From 7fcc6a62b1762fda0494285d42f39d7ddcb88e5d Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Sat, 17 Feb 2024 02:19:10 -0500 Subject: [PATCH 01/51] Update Dockerfile to use Python 3.11 image and install required packages --- Dockerfile | 60 ++++++++++++++++-------------------------------------- 1 file changed, 17 insertions(+), 43 deletions(-) diff --git a/Dockerfile b/Dockerfile index dd0de0d7..466445eb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,48 +1,22 @@ -# Using the ubuntu:20.04 base image for compatibility with the ICESat-2 SlideRule software -# Some code to add conda from https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile -# This file builds the docker image for the ICESat-2 tracks project. Includes the ICESat-2 SlideRule tool, conda, and the python3.11 environment for the project with dependencies provided in the environment_small.yml file. -FROM ubuntu:20.04 -ARG DEBIAN_FRONTEND=noninteractive -ARG MINIFORGE_NAME=Miniforge3 -ARG MINIFORGE_VERSION=23.3.1-0 -ARG TARGETPLATFORM +# Use the official Python 3.11 image from the Docker Hub +FROM python:3.11 -ENV CONDA_DIR=/opt/conda -ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 -ENV PATH=${CONDA_DIR}/bin:${PATH} -ENV ENVNAME=2021-icesat2-tracks -RUN apt-get update && \ - apt-get install -y git curl wget +# Update the system and install the packages +RUN apt-get update && apt-get install -y \ + openmpi-bin \ + openmpi-doc \ + libopenmpi-dev -# Install sliderule dependencies -RUN apt-get install -y build-essential libreadline-dev liblua5.3-dev zlib1g-dev cmake -RUN git clone https://github.com/ICESat2-SlideRule/sliderule.git -WORKDIR /sliderule/ -RUN make config && \ - make && \ - make install +# Set the working directory to /app +WORKDIR /app -# Install conda -RUN apt-get update > /dev/null && \ - apt-get install --no-install-recommends --yes \ - bzip2 ca-certificates \ - tini \ - > /dev/null && \ - apt-get clean && \ - rm -rf /var/lib/apt/lists/* && \ - wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/${MINIFORGE_NAME}-${MINIFORGE_VERSION}-Linux-$(uname -m).sh -O /tmp/miniforge.sh && \ - /bin/bash /tmp/miniforge.sh -b -p ${CONDA_DIR} && \ - rm /tmp/miniforge.sh && \ - conda clean --tarballs --index-cache --packages --yes && \ - find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ - find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \ - conda clean --force-pkgs-dirs --all --yes && \ - echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> /etc/skel/.bashrc && \ - echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc +# Copy the current directory contents into the container at /app +COPY . /app -# Install conda environment -COPY environment_small.yml /tmp/environment.yml -RUN mamba env create -f /tmp/environment.yml +# Create the output directory +RUN mkdir -p /app/output -ENTRYPOINT ["tini", "--"] -CMD ["/bin/bash"] +# Install any needed packages specified in pyproject.toml +RUN pip install . + +CMD ["/bin/bash"] \ No newline at end of file From 2aed3e7ee0033152170515d50becf6456ef02a89 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Mon, 26 Feb 2024 03:57:09 -0500 Subject: [PATCH 02/51] cleaning and formating files form the ICEsat2_SI_tools folder --- .../ICEsat2_SI_tools/angle_optimizer.py | 260 ++-- .../ICEsat2_SI_tools/beam_stats.py | 5 - .../ICEsat2_SI_tools/convert_GPS_time.py | 179 +-- .../ICEsat2_SI_tools/convert_julian.py | 110 +- .../ICEsat2_SI_tools/filter_regrid.py | 393 +++--- .../ICEsat2_SI_tools/iotools.py | 19 +- .../ICEsat2_SI_tools/lanczos.py | 75 +- .../ICEsat2_SI_tools/read_ground_tracks.py | 112 +- .../sliderule_converter_tools.py | 1 - .../ICEsat2_SI_tools/spectral_estimates.py | 1152 ++++++++++------- .../ICEsat2_SI_tools/spicke_remover.py | 102 +- .../ICEsat2_SI_tools/wave_tools.py | 32 +- 12 files changed, 1325 insertions(+), 1115 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py index 7ec54aa2..e3e28b53 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py @@ -1,13 +1,15 @@ """ This library contains method, and classes used to search for the best angle given x,y data using single frequecy fits. """ + from numba import jit import numpy as np numba_parallel = False -def get_wavenumbers_polar( amp, angle_rad): + +def get_wavenumbers_polar(amp, angle_rad): """ inputs: @@ -18,108 +20,126 @@ def get_wavenumbers_polar( amp, angle_rad): wavenumber k,l """ import numpy as np + k0 = amp * np.cos(angle_rad) l0 = amp * np.sin(angle_rad) return k0, l0 -def wavemodel(XX, YY, ks, ls, amps, group_phase = 0): - import numpy as np +def wavemodel(XX, YY, ks, ls, amps, group_phase=0): - G = np.vstack([ np.cos(np.outer(XX, ks) + np.outer(YY, ls) ).T , np.sin(np.outer(XX, ks) + np.outer(YY, ls) ).T ] ).T + import numpy as np - #phase1 = np.random.rand(1, amp_list.size) * np.pi*2 - #phase = np.arange(0, amp_list.size) * np.pi/2 + G = np.vstack( + [ + np.cos(np.outer(XX, ks) + np.outer(YY, ls)).T, + np.sin(np.outer(XX, ks) + np.outer(YY, ls)).T, + ] + ).T - b = np.hstack([ np.cos(group_phase) * amps , np.sin(group_phase) * amps ]).squeeze() - z_model = (G @ b) + b = np.hstack([np.cos(group_phase) * amps, np.sin(group_phase) * amps]).squeeze() + z_model = G @ b return z_model -@jit(nopython=True, parallel= numba_parallel) -def wavemodel_single_wave(XX, YY, ks, ls, amps, group_phase = 0): - z_model = amps * np.cos(XX * ks + YY * ls + group_phase ) - return z_model#.squeeze() + +@jit(nopython=True, parallel=numba_parallel) +def wavemodel_single_wave(XX, YY, ks, ls, amps, group_phase=0): + z_model = amps * np.cos(XX * ks + YY * ls + group_phase) + return z_model -def get_z_model(x_positions, y_position, K_prime, K_amp, alpha_rad, group_phase): +def get_z_model(x_positions, y_position, K_prime, K_amp, alpha_rad, group_phase): - K_abs = K_prime / np.cos(alpha_rad) + K_abs = K_prime / np.cos(alpha_rad) k = K_abs * np.cos(alpha_rad) l = K_abs * np.sin(alpha_rad) - return wavemodel( x_positions,y_position, k, l, np.array(K_amp ), group_phase= group_phase) + return wavemodel( + x_positions, y_position, k, l, np.array(K_amp), group_phase=group_phase + ) + -@jit(nopython=True, parallel= False) -def get_z_model_single_wave(x_positions, y_position, K_prime, K_amp, alpha_rad, group_phase): +@jit(nopython=True, parallel=False) +def get_z_model_single_wave( + x_positions, y_position, K_prime, K_amp, alpha_rad, group_phase +): - K_abs = K_prime / np.cos(alpha_rad) + K_abs = K_prime / np.cos(alpha_rad) k = K_abs * np.cos(alpha_rad) l = K_abs * np.sin(alpha_rad) - return wavemodel_single_wave( x_positions,y_position, k, l, K_amp, group_phase= group_phase) - + return wavemodel_single_wave( + x_positions, y_position, k, l, K_amp, group_phase=group_phase + ) -def objective_func(pars, x, y, z, test_flag= False , prior= None, prior_weight = 2 ): +def objective_func(pars, x, y, z, test_flag=False, prior=None, prior_weight=2): "objective function that returns the residual array" - z_model = get_z_model_single_wave(x, y, pars['K_prime'].value, pars['K_amp'].value, pars['alpha'].value,pars['phase'].value) + z_model = get_z_model_single_wave( + x, + y, + pars["K_prime"].value, + pars["K_amp"].value, + pars["alpha"].value, + pars["phase"].value, + ) if prior is not None: - a_0, a_std = prior['alpha'] - penalties = np.array([ (abs(a_0 - pars['alpha'] )**2 / a_std**2) ]) + a_0, a_std = prior["alpha"] + penalties = np.array([(abs(a_0 - pars["alpha"]) ** 2 / a_std**2)]) else: - penalties = np.array([0]) + penalties = np.array([0]) - cost =( abs(z - z_model) )**2 /z.std()**2 + cost = (abs(z - z_model)) ** 2 / z.std() ** 2 if test_flag: return z_model else: - return np.concatenate([cost , prior_weight * penalties]) + return np.concatenate([cost, prior_weight * penalties]) -# def gaussian_prior(x, x0, sigma): -# return np.exp(-np.power((x - x0)/sigma, 2.)/2.) - -def likelyhood_func(pars, x, y, z, z_error= None, test_flag= False , prior= None , prior_weight = 2): +def likelyhood_func( + pars, x, y, z, z_error=None, test_flag=False, prior=None, prior_weight=2 +): """ ---not well testet --- likelyhood function using log(p) """ # get model - z_model = get_z_model(x, y, pars['K_prime'], pars['K_amp'], pars['alpha'],pars['phase']) + z_model = get_z_model( + x, y, pars["K_prime"], pars["K_amp"], pars["alpha"], pars["phase"] + ) # define cost - cost_sqrt =( abs(z - z_model) )**2 + cost_sqrt = (abs(z - z_model)) ** 2 # estimate total variance if z_error is None: - tot_var = z.std()**2* 0.01 + z_model**2 + tot_var = z.std() ** 2 * 0.01 + z_model**2 else: - tot_var = z_error**2 + z_model**2 + tot_var = z_error**2 + z_model**2 - #cost_sqrt.sum()/tot_var.sum() - # (cost_sqrt/tot_var).sum() - # - # np.log(tot_var).sum() def simple_log_panelty(x, x0, sigma): - return -np.power((x - x0)/sigma, 2.)/2. + return -np.power((x - x0) / sigma, 2.0) / 2.0 # try ot get prior if prior is not None: - a_0, a_std = prior['alpha'] + a_0, a_std = prior["alpha"] # this corresponds to the the panelty log( p(alpha) ) - penalties = simple_log_panelty(pars['alpha'], a_0,a_std ) + penalties = simple_log_panelty(pars["alpha"], a_0, a_std) else: - penalties = np.array([0]) + penalties = np.array([0]) if test_flag: return z_model else: - return - 0.5 * (cost_sqrt/tot_var + np.log(tot_var) ).sum() + prior_weight * penalties + return ( + -0.5 * (cost_sqrt / tot_var + np.log(tot_var)).sum() + + prior_weight * penalties + ) class sample_with_mcmc: @@ -156,6 +176,7 @@ class sample_with_mcmc: def __init__(self, params): import lmfit as LM + self.LM = LM self.set_parameters(params) @@ -165,14 +186,7 @@ def __init__(self, params): def set_objective_func(self, ofunc): self.objective_func = ofunc - # def objective_func(self, ): - # sn2 = 0.1**2 - # return - cost(params['x'], params['y']) + np.log(sn2) - - # def test_ojective_func(self, model_func): - # return self.objective_func(self.params, self.data, model_func, self.freq) - - def set_parameters(self, par_dict, verbose= False): + def set_parameters(self, par_dict, verbose=False): """ defines params object at inital seed for mcmc par_dict should contain: var_name : [min, max, nseed] @@ -181,97 +195,129 @@ def set_parameters(self, par_dict, verbose= False): params = self.LM.Parameters() var_seeds = list() - for k,I in par_dict.items(): - params.add(k, (I[0]+ I[1])/2, vary=True , min=I[0], max=I[1]) - - var_seeds.append( np.linspace(I[0],I[1], I[2])) + for k, I in par_dict.items(): + params.add(k, (I[0] + I[1]) / 2, vary=True, min=I[0], max=I[1]) + var_seeds.append(np.linspace(I[0], I[1], I[2])) if len(var_seeds) > 2: - raise ValueError('nor proframmed for 3d') + raise ValueError("nor proframmed for 3d") - self.nwalkers= int(var_seeds[0].size * var_seeds[1].size) + self.nwalkers = int(var_seeds[0].size * var_seeds[1].size) pxx, pyy = np.meshgrid(var_seeds[0], var_seeds[1]) - self.seeds = np.vstack([pxx.flatten(), pyy.flatten() ]).T + self.seeds = np.vstack([pxx.flatten(), pyy.flatten()]).T self.params = params if verbose: - print('Nwalker: ', self.nwalkers) - print('Seeds: ', self.seeds.shape) + print("Nwalker: ", self.nwalkers) + print("Seeds: ", self.seeds.shape) print(self.params) def test_objective_func(self): - return self.objective_func(self.params, *self.fitting_args, **self.fitting_kargs) + return self.objective_func( + self.params, *self.fitting_args, **self.fitting_kargs + ) - def sample(self, fitting_args= None , method='emcee', steps=100, verbose= True, **kargs): + def sample( + self, fitting_args=None, method="emcee", steps=100, verbose=True, **kargs + ): - fitting_args, fitting_kargs = self.fitting_args, self.fitting_kargs - # TODO: this funciton throws an error in CI. The nan_policy='omit' policiy was added to avoid this issue + fitting_args, fitting_kargs = self.fitting_args, self.fitting_kargs + # TODO: this funciton throws an error in CI. The nan_policy='omit' policiy was added to avoid this issue # according to the guidelines in https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do - self.fitter = self.LM.minimize(self.objective_func, self.params, method=method, - args=fitting_args, kws=fitting_kargs , - nwalkers=self.nwalkers, steps=steps, pos= self.seeds,nan_policy='omit' , **kargs) + self.fitter = self.LM.minimize( + self.objective_func, + self.params, + method=method, + args=fitting_args, + kws=fitting_kargs, + nwalkers=self.nwalkers, + steps=steps, + pos=self.seeds, + nan_policy="omit", + **kargs, + ) if verbose: print(self.LM.report_fit(self.fitter)) - print('results at self.fitter') + print("results at self.fitter") - def plot_sample(self, **kargs ): + def plot_sample(self, **kargs): import matplotlib.pyplot as plt + chain = self.chain() nwalkers = self.nwalkers for n in np.arange(nwalkers): - plt.plot(chain[:,n,1], chain[:,n,0] , '-', **kargs) - plt.plot(chain[:,n,1], chain[:,n,0] , '.', **kargs) + plt.plot(chain[:, n, 1], chain[:, n, 0], "-", **kargs) + plt.plot(chain[:, n, 1], chain[:, n, 0], ".", **kargs) + def optimize(self, fitting_args=None, method="dual_annealing", verbose=True): - def optimize(self, fitting_args= None , method='dual_annealing', verbose= True): + fitting_args = self.fitting_args + fitting_kargs = self.fitting_kargs - fitting_args = self.fitting_args - fitting_kargs = self.fitting_kargs - - self.fitter_optimize = self.LM.minimize(self.objective_func, self.params, method=method, - args=fitting_args, kws=fitting_kargs ) + self.fitter_optimize = self.LM.minimize( + self.objective_func, + self.params, + method=method, + args=fitting_args, + kws=fitting_kargs, + ) if verbose: print(self.LM.report_fit(self.fitter_optimize)) - print('results at self.fitter_optimize') + print("results at self.fitter_optimize") def plot_optimze(self, **kargs): import matplotlib.pyplot as plt - plt.plot(self.fitter_optimize.params['phase'].value, self.fitter_optimize.params['alpha'].value, '.', **kargs) + plt.plot( + self.fitter_optimize.params["phase"].value, + self.fitter_optimize.params["alpha"].value, + ".", + **kargs, + ) - def brute(self, fitting_args= None , method='brute', verbose= True, N_grid = 30): + def brute(self, fitting_args=None, method="brute", verbose=True, N_grid=30): - fitting_args = self.fitting_args - fitting_kargs = self.fitting_kargs + fitting_args = self.fitting_args + fitting_kargs = self.fitting_kargs - self.fitter_brute = self.LM.minimize(self.objective_func, self.params, method=method, - args=fitting_args, kws=fitting_kargs, Ns=N_grid ) + self.fitter_brute = self.LM.minimize( + self.objective_func, + self.params, + method=method, + args=fitting_args, + kws=fitting_kargs, + Ns=N_grid, + ) if verbose: print(self.LM.report_fit(self.fitter_brute)) - print('results at self.fitter_brute') - + print("results at self.fitter_brute") - def plot_brute(self, clevel = np.linspace(-3.2, 3.2, 30), **kargs): + def plot_brute(self, clevel=np.linspace(-3.2, 3.2, 30), **kargs): import matplotlib.pyplot as plt - fitter_brute =self.fitter_brute - - dd = (fitter_brute.brute_Jout- fitter_brute.brute_Jout.mean())/fitter_brute.brute_Jout.std() - plt.contourf(fitter_brute.brute_grid[1,:,:], fitter_brute.brute_grid[0,:,:], dd , clevel, cmap= plt.cm.YlGnBu_r ) - #plt.scatter(fitter_brute.brute_grid[1,:,:], fitter_brute.brute_grid[0,:,:], s=0.2, alpha= 0.4, color='black') - #plt.plot(fitter_brute.brute_x0[1], fitter_brute.brute_x0[0], **kargs) - x_name, y_name = list(fitter_brute.params.keys())[1], list(fitter_brute.params.keys())[0] + fitter_brute = self.fitter_brute + + dd = ( + fitter_brute.brute_Jout - fitter_brute.brute_Jout.mean() + ) / fitter_brute.brute_Jout.std() + plt.contourf( + fitter_brute.brute_grid[1, :, :], + fitter_brute.brute_grid[0, :, :], + dd, + clevel, + cmap=plt.cm.YlGnBu_r, + ) + + x_name, y_name = ( + list(fitter_brute.params.keys())[1], + list(fitter_brute.params.keys())[0], + ) plt.xlabel(x_name) plt.ylabel(y_name) - # plt.xlabel('Phase (rad)') - # plt.ylabel('Angle (rad)') - - - def chain(self, burn=None): "return results as nparray contains walk of each walker" if burn is not None: @@ -286,8 +332,9 @@ def flatchain(self, burn=None): else: return self.fitter.flatchain - def get_marginal_dist(self, var, var_dx, burn = None, plot_flag= False, normalize = True): - + def get_marginal_dist( + self, var, var_dx, burn=None, plot_flag=False, normalize=True + ): """ retrurn the marginal distribution from self.params object @@ -300,18 +347,17 @@ def get_marginal_dist(self, var, var_dx, burn = None, plot_flag= False, normaliz otherwise it returns the rar histogram """ - data = self.flatchain(burn) - #fitter.flatchain.loc[100:][var] - bins = np.arange(self.params[var].min,self.params[var].max+ var_dx,var_dx) + bins = np.arange(self.params[var].min, self.params[var].max + var_dx, var_dx) y_hist, _ = np.histogram(self.fitter.flatchain.loc[burn:][var], bins) - bins_pos = (bins[0:-1] + np.diff(bins)/2) + bins_pos = bins[0:-1] + np.diff(bins) / 2 if normalize: - y_hist = y_hist/var_dx/y_hist.sum() + y_hist = y_hist / var_dx / y_hist.sum() if plot_flag: import matplotlib.pyplot as plt + plt.stairs(y_hist, bins) return y_hist, bins, bins_pos diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py index 3f815e15..90473ffa 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py @@ -145,9 +145,6 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): plt.title("low beams N", loc="left") plt.xlabel("along track distance (km)") - # plt.ylabel('Point density (m)') - - ax5 = plt.subplot(gs[0:2, 2]) lat_shift = 0 for k in low_beams: @@ -184,8 +181,6 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): ## plot track stats basics for sliderules ATL06 output - - def plot_ATL06_track_data(G2, cdict): """ Plots the beam statistics in a 3 x 3 plot diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py b/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py index a1e491c8..7a2b7bc8 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -u""" +""" convert_GPS_time.py (10/2017) Return the calendar date and time for given GPS time. Based on Tiffany Summerscales's PHP conversion algorithm @@ -33,88 +33,109 @@ from .convert_julian import convert_julian import pdb -#-- PURPOSE: Define GPS leap seconds + +# -- PURPOSE: Define GPS leap seconds def get_leaps(): - leaps = [46828800, 78364801, 109900802, 173059203, 252028804, 315187205, - 346723206, 393984007, 425520008, 457056009, 504489610, 551750411, - 599184012, 820108813, 914803214, 1025136015, 1119744016, 1167264017] - return leaps + leaps = [ + 46828800, + 78364801, + 109900802, + 173059203, + 252028804, + 315187205, + 346723206, + 393984007, + 425520008, + 457056009, + 504489610, + 551750411, + 599184012, + 820108813, + 914803214, + 1025136015, + 1119744016, + 1167264017, + ] + return leaps + -#-- PURPOSE: Test to see if any GPS seconds are leap seconds +# -- PURPOSE: Test to see if any GPS seconds are leap seconds def is_leap(GPS_Time): - leaps = get_leaps() - Flag = np.zeros_like(GPS_Time, dtype=np.bool_) - for leap in leaps: - count = np.count_nonzero(np.floor(GPS_Time) == leap) - if (count > 0): - indices, = np.nonzero(np.floor(GPS_Time) == leap) - Flag[indices] = True - return Flag - -#-- PURPOSE: Count number of leap seconds that have passed for each GPS time + leaps = get_leaps() + Flag = np.zeros_like(GPS_Time, dtype=np.bool_) + for leap in leaps: + count = np.count_nonzero(np.floor(GPS_Time) == leap) + if count > 0: + (indices,) = np.nonzero(np.floor(GPS_Time) == leap) + Flag[indices] = True + return Flag + + +# -- PURPOSE: Count number of leap seconds that have passed for each GPS time def count_leaps(GPS_Time): - leaps = get_leaps() - #-- number of leap seconds prior to GPS_Time - n_leaps = np.zeros_like(GPS_Time, dtype=np.uint) - for i,leap in enumerate(leaps): - count = np.count_nonzero(GPS_Time >= leap) - if (count > 0): - indices, = np.nonzero(GPS_Time >= leap) - # print(indices) - # pdb.set_trace() - n_leaps[indices] += 1 - return n_leaps - -#-- PURPOSE: Convert UNIX Time to GPS Time + leaps = get_leaps() + # -- number of leap seconds prior to GPS_Time + n_leaps = np.zeros_like(GPS_Time, dtype=np.uint) + for i, leap in enumerate(leaps): + count = np.count_nonzero(GPS_Time >= leap) + if count > 0: + (indices,) = np.nonzero(GPS_Time >= leap) + n_leaps[indices] += 1 + return n_leaps + + +# -- PURPOSE: Convert UNIX Time to GPS Time def convert_UNIX_to_GPS(UNIX_Time): - #-- calculate offsets for UNIX times that occur during leap seconds - offset = np.zeros_like(UNIX_Time) - count = np.count_nonzero((UNIX_Time % 1) != 0) - if (count > 0): - indices, = np.nonzero((UNIX_Time % 1) != 0) - UNIX_Time[indices] -= 0.5 - offset[indices] = 1.0 - #-- convert UNIX_Time to GPS without taking into account leap seconds - #-- (UNIX epoch: Jan 1, 1970 00:00:00, GPS epoch: Jan 6, 1980 00:00:00) - GPS_Time = UNIX_Time - 315964800 - leaps = get_leaps() - #-- calculate number of leap seconds prior to GPS_Time - n_leaps = np.zeros_like(GPS_Time, dtype=np.uint) - for i,leap in enumerate(leaps): - count = np.count_nonzero(GPS_Time >= (leap - i)) - if (count > 0): - indices, = np.nonzero(GPS_Time >= (leap - i)) - n_leaps[indices] += 1 - #-- take into account leap seconds and offsets - GPS_Time += n_leaps + offset - return GPS_Time - -#-- PURPOSE: Convert GPS Time to UNIX Time + # -- calculate offsets for UNIX times that occur during leap seconds + offset = np.zeros_like(UNIX_Time) + count = np.count_nonzero((UNIX_Time % 1) != 0) + if count > 0: + (indices,) = np.nonzero((UNIX_Time % 1) != 0) + UNIX_Time[indices] -= 0.5 + offset[indices] = 1.0 + # -- convert UNIX_Time to GPS without taking into account leap seconds + # -- (UNIX epoch: Jan 1, 1970 00:00:00, GPS epoch: Jan 6, 1980 00:00:00) + GPS_Time = UNIX_Time - 315964800 + leaps = get_leaps() + # -- calculate number of leap seconds prior to GPS_Time + n_leaps = np.zeros_like(GPS_Time, dtype=np.uint) + for i, leap in enumerate(leaps): + count = np.count_nonzero(GPS_Time >= (leap - i)) + if count > 0: + (indices,) = np.nonzero(GPS_Time >= (leap - i)) + n_leaps[indices] += 1 + # -- take into account leap seconds and offsets + GPS_Time += n_leaps + offset + return GPS_Time + + +# -- PURPOSE: Convert GPS Time to UNIX Time def convert_GPS_to_UNIX(GPS_Time): - #-- convert GPS_Time to UNIX without taking into account leap seconds - #-- (UNIX epoch: Jan 1, 1970 00:00:00, GPS epoch: Jan 6, 1980 00:00:00) - UNIX_Time = GPS_Time + 315964800 - #-- number of leap seconds prior to GPS_Time - n_leaps = count_leaps(GPS_Time) - UNIX_Time -= n_leaps - #-- check if GPS Time is leap second - Flag = is_leap(GPS_Time) - if Flag.any(): - #-- for leap seconds: add a half second offset - indices, = np.nonzero(Flag) - UNIX_Time[indices] += 0.5 - return UNIX_Time - -#-- PURPOSE: convert from GPS time to calendar dates + # -- convert GPS_Time to UNIX without taking into account leap seconds + # -- (UNIX epoch: Jan 1, 1970 00:00:00, GPS epoch: Jan 6, 1980 00:00:00) + UNIX_Time = GPS_Time + 315964800 + # -- number of leap seconds prior to GPS_Time + n_leaps = count_leaps(GPS_Time) + UNIX_Time -= n_leaps + # -- check if GPS Time is leap second + Flag = is_leap(GPS_Time) + if Flag.any(): + # -- for leap seconds: add a half second offset + (indices,) = np.nonzero(Flag) + UNIX_Time[indices] += 0.5 + return UNIX_Time + + +# -- PURPOSE: convert from GPS time to calendar dates def convert_GPS_time(GPS_Time, OFFSET=0.0): - #-- convert from standard GPS time to UNIX time accounting for leap seconds - #-- and adding the specified offset to GPS_Time - UNIX_Time = convert_GPS_to_UNIX(np.array(GPS_Time) + OFFSET) - #-- calculate Julian date from UNIX time and convert into calendar dates - #-- UNIX time: seconds from 1970-01-01 00:00:00 UTC - julian_date = (UNIX_Time/86400.0) + 2440587.500000 - cal_date = convert_julian(julian_date) - #-- include UNIX times in output - cal_date['UNIX'] = UNIX_Time - #-- return the calendar dates and UNIX time - return cal_date + # -- convert from standard GPS time to UNIX time accounting for leap seconds + # -- and adding the specified offset to GPS_Time + UNIX_Time = convert_GPS_to_UNIX(np.array(GPS_Time) + OFFSET) + # -- calculate Julian date from UNIX time and convert into calendar dates + # -- UNIX time: seconds from 1970-01-01 00:00:00 UTC + julian_date = (UNIX_Time / 86400.0) + 2440587.500000 + cal_date = convert_julian(julian_date) + # -- include UNIX times in output + cal_date["UNIX"] = UNIX_Time + # -- return the calendar dates and UNIX time + return cal_date diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/convert_julian.py b/src/icesat2_tracks/ICEsat2_SI_tools/convert_julian.py index 74b3fd81..b5d6c7bc 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/convert_julian.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/convert_julian.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -u""" +""" convert_julian.py Written by Tyler Sutterley (10/2017) @@ -50,60 +50,62 @@ """ import numpy as np -def convert_julian(JD, ASTYPE=None, FORMAT='dict'): - #-- convert to array if only a single value was imported - if (np.ndim(JD) == 0): - JD = np.array([JD]) - SINGLE_VALUE = True - else: - SINGLE_VALUE = False - JDO = np.floor(JD + 0.5) - C = np.zeros_like(JD) - #-- calculate C for dates before and after the switch to Gregorian - IGREG = 2299161.0 - ind1, = np.nonzero(JDO < IGREG) - C[ind1] = JDO[ind1] + 1524.0 - ind2, = np.nonzero(JDO >= IGREG) - B = np.floor((JDO[ind2] - 1867216.25)/36524.25) - C[ind2] = JDO[ind2] + B - np.floor(B/4.0) + 1525.0 - #-- calculate coefficients for date conversion - D = np.floor((C - 122.1)/365.25) - E = np.floor((365.0 * D) + np.floor(D/4.0)) - F = np.floor((C - E)/30.6001) - #-- calculate day, month, year and hour - DAY = np.floor(C - E + 0.5) - np.floor(30.6001*F) - MONTH = F - 1.0 - 12.0*np.floor(F/14.0) - YEAR = D - 4715.0 - np.floor((7.0+MONTH)/10.0) - HOUR = np.floor(24.0*(JD + 0.5 - JDO)) - #-- calculate minute and second - G = (JD + 0.5 - JDO) - HOUR/24.0 - MINUTE = np.floor(G*1440.0) - SECOND = (G - MINUTE/1440.0) * 86400.0 +def convert_julian(JD, ASTYPE=None, FORMAT="dict"): + # -- convert to array if only a single value was imported + if np.ndim(JD) == 0: + JD = np.array([JD]) + SINGLE_VALUE = True + else: + SINGLE_VALUE = False + + JDO = np.floor(JD + 0.5) + C = np.zeros_like(JD) + # -- calculate C for dates before and after the switch to Gregorian + IGREG = 2299161.0 + (ind1,) = np.nonzero(JDO < IGREG) + C[ind1] = JDO[ind1] + 1524.0 + (ind2,) = np.nonzero(JDO >= IGREG) + B = np.floor((JDO[ind2] - 1867216.25) / 36524.25) + C[ind2] = JDO[ind2] + B - np.floor(B / 4.0) + 1525.0 + # -- calculate coefficients for date conversion + D = np.floor((C - 122.1) / 365.25) + E = np.floor((365.0 * D) + np.floor(D / 4.0)) + F = np.floor((C - E) / 30.6001) + # -- calculate day, month, year and hour + DAY = np.floor(C - E + 0.5) - np.floor(30.6001 * F) + MONTH = F - 1.0 - 12.0 * np.floor(F / 14.0) + YEAR = D - 4715.0 - np.floor((7.0 + MONTH) / 10.0) + HOUR = np.floor(24.0 * (JD + 0.5 - JDO)) + # -- calculate minute and second + G = (JD + 0.5 - JDO) - HOUR / 24.0 + MINUTE = np.floor(G * 1440.0) + SECOND = (G - MINUTE / 1440.0) * 86400.0 - #-- convert all variables to output type (from float) - if ASTYPE is not None: - YEAR = YEAR.astype(ASTYPE) - MONTH = MONTH.astype(ASTYPE) - DAY = DAY.astype(ASTYPE) - HOUR = HOUR.astype(ASTYPE) - MINUTE = MINUTE.astype(ASTYPE) - SECOND = SECOND.astype(ASTYPE) + # -- convert all variables to output type (from float) + if ASTYPE is not None: + YEAR = YEAR.astype(ASTYPE) + MONTH = MONTH.astype(ASTYPE) + DAY = DAY.astype(ASTYPE) + HOUR = HOUR.astype(ASTYPE) + MINUTE = MINUTE.astype(ASTYPE) + SECOND = SECOND.astype(ASTYPE) - #-- if only a single value was imported initially: remove singleton dims - if SINGLE_VALUE: - YEAR = YEAR.item(0) - MONTH = MONTH.item(0) - DAY = DAY.item(0) - HOUR = HOUR.item(0) - MINUTE = MINUTE.item(0) - SECOND = SECOND.item(0) + # -- if only a single value was imported initially: remove singleton dims + if SINGLE_VALUE: + YEAR = YEAR.item(0) + MONTH = MONTH.item(0) + DAY = DAY.item(0) + HOUR = HOUR.item(0) + MINUTE = MINUTE.item(0) + SECOND = SECOND.item(0) - #-- return date variables in output format (default python dictionary) - if (FORMAT == 'dict'): - return dict(year=YEAR, month=MONTH, day=DAY, - hour=HOUR, minute=MINUTE, second=SECOND) - elif (FORMAT == 'tuple'): - return (YEAR, MONTH, DAY, HOUR, MINUTE, SECOND) - elif (FORMAT == 'zip'): - return zip(YEAR, MONTH, DAY, HOUR, MINUTE, SECOND) + # -- return date variables in output format (default python dictionary) + if FORMAT == "dict": + return dict( + year=YEAR, month=MONTH, day=DAY, hour=HOUR, minute=MINUTE, second=SECOND + ) + elif FORMAT == "tuple": + return (YEAR, MONTH, DAY, HOUR, MINUTE, SECOND) + elif FORMAT == "zip": + return zip(YEAR, MONTH, DAY, HOUR, MINUTE, SECOND) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py index 1c276853..77766490 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py @@ -1,55 +1,48 @@ - import numpy as np from numba import jit -def correct_heights(T03, T03c, coord = 'delta_time'): +def correct_heights(T03, T03c, coord="delta_time"): """ returns the corrected photon heigts in T03 given SSSH approxiamtion 'dem_h' in T03c """ - T03['heights_c']= T03['heights'] - np.interp( T03[coord],T03c[coord], T03c['dem_h'] ) + T03["heights_c"] = T03["heights"] - np.interp( + T03[coord], T03c[coord], T03c["dem_h"] + ) return T03 -# def track_type_beam(hdf5_file): -# """ -# Returns True if track is acending -# hdf5_file is a hdf5 beam file -# -# sc_orient - spacecraft orientation -# This parameter tracks the spacecraft orientation between ‘forward’ and ‘backward’ orientations, to allow mapping between ATLAS hardware and the beam orientation on the ground. Forward == 1; backward == 0; transition ==2. -# -# -# """ -# return hdf5_file['orbit_info/sc_orient'][:][0] ==0 - -def track_pole_ward_file(hdf5_file, product='ALT03'): +def track_pole_ward_file(hdf5_file, product="ALT03"): """ Returns true if track goes poleward hdf5_file is a an HFD5 object in read mode """ - if product == 'ALT03': - T_lat = hdf5_file['gt1r/geolocation/reference_photon_lat'][:] - T_time = hdf5_file['gt1r/geolocation/delta_time'][:] - elif product == 'ALT10': - T_lat = hdf5_file['gt1r/freeboard_beam_segment/latitude'][:] - T_time = hdf5_file['gt1r/freeboard_beam_segment/delta_time'][:] - #return ( T_lat[T_time.argmax()] - T_lat[T_time.argmin()] ) < 0 - print('1st lat =' + str(abs(T_lat[T_time.argmin()])) , ';last lat =' + str(abs(T_lat[T_time.argmax()])) ) + if product == "ALT03": + T_lat = hdf5_file["gt1r/geolocation/reference_photon_lat"][:] + T_time = hdf5_file["gt1r/geolocation/delta_time"][:] + elif product == "ALT10": + T_lat = hdf5_file["gt1r/freeboard_beam_segment/latitude"][:] + T_time = hdf5_file["gt1r/freeboard_beam_segment/delta_time"][:] + + print( + "1st lat =" + str(abs(T_lat[T_time.argmin()])), + ";last lat =" + str(abs(T_lat[T_time.argmax()])), + ) return abs(T_lat[T_time.argmax()]) > abs(T_lat[T_time.argmin()]) - def track_type(T): """ Returns if track acending or desending T is a pandas table """ - #T = B[k] - #T = B[beams_list[0]] - return (T['lats'].iloc[T['delta_time'].argmax()] - T['lats'].iloc[T['delta_time'].argmin()] ) < 0 + return ( + T["lats"].iloc[T["delta_time"].argmax()] + - T["lats"].iloc[T["delta_time"].argmin()] + ) < 0 + def lat_min_max_extended(B, beams_list, accent=None): """ @@ -62,57 +55,63 @@ def lat_min_max_extended(B, beams_list, accent=None): returns: min_lat, max_lat, accent min and max latitudes of the beams, (True/False) True if the track is accending """ - #B, beams_list = B , high_beams - accent = regrid.track_type( B[beams_list[0]] ) if accent is None else accent - if B[beams_list[0]]['lats'].iloc[0] < 0: - hemis = 'SH' + accent = regrid.track_type(B[beams_list[0]]) if accent is None else accent + + if B[beams_list[0]]["lats"].iloc[0] < 0: + hemis = "SH" else: - hemis = 'NH' + hemis = "NH" - track_pos_start, track_pos_end= list(), list() + track_pos_start, track_pos_end = list(), list() for k in beams_list: - if (hemis == 'SH'): - track_pos_start.append( B[k].loc[B[k]['lats'].argmax()][ ['lats', 'lons']] ) - track_pos_end.append( B[k].loc[B[k]['lats'].argmin()][ ['lats', 'lons']] ) + if hemis == "SH": + track_pos_start.append(B[k].loc[B[k]["lats"].argmax()][["lats", "lons"]]) + track_pos_end.append(B[k].loc[B[k]["lats"].argmin()][["lats", "lons"]]) else: - track_pos_start.append( B[k].loc[B[k]['lats'].argmin()][ ['lats', 'lons']] ) - track_pos_end.append( B[k].loc[B[k]['lats'].argmax()][ ['lats', 'lons']] ) - + track_pos_start.append(B[k].loc[B[k]["lats"].argmin()][["lats", "lons"]]) + track_pos_end.append(B[k].loc[B[k]["lats"].argmax()][["lats", "lons"]]) track_lat_start, track_lat_end = list(), list() track_lon_start, track_lon_end = list(), list() for ll in track_pos_start: - track_lat_start.append(ll['lats']) - track_lon_start.append(ll['lons']) - + track_lat_start.append(ll["lats"]) + track_lon_start.append(ll["lons"]) for ll in track_pos_end: - track_lat_end.append(ll['lats']) - track_lon_end.append(ll['lons']) - - # track_lat_start.append( B[k]['lats'].min() ) - # track_lat_end.append( B[k]['lats'].max() ) - # - # track_lon_left.append(B[k]['lons'].min()) - # track_lon_right.append(B[k]['lons'].max()) + track_lat_end.append(ll["lats"]) + track_lon_end.append(ll["lons"]) if accent: track_lon_start - #track_lat_start.min(), track_lon_right.max() - - if (hemis == 'SH') & accent: - return [max(track_lat_start) , min(track_lat_end)], [max(track_lon_start), min(track_lon_end)], accent # accenting SH mean start is in the top right - elif (hemis == 'SH') & ~accent: - return [max(track_lat_start) , min(track_lat_end)], [min(track_lon_start), max(track_lon_end)], accent # decent SH mean start is in the top left - elif (hemis == 'NH') & accent: - return [min(track_lat_start) , max(track_lat_end)], [min(track_lon_start), max(track_lon_end)], accent # accent NH mean start is in the lower left - elif (hemis == 'NH') & ~accent: - return [min(track_lat_start) , max(track_lat_end)], [max(track_lon_start), min(track_lon_end)], accent # decent NH mean start is in the lower right - else: - raise ValueError('some defintions went wrong') + if (hemis == "SH") & accent: + return ( + [max(track_lat_start), min(track_lat_end)], + [max(track_lon_start), min(track_lon_end)], + accent, + ) # accenting SH mean start is in the top right + elif (hemis == "SH") & ~accent: + return ( + [max(track_lat_start), min(track_lat_end)], + [min(track_lon_start), max(track_lon_end)], + accent, + ) # decent SH mean start is in the top left + elif (hemis == "NH") & accent: + return ( + [min(track_lat_start), max(track_lat_end)], + [min(track_lon_start), max(track_lon_end)], + accent, + ) # accent NH mean start is in the lower left + elif (hemis == "NH") & ~accent: + return ( + [min(track_lat_start), max(track_lat_end)], + [max(track_lon_start), min(track_lon_end)], + accent, + ) # decent NH mean start is in the lower right + else: + raise ValueError("some defintions went wrong") def lat_min_max(B, beams_list, accent=None): @@ -126,25 +125,26 @@ def lat_min_max(B, beams_list, accent=None): returns: min_lat, max_lat, accent min and max latitudes of the beams, (True/False) True if the track is accending """ - #B, beams_list = B , high_beams - accent = track_type( B[beams_list[0]] ) if accent is None else accent - if B[beams_list[0]]['lats'].iloc[0] < 0: - hemis = 'SH' + accent = track_type(B[beams_list[0]]) if accent is None else accent + + if B[beams_list[0]]["lats"].iloc[0] < 0: + hemis = "SH" else: - hemis = 'NH' + hemis = "NH" - track_lat_mins, track_lat_maxs= list(), list() + track_lat_mins, track_lat_maxs = list(), list() for k in beams_list: - track_lat_mins.append( B[k]['lats'].min() ) - track_lat_maxs.append( B[k]['lats'].max() ) + track_lat_mins.append(B[k]["lats"].min()) + track_lat_maxs.append(B[k]["lats"].max()) - if hemis == 'SH': - return max(track_lat_maxs) , min(track_lat_mins), accent + if hemis == "SH": + return max(track_lat_maxs), min(track_lat_mins), accent else: return min(track_lat_mins), max(track_lat_maxs), accent -def derive_axis(TT, lat_lims = None): + +def derive_axis(TT, lat_lims=None): """ returns TT distance along track 'dist' in meters input: @@ -153,43 +153,38 @@ def derive_axis(TT, lat_lims = None): returns: TT with x,y,dist and order by dist """ - #TT, lat_lims = B[key], lat_lims_high + # derive distances in meters - r_e= 6.3710E+6 - dy= r_e*2*np.pi/360.0 - #deglon_in_m= np.cos(T2['lats']*np.pi/180.0)*dy + r_e = 6.3710e6 + dy = r_e * 2 * np.pi / 360.0 # either use position of the 1st photon or use defined start latitude if lat_lims is None: - TT['y']=(TT['lats'].max() - TT['lats']) *dy + TT["y"] = (TT["lats"].max() - TT["lats"]) * dy else: - TT['y']=(lat_lims[0] - TT['lats']) *dy + TT["y"] = (lat_lims[0] - TT["lats"]) * dy - #TT['y'] = (TT['lats']) *dy - - - if (lat_lims[2] == True): + if lat_lims[2] == True: # accending track - lon_min = TT['lons'].max() + lon_min = TT["lons"].max() else: # decending track - lon_min = TT['lons'].min() + lon_min = TT["lons"].min() - #print(lon_min) - TT['x'] = (TT['lons'] - lon_min) * np.cos( TT['lats']*np.pi/180.0 ) * dy - #TT['x'] = (TT['lons'] ) * np.cos( TT['lats']*np.pi/180.0 ) * dy - TT['dist'] = np.sqrt(TT['x']**2 + TT['y']**2) + TT["x"] = (TT["lons"] - lon_min) * np.cos(TT["lats"] * np.pi / 180.0) * dy + TT["dist"] = np.sqrt(TT["x"] ** 2 + TT["y"] ** 2) # set 1st dist to 0, not used if global limits are used if lat_lims is None: - TT['dist']= TT['dist']- TT['dist'].min() + TT["dist"] = TT["dist"] - TT["dist"].min() else: - TT['dist']= TT['dist']#- lat_lims[0] + TT["dist"] = TT["dist"] # - lat_lims[0] - TT=TT.sort_values(by='dist') + TT = TT.sort_values(by="dist") return TT -def reduce_to_height_distance(TT, key, dx=1, lat_lims = None): + +def reduce_to_height_distance(TT, key, dx=1, lat_lims=None): """ interpolates key (photos heights) to regular grid using 'dist' in pandas table TT. dx is the interpolation interval @@ -200,17 +195,18 @@ def reduce_to_height_distance(TT, key, dx=1, lat_lims = None): x1, y1 position, height """ from scipy.interpolate import interp1d + if type(dx) is np.ndarray: x1 = dx else: - x1 = np.arange(0,TT['dist'].max(), dx) - y1 = np.interp(x1, TT['dist'], TT[key] ) + x1 = np.arange(0, TT["dist"].max(), dx) + y1 = np.interp(x1, TT["dist"], TT[key]) return x1, y1 + # this is not need anymore def poly_correct(x, y, poly_order=7, plot_flag=False): - """ subtracts a fitted polynom to y inputs: @@ -220,38 +216,58 @@ def poly_correct(x, y, poly_order=7, plot_flag=False): returns y' y - polynom fit """ - z = np.polyfit(x , y , poly_order) + z = np.polyfit(x, y, poly_order) p = np.poly1d(z) if plot_flag: - plt.plot(x,y, '.', markersize=0.2,) - plt.plot(x, p(x), '-', markersize=0.2,) - #return z + plt.plot( + x, + y, + ".", + markersize=0.2, + ) + plt.plot( + x, + p(x), + "-", + markersize=0.2, + ) + return y - p(x) ### regridding -#@jit(nopython=True) -def get_mode(y, bins = np.arange(-5,5, 0.1)): + +# @jit(nopython=True) +def get_mode(y, bins=np.arange(-5, 5, 0.1)): "returns modes of histogram of y defined by bins" - hist, xbin = np.histogram(y, bins = bins ) + hist, xbin = np.histogram(y, bins=bins) return xbin[hist.argmax()] -@jit(nopython=True, parallel= False) + +@jit(nopython=True, parallel=False) def weighted_mean(x_rel, y): "returns the gaussian weighted mean for stencil" - #@jit(nopython=True, parallel= False) + # @jit(nopython=True, parallel= False) def weight_fnk(x): "returns gaussian weight given the distance to the center x" - return np.exp(- (x/.5)**2 ) + return np.exp(-((x / 0.5) ** 2)) w = weight_fnk(x_rel) - return np.sum(w*y)/np.sum(w) + return np.sum(w * y) / np.sum(w) -# this function is applied to beam: -def get_stencil_stats_shift( T2, stencil_iter, key_var , key_x_coord, stancil_width , Nphoton_min = 5, plot_flag= False): +# this function is applied to beam: +def get_stencil_stats_shift( + T2, + stencil_iter, + key_var, + key_x_coord, + stancil_width, + Nphoton_min=5, + plot_flag=False, +): """ T2 pd.Dataframe with beam data needs at least 'dist' and key stencil_iter np.array that constains the stancil boundaries and center [left boundary, center, right boundary] @@ -272,42 +288,35 @@ def get_stencil_stats_shift( T2, stencil_iter, key_var , key_x_coord, stancil_w """ import pandas as pd - stencil_1 = stencil_iter[:, ::2] - stencil_1half = stencil_iter[:, 1::2] - def calc_stencil_stats(group, key, key_x_coord, stancil_width, stancils): + stencil_1 = stencil_iter[:, ::2] + stencil_1half = stencil_iter[:, 1::2] - "returns stats per stencil" - #import time - #tstart = time.time() - Nphoton = group.shape[0] - istancil = group['x_bins'].iloc[int(Nphoton/2)] - stencil_center = stancils[1, istancil-1] + def calc_stencil_stats(group, key, key_x_coord, stancil_width, stancils): + "returns stats per stencil" + Nphoton = group.shape[0] + istancil = group["x_bins"].iloc[int(Nphoton / 2)] + stencil_center = stancils[1, istancil - 1] if Nphoton > Nphoton_min: - x_rel = (group[key_x_coord] - stencil_center)/ stancil_width - y = group[key] - - #Tmedian[key+ '_weighted_mean'] + x_rel = (group[key_x_coord] - stencil_center) / stancil_width + y = group[key] key_weighted_mean = weighted_mean(np.array(x_rel), np.array(y)) - key_std = y.std() - key_mode = get_mode(y) + key_std = y.std() + key_mode = get_mode(y) else: - - #Nphoton = 0 key_weighted_mean = np.nan - #Tmedian[key+ '_mode'] = np.nan - key_std = np.nan - key_mode = np.nan - - #Tweight = pd.DataFrame([key_weighted_mean, key_std, Nphoton], index= [key+ '_weighted_mean', key+ '_std', 'N_photos' ]) - Tweight = pd.Series([key_weighted_mean, key_std, Nphoton, key_mode], index= [key+ '_weighted_mean', key+ '_std', 'N_photos', key+ '_mode' ]) + key_std = np.nan + key_mode = np.nan + Tweight = pd.Series( + [key_weighted_mean, key_std, Nphoton, key_mode], + index=[key + "_weighted_mean", key + "_std", "N_photos", key + "_mode"], + ) - #print ( str( istancil) + ' s' + str(time.time() - tstart)) return Tweight.T T_sets = list() @@ -315,55 +324,56 @@ def calc_stencil_stats(group, key, key_x_coord, stancil_width, stancils): for stancil_set in [stencil_1, stencil_1half]: # select photons that are in bins - Ti_sel = T2[ (stancil_set[0,0] < T2['x']) & (T2['x'] < stancil_set[2,-1]) ] + Ti_sel = T2[(stancil_set[0, 0] < T2["x"]) & (T2["x"] < stancil_set[2, -1])] # put each photon in a bin - bin_labels = np.searchsorted(stancil_set[0,:], Ti_sel['x']) - #bin_labels2 = np.digitize( Ti_sel['x'], stancil_set[0,:], right = True ) + bin_labels = np.searchsorted(stancil_set[0, :], Ti_sel["x"]) - Ti_sel['x_bins'] =bin_labels + Ti_sel["x_bins"] = bin_labels # group data by this bin - Ti_g = Ti_sel.groupby(Ti_sel['x_bins'], dropna= False , as_index = True )#.median() - + Ti_g = Ti_sel.groupby(Ti_sel["x_bins"], dropna=False, as_index=True) # take median of the data Ti_median = Ti_g.median() # apply weighted mean and count photons - args = [ key_var, key_x_coord, stancil_width, stancil_set] + args = [key_var, key_x_coord, stancil_width, stancil_set] - #%timeit -r 1 -n 1 Ti_weight = Ti_g.apply(calc_stencil_stats, *args) - Ti_weight = Ti_g.apply(calc_stencil_stats, *args) + Ti_weight = Ti_g.apply(calc_stencil_stats, *args) - #merge both datasets - T_merged = pd.concat( [Ti_median, Ti_weight], axis= 1) + # merge both datasets + T_merged = pd.concat([Ti_median, Ti_weight], axis=1) # rename columns - T_merged = T_merged.rename(columns={key_var: key_var+'_median', key_x_coord: key_x_coord+ '_median'}) - T_merged[ key_var+ '_median'][ np.isnan(T_merged[key_var+ '_std']) ] = np.nan # replace median calculation with nans + T_merged = T_merged.rename( + columns={key_var: key_var + "_median", key_x_coord: key_x_coord + "_median"} + ) + T_merged[key_var + "_median"][ + np.isnan(T_merged[key_var + "_std"]) + ] = np.nan # replace median calculation with nans # set stancil center an new x-coodinate - T_merged['x'] = stancil_set[1, T_merged.index-1] + T_merged["x"] = stancil_set[1, T_merged.index - 1] T_sets.append(T_merged) # mergeboth stancils - T3 = pd.concat(T_sets ).sort_values(by= 'x').reset_index() + T3 = pd.concat(T_sets).sort_values(by="x").reset_index() if plot_flag: - Ti_1, Ti_1half = T_sets - - plt.plot( Ti_1half.iloc[0:60].x, Ti_1half.iloc[0:60]['heights_c_median'], '.' ) - plt.plot( Ti_1.iloc[0:60].x, Ti_1.iloc[0:60]['heights_c_median'], '.' ) - plt.plot( T3.iloc[0:120].x, T3.iloc[0:120]['heights_c_median'], '-' ) + Ti_1, Ti_1half = T_sets + plt.plot(Ti_1half.iloc[0:60].x, Ti_1half.iloc[0:60]["heights_c_median"], ".") + plt.plot(Ti_1.iloc[0:60].x, Ti_1.iloc[0:60]["heights_c_median"], ".") + plt.plot(T3.iloc[0:120].x, T3.iloc[0:120]["heights_c_median"], "-") return T3 # this function is applied to beam: -#old version -def get_stencil_stats(T2, stencil_iter, key , key_x_coord, stancil_width , Nphoton_min = 5, map_func=None): - +# old version +def get_stencil_stats( + T2, stencil_iter, key, key_x_coord, stancil_width, Nphoton_min=5, map_func=None +): """ T2 pd.DAtaframe with beam data needs at least 'dist' and key stencil_iter iterable that constains the stancil boundaries and center [left boundary, center, right boundary] @@ -396,67 +406,64 @@ def calc_stencil_stats(istencil): "returns stats per stencil" tstart = time.time() - i_mask = (x_data >= istencil[0]) & (x_data < istencil[2]) - Nphoton = sum(i_mask) + i_mask = (x_data >= istencil[0]) & (x_data < istencil[2]) + Nphoton = sum(i_mask) if Nphoton < Nphoton_min: Tmedian = T2[i_mask].median() - Tmedian[key+ '_weighted_mean'] = np.nan - Tmedian[key+ '_mode'] = np.nan - Tmedian['N_photos'] = Nphoton - Tmedian[key+ '_std'] = np.nan + Tmedian[key + "_weighted_mean"] = np.nan + Tmedian[key + "_mode"] = np.nan + Tmedian["N_photos"] = Nphoton + Tmedian[key + "_std"] = np.nan return istencil[1], Tmedian + x_rel = (x_data[i_mask] - istencil[1]) / stancil_width + y = y_data[i_mask] - x_rel = (x_data[i_mask] - istencil[1])/ stancil_width - y = y_data[i_mask] + Tmedian = T2[i_mask].median() + Tmedian[key + "_weighted_mean"] = weighted_mean(x_rel, y) + Tmedian[key + "_mode"] = get_mode(y) + Tmedian["N_photos"] = Nphoton + Tmedian[key + "_std"] = y.std() - Tmedian = T2[i_mask].median() - Tmedian[key+ '_weighted_mean'] = weighted_mean(x_rel, y) - Tmedian[key+ '_mode'] = get_mode(y) - Tmedian['N_photos'] = Nphoton - Tmedian[key+ '_std'] = y.std() - #Tmedian[key+ '_median'][ np.isnan(Tmedian[key+ 'std']) ]= np.nan # replace median calculation with nans - print ( str( istencil[1]) + ' s' + str(time.time() - tstart)) + print(str(istencil[1]) + " s" + str(time.time() - tstart)) return istencil[1], Tmedian # apply func to all stancils map_func = map if map_func is None else map_func - D_filt = dict(map_func(calc_stencil_stats, stencil_iter)) - - DF_filt = pd.DataFrame.from_dict(D_filt, orient='index') - DF_filt = DF_filt.rename(columns={key: key+'_median', key_x_coord: 'median_'+key_x_coord}) - DF_filt[ key+ '_median'][ np.isnan(DF_filt[key+ '_std']) ] = np.nan # replace median calculation with nans + D_filt = dict(map_func(calc_stencil_stats, stencil_iter)) + + DF_filt = pd.DataFrame.from_dict(D_filt, orient="index") + DF_filt = DF_filt.rename( + columns={key: key + "_median", key_x_coord: "median_" + key_x_coord} + ) + DF_filt[key + "_median"][ + np.isnan(DF_filt[key + "_std"]) + ] = np.nan # replace median calculation with nans DF_filt[key_x_coord] = DF_filt.index - DF_filt = DF_filt.reset_index() + DF_filt = DF_filt.reset_index() return DF_filt -# %% old version -# define common dist_grid: -#dx= 5 # 2 * resolution in meters, datapoint +-dx are used to take the mean -#dist_grid = np.arange( np.nanmin(dist_list[:, 0], 0) , np.nanmax(dist_list[:, 1], 0), dx ) # derive bin means def bin_means(T2, dist_grid): - dF_mean = pd.DataFrame(index =T2.columns) - ilim = int(len(dist_grid)) - N_i = list() + dF_mean = pd.DataFrame(index=T2.columns) + ilim = int(len(dist_grid)) + N_i = list() - for i in np.arange(1,ilim-1, 1): - if i % 5000 ==0: + for i in np.arange(1, ilim - 1, 1): + if i % 5000 == 0: print(i) - i_mask=(T2['dist'] >= dist_grid[i-1]) & (T2['dist'] < dist_grid[i+1]) - #if ( (T2['dist'] >= dist_grid[i-1]) & (T2['dist'] < dist_grid[i+1]) ).sum() > 0: + i_mask = (T2["dist"] >= dist_grid[i - 1]) & (T2["dist"] < dist_grid[i + 1]) dF_mean[i] = T2[i_mask].mean() - #dF_median[i] = T2[i_mask].median() N_i.append(i_mask.sum()) - dF_mean = dF_mean.T - dF_mean['N_photos'] = N_i - dF_mean['dist'] = dist_grid[np.arange(1,ilim-1, 1)] + dF_mean = dF_mean.T + dF_mean["N_photos"] = N_i + dF_mean["dist"] = dist_grid[np.arange(1, ilim - 1, 1)] return dF_mean diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py b/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py index 45444490..3fb63f35 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py @@ -37,9 +37,6 @@ def init_from_input(arguments): else: track_name = arguments[1] batch_key = arguments[2] - # $(hemisphere) $(coords) $(config) - - # print("read vars from file: " + str(arguments[1])) if len(arguments) >= 4: if arguments[3] == "True": @@ -49,16 +46,9 @@ def init_from_input(arguments): else: test_flag = arguments[3] - # print("test_flag found, test_flag= " + str(test_flag)) else: test_flag = False - # TODO: print statements to be handled with logger - # # print(track_name) - - # print("----- batch =" + batch_key) - # print("----- test_flag: " + str(test_flag)) - return track_name, batch_key, test_flag @@ -193,7 +183,7 @@ def set_ATL03_trackname(self): def set_ATL10_trackname(self): block1 = (self.YY, self.MM, self.DD) block1b = (self.HH, self.MN, self.SS) - block2 = (self.TRK, self.CYC, "01") # granule is alwasy '01' for ATL10 + block2 = (self.TRK, self.CYC, "01") if self.RL is "": raise ValueError("RL not set") if self.VRS is "": @@ -499,7 +489,7 @@ def getATL03_beam(fileT, numpy=False, beam="gt1l", maxElev=1e6): "signal_confidence": signal_confidence, "mask_seaice": mask_seaice, "delta_time": delta_time, - "along_track_distance": along_track_distance, #'delta_time_granule':delta_time_granule, + "along_track_distance": along_track_distance, "across_track_distance": across_track_distance, "ph_id_count": ph_id_count, } @@ -520,11 +510,6 @@ def getATL03_beam(fileT, numpy=False, beam="gt1l", maxElev=1e6): print("df shape ", dF.shape) dF = dF[mask_total] - # dF_seg = dF_seg[mask_total] - # print('df[mask] shape ',dF.shape) - - # Reset row indexing - # dF=dF#.reset_index(drop=True) return dF, dF_seg diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py index 3396b57f..f8ade32a 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py @@ -1,6 +1,7 @@ import numpy as np -def lanczos_1d(width, dx, a=2): + +def lanczos_1d(width, dx, a=2): """ This is a 1D lanczos Filter for time series analysis. it generates the Filter to be convolved with the timeseries @@ -18,25 +19,26 @@ def lanczos_1d(width, dx, a=2): # a= 1 # Lanczos parameter. the length of the filter is a*width # dx= .1 # deltax of the to be filtered timeseries - r=width/2.0 - xl=a*r - x= np.arange(-xl, xl, dx) - xprime=x/r + r = width / 2.0 + xl = a * r + x = np.arange(-xl, xl, dx) + xprime = x / r # define the filter - L = np.sinc(xprime) * np.sinc(xprime/a) - L = np.where((xprime > -a) & (xprime < a),L, 0) + L = np.sinc(xprime) * np.sinc(xprime / a) + L = np.where((xprime > -a) & (xprime < a), L, 0) - return x, L/L.sum() + return x, L / L.sum() -def lanczos_2d(width , dx, a=2): - x , L =lanczos_1d(width, dx, a=a) - L2d =np.outer(L ,L.T) +def lanczos_2d(width, dx, a=2): + x, L = lanczos_1d(width, dx, a=a) + L2d = np.outer(L, L.T) return x, L2d -def lanczos_filter_1d(x, data, width, a=2 , mode='same', method='direct'): + +def lanczos_filter_1d(x, data, width, a=2, mode="same", method="direct"): """ colvolves the lanzcos filter with data. inputs @@ -52,15 +54,16 @@ def lanczos_filter_1d(x, data, width, a=2 , mode='same', method='direct'): data_lp low-passed data, same size as before. """ import scipy.signal as signal - dx = np.diff(x).mean() - x , L = lanczos_1d(width, dx, a=a) + dx = np.diff(x).mean() + x, L = lanczos_1d(width, dx, a=a) - data_lp= signal.convolve(data, L, mode=mode, method=method)#* + data_lp = signal.convolve(data, L, mode=mode, method=method) # * return data_lp -def lanczos_filter_1d_wrapping(x, data, width, a=2 , mode='wrap'): + +def lanczos_filter_1d_wrapping(x, data, width, a=2, mode="wrap"): """ colvolves the lanzcos filter with data. same as lanczos_filter_1d but can wrap around @@ -78,16 +81,16 @@ def lanczos_filter_1d_wrapping(x, data, width, a=2 , mode='wrap'): data_lp low-passed data, same size as before. """ import scipy.ndimage - dx = np.diff(x).mean() - x , L = lanczos_1d(width, dx, a=a) - data_lp= scipy.ndimage.convolve(data, L, mode=mode)#* + dx = np.diff(x).mean() + x, L = lanczos_1d(width, dx, a=a) - return data_lp + data_lp = scipy.ndimage.convolve(data, L, mode=mode) # * + return data_lp -def lanczos_filter_2d(x, data, width, a=2 , mode='same'): +def lanczos_filter_2d(x, data, width, a=2, mode="same"): """ colvolves the lanzcos filter with data in 3 dimensions. inputs @@ -104,27 +107,27 @@ def lanczos_filter_2d(x, data, width, a=2 , mode='same'): """ import scipy.ndimage.filters as signal - #import scipy.ndimage.filters as signal - dx = abs(np.diff(x).mean()) - x , L2d = lanczos_2d(width, dx, a=a) + dx = abs(np.diff(x).mean()) + x, L2d = lanczos_2d(width, dx, a=a) - - data_lp= signal.convolve(data, L2d, mode=mode)#* + data_lp = signal.convolve(data, L2d, mode=mode) # * return data_lp -def lanczos_filter_2d_apply(data, x, width, a=2 , mode='same'): - return lanczos_filter_2d(x, data, width, a=a , mode=mode) -def lanczos_3d(width , dx, a=2): - x , L =lanczos_1d(width, dx, a=a) - L2d =np.outer(L ,L.T) +def lanczos_filter_2d_apply(data, x, width, a=2, mode="same"): + return lanczos_filter_2d(x, data, width, a=a, mode=mode) + + +def lanczos_3d(width, dx, a=2): + x, L = lanczos_1d(width, dx, a=a) + L2d = np.outer(L, L.T) L3d = np.multiply.outer(L2d, L.T) return x, L3d -def lanczos_filter_3d(x, data, width, a=2 , mode='same'): +def lanczos_filter_3d(x, data, width, a=2, mode="same"): """ colvolves the lanzcos filter with data in 3 dimensions. inputs @@ -141,11 +144,9 @@ def lanczos_filter_3d(x, data, width, a=2 , mode='same'): """ import scipy.ndimage.filters as signal - #import scipy.ndimage.filters as signal - dx = abs(np.diff(x).mean()) - x , L3d = lanczos_3d(width, dx, a=a) - + dx = abs(np.diff(x).mean()) + x, L3d = lanczos_3d(width, dx, a=a) - data_lp= signal.convolve(data, L3d, mode=mode)#* + data_lp = signal.convolve(data, L3d, mode=mode) # * return data_lp diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py b/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py index e449fef6..1777d1f6 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py @@ -8,130 +8,146 @@ import osgeo.ogr import matplotlib.pyplot as plt + # PURPOSE: read ICESat-2 ground tracks for TRACK and BEAM def read_ICESat2_groundtrack(input_file): # decompress and parse KMZ file input_file = pathlib.Path(input_file).expanduser().absolute() - kmls = zipfile.ZipFile(str(input_file), 'r') + kmls = zipfile.ZipFile(str(input_file), "r") parser = lxml.etree.XMLParser(recover=True, remove_blank_text=True) # list of geodataframes for all RGTs RGTS = [] # for each kml in the zipfile (per RGT) for kml in kmls.filelist: - tree = lxml.etree.parse(kmls.open(kml, 'r'), parser) + tree = lxml.etree.parse(kmls.open(kml, "r"), parser) root = tree.getroot() # create list of rows rows = [] # find documents within kmz file - for document in root.iterfind('.//kml:Document//Folder//Placemark', root.nsmap): + for document in root.iterfind(".//kml:Document//Folder//Placemark", root.nsmap): # extract laser name, satellite track and coordinates of line strings - description = document.find('description', root.nsmap).text + description = document.find("description", root.nsmap).text columns = {} - columns['RGT'], = re.findall(r'RGT\s(\d+)',description) + (columns["RGT"],) = re.findall(r"RGT\s(\d+)", description) # get date and time - date = re.findall(r'\d{2}\-\w{3}\-\d{4}\s\d{2}\:\d{2}\:\d{2}', description).pop() - columns['date'] = geopandas.pd.to_datetime(date, format='%d-%b-%Y %H:%M:%S') - columns['DOY'], = re.findall(r'DOY\s(\d+)', description) - columns['cycle'], = re.findall(r'Cycle\s(\d+)', description) - coords = document.findall('Point/coordinates',root.nsmap) + date = re.findall( + r"\d{2}\-\w{3}\-\d{4}\s\d{2}\:\d{2}\:\d{2}", description + ).pop() + columns["date"] = geopandas.pd.to_datetime(date, format="%d-%b-%Y %H:%M:%S") + (columns["DOY"],) = re.findall(r"DOY\s(\d+)", description) + (columns["cycle"],) = re.findall(r"Cycle\s(\d+)", description) + coords = document.findall("Point/coordinates", root.nsmap) # for each set of coordinates - for i,c in enumerate(coords): - points = np.array([x.split(',')[:2] for x in c.text.split()],dtype='f8') - columns['geometry'], = geopandas.points_from_xy(points[:,0],points[:,1]) + for i, c in enumerate(coords): + points = np.array( + [x.split(",")[:2] for x in c.text.split()], dtype="f8" + ) + (columns["geometry"],) = geopandas.points_from_xy( + points[:, 0], points[:, 1] + ) rows.append(columns) # create geopandas geodataframe for points gdf = geopandas.GeoDataFrame(rows) RGTS.append(gdf) # return the concatenated geodataframe - return geopandas.pd.concat(RGTS).set_index('date') + return geopandas.pd.concat(RGTS).set_index("date") # PURPOSE: read ICESat-2 ground tracks def ICESat2_mission_groundtrack(input_file): # decompress and parse KMZ file input_file = pathlib.Path(input_file).expanduser().absolute() - kmzs = zipfile.ZipFile(str(input_file), 'r') + kmzs = zipfile.ZipFile(str(input_file), "r") parser = lxml.etree.XMLParser(recover=True, remove_blank_text=True) # for each kml in the zipfile (per GT) GTs = [] for kmz in kmzs.filelist: - kmls = zipfile.ZipFile(kmzs.open(kmz, 'r')) + kmls = zipfile.ZipFile(kmzs.open(kmz, "r")) for kml in kmls.filelist: - tree = lxml.etree.parse(kmls.open(kml, 'r'), parser) + tree = lxml.etree.parse(kmls.open(kml, "r"), parser) root = tree.getroot() # find documents within kmz file - for document in root.iterfind('.//kml:Document', root.nsmap): + for document in root.iterfind(".//kml:Document", root.nsmap): # extract laser name, satellite track and coordinates of line strings - name = document.find('name',root.nsmap).text - placemarks = document.findall('Placemark/name',root.nsmap) - coords = document.findall('Placemark/LineString/coordinates',root.nsmap) + name = document.find("name", root.nsmap).text + placemarks = document.findall("Placemark/name", root.nsmap) + coords = document.findall( + "Placemark/LineString/coordinates", root.nsmap + ) # create list of rows rows = [] wkt = [] # for each set of coordinates - for i,c in enumerate(coords): + for i, c in enumerate(coords): columns = {} - columns['Laser'], = re.findall(r'laser(\d+)', name) - columns['GT'], = re.findall(r'GT\d[LR]?', kmz.filename) - columns['RGT'] = int(placemarks[i].text) - coords = document.findall('Point/coordinates',root.nsmap) + (columns["Laser"],) = re.findall(r"laser(\d+)", name) + (columns["GT"],) = re.findall(r"GT\d[LR]?", kmz.filename) + columns["RGT"] = int(placemarks[i].text) + coords = document.findall("Point/coordinates", root.nsmap) # create LineString object linestring = osgeo.ogr.Geometry(osgeo.ogr.wkbLineString) - line = np.array([x.split(',')[:2] for x in c.text.split()],dtype='f8') - for ln,lt in zip(line[:,0],line[:,1]): + line = np.array( + [x.split(",")[:2] for x in c.text.split()], dtype="f8" + ) + for ln, lt in zip(line[:, 0], line[:, 1]): linestring.AddPoint(ln, lt) # convert to wkt and then add to geometry wkt.append(linestring.ExportToWkt()) rows.append(columns) # create geopandas geodataframe for points - gdf = geopandas.GeoDataFrame(rows, - geometry=geopandas.GeoSeries.from_wkt(wkt) + gdf = geopandas.GeoDataFrame( + rows, geometry=geopandas.GeoSeries.from_wkt(wkt) ) GTs.append(gdf) # return the concatenated geodataframe return geopandas.pd.concat(GTs) + # PURPOSE: read ICESat-2 mission ground tracks as points def ICESat2_mission_points(input_file): # decompress and parse KMZ file input_file = pathlib.Path(input_file).expanduser().absolute() - kmzs = zipfile.ZipFile(str(input_file), 'r') + kmzs = zipfile.ZipFile(str(input_file), "r") parser = lxml.etree.XMLParser(recover=True, remove_blank_text=True) # for each kml in the zipfile (per GT) GTs = [] for kmz in kmzs.filelist: - kmls = zipfile.ZipFile(kmzs.open(kmz, 'r')) + kmls = zipfile.ZipFile(kmzs.open(kmz, "r")) for kml in kmls.filelist: - tree = lxml.etree.parse(kmls.open(kml, 'r'), parser) + tree = lxml.etree.parse(kmls.open(kml, "r"), parser) root = tree.getroot() # find documents within kmz file - for document in root.iterfind('.//kml:Document', root.nsmap): + for document in root.iterfind(".//kml:Document", root.nsmap): # extract laser name, satellite track and coordinates of line strings - name = document.find('name', root.nsmap).text - placemarks = document.findall('Placemark/name', root.nsmap) - coords = document.findall('Placemark/LineString/coordinates', root.nsmap) + name = document.find("name", root.nsmap).text + placemarks = document.findall("Placemark/name", root.nsmap) + coords = document.findall( + "Placemark/LineString/coordinates", root.nsmap + ) # create list of rows rows = [] - x = []; y = [] + x = [] + y = [] # for each set of coordinates - for i,c in enumerate(coords): + for i, c in enumerate(coords): # create a line string of coordinates - line = np.array([x.split(',')[:2] for x in c.text.split()], dtype='f8') - for ln,lt in zip(line[:,0], line[:,1]): + line = np.array( + [x.split(",")[:2] for x in c.text.split()], dtype="f8" + ) + for ln, lt in zip(line[:, 0], line[:, 1]): columns = {} - columns['Laser'], = re.findall(r'laser(\d+)', name) - columns['GT'], = re.findall(r'GT\d[LR]?', kmz.filename) - columns['RGT'] = int(placemarks[i].text) + (columns["Laser"],) = re.findall(r"laser(\d+)", name) + (columns["GT"],) = re.findall(r"GT\d[LR]?", kmz.filename) + columns["RGT"] = int(placemarks[i].text) rows.append(columns) x.append(ln) y.append(lt) # create geopandas geodataframe for points - gdf = geopandas.GeoDataFrame(rows, - geometry=geopandas.points_from_xy(x,y) + gdf = geopandas.GeoDataFrame( + rows, geometry=geopandas.points_from_xy(x, y) ) GTs.append(gdf) # return the concatenated and georefernced geodataframe G = geopandas.pd.concat(GTs) - G.geometry.crs = {'init': 'epsg:4326'} + G.geometry.crs = {"init": "epsg:4326"} return G - diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py b/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py index a370c3cc..f084db97 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py @@ -406,7 +406,6 @@ def define_x_coordinate_in_polygon(table_data, polygon, round=True): if ascending_test(table_data): table_data["x"] = table_data["x_atc"] - min_eq_dist else: - # print('descending') table_data["x"] = ((np.pi * 6371 * 1e3) - min_eq_dist) - table_data["x_atc"] return table_data diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index d46d9ea2..bcc8afde 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -2,7 +2,7 @@ # basic functions -def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): +def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): """ returns all need chunk boudaries and center position given L, and ov inputs: @@ -13,17 +13,18 @@ def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): if iter_flag True returns iter else it returns an ndarray """ - ov=int(np.round(L/2)) if ov is None else ov + ov = int(np.round(L / 2)) if ov is None else ov - - xleft = np.arange(0,dsize-int(L-ov),int(L-ov)) - xright = np.arange(int(L-ov)*2,dsize+1,int(L-ov)) - xcenter_pos = np.arange(int(L-ov),dsize-int(L-ov)+1,int(L-ov)) - max_size = min([xleft.size , xcenter_pos.size, xright.size]) + xleft = np.arange(0, dsize - int(L - ov), int(L - ov)) + xright = np.arange(int(L - ov) * 2, dsize + 1, int(L - ov)) + xcenter_pos = np.arange(int(L - ov), dsize - int(L - ov) + 1, int(L - ov)) + max_size = min([xleft.size, xcenter_pos.size, xright.size]) # if xright[max_size-1] < dsize: # print('left out last ' + str(dsize- xright[max_size-1]) + ' data points' ) - #print([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) - position_stancil = np.vstack([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) + # print([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) + position_stancil = np.vstack( + [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] + ) if iter_flag is True: return iter(position_stancil.T.tolist()) @@ -31,7 +32,7 @@ def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): return position_stancil -def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov= None, iter_flag=True): +def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag=True): """ returns all need chunk boudaries and center position given L, and ov inputs: @@ -42,74 +43,78 @@ def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov= None, iter_fl if iter_flag True returns iter else it returns an ndarray """ - L= L_unit - ov=np.round(L/2) if ov is None else ov - #print(ov) - dl = (L-ov) - xleft = np.arange(data_limits[0] , data_limits[1]-dl, dl ) - xcenter_pos = np.arange(data_limits[0]+ L/2 , data_limits[1]-dl+1, dl ) - xright = np.arange(data_limits[0] + L , data_limits[1]+1, dl ) - - - max_size = min([xleft.size , xcenter_pos.size, xright.size]) + L = L_unit + ov = np.round(L / 2) if ov is None else ov + # print(ov) + dl = L - ov + xleft = np.arange(data_limits[0], data_limits[1] - dl, dl) + xcenter_pos = np.arange(data_limits[0] + L / 2, data_limits[1] - dl + 1, dl) + xright = np.arange(data_limits[0] + L, data_limits[1] + 1, dl) + + max_size = min([xleft.size, xcenter_pos.size, xright.size]) # if xright[max_size-1] < data_limits[1]: # print('left out last ' + str(data_limits[1]- xright[max_size-1]) + ' data points' ) - #print([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) - position_stancil = np.vstack([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) + # print([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) + position_stancil = np.vstack( + [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] + ) if iter_flag is True: return iter(position_stancil.T.tolist()) else: return position_stancil + def Z_to_power(Z, df, N): - """ compute the 1d spectrum of a field phi + """compute the 1d spectrum of a field phi inputs: Z complex fourier coefficients df frequency / or wavenumber step N length of data vector in real space (= L) """ - spec = 2.*(Z*Z.conj()).real / df /N**2 - neven = True if (N%2) else False + spec = 2.0 * (Z * Z.conj()).real / df / N**2 + neven = True if (N % 2) else False # the zeroth frequency should be counted only once - spec[0] = spec[0]/2. + spec[0] = spec[0] / 2.0 if neven: - spec[-1] = spec[-1]/2. + spec[-1] = spec[-1] / 2.0 return spec + # 2nd cal spectra def calc_spectrum_fft(phi, df, N): - """ compute the 1d spectrum of a field phi + """compute the 1d spectrum of a field phi inputs: df frequency / or wavenumber step N length of data vector in real space (= L) neven bool, if True """ - neven = True if (N%2) else False + neven = True if (N % 2) else False phih = np.fft.rfft(phi) # the factor of 2 comes from the symmetry of the Fourier coeffs - spec = 2.*(phih*phih.conj()).real / df /N**2 + spec = 2.0 * (phih * phih.conj()).real / df / N**2 # the zeroth frequency should be counted only once - spec[0] = spec[0]/2. + spec[0] = spec[0] / 2.0 if neven: - spec[-1] = spec[-1]/2. + spec[-1] = spec[-1] / 2.0 return spec -def LS_power_to_PSD( ls_power, L , dff): +def LS_power_to_PSD(ls_power, L, dff): """ returns Power spectral density (unit^2/dfreq) ls_power output of astropy.timeseries.LombScargle.power with normalization='psd' """ - return 2 * ls_power / L /dff + return 2 * ls_power / L / dff -def calc_spectrum_LS( x, y, k, err=None, LS= None, dk =None): + +def calc_spectrum_LS(x, y, k, err=None, LS=None, dk=None): """ returns: Power spectral density of y given postitions x, for wanumbers k @@ -119,16 +124,18 @@ def calc_spectrum_LS( x, y, k, err=None, LS= None, dk =None): """ if LS is None: from astropy.timeseries import LombScargle - LS = LombScargle(x , y, dy = err, fit_mean=False, center_data=True) + + LS = LombScargle(x, y, dy=err, fit_mean=False, center_data=True) else: LS.t = x LS.y = y - LS.dy= err + LS.dy = err + + ls_power = LS.power(k, normalization="psd", assume_regular_frequency="False") - ls_power = LS.power(k, normalization='psd', assume_regular_frequency='False') + dk = np.diff(k).mean() if dk is None else dk + return 2 * ls_power / y.size / dk, LS - dk = np.diff(k).mean() if dk is None else dk - return 2 * ls_power / y.size / dk , LS def reconstruct_data_from_LS(LS, x_real_axis, freq): """ @@ -141,16 +148,18 @@ def reconstruct_data_from_LS(LS, x_real_axis, freq): y_reconstruct = LS.offset() * np.ones(len(x_real_axis)) freq_seq = freq[1:] if freq[0] == 0 else freq - freq_mask= freq <= 1/100 + freq_mask = freq <= 1 / 100 - #print(freq_seq) + # print(freq_seq) for fi in freq_seq: try: theta = LS.model_parameters(fi) except: - theta = [0,0] - y_reconstruct += theta[0] * np.sin(x_real_axis * 2 * np.pi *fi ) + theta[1]* np.cos(x_real_axis * 2 * np.pi *fi) - #y_reconstruct += LS.model(x_real_axis, fi) + theta = [0, 0] + y_reconstruct += theta[0] * np.sin(x_real_axis * 2 * np.pi * fi) + theta[ + 1 + ] * np.cos(x_real_axis * 2 * np.pi * fi) + # y_reconstruct += LS.model(x_real_axis, fi) # for fi in freq_seq[:]: # theta = LS.model_parameters(fi) @@ -159,20 +168,22 @@ def reconstruct_data_from_LS(LS, x_real_axis, freq): return y_reconstruct + def calc_freq_fft(x_grid, N): - """ calculate array of spectral variable (frequency or - wavenumber) in cycles per unit of L """ + """calculate array of spectral variable (frequency or + wavenumber) in cycles per unit of L""" - neven = True if (N%2) else False - #dx=np.diff(x_grid).mean() - dx = np.round(np.median(np.diff(x_grid) ), 1) - df = 1./((N-1)*dx) + neven = True if (N % 2) else False + # dx=np.diff(x_grid).mean() + dx = np.round(np.median(np.diff(x_grid)), 1) + df = 1.0 / ((N - 1) * dx) if neven: - f = df*np.arange(N/2+1) + f = df * np.arange(N / 2 + 1) else: - f = df*np.arange( (N-1)/2. + 1 ) - return f,df + f = df * np.arange((N - 1) / 2.0 + 1) + return f, df + def calc_freq_fft_given_dx(dx, N): """ @@ -182,17 +193,25 @@ def calc_freq_fft_given_dx(dx, N): N number of datapoints used in window """ - neven = True if (N%2) else False - df = 1./((N-1)*dx) + neven = True if (N % 2) else False + df = 1.0 / ((N - 1) * dx) if neven: - f = df*np.arange(N/2+1) + f = df * np.arange(N / 2 + 1) else: - f = df*np.arange( (N-1)/2. + 1 ) - return f,df - - -def calc_freq_LS(x, N, method='fftX2', dx=None, minimum_frequency=None, maximum_frequency=None, samples_per_peak=0.01): + f = df * np.arange((N - 1) / 2.0 + 1) + return f, df + + +def calc_freq_LS( + x, + N, + method="fftX2", + dx=None, + minimum_frequency=None, + maximum_frequency=None, + samples_per_peak=0.01, +): """ calculate array of spectral variable (frequency or wavenumber) in cycles per unit of N (window length in number of data points) @@ -204,42 +223,48 @@ def calc_freq_LS(x, N, method='fftX2', dx=None, minimum_frequency=None, maximum_ minimum_frequency, maximum_frequency only used for LS_auto """ - if method is 'fftX2': - neven = True if (N%2) else False + if method is "fftX2": + neven = True if (N % 2) else False dx = np.diff(x).mean() if dx is None else dx - df = 1./((N-1)*dx) /2 + df = 1.0 / ((N - 1) * dx) / 2 if neven: - f = df*np.arange(df, N+1) + f = df * np.arange(df, N + 1) else: - f = df* np.arange(df, (N-1) + 1 ) + f = df * np.arange(df, (N - 1) + 1) - elif method is 'fft': - neven = True if (N%2) else False + elif method is "fft": + neven = True if (N % 2) else False dx = np.diff(x).mean() if dx is None else dx - df = 1./((N-1)*dx) + df = 1.0 / ((N - 1) * dx) if neven: - f = df*np.arange(N/2+1) + f = df * np.arange(N / 2 + 1) else: - f = df*np.arange( (N-1)/2. + 1 ) + f = df * np.arange((N - 1) / 2.0 + 1) - elif method is 'LS_auto': + elif method is "LS_auto": from astropy.timeseries import LombScargle - f = LombScargle(x , np.random.randn(len(x)), fit_mean=True).autofrequency(minimum_frequency=minimum_frequency, maximum_frequency=maximum_frequency, samples_per_peak=samples_per_peak)##0.1) + + f = LombScargle(x, np.random.randn(len(x)), fit_mean=True).autofrequency( + minimum_frequency=minimum_frequency, + maximum_frequency=maximum_frequency, + samples_per_peak=samples_per_peak, + ) ##0.1) df = np.diff(f).mean() df = np.round(df, 5) - elif method is 'fixed_ratio': + elif method is "fixed_ratio": - neven = True if (N%2) else False + neven = True if (N % 2) else False dx = np.diff(x).mean() if dx is None else dx df = dx / 50 if neven: - f = df*np.arange(df, N +1) + f = df * np.arange(df, N + 1) else: - f = df* np.arange(df, N ) + f = df * np.arange(df, N) + + return f, df - return f ,df def create_window(L, window=None): """ @@ -247,65 +272,66 @@ def create_window(L, window=None): if window is not None it show have a length of N """ if window is None: - win=np.hanning(L) + win = np.hanning(L) else: - win=window + win = window - factor=np.sqrt(L/(win**2).sum()) - win*=factor + factor = np.sqrt(L / (win**2).sum()) + win *= factor return win + def create_weighted_window(data, window=None): """ define window function and weight it to conserve variance if window is not None it show have a length of N """ import scipy.signal.windows as WINDOWS + L = data.size if window is None: - #win=np.hanning(L) - win = WINDOWS.tukey(L, alpha=0.1, sym=True) + # win=np.hanning(L) + win = WINDOWS.tukey(L, alpha=0.1, sym=True) else: - win=window + win = window - factor = np.sqrt( np.var(data) / np.var(( data* win) ) ) - #factor=np.sqrt( L/(win**2).sum()) - win *= factor + factor = np.sqrt(np.var(data) / np.var((data * win))) + # factor=np.sqrt( L/(win**2).sum()) + win *= factor return win -def spec_error(E,sn,ci=.95): - - """ Computes confidence interval for one-dimensional spectral - estimate E (the power spectra). - Parameters - =========== - - sn is the number of spectral realizations; - it can be either an scalar or an array of size(E) - - ci = .95 for 95 % confidence interval +def spec_error(E, sn, ci=0.95): + """Computes confidence interval for one-dimensional spectral + estimate E (the power spectra). - Output - ========== - lower (El) and upper (Eu) bounds on E """ + Parameters + =========== + - sn is the number of spectral realizations; + it can be either an scalar or an array of size(E) + - ci = .95 for 95 % confidence interval + Output + ========== + lower (El) and upper (Eu) bounds on E""" - - def yNlu(sn,yN,ci): - """ compute yN[l] yN[u], that is, the lower and - upper limit of yN """ + def yNlu(sn, yN, ci): + """compute yN[l] yN[u], that is, the lower and + upper limit of yN""" from scipy.special import gammainc + # cdf of chi^2 dist. with 2*sn DOF - cdf = gammainc(sn,sn*yN) + cdf = gammainc(sn, sn * yN) # indices that delimit the wedge of the conf. interval fl = np.abs(cdf - ci).argmin() - fu = np.abs(cdf - 1. + ci).argmin() + fu = np.abs(cdf - 1.0 + ci).argmin() - return yN[fl],yN[fu] + return yN[fl], yN[fu] - dbin = .005 - yN = np.arange(0,2.+dbin,dbin) + dbin = 0.005 + yN = np.arange(0, 2.0 + dbin, dbin) El, Eu = np.empty_like(E), np.empty_like(E) @@ -319,19 +345,19 @@ def yNlu(sn,yN,ci): assert n == E.size, " *** sn has different size than E " for i in range(n): - yNl,yNu = yNlu(sn[i],yN=yN,ci=ci) - El[i] = E[i]/yNl - Eu[i] = E[i]/yNu + yNl, yNu = yNlu(sn[i], yN=yN, ci=ci) + El[i] = E[i] / yNl + Eu[i] = E[i] / yNu else: - yNl,yNu = yNlu(sn,yN=yN,ci=ci) - El = E/yNl - Eu = E/yNu + yNl, yNu = yNlu(sn, yN=yN, ci=ci) + El = E / yNl + Eu = E / yNu return El, Eu -def linear_gap_fill(F, key_lead, key_int): +def linear_gap_fill(F, key_lead, key_int): """ F pd.DataFrame key_lead key in F that determined the independent coordindate @@ -339,13 +365,13 @@ def linear_gap_fill(F, key_lead, key_int): """ y_g = np.array(F[key_int]) - nans, x2= np.isnan(y_g), lambda z: z.nonzero()[0] - y_g[nans]= np.interp(x2(nans), x2(~nans), y_g[~nans]) + nans, x2 = np.isnan(y_g), lambda z: z.nonzero()[0] + y_g[nans] = np.interp(x2(nans), x2(~nans), y_g[~nans]) return y_g -def sub_sample_coords(X, lons, lats, stancils, map_func =None): +def sub_sample_coords(X, lons, lats, stancils, map_func=None): """ X non-nan array of coodinate along beam lons, lats arrays of postion data that should be mapped. must have same size as X @@ -357,20 +383,21 @@ def sub_sample_coords(X, lons, lats, stancils, map_func =None): """ import copy + def get_lon_lat_coords(stancil): - x_mask= (stancil[0] <= X) & (X <= stancil[-1]) - #print(stancil[1]) - if sum(x_mask) ==0: # if there are not enough photos set results to nan + x_mask = (stancil[0] <= X) & (X <= stancil[-1]) + # print(stancil[1]) + if sum(x_mask) == 0: # if there are not enough photos set results to nan return np.array([stancil[1], np.nan, np.nan]) lon_bin, lat_bin = lons[x_mask].mean(), lats[x_mask].mean() - return np.array([stancil[1],lon_bin, lat_bin]) + return np.array([stancil[1], lon_bin, lat_bin]) map_func = map if map_func is None else map_func - #print(map_func) - coord_positions = list(map_func( get_lon_lat_coords, copy.copy(stancils) )) + # print(map_func) + coord_positions = list(map_func(get_lon_lat_coords, copy.copy(stancils))) coord_positions = np.vstack(coord_positions) return coord_positions @@ -394,23 +421,26 @@ def __init__(self, x_grid, data, Lpoints, ov=None, window=None): other arributes are in the .attr dict. """ - self.Lpoints = Lpoints - self.ov = int(Lpoints/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 + self.Lpoints = Lpoints + self.ov = ( + int(Lpoints / 2) if ov is None else ov + ) # when not defined in create_chunk_boundaries then L/2 - self.data = data + self.data = data # create subsample k - self.k, self.dk = calc_freq_fft(x_grid, Lpoints) # return 1/ unit of frid points + self.k, self.dk = calc_freq_fft( + x_grid, Lpoints + ) # return 1/ unit of frid points # to get the waveumber units (2 pi/ lambda), multiply by 2 pi - self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi + self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi # print(self.k[0], self.k[-1]) # print(self.dk) # create window - self.win = create_window(Lpoints) + self.win = create_window(Lpoints) def cal_spectrogram(self, data=None, name=None): - """ defines apply function and calculated all sub-sample sprectra using map """ @@ -418,102 +448,109 @@ def cal_spectrogram(self, data=None, name=None): DATA = self.data if data is None else data Lpoints, dk = self.Lpoints, self.dk - win =self.win + win = self.win def calc_spectrum_apply(stancil): "returns spectrum per stencil, detrends and windows the data" from scipy.signal import detrend - idata = DATA[stancil[0]:stancil[-1]] + idata = DATA[stancil[0] : stancil[-1]] idata = detrend(idata) * win - return stancil[1], calc_spectrum_fft(idata , dk, Lpoints) + return stancil[1], calc_spectrum_fft(idata, dk, Lpoints) # def test_func(i_stancil): # return i_stancil[1], yy[i_stancil[0]:i_stancil[-1]].shape # %% derive L2 stancil - stancil_iter = create_chunk_boundaries(Lpoints, DATA.size, ov= self.ov) + stancil_iter = create_chunk_boundaries(Lpoints, DATA.size, ov=self.ov) # apply func to all stancils - D_specs = dict(map(calc_spectrum_apply,stancil_iter)) + D_specs = dict(map(calc_spectrum_apply, stancil_iter)) chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectal relazations + self.N_stancils = len(chunk_positions) # number of spectal relazations # repack data, create xarray - self.spec_name = 'power_spec' if name is None else name - G =dict() - for xi,I in D_specs.items(): - G[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi } , name=self.spec_name) - - self.G = xr.concat(G.values(), dim='x').T#.to_dataset() + self.spec_name = "power_spec" if name is None else name + G = dict() + for xi, I in D_specs.items(): + G[xi] = xr.DataArray( + I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name + ) + + self.G = xr.concat(G.values(), dim="x").T # .to_dataset() if self.G.k[0] == 0: self.G = self.G[1:, :] - self.G.attrs['ov'] = self.ov - self.G.attrs['L'] = self.Lpoints + self.G.attrs["ov"] = self.ov + self.G.attrs["L"] = self.Lpoints return self.G # cal variance def calc_var(self): - """ Compute total variance from spectragram """ - return self.dk*self.G.mean('x').sum().data # do not consider zeroth frequency + """Compute total variance from spectragram""" + return self.dk * self.G.mean("x").sum().data # do not consider zeroth frequency - def mean_spectral_error(self, mask=None, confidence = 0.95): + def mean_spectral_error(self, mask=None, confidence=0.95): "retrurns spetral error for the x-mean spectral estimate and stores it as coordindate in the dataarray" # make error estimate if mask is not None: - meanspec= self.G.isel(x=mask).mean('x') + meanspec = self.G.isel(x=mask).mean("x") N = int(sum(mask)) else: - meanspec= self.G.mean('x') + meanspec = self.G.mean("x") N = self.N_stancils - El_of_mean, Eu_of_mean = spec_error(meanspec, N , confidence ) - El_of_mean.name = 'El_mean' - Eu_of_mean.name = 'Eu_mean' + El_of_mean, Eu_of_mean = spec_error(meanspec, N, confidence) + El_of_mean.name = "El_mean" + Eu_of_mean.name = "Eu_mean" - self.G.coords['mean_El'] = (('k'), El_of_mean.data) - self.G.coords['mean_Eu'] = (('k'), Eu_of_mean.data) + self.G.coords["mean_El"] = (("k"), El_of_mean.data) + self.G.coords["mean_Eu"] = (("k"), Eu_of_mean.data) - def parceval(self, add_attrs=True ): + def parceval(self, add_attrs=True): "test Parceval theorem" DATA = self.data L = self.Lpoints - # derive mean variances of stancils stancil_iter = create_chunk_boundaries(L, DATA.size) def get_stancil_var_apply(stancil): from scipy.signal import detrend + "returns the variance of yy for stancil" - idata = DATA[stancil[0]:stancil[-1]] - idata = detrend(idata)# * win + idata = DATA[stancil[0] : stancil[-1]] + idata = detrend(idata) # * win return stancil[1], idata.var() - D_vars = dict(map(get_stancil_var_apply,stancil_iter)) + D_vars = dict(map(get_stancil_var_apply, stancil_iter)) - stancil_vars =list() + stancil_vars = list() for I in D_vars.values(): stancil_vars.append(I) - print('Parcevals Theorem:') - print('variance of unweighted timeseries: ',DATA.var()) - print('mean variance of detrended chunks: ', np.array(stancil_vars).mean()) - #print('variance of weighted timeseries: ',self.phi.var() ) - #self.calc_var(self) - print('variance of the pwelch Spectrum: ', self.calc_var()) + print("Parcevals Theorem:") + print("variance of unweighted timeseries: ", DATA.var()) + print("mean variance of detrended chunks: ", np.array(stancil_vars).mean()) + # print('variance of weighted timeseries: ',self.phi.var() ) + # self.calc_var(self) + print("variance of the pwelch Spectrum: ", self.calc_var()) if add_attrs: - self.G.attrs['variance_unweighted_data'] = DATA.var() - self.G.attrs['mean_variance_detrended_chunks'] = np.array(stancil_vars).mean() - self.G.attrs['mean_variance_pwelch_spectrum'] = self.calc_var() + self.G.attrs["variance_unweighted_data"] = DATA.var() + self.G.attrs["mean_variance_detrended_chunks"] = np.array( + stancil_vars + ).mean() + self.G.attrs["mean_variance_pwelch_spectrum"] = self.calc_var() + class wavenumber_spectrogram_LS_even: - def __init__(self, x, data, L, waven_method = 'fftX2' , dy=None , ov=None, window=None, kjumps=1): + def __init__( + self, x, data, L, waven_method="fftX2", dy=None, ov=None, window=None, kjumps=1 + ): """ returns a wavenumber spectrogram with the resolution L-ov this uses Lombscargle @@ -532,29 +569,30 @@ def __init__(self, x, data, L, waven_method = 'fftX2' , dy=None , ov=None, wind other arributes are in the .attr dict. """ from astropy.timeseries import LombScargle - self.L = L - self.ov = int(L/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.x = x - self.data = data - self.dy = dy + self.L = L + self.ov = ( + int(L / 2) if ov is None else ov + ) # when not defined in create_chunk_boundaries then L/2 + self.x = x + self.data = data + self.dy = dy # create subsample k - #print(waven_method) + # print(waven_method) if type(waven_method) is str: - self.k, self.dk = calc_freq_LS(x, L, method = waven_method ) + self.k, self.dk = calc_freq_LS(x, L, method=waven_method) elif type(waven_method) is np.ndarray: - self.k, self.dk = waven_method, np.diff(waven_method).mean() + self.k, self.dk = waven_method, np.diff(waven_method).mean() else: - raise ValueError('waven_method is neither string nor an array') + raise ValueError("waven_method is neither string nor an array") - self.k, self.dk = self.k[::kjumps], self.dk*kjumps + self.k, self.dk = self.k[::kjumps], self.dk * kjumps # create window - self.win = None #create_window(L) - - def cal_spectrogram(self, x = None, data=None, name=None, dx=1): + self.win = None # create_window(L) + def cal_spectrogram(self, x=None, data=None, name=None, dx=1): """ defines apply function and calculated all sub-sample sprectra using map dx nominal resolution of the data resolutionif not set, dx= 1 @@ -562,64 +600,71 @@ def cal_spectrogram(self, x = None, data=None, name=None, dx=1): from astropy.timeseries import LombScargle import xarray as xr - X = self.x if x is None else x # all x positions - DATA = self.data if data is None else data # all data points - L, dk = self.L, self.dk - win = self.win + X = self.x if x is None else x # all x positions + DATA = self.data if data is None else data # all data points + L, dk = self.L, self.dk + win = self.win self.dx = dx # init Lomb scargle object with noise as nummy data () - #dy_fake= np.random.randn(len(dy))*0.001 if self.dy is not None else None - self.LS = LombScargle(X[0:L] , np.random.randn(L)*0.001, fit_mean=True) - + # dy_fake= np.random.randn(len(dy))*0.001 if self.dy is not None else None + self.LS = LombScargle(X[0:L], np.random.randn(L) * 0.001, fit_mean=True) def calc_spectrum_apply(stancil): "returns spectrum per stencil, detrends and windows the data" from scipy.signal import detrend - x = X[stancil[0]:stancil[-1]] - #x_mask= (stancil[0] < X) & (X <= stancil[-1]) - #x = X[x_mask] - idata = DATA[stancil[0]:stancil[-1]] - y = detrend(idata)# * win + x = X[stancil[0] : stancil[-1]] + # x_mask= (stancil[0] < X) & (X <= stancil[-1]) + # x = X[x_mask] + idata = DATA[stancil[0] : stancil[-1]] + y = detrend(idata) # * win - LS_PSD, LS_object = calc_spectrum_LS( x, y, self.k, LS= self.LS, dk =self.dk) + LS_PSD, LS_object = calc_spectrum_LS(x, y, self.k, LS=self.LS, dk=self.dk) return stancil[1], LS_PSD # % derive L2 stancil - stancil_iter = create_chunk_boundaries(L, DATA.size, ov= self.ov) + stancil_iter = create_chunk_boundaries(L, DATA.size, ov=self.ov) # apply func to all stancils - D_specs = dict(map(calc_spectrum_apply,stancil_iter)) + D_specs = dict(map(calc_spectrum_apply, stancil_iter)) chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectal relazations + self.N_stancils = len(chunk_positions) # number of spectal relazations # repack data, create xarray - self.spec_name = 'power_spec' if name is None else name - G =dict() - for xi,I in D_specs.items(): - G[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi * self.dx } , name=self.spec_name) - - self.G = xr.concat(G.values(), dim='x').T#.to_dataset() + self.spec_name = "power_spec" if name is None else name + G = dict() + for xi, I in D_specs.items(): + G[xi] = xr.DataArray( + I, + dims=["k"], + coords={"k": self.k, "x": xi * self.dx}, + name=self.spec_name, + ) + + self.G = xr.concat(G.values(), dim="x").T # .to_dataset() if self.G.k[0] == 0: self.G = self.G[1:, :] - self.G.attrs['ov'] = self.ov - self.G.attrs['L'] = self.L + self.G.attrs["ov"] = self.ov + self.G.attrs["L"] = self.L return self.G def calc_var(self): return wavenumber_spectrogram.calc_var(self) - def parceval(self, add_attrs=True ): - return wavenumber_spectrogram.parceval(self, add_attrs= add_attrs ) + def parceval(self, add_attrs=True): + return wavenumber_spectrogram.parceval(self, add_attrs=add_attrs) + + def mean_spectral_error(self, confidence=0.95): + return wavenumber_spectrogram.mean_spectral_error(self, confidence=confidence) - def mean_spectral_error(self, confidence = 0.95 ): - return wavenumber_spectrogram.mean_spectral_error(self, confidence= confidence ) class wavenumber_spectrogram_LS: - def __init__(self, x, data, L, dx, dy = None, waven_method = 'fftX2', ov=None, window=None): + def __init__( + self, x, data, L, dx, dy=None, waven_method="fftX2", ov=None, window=None + ): """ returns a wavenumber spectrogram with the resolution L-ov this uses Lombscargle @@ -639,31 +684,42 @@ def __init__(self, x, data, L, dx, dy = None, waven_method = 'fftX2', ov=None, w other arributes are in the .attr dict. """ from astropy.timeseries import LombScargle - self.L = L - self.ov = int(L/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.x = x - self.dx = dx - self.data = data - self.error = dy if dy is not None else None - self.Lpoints= int(self.L/self.dx) + self.L = L + self.ov = ( + int(L / 2) if ov is None else ov + ) # when not defined in create_chunk_boundaries then L/2 + self.x = x + self.dx = dx + self.data = data + self.error = dy if dy is not None else None + self.Lpoints = int(self.L / self.dx) # create subsample k - #print(waven_method) + # print(waven_method) if type(waven_method) is str: - self.k, self.dk = calc_freq_LS(x, self.Lpoints, method = waven_method ) + self.k, self.dk = calc_freq_LS(x, self.Lpoints, method=waven_method) elif type(waven_method) is np.ndarray: - self.k, self.dk = waven_method, np.diff(waven_method).mean() + self.k, self.dk = waven_method, np.diff(waven_method).mean() else: - raise ValueError('waven_method is neither string nor an array') + raise ValueError("waven_method is neither string nor an array") - #self.k, self.dk = self.k[::kjumps], self.dk*kjumps + # self.k, self.dk = self.k[::kjumps], self.dk*kjumps # create window - self.win = None #create_window(L) - - def cal_spectrogram(self, x = None, data=None, error=None, name=None, xlims =None, weight_data= True, max_nfev = None, map_func=None): - + self.win = None # create_window(L) + + def cal_spectrogram( + self, + x=None, + data=None, + error=None, + name=None, + xlims=None, + weight_data=True, + max_nfev=None, + map_func=None, + ): """ defines apply function and calculated all sub-sample sprectra using map @@ -687,77 +743,81 @@ def cal_spectrogram(self, x = None, data=None, error=None, name=None, xlims =Non import copy import pandas as pd - X = self.x if x is None else x # all x positions - DATA = self.data if data is None else data # all data points - ERR = self.error if error is None else error # all error for points - L, dk = self.L, self.dk - #win = self.win - self.xlims = ( np.round(X.min()), X.max() ) if xlims is None else xlims + X = self.x if x is None else x # all x positions + DATA = self.data if data is None else data # all data points + ERR = self.error if error is None else error # all error for points + L, dk = self.L, self.dk + # win = self.win + self.xlims = (np.round(X.min()), X.max()) if xlims is None else xlims # init Lomb scargle object with noise as nummy data () - #dy_fake= np.random.randn(len(dy))*0.001 if self.dy is not None else None - #self.LS = LombScargle(X[0:L] , np.random.randn(L)*0.001, fit_mean=True) + # dy_fake= np.random.randn(len(dy))*0.001 if self.dy is not None else None + # self.LS = LombScargle(X[0:L] , np.random.randn(L)*0.001, fit_mean=True) # define window import scipy.signal.windows as WINDOWS - self.win = WINDOWS.tukey(self.Lpoints, alpha=0.1, sym=True) + self.win = WINDOWS.tukey(self.Lpoints, alpha=0.1, sym=True) def calc_spectrum_and_field_apply(stancil): - """ windows the data accoding to stencil and applies LS spectrogram returns: stancil center, spectrum for this stencil, number of datapoints in stancil """ from scipy.signal import detrend - #x = X[stancil[0]:stancil[-1]] - x_mask= (stancil[0] <= X) & (X <= stancil[-1]) + # x = X[stancil[0]:stancil[-1]] + x_mask = (stancil[0] <= X) & (X <= stancil[-1]) - #print(stancil[1]) + # print(stancil[1]) x = X[x_mask] - if x.size < 200: # if there are not enough photos set results to nan - #return stancil[1], self.k*np.nan, np.fft.rfftfreq( int(self.Lpoints), d=self.dx)*np.nan, x.size - return stancil[1], self.k*np.nan, self.k*np.nan, np.nan, x.size + if x.size < 200: # if there are not enough photos set results to nan + # return stancil[1], self.k*np.nan, np.fft.rfftfreq( int(self.Lpoints), d=self.dx)*np.nan, x.size + return stancil[1], self.k * np.nan, self.k * np.nan, np.nan, x.size y = DATA[x_mask] - #make x positions - x_pos = (np.round( (x - stancil[0])/ 10.0 -1 , 0) ).astype('int') + # make x positions + x_pos = (np.round((x - stancil[0]) / 10.0 - 1, 0)).astype("int") # weight data if weight_data: window = self.win[x_pos] - y = y * window * np.sqrt( np.var(y) / np.var(( y* window) ) ) + y = y * window * np.sqrt(np.var(y) / np.var((y * window))) - #make y gridded - x_model = np.arange(stancil[0], stancil[-1], self.dx) - y_gridded = np.copy(x_model) * np.nan + # make y gridded + x_model = np.arange(stancil[0], stancil[-1], self.dx) + y_gridded = np.copy(x_model) * np.nan y_gridded[x_pos] = y - nan_mask =np.isnan(y_gridded) + nan_mask = np.isnan(y_gridded) err = ERR[x_mask] if ERR is not None else None - #print(x.shape, y.shape, self.k, self.LS) - LS_PSD, LS_object = calc_spectrum_LS( x, y, self.k, err=err, LS= None, dk =self.dk) - - y_model = reconstruct_data_from_LS(LS_object, x_model, self.k) + # print(x.shape, y.shape, self.k, self.LS) + LS_PSD, LS_object = calc_spectrum_LS( + x, y, self.k, err=err, LS=None, dk=self.dk + ) + y_model = reconstruct_data_from_LS(LS_object, x_model, self.k) # print(stancil[-1], x_model[-1]) # print(stancil[0], x_model[0]) # print(np.fft.rfft(y_model).size , kk.size) # print(x_model.size, y_gridded.size, y_model.size) # print('--') - P = conserve_variance(np.fft.rfft(y_model), self.k, y_gridded, nan_mask = nan_mask ) + P = conserve_variance( + np.fft.rfft(y_model), self.k, y_gridded, nan_mask=nan_mask + ) P.set_parameters() - #P.test_ojective_func(P.tanh_weight_function, plot_flag=False) + # P.test_ojective_func(P.tanh_weight_function, plot_flag=False) fitter = P.optimize(max_nfev=max_nfev) return stancil[1], LS_PSD, P.best_guess_Z(), fitter.params, x.size # % derive L2 stancil - self.stancil_iter = create_chunk_boundaries_unit_lengths(L, self.xlims, ov= self.ov, iter_flag=True) - #stancil_iter = create_chunk_boundaries_unit_lengths(L, ( np.round(X.min()), X.max() ), ov= self.ov, iter_flag=True) + self.stancil_iter = create_chunk_boundaries_unit_lengths( + L, self.xlims, ov=self.ov, iter_flag=True + ) + # stancil_iter = create_chunk_boundaries_unit_lengths(L, ( np.round(X.min()), X.max() ), ov= self.ov, iter_flag=True) # apply func to all stancils # Spec_returns=list() @@ -767,34 +827,38 @@ def calc_spectrum_and_field_apply(stancil): map_func = map if map_func is None else map_func print(map_func) - Spec_returns = list(map_func( calc_spectrum_and_field_apply, copy.copy(self.stancil_iter) )) + Spec_returns = list( + map_func(calc_spectrum_and_field_apply, copy.copy(self.stancil_iter)) + ) # # linear version - #Spec_returns = list(map( calc_spectrum_and_field_apply, copy.copy(self.stancil_iter) )) + # Spec_returns = list(map( calc_spectrum_and_field_apply, copy.copy(self.stancil_iter) )) # unpack resutls of the mapping: - D_specs = dict() - Y_model = dict() - Pars = dict() - N_per_stancil = list() + D_specs = dict() + Y_model = dict() + Pars = dict() + N_per_stancil = list() for I in Spec_returns: - #print(I[1].shape, I[2].shape) - D_specs[I[0]] = I[1] - Y_model[I[0]] = I[2] - Pars[I[0]] = I[3] + # print(I[1].shape, I[2].shape) + D_specs[I[0]] = I[1] + Y_model[I[0]] = I[2] + Pars[I[0]] = I[3] N_per_stancil.append(I[4]) self.N_per_stancil = N_per_stancil chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectral realizatiobs + self.N_stancils = len(chunk_positions) # number of spectral realizatiobs # repack data, create xarray # 1st LS spectal estimates - self.spec_name = 'LS_spectal_power' if name is None else name - G_LS_power =dict() - for xi,I in D_specs.items(): - G_LS_power[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi } , name=self.spec_name) + self.spec_name = "LS_spectal_power" if name is None else name + G_LS_power = dict() + for xi, I in D_specs.items(): + G_LS_power[xi] = xr.DataArray( + I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name + ) - G_LS_power = xr.concat(G_LS_power.values(), dim='x').T#.to_dataset() + G_LS_power = xr.concat(G_LS_power.values(), dim="x").T # .to_dataset() # 2nd Y_model # G_model =dict() @@ -816,52 +880,52 @@ def calc_spectrum_and_field_apply(stancil): # self.G_model.attrs['Lpoints'] = self.Lpoints # self.G_model.coords['N_per_stancil'] = ( ('x'), N_per_stancil) - - #2nd FFT(Y_model) - G_fft =dict() - Y_model_k_fft = np.fft.rfftfreq( int(self.Lpoints), d=self.dx) - for xi,I in Y_model.items(): + # 2nd FFT(Y_model) + G_fft = dict() + Y_model_k_fft = np.fft.rfftfreq(int(self.Lpoints), d=self.dx) + for xi, I in Y_model.items(): if I.size < Y_model_k_fft.size: I = np.insert(I, -1, I[-1]) - G_fft[xi] = xr.DataArray(I, dims=['k'], coords={'k': Y_model_k_fft, 'x': xi } , name='Y_model_hat') + G_fft[xi] = xr.DataArray( + I, dims=["k"], coords={"k": Y_model_k_fft, "x": xi}, name="Y_model_hat" + ) - G_fft = xr.concat(G_fft.values(), dim='x').T#.to_dataset() + G_fft = xr.concat(G_fft.values(), dim="x").T # .to_dataset() # generate power spec as well self.G = Z_to_power(G_fft, self.dk, self.Lpoints) - self.G.name = 'spectral_power_optm' - + self.G.name = "spectral_power_optm" # merge both datasets self.GG = xr.merge([G_LS_power, G_fft, self.G]) - self.GG.attrs['ov'] = self.ov - self.GG.attrs['L'] = self.L - self.GG.attrs['Lpoints'] = self.Lpoints - self.GG.coords['N_per_stancil'] = ( ('x'), N_per_stancil) - - self.GG.expand_dims(dim='eta') - self.GG.coords['eta'] = ( ('eta'), np.arange(0, self.L + self.dx, self.dx) - self.L/2 ) - self.GG['win'] = ( ('eta'), np.insert(self.win, -1, self.win[-1])) + self.GG.attrs["ov"] = self.ov + self.GG.attrs["L"] = self.L + self.GG.attrs["Lpoints"] = self.Lpoints + self.GG.coords["N_per_stancil"] = (("x"), N_per_stancil) + + self.GG.expand_dims(dim="eta") + self.GG.coords["eta"] = ( + ("eta"), + np.arange(0, self.L + self.dx, self.dx) - self.L / 2, + ) + self.GG["win"] = (("eta"), np.insert(self.win, -1, self.win[-1])) # create dataframe with fitted parameters - PP2= dict() + PP2 = dict() for k, I in Pars.items(): if I is not np.nan: - PP2[k] =I + PP2[k] = I keys = PP2[next(iter(PP2))].keys() - params_dataframe = pd.DataFrame(index =keys) + params_dataframe = pd.DataFrame(index=keys) - for k,I in PP2.items(): + for k, I in PP2.items(): I.values() params_dataframe[k] = list(I.valuesdict().values()) return self.GG, params_dataframe - - - def calc_var(self): Gmean = np.nanmean(self.G, 1) @@ -872,61 +936,67 @@ def calc_var(self): # def parceval(self, add_attrs=True ): # return wavenumber_spectrogram.parceval(self, add_attrs= add_attrs ) - def parceval(self, add_attrs=True, weight_data=False ): + def parceval(self, add_attrs=True, weight_data=False): "test Parceval theorem" import copy + DATA = self.data L = self.L X = self.x # derive mean variances of stancils - #stancil_iter = create_chunk_boundaries_unit_lengths(L, self.xlims, ov= self.ov ) + # stancil_iter = create_chunk_boundaries_unit_lengths(L, self.xlims, ov= self.ov ) def get_stancil_var_apply(stancil): from scipy.signal import detrend + "returns the variance of yy for stancil" - x_mask= (stancil[0] < X) & (X <= stancil[-1]) + x_mask = (stancil[0] < X) & (X <= stancil[-1]) idata = DATA[x_mask] if len(idata) < 1: return stancil[1], np.nan, len(idata) idata = detrend(idata) # weight data - x_pos = (np.round( (X[x_mask] - stancil[0])/ 10.0 , 0) ).astype('int') + x_pos = (np.round((X[x_mask] - stancil[0]) / 10.0, 0)).astype("int") if weight_data: window = self.win[x_pos] - idata = idata * window * np.sqrt( np.var(idata) / np.var(( idata* window) ) ) + idata = ( + idata * window * np.sqrt(np.var(idata) / np.var((idata * window))) + ) return stancil[1], idata.var(), len(idata) - D_vars = list(map(get_stancil_var_apply, copy.copy(self.stancil_iter) )) + D_vars = list(map(get_stancil_var_apply, copy.copy(self.stancil_iter))) - stancil_vars, Nphotons =list(), 0 + stancil_vars, Nphotons = list(), 0 for I in D_vars: - stancil_vars.append(I[1] * I[2]) - Nphotons += I[2] + stancil_vars.append(I[1] * I[2]) + Nphotons += I[2] - stancil_weighted_variance = np.nansum(np.array(stancil_vars))/Nphotons + stancil_weighted_variance = np.nansum(np.array(stancil_vars)) / Nphotons - print('Parcevals Theorem:') - print('variance of timeseries: ', DATA.var()) - print('mean variance of stancils: ', stancil_weighted_variance ) - #print('variance of weighted timeseries: ',self.phi.var() ) - #self.calc_var(self) - print('variance of the optimzed windowed LS Spectrum: ', self.calc_var()) + print("Parcevals Theorem:") + print("variance of timeseries: ", DATA.var()) + print("mean variance of stancils: ", stancil_weighted_variance) + # print('variance of weighted timeseries: ',self.phi.var() ) + # self.calc_var(self) + print("variance of the optimzed windowed LS Spectrum: ", self.calc_var()) if add_attrs: - self.G.attrs['variance_unweighted_data'] = DATA.var() - self.G.attrs['mean_variance_stancils'] = np.nanmean(np.array(stancil_vars) ) - self.G.attrs['mean_variance_LS_pwelch_spectrum'] = self.calc_var() - - - def mean_spectral_error(self, mask=None, confidence = 0.95 ): - return wavenumber_spectrogram.mean_spectral_error(self, mask=mask, confidence= confidence ) + self.G.attrs["variance_unweighted_data"] = DATA.var() + self.G.attrs["mean_variance_stancils"] = np.nanmean(np.array(stancil_vars)) + self.G.attrs["mean_variance_LS_pwelch_spectrum"] = self.calc_var() + def mean_spectral_error(self, mask=None, confidence=0.95): + return wavenumber_spectrogram.mean_spectral_error( + self, mask=mask, confidence=confidence + ) # class for getting standard Pwelch spectrum. old version, deprechiate class wavenumber_pwelch: - def __init__(self,data, x, L, ov=None, window=None, save_chunks=False, plot_chunks=False): + def __init__( + self, data, x, L, ov=None, window=None, save_chunks=False, plot_chunks=False + ): """ returns a wavenumber spectrum using the pwelch method @@ -948,93 +1018,90 @@ def __init__(self,data, x, L, ov=None, window=None, save_chunks=False, plot_chun """ from scipy import signal + self.data = data # field to be analyzed + self.dx = np.diff(x)[0] # sampling interval + self.save_chunks = save_chunks + dsize = data.size - self.data = data # field to be analyzed - self.dx = np.diff(x)[0] # sampling interval - self.save_chunks= save_chunks - dsize = data.size - - ov=int(np.round(L/2)) if ov is None else ov + ov = int(np.round(L / 2)) if ov is None else ov self.n = L if window is None: - win=np.hanning(self.n) + win = np.hanning(self.n) else: - win=window + win = window - factor=np.sqrt(self.n/(win**2).sum()) - win*=factor + factor = np.sqrt(self.n / (win**2).sum()) + win *= factor # test if n is even - if (self.n%2): + if self.n % 2: self.neven = False else: self.neven = True - #calculate freq - self.k = self.calc_freq() - #del(self.df) + # calculate freq + self.k = self.calc_freq() + # del(self.df) - #print(data.size, L, ov, int(L-ov) ) - nbin=int(np.floor(dsize/(L-ov))) - #print(nbin) + # print(data.size, L, ov, int(L-ov) ) + nbin = int(np.floor(dsize / (L - ov))) + # print(nbin) if save_chunks: - chunks=np.empty([int(nbin),int(L)]) - - self.specs=np.empty([int(nbin),self.k.size]) - #print(chunks.shape) - #result_array = np.empty((0, 100)) - #if plot_chunks: - #M.figure_axis_xy() - last_k=0 - k=0 - #print('iter range', np.arange(0,data.size,int(L-ov))) - for i in np.arange(0,dsize-int(L-ov)+1,int(L-ov)): - - if (plot_chunks) and (i >= dsize-6*int(L-ov)): + chunks = np.empty([int(nbin), int(L)]) + + self.specs = np.empty([int(nbin), self.k.size]) + # print(chunks.shape) + # result_array = np.empty((0, 100)) + # if plot_chunks: + # M.figure_axis_xy() + last_k = 0 + k = 0 + # print('iter range', np.arange(0,data.size,int(L-ov))) + for i in np.arange(0, dsize - int(L - ov) + 1, int(L - ov)): + + if (plot_chunks) and (i >= dsize - 6 * int(L - ov)): M.figure_axis_xy() - self.phi=data[int(i):int(i+L)] + self.phi = data[int(i) : int(i + L)] - #self.ii=np.append(self.ii,[i,i+L]) - #print(self.phi.max()) + # self.ii=np.append(self.ii,[i,i+L]) + # print(self.phi.max()) - #print(self.phi.mean()) - #print(self.phi.shape) - #print('i',int(i), int(i+L)) - #print(chunk.size, l) - if int(i+L) <= data.size-1: + # print(self.phi.mean()) + # print(self.phi.shape) + # print('i',int(i), int(i+L)) + # print(chunk.size, l) + if int(i + L) <= data.size - 1: if save_chunks: - chunks[k,:]=self.phi - + chunks[k, :] = self.phi - self.phi=signal.detrend(self.phi)*win + self.phi = signal.detrend(self.phi) * win if plot_chunks: - #MT.stats_format(self.phi, 'chunk '+str(i)) + # MT.stats_format(self.phi, 'chunk '+str(i)) plt.plot(self.phi) - self.specs[k,:]= self.calc_spectrum() - last_k=k - last_used_TS=int(i+L) - #if plot_chunks: + self.specs[k, :] = self.calc_spectrum() + last_k = k + last_used_TS = int(i + L) + # if plot_chunks: # MT.stats_format(self.spec, 'spec '+str(i)) else: if plot_chunks: - print('end of TS is reached') - print('last spec No: '+str(last_k)) - print('spec container: '+str(specs.shape)) - print('last used Timestep: '+str(last_used_TS)) - print('length of TS '+ str(dsize) +'ms') - - k+=1 + print("end of TS is reached") + print("last spec No: " + str(last_k)) + print("spec container: " + str(specs.shape)) + print("last used Timestep: " + str(last_used_TS)) + print("length of TS " + str(dsize) + "ms") + k += 1 if save_chunks: - self.chunks=chunks - #del(chunks) + self.chunks = chunks + # del(chunks) - self.spec_est=self.specs.mean(axis=0) + self.spec_est = self.specs.mean(axis=0) # if prewhite is None: # self.specs=specs[:last_k,:] # self.spec_est=self.specs.mean(axis=0) @@ -1045,69 +1112,74 @@ def __init__(self,data, x, L, ov=None, window=None, save_chunks=False, plot_chun # self.specs=specs[:last_k,:]*(2*np.pi*self.f)**2 # self.spec_est=self.specs.mean(axis=0) - - self.n_spec,_=self.specs.shape + self.n_spec, _ = self.specs.shape self.calc_var() - #self.phi=self.data - #self.phi*=win*np.sqrt(factor) + # self.phi=self.data + # self.phi*=win*np.sqrt(factor) def calc_freq(self): - """ calculate array of spectral variable (frequency or - wavenumber) in cycles per unit of L """ + """calculate array of spectral variable (frequency or + wavenumber) in cycles per unit of L""" - self.df = 1./((self.n-1)*self.dx) + self.df = 1.0 / ((self.n - 1) * self.dx) if self.neven: - f = self.df*np.arange(self.n/2+1) + f = self.df * np.arange(self.n / 2 + 1) else: - f = self.df*np.arange( (self.n-1)/2. + 1 ) + f = self.df * np.arange((self.n - 1) / 2.0 + 1) return f def calc_spectrum(self): - """ compute the 1d spectrum of a field phi """ + """compute the 1d spectrum of a field phi""" self.phih = np.fft.rfft(self.phi) # the factor of 2 comes from the symmetry of the Fourier coeffs - spec = 2.*(self.phih*self.phih.conj()).real / self.df /self.n**2 + spec = 2.0 * (self.phih * self.phih.conj()).real / self.df / self.n**2 # the zeroth frequency should be counted only once - spec[0] = spec[0]/2. + spec[0] = spec[0] / 2.0 if self.neven: - spec[-1] = spec[-1]/2. + spec[-1] = spec[-1] / 2.0 return spec - def error(self, ci=0.95): - self.El, self.Eu =spec_error(self.spec_est,self.n_spec,ci=ci) + self.El, self.Eu = spec_error(self.spec_est, self.n_spec, ci=ci) def parceval(self): - print('Parcevals Theorem:') - print('variance of unweighted timeseries: ',self.data.var()) - print('mean variance of timeseries chunks: ',self.chunks.var(axis=1).mean() if self.save_chunks is True else 'data not saved') - #print('variance of weighted timeseries: ',self.phi.var() ) - #self.calc_var(self) - print('variance of the pwelch Spectrum: ',self.var) + print("Parcevals Theorem:") + print("variance of unweighted timeseries: ", self.data.var()) + print( + "mean variance of timeseries chunks: ", + ( + self.chunks.var(axis=1).mean() + if self.save_chunks is True + else "data not saved" + ), + ) + # print('variance of weighted timeseries: ',self.phi.var() ) + # self.calc_var(self) + print("variance of the pwelch Spectrum: ", self.var) def calc_var(self): - """ Compute total variance from spectrum """ - self.var = self.df* np.nanmean(self.specs[1:], 0).sum() # do not consider zeroth frequency - + """Compute total variance from spectrum""" + self.var = ( + self.df * np.nanmean(self.specs[1:], 0).sum() + ) # do not consider zeroth frequency # %% optimze spectral variance -class conserve_variance: - def __init__(self,Z, freq, data, nan_mask= None): - - """ - """ +class conserve_variance: + def __init__(self, Z, freq, data, nan_mask=None): + """ """ import lmfit as LM - self.LM =LM + + self.LM = LM self.data = data - self.Z = Z + self.Z = Z self.freq = freq self.nan_mask = nan_mask @@ -1115,59 +1187,79 @@ def set_parameters(self): params = self.LM.Parameters() - p_smothed = self.runningmean(np.abs(self.Z ), 20, tailcopy=True) + p_smothed = self.runningmean(np.abs(self.Z), 20, tailcopy=True) f_max = self.freq[p_smothed[~np.isnan(p_smothed)].argmax()] - - lambda_max = 9.81 * 5 **2/ (2* np.pi) - params.add('x_cutoff', 1/lambda_max , min=0, max=1, vary=False) - params.add('x_max_pos', f_max , min=f_max*0.75, max=f_max*5+0.001, vary=False) - params.add('LF_amp', 1 , min=0.5 , max=1.2, vary= True) - params.add('HF_amp', 0.5 , min=0 , max=1.5, vary= True) - params.add('sigma_g', 0.002 , min=0.001 , max=0.05, vary= False) - params.add('Gauss_amp', 0.5 , min=0.01 , max=2, vary= True) - + lambda_max = 9.81 * 5**2 / (2 * np.pi) + params.add("x_cutoff", 1 / lambda_max, min=0, max=1, vary=False) + params.add( + "x_max_pos", f_max, min=f_max * 0.75, max=f_max * 5 + 0.001, vary=False + ) + params.add("LF_amp", 1, min=0.5, max=1.2, vary=True) + params.add("HF_amp", 0.5, min=0, max=1.5, vary=True) + params.add("sigma_g", 0.002, min=0.001, max=0.05, vary=False) + params.add("Gauss_amp", 0.5, min=0.01, max=2, vary=True) self.params = params return params def test_ojective_func(self, weight_func, plot_flag=True): - self.objective_func(self.params, self.data, self.Z, weight_func, self.freq, self.nan_mask, plot_flag=plot_flag) - - def tanh_weight_function(self,ff, params): - return self.tanh_weight(ff, params['x_cutoff'].value, - params['x_max_pos'].value, - params['LF_amp'].value, - params['HF_amp'].value, - params['Gauss_amp'].value, - params['sigma_g'].value ) - - def tanh_weight(self,x, x_cutoff , x_max_pos, LF_amp, HF_amp, Gauss_amp, sigma_g): + self.objective_func( + self.params, + self.data, + self.Z, + weight_func, + self.freq, + self.nan_mask, + plot_flag=plot_flag, + ) + + def tanh_weight_function(self, ff, params): + return self.tanh_weight( + ff, + params["x_cutoff"].value, + params["x_max_pos"].value, + params["LF_amp"].value, + params["HF_amp"].value, + params["Gauss_amp"].value, + params["sigma_g"].value, + ) + + def tanh_weight(self, x, x_cutoff, x_max_pos, LF_amp, HF_amp, Gauss_amp, sigma_g): """ - zdgfsg + zdgfsg """ - HF_amp1 = (LF_amp-HF_amp) - decay = 0.5 - np.tanh( (x-x_cutoff)/sigma_g )/2 - y = decay * HF_amp1 + (1 - HF_amp1) - y = y- y[0] +LF_amp + HF_amp1 = LF_amp - HF_amp + decay = 0.5 - np.tanh((x - x_cutoff) / sigma_g) / 2 + y = decay * HF_amp1 + (1 - HF_amp1) + y = y - y[0] + LF_amp - def gaus(x, x_0, amp, sigma_g ): - return amp* np.exp(-0.5 * ( (x-x_0)/sigma_g)**2) + def gaus(x, x_0, amp, sigma_g): + return amp * np.exp(-0.5 * ((x - x_0) / sigma_g) ** 2) - y += gaus(x, x_max_pos, Gauss_amp, sigma_g ) + y += gaus(x, x_max_pos, Gauss_amp, sigma_g) - #y = y * LF_amp + # y = y * LF_amp return y + def objective_func( + self, + params, + data_x, + Z_results, + weight_func, + freq, + nan_mask=None, + plot_flag=False, + ): - def objective_func(self, params, data_x, Z_results, weight_func, freq, nan_mask = None, plot_flag=False): + alpha = 1e7 - alpha =1e7 def model_real_space(Z, weights, n=None): """ Both inputs must have the same length """ - return np.fft.irfft(Z*weights, n = n) + return np.fft.irfft(Z * weights, n=n) weights = weight_func(freq, params) @@ -1175,10 +1267,10 @@ def model_real_space(Z, weights, n=None): weights = np.insert(weights, -1, weights[-1]) if nan_mask is not None: - model = model_real_space(Z_results, weights, n= data_x.size)[~nan_mask] + model = model_real_space(Z_results, weights, n=data_x.size)[~nan_mask] dd = data_x[~nan_mask][:] else: - model = model_real_space(Z_results, weights, n= data_x.size)[:] + model = model_real_space(Z_results, weights, n=data_x.size)[:] dd = data_x[:] if model.size > dd.size: @@ -1190,102 +1282,156 @@ def model_real_space(Z, weights, n=None): import m_general_ph3 as M from matplotlib.gridspec import GridSpec import matplotlib.pyplot as plt - F= M.figure_axis_xy(10, 4.1 * 2.5, view_scale= 0.5, container = True) - gs = GridSpec(5,1, wspace=0.1, hspace=0.4)#figure=fig, - pos0,pos1,pos2 = gs[0:3, 0],gs[3, 0],gs[4, 0]#,gs[3, 0] + F = M.figure_axis_xy(10, 4.1 * 2.5, view_scale=0.5, container=True) + + gs = GridSpec(5, 1, wspace=0.1, hspace=0.4) # figure=fig, + pos0, pos1, pos2 = gs[0:3, 0], gs[3, 0], gs[4, 0] # ,gs[3, 0] ax1 = F.fig.add_subplot(pos0) - plt.title('Stacked Timeseries', loc='left') + plt.title("Stacked Timeseries", loc="left") - chunk_l= 400 - chunk_iter = create_chunk_boundaries(chunk_l, data_x.size, ov=0, iter_flag = True) + chunk_l = 400 + chunk_iter = create_chunk_boundaries( + chunk_l, data_x.size, ov=0, iter_flag=True + ) - ofsett0= 6 + ofsett0 = 6 ofsett = np.copy(ofsett0) for chi in chunk_iter: - v1= np.round(np.nanvar(dd), 4) - plt.plot(ofsett+ data_x[chi[0]:chi[-1]] , linewidth=3, alpha=0.5 , c='black', label=' org. data (var:'+str(v1)+')') - - v1= np.round(model_real_space(Z_results, weights*0 +1)[~nan_mask[1:]].var(), 4) - plt.plot(ofsett + model_real_space(Z_results, weights*0 +1)[chi[0]:chi[-1]] ,linewidth= 0.8, c='red', label='LS model init (var:'+str(v1)+')') - - v1= np.round(model.var(), 4) - plt.plot(ofsett + model_real_space(Z_results, weights)[chi[0]:chi[-1]],linewidth= 0.8, c='blue', label='LS model weighted (var:'+str(v1)+')') + v1 = np.round(np.nanvar(dd), 4) + plt.plot( + ofsett + data_x[chi[0] : chi[-1]], + linewidth=3, + alpha=0.5, + c="black", + label=" org. data (var:" + str(v1) + ")", + ) + + v1 = np.round( + model_real_space(Z_results, weights * 0 + 1)[~nan_mask[1:]].var(), 4 + ) + plt.plot( + ofsett + + model_real_space(Z_results, weights * 0 + 1)[chi[0] : chi[-1]], + linewidth=0.8, + c="red", + label="LS model init (var:" + str(v1) + ")", + ) + + v1 = np.round(model.var(), 4) + plt.plot( + ofsett + model_real_space(Z_results, weights)[chi[0] : chi[-1]], + linewidth=0.8, + c="blue", + label="LS model weighted (var:" + str(v1) + ")", + ) if ofsett == ofsett0: plt.legend() ofsett -= 1 - plt.ylim(ofsett, ofsett0+1) - plt.xlim(0, chunk_l*2) - + plt.ylim(ofsett, ofsett0 + 1) + plt.xlim(0, chunk_l * 2) ax2 = F.fig.add_subplot(pos1) - #ax2 = plt.subplot(3, 1, 2) - plt.title('Amplitude Weight Function', loc='left') - plt.plot(weights , c='black') - ax2.set_xscale('log') + # ax2 = plt.subplot(3, 1, 2) + plt.title("Amplitude Weight Function", loc="left") + plt.plot(weights, c="black") + ax2.set_xscale("log") ax3 = F.fig.add_subplot(pos2) - plt.title('Initial and tuned |Z|', loc='left') + plt.title("Initial and tuned |Z|", loc="left") - #ax3 = plt.subplot(3, 1, 3) + # ax3 = plt.subplot(3, 1, 3) # v2_fft= np.fft.rfft(data_x) # v2 = np.round( (2.*(v2_fft*v2_fft.conj()).real /data_x.size**2 ).sum(), 4) # plt.plot(abs(v2_fft) , linewidth=2, alpha=0.5 , c='black', label='org data (var: '+str(v2) +')') - v2 = np.round( (4.*(Z_results*Z_results.conj()).real /data_x.size**2 ).sum(), 4) - plt.plot(abs(Z_results), linewidth= 0.8, c='red', label='Z (var: '+str(v2) +')') - plt.plot(M.runningmean(abs(Z_results) , 20, tailcopy=True), linewidth= 1.5, c='red', zorder=12) - - Z2= Z_results* weights - v2 = np.round( (4.*(Z2*Z2.conj()).real /data_x.size**2 ).sum(), 4) - plt.plot(abs(Z2), linewidth= 0.8, c='blue', label='weighted Z(var: '+str(v2) +')') - plt.plot(M.runningmean(abs(Z2) , 20, tailcopy=True), linewidth= 1.5, c='blue', zorder=12) + v2 = np.round( + (4.0 * (Z_results * Z_results.conj()).real / data_x.size**2).sum(), 4 + ) + plt.plot( + abs(Z_results), linewidth=0.8, c="red", label="Z (var: " + str(v2) + ")" + ) + plt.plot( + M.runningmean(abs(Z_results), 20, tailcopy=True), + linewidth=1.5, + c="red", + zorder=12, + ) + + Z2 = Z_results * weights + v2 = np.round((4.0 * (Z2 * Z2.conj()).real / data_x.size**2).sum(), 4) + plt.plot( + abs(Z2), + linewidth=0.8, + c="blue", + label="weighted Z(var: " + str(v2) + ")", + ) + plt.plot( + M.runningmean(abs(Z2), 20, tailcopy=True), + linewidth=1.5, + c="blue", + zorder=12, + ) plt.legend() - plt.ylim( np.percentile(abs(Z_results), 0.5), abs(Z_results).max()*1.3 ) - plt.xlabel('wavenumber k') - ax3.set_xscale('log') - ax3.set_yscale('log') - - fitting_cost =( abs(dd - model) / dd.std() )**2 - variance_cost =( abs(dd.var() - model.var()) / dd.std() ) **2 + plt.ylim(np.percentile(abs(Z_results), 0.5), abs(Z_results).max() * 1.3) + plt.xlabel("wavenumber k") + ax3.set_xscale("log") + ax3.set_yscale("log") - return fitting_cost.sum() , alpha* variance_cost + fitting_cost = (abs(dd - model) / dd.std()) ** 2 + variance_cost = (abs(dd.var() - model.var()) / dd.std()) ** 2 - def optimize(self, fitting_args= None , method='dual_annealing', max_nfev=None): + return fitting_cost.sum(), alpha * variance_cost + def optimize(self, fitting_args=None, method="dual_annealing", max_nfev=None): if fitting_args is None: fitting_args = (self.data, self.Z, self.tanh_weight_function, self.freq) self.weight_func = fitting_args[2] - self.fitter = self.LM.minimize(self.objective_func, self.params, args=fitting_args, kws={'nan_mask':self.nan_mask} , method=method, max_nfev=max_nfev) + self.fitter = self.LM.minimize( + self.objective_func, + self.params, + args=fitting_args, + kws={"nan_mask": self.nan_mask}, + method=method, + max_nfev=max_nfev, + ) return self.fitter def plot_result(self): - self.objective_func(self.fitter.params, self.data, self.Z, self.weight_func, self.freq, self.nan_mask, plot_flag=True) + self.objective_func( + self.fitter.params, + self.data, + self.Z, + self.weight_func, + self.freq, + self.nan_mask, + plot_flag=True, + ) def best_guess_Z(self): return self.Z * self.weight_func(self.freq, self.fitter.params) def runningmean(self, var, m, tailcopy=False): - m=int(m) - s =var.shape - if s[0] <= 2*m: - print('0 Dimension is smaller then averaging length') + m = int(m) + s = var.shape + if s[0] <= 2 * m: + print("0 Dimension is smaller then averaging length") return - rr=np.asarray(var)*np.nan - #print(type(rr)) - var_range=np.arange(m,int(s[0])-m-1,1) - for i in var_range[np.isfinite(var[m:int(s[0])-m-1])]: - #rm.append(var[i-m:i+m].mean()) - rr[int(i)]=np.nanmean(var[i-m:i+m]) + rr = np.asarray(var) * np.nan + # print(type(rr)) + var_range = np.arange(m, int(s[0]) - m - 1, 1) + for i in var_range[np.isfinite(var[m : int(s[0]) - m - 1])]: + # rm.append(var[i-m:i+m].mean()) + rr[int(i)] = np.nanmean(var[i - m : i + m]) if tailcopy: - rr[0:m]=rr[m+1] - rr[-m-1:-1]=rr[-m-2] + rr[0:m] = rr[m + 1] + rr[-m - 1 : -1] = rr[-m - 2] return rr diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py b/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py index deb19bb7..1964383e 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py @@ -1,7 +1,7 @@ - import numpy as np -def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0 , verbose=False): + +def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0, verbose=False): """ This function removes spickes from timeseries based on its std and maximum values inputs: @@ -10,81 +10,77 @@ def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0 , verbose=False spreed width of data between wich will be linear interpolated around the spike. width is in units of data points (dt) max_loops number of maximum possible loobs until the spike removal is stopped, even it the first creteria is not true """ - datastd=np.nanstd(data) - data2=np.copy(data) + datastd = np.nanstd(data) + data2 = np.copy(data) - peak_remove=True - looper_count=0 - act_flag=False + peak_remove = True + looper_count = 0 + act_flag = False while peak_remove is True: - if nstd* datastd < np.nanmax(np.abs(data2)): - act_flag=True + if nstd * datastd < np.nanmax(np.abs(data2)): + act_flag = True if verbose: - print('true: '+ str(nstd* datastd) +' < '+str( np.nanmax(np.abs(data)) ) ) - data2=spickes_to_mean(data2, nloop=0, spreed=spreed, gaussian=False) - looper_count+=1 + print( + "true: " + + str(nstd * datastd) + + " < " + + str(np.nanmax(np.abs(data))) + ) + data2 = spickes_to_mean(data2, nloop=0, spreed=spreed, gaussian=False) + looper_count += 1 else: if verbose: - print('False: '+ str(nstd* datastd) +' > '+str( np.nanmax(np.abs(data)) ) ) - peak_remove=False + print( + "False: " + + str(nstd * datastd) + + " > " + + str(np.nanmax(np.abs(data))) + ) + peak_remove = False if looper_count > max_loops: - peak_remove=False + peak_remove = False if verbose: - print('stoped by max#') - + print("stoped by max#") if verbose: import matplotlib.pyplot as plt - plt.plot(data, 'r') - plt.plot(data2, 'b') - return data2 , act_flag + plt.plot(data, "r") + plt.plot(data2, "b") + + return data2, act_flag def spickes_to_mean(ts, nloop=None, spreed=1, gaussian=True): from scipy import signal - nloop=0 if nloop is None else nloop - i=0 - tsmean=ts.mean() - b=2*spreed - gaus=signal.gaussian(b, std=b/10) + nloop = 0 if nloop is None else nloop + i = 0 + tsmean = ts.mean() + b = 2 * spreed + gaus = signal.gaussian(b, std=b / 10) while i <= nloop: - #print(i) - #ts.max() - #print(np.where(ts == ts.max())) - tsabs=np.abs(ts) - tmax=np.nanmax(tsabs) - #print(tsabs, tmax) - pa=np.where(tsabs == tmax)[0][0] + tsabs = np.abs(ts) + tmax = np.nanmax(tsabs) + pa = np.where(tsabs == tmax)[0][0] if gaussian: - tsm=np.mean([ts[pa-spreed],ts[pa+spreed]]) #ts[pa-spreed:pa+spreed] - #print(ts[pa-spreed:pa+spreed].shape) - #print((gaus*(tmax-tsm)).shape) - #print(np.shape(gaus*(tmax-tsm))) - le=int(pa-spreed) - ue=int(pa+spreed) + tsm = np.mean([ts[pa - spreed], ts[pa + spreed]]) + le = int(pa - spreed) + ue = int(pa + spreed) - ts[le:ue]=ts[le:ue]-gaus*(tmax-tsm) + ts[le:ue] = ts[le:ue] - gaus * (tmax - tsm) else: - #tsm=np.mean([ts[pa-spreed],ts[pa+spreed]]) #ts[pa-spreed:pa+spreed] - #print(ts[pa-spreed:pa+spreed].shape) - #print((gaus*(tmax-tsm)).shape) - #print(np.shape(gaus*(tmax-tsm))) - #print(len(ts)) - #print(pa+spreed) - if pa+spreed > len(ts): - le= int(pa-spreed) - ts[le:-1]=np.linspace(ts[le],ts[-1],len(ts[le:-1])) + if pa + spreed > len(ts): + le = int(pa - spreed) + ts[le:-1] = np.linspace(ts[le], ts[-1], len(ts[le:-1])) else: - le=int(pa-spreed) - ue=int(pa+spreed) - #print(le, ue) - ts[ le : ue ]=np.linspace(ts[le],ts[ue],len(ts[le:ue])) + le = int(pa - spreed) + ue = int(pa + spreed) + ts[le:ue] = np.linspace(ts[le], ts[ue], len(ts[le:ue])) - i=i+1 + i = i + 1 return ts diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py b/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py index 62732c16..09288f95 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py @@ -1,17 +1,17 @@ -def to_vec(amp, angle, deg = True): +def to_vec(amp, angle, deg=True): "from anlge deg to vect" import numpy as np if deg: - u, v = amp * np.cos(angle * np.pi/180), amp * np.sin(angle * np.pi/180) + u, v = amp * np.cos(angle * np.pi / 180), amp * np.sin(angle * np.pi / 180) else: - u, v = amp * np.cos(angle ), amp * np.sin(angle ) + u, v = amp * np.cos(angle), amp * np.sin(angle) - return u,v + return u, v -def to_deg(u,v, deg = True): +def to_deg(u, v, deg=True): """ from vect to angle, amp angle is -180 to 180 @@ -20,26 +20,22 @@ def to_deg(u,v, deg = True): import numpy as np amp = np.sqrt(u**2 + v**2) - angle = np.arctan2(v, u)# + 2 * np.pi - - # nan_mask = np.isnan(angle) - # angle= np.where(angle > np.pi, angle - 2 * np.pi , angle) - # angle= np.where(angle <= - np.pi, angle + 2 * np.pi , angle) - # angle= np.where(nan_mask, np.nan , angle) + angle = np.arctan2(v, u) if deg: - angle = angle * 180/np.pi + angle = angle * 180 / np.pi return amp, angle -def get_ave_amp_angle(amp, angle, deg = True): + +def get_ave_amp_angle(amp, angle, deg=True): import numpy as np - u,v = to_vec(amp, angle , deg= deg) + + u, v = to_vec(amp, angle, deg=deg) # average angle in vector space - #print(u, v) - _ , ave_deg = to_deg( np.nanmean(u) , np.nanmean(v), deg = deg) - _ , std_deg = to_deg( np.nanstd(u) , np.nanstd(v) , deg = deg) + _, ave_deg = to_deg(np.nanmean(u), np.nanmean(v), deg=deg) + _, std_deg = to_deg(np.nanstd(u), np.nanstd(v), deg=deg) - #average amp in angle space + # average amp in angle space ave_amp = np.nanmean(amp) std_amp = np.nanstd(amp) From 45dca27d200e13d31bb7d097c79799dba3382a1d Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Mon, 26 Feb 2024 07:53:58 -0500 Subject: [PATCH 03/51] applying review comments --- src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py | 3 +-- src/icesat2_tracks/ICEsat2_SI_tools/iotools.py | 2 +- src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py | 10 +++++----- src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py | 2 +- 4 files changed, 8 insertions(+), 9 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py index e3e28b53..44ace1ef 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py @@ -19,7 +19,6 @@ def get_wavenumbers_polar(amp, angle_rad): returns: wavenumber k,l """ - import numpy as np k0 = amp * np.cos(angle_rad) l0 = amp * np.sin(angle_rad) @@ -105,7 +104,7 @@ def likelyhood_func( pars, x, y, z, z_error=None, test_flag=False, prior=None, prior_weight=2 ): """ - ---not well testet --- + ---not well tested --- likelyhood function using log(p) """ diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py b/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py index 3fb63f35..27e2653b 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py @@ -183,7 +183,7 @@ def set_ATL03_trackname(self): def set_ATL10_trackname(self): block1 = (self.YY, self.MM, self.DD) block1b = (self.HH, self.MN, self.SS) - block2 = (self.TRK, self.CYC, "01") + block2 = (self.TRK, self.CYC, "01") # granule is always '01' for ATL10 if self.RL is "": raise ValueError("RL not set") if self.VRS is "": diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py index f8ade32a..ad5bd1d0 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py @@ -1,5 +1,5 @@ import numpy as np - +import scipy.signal as signal def lanczos_1d(width, dx, a=2): """ @@ -53,12 +53,12 @@ def lanczos_filter_1d(x, data, width, a=2, mode="same", method="direct"): returns data_lp low-passed data, same size as before. """ - import scipy.signal as signal + dx = np.diff(x).mean() x, L = lanczos_1d(width, dx, a=a) - data_lp = signal.convolve(data, L, mode=mode, method=method) # * + data_lp = signal.convolve(data, L, mode=mode, method=method) return data_lp @@ -110,7 +110,7 @@ def lanczos_filter_2d(x, data, width, a=2, mode="same"): dx = abs(np.diff(x).mean()) x, L2d = lanczos_2d(width, dx, a=a) - data_lp = signal.convolve(data, L2d, mode=mode) # * + data_lp = signal.convolve(data, L2d, mode=mode) return data_lp @@ -147,6 +147,6 @@ def lanczos_filter_3d(x, data, width, a=2, mode="same"): dx = abs(np.diff(x).mean()) x, L3d = lanczos_3d(width, dx, a=a) - data_lp = signal.convolve(data, L3d, mode=mode) # * + data_lp = signal.convolve(data, L3d, mode=mode) return data_lp diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py b/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py index 1964383e..9ea22e47 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py @@ -3,7 +3,7 @@ def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0, verbose=False): """ - This function removes spickes from timeseries based on its std and maximum values + This function removes spikes from timeseries based on its std and maximum values inputs: data timeseries as1d arrays nstd number of standard deviations that have to be exceeded by the maximum data value From d2dcd3696b1da2eaf0aee2b05b2c4674c0b3c5ce Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Wed, 28 Feb 2024 15:40:19 -0500 Subject: [PATCH 04/51] applying suggested changed in review --- .../ICEsat2_SI_tools/angle_optimizer.py | 13 +--- .../ICEsat2_SI_tools/beam_stats.py | 21 +++--- .../ICEsat2_SI_tools/filter_regrid.py | 65 ++++++++----------- .../ICEsat2_SI_tools/generalized_FT.py | 2 +- .../ICEsat2_SI_tools/lanczos.py | 13 ++-- .../ICEsat2_SI_tools/read_ground_tracks.py | 6 +- .../sliderule_converter_tools.py | 38 ++++------- .../ICEsat2_SI_tools/spicke_remover.py | 5 +- .../ICEsat2_SI_tools/wave_tools.py | 7 +- .../analysis_db/B02_make_spectra_gFT.py | 2 +- 10 files changed, 67 insertions(+), 105 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py index 44ace1ef..dac43084 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py @@ -4,7 +4,8 @@ from numba import jit import numpy as np - +import lmfit as LM +import matplotlib.pyplot as plt numba_parallel = False @@ -28,8 +29,6 @@ def get_wavenumbers_polar(amp, angle_rad): def wavemodel(XX, YY, ks, ls, amps, group_phase=0): - import numpy as np - G = np.vstack( [ np.cos(np.outer(XX, ks) + np.outer(YY, ls)).T, @@ -174,8 +173,6 @@ class sample_with_mcmc: def __init__(self, params): - import lmfit as LM - self.LM = LM self.set_parameters(params) @@ -241,7 +238,6 @@ def sample( print("results at self.fitter") def plot_sample(self, **kargs): - import matplotlib.pyplot as plt chain = self.chain() nwalkers = self.nwalkers @@ -266,7 +262,6 @@ def optimize(self, fitting_args=None, method="dual_annealing", verbose=True): print("results at self.fitter_optimize") def plot_optimze(self, **kargs): - import matplotlib.pyplot as plt plt.plot( self.fitter_optimize.params["phase"].value, @@ -295,8 +290,6 @@ def brute(self, fitting_args=None, method="brute", verbose=True, N_grid=30): def plot_brute(self, clevel=np.linspace(-3.2, 3.2, 30), **kargs): - import matplotlib.pyplot as plt - fitter_brute = self.fitter_brute dd = ( @@ -355,8 +348,6 @@ def get_marginal_dist( y_hist = y_hist / var_dx / y_hist.sum() if plot_flag: - import matplotlib.pyplot as plt - plt.stairs(y_hist, bins) return y_hist, bins, bins_pos diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py index 90473ffa..8b13e3cf 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py @@ -5,6 +5,7 @@ import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec +import h5py def derive_beam_statistics(Gd, all_beams, Lmeter=10e3, dx=10): @@ -15,7 +16,6 @@ def derive_beam_statistics(Gd, all_beams, Lmeter=10e3, dx=10): Lemter is the length of the segment in meters for the statistics dx is the nominal resolution of the ATL06 data in meters """ - import h5py D = dict() for k in all_beams: @@ -82,13 +82,10 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): col_dict is a dict with the colors for the beams track_name is the name of the track """ - import matplotlib.pyplot as plt if track_name is not None: plt.suptitle(track_name, fontsize=10) - import matplotlib.gridspec as gridspec - gs = gridspec.GridSpec(2, 3) # make 2 x 2 plot @@ -146,10 +143,12 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): plt.title("low beams N", loc="left") plt.xlabel("along track distance (km)") + ax5 = plt.subplot(gs[0:2, 2]) + lat_shift = 0 for k in low_beams: Di = D[k] - plt.scatter( + ax5.scatter( Di["x"] / 1e3, Di["lat"] + lat_shift, s=np.exp(Di["N"] * 5), @@ -162,7 +161,7 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): for k in high_beams: Di = D[k] - plt.scatter( + ax5.scatter( Di["x"] / 1e3, Di["lat"] + lat_shift, s=np.exp(Di["N"] * 5), @@ -173,11 +172,11 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): ) lat_shift = lat_shift + 2 - plt.title("Density in space", loc="left") - plt.ylabel("Latitude (deg)") - plt.xlabel("along track distance (km)") - plt.legend() - plt.show() + ax5.title("Density in space", loc="left") + ax5.ylabel("Latitude (deg)") + ax5.xlabel("along track distance (km)") + ax5.legend() + ax5.show() ## plot track stats basics for sliderules ATL06 output diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py index 77766490..5799f0ca 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py @@ -1,5 +1,10 @@ import numpy as np from numba import jit +import pandas as pd + + +def get_hemis(B, beams_list): + return "SH" if B[beams_list[0]]["lats"].iloc[0] < 0 else "NH" def correct_heights(T03, T03c, coord="delta_time"): @@ -58,10 +63,7 @@ def lat_min_max_extended(B, beams_list, accent=None): accent = regrid.track_type(B[beams_list[0]]) if accent is None else accent - if B[beams_list[0]]["lats"].iloc[0] < 0: - hemis = "SH" - else: - hemis = "NH" + hemis = get_hemis(B, beams_list) track_pos_start, track_pos_end = list(), list() for k in beams_list: @@ -83,9 +85,6 @@ def lat_min_max_extended(B, beams_list, accent=None): track_lat_end.append(ll["lats"]) track_lon_end.append(ll["lons"]) - if accent: - track_lon_start - if (hemis == "SH") & accent: return ( [max(track_lat_start), min(track_lat_end)], @@ -117,26 +116,22 @@ def lat_min_max_extended(B, beams_list, accent=None): def lat_min_max(B, beams_list, accent=None): """ defines common boundaries for beams_list in B - iunputs: - beams_list list of concidered beams + inputs: + beams_list list of considered beams B is dict of Pandas tables with beams - accent if track is accending or decending. if None, this will try to use the track time to get this + accent if track is ascending or descending. if None, this will try to use the track time to get this returns: - min_lat, max_lat, accent min and max latitudes of the beams, (True/False) True if the track is accending + min_lat, max_lat, accent min and max latitudes of the beams, (True/False) True if the track is ascending """ accent = track_type(B[beams_list[0]]) if accent is None else accent - if B[beams_list[0]]["lats"].iloc[0] < 0: - hemis = "SH" - else: - hemis = "NH" + hemis = get_hemis(B, beams_list) - track_lat_mins, track_lat_maxs = list(), list() - for k in beams_list: - track_lat_mins.append(B[k]["lats"].min()) - track_lat_maxs.append(B[k]["lats"].max()) + track_lat_mins, track_lat_maxs = zip( + *[(B[k]["lats"].min(), B[k]["lats"].max()) for k in beams_list] + ) if hemis == "SH": return max(track_lat_maxs), min(track_lat_mins), accent @@ -177,8 +172,6 @@ def derive_axis(TT, lat_lims=None): # set 1st dist to 0, not used if global limits are used if lat_lims is None: TT["dist"] = TT["dist"] - TT["dist"].min() - else: - TT["dist"] = TT["dist"] # - lat_lims[0] TT = TT.sort_values(by="dist") return TT @@ -194,12 +187,9 @@ def reduce_to_height_distance(TT, key, dx=1, lat_lims=None): returns: x1, y1 position, height """ - from scipy.interpolate import interp1d - if type(dx) is np.ndarray: - x1 = dx - else: - x1 = np.arange(0, TT["dist"].max(), dx) + x1 = dx if isinstance(dx, np.ndarray) else np.arange(0, TT["dist"].max(), dx) + y1 = np.interp(x1, TT["dist"], TT[key]) return x1, y1 @@ -238,7 +228,6 @@ def poly_correct(x, y, poly_order=7, plot_flag=False): ### regridding -# @jit(nopython=True) def get_mode(y, bins=np.arange(-5, 5, 0.1)): "returns modes of histogram of y defined by bins" hist, xbin = np.histogram(y, bins=bins) @@ -249,7 +238,6 @@ def get_mode(y, bins=np.arange(-5, 5, 0.1)): def weighted_mean(x_rel, y): "returns the gaussian weighted mean for stencil" - # @jit(nopython=True, parallel= False) def weight_fnk(x): "returns gaussian weight given the distance to the center x" return np.exp(-((x / 0.5) ** 2)) @@ -287,7 +275,6 @@ def get_stencil_stats_shift( the column 'key' is rename to key+'_median' """ - import pandas as pd stencil_1 = stencil_iter[:, ::2] stencil_1half = stencil_iter[:, 1::2] @@ -320,7 +307,7 @@ def calc_stencil_stats(group, key, key_x_coord, stancil_width, stancils): return Tweight.T T_sets = list() - stancil_set = stencil_1 + for stancil_set in [stencil_1, stencil_1half]: # select photons that are in bins @@ -424,12 +411,12 @@ def calc_stencil_stats(istencil): y = y_data[i_mask] Tmedian = T2[i_mask].median() - Tmedian[key + "_weighted_mean"] = weighted_mean(x_rel, y) - Tmedian[key + "_mode"] = get_mode(y) + Tmedian[f"{key}_weighted_mean"] = weighted_mean(x_rel, y) + Tmedian[f"{key}_mode"] = get_mode(y) Tmedian["N_photos"] = Nphoton - Tmedian[key + "_std"] = y.std() + Tmedian[f"{key}_std"] = y.std() - print(str(istencil[1]) + " s" + str(time.time() - tstart)) + print(f"{istencil[1]} s{time.time() - tstart}") return istencil[1], Tmedian # apply func to all stancils @@ -438,10 +425,10 @@ def calc_stencil_stats(istencil): DF_filt = pd.DataFrame.from_dict(D_filt, orient="index") DF_filt = DF_filt.rename( - columns={key: key + "_median", key_x_coord: "median_" + key_x_coord} + columns={key: f"{key}_median", key_x_coord: f"median_{key_x_coord}"} ) - DF_filt[key + "_median"][ - np.isnan(DF_filt[key + "_std"]) + DF_filt[f"{key}_median"][ + np.isnan(DF_filt[f"{key}_std"]) ] = np.nan # replace median calculation with nans DF_filt[key_x_coord] = DF_filt.index DF_filt = DF_filt.reset_index() @@ -452,10 +439,10 @@ def calc_stencil_stats(istencil): # derive bin means def bin_means(T2, dist_grid): dF_mean = pd.DataFrame(index=T2.columns) - ilim = int(len(dist_grid)) + ilim = len(dist_grid) N_i = list() - for i in np.arange(1, ilim - 1, 1): + for i in np.arange(1, ilim - 1): if i % 5000 == 0: print(i) i_mask = (T2["dist"] >= dist_grid[i - 1]) & (T2["dist"] < dist_grid[i + 1]) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py b/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py index abec0dbc..bcb174da 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py @@ -668,7 +668,7 @@ def get_stancil_var_apply(stancil): self.G.attrs["mean_variance_LS_pwelch_spectrum"] = self.calc_var() def mean_spectral_error(self, mask=None, confidence=0.95): - return spec.wavenumber_spectrogram.mean_spectral_error( + return spec.WavenumberSpectrogram.mean_spectral_error( self, mask=mask, confidence=confidence ) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py index ad5bd1d0..5a7771ee 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py @@ -1,5 +1,8 @@ import numpy as np import scipy.signal as signal +import scipy.ndimage +import scipy.ndimage.filters as signal + def lanczos_1d(width, dx, a=2): """ @@ -53,12 +56,11 @@ def lanczos_filter_1d(x, data, width, a=2, mode="same", method="direct"): returns data_lp low-passed data, same size as before. """ - dx = np.diff(x).mean() x, L = lanczos_1d(width, dx, a=a) - data_lp = signal.convolve(data, L, mode=mode, method=method) + data_lp = signal.convolve(data, L, mode=mode, method=method) return data_lp @@ -80,7 +82,6 @@ def lanczos_filter_1d_wrapping(x, data, width, a=2, mode="wrap"): returns data_lp low-passed data, same size as before. """ - import scipy.ndimage dx = np.diff(x).mean() x, L = lanczos_1d(width, dx, a=a) @@ -105,12 +106,11 @@ def lanczos_filter_2d(x, data, width, a=2, mode="same"): returns data_lp low-passed data, same size as before. """ - import scipy.ndimage.filters as signal dx = abs(np.diff(x).mean()) x, L2d = lanczos_2d(width, dx, a=a) - data_lp = signal.convolve(data, L2d, mode=mode) + data_lp = signal.convolve(data, L2d, mode=mode) return data_lp @@ -142,11 +142,10 @@ def lanczos_filter_3d(x, data, width, a=2, mode="same"): returns data_lp low-passed data, same size as before. """ - import scipy.ndimage.filters as signal dx = abs(np.diff(x).mean()) x, L3d = lanczos_3d(width, dx, a=a) - data_lp = signal.convolve(data, L3d, mode=mode) + data_lp = signal.convolve(data, L3d, mode=mode) return data_lp diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py b/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py index 1777d1f6..85fdf230 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py @@ -50,7 +50,8 @@ def read_ICESat2_groundtrack(input_file): gdf = geopandas.GeoDataFrame(rows) RGTS.append(gdf) # return the concatenated geodataframe - return geopandas.pd.concat(RGTS).set_index("date") + concatenated_df = geopandas.pd.concat(RGTS).set_index("date") + return concatenated_df # PURPOSE: read ICESat-2 ground tracks @@ -100,7 +101,8 @@ def ICESat2_mission_groundtrack(input_file): ) GTs.append(gdf) # return the concatenated geodataframe - return geopandas.pd.concat(GTs) + concatenated_df = geopandas.pd.concat(GTs) + return concatenated_df # PURPOSE: read ICESat-2 mission ground tracks as points diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py b/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py index f084db97..47b25490 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py @@ -1,4 +1,15 @@ -from ipyleaflet import basemaps +from ipyleaflet import ( + Map, + basemaps, + Polygon, +) +import numpy as np +from math import radians, cos, sin, asin, sqrt +from shapely.geometry import Polygon +import pandas as pd +import geopandas as gpd + +import matplotlib.pyplot as plt # height correction tools @@ -17,8 +28,6 @@ def correct_and_remove_height(Gi, height_limit): def make_plot_polygon(poly_test, color="green"): """create a plot polygon from the given coordinates""" - from ipyleaflet import Polygon - bb = [ poly_test[0]["lon"], poly_test[0]["lat"], @@ -32,20 +41,7 @@ def make_plot_polygon(poly_test, color="green"): def plot_polygon(poly_test, basemap=basemaps.Esri.WorldImagery, zoom=3): """plots polygon in the map""" - from ipyleaflet import ( - Map, - GeoData, - LayersControl, - Rectangle, - basemaps, - basemap_to_tiles, - TileLayer, - SplitMapControl, - Polygon, - ) - # icepx will want a bounding box with LL lon/lat, UR lon/lat - import numpy as np polygon_plot = make_plot_polygon(poly_test, color="green") @@ -60,8 +56,6 @@ def plot_polygon(poly_test, basemap=basemaps.Esri.WorldImagery, zoom=3): # gemetric tools def haversine(lon1, lat1, lon2, lat2, arc=False): - from math import radians, cos, sin, asin, sqrt - """ Calculate the great circle distance between two points on the earth (specified in decimal degrees) @@ -98,7 +92,6 @@ def get_min_eq_dist(ppoly): def create_polygons(latR, lonR): - from shapely.geometry import Polygon, Point latR.sort() lonR.sort() @@ -123,8 +116,6 @@ def find_highest_point_on_RGT(Gs, RGT): # find_lowest_point_on_RGT(Gs, 2).geometry def get_RGT_start_points(Gs, RGT="RGT"): - import pandas as pd - import geopandas as gpd G_lowest = pd.concat( [find_lowest_point_on_RGT(Gs, rgt).T for rgt in Gs[RGT].unique()], axis=1 @@ -134,8 +125,6 @@ def get_RGT_start_points(Gs, RGT="RGT"): def get_RGT_end_points(Gs, RGT="RGT"): - import pandas as pd - import geopandas as gpd G_lowest = pd.concat( [find_highest_point_on_RGT(Gs, rgt).T for rgt in Gs[RGT].unique()], axis=1 @@ -225,7 +214,6 @@ def plot_reference_point_coordinates(tmp, start_point_dist, start_point): start_point_dist: the distance from the equator to the reference point start_point: the reference point (GeoDataFrame) """ - import matplotlib.pyplot as plt rgt = tmp["rgt"].unique()[0] spoint_color = "black" @@ -273,7 +261,6 @@ def plot_data_in_domain(gdf2, polygon_list): inputs: gdf: GeoDataFrame with the down """ - import matplotlib.pyplot as plt # make two panel figure, on the left plot the photon postions, on the the hoffmoeller diagram fig, axx = plt.subplots(1, 2, figsize=(8, 4)) @@ -368,7 +355,6 @@ def check_RGT_in_domain(Gtrack_lowest, gdf): returns: result: set of RGT that are in both Gtrack_lowest and gdf """ - import collections gdf_list = list(gdf["rgt"].unique()) result = set(gdf_list).intersection(set(Gtrack_lowest["RGT"])) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py b/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py index 9ea22e47..13828fe5 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py @@ -1,4 +1,6 @@ import numpy as np +import matplotlib.pyplot as plt +from scipy import signal def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0, verbose=False): @@ -45,7 +47,6 @@ def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0, verbose=False) print("stoped by max#") if verbose: - import matplotlib.pyplot as plt plt.plot(data, "r") plt.plot(data2, "b") @@ -55,8 +56,6 @@ def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0, verbose=False) def spickes_to_mean(ts, nloop=None, spreed=1, gaussian=True): - from scipy import signal - nloop = 0 if nloop is None else nloop i = 0 tsmean = ts.mean() diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py b/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py index 09288f95..42d9f8ff 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py @@ -1,8 +1,9 @@ +import numpy as np + + def to_vec(amp, angle, deg=True): "from anlge deg to vect" - import numpy as np - if deg: u, v = amp * np.cos(angle * np.pi / 180), amp * np.sin(angle * np.pi / 180) else: @@ -17,7 +18,6 @@ def to_deg(u, v, deg=True): angle is -180 to 180 this is a different definiton then WW3 [0, 360 ), but (-180, 180] is more convient for the problem """ - import numpy as np amp = np.sqrt(u**2 + v**2) angle = np.arctan2(v, u) @@ -28,7 +28,6 @@ def to_deg(u, v, deg=True): def get_ave_amp_angle(amp, angle, deg=True): - import numpy as np u, v = to_vec(amp, angle, deg=deg) # average angle in vector space diff --git a/src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py b/src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py index fca302da..b5c2f8eb 100644 --- a/src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py +++ b/src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py @@ -459,7 +459,7 @@ def _get_stancil_nans(stancil, Gd_cut=Gd_cut): print("FFT") dd[dd_nans] = 0 - S = spec.wavenumber_spectrogram(x, dd, Lpoints) + S = spec.WavenumberSpectrogram(x, dd, Lpoints) G = S.cal_spectrogram() S.mean_spectral_error() # add x-mean spectral error estimate to xarray S.parceval(add_attrs=True) From 9aef485ed17d4658e722ed4c790c425430524ae0 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Wed, 28 Feb 2024 17:03:46 -0500 Subject: [PATCH 05/51] fix bug on beam_stats.py --- src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py index 8b13e3cf..6315da16 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py @@ -7,7 +7,6 @@ import matplotlib.gridspec as gridspec import h5py - def derive_beam_statistics(Gd, all_beams, Lmeter=10e3, dx=10): """ this method returns a dict of dataframes with the beam statistics @@ -16,6 +15,7 @@ def derive_beam_statistics(Gd, all_beams, Lmeter=10e3, dx=10): Lemter is the length of the segment in meters for the statistics dx is the nominal resolution of the ATL06 data in meters """ + D = dict() for k in all_beams: @@ -86,6 +86,7 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): if track_name is not None: plt.suptitle(track_name, fontsize=10) + gs = gridspec.GridSpec(2, 3) # make 2 x 2 plot @@ -172,7 +173,7 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): ) lat_shift = lat_shift + 2 - ax5.title("Density in space", loc="left") + ax5.set_title("Density in space", loc="left") ax5.ylabel("Latitude (deg)") ax5.xlabel("along track distance (km)") ax5.legend() From 2f471626b5bbc82fe228da3d7dc9f8fb1cf5b34e Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Wed, 28 Feb 2024 18:49:18 -0500 Subject: [PATCH 06/51] fix: update xlabel, ylabel to set_xlabel, set_ylabel --- src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py index 6315da16..28c8bc6e 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py @@ -174,10 +174,10 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): lat_shift = lat_shift + 2 ax5.set_title("Density in space", loc="left") - ax5.ylabel("Latitude (deg)") - ax5.xlabel("along track distance (km)") + ax5.set_ylabel("Latitude (deg)") + ax5.set_xlabel("along track distance (km)") ax5.legend() - ax5.show() + plt.show() ## plot track stats basics for sliderules ATL06 output From f5953705ad8f0991d3b7d2a25674323ee7b1fbd5 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 29 Feb 2024 09:29:13 -0500 Subject: [PATCH 07/51] it seems spectral_estimates.py was not included in the last commit --- .../ICEsat2_SI_tools/spectral_estimates.py | 1276 +++++++---------- 1 file changed, 518 insertions(+), 758 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index bcc8afde..2e9e54bd 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -1,10 +1,50 @@ import numpy as np +from astropy.timeseries import LombScargle +import scipy.signal.windows as WINDOWS +from scipy.special import gammainc +import copy +import xarray as xr +from scipy.signal import detrend +import pandas as pd +from scipy import signal +import lmfit as LM +import icesat2_tracks.local_modules.m_general_ph3 as M + + +def is_even(number): + return not (number % 2) + +def define_chunk_boundaries_per_type(L_unit, ov, limits_size): + + ov = int(np.round(L_unit / 2)) if ov is None else ov + dl = L_unit - ov + boundaries = [] + + # Handling when limits_size is an integer + if isinstance(limits_size, int): + boundaries = [ + (0, limits_size - dl,dl), + (dl, limits_size - dl + 1,dl), + (dl * 2, limits_size + 1,dl) + ] + + # Handling when limits_size is a list + elif isinstance(limits_size, list) and len(limits_size) == 2: + start, end = limits_size + boundaries = [ + (start, end - dl,dl), + (start + L_unit / 2, end - dl + 1,dl), + (start + L_unit, end + 1,dl) + ] + else: + raise ValueError("limits_size must be either an int or a list of two elements") + return boundaries # basic functions -def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): +def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): """ - returns all need chunk boudaries and center position given L, and ov + returns all need chunk boundaries and center position given L, and ov inputs: L desired length of window, dsize size of the data @@ -13,108 +53,68 @@ def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): if iter_flag True returns iter else it returns an ndarray """ - ov = int(np.round(L / 2)) if ov is None else ov - - xleft = np.arange(0, dsize - int(L - ov), int(L - ov)) - xright = np.arange(int(L - ov) * 2, dsize + 1, int(L - ov)) - xcenter_pos = np.arange(int(L - ov), dsize - int(L - ov) + 1, int(L - ov)) - max_size = min([xleft.size, xcenter_pos.size, xright.size]) - # if xright[max_size-1] < dsize: - # print('left out last ' + str(dsize- xright[max_size-1]) + ' data points' ) - # print([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) - position_stancil = np.vstack( - [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] - ) - - if iter_flag is True: - return iter(position_stancil.T.tolist()) - else: - return position_stancil + boundaries = define_chunk_boundaries_per_type(L,ov,dsize) + + xleft = np.arange(boundaries[0]) + xcenter_pos = np.arange(boundaries[1]) + xright = np.arange(boundaries[3]) + + max_size = min([xleft.size , xcenter_pos.size, xright.size]) -def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag=True): - """ - returns all need chunk boudaries and center position given L, and ov - inputs: - L desired length of window in units of the x axis of the data, - data_limits (x_min, x_max) tuple with the beginning and end the the derived window stancils - - if ov is None, = L/2 - if iter_flag True returns iter else it returns an ndarray + position_stancil = np.vstack([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) - """ - L = L_unit - ov = np.round(L / 2) if ov is None else ov - # print(ov) - dl = L - ov - xleft = np.arange(data_limits[0], data_limits[1] - dl, dl) - xcenter_pos = np.arange(data_limits[0] + L / 2, data_limits[1] - dl + 1, dl) - xright = np.arange(data_limits[0] + L, data_limits[1] + 1, dl) - - max_size = min([xleft.size, xcenter_pos.size, xright.size]) - # if xright[max_size-1] < data_limits[1]: - # print('left out last ' + str(data_limits[1]- xright[max_size-1]) + ' data points' ) - # print([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) - position_stancil = np.vstack( - [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] - ) - - if iter_flag is True: - return iter(position_stancil.T.tolist()) - else: - return position_stancil + return iter(position_stancil.T.tolist()) if iter_flag else position_stancil def Z_to_power(Z, df, N): - """compute the 1d spectrum of a field phi + """ compute the 1d spectrum of a field phi inputs: Z complex fourier coefficients df frequency / or wavenumber step N length of data vector in real space (= L) """ - spec = 2.0 * (Z * Z.conj()).real / df / N**2 - neven = True if (N % 2) else False + spec = 2.*(Z*Z.conj()).real / df /N**2 + neven = is_even(N) # the zeroth frequency should be counted only once - spec[0] = spec[0] / 2.0 + spec[0] = spec[0]/2. if neven: - spec[-1] = spec[-1] / 2.0 + spec[-1] = spec[-1]/2. return spec - # 2nd cal spectra def calc_spectrum_fft(phi, df, N): - """compute the 1d spectrum of a field phi + """ compute the 1d spectrum of a field phi inputs: df frequency / or wavenumber step N length of data vector in real space (= L) neven bool, if True """ - neven = True if (N % 2) else False + neven = is_even(N) phih = np.fft.rfft(phi) # the factor of 2 comes from the symmetry of the Fourier coeffs - spec = 2.0 * (phih * phih.conj()).real / df / N**2 + spec = 2.*(phih*phih.conj()).real / df /N**2 # the zeroth frequency should be counted only once - spec[0] = spec[0] / 2.0 + spec[0] = spec[0]/2. if neven: - spec[-1] = spec[-1] / 2.0 + spec[-1] = spec[-1]/2. return spec -def LS_power_to_PSD(ls_power, L, dff): +def LS_power_to_PSD( ls_power, L , dff): """ returns Power spectral density (unit^2/dfreq) ls_power output of astropy.timeseries.LombScargle.power with normalization='psd' """ - return 2 * ls_power / L / dff - + return 2 * ls_power / L /dff -def calc_spectrum_LS(x, y, k, err=None, LS=None, dk=None): +def calc_spectrum_LS( x, y, k, err=None, LS= None, dk =None): """ returns: Power spectral density of y given postitions x, for wanumbers k @@ -123,19 +123,16 @@ def calc_spectrum_LS(x, y, k, err=None, LS=None, dk=None): LS LombScargle object """ if LS is None: - from astropy.timeseries import LombScargle - - LS = LombScargle(x, y, dy=err, fit_mean=False, center_data=True) + LS = LombScargle(x , y, dy = err, fit_mean=False, center_data=True) else: LS.t = x LS.y = y - LS.dy = err - - ls_power = LS.power(k, normalization="psd", assume_regular_frequency="False") + LS.dy= err - dk = np.diff(k).mean() if dk is None else dk - return 2 * ls_power / y.size / dk, LS + ls_power = LS.power(k, normalization='psd', assume_regular_frequency='False') + dk = np.diff(k).mean() if dk is None else dk + return 2 * ls_power / y.size / dk , LS def reconstruct_data_from_LS(LS, x_real_axis, freq): """ @@ -148,42 +145,32 @@ def reconstruct_data_from_LS(LS, x_real_axis, freq): y_reconstruct = LS.offset() * np.ones(len(x_real_axis)) freq_seq = freq[1:] if freq[0] == 0 else freq - freq_mask = freq <= 1 / 100 + freq_mask= freq <= 1/100 - # print(freq_seq) for fi in freq_seq: try: theta = LS.model_parameters(fi) except: - theta = [0, 0] - y_reconstruct += theta[0] * np.sin(x_real_axis * 2 * np.pi * fi) + theta[ - 1 - ] * np.cos(x_real_axis * 2 * np.pi * fi) - # y_reconstruct += LS.model(x_real_axis, fi) - - # for fi in freq_seq[:]: - # theta = LS.model_parameters(fi) - # y_reconstruct += theta[0] + theta[1] * np.sin(x_real_axis * 2 * np.pi *fi ) + theta[2]* np.cos(x_real_axis * 2 * np.pi *fi) - # #y_reconstruct += LS.model(x_real_axis, fi) + theta = [0,0] + y_reconstruct += theta[0] * np.sin(x_real_axis * 2 * np.pi *fi ) + theta[1]* np.cos(x_real_axis * 2 * np.pi *fi) + return y_reconstruct - def calc_freq_fft(x_grid, N): - """calculate array of spectral variable (frequency or - wavenumber) in cycles per unit of L""" + """ calculate array of spectral variable (frequency or + wavenumber) in cycles per unit of L """ - neven = True if (N % 2) else False - # dx=np.diff(x_grid).mean() - dx = np.round(np.median(np.diff(x_grid)), 1) - df = 1.0 / ((N - 1) * dx) + neven = is_even(N) + + dx = np.round(np.median(np.diff(x_grid) ), 1) + df = 1./((N-1)*dx) if neven: - f = df * np.arange(N / 2 + 1) + f = df*np.arange(N/2+1) else: - f = df * np.arange((N - 1) / 2.0 + 1) - return f, df - + f = df*np.arange( (N-1)/2. + 1 ) + return f,df def calc_freq_fft_given_dx(dx, N): """ @@ -193,25 +180,17 @@ def calc_freq_fft_given_dx(dx, N): N number of datapoints used in window """ - neven = True if (N % 2) else False - df = 1.0 / ((N - 1) * dx) + neven = is_even(N) + df = 1./((N-1)*dx) if neven: - f = df * np.arange(N / 2 + 1) + f = df*np.arange(N/2+1) else: - f = df * np.arange((N - 1) / 2.0 + 1) - return f, df - - -def calc_freq_LS( - x, - N, - method="fftX2", - dx=None, - minimum_frequency=None, - maximum_frequency=None, - samples_per_peak=0.01, -): + f = df*np.arange( (N-1)/2. + 1 ) + return f,df + + +def calc_freq_LS(x, N, method='fftX2', dx=None, minimum_frequency=None, maximum_frequency=None, samples_per_peak=0.01): """ calculate array of spectral variable (frequency or wavenumber) in cycles per unit of N (window length in number of data points) @@ -223,48 +202,40 @@ def calc_freq_LS( minimum_frequency, maximum_frequency only used for LS_auto """ - if method is "fftX2": - neven = True if (N % 2) else False + if method is 'fftX2': + neven = is_even(N) dx = np.diff(x).mean() if dx is None else dx - df = 1.0 / ((N - 1) * dx) / 2 + df = 1./((N-1)*dx) /2 if neven: - f = df * np.arange(df, N + 1) + f = df*np.arange(df, N+1) else: - f = df * np.arange(df, (N - 1) + 1) + f = df* np.arange(df, (N-1) + 1 ) - elif method is "fft": - neven = True if (N % 2) else False + elif method is 'fft': + neven = is_even(N) dx = np.diff(x).mean() if dx is None else dx - df = 1.0 / ((N - 1) * dx) + df = 1./((N-1)*dx) if neven: - f = df * np.arange(N / 2 + 1) + f = df*np.arange(N/2+1) else: - f = df * np.arange((N - 1) / 2.0 + 1) + f = df*np.arange( (N-1)/2. + 1 ) - elif method is "LS_auto": - from astropy.timeseries import LombScargle - - f = LombScargle(x, np.random.randn(len(x)), fit_mean=True).autofrequency( - minimum_frequency=minimum_frequency, - maximum_frequency=maximum_frequency, - samples_per_peak=samples_per_peak, - ) ##0.1) + elif method is 'LS_auto': + + f = LombScargle(x , np.random.randn(len(x)), fit_mean=True).autofrequency(minimum_frequency=minimum_frequency, maximum_frequency=maximum_frequency, samples_per_peak=samples_per_peak)##0.1) df = np.diff(f).mean() df = np.round(df, 5) - elif method is "fixed_ratio": + elif method is 'fixed_ratio': - neven = True if (N % 2) else False + neven = is_even(N) dx = np.diff(x).mean() if dx is None else dx df = dx / 50 - if neven: - f = df * np.arange(df, N + 1) - else: - f = df * np.arange(df, N) - - return f, df + f = df * np.arange(df, N + 1) if neven else df * np.arange(df, N) + + return f ,df def create_window(L, window=None): """ @@ -272,66 +243,63 @@ def create_window(L, window=None): if window is not None it show have a length of N """ if window is None: - win = np.hanning(L) + win=np.hanning(L) else: - win = window + win=window - factor = np.sqrt(L / (win**2).sum()) - win *= factor + factor=np.sqrt(L/(win**2).sum()) + win*=factor return win - def create_weighted_window(data, window=None): """ define window function and weight it to conserve variance if window is not None it show have a length of N """ - import scipy.signal.windows as WINDOWS - + L = data.size if window is None: - # win=np.hanning(L) - win = WINDOWS.tukey(L, alpha=0.1, sym=True) + win = WINDOWS.tukey(L, alpha=0.1, sym=True) else: - win = window + win=window - factor = np.sqrt(np.var(data) / np.var((data * win))) - # factor=np.sqrt( L/(win**2).sum()) - win *= factor + factor = np.sqrt( np.var(data) / np.var(( data* win) ) ) + win *= factor return win +def spec_error(E,sn,ci=.95): + + """ Computes confidence interval for one-dimensional spectral + estimate E (the power spectra). -def spec_error(E, sn, ci=0.95): - """Computes confidence interval for one-dimensional spectral - estimate E (the power spectra). + Parameters + =========== + - sn is the number of spectral realizations; + it can be either an scalar or an array of size(E) + - ci = .95 for 95 % confidence interval - Parameters - =========== - - sn is the number of spectral realizations; - it can be either an scalar or an array of size(E) - - ci = .95 for 95 % confidence interval + Output + ========== + lower (El) and upper (Eu) bounds on E """ - Output - ========== - lower (El) and upper (Eu) bounds on E""" - def yNlu(sn, yN, ci): - """compute yN[l] yN[u], that is, the lower and - upper limit of yN""" - from scipy.special import gammainc + def yNlu(sn,yN,ci): + """ compute yN[l] yN[u], that is, the lower and + upper limit of yN """ + # cdf of chi^2 dist. with 2*sn DOF - cdf = gammainc(sn, sn * yN) + cdf = gammainc(sn,sn*yN) # indices that delimit the wedge of the conf. interval fl = np.abs(cdf - ci).argmin() - fu = np.abs(cdf - 1.0 + ci).argmin() + fu = np.abs(cdf - 1. + ci).argmin() - return yN[fl], yN[fu] + return yN[fl],yN[fu] - dbin = 0.005 - yN = np.arange(0, 2.0 + dbin, dbin) + dbin = .005 + yN = np.arange(0,2.+dbin,dbin) El, Eu = np.empty_like(E), np.empty_like(E) @@ -345,19 +313,19 @@ def yNlu(sn, yN, ci): assert n == E.size, " *** sn has different size than E " for i in range(n): - yNl, yNu = yNlu(sn[i], yN=yN, ci=ci) - El[i] = E[i] / yNl - Eu[i] = E[i] / yNu + yNl,yNu = yNlu(sn[i],yN=yN,ci=ci) + El[i] = E[i]/yNl + Eu[i] = E[i]/yNu else: - yNl, yNu = yNlu(sn, yN=yN, ci=ci) - El = E / yNl - Eu = E / yNu + yNl,yNu = yNlu(sn,yN=yN,ci=ci) + El = E/yNl + Eu = E/yNu return El, Eu - def linear_gap_fill(F, key_lead, key_int): + """ F pd.DataFrame key_lead key in F that determined the independent coordindate @@ -365,13 +333,13 @@ def linear_gap_fill(F, key_lead, key_int): """ y_g = np.array(F[key_int]) - nans, x2 = np.isnan(y_g), lambda z: z.nonzero()[0] - y_g[nans] = np.interp(x2(nans), x2(~nans), y_g[~nans]) + nans, x2= np.isnan(y_g), lambda z: z.nonzero()[0] + y_g[nans]= np.interp(x2(nans), x2(~nans), y_g[~nans]) return y_g +def sub_sample_coords(X, lons, lats, stancils, map_func =None): -def sub_sample_coords(X, lons, lats, stancils, map_func=None): """ X non-nan array of coodinate along beam lons, lats arrays of postion data that should be mapped. must have same size as X @@ -382,28 +350,25 @@ def sub_sample_coords(X, lons, lats, stancils, map_func=None): nparray(3, N) 1st column is the stancil center, 2nd and 3rd collumn are the mapped lons and lats """ - import copy - + def get_lon_lat_coords(stancil): - x_mask = (stancil[0] <= X) & (X <= stancil[-1]) - # print(stancil[1]) - if sum(x_mask) == 0: # if there are not enough photos set results to nan + x_mask= (stancil[0] <= X) & (X <= stancil[-1]) + if sum(x_mask) ==0: # if there are not enough photos set results to nan return np.array([stancil[1], np.nan, np.nan]) lon_bin, lat_bin = lons[x_mask].mean(), lats[x_mask].mean() - return np.array([stancil[1], lon_bin, lat_bin]) + return np.array([stancil[1],lon_bin, lat_bin]) map_func = map if map_func is None else map_func - # print(map_func) - coord_positions = list(map_func(get_lon_lat_coords, copy.copy(stancils))) + coord_positions = list(map_func( get_lon_lat_coords, copy.copy(stancils) )) coord_positions = np.vstack(coord_positions) return coord_positions -class wavenumber_spectrogram: +class WavenumberSpectrogram: def __init__(self, x_grid, data, Lpoints, ov=None, window=None): """ returns a wavenumber spectrogram with the resolution L-ov @@ -421,136 +386,119 @@ def __init__(self, x_grid, data, Lpoints, ov=None, window=None): other arributes are in the .attr dict. """ - self.Lpoints = Lpoints - self.ov = ( - int(Lpoints / 2) if ov is None else ov - ) # when not defined in create_chunk_boundaries then L/2 + self.Lpoints = Lpoints + self.ov = int(Lpoints/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.data = data + self.data = data # create subsample k - self.k, self.dk = calc_freq_fft( - x_grid, Lpoints - ) # return 1/ unit of frid points + self.k, self.dk = calc_freq_fft(x_grid, Lpoints) # return 1/ unit of frid points # to get the waveumber units (2 pi/ lambda), multiply by 2 pi - self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi + self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi - # print(self.k[0], self.k[-1]) - # print(self.dk) # create window - self.win = create_window(Lpoints) + self.win = create_window(Lpoints) def cal_spectrogram(self, data=None, name=None): + """ defines apply function and calculated all sub-sample sprectra using map """ - import xarray as xr + DATA = self.data if data is None else data Lpoints, dk = self.Lpoints, self.dk - win = self.win + win =self.win def calc_spectrum_apply(stancil): "returns spectrum per stencil, detrends and windows the data" - from scipy.signal import detrend + - idata = DATA[stancil[0] : stancil[-1]] + idata = DATA[stancil[0]:stancil[-1]] idata = detrend(idata) * win - return stancil[1], calc_spectrum_fft(idata, dk, Lpoints) + return stancil[1], calc_spectrum_fft(idata , dk, Lpoints) - # def test_func(i_stancil): - # return i_stancil[1], yy[i_stancil[0]:i_stancil[-1]].shape - - # %% derive L2 stancil - stancil_iter = create_chunk_boundaries(Lpoints, DATA.size, ov=self.ov) + # derive L2 stancil + stancil_iter = create_chunk_boundaries(Lpoints, DATA.size, ov= self.ov) # apply func to all stancils - D_specs = dict(map(calc_spectrum_apply, stancil_iter)) + D_specs = dict(map(calc_spectrum_apply,stancil_iter)) chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectal relazations + self.N_stancils = len(chunk_positions) # number of spectal relazations # repack data, create xarray - self.spec_name = "power_spec" if name is None else name - G = dict() - for xi, I in D_specs.items(): - G[xi] = xr.DataArray( - I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name - ) + self.spec_name = 'power_spec' if name is None else name + G =dict() + for xi,I in D_specs.items(): + G[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi } , name=self.spec_name) - self.G = xr.concat(G.values(), dim="x").T # .to_dataset() + self.G = xr.concat(G.values(), dim='x').T if self.G.k[0] == 0: self.G = self.G[1:, :] - self.G.attrs["ov"] = self.ov - self.G.attrs["L"] = self.Lpoints + self.G.attrs['ov'] = self.ov + self.G.attrs['L'] = self.Lpoints return self.G - # cal variance + def calc_var(self): - """Compute total variance from spectragram""" - return self.dk * self.G.mean("x").sum().data # do not consider zeroth frequency + """ Compute total variance from spectragram """ + return self.dk*self.G.mean('x').sum().data # do not consider zeroth frequency - def mean_spectral_error(self, mask=None, confidence=0.95): + def mean_spectral_error(self, mask=None, confidence = 0.95): "retrurns spetral error for the x-mean spectral estimate and stores it as coordindate in the dataarray" # make error estimate if mask is not None: - meanspec = self.G.isel(x=mask).mean("x") + meanspec= self.G.isel(x=mask).mean('x') N = int(sum(mask)) else: - meanspec = self.G.mean("x") + meanspec= self.G.mean('x') N = self.N_stancils - El_of_mean, Eu_of_mean = spec_error(meanspec, N, confidence) - El_of_mean.name = "El_mean" - Eu_of_mean.name = "Eu_mean" + El_of_mean, Eu_of_mean = spec_error(meanspec, N , confidence ) + El_of_mean.name = 'El_mean' + Eu_of_mean.name = 'Eu_mean' - self.G.coords["mean_El"] = (("k"), El_of_mean.data) - self.G.coords["mean_Eu"] = (("k"), Eu_of_mean.data) + self.G.coords['mean_El'] = (('k'), El_of_mean.data) + self.G.coords['mean_Eu'] = (('k'), Eu_of_mean.data) - def parceval(self, add_attrs=True): + def parceval(self, add_attrs=True ): "test Parceval theorem" DATA = self.data L = self.Lpoints + # derive mean variances of stancils stancil_iter = create_chunk_boundaries(L, DATA.size) def get_stancil_var_apply(stancil): - from scipy.signal import detrend - + "returns the variance of yy for stancil" - idata = DATA[stancil[0] : stancil[-1]] - idata = detrend(idata) # * win + idata = DATA[stancil[0]:stancil[-1]] + idata = detrend(idata) return stancil[1], idata.var() - D_vars = dict(map(get_stancil_var_apply, stancil_iter)) + D_vars = dict(map(get_stancil_var_apply,stancil_iter)) - stancil_vars = list() + stancil_vars =list() for I in D_vars.values(): stancil_vars.append(I) - print("Parcevals Theorem:") - print("variance of unweighted timeseries: ", DATA.var()) - print("mean variance of detrended chunks: ", np.array(stancil_vars).mean()) - # print('variance of weighted timeseries: ',self.phi.var() ) - # self.calc_var(self) - print("variance of the pwelch Spectrum: ", self.calc_var()) + print('Parcevals Theorem:') + print('variance of unweighted timeseries: ',DATA.var()) + print('mean variance of detrended chunks: ', np.array(stancil_vars).mean()) + print('variance of the pwelch Spectrum: ', self.calc_var()) if add_attrs: - self.G.attrs["variance_unweighted_data"] = DATA.var() - self.G.attrs["mean_variance_detrended_chunks"] = np.array( - stancil_vars - ).mean() - self.G.attrs["mean_variance_pwelch_spectrum"] = self.calc_var() + self.G.attrs['variance_unweighted_data'] = DATA.var() + self.G.attrs['mean_variance_detrended_chunks'] = np.array(stancil_vars).mean() + self.G.attrs['mean_variance_pwelch_spectrum'] = self.calc_var() - -class wavenumber_spectrogram_LS_even: - def __init__( - self, x, data, L, waven_method="fftX2", dy=None, ov=None, window=None, kjumps=1 - ): +class WavenumberSpectrogramLSEven: + def __init__(self, x, data, L, waven_method = 'fftX2' , dy=None , ov=None, window=None, kjumps=1): """ returns a wavenumber spectrogram with the resolution L-ov this uses Lombscargle @@ -568,103 +516,96 @@ def __init__( xr.Dataset with x, k as cooridates of the spectrogram and the mean error other arributes are in the .attr dict. """ - from astropy.timeseries import LombScargle + + self.L = L + self.ov = int(L/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.L = L - self.ov = ( - int(L / 2) if ov is None else ov - ) # when not defined in create_chunk_boundaries then L/2 + self.x = x + self.data = data + self.dy = dy - self.x = x - self.data = data - self.dy = dy # create subsample k - # print(waven_method) if type(waven_method) is str: - self.k, self.dk = calc_freq_LS(x, L, method=waven_method) + self.k, self.dk = calc_freq_LS(x, L, method = waven_method ) elif type(waven_method) is np.ndarray: - self.k, self.dk = waven_method, np.diff(waven_method).mean() + self.k, self.dk = waven_method, np.diff(waven_method).mean() else: - raise ValueError("waven_method is neither string nor an array") + raise ValueError('waven_method is neither string nor an array') - self.k, self.dk = self.k[::kjumps], self.dk * kjumps + self.k, self.dk = self.k[::kjumps], self.dk*kjumps # create window - self.win = None # create_window(L) + self.win = None + + def cal_spectrogram(self, x = None, data=None, name=None, dx=1): - def cal_spectrogram(self, x=None, data=None, name=None, dx=1): """ defines apply function and calculated all sub-sample sprectra using map dx nominal resolution of the data resolutionif not set, dx= 1 """ - from astropy.timeseries import LombScargle - import xarray as xr + - X = self.x if x is None else x # all x positions - DATA = self.data if data is None else data # all data points - L, dk = self.L, self.dk - win = self.win + X = self.x if x is None else x # all x positions + DATA = self.data if data is None else data # all data points + L, dk = self.L, self.dk + win = self.win self.dx = dx # init Lomb scargle object with noise as nummy data () - # dy_fake= np.random.randn(len(dy))*0.001 if self.dy is not None else None - self.LS = LombScargle(X[0:L], np.random.randn(L) * 0.001, fit_mean=True) + self.LS = LombScargle(X[0:L] , np.random.randn(L)*0.001, fit_mean=True) + def calc_spectrum_apply(stancil): "returns spectrum per stencil, detrends and windows the data" - from scipy.signal import detrend + - x = X[stancil[0] : stancil[-1]] - # x_mask= (stancil[0] < X) & (X <= stancil[-1]) - # x = X[x_mask] - idata = DATA[stancil[0] : stancil[-1]] - y = detrend(idata) # * win + x = X[stancil[0]:stancil[-1]] + idata = DATA[stancil[0]:stancil[-1]] + y = detrend(idata) - LS_PSD, LS_object = calc_spectrum_LS(x, y, self.k, LS=self.LS, dk=self.dk) + LS_PSD, LS_object = calc_spectrum_LS( x, y, self.k, LS= self.LS, dk =self.dk) return stancil[1], LS_PSD # % derive L2 stancil - stancil_iter = create_chunk_boundaries(L, DATA.size, ov=self.ov) + stancil_iter = create_chunk_boundaries(L, DATA.size, ov= self.ov) # apply func to all stancils - D_specs = dict(map(calc_spectrum_apply, stancil_iter)) + D_specs = dict(map(calc_spectrum_apply,stancil_iter)) chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectal relazations + self.N_stancils = len(chunk_positions) # number of spectal relazations # repack data, create xarray - self.spec_name = "power_spec" if name is None else name - G = dict() - for xi, I in D_specs.items(): - G[xi] = xr.DataArray( + self.spec_name = 'power_spec' if name is None else name + G = { + xi: xr.DataArray( I, dims=["k"], coords={"k": self.k, "x": xi * self.dx}, name=self.spec_name, ) + for xi, I in D_specs.items() + } - self.G = xr.concat(G.values(), dim="x").T # .to_dataset() + self.G = xr.concat(G.values(), dim='x').T if self.G.k[0] == 0: self.G = self.G[1:, :] - self.G.attrs["ov"] = self.ov - self.G.attrs["L"] = self.L + self.G.attrs['ov'] = self.ov + self.G.attrs['L'] = self.L return self.G def calc_var(self): - return wavenumber_spectrogram.calc_var(self) + return WavenumberSpectrogram.calc_var(self) - def parceval(self, add_attrs=True): - return wavenumber_spectrogram.parceval(self, add_attrs=add_attrs) + def parceval(self, add_attrs=True ): + return WavenumberSpectrogram.parceval(self, add_attrs= add_attrs ) - def mean_spectral_error(self, confidence=0.95): - return wavenumber_spectrogram.mean_spectral_error(self, confidence=confidence) + def mean_spectral_error(self, confidence = 0.95 ): + return WavenumberSpectrogram.mean_spectral_error(self, confidence= confidence ) - -class wavenumber_spectrogram_LS: - def __init__( - self, x, data, L, dx, dy=None, waven_method="fftX2", ov=None, window=None - ): +class WavenumberSpectrogramLS: + def __init__(self, x, data, L, dx, dy = None, waven_method = 'fftX2', ov=None, window=None): """ returns a wavenumber spectrogram with the resolution L-ov this uses Lombscargle @@ -683,43 +624,31 @@ def __init__( xr.Dataset with x, k as cooridates of the spectrogram and the mean error other arributes are in the .attr dict. """ - from astropy.timeseries import LombScargle - - self.L = L - self.ov = ( - int(L / 2) if ov is None else ov - ) # when not defined in create_chunk_boundaries then L/2 + + self.L = L + self.ov = int(L/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.x = x - self.dx = dx - self.data = data + self.x = x + self.dx = dx + self.data = data self.error = dy if dy is not None else None - self.Lpoints = int(self.L / self.dx) + self.Lpoints= int(self.L/self.dx) - # create subsample k - # print(waven_method) + + # create subsample k if type(waven_method) is str: - self.k, self.dk = calc_freq_LS(x, self.Lpoints, method=waven_method) + self.k, self.dk = calc_freq_LS(x, self.Lpoints, method = waven_method ) elif type(waven_method) is np.ndarray: - self.k, self.dk = waven_method, np.diff(waven_method).mean() + self.k, self.dk = waven_method, np.diff(waven_method).mean() else: - raise ValueError("waven_method is neither string nor an array") + raise ValueError('waven_method is neither string nor an array') - # self.k, self.dk = self.k[::kjumps], self.dk*kjumps + # create window - self.win = None # create_window(L) - - def cal_spectrogram( - self, - x=None, - data=None, - error=None, - name=None, - xlims=None, - weight_data=True, - max_nfev=None, - map_func=None, - ): + self.win = None + + def cal_spectrogram(self, x = None, data=None, error=None, name=None, xlims =None, weight_data= True, max_nfev = None, map_func=None): + """ defines apply function and calculated all sub-sample sprectra using map @@ -738,194 +667,143 @@ def cal_spectrogram( self.GG, params_dataframe params_dataframe is a pd.DataFrame that containes all the parameters of the fitting process (and may contain uncertainties too once they are calculated) """ - from astropy.timeseries import LombScargle - import xarray as xr - import copy - import pandas as pd - - X = self.x if x is None else x # all x positions - DATA = self.data if data is None else data # all data points - ERR = self.error if error is None else error # all error for points - L, dk = self.L, self.dk - # win = self.win - self.xlims = (np.round(X.min()), X.max()) if xlims is None else xlims + + - # init Lomb scargle object with noise as nummy data () - # dy_fake= np.random.randn(len(dy))*0.001 if self.dy is not None else None - # self.LS = LombScargle(X[0:L] , np.random.randn(L)*0.001, fit_mean=True) + X = self.x if x is None else x # all x positions + DATA = self.data if data is None else data # all data points + ERR = self.error if error is None else error # all error for points + L, dk = self.L, self.dk + self.xlims = ( np.round(X.min()), X.max() ) if xlims is None else xlims - # define window - import scipy.signal.windows as WINDOWS + # define window self.win = WINDOWS.tukey(self.Lpoints, alpha=0.1, sym=True) + def calc_spectrum_and_field_apply(stancil): + """ windows the data accoding to stencil and applies LS spectrogram returns: stancil center, spectrum for this stencil, number of datapoints in stancil """ - from scipy.signal import detrend + - # x = X[stancil[0]:stancil[-1]] - x_mask = (stancil[0] <= X) & (X <= stancil[-1]) + x_mask= (stancil[0] <= X) & (X <= stancil[-1]) - # print(stancil[1]) x = X[x_mask] - if x.size < 200: # if there are not enough photos set results to nan - # return stancil[1], self.k*np.nan, np.fft.rfftfreq( int(self.Lpoints), d=self.dx)*np.nan, x.size - return stancil[1], self.k * np.nan, self.k * np.nan, np.nan, x.size + if x.size < 200: # if there are not enough photos set results to nan + return stancil[1], self.k*np.nan, self.k*np.nan, np.nan, x.size y = DATA[x_mask] - # make x positions - x_pos = (np.round((x - stancil[0]) / 10.0 - 1, 0)).astype("int") + #make x positions + x_pos = (np.round( (x - stancil[0])/ 10.0 -1 , 0) ).astype('int') # weight data if weight_data: window = self.win[x_pos] - y = y * window * np.sqrt(np.var(y) / np.var((y * window))) + y = y * window * np.sqrt( np.var(y) / np.var(( y* window) ) ) - # make y gridded - x_model = np.arange(stancil[0], stancil[-1], self.dx) - y_gridded = np.copy(x_model) * np.nan + #make y gridded + x_model = np.arange(stancil[0], stancil[-1], self.dx) + y_gridded = np.copy(x_model) * np.nan y_gridded[x_pos] = y - nan_mask = np.isnan(y_gridded) + nan_mask =np.isnan(y_gridded) err = ERR[x_mask] if ERR is not None else None - # print(x.shape, y.shape, self.k, self.LS) - LS_PSD, LS_object = calc_spectrum_LS( - x, y, self.k, err=err, LS=None, dk=self.dk - ) + LS_PSD, LS_object = calc_spectrum_LS( x, y, self.k, err=err, LS= None, dk =self.dk) - y_model = reconstruct_data_from_LS(LS_object, x_model, self.k) + y_model = reconstruct_data_from_LS(LS_object, x_model, self.k) - # print(stancil[-1], x_model[-1]) - # print(stancil[0], x_model[0]) - # print(np.fft.rfft(y_model).size , kk.size) - # print(x_model.size, y_gridded.size, y_model.size) - # print('--') - P = conserve_variance( - np.fft.rfft(y_model), self.k, y_gridded, nan_mask=nan_mask - ) + + + P = conserve_variance(np.fft.rfft(y_model), self.k, y_gridded, nan_mask = nan_mask ) P.set_parameters() - # P.test_ojective_func(P.tanh_weight_function, plot_flag=False) fitter = P.optimize(max_nfev=max_nfev) return stancil[1], LS_PSD, P.best_guess_Z(), fitter.params, x.size - # % derive L2 stancil - self.stancil_iter = create_chunk_boundaries_unit_lengths( - L, self.xlims, ov=self.ov, iter_flag=True - ) - # stancil_iter = create_chunk_boundaries_unit_lengths(L, ( np.round(X.min()), X.max() ), ov= self.ov, iter_flag=True) + # derive L2 stancil + self.stancil_iter = create_chunk_boundaries(L, self.xlims, ov= self.ov, iter_flag=True) - # apply func to all stancils - # Spec_returns=list() - # for ss in stancil_iter: - # print(ss) - # Spec_returns.append( calc_spectrum_apply(ss) ) map_func = map if map_func is None else map_func print(map_func) - Spec_returns = list( - map_func(calc_spectrum_and_field_apply, copy.copy(self.stancil_iter)) - ) - # # linear version - # Spec_returns = list(map( calc_spectrum_and_field_apply, copy.copy(self.stancil_iter) )) + Spec_returns = list(map_func( calc_spectrum_and_field_apply, copy.copy(self.stancil_iter) )) + # unpack resutls of the mapping: - D_specs = dict() - Y_model = dict() - Pars = dict() - N_per_stancil = list() + D_specs = dict() + Y_model = dict() + Pars = dict() + N_per_stancil = list() for I in Spec_returns: - # print(I[1].shape, I[2].shape) - D_specs[I[0]] = I[1] - Y_model[I[0]] = I[2] - Pars[I[0]] = I[3] + D_specs[I[0]] = I[1] + Y_model[I[0]] = I[2] + Pars[I[0]] = I[3] N_per_stancil.append(I[4]) self.N_per_stancil = N_per_stancil chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectral realizatiobs + self.N_stancils = len(chunk_positions) # number of spectral realizatiobs # repack data, create xarray # 1st LS spectal estimates - self.spec_name = "LS_spectal_power" if name is None else name - G_LS_power = dict() - for xi, I in D_specs.items(): - G_LS_power[xi] = xr.DataArray( - I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name - ) + self.spec_name = 'LS_spectal_power' if name is None else name + G_LS_power =dict() + for xi,I in D_specs.items(): + G_LS_power[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi } , name=self.spec_name) + + G_LS_power = xr.concat(G_LS_power.values(), dim='x').T + + - G_LS_power = xr.concat(G_LS_power.values(), dim="x").T # .to_dataset() - - # 2nd Y_model - # G_model =dict() - # # define relative x-coodinate. relative to center - # #eta = np.arange(0, self.L, self.dx) - self.L/2 - # eta = np.arange(0, self.L + self.dx, self.dx) - self.L/2 - # for xi,I in Y_model.items(): - # if I.size < eta.size: - # I = np.insert(I, -1, I[-1]) - # - # G_model[xi] = xr.DataArray(I, dims=['eta'], coords={'eta': eta, 'x': xi } , name="y_model") - # - # self.G_model = xr.concat(G_model.values(), dim='x').T#.to_dataset() - # # if self.G_fft.k[0] == 0: - # # self.G_fft = self.G_fft[1:, :] - # - # self.G_model.attrs['ov'] = self.ov - # self.G_model.attrs['L'] = self.L - # self.G_model.attrs['Lpoints'] = self.Lpoints - # self.G_model.coords['N_per_stancil'] = ( ('x'), N_per_stancil) - - # 2nd FFT(Y_model) - G_fft = dict() - Y_model_k_fft = np.fft.rfftfreq(int(self.Lpoints), d=self.dx) - for xi, I in Y_model.items(): + #2nd FFT(Y_model) + G_fft =dict() + Y_model_k_fft = np.fft.rfftfreq( int(self.Lpoints), d=self.dx) + for xi,I in Y_model.items(): if I.size < Y_model_k_fft.size: I = np.insert(I, -1, I[-1]) - G_fft[xi] = xr.DataArray( - I, dims=["k"], coords={"k": Y_model_k_fft, "x": xi}, name="Y_model_hat" - ) + G_fft[xi] = xr.DataArray(I, dims=['k'], coords={'k': Y_model_k_fft, 'x': xi } , name='Y_model_hat') - G_fft = xr.concat(G_fft.values(), dim="x").T # .to_dataset() + G_fft = xr.concat(G_fft.values(), dim='x').T # generate power spec as well self.G = Z_to_power(G_fft, self.dk, self.Lpoints) - self.G.name = "spectral_power_optm" + self.G.name = 'spectral_power_optm' + # merge both datasets self.GG = xr.merge([G_LS_power, G_fft, self.G]) - self.GG.attrs["ov"] = self.ov - self.GG.attrs["L"] = self.L - self.GG.attrs["Lpoints"] = self.Lpoints - self.GG.coords["N_per_stancil"] = (("x"), N_per_stancil) - - self.GG.expand_dims(dim="eta") - self.GG.coords["eta"] = ( - ("eta"), - np.arange(0, self.L + self.dx, self.dx) - self.L / 2, - ) - self.GG["win"] = (("eta"), np.insert(self.win, -1, self.win[-1])) + self.GG.attrs['ov'] = self.ov + self.GG.attrs['L'] = self.L + self.GG.attrs['Lpoints'] = self.Lpoints + self.GG.coords['N_per_stancil'] = ( ('x'), N_per_stancil) + + self.GG.expand_dims(dim='eta') + self.GG.coords['eta'] = ( ('eta'), np.arange(0, self.L + self.dx, self.dx) - self.L/2 ) + self.GG['win'] = ( ('eta'), np.insert(self.win, -1, self.win[-1])) # create dataframe with fitted parameters - PP2 = dict() + PP2= dict() for k, I in Pars.items(): if I is not np.nan: - PP2[k] = I + PP2[k] =I keys = PP2[next(iter(PP2))].keys() - params_dataframe = pd.DataFrame(index=keys) + params_dataframe = pd.DataFrame(index =keys) - for k, I in PP2.items(): + for k,I in PP2.items(): I.values() params_dataframe[k] = list(I.valuesdict().values()) return self.GG, params_dataframe + + + def calc_var(self): Gmean = np.nanmean(self.G, 1) @@ -933,70 +811,60 @@ def calc_var(self): return self.dk * Gmean[~infmask].sum().data - # def parceval(self, add_attrs=True ): - # return wavenumber_spectrogram.parceval(self, add_attrs= add_attrs ) + - def parceval(self, add_attrs=True, weight_data=False): + def parceval(self, add_attrs=True, weight_data=False ): "test Parceval theorem" - import copy - + DATA = self.data L = self.L X = self.x - # derive mean variances of stancils - # stancil_iter = create_chunk_boundaries_unit_lengths(L, self.xlims, ov= self.ov ) def get_stancil_var_apply(stancil): - from scipy.signal import detrend - + "returns the variance of yy for stancil" - x_mask = (stancil[0] < X) & (X <= stancil[-1]) + x_mask= (stancil[0] < X) & (X <= stancil[-1]) idata = DATA[x_mask] if len(idata) < 1: return stancil[1], np.nan, len(idata) idata = detrend(idata) # weight data - x_pos = (np.round((X[x_mask] - stancil[0]) / 10.0, 0)).astype("int") + x_pos = (np.round( (X[x_mask] - stancil[0])/ 10.0 , 0) ).astype('int') if weight_data: window = self.win[x_pos] - idata = ( - idata * window * np.sqrt(np.var(idata) / np.var((idata * window))) - ) + idata = idata * window * np.sqrt( np.var(idata) / np.var(( idata* window) ) ) return stancil[1], idata.var(), len(idata) - D_vars = list(map(get_stancil_var_apply, copy.copy(self.stancil_iter))) + D_vars = list(map(get_stancil_var_apply, copy.copy(self.stancil_iter) )) - stancil_vars, Nphotons = list(), 0 + stancil_vars, Nphotons =list(), 0 for I in D_vars: - stancil_vars.append(I[1] * I[2]) - Nphotons += I[2] + stancil_vars.append(I[1] * I[2]) + Nphotons += I[2] - stancil_weighted_variance = np.nansum(np.array(stancil_vars)) / Nphotons + stancil_weighted_variance = np.nansum(np.array(stancil_vars))/Nphotons - print("Parcevals Theorem:") - print("variance of timeseries: ", DATA.var()) - print("mean variance of stancils: ", stancil_weighted_variance) - # print('variance of weighted timeseries: ',self.phi.var() ) - # self.calc_var(self) - print("variance of the optimzed windowed LS Spectrum: ", self.calc_var()) + print('Parcevals Theorem:') + print('variance of timeseries: ', DATA.var()) + print('mean variance of stancils: ', stancil_weighted_variance ) + + print('variance of the optimzed windowed LS Spectrum: ', self.calc_var()) if add_attrs: - self.G.attrs["variance_unweighted_data"] = DATA.var() - self.G.attrs["mean_variance_stancils"] = np.nanmean(np.array(stancil_vars)) - self.G.attrs["mean_variance_LS_pwelch_spectrum"] = self.calc_var() + self.G.attrs['variance_unweighted_data'] = DATA.var() + self.G.attrs['mean_variance_stancils'] = np.nanmean(np.array(stancil_vars) ) + self.G.attrs['mean_variance_LS_pwelch_spectrum'] = self.calc_var() + + + def mean_spectral_error(self, mask=None, confidence = 0.95 ): + return WavenumberSpectrogram.mean_spectral_error(self, mask=mask, confidence= confidence ) - def mean_spectral_error(self, mask=None, confidence=0.95): - return wavenumber_spectrogram.mean_spectral_error( - self, mask=mask, confidence=confidence - ) # class for getting standard Pwelch spectrum. old version, deprechiate -class wavenumber_pwelch: - def __init__( - self, data, x, L, ov=None, window=None, save_chunks=False, plot_chunks=False - ): +class WavenumberPwelch: + def __init__(self,data, x, L, ov=None, window=None, save_chunks=False, plot_chunks=False): """ returns a wavenumber spectrum using the pwelch method @@ -1016,170 +884,143 @@ def __init__( self.dx self.n_spec """ - from scipy import signal + + - self.data = data # field to be analyzed - self.dx = np.diff(x)[0] # sampling interval - self.save_chunks = save_chunks - dsize = data.size + self.data = data # field to be analyzed + self.dx = np.diff(x)[0] # sampling interval + self.save_chunks= save_chunks + dsize = data.size - ov = int(np.round(L / 2)) if ov is None else ov + ov=int(np.round(L/2)) if ov is None else ov self.n = L if window is None: - win = np.hanning(self.n) + win=np.hanning(self.n) else: - win = window + win=window - factor = np.sqrt(self.n / (win**2).sum()) - win *= factor + factor=np.sqrt(self.n/(win**2).sum()) + win*=factor # test if n is even - if self.n % 2: + if (self.n%2): self.neven = False else: self.neven = True - # calculate freq - self.k = self.calc_freq() - # del(self.df) + #calculate freq + self.k = self.calc_freq() + nbin=int(np.floor(dsize/(L-ov))) - # print(data.size, L, ov, int(L-ov) ) - nbin = int(np.floor(dsize / (L - ov))) - # print(nbin) if save_chunks: - chunks = np.empty([int(nbin), int(L)]) - - self.specs = np.empty([int(nbin), self.k.size]) - # print(chunks.shape) - # result_array = np.empty((0, 100)) - # if plot_chunks: - # M.figure_axis_xy() - last_k = 0 - k = 0 - # print('iter range', np.arange(0,data.size,int(L-ov))) - for i in np.arange(0, dsize - int(L - ov) + 1, int(L - ov)): - - if (plot_chunks) and (i >= dsize - 6 * int(L - ov)): + chunks=np.empty([int(nbin),int(L)]) + + self.specs=np.empty([int(nbin),self.k.size]) + + last_k=0 + k=0 + + for i in np.arange(0,dsize-int(L-ov)+1,int(L-ov)): + + if (plot_chunks) and (i >= dsize-6*int(L-ov)): M.figure_axis_xy() - self.phi = data[int(i) : int(i + L)] + self.phi=data[int(i):int(i+L)] - # self.ii=np.append(self.ii,[i,i+L]) - # print(self.phi.max()) - # print(self.phi.mean()) - # print(self.phi.shape) - # print('i',int(i), int(i+L)) - # print(chunk.size, l) - if int(i + L) <= data.size - 1: + if int(i+L) <= data.size-1: if save_chunks: - chunks[k, :] = self.phi + chunks[k,:]=self.phi - self.phi = signal.detrend(self.phi) * win + + self.phi=signal.detrend(self.phi)*win if plot_chunks: - # MT.stats_format(self.phi, 'chunk '+str(i)) plt.plot(self.phi) - self.specs[k, :] = self.calc_spectrum() - last_k = k - last_used_TS = int(i + L) - # if plot_chunks: - # MT.stats_format(self.spec, 'spec '+str(i)) + self.specs[k,:]= self.calc_spectrum() + last_k=k + last_used_TS=int(i+L) + else: if plot_chunks: - print("end of TS is reached") - print("last spec No: " + str(last_k)) - print("spec container: " + str(specs.shape)) - print("last used Timestep: " + str(last_used_TS)) - print("length of TS " + str(dsize) + "ms") + print('end of TS is reached') + print('last spec No: '+str(last_k)) + print('spec container: '+str(specs.shape)) + print('last used Timestep: '+str(last_used_TS)) + print('length of TS '+ str(dsize) +'ms') + + k+=1 - k += 1 if save_chunks: - self.chunks = chunks - # del(chunks) - - self.spec_est = self.specs.mean(axis=0) - # if prewhite is None: - # self.specs=specs[:last_k,:] - # self.spec_est=self.specs.mean(axis=0) - # elif prewhite ==1: - # self.specs=specs[:last_k,:]*(2*np.pi*self.f) - # self.spec_est=self.specs.mean(axis=0) - # elif prewhite ==2: - # self.specs=specs[:last_k,:]*(2*np.pi*self.f)**2 - # self.spec_est=self.specs.mean(axis=0) - - self.n_spec, _ = self.specs.shape + self.chunks=chunks + + + self.spec_est=self.specs.mean(axis=0) + + + + self.n_spec,_=self.specs.shape self.calc_var() - # self.phi=self.data - # self.phi*=win*np.sqrt(factor) + def calc_freq(self): - """calculate array of spectral variable (frequency or - wavenumber) in cycles per unit of L""" + """ calculate array of spectral variable (frequency or + wavenumber) in cycles per unit of L """ - self.df = 1.0 / ((self.n - 1) * self.dx) + self.df = 1./((self.n-1)*self.dx) if self.neven: - f = self.df * np.arange(self.n / 2 + 1) + f = self.df*np.arange(self.n/2+1) else: - f = self.df * np.arange((self.n - 1) / 2.0 + 1) + f = self.df*np.arange( (self.n-1)/2. + 1 ) return f def calc_spectrum(self): - """compute the 1d spectrum of a field phi""" + """ compute the 1d spectrum of a field phi """ self.phih = np.fft.rfft(self.phi) # the factor of 2 comes from the symmetry of the Fourier coeffs - spec = 2.0 * (self.phih * self.phih.conj()).real / self.df / self.n**2 + spec = 2.*(self.phih*self.phih.conj()).real / self.df /self.n**2 # the zeroth frequency should be counted only once - spec[0] = spec[0] / 2.0 + spec[0] = spec[0]/2. if self.neven: - spec[-1] = spec[-1] / 2.0 + spec[-1] = spec[-1]/2. return spec + def error(self, ci=0.95): - self.El, self.Eu = spec_error(self.spec_est, self.n_spec, ci=ci) + self.El, self.Eu =spec_error(self.spec_est,self.n_spec,ci=ci) def parceval(self): - print("Parcevals Theorem:") - print("variance of unweighted timeseries: ", self.data.var()) - print( - "mean variance of timeseries chunks: ", - ( - self.chunks.var(axis=1).mean() - if self.save_chunks is True - else "data not saved" - ), - ) - # print('variance of weighted timeseries: ',self.phi.var() ) - # self.calc_var(self) - print("variance of the pwelch Spectrum: ", self.var) + print('Parcevals Theorem:') + print('variance of unweighted timeseries: ',self.data.var()) + print('mean variance of timeseries chunks: ',self.chunks.var(axis=1).mean() if self.save_chunks is True else 'data not saved') + print('variance of the pwelch Spectrum: ',self.var) def calc_var(self): - """Compute total variance from spectrum""" - self.var = ( - self.df * np.nanmean(self.specs[1:], 0).sum() - ) # do not consider zeroth frequency + """ Compute total variance from spectrum """ + self.var = self.df* np.nanmean(self.specs[1:], 0).sum() # do not consider zeroth frequency -# %% optimze spectral variance +# optimze spectral variance class conserve_variance: - def __init__(self, Z, freq, data, nan_mask=None): - """ """ - import lmfit as LM + def __init__(self,Z, freq, data, nan_mask= None): - self.LM = LM + """ + + """ + + self.LM =LM self.data = data - self.Z = Z + self.Z = Z self.freq = freq self.nan_mask = nan_mask @@ -1187,79 +1028,58 @@ def set_parameters(self): params = self.LM.Parameters() - p_smothed = self.runningmean(np.abs(self.Z), 20, tailcopy=True) + p_smothed = self.runningmean(np.abs(self.Z ), 20, tailcopy=True) f_max = self.freq[p_smothed[~np.isnan(p_smothed)].argmax()] - lambda_max = 9.81 * 5**2 / (2 * np.pi) - params.add("x_cutoff", 1 / lambda_max, min=0, max=1, vary=False) - params.add( - "x_max_pos", f_max, min=f_max * 0.75, max=f_max * 5 + 0.001, vary=False - ) - params.add("LF_amp", 1, min=0.5, max=1.2, vary=True) - params.add("HF_amp", 0.5, min=0, max=1.5, vary=True) - params.add("sigma_g", 0.002, min=0.001, max=0.05, vary=False) - params.add("Gauss_amp", 0.5, min=0.01, max=2, vary=True) + + lambda_max = 9.81 * 5 **2/ (2* np.pi) + params.add('x_cutoff', 1/lambda_max , min=0, max=1, vary=False) + params.add('x_max_pos', f_max , min=f_max*0.75, max=f_max*5+0.001, vary=False) + params.add('LF_amp', 1 , min=0.5 , max=1.2, vary= True) + params.add('HF_amp', 0.5 , min=0 , max=1.5, vary= True) + params.add('sigma_g', 0.002 , min=0.001 , max=0.05, vary= False) + params.add('Gauss_amp', 0.5 , min=0.01 , max=2, vary= True) + self.params = params return params def test_ojective_func(self, weight_func, plot_flag=True): - self.objective_func( - self.params, - self.data, - self.Z, - weight_func, - self.freq, - self.nan_mask, - plot_flag=plot_flag, - ) - - def tanh_weight_function(self, ff, params): - return self.tanh_weight( - ff, - params["x_cutoff"].value, - params["x_max_pos"].value, - params["LF_amp"].value, - params["HF_amp"].value, - params["Gauss_amp"].value, - params["sigma_g"].value, - ) - - def tanh_weight(self, x, x_cutoff, x_max_pos, LF_amp, HF_amp, Gauss_amp, sigma_g): + self.objective_func(self.params, self.data, self.Z, weight_func, self.freq, self.nan_mask, plot_flag=plot_flag) + + def tanh_weight_function(self,ff, params): + return self.tanh_weight(ff, params['x_cutoff'].value, + params['x_max_pos'].value, + params['LF_amp'].value, + params['HF_amp'].value, + params['Gauss_amp'].value, + params['sigma_g'].value ) + + def tanh_weight(self,x, x_cutoff , x_max_pos, LF_amp, HF_amp, Gauss_amp, sigma_g): """ - zdgfsg + zdgfsg """ - HF_amp1 = LF_amp - HF_amp - decay = 0.5 - np.tanh((x - x_cutoff) / sigma_g) / 2 - y = decay * HF_amp1 + (1 - HF_amp1) - y = y - y[0] + LF_amp + HF_amp1 = (LF_amp-HF_amp) + decay = 0.5 - np.tanh( (x-x_cutoff)/sigma_g )/2 + y = decay * HF_amp1 + (1 - HF_amp1) + y = y- y[0] +LF_amp - def gaus(x, x_0, amp, sigma_g): - return amp * np.exp(-0.5 * ((x - x_0) / sigma_g) ** 2) + def gaus(x, x_0, amp, sigma_g ): + return amp* np.exp(-0.5 * ( (x-x_0)/sigma_g)**2) - y += gaus(x, x_max_pos, Gauss_amp, sigma_g) + y += gaus(x, x_max_pos, Gauss_amp, sigma_g ) - # y = y * LF_amp return y - def objective_func( - self, - params, - data_x, - Z_results, - weight_func, - freq, - nan_mask=None, - plot_flag=False, - ): - alpha = 1e7 + def objective_func(self, params, data_x, Z_results, weight_func, freq, nan_mask = None, plot_flag=False): + alpha =1e7 def model_real_space(Z, weights, n=None): """ Both inputs must have the same length """ - return np.fft.irfft(Z * weights, n=n) + return np.fft.irfft(Z*weights, n = n) weights = weight_func(freq, params) @@ -1267,10 +1087,10 @@ def model_real_space(Z, weights, n=None): weights = np.insert(weights, -1, weights[-1]) if nan_mask is not None: - model = model_real_space(Z_results, weights, n=data_x.size)[~nan_mask] + model = model_real_space(Z_results, weights, n= data_x.size)[~nan_mask] dd = data_x[~nan_mask][:] else: - model = model_real_space(Z_results, weights, n=data_x.size)[:] + model = model_real_space(Z_results, weights, n= data_x.size)[:] dd = data_x[:] if model.size > dd.size: @@ -1279,159 +1099,99 @@ def model_real_space(Z, weights, n=None): dd = dd[:-1] if plot_flag: - import m_general_ph3 as M + from matplotlib.gridspec import GridSpec import matplotlib.pyplot as plt + F= M.figure_axis_xy(10, 4.1 * 2.5, view_scale= 0.5, container = True) - F = M.figure_axis_xy(10, 4.1 * 2.5, view_scale=0.5, container=True) - - gs = GridSpec(5, 1, wspace=0.1, hspace=0.4) # figure=fig, - pos0, pos1, pos2 = gs[0:3, 0], gs[3, 0], gs[4, 0] # ,gs[3, 0] + gs = GridSpec(5,1, wspace=0.1, hspace=0.4) + pos0,pos1,pos2 = gs[0:3, 0],gs[3, 0],gs[4, 0] ax1 = F.fig.add_subplot(pos0) - plt.title("Stacked Timeseries", loc="left") + plt.title('Stacked Timeseries', loc='left') - chunk_l = 400 - chunk_iter = create_chunk_boundaries( - chunk_l, data_x.size, ov=0, iter_flag=True - ) + chunk_l= 400 + chunk_iter = create_chunk_boundaries(chunk_l, data_x.size, ov=0, iter_flag = True) - ofsett0 = 6 + ofsett0= 6 ofsett = np.copy(ofsett0) for chi in chunk_iter: - v1 = np.round(np.nanvar(dd), 4) - plt.plot( - ofsett + data_x[chi[0] : chi[-1]], - linewidth=3, - alpha=0.5, - c="black", - label=" org. data (var:" + str(v1) + ")", - ) - - v1 = np.round( - model_real_space(Z_results, weights * 0 + 1)[~nan_mask[1:]].var(), 4 - ) - plt.plot( - ofsett - + model_real_space(Z_results, weights * 0 + 1)[chi[0] : chi[-1]], - linewidth=0.8, - c="red", - label="LS model init (var:" + str(v1) + ")", - ) - - v1 = np.round(model.var(), 4) - plt.plot( - ofsett + model_real_space(Z_results, weights)[chi[0] : chi[-1]], - linewidth=0.8, - c="blue", - label="LS model weighted (var:" + str(v1) + ")", - ) + v1= np.round(np.nanvar(dd), 4) + plt.plot(ofsett+ data_x[chi[0]:chi[-1]] , linewidth=3, alpha=0.5 , c='black', label=' org. data (var:'+str(v1)+')') + + v1= np.round(model_real_space(Z_results, weights*0 +1)[~nan_mask[1:]].var(), 4) + plt.plot(ofsett + model_real_space(Z_results, weights*0 +1)[chi[0]:chi[-1]] ,linewidth= 0.8, c='red', label='LS model init (var:'+str(v1)+')') + + v1= np.round(model.var(), 4) + plt.plot(ofsett + model_real_space(Z_results, weights)[chi[0]:chi[-1]],linewidth= 0.8, c='blue', label='LS model weighted (var:'+str(v1)+')') if ofsett == ofsett0: plt.legend() ofsett -= 1 - plt.ylim(ofsett, ofsett0 + 1) - plt.xlim(0, chunk_l * 2) + plt.ylim(ofsett, ofsett0+1) + plt.xlim(0, chunk_l*2) + ax2 = F.fig.add_subplot(pos1) - # ax2 = plt.subplot(3, 1, 2) - plt.title("Amplitude Weight Function", loc="left") - plt.plot(weights, c="black") - ax2.set_xscale("log") + plt.title('Amplitude Weight Function', loc='left') + plt.plot(weights , c='black') + ax2.set_xscale('log') ax3 = F.fig.add_subplot(pos2) - plt.title("Initial and tuned |Z|", loc="left") + plt.title('Initial and tuned |Z|', loc='left') - # ax3 = plt.subplot(3, 1, 3) - # v2_fft= np.fft.rfft(data_x) - # v2 = np.round( (2.*(v2_fft*v2_fft.conj()).real /data_x.size**2 ).sum(), 4) - # plt.plot(abs(v2_fft) , linewidth=2, alpha=0.5 , c='black', label='org data (var: '+str(v2) +')') + v2 = np.round( (4.*(Z_results*Z_results.conj()).real /data_x.size**2 ).sum(), 4) + plt.plot(abs(Z_results), linewidth= 0.8, c='red', label='Z (var: '+str(v2) +')') + plt.plot(M.runningmean(abs(Z_results) , 20, tailcopy=True), linewidth= 1.5, c='red', zorder=12) - v2 = np.round( - (4.0 * (Z_results * Z_results.conj()).real / data_x.size**2).sum(), 4 - ) - plt.plot( - abs(Z_results), linewidth=0.8, c="red", label="Z (var: " + str(v2) + ")" - ) - plt.plot( - M.runningmean(abs(Z_results), 20, tailcopy=True), - linewidth=1.5, - c="red", - zorder=12, - ) - - Z2 = Z_results * weights - v2 = np.round((4.0 * (Z2 * Z2.conj()).real / data_x.size**2).sum(), 4) - plt.plot( - abs(Z2), - linewidth=0.8, - c="blue", - label="weighted Z(var: " + str(v2) + ")", - ) - plt.plot( - M.runningmean(abs(Z2), 20, tailcopy=True), - linewidth=1.5, - c="blue", - zorder=12, - ) + Z2= Z_results* weights + v2 = np.round( (4.*(Z2*Z2.conj()).real /data_x.size**2 ).sum(), 4) + plt.plot(abs(Z2), linewidth= 0.8, c='blue', label='weighted Z(var: '+str(v2) +')') + plt.plot(M.runningmean(abs(Z2) , 20, tailcopy=True), linewidth= 1.5, c='blue', zorder=12) plt.legend() - plt.ylim(np.percentile(abs(Z_results), 0.5), abs(Z_results).max() * 1.3) - plt.xlabel("wavenumber k") - ax3.set_xscale("log") - ax3.set_yscale("log") + plt.ylim( np.percentile(abs(Z_results), 0.5), abs(Z_results).max()*1.3 ) + plt.xlabel('wavenumber k') + ax3.set_xscale('log') + ax3.set_yscale('log') + + fitting_cost =( abs(dd - model) / dd.std() )**2 + variance_cost =( abs(dd.var() - model.var()) / dd.std() ) **2 - fitting_cost = (abs(dd - model) / dd.std()) ** 2 - variance_cost = (abs(dd.var() - model.var()) / dd.std()) ** 2 + return fitting_cost.sum() , alpha* variance_cost - return fitting_cost.sum(), alpha * variance_cost + def optimize(self, fitting_args= None , method='dual_annealing', max_nfev=None): - def optimize(self, fitting_args=None, method="dual_annealing", max_nfev=None): if fitting_args is None: fitting_args = (self.data, self.Z, self.tanh_weight_function, self.freq) self.weight_func = fitting_args[2] - self.fitter = self.LM.minimize( - self.objective_func, - self.params, - args=fitting_args, - kws={"nan_mask": self.nan_mask}, - method=method, - max_nfev=max_nfev, - ) + self.fitter = self.LM.minimize(self.objective_func, self.params, args=fitting_args, kws={'nan_mask':self.nan_mask} , method=method, max_nfev=max_nfev) return self.fitter def plot_result(self): - self.objective_func( - self.fitter.params, - self.data, - self.Z, - self.weight_func, - self.freq, - self.nan_mask, - plot_flag=True, - ) + self.objective_func(self.fitter.params, self.data, self.Z, self.weight_func, self.freq, self.nan_mask, plot_flag=True) def best_guess_Z(self): return self.Z * self.weight_func(self.freq, self.fitter.params) def runningmean(self, var, m, tailcopy=False): - m = int(m) - s = var.shape - if s[0] <= 2 * m: - print("0 Dimension is smaller then averaging length") + m=int(m) + s =var.shape + if s[0] <= 2*m: + print('0 Dimension is smaller then averaging length') return - rr = np.asarray(var) * np.nan - # print(type(rr)) + rr=np.asarray(var)*np.nan + var_range = np.arange(m, int(s[0]) - m - 1, 1) for i in var_range[np.isfinite(var[m : int(s[0]) - m - 1])]: - # rm.append(var[i-m:i+m].mean()) rr[int(i)] = np.nanmean(var[i - m : i + m]) + if tailcopy: - rr[0:m] = rr[m + 1] - rr[-m - 1 : -1] = rr[-m - 2] + rr[0:m]=rr[m+1] + rr[-m-1:-1]=rr[-m-2] return rr From 708e6a9847f388cf40697a14f0bbd12d709fa14d Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 29 Feb 2024 09:47:08 -0500 Subject: [PATCH 08/51] added astropy dependency --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index e340d58d..c10d9f40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -123,6 +123,8 @@ dependencies = [ # Optional "h5py >=3.5.0, < 4.0.0", "termcolor >=2.4.0, < 3.0.0", "typer >=0.9.0, < 1.0.0", + "getmem >=1.0, <= 1.0.0", + "astropy >=5.2, <= 6.0.0" ] # List additional groups of dependencies here (e.g. development From 0e5dc6d4117105379c0bae5421a265af32732c6e Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 29 Feb 2024 10:20:06 -0500 Subject: [PATCH 09/51] removing calls to create_chunk_boundaries --- src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py | 8 ++++---- src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py | 2 +- .../analysis_db/A01b_ALT07_SHNH_variance_tester.py | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py index 28c8bc6e..aed0c10e 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py @@ -42,21 +42,21 @@ def get_lat(sti): mask = (sti[0] < xx) & (xx <= sti[1]) return np.nanmean(Gi["lats"][mask]) - iter_x = spec.create_chunk_boundaries_unit_lengths( + iter_x = spec.create_chunk_boundaries( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=False )[1, :] - stencil_iter = spec.create_chunk_boundaries_unit_lengths( + stencil_iter = spec.create_chunk_boundaries( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=True ) var_list = np.array(list(map(get_var, stencil_iter))) - stencil_iter = spec.create_chunk_boundaries_unit_lengths( + stencil_iter = spec.create_chunk_boundaries( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=True ) N_list = np.array(list(map(get_N, stencil_iter))) - stencil_iter = spec.create_chunk_boundaries_unit_lengths( + stencil_iter = spec.create_chunk_boundaries( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=True ) lat_list = np.array(list(map(get_lat, stencil_iter))) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py b/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py index bcb174da..153eb4a6 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py @@ -384,7 +384,7 @@ def calc_gFT_apply(stancil, prior): return return_dict # derive L2 stancil - self.stancil_iter_list = spec.create_chunk_boundaries_unit_lengths( + self.stancil_iter_list = spec.create_chunk_boundaries( Lmeters, self.xlims, ov=self.ov, iter_flag=False ) self.stancil_iter = iter(self.stancil_iter_list.T.tolist()) diff --git a/src/icesat2_tracks/analysis_db/A01b_ALT07_SHNH_variance_tester.py b/src/icesat2_tracks/analysis_db/A01b_ALT07_SHNH_variance_tester.py index 21abbaa1..d455ee37 100644 --- a/src/icesat2_tracks/analysis_db/A01b_ALT07_SHNH_variance_tester.py +++ b/src/icesat2_tracks/analysis_db/A01b_ALT07_SHNH_variance_tester.py @@ -20,8 +20,8 @@ from random import sample import imp import icesat2_tracks.ICEsat2_SI_tools.convert_GPS_time as cGPS -import icesat2_tracks.ICEsat2_SI_tools.io as io -from icesat2_tracks.ICEsat2_SI_tools.spectral_estimates import create_chunk_boundaries_unit_lengths, create_chunk_boundaries +import icesat2_tracks.ICEsat2_SI_tools.iotools as io +from icesat2_tracks.ICEsat2_SI_tools.spectral_estimates import create_chunk_boundaries import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec import icesat2_tracks.ICEsat2_SI_tools.filter_regrid as regrid @@ -149,8 +149,8 @@ def get_var(sti): def get_breakingpoints(xx, dd ,Lmeter= 3000): nsize = dd.size - stencil_iter = spec.create_chunk_boundaries_unit_lengths( Lmeter, [ xx.min(), xx.max()],ov =Lmeter*3/4, iter_flag= True) - iter_x = spec.create_chunk_boundaries_unit_lengths( Lmeter, [ xx.min(), xx.max()],ov =Lmeter*3/4, iter_flag= False)[1,:] + stencil_iter = spec.create_chunk_boundaries( Lmeter, [ xx.min(), xx.max()],ov =Lmeter*3/4, iter_flag= True) + iter_x = spec.create_chunk_boundaries( Lmeter, [ xx.min(), xx.max()],ov =Lmeter*3/4, iter_flag= False)[1,:] def get_var(sti): mask = (sti[0] < xx) & (xx <= sti[1]) From d3e5d55b1b46437fdf1de0407613c0bdba530243 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 29 Feb 2024 11:10:16 -0500 Subject: [PATCH 10/51] Fixed create_chunk_boundaries implementaiton --- src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 2e9e54bd..1e4bfbba 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -55,10 +55,10 @@ def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): """ boundaries = define_chunk_boundaries_per_type(L,ov,dsize) - - xleft = np.arange(boundaries[0]) - xcenter_pos = np.arange(boundaries[1]) - xright = np.arange(boundaries[3]) + + xleft, xcenter_pos, xright = [ + np.arange(*boundary) for boundary in boundaries + ] max_size = min([xleft.size , xcenter_pos.size, xright.size]) From 4beefa8875a21353aeeb79402fd81ace2565ba78 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 29 Feb 2024 13:14:55 -0500 Subject: [PATCH 11/51] fixed imports and function argument types --- src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py | 14 +++++++------- .../ICEsat2_SI_tools/spectral_estimates.py | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py index 5a7771ee..530b4e32 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py @@ -1,7 +1,7 @@ import numpy as np import scipy.signal as signal -import scipy.ndimage -import scipy.ndimage.filters as signal +from scipy.ndimage import convolve +import scipy.ndimage.filters as filters def lanczos_1d(width, dx, a=2): @@ -59,8 +59,8 @@ def lanczos_filter_1d(x, data, width, a=2, mode="same", method="direct"): dx = np.diff(x).mean() x, L = lanczos_1d(width, dx, a=a) - - data_lp = signal.convolve(data, L, mode=mode, method=method) + _method = method + data_lp = signal.convolve(data, L, mode=mode, method=_method) return data_lp @@ -86,7 +86,7 @@ def lanczos_filter_1d_wrapping(x, data, width, a=2, mode="wrap"): dx = np.diff(x).mean() x, L = lanczos_1d(width, dx, a=a) - data_lp = scipy.ndimage.convolve(data, L, mode=mode) # * + data_lp = convolve(data, L, mode=mode) # * return data_lp @@ -110,7 +110,7 @@ def lanczos_filter_2d(x, data, width, a=2, mode="same"): dx = abs(np.diff(x).mean()) x, L2d = lanczos_2d(width, dx, a=a) - data_lp = signal.convolve(data, L2d, mode=mode) + data_lp = filters.convolve(data, L2d, mode=mode) return data_lp @@ -146,6 +146,6 @@ def lanczos_filter_3d(x, data, width, a=2, mode="same"): dx = abs(np.diff(x).mean()) x, L3d = lanczos_3d(width, dx, a=a) - data_lp = signal.convolve(data, L3d, mode=mode) + data_lp = filters.convolve(data, L3d, mode=mode) return data_lp diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 1e4bfbba..f705c575 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -29,7 +29,7 @@ def define_chunk_boundaries_per_type(L_unit, ov, limits_size): ] # Handling when limits_size is a list - elif isinstance(limits_size, list) and len(limits_size) == 2: + elif isinstance(limits_size, tuple) and len(limits_size) == 2: start, end = limits_size boundaries = [ (start, end - dl,dl), From 8c05ea45e012df4ce49c70d1b74f0960d5df039c Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 29 Feb 2024 15:42:35 -0500 Subject: [PATCH 12/51] refactor create_chunk_boundaries function --- .../ICEsat2_SI_tools/spectral_estimates.py | 48 ++++++++++--------- 1 file changed, 26 insertions(+), 22 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index f705c575..47797b58 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -9,40 +9,42 @@ from scipy import signal import lmfit as LM import icesat2_tracks.local_modules.m_general_ph3 as M - +from functools import singledispatch def is_even(number): return not (number % 2) -def define_chunk_boundaries_per_type(L_unit, ov, limits_size): - - ov = int(np.round(L_unit / 2)) if ov is None else ov - dl = L_unit - ov - boundaries = [] +@singledispatch +def define_chunk_boundaries(L_unit,dl, limits_size): + raise ValueError("limits_size must be either an int or a list of two elements") - # Handling when limits_size is an integer - if isinstance(limits_size, int): - boundaries = [ - (0, limits_size - dl,dl), +@define_chunk_boundaries.register +def _(limits_size:int,L_unit:int,dl:int): + L_unit = 0 + boundaries = [ + (L_unit, limits_size - dl,dl), (dl, limits_size - dl + 1,dl), (dl * 2, limits_size + 1,dl) ] - - # Handling when limits_size is a list - elif isinstance(limits_size, tuple) and len(limits_size) == 2: - start, end = limits_size - boundaries = [ + return boundaries + +@define_chunk_boundaries.register +def _( limits_size:tuple,L_unit:int,dl:int): + return define_chunk_boundaries(list(limits_size),L_unit,dl) + +@define_chunk_boundaries.register +def _(limits_size:list, L_unit:int,dl:int ): + start, end = limits_size + boundaries = [ (start, end - dl,dl), (start + L_unit / 2, end - dl + 1,dl), (start + L_unit, end + 1,dl) - ] - else: - raise ValueError("limits_size must be either an int or a list of two elements") - + ] return boundaries + # basic functions -def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): +def create_chunk_boundaries(L_unit, dsize, ov= None, iter_flag=True): """ returns all need chunk boundaries and center position given L, and ov inputs: @@ -53,8 +55,10 @@ def create_chunk_boundaries(L, dsize, ov= None, iter_flag=True): if iter_flag True returns iter else it returns an ndarray """ - - boundaries = define_chunk_boundaries_per_type(L,ov,dsize) + ov = int(np.round(L_unit / 2)) if ov is None else ov + dl = int( L_unit - ov) + + boundaries = define_chunk_boundaries(dsize,int(L_unit),dl) xleft, xcenter_pos, xright = [ np.arange(*boundary) for boundary in boundaries From e9ddc4e40f99cf5e3edd1589423956e74a78c69c Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Fri, 1 Mar 2024 06:56:30 -0500 Subject: [PATCH 13/51] added review suggestions --- .../ICEsat2_SI_tools/convert_GPS_time.py | 1 - .../ICEsat2_SI_tools/filter_regrid.py | 136 +++++++++--------- 2 files changed, 72 insertions(+), 65 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py b/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py index 7a2b7bc8..0aa326f5 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py @@ -31,7 +31,6 @@ """ import numpy as np from .convert_julian import convert_julian -import pdb # -- PURPOSE: Define GPS leap seconds diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py index 5799f0ca..e70bf994 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py @@ -1,6 +1,42 @@ import numpy as np from numba import jit import pandas as pd +import matplotlib as plt + +def process_single_stencil_set( + stancil_set, T2, key_var, key_x_coord, stancil_width, calc_stencil_stats +): + # Select photons that are in bins + Ti_sel = T2[(stancil_set[0, 0] < T2["x"]) & (T2["x"] < stancil_set[2, -1])] + + # Put each photon in a bin + bin_labels = np.searchsorted(stancil_set[0, :], Ti_sel["x"]) + Ti_sel["x_bins"] = bin_labels + + # Group data by this bin + Ti_g = Ti_sel.groupby("x_bins", dropna=False, as_index=True) + + # Take median of the data + Ti_median = Ti_g.median() + + # Apply weighted mean and count photons + Ti_weight = Ti_g.apply( + calc_stencil_stats, key_var, key_x_coord, stancil_width, stancil_set + ) + + # Merge both datasets + T_merged = pd.concat([Ti_median, Ti_weight], axis=1) + + # Rename columns + T_merged = T_merged.rename( + columns={key_var: key_var + "_median", key_x_coord: key_x_coord + "_median"} + ) + T_merged[key_var + "_median"][np.isnan(T_merged[key_var + "_std"])] = np.nan + + # Set stencil center as new x-coordinate + T_merged["x"] = stancil_set[1, T_merged.index - 1] + + return T_merged def get_hemis(B, beams_list): @@ -61,7 +97,7 @@ def lat_min_max_extended(B, beams_list, accent=None): min_lat, max_lat, accent min and max latitudes of the beams, (True/False) True if the track is accending """ - accent = regrid.track_type(B[beams_list[0]]) if accent is None else accent + accent = track_type(B[beams_list[0]]) if accent is None else accent hemis = get_hemis(B, beams_list) @@ -85,32 +121,36 @@ def lat_min_max_extended(B, beams_list, accent=None): track_lat_end.append(ll["lats"]) track_lon_end.append(ll["lons"]) - if (hemis == "SH") & accent: - return ( - [max(track_lat_start), min(track_lat_end)], - [max(track_lon_start), min(track_lon_end)], - accent, - ) # accenting SH mean start is in the top right - elif (hemis == "SH") & ~accent: - return ( - [max(track_lat_start), min(track_lat_end)], - [min(track_lon_start), max(track_lon_end)], - accent, - ) # decent SH mean start is in the top left - elif (hemis == "NH") & accent: - return ( - [min(track_lat_start), max(track_lat_end)], - [min(track_lon_start), max(track_lon_end)], - accent, - ) # accent NH mean start is in the lower left - elif (hemis == "NH") & ~accent: - return ( - [min(track_lat_start), max(track_lat_end)], - [max(track_lon_start), min(track_lon_end)], - accent, - ) # decent NH mean start is in the lower right - else: - raise ValueError("some defintions went wrong") + # Define a dictionary to map the conditions to the functions + func_map = { + ("SH", True): ( + max, + min, + max, + min, + ), # accenting SH mean start is in the top right + ("SH", False): (max, min, min, max), # decent SH mean start is in the top left + ("NH", True): (min, max, min, max), # accent NH mean start is in the lower left + ("NH", False): ( + min, + max, + max, + min, + ), # decent NH mean start is in the lower right + } + # Get the functions based on the conditions + funcs = func_map.get((hemis, accent)) + # If the key is not found in the dictionary, raise an error + if funcs is None: + raise ValueError("some definitions went wrong") + lat_start_func, lat_end_func, lon_start_func, lon_end_func = funcs + # Use the functions to calculate the start and end of latitude and longitude + # Return these values along with accent + return ( + [lat_start_func(track_lat_start), lat_end_func(track_lat_end)], + [lon_start_func(track_lon_start), lon_end_func(track_lon_end)], + accent, + ) def lat_min_max(B, beams_list, accent=None): @@ -306,42 +346,12 @@ def calc_stencil_stats(group, key, key_x_coord, stancil_width, stancils): return Tweight.T - T_sets = list() - - for stancil_set in [stencil_1, stencil_1half]: - - # select photons that are in bins - Ti_sel = T2[(stancil_set[0, 0] < T2["x"]) & (T2["x"] < stancil_set[2, -1])] - - # put each photon in a bin - bin_labels = np.searchsorted(stancil_set[0, :], Ti_sel["x"]) - - Ti_sel["x_bins"] = bin_labels - # group data by this bin - Ti_g = Ti_sel.groupby(Ti_sel["x_bins"], dropna=False, as_index=True) - # take median of the data - Ti_median = Ti_g.median() - - # apply weighted mean and count photons - args = [key_var, key_x_coord, stancil_width, stancil_set] - - Ti_weight = Ti_g.apply(calc_stencil_stats, *args) - - # merge both datasets - T_merged = pd.concat([Ti_median, Ti_weight], axis=1) - - # rename columns - T_merged = T_merged.rename( - columns={key_var: key_var + "_median", key_x_coord: key_x_coord + "_median"} + T_sets = [ + process_single_stencil_set( + stancil_set, T2, key_var, key_x_coord, stancil_width, calc_stencil_stats ) - T_merged[key_var + "_median"][ - np.isnan(T_merged[key_var + "_std"]) - ] = np.nan # replace median calculation with nans - - # set stancil center an new x-coodinate - T_merged["x"] = stancil_set[1, T_merged.index - 1] - - T_sets.append(T_merged) + for stancil_set in [stencil_1, stencil_1half] + ] # mergeboth stancils T3 = pd.concat(T_sets).sort_values(by="x").reset_index() @@ -443,8 +453,6 @@ def bin_means(T2, dist_grid): N_i = list() for i in np.arange(1, ilim - 1): - if i % 5000 == 0: - print(i) i_mask = (T2["dist"] >= dist_grid[i - 1]) & (T2["dist"] < dist_grid[i + 1]) dF_mean[i] = T2[i_mask].mean() N_i.append(i_mask.sum()) From 082478fbc508cba983da4dd56a5d5bcb1f15427d Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Wed, 28 Feb 2024 18:49:18 -0500 Subject: [PATCH 14/51] fix: update xlabel, ylabel to set_xlabel, set_ylabel From 99c2eb7b9d7e3de377edd9a2c7097754d77d0ff6 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Fri, 1 Mar 2024 13:22:24 -0500 Subject: [PATCH 15/51] cleaning and formatting more files in ICEsat2_SI_tools folder --- .../ICEsat2_SI_tools/beam_stats.py | 11 +- .../ICEsat2_SI_tools/generalized_FT.py | 2 +- .../ICEsat2_SI_tools/spectral_estimates.py | 1123 +++++++++-------- 3 files changed, 615 insertions(+), 521 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py index aed0c10e..4cc0ba97 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py @@ -7,6 +7,7 @@ import matplotlib.gridspec as gridspec import h5py + def derive_beam_statistics(Gd, all_beams, Lmeter=10e3, dx=10): """ this method returns a dict of dataframes with the beam statistics @@ -15,7 +16,6 @@ def derive_beam_statistics(Gd, all_beams, Lmeter=10e3, dx=10): Lemter is the length of the segment in meters for the statistics dx is the nominal resolution of the ATL06 data in meters """ - D = dict() for k in all_beams: @@ -42,21 +42,21 @@ def get_lat(sti): mask = (sti[0] < xx) & (xx <= sti[1]) return np.nanmean(Gi["lats"][mask]) - iter_x = spec.create_chunk_boundaries( + iter_x = spec.create_chunk_boundaries_unit_lengths( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=False )[1, :] - stencil_iter = spec.create_chunk_boundaries( + stencil_iter = spec.create_chunk_boundaries_unit_lengths( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=True ) var_list = np.array(list(map(get_var, stencil_iter))) - stencil_iter = spec.create_chunk_boundaries( + stencil_iter = spec.create_chunk_boundaries_unit_lengths( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=True ) N_list = np.array(list(map(get_N, stencil_iter))) - stencil_iter = spec.create_chunk_boundaries( + stencil_iter = spec.create_chunk_boundaries_unit_lengths( Lmeter, [xx.min(), xx.max()], ov=0, iter_flag=True ) lat_list = np.array(list(map(get_lat, stencil_iter))) @@ -86,7 +86,6 @@ def plot_beam_statistics(D, high_beams, low_beams, col_dict, track_name=None): if track_name is not None: plt.suptitle(track_name, fontsize=10) - gs = gridspec.GridSpec(2, 3) # make 2 x 2 plot diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py b/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py index 153eb4a6..bcb174da 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py @@ -384,7 +384,7 @@ def calc_gFT_apply(stancil, prior): return return_dict # derive L2 stancil - self.stancil_iter_list = spec.create_chunk_boundaries( + self.stancil_iter_list = spec.create_chunk_boundaries_unit_lengths( Lmeters, self.xlims, ov=self.ov, iter_flag=False ) self.stancil_iter = iter(self.stancil_iter_list.T.tolist()) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 47797b58..9759b3c5 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -9,44 +9,18 @@ from scipy import signal import lmfit as LM import icesat2_tracks.local_modules.m_general_ph3 as M -from functools import singledispatch - -def is_even(number): - return not (number % 2) - -@singledispatch -def define_chunk_boundaries(L_unit,dl, limits_size): - raise ValueError("limits_size must be either an int or a list of two elements") - -@define_chunk_boundaries.register -def _(limits_size:int,L_unit:int,dl:int): - L_unit = 0 - boundaries = [ - (L_unit, limits_size - dl,dl), - (dl, limits_size - dl + 1,dl), - (dl * 2, limits_size + 1,dl) - ] - return boundaries - -@define_chunk_boundaries.register -def _( limits_size:tuple,L_unit:int,dl:int): - return define_chunk_boundaries(list(limits_size),L_unit,dl) - -@define_chunk_boundaries.register -def _(limits_size:list, L_unit:int,dl:int ): - start, end = limits_size - boundaries = [ - (start, end - dl,dl), - (start + L_unit / 2, end - dl + 1,dl), - (start + L_unit, end + 1,dl) - ] - return boundaries +from matplotlib.gridspec import GridSpec +import matplotlib.pyplot as plt + + +def is_not_even(number): + return True if (number % 2) else False # basic functions -def create_chunk_boundaries(L_unit, dsize, ov= None, iter_flag=True): +def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): """ - returns all need chunk boundaries and center position given L, and ov + returns all need chunk boudaries and center position given L, and ov inputs: L desired length of window, dsize size of the data @@ -55,70 +29,101 @@ def create_chunk_boundaries(L_unit, dsize, ov= None, iter_flag=True): if iter_flag True returns iter else it returns an ndarray """ - ov = int(np.round(L_unit / 2)) if ov is None else ov - dl = int( L_unit - ov) - - boundaries = define_chunk_boundaries(dsize,int(L_unit),dl) + ov = int(np.round(L / 2)) if ov is None else ov + + xleft = np.arange(0, dsize - int(L - ov), int(L - ov)) + xright = np.arange(int(L - ov) * 2, dsize + 1, int(L - ov)) + xcenter_pos = np.arange(int(L - ov), dsize - int(L - ov) + 1, int(L - ov)) + max_size = min([xleft.size, xcenter_pos.size, xright.size]) + position_stancil = np.vstack( + [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] + ) + + if iter_flag is True: + return iter(position_stancil.T.tolist()) + else: + return position_stancil - xleft, xcenter_pos, xright = [ - np.arange(*boundary) for boundary in boundaries - ] - - max_size = min([xleft.size , xcenter_pos.size, xright.size]) - position_stancil = np.vstack([xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]]) +def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag=True): + """ + returns all need chunk boudaries and center position given L, and ov + inputs: + L desired length of window in units of the x axis of the data, + data_limits (x_min, x_max) tuple with the beginning and end the the derived window stancils - return iter(position_stancil.T.tolist()) if iter_flag else position_stancil + if ov is None, = L/2 + if iter_flag True returns iter else it returns an ndarray + + """ + L = L_unit + ov = np.round(L / 2) if ov is None else ov + dl = L - ov + xleft = np.arange(data_limits[0], data_limits[1] - dl, dl) + xcenter_pos = np.arange(data_limits[0] + L / 2, data_limits[1] - dl + 1, dl) + xright = np.arange(data_limits[0] + L, data_limits[1] + 1, dl) + + max_size = min([xleft.size, xcenter_pos.size, xright.size]) + + position_stancil = np.vstack( + [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] + ) + + if iter_flag is True: + return iter(position_stancil.T.tolist()) + else: + return position_stancil def Z_to_power(Z, df, N): - """ compute the 1d spectrum of a field phi + """compute the 1d spectrum of a field phi inputs: Z complex fourier coefficients df frequency / or wavenumber step N length of data vector in real space (= L) """ - spec = 2.*(Z*Z.conj()).real / df /N**2 - neven = is_even(N) - # the zeroth frequency should be counted only once - spec[0] = spec[0]/2. + spec = 2.0 * (Z * Z.conj()).real / df / N**2 + neven = is_not_even(N) + spec[0] = spec[0] / 2.0 if neven: - spec[-1] = spec[-1]/2. + spec[-1] = spec[-1] / 2.0 return spec + # 2nd cal spectra def calc_spectrum_fft(phi, df, N): - """ compute the 1d spectrum of a field phi + """compute the 1d spectrum of a field phi inputs: df frequency / or wavenumber step N length of data vector in real space (= L) neven bool, if True """ - neven = is_even(N) + neven = is_not_even(N) phih = np.fft.rfft(phi) # the factor of 2 comes from the symmetry of the Fourier coeffs - spec = 2.*(phih*phih.conj()).real / df /N**2 + spec = 2.0 * (phih * phih.conj()).real / df / N**2 # the zeroth frequency should be counted only once - spec[0] = spec[0]/2. + spec[0] = spec[0] / 2.0 if neven: - spec[-1] = spec[-1]/2. + spec[-1] = spec[-1] / 2.0 return spec -def LS_power_to_PSD( ls_power, L , dff): +def LS_power_to_PSD(ls_power, L, dff): """ returns Power spectral density (unit^2/dfreq) ls_power output of astropy.timeseries.LombScargle.power with normalization='psd' """ - return 2 * ls_power / L /dff + return 2 * ls_power / L / dff -def calc_spectrum_LS( x, y, k, err=None, LS= None, dk =None): + +def calc_spectrum_LS(x, y, k, err=None, LS=None, dk=None): """ returns: Power spectral density of y given postitions x, for wanumbers k @@ -127,16 +132,17 @@ def calc_spectrum_LS( x, y, k, err=None, LS= None, dk =None): LS LombScargle object """ if LS is None: - LS = LombScargle(x , y, dy = err, fit_mean=False, center_data=True) + LS = LombScargle(x, y, dy=err, fit_mean=False, center_data=True) else: LS.t = x LS.y = y - LS.dy= err + LS.dy = err + + ls_power = LS.power(k, normalization="psd", assume_regular_frequency="False") - ls_power = LS.power(k, normalization='psd', assume_regular_frequency='False') + dk = np.diff(k).mean() if dk is None else dk + return 2 * ls_power / y.size / dk, LS - dk = np.diff(k).mean() if dk is None else dk - return 2 * ls_power / y.size / dk , LS def reconstruct_data_from_LS(LS, x_real_axis, freq): """ @@ -145,36 +151,39 @@ def reconstruct_data_from_LS(LS, x_real_axis, freq): x_real_axis is the x coordinate of the original data (np.array) freq is the frequency grid on which the field is reconstructed """ - # t_base =np.array(Gi['dist']) + y_reconstruct = LS.offset() * np.ones(len(x_real_axis)) freq_seq = freq[1:] if freq[0] == 0 else freq - freq_mask= freq <= 1/100 + freq_mask = freq <= 1 / 100 for fi in freq_seq: try: theta = LS.model_parameters(fi) except: - theta = [0,0] - y_reconstruct += theta[0] * np.sin(x_real_axis * 2 * np.pi *fi ) + theta[1]* np.cos(x_real_axis * 2 * np.pi *fi) - + theta = [0, 0] + y_reconstruct += theta[0] * np.sin(x_real_axis * 2 * np.pi * fi) + theta[ + 1 + ] * np.cos(x_real_axis * 2 * np.pi * fi) return y_reconstruct + def calc_freq_fft(x_grid, N): - """ calculate array of spectral variable (frequency or - wavenumber) in cycles per unit of L """ + """calculate array of spectral variable (frequency or + wavenumber) in cycles per unit of L""" - neven = is_even(N) - - dx = np.round(np.median(np.diff(x_grid) ), 1) - df = 1./((N-1)*dx) + neven = is_not_even(N) + + dx = np.round(np.median(np.diff(x_grid)), 1) + df = 1.0 / ((N - 1) * dx) if neven: - f = df*np.arange(N/2+1) + f = df * np.arange(N / 2 + 1) else: - f = df*np.arange( (N-1)/2. + 1 ) - return f,df + f = df * np.arange((N - 1) / 2.0 + 1) + return f, df + def calc_freq_fft_given_dx(dx, N): """ @@ -184,17 +193,25 @@ def calc_freq_fft_given_dx(dx, N): N number of datapoints used in window """ - neven = is_even(N) - df = 1./((N-1)*dx) + neven = is_not_even(N) + df = 1.0 / ((N - 1) * dx) if neven: - f = df*np.arange(N/2+1) + f = df * np.arange(N / 2 + 1) else: - f = df*np.arange( (N-1)/2. + 1 ) - return f,df - - -def calc_freq_LS(x, N, method='fftX2', dx=None, minimum_frequency=None, maximum_frequency=None, samples_per_peak=0.01): + f = df * np.arange((N - 1) / 2.0 + 1) + return f, df + + +def calc_freq_LS( + x, + N, + method="fftX2", + dx=None, + minimum_frequency=None, + maximum_frequency=None, + samples_per_peak=0.01, +): """ calculate array of spectral variable (frequency or wavenumber) in cycles per unit of N (window length in number of data points) @@ -206,40 +223,47 @@ def calc_freq_LS(x, N, method='fftX2', dx=None, minimum_frequency=None, maximum_ minimum_frequency, maximum_frequency only used for LS_auto """ - if method is 'fftX2': - neven = is_even(N) + if method is "fftX2": + neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx - df = 1./((N-1)*dx) /2 + df = 1.0 / ((N - 1) * dx) / 2 if neven: - f = df*np.arange(df, N+1) + f = df * np.arange(df, N + 1) else: - f = df* np.arange(df, (N-1) + 1 ) + f = df * np.arange(df, (N - 1) + 1) - elif method is 'fft': - neven = is_even(N) + elif method is "fft": + neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx - df = 1./((N-1)*dx) + df = 1.0 / ((N - 1) * dx) if neven: - f = df*np.arange(N/2+1) + f = df * np.arange(N / 2 + 1) else: - f = df*np.arange( (N-1)/2. + 1 ) + f = df * np.arange((N - 1) / 2.0 + 1) + + elif method is "LS_auto": - elif method is 'LS_auto': - - f = LombScargle(x , np.random.randn(len(x)), fit_mean=True).autofrequency(minimum_frequency=minimum_frequency, maximum_frequency=maximum_frequency, samples_per_peak=samples_per_peak)##0.1) + f = LombScargle(x, np.random.randn(len(x)), fit_mean=True).autofrequency( + minimum_frequency=minimum_frequency, + maximum_frequency=maximum_frequency, + samples_per_peak=samples_per_peak, + ) df = np.diff(f).mean() df = np.round(df, 5) - elif method is 'fixed_ratio': + elif method is "fixed_ratio": - neven = is_even(N) + neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx df = dx / 50 - f = df * np.arange(df, N + 1) if neven else df * np.arange(df, N) - + if neven: + f = df * np.arange(df, N + 1) + else: + f = df * np.arange(df, N) + + return f, df - return f ,df def create_window(L, window=None): """ @@ -247,63 +271,61 @@ def create_window(L, window=None): if window is not None it show have a length of N """ if window is None: - win=np.hanning(L) + win = np.hanning(L) else: - win=window + win = window - factor=np.sqrt(L/(win**2).sum()) - win*=factor + factor = np.sqrt(L / (win**2).sum()) + win *= factor return win + def create_weighted_window(data, window=None): """ define window function and weight it to conserve variance if window is not None it show have a length of N """ - + L = data.size if window is None: - win = WINDOWS.tukey(L, alpha=0.1, sym=True) + win = WINDOWS.tukey(L, alpha=0.1, sym=True) else: - win=window + win = window - factor = np.sqrt( np.var(data) / np.var(( data* win) ) ) - win *= factor + factor = np.sqrt(np.var(data) / np.var((data * win))) + win *= factor return win -def spec_error(E,sn,ci=.95): - """ Computes confidence interval for one-dimensional spectral - estimate E (the power spectra). +def spec_error(E, sn, ci=0.95): + """Computes confidence interval for one-dimensional spectral + estimate E (the power spectra). - Parameters - =========== - - sn is the number of spectral realizations; - it can be either an scalar or an array of size(E) - - ci = .95 for 95 % confidence interval + Parameters + =========== + - sn is the number of spectral realizations; + it can be either an scalar or an array of size(E) + - ci = .95 for 95 % confidence interval - Output - ========== - lower (El) and upper (Eu) bounds on E """ + Output + ========== + lower (El) and upper (Eu) bounds on E""" + def yNlu(sn, yN, ci): + """compute yN[l] yN[u], that is, the lower and + upper limit of yN""" - - def yNlu(sn,yN,ci): - """ compute yN[l] yN[u], that is, the lower and - upper limit of yN """ - - # cdf of chi^2 dist. with 2*sn DOF - cdf = gammainc(sn,sn*yN) + cdf = gammainc(sn, sn * yN) # indices that delimit the wedge of the conf. interval fl = np.abs(cdf - ci).argmin() - fu = np.abs(cdf - 1. + ci).argmin() + fu = np.abs(cdf - 1.0 + ci).argmin() - return yN[fl],yN[fu] + return yN[fl], yN[fu] - dbin = .005 - yN = np.arange(0,2.+dbin,dbin) + dbin = 0.005 + yN = np.arange(0, 2.0 + dbin, dbin) El, Eu = np.empty_like(E), np.empty_like(E) @@ -317,19 +339,19 @@ def yNlu(sn,yN,ci): assert n == E.size, " *** sn has different size than E " for i in range(n): - yNl,yNu = yNlu(sn[i],yN=yN,ci=ci) - El[i] = E[i]/yNl - Eu[i] = E[i]/yNu + yNl, yNu = yNlu(sn[i], yN=yN, ci=ci) + El[i] = E[i] / yNl + Eu[i] = E[i] / yNu else: - yNl,yNu = yNlu(sn,yN=yN,ci=ci) - El = E/yNl - Eu = E/yNu + yNl, yNu = yNlu(sn, yN=yN, ci=ci) + El = E / yNl + Eu = E / yNu return El, Eu -def linear_gap_fill(F, key_lead, key_int): +def linear_gap_fill(F, key_lead, key_int): """ F pd.DataFrame key_lead key in F that determined the independent coordindate @@ -337,13 +359,13 @@ def linear_gap_fill(F, key_lead, key_int): """ y_g = np.array(F[key_int]) - nans, x2= np.isnan(y_g), lambda z: z.nonzero()[0] - y_g[nans]= np.interp(x2(nans), x2(~nans), y_g[~nans]) + nans, x2 = np.isnan(y_g), lambda z: z.nonzero()[0] + y_g[nans] = np.interp(x2(nans), x2(~nans), y_g[~nans]) return y_g -def sub_sample_coords(X, lons, lats, stancils, map_func =None): +def sub_sample_coords(X, lons, lats, stancils, map_func=None): """ X non-nan array of coodinate along beam lons, lats arrays of postion data that should be mapped. must have same size as X @@ -354,19 +376,18 @@ def sub_sample_coords(X, lons, lats, stancils, map_func =None): nparray(3, N) 1st column is the stancil center, 2nd and 3rd collumn are the mapped lons and lats """ - def get_lon_lat_coords(stancil): - x_mask= (stancil[0] <= X) & (X <= stancil[-1]) - if sum(x_mask) ==0: # if there are not enough photos set results to nan + x_mask = (stancil[0] <= X) & (X <= stancil[-1]) + if sum(x_mask) == 0: return np.array([stancil[1], np.nan, np.nan]) lon_bin, lat_bin = lons[x_mask].mean(), lats[x_mask].mean() - return np.array([stancil[1],lon_bin, lat_bin]) + return np.array([stancil[1], lon_bin, lat_bin]) map_func = map if map_func is None else map_func - coord_positions = list(map_func( get_lon_lat_coords, copy.copy(stancils) )) + coord_positions = list(map_func(get_lon_lat_coords, copy.copy(stancils))) coord_positions = np.vstack(coord_positions) return coord_positions @@ -390,119 +411,124 @@ def __init__(self, x_grid, data, Lpoints, ov=None, window=None): other arributes are in the .attr dict. """ - self.Lpoints = Lpoints - self.ov = int(Lpoints/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 + self.Lpoints = Lpoints + self.ov = int(Lpoints / 2) if ov is None else ov - self.data = data + self.data = data # create subsample k - self.k, self.dk = calc_freq_fft(x_grid, Lpoints) # return 1/ unit of frid points + self.k, self.dk = calc_freq_fft(x_grid, Lpoints) # to get the waveumber units (2 pi/ lambda), multiply by 2 pi - self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi + self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi # create window - self.win = create_window(Lpoints) + self.win = create_window(Lpoints) def cal_spectrogram(self, data=None, name=None): - """ defines apply function and calculated all sub-sample sprectra using map """ - DATA = self.data if data is None else data Lpoints, dk = self.Lpoints, self.dk - win =self.win + win = self.win def calc_spectrum_apply(stancil): "returns spectrum per stencil, detrends and windows the data" - - - idata = DATA[stancil[0]:stancil[-1]] + idata = DATA[stancil[0] : stancil[-1]] idata = detrend(idata) * win - return stancil[1], calc_spectrum_fft(idata , dk, Lpoints) + return stancil[1], calc_spectrum_fft(idata, dk, Lpoints) - # derive L2 stancil - stancil_iter = create_chunk_boundaries(Lpoints, DATA.size, ov= self.ov) + # derive L2 stancil + stancil_iter = create_chunk_boundaries(Lpoints, DATA.size, ov=self.ov) # apply func to all stancils - D_specs = dict(map(calc_spectrum_apply,stancil_iter)) + D_specs = dict(map(calc_spectrum_apply, stancil_iter)) chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectal relazations + + # number of spectal relazations + self.N_stancils = len(chunk_positions) # repack data, create xarray - self.spec_name = 'power_spec' if name is None else name - G =dict() - for xi,I in D_specs.items(): - G[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi } , name=self.spec_name) + self.spec_name = "power_spec" if name is None else name + G = dict() + for xi, I in D_specs.items(): + G[xi] = xr.DataArray( + I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name + ) - self.G = xr.concat(G.values(), dim='x').T + self.G = xr.concat(G.values(), dim="x").T if self.G.k[0] == 0: self.G = self.G[1:, :] - self.G.attrs['ov'] = self.ov - self.G.attrs['L'] = self.Lpoints + self.G.attrs["ov"] = self.ov + self.G.attrs["L"] = self.Lpoints return self.G - + # cal variance def calc_var(self): - """ Compute total variance from spectragram """ - return self.dk*self.G.mean('x').sum().data # do not consider zeroth frequency + """Compute total variance from spectragram""" + # do not consider zeroth frequency + return self.dk * self.G.mean("x").sum().data - def mean_spectral_error(self, mask=None, confidence = 0.95): + def mean_spectral_error(self, mask=None, confidence=0.95): "retrurns spetral error for the x-mean spectral estimate and stores it as coordindate in the dataarray" # make error estimate if mask is not None: - meanspec= self.G.isel(x=mask).mean('x') + meanspec = self.G.isel(x=mask).mean("x") N = int(sum(mask)) else: - meanspec= self.G.mean('x') + meanspec = self.G.mean("x") N = self.N_stancils - El_of_mean, Eu_of_mean = spec_error(meanspec, N , confidence ) - El_of_mean.name = 'El_mean' - Eu_of_mean.name = 'Eu_mean' + El_of_mean, Eu_of_mean = spec_error(meanspec, N, confidence) + El_of_mean.name = "El_mean" + Eu_of_mean.name = "Eu_mean" - self.G.coords['mean_El'] = (('k'), El_of_mean.data) - self.G.coords['mean_Eu'] = (('k'), Eu_of_mean.data) + self.G.coords["mean_El"] = (("k"), El_of_mean.data) + self.G.coords["mean_Eu"] = (("k"), Eu_of_mean.data) - def parceval(self, add_attrs=True ): + def parceval(self, add_attrs=True): "test Parceval theorem" DATA = self.data L = self.Lpoints - # derive mean variances of stancils stancil_iter = create_chunk_boundaries(L, DATA.size) def get_stancil_var_apply(stancil): - + "returns the variance of yy for stancil" - idata = DATA[stancil[0]:stancil[-1]] + idata = DATA[stancil[0] : stancil[-1]] idata = detrend(idata) return stancil[1], idata.var() - D_vars = dict(map(get_stancil_var_apply,stancil_iter)) + D_vars = dict(map(get_stancil_var_apply, stancil_iter)) - stancil_vars =list() + stancil_vars = list() for I in D_vars.values(): stancil_vars.append(I) - print('Parcevals Theorem:') - print('variance of unweighted timeseries: ',DATA.var()) - print('mean variance of detrended chunks: ', np.array(stancil_vars).mean()) - print('variance of the pwelch Spectrum: ', self.calc_var()) + print("Parcevals Theorem:") + print("variance of unweighted timeseries: ", DATA.var()) + print("mean variance of detrended chunks: ", np.array(stancil_vars).mean()) + print("variance of the pwelch Spectrum: ", self.calc_var()) if add_attrs: - self.G.attrs['variance_unweighted_data'] = DATA.var() - self.G.attrs['mean_variance_detrended_chunks'] = np.array(stancil_vars).mean() - self.G.attrs['mean_variance_pwelch_spectrum'] = self.calc_var() + self.G.attrs["variance_unweighted_data"] = DATA.var() + self.G.attrs["mean_variance_detrended_chunks"] = np.array( + stancil_vars + ).mean() + self.G.attrs["mean_variance_pwelch_spectrum"] = self.calc_var() + class WavenumberSpectrogramLSEven: - def __init__(self, x, data, L, waven_method = 'fftX2' , dy=None , ov=None, window=None, kjumps=1): + def __init__( + self, x, data, L, waven_method="fftX2", dy=None, ov=None, window=None, kjumps=1 + ): """ returns a wavenumber spectrogram with the resolution L-ov this uses Lombscargle @@ -520,96 +546,96 @@ def __init__(self, x, data, L, waven_method = 'fftX2' , dy=None , ov=None, wind xr.Dataset with x, k as cooridates of the spectrogram and the mean error other arributes are in the .attr dict. """ - - self.L = L - self.ov = int(L/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.x = x - self.data = data - self.dy = dy + self.L = L + self.ov = ( + int(L / 2) if ov is None else ov + ) # when not defined in create_chunk_boundaries then L/2 + self.x = x + self.data = data + self.dy = dy # create subsample k if type(waven_method) is str: - self.k, self.dk = calc_freq_LS(x, L, method = waven_method ) + self.k, self.dk = calc_freq_LS(x, L, method=waven_method) elif type(waven_method) is np.ndarray: - self.k, self.dk = waven_method, np.diff(waven_method).mean() + self.k, self.dk = waven_method, np.diff(waven_method).mean() else: - raise ValueError('waven_method is neither string nor an array') + raise ValueError("waven_method is neither string nor an array") - self.k, self.dk = self.k[::kjumps], self.dk*kjumps - # create window - self.win = None - - def cal_spectrogram(self, x = None, data=None, name=None, dx=1): + self.k, self.dk = self.k[::kjumps], self.dk * kjumps + self.win = None + def cal_spectrogram(self, x=None, data=None, name=None, dx=1): """ defines apply function and calculated all sub-sample sprectra using map dx nominal resolution of the data resolutionif not set, dx= 1 """ - - X = self.x if x is None else x # all x positions - DATA = self.data if data is None else data # all data points - L, dk = self.L, self.dk - win = self.win + X = self.x if x is None else x # all x positions + DATA = self.data if data is None else data # all data points + L, dk = self.L, self.dk + win = self.win self.dx = dx - # init Lomb scargle object with noise as nummy data () - self.LS = LombScargle(X[0:L] , np.random.randn(L)*0.001, fit_mean=True) + self.LS = LombScargle(X[0:L], np.random.randn(L) * 0.001, fit_mean=True) def calc_spectrum_apply(stancil): "returns spectrum per stencil, detrends and windows the data" - - x = X[stancil[0]:stancil[-1]] - idata = DATA[stancil[0]:stancil[-1]] + x = X[stancil[0] : stancil[-1]] + idata = DATA[stancil[0] : stancil[-1]] y = detrend(idata) - LS_PSD, LS_object = calc_spectrum_LS( x, y, self.k, LS= self.LS, dk =self.dk) + LS_PSD, LS_object = calc_spectrum_LS(x, y, self.k, LS=self.LS, dk=self.dk) return stancil[1], LS_PSD # % derive L2 stancil - stancil_iter = create_chunk_boundaries(L, DATA.size, ov= self.ov) + stancil_iter = create_chunk_boundaries(L, DATA.size, ov=self.ov) # apply func to all stancils - D_specs = dict(map(calc_spectrum_apply,stancil_iter)) + D_specs = dict(map(calc_spectrum_apply, stancil_iter)) chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectal relazations + + # number of spectal relazations + self.N_stancils = len(chunk_positions) # repack data, create xarray - self.spec_name = 'power_spec' if name is None else name - G = { - xi: xr.DataArray( + self.spec_name = "power_spec" if name is None else name + G = dict() + for xi, I in D_specs.items(): + G[xi] = xr.DataArray( I, dims=["k"], coords={"k": self.k, "x": xi * self.dx}, name=self.spec_name, ) - for xi, I in D_specs.items() - } - self.G = xr.concat(G.values(), dim='x').T + self.G = xr.concat(G.values(), dim="x").T if self.G.k[0] == 0: self.G = self.G[1:, :] - self.G.attrs['ov'] = self.ov - self.G.attrs['L'] = self.L + self.G.attrs["ov"] = self.ov + self.G.attrs["L"] = self.L return self.G def calc_var(self): return WavenumberSpectrogram.calc_var(self) - def parceval(self, add_attrs=True ): - return WavenumberSpectrogram.parceval(self, add_attrs= add_attrs ) + def parceval(self, add_attrs=True): + return WavenumberSpectrogram.parceval(self, add_attrs=add_attrs) + + def mean_spectral_error(self, confidence=0.95): + return WavenumberSpectrogram.mean_spectral_error(self, confidence=confidence) - def mean_spectral_error(self, confidence = 0.95 ): - return WavenumberSpectrogram.mean_spectral_error(self, confidence= confidence ) class WavenumberSpectrogramLS: - def __init__(self, x, data, L, dx, dy = None, waven_method = 'fftX2', ov=None, window=None): + def __init__( + self, x, data, L, dx, dy=None, waven_method="fftX2", ov=None, window=None + ): """ returns a wavenumber spectrogram with the resolution L-ov this uses Lombscargle @@ -628,31 +654,38 @@ def __init__(self, x, data, L, dx, dy = None, waven_method = 'fftX2', ov=None, w xr.Dataset with x, k as cooridates of the spectrogram and the mean error other arributes are in the .attr dict. """ - - self.L = L - self.ov = int(L/2) if ov is None else ov #when not defined in create_chunk_boundaries then L/2 - self.x = x - self.dx = dx - self.data = data - self.error = dy if dy is not None else None - self.Lpoints= int(self.L/self.dx) + self.L = L + self.ov = ( + int(L / 2) if ov is None else ov + ) # when not defined in create_chunk_boundaries then L/2 + self.x = x + self.dx = dx + self.data = data + self.error = dy if dy is not None else None + self.Lpoints = int(self.L / self.dx) - # create subsample k + # create subsample k if type(waven_method) is str: - self.k, self.dk = calc_freq_LS(x, self.Lpoints, method = waven_method ) + self.k, self.dk = calc_freq_LS(x, self.Lpoints, method=waven_method) elif type(waven_method) is np.ndarray: - self.k, self.dk = waven_method, np.diff(waven_method).mean() + self.k, self.dk = waven_method, np.diff(waven_method).mean() else: - raise ValueError('waven_method is neither string nor an array') - - - # create window - self.win = None - - def cal_spectrogram(self, x = None, data=None, error=None, name=None, xlims =None, weight_data= True, max_nfev = None, map_func=None): - + raise ValueError("waven_method is neither string nor an array") + self.win = None + + def cal_spectrogram( + self, + x=None, + data=None, + error=None, + name=None, + xlims=None, + weight_data=True, + max_nfev=None, + map_func=None, + ): """ defines apply function and calculated all sub-sample sprectra using map @@ -671,143 +704,144 @@ def cal_spectrogram(self, x = None, data=None, error=None, name=None, xlims =Non self.GG, params_dataframe params_dataframe is a pd.DataFrame that containes all the parameters of the fitting process (and may contain uncertainties too once they are calculated) """ - - - X = self.x if x is None else x # all x positions - DATA = self.data if data is None else data # all data points - ERR = self.error if error is None else error # all error for points - L, dk = self.L, self.dk - self.xlims = ( np.round(X.min()), X.max() ) if xlims is None else xlims + X = self.x if x is None else x # all x positions + DATA = self.data if data is None else data # all data points + ERR = self.error if error is None else error # all error for points + L, dk = self.L, self.dk + self.xlims = (np.round(X.min()), X.max()) if xlims is None else xlims # define window self.win = WINDOWS.tukey(self.Lpoints, alpha=0.1, sym=True) - def calc_spectrum_and_field_apply(stancil): - """ windows the data accoding to stencil and applies LS spectrogram returns: stancil center, spectrum for this stencil, number of datapoints in stancil """ - - x_mask= (stancil[0] <= X) & (X <= stancil[-1]) + x_mask = (stancil[0] <= X) & (X <= stancil[-1]) x = X[x_mask] - if x.size < 200: # if there are not enough photos set results to nan - return stancil[1], self.k*np.nan, self.k*np.nan, np.nan, x.size + if x.size < 200: # if there are not enough photos set results to nan + return stancil[1], self.k * np.nan, self.k * np.nan, np.nan, x.size y = DATA[x_mask] - #make x positions - x_pos = (np.round( (x - stancil[0])/ 10.0 -1 , 0) ).astype('int') + # make x positions + x_pos = (np.round((x - stancil[0]) / 10.0 - 1, 0)).astype("int") # weight data if weight_data: window = self.win[x_pos] - y = y * window * np.sqrt( np.var(y) / np.var(( y* window) ) ) + y = y * window * np.sqrt(np.var(y) / np.var((y * window))) - #make y gridded - x_model = np.arange(stancil[0], stancil[-1], self.dx) - y_gridded = np.copy(x_model) * np.nan + # make y gridded + x_model = np.arange(stancil[0], stancil[-1], self.dx) + y_gridded = np.copy(x_model) * np.nan y_gridded[x_pos] = y - nan_mask =np.isnan(y_gridded) + nan_mask = np.isnan(y_gridded) err = ERR[x_mask] if ERR is not None else None - LS_PSD, LS_object = calc_spectrum_LS( x, y, self.k, err=err, LS= None, dk =self.dk) - - y_model = reconstruct_data_from_LS(LS_object, x_model, self.k) - + LS_PSD, LS_object = calc_spectrum_LS( + x, y, self.k, err=err, LS=None, dk=self.dk + ) + y_model = reconstruct_data_from_LS(LS_object, x_model, self.k) - P = conserve_variance(np.fft.rfft(y_model), self.k, y_gridded, nan_mask = nan_mask ) + P = ConserveVariance( + np.fft.rfft(y_model), self.k, y_gridded, nan_mask=nan_mask + ) P.set_parameters() + fitter = P.optimize(max_nfev=max_nfev) return stancil[1], LS_PSD, P.best_guess_Z(), fitter.params, x.size # derive L2 stancil - self.stancil_iter = create_chunk_boundaries(L, self.xlims, ov= self.ov, iter_flag=True) - + self.stancil_iter = create_chunk_boundaries_unit_lengths( + L, self.xlims, ov=self.ov, iter_flag=True + ) map_func = map if map_func is None else map_func print(map_func) - Spec_returns = list(map_func( calc_spectrum_and_field_apply, copy.copy(self.stancil_iter) )) - + Spec_returns = list( + map_func(calc_spectrum_and_field_apply, copy.copy(self.stancil_iter)) + ) # unpack resutls of the mapping: - D_specs = dict() - Y_model = dict() - Pars = dict() - N_per_stancil = list() + D_specs = dict() + Y_model = dict() + Pars = dict() + N_per_stancil = list() for I in Spec_returns: - D_specs[I[0]] = I[1] - Y_model[I[0]] = I[2] - Pars[I[0]] = I[3] + D_specs[I[0]] = I[1] + Y_model[I[0]] = I[2] + Pars[I[0]] = I[3] N_per_stancil.append(I[4]) self.N_per_stancil = N_per_stancil chunk_positions = np.array(list(D_specs.keys())) - self.N_stancils = len(chunk_positions) # number of spectral realizatiobs + self.N_stancils = len(chunk_positions) # number of spectral realizatiobs # repack data, create xarray # 1st LS spectal estimates - self.spec_name = 'LS_spectal_power' if name is None else name - G_LS_power =dict() - for xi,I in D_specs.items(): - G_LS_power[xi] = xr.DataArray(I, dims=['k'], coords={'k': self.k, 'x': xi } , name=self.spec_name) - - G_LS_power = xr.concat(G_LS_power.values(), dim='x').T - + self.spec_name = "LS_spectal_power" if name is None else name + G_LS_power = dict() + for xi, I in D_specs.items(): + G_LS_power[xi] = xr.DataArray( + I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name + ) + G_LS_power = xr.concat(G_LS_power.values(), dim="x").T - #2nd FFT(Y_model) - G_fft =dict() - Y_model_k_fft = np.fft.rfftfreq( int(self.Lpoints), d=self.dx) - for xi,I in Y_model.items(): + # 2nd FFT(Y_model) + G_fft = dict() + Y_model_k_fft = np.fft.rfftfreq(int(self.Lpoints), d=self.dx) + for xi, I in Y_model.items(): if I.size < Y_model_k_fft.size: I = np.insert(I, -1, I[-1]) - G_fft[xi] = xr.DataArray(I, dims=['k'], coords={'k': Y_model_k_fft, 'x': xi } , name='Y_model_hat') + G_fft[xi] = xr.DataArray( + I, dims=["k"], coords={"k": Y_model_k_fft, "x": xi}, name="Y_model_hat" + ) - G_fft = xr.concat(G_fft.values(), dim='x').T + G_fft = xr.concat(G_fft.values(), dim="x").T # generate power spec as well self.G = Z_to_power(G_fft, self.dk, self.Lpoints) - self.G.name = 'spectral_power_optm' - + self.G.name = "spectral_power_optm" # merge both datasets self.GG = xr.merge([G_LS_power, G_fft, self.G]) - self.GG.attrs['ov'] = self.ov - self.GG.attrs['L'] = self.L - self.GG.attrs['Lpoints'] = self.Lpoints - self.GG.coords['N_per_stancil'] = ( ('x'), N_per_stancil) - - self.GG.expand_dims(dim='eta') - self.GG.coords['eta'] = ( ('eta'), np.arange(0, self.L + self.dx, self.dx) - self.L/2 ) - self.GG['win'] = ( ('eta'), np.insert(self.win, -1, self.win[-1])) + self.GG.attrs["ov"] = self.ov + self.GG.attrs["L"] = self.L + self.GG.attrs["Lpoints"] = self.Lpoints + self.GG.coords["N_per_stancil"] = (("x"), N_per_stancil) + + self.GG.expand_dims(dim="eta") + self.GG.coords["eta"] = ( + ("eta"), + np.arange(0, self.L + self.dx, self.dx) - self.L / 2, + ) + self.GG["win"] = (("eta"), np.insert(self.win, -1, self.win[-1])) # create dataframe with fitted parameters - PP2= dict() + PP2 = dict() for k, I in Pars.items(): if I is not np.nan: - PP2[k] =I + PP2[k] = I keys = PP2[next(iter(PP2))].keys() - params_dataframe = pd.DataFrame(index =keys) + params_dataframe = pd.DataFrame(index=keys) - for k,I in PP2.items(): + for k, I in PP2.items(): I.values() params_dataframe[k] = list(I.valuesdict().values()) return self.GG, params_dataframe - - - def calc_var(self): Gmean = np.nanmean(self.G, 1) @@ -815,60 +849,59 @@ def calc_var(self): return self.dk * Gmean[~infmask].sum().data - - - def parceval(self, add_attrs=True, weight_data=False ): + def parceval(self, add_attrs=True, weight_data=False): "test Parceval theorem" - + DATA = self.data - L = self.L X = self.x - def get_stancil_var_apply(stancil): - + "returns the variance of yy for stancil" - x_mask= (stancil[0] < X) & (X <= stancil[-1]) + x_mask = (stancil[0] < X) & (X <= stancil[-1]) idata = DATA[x_mask] if len(idata) < 1: return stancil[1], np.nan, len(idata) idata = detrend(idata) # weight data - x_pos = (np.round( (X[x_mask] - stancil[0])/ 10.0 , 0) ).astype('int') + x_pos = (np.round((X[x_mask] - stancil[0]) / 10.0, 0)).astype("int") if weight_data: window = self.win[x_pos] - idata = idata * window * np.sqrt( np.var(idata) / np.var(( idata* window) ) ) + idata = ( + idata * window * np.sqrt(np.var(idata) / np.var((idata * window))) + ) return stancil[1], idata.var(), len(idata) - D_vars = list(map(get_stancil_var_apply, copy.copy(self.stancil_iter) )) + D_vars = list(map(get_stancil_var_apply, copy.copy(self.stancil_iter))) - stancil_vars, Nphotons =list(), 0 + stancil_vars, Nphotons = list(), 0 for I in D_vars: - stancil_vars.append(I[1] * I[2]) - Nphotons += I[2] - - stancil_weighted_variance = np.nansum(np.array(stancil_vars))/Nphotons + stancil_vars.append(I[1] * I[2]) + Nphotons += I[2] - print('Parcevals Theorem:') - print('variance of timeseries: ', DATA.var()) - print('mean variance of stancils: ', stancil_weighted_variance ) + stancil_weighted_variance = np.nansum(np.array(stancil_vars)) / Nphotons - print('variance of the optimzed windowed LS Spectrum: ', self.calc_var()) + print("Parcevals Theorem:") + print("variance of timeseries: ", DATA.var()) + print("mean variance of stancils: ", stancil_weighted_variance) + print("variance of the optimzed windowed LS Spectrum: ", self.calc_var()) if add_attrs: - self.G.attrs['variance_unweighted_data'] = DATA.var() - self.G.attrs['mean_variance_stancils'] = np.nanmean(np.array(stancil_vars) ) - self.G.attrs['mean_variance_LS_pwelch_spectrum'] = self.calc_var() - - - def mean_spectral_error(self, mask=None, confidence = 0.95 ): - return WavenumberSpectrogram.mean_spectral_error(self, mask=mask, confidence= confidence ) + self.G.attrs["variance_unweighted_data"] = DATA.var() + self.G.attrs["mean_variance_stancils"] = np.nanmean(np.array(stancil_vars)) + self.G.attrs["mean_variance_LS_pwelch_spectrum"] = self.calc_var() + def mean_spectral_error(self, mask=None, confidence=0.95): + return WavenumberSpectrogram.mean_spectral_error( + self, mask=mask, confidence=confidence + ) # class for getting standard Pwelch spectrum. old version, deprechiate class WavenumberPwelch: - def __init__(self,data, x, L, ov=None, window=None, save_chunks=False, plot_chunks=False): + def __init__( + self, data, x, L, ov=None, window=None, save_chunks=False, plot_chunks=False + ): """ returns a wavenumber spectrum using the pwelch method @@ -888,143 +921,137 @@ def __init__(self,data, x, L, ov=None, window=None, save_chunks=False, plot_chun self.dx self.n_spec """ - - - - self.data = data # field to be analyzed - self.dx = np.diff(x)[0] # sampling interval - self.save_chunks= save_chunks - dsize = data.size + # field to be analyzed + self.data = data + # sampling interval + self.dx = np.diff(x)[0] + self.save_chunks = save_chunks + dsize = data.size - ov=int(np.round(L/2)) if ov is None else ov + ov = int(np.round(L / 2)) if ov is None else ov self.n = L if window is None: - win=np.hanning(self.n) + win = np.hanning(self.n) else: - win=window + win = window - factor=np.sqrt(self.n/(win**2).sum()) - win*=factor + factor = np.sqrt(self.n / (win**2).sum()) + win *= factor # test if n is even - if (self.n%2): + if self.n % 2: self.neven = False else: self.neven = True - #calculate freq - self.k = self.calc_freq() - nbin=int(np.floor(dsize/(L-ov))) + # calculate freq + self.k = self.calc_freq() + nbin = int(np.floor(dsize / (L - ov))) if save_chunks: - chunks=np.empty([int(nbin),int(L)]) + chunks = np.empty([int(nbin), int(L)]) - self.specs=np.empty([int(nbin),self.k.size]) + self.specs = np.empty([int(nbin), self.k.size]) - last_k=0 - k=0 + last_k = 0 + k = 0 - for i in np.arange(0,dsize-int(L-ov)+1,int(L-ov)): + for i in np.arange(0, dsize - int(L - ov) + 1, int(L - ov)): - if (plot_chunks) and (i >= dsize-6*int(L-ov)): + if (plot_chunks) and (i >= dsize - 6 * int(L - ov)): M.figure_axis_xy() - self.phi=data[int(i):int(i+L)] + self.phi = data[int(i) : int(i + L)] - - if int(i+L) <= data.size-1: + if int(i + L) <= data.size - 1: if save_chunks: - chunks[k,:]=self.phi - + chunks[k, :] = self.phi - self.phi=signal.detrend(self.phi)*win + self.phi = signal.detrend(self.phi) * win if plot_chunks: plt.plot(self.phi) - self.specs[k,:]= self.calc_spectrum() - last_k=k - last_used_TS=int(i+L) - + self.specs[k, :] = self.calc_spectrum() + last_k = k + last_used_TS = int(i + L) else: if plot_chunks: - print('end of TS is reached') - print('last spec No: '+str(last_k)) - print('spec container: '+str(specs.shape)) - print('last used Timestep: '+str(last_used_TS)) - print('length of TS '+ str(dsize) +'ms') - - k+=1 + print("end of TS is reached") + print("last spec No: " + str(last_k)) + print("spec container: " + str(specs.shape)) + print("last used Timestep: " + str(last_used_TS)) + print("length of TS " + str(dsize) + "ms") + k += 1 if save_chunks: - self.chunks=chunks - - - self.spec_est=self.specs.mean(axis=0) - + self.chunks = chunks + self.spec_est = self.specs.mean(axis=0) - self.n_spec,_=self.specs.shape + self.n_spec, _ = self.specs.shape self.calc_var() - def calc_freq(self): - """ calculate array of spectral variable (frequency or - wavenumber) in cycles per unit of L """ + """calculate array of spectral variable (frequency or + wavenumber) in cycles per unit of L""" - self.df = 1./((self.n-1)*self.dx) + self.df = 1.0 / ((self.n - 1) * self.dx) if self.neven: - f = self.df*np.arange(self.n/2+1) + f = self.df * np.arange(self.n / 2 + 1) else: - f = self.df*np.arange( (self.n-1)/2. + 1 ) + f = self.df * np.arange((self.n - 1) / 2.0 + 1) return f def calc_spectrum(self): - """ compute the 1d spectrum of a field phi """ + """compute the 1d spectrum of a field phi""" self.phih = np.fft.rfft(self.phi) # the factor of 2 comes from the symmetry of the Fourier coeffs - spec = 2.*(self.phih*self.phih.conj()).real / self.df /self.n**2 + spec = 2.0 * (self.phih * self.phih.conj()).real / self.df / self.n**2 # the zeroth frequency should be counted only once - spec[0] = spec[0]/2. + spec[0] = spec[0] / 2.0 if self.neven: - spec[-1] = spec[-1]/2. + spec[-1] = spec[-1] / 2.0 return spec - def error(self, ci=0.95): - self.El, self.Eu =spec_error(self.spec_est,self.n_spec,ci=ci) + self.El, self.Eu = spec_error(self.spec_est, self.n_spec, ci=ci) def parceval(self): - print('Parcevals Theorem:') - print('variance of unweighted timeseries: ',self.data.var()) - print('mean variance of timeseries chunks: ',self.chunks.var(axis=1).mean() if self.save_chunks is True else 'data not saved') - print('variance of the pwelch Spectrum: ',self.var) + print("Parcevals Theorem:") + print("variance of unweighted timeseries: ", self.data.var()) + print( + "mean variance of timeseries chunks: ", + ( + self.chunks.var(axis=1).mean() + if self.save_chunks is True + else "data not saved" + ), + ) + print("variance of the pwelch Spectrum: ", self.var) def calc_var(self): - """ Compute total variance from spectrum """ - self.var = self.df* np.nanmean(self.specs[1:], 0).sum() # do not consider zeroth frequency - + """Compute total variance from spectrum""" + self.var = ( + self.df * np.nanmean(self.specs[1:], 0).sum() + ) # do not consider zeroth frequency # optimze spectral variance +class ConserveVariance: + def __init__(self, Z, freq, data, nan_mask=None): + """ """ -class conserve_variance: - def __init__(self,Z, freq, data, nan_mask= None): - - """ - - """ - - self.LM =LM + self.LM = LM self.data = data - self.Z = Z + self.Z = Z self.freq = freq self.nan_mask = nan_mask @@ -1032,58 +1059,78 @@ def set_parameters(self): params = self.LM.Parameters() - p_smothed = self.runningmean(np.abs(self.Z ), 20, tailcopy=True) + p_smothed = self.runningmean(np.abs(self.Z), 20, tailcopy=True) f_max = self.freq[p_smothed[~np.isnan(p_smothed)].argmax()] - - lambda_max = 9.81 * 5 **2/ (2* np.pi) - params.add('x_cutoff', 1/lambda_max , min=0, max=1, vary=False) - params.add('x_max_pos', f_max , min=f_max*0.75, max=f_max*5+0.001, vary=False) - params.add('LF_amp', 1 , min=0.5 , max=1.2, vary= True) - params.add('HF_amp', 0.5 , min=0 , max=1.5, vary= True) - params.add('sigma_g', 0.002 , min=0.001 , max=0.05, vary= False) - params.add('Gauss_amp', 0.5 , min=0.01 , max=2, vary= True) - + lambda_max = 9.81 * 5**2 / (2 * np.pi) + params.add("x_cutoff", 1 / lambda_max, min=0, max=1, vary=False) + params.add( + "x_max_pos", f_max, min=f_max * 0.75, max=f_max * 5 + 0.001, vary=False + ) + params.add("LF_amp", 1, min=0.5, max=1.2, vary=True) + params.add("HF_amp", 0.5, min=0, max=1.5, vary=True) + params.add("sigma_g", 0.002, min=0.001, max=0.05, vary=False) + params.add("Gauss_amp", 0.5, min=0.01, max=2, vary=True) self.params = params return params def test_ojective_func(self, weight_func, plot_flag=True): - self.objective_func(self.params, self.data, self.Z, weight_func, self.freq, self.nan_mask, plot_flag=plot_flag) - - def tanh_weight_function(self,ff, params): - return self.tanh_weight(ff, params['x_cutoff'].value, - params['x_max_pos'].value, - params['LF_amp'].value, - params['HF_amp'].value, - params['Gauss_amp'].value, - params['sigma_g'].value ) - - def tanh_weight(self,x, x_cutoff , x_max_pos, LF_amp, HF_amp, Gauss_amp, sigma_g): + self.objective_func( + self.params, + self.data, + self.Z, + weight_func, + self.freq, + self.nan_mask, + plot_flag=plot_flag, + ) + + def tanh_weight_function(self, ff, params): + return self.tanh_weight( + ff, + params["x_cutoff"].value, + params["x_max_pos"].value, + params["LF_amp"].value, + params["HF_amp"].value, + params["Gauss_amp"].value, + params["sigma_g"].value, + ) + + def tanh_weight(self, x, x_cutoff, x_max_pos, LF_amp, HF_amp, Gauss_amp, sigma_g): """ - zdgfsg + zdgfsg """ - HF_amp1 = (LF_amp-HF_amp) - decay = 0.5 - np.tanh( (x-x_cutoff)/sigma_g )/2 - y = decay * HF_amp1 + (1 - HF_amp1) - y = y- y[0] +LF_amp + HF_amp1 = LF_amp - HF_amp + decay = 0.5 - np.tanh((x - x_cutoff) / sigma_g) / 2 + y = decay * HF_amp1 + (1 - HF_amp1) + y = y - y[0] + LF_amp - def gaus(x, x_0, amp, sigma_g ): - return amp* np.exp(-0.5 * ( (x-x_0)/sigma_g)**2) + def gaus(x, x_0, amp, sigma_g): + return amp * np.exp(-0.5 * ((x - x_0) / sigma_g) ** 2) - y += gaus(x, x_max_pos, Gauss_amp, sigma_g ) + y += gaus(x, x_max_pos, Gauss_amp, sigma_g) return y + def objective_func( + self, + params, + data_x, + Z_results, + weight_func, + freq, + nan_mask=None, + plot_flag=False, + ): - def objective_func(self, params, data_x, Z_results, weight_func, freq, nan_mask = None, plot_flag=False): + alpha = 1e7 - alpha =1e7 def model_real_space(Z, weights, n=None): """ Both inputs must have the same length """ - return np.fft.irfft(Z*weights, n = n) + return np.fft.irfft(Z * weights, n=n) weights = weight_func(freq, params) @@ -1091,10 +1138,10 @@ def model_real_space(Z, weights, n=None): weights = np.insert(weights, -1, weights[-1]) if nan_mask is not None: - model = model_real_space(Z_results, weights, n= data_x.size)[~nan_mask] + model = model_real_space(Z_results, weights, n=data_x.size)[~nan_mask] dd = data_x[~nan_mask][:] else: - model = model_real_space(Z_results, weights, n= data_x.size)[:] + model = model_real_space(Z_results, weights, n=data_x.size)[:] dd = data_x[:] if model.size > dd.size: @@ -1103,99 +1150,147 @@ def model_real_space(Z, weights, n=None): dd = dd[:-1] if plot_flag: - - from matplotlib.gridspec import GridSpec - import matplotlib.pyplot as plt - F= M.figure_axis_xy(10, 4.1 * 2.5, view_scale= 0.5, container = True) - gs = GridSpec(5,1, wspace=0.1, hspace=0.4) - pos0,pos1,pos2 = gs[0:3, 0],gs[3, 0],gs[4, 0] + F = M.figure_axis_xy(10, 4.1 * 2.5, view_scale=0.5, container=True) + + gs = GridSpec(5, 1, wspace=0.1, hspace=0.4) + pos0, pos1, pos2 = gs[0:3, 0], gs[3, 0], gs[4, 0] ax1 = F.fig.add_subplot(pos0) - plt.title('Stacked Timeseries', loc='left') + plt.title("Stacked Timeseries", loc="left") - chunk_l= 400 - chunk_iter = create_chunk_boundaries(chunk_l, data_x.size, ov=0, iter_flag = True) + chunk_l = 400 + chunk_iter = create_chunk_boundaries( + chunk_l, data_x.size, ov=0, iter_flag=True + ) - ofsett0= 6 + ofsett0 = 6 ofsett = np.copy(ofsett0) for chi in chunk_iter: - v1= np.round(np.nanvar(dd), 4) - plt.plot(ofsett+ data_x[chi[0]:chi[-1]] , linewidth=3, alpha=0.5 , c='black', label=' org. data (var:'+str(v1)+')') - - v1= np.round(model_real_space(Z_results, weights*0 +1)[~nan_mask[1:]].var(), 4) - plt.plot(ofsett + model_real_space(Z_results, weights*0 +1)[chi[0]:chi[-1]] ,linewidth= 0.8, c='red', label='LS model init (var:'+str(v1)+')') - - v1= np.round(model.var(), 4) - plt.plot(ofsett + model_real_space(Z_results, weights)[chi[0]:chi[-1]],linewidth= 0.8, c='blue', label='LS model weighted (var:'+str(v1)+')') + v1 = np.round(np.nanvar(dd), 4) + plt.plot( + ofsett + data_x[chi[0] : chi[-1]], + linewidth=3, + alpha=0.5, + c="black", + label=" org. data (var:" + str(v1) + ")", + ) + + v1 = np.round( + model_real_space(Z_results, weights * 0 + 1)[~nan_mask[1:]].var(), 4 + ) + plt.plot( + ofsett + + model_real_space(Z_results, weights * 0 + 1)[chi[0] : chi[-1]], + linewidth=0.8, + c="red", + label="LS model init (var:" + str(v1) + ")", + ) + + v1 = np.round(model.var(), 4) + plt.plot( + ofsett + model_real_space(Z_results, weights)[chi[0] : chi[-1]], + linewidth=0.8, + c="blue", + label="LS model weighted (var:" + str(v1) + ")", + ) if ofsett == ofsett0: plt.legend() ofsett -= 1 - plt.ylim(ofsett, ofsett0+1) - plt.xlim(0, chunk_l*2) - + plt.ylim(ofsett, ofsett0 + 1) + plt.xlim(0, chunk_l * 2) ax2 = F.fig.add_subplot(pos1) - plt.title('Amplitude Weight Function', loc='left') - plt.plot(weights , c='black') - ax2.set_xscale('log') + plt.title("Amplitude Weight Function", loc="left") + plt.plot(weights, c="black") + ax2.set_xscale("log") ax3 = F.fig.add_subplot(pos2) - plt.title('Initial and tuned |Z|', loc='left') - + plt.title("Initial and tuned |Z|", loc="left") - v2 = np.round( (4.*(Z_results*Z_results.conj()).real /data_x.size**2 ).sum(), 4) - plt.plot(abs(Z_results), linewidth= 0.8, c='red', label='Z (var: '+str(v2) +')') - plt.plot(M.runningmean(abs(Z_results) , 20, tailcopy=True), linewidth= 1.5, c='red', zorder=12) + v2 = np.round( + (4.0 * (Z_results * Z_results.conj()).real / data_x.size**2).sum(), 4 + ) + plt.plot( + abs(Z_results), linewidth=0.8, c="red", label="Z (var: " + str(v2) + ")" + ) + plt.plot( + M.runningmean(abs(Z_results), 20, tailcopy=True), + linewidth=1.5, + c="red", + zorder=12, + ) - Z2= Z_results* weights - v2 = np.round( (4.*(Z2*Z2.conj()).real /data_x.size**2 ).sum(), 4) - plt.plot(abs(Z2), linewidth= 0.8, c='blue', label='weighted Z(var: '+str(v2) +')') - plt.plot(M.runningmean(abs(Z2) , 20, tailcopy=True), linewidth= 1.5, c='blue', zorder=12) + Z2 = Z_results * weights + v2 = np.round((4.0 * (Z2 * Z2.conj()).real / data_x.size**2).sum(), 4) + plt.plot( + abs(Z2), + linewidth=0.8, + c="blue", + label="weighted Z(var: " + str(v2) + ")", + ) + plt.plot( + M.runningmean(abs(Z2), 20, tailcopy=True), + linewidth=1.5, + c="blue", + zorder=12, + ) plt.legend() - plt.ylim( np.percentile(abs(Z_results), 0.5), abs(Z_results).max()*1.3 ) - plt.xlabel('wavenumber k') - ax3.set_xscale('log') - ax3.set_yscale('log') - - fitting_cost =( abs(dd - model) / dd.std() )**2 - variance_cost =( abs(dd.var() - model.var()) / dd.std() ) **2 + plt.ylim(np.percentile(abs(Z_results), 0.5), abs(Z_results).max() * 1.3) + plt.xlabel("wavenumber k") + ax3.set_xscale("log") + ax3.set_yscale("log") - return fitting_cost.sum() , alpha* variance_cost + fitting_cost = (abs(dd - model) / dd.std()) ** 2 + variance_cost = (abs(dd.var() - model.var()) / dd.std()) ** 2 - def optimize(self, fitting_args= None , method='dual_annealing', max_nfev=None): + return fitting_cost.sum(), alpha * variance_cost + def optimize(self, fitting_args=None, method="dual_annealing", max_nfev=None): if fitting_args is None: fitting_args = (self.data, self.Z, self.tanh_weight_function, self.freq) self.weight_func = fitting_args[2] - self.fitter = self.LM.minimize(self.objective_func, self.params, args=fitting_args, kws={'nan_mask':self.nan_mask} , method=method, max_nfev=max_nfev) + self.fitter = self.LM.minimize( + self.objective_func, + self.params, + args=fitting_args, + kws={"nan_mask": self.nan_mask}, + method=method, + max_nfev=max_nfev, + ) return self.fitter def plot_result(self): - self.objective_func(self.fitter.params, self.data, self.Z, self.weight_func, self.freq, self.nan_mask, plot_flag=True) + self.objective_func( + self.fitter.params, + self.data, + self.Z, + self.weight_func, + self.freq, + self.nan_mask, + plot_flag=True, + ) def best_guess_Z(self): return self.Z * self.weight_func(self.freq, self.fitter.params) def runningmean(self, var, m, tailcopy=False): - m=int(m) - s =var.shape - if s[0] <= 2*m: - print('0 Dimension is smaller then averaging length') + m = int(m) + s = var.shape + if s[0] <= 2 * m: + print("0 Dimension is smaller then averaging length") return - rr=np.asarray(var)*np.nan - + rr = np.asarray(var) * np.nan var_range = np.arange(m, int(s[0]) - m - 1, 1) for i in var_range[np.isfinite(var[m : int(s[0]) - m - 1])]: rr[int(i)] = np.nanmean(var[i - m : i + m]) - if tailcopy: - rr[0:m]=rr[m+1] - rr[-m-1:-1]=rr[-m-2] + rr[0:m] = rr[m + 1] + rr[-m - 1 : -1] = rr[-m - 2] return rr From 18c665d802a6f70ecbaf996eb5f933b93578cb38 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Sun, 3 Mar 2024 08:26:36 -0500 Subject: [PATCH 16/51] applied suggested changes in review --- .../ICEsat2_SI_tools/angle_optimizer.py | 36 ++++++++++--------- .../ICEsat2_SI_tools/filter_regrid.py | 14 +++++--- src/icesat2_tracks/analysis_db/B04_angle.py | 2 +- 3 files changed, 30 insertions(+), 22 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py index dac43084..a3b40d86 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py @@ -55,9 +55,10 @@ def get_z_model(x_positions, y_position, K_prime, K_amp, alpha_rad, group_phase) k = K_abs * np.cos(alpha_rad) l = K_abs * np.sin(alpha_rad) - return wavemodel( + _wavemodel = wavemodel( x_positions, y_position, k, l, np.array(K_amp), group_phase=group_phase ) + return _wavemodel @jit(nopython=True, parallel=False) @@ -70,10 +71,12 @@ def get_z_model_single_wave( k = K_abs * np.cos(alpha_rad) l = K_abs * np.sin(alpha_rad) - return wavemodel_single_wave( + _wavemodel_single_wave = wavemodel_single_wave( x_positions, y_position, k, l, K_amp, group_phase=group_phase ) + return _wavemodel_single_wave + def objective_func(pars, x, y, z, test_flag=False, prior=None, prior_weight=2): @@ -88,15 +91,16 @@ def objective_func(pars, x, y, z, test_flag=False, prior=None, prior_weight=2): ) if prior is not None: a_0, a_std = prior["alpha"] - penalties = np.array([(abs(a_0 - pars["alpha"]) ** 2 / a_std**2)]) + penalties = np.array([((a_0 - pars["alpha"]) / a_std) ** 2]) else: penalties = np.array([0]) - cost = (abs(z - z_model)) ** 2 / z.std() ** 2 + cost = ((z - z_model) / z.std()) ** 2 if test_flag: return z_model else: - return np.concatenate([cost, prior_weight * penalties]) + residual = np.concatenate([cost, prior_weight * penalties]) + return residual def likelyhood_func( @@ -112,7 +116,7 @@ def likelyhood_func( x, y, pars["K_prime"], pars["K_amp"], pars["alpha"], pars["phase"] ) # define cost - cost_sqrt = (abs(z - z_model)) ** 2 + cost_sqrt = (z - z_model) ** 2 # estimate total variance if z_error is None: @@ -140,7 +144,7 @@ def simple_log_panelty(x, x0, sigma): ) -class sample_with_mcmc: +class SampleWithMcmc: """ sample a 2nd surface using mcmc and other methods. its made for getting a quick estimate! @@ -190,14 +194,13 @@ def set_parameters(self, par_dict, verbose=False): params = self.LM.Parameters() - var_seeds = list() for k, I in par_dict.items(): params.add(k, (I[0] + I[1]) / 2, vary=True, min=I[0], max=I[1]) - var_seeds.append(np.linspace(I[0], I[1], I[2])) + var_seeds = [np.linspace(I[0], I[1], I[2]) for _, I in par_dict.items()] if len(var_seeds) > 2: - raise ValueError("nor proframmed for 3d") + raise ValueError("Dimensions larger than 2 not supported") self.nwalkers = int(var_seeds[0].size * var_seeds[1].size) @@ -210,12 +213,13 @@ def set_parameters(self, par_dict, verbose=False): print(self.params) def test_objective_func(self): - return self.objective_func( + obj_func = self.objective_func( self.params, *self.fitting_args, **self.fitting_kargs ) + return obj_func def sample( - self, fitting_args=None, method="emcee", steps=100, verbose=True, **kargs + self, fitting_args=None, method="emcee", steps=100, verbose=True, **kwargs ): fitting_args, fitting_kargs = self.fitting_args, self.fitting_kargs @@ -231,19 +235,19 @@ def sample( steps=steps, pos=self.seeds, nan_policy="omit", - **kargs, + **kwargs, ) if verbose: print(self.LM.report_fit(self.fitter)) print("results at self.fitter") - def plot_sample(self, **kargs): + def plot_sample(self, **kwargs): chain = self.chain() nwalkers = self.nwalkers for n in np.arange(nwalkers): - plt.plot(chain[:, n, 1], chain[:, n, 0], "-", **kargs) - plt.plot(chain[:, n, 1], chain[:, n, 0], ".", **kargs) + plt.plot(chain[:, n, 1], chain[:, n, 0], "-", **kwargs) + plt.plot(chain[:, n, 1], chain[:, n, 0], ".", **kwargs) def optimize(self, fitting_args=None, method="dual_annealing", verbose=True): diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py index e70bf994..50c60b79 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py @@ -71,7 +71,10 @@ def track_pole_ward_file(hdf5_file, product="ALT03"): "1st lat =" + str(abs(T_lat[T_time.argmin()])), ";last lat =" + str(abs(T_lat[T_time.argmax()])), ) - return abs(T_lat[T_time.argmax()]) > abs(T_lat[T_time.argmin()]) + + _lhs = abs(T_lat[T_time.argmax()]) + _rhs = abs(T_lat[T_time.argmin()]) + return _lhs > _rhs def track_type(T): @@ -79,10 +82,11 @@ def track_type(T): Returns if track acending or desending T is a pandas table """ - return ( - T["lats"].iloc[T["delta_time"].argmax()] - - T["lats"].iloc[T["delta_time"].argmin()] - ) < 0 + + max_lat = T["lats"].iloc[T["delta_time"].argmax()] + min_lat = T["lats"].iloc[T["delta_time"].argmin()] + delta_lat = max_lat - min_lat + return delta_lat < 0 def lat_min_max_extended(B, beams_list, accent=None): diff --git a/src/icesat2_tracks/analysis_db/B04_angle.py b/src/icesat2_tracks/analysis_db/B04_angle.py index 6c85ec8a..38905c5d 100644 --- a/src/icesat2_tracks/analysis_db/B04_angle.py +++ b/src/icesat2_tracks/analysis_db/B04_angle.py @@ -615,7 +615,7 @@ def plot_instance( Marginals[ikey] = make_fake_data(xi, group) continue - SM = angle_optimizer.sample_with_mcmc(params_dict) + SM = angle_optimizer.SampleWithMcmc(params_dict) SM.set_objective_func(angle_optimizer.objective_func) nan_list = np.isnan(x_concat) | np.isnan(y_concat) | np.isnan(y_concat) x_concat[nan_list] = [] From 8988ae7acaa0aaeb0bf2785f522682b457f1e119 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Sun, 3 Mar 2024 08:30:36 -0500 Subject: [PATCH 17/51] remove int cast --- src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py index a3b40d86..b7cfbfd8 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py @@ -202,7 +202,7 @@ def set_parameters(self, par_dict, verbose=False): if len(var_seeds) > 2: raise ValueError("Dimensions larger than 2 not supported") - self.nwalkers = int(var_seeds[0].size * var_seeds[1].size) + self.nwalkers = var_seeds[0].size * var_seeds[1].size pxx, pyy = np.meshgrid(var_seeds[0], var_seeds[1]) self.seeds = np.vstack([pxx.flatten(), pyy.flatten()]).T @@ -223,7 +223,7 @@ def sample( ): fitting_args, fitting_kargs = self.fitting_args, self.fitting_kargs - # TODO: this funciton throws an error in CI. The nan_policy='omit' policiy was added to avoid this issue + # TODO: this function throws an error in CI. The nan_policy='omit' policy was added to avoid this issue # according to the guidelines in https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do self.fitter = self.LM.minimize( self.objective_func, From 8b921091c770f82644c160670191643ece60ecda Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Sun, 3 Mar 2024 17:04:01 -0500 Subject: [PATCH 18/51] removed track_list folder --- track_lists/ATL10_tracks_complete.txt | 28776 ----------------- track_lists/Batch02_alex_tracks.json | 1 - track_lists/alex_ATL07_filelist.txt | 629 - track_lists/batch02_tracks.json | 1 - track_lists/batch02_tracks_test.json | 1 - track_lists/batch03_ATL03_A00.json | 1 - track_lists/batch03_ATL07_filelist.txt | 2 - track_lists/batch03_tracks_components.json | 1 - track_lists/batch04_ATL10_A00.h5 | Bin 11862366 -> 0 bytes track_lists/batch04_ATL10_A00.json | 1 - track_lists/batch04_test_ATL07_A00.h5 | Bin 10545832 -> 0 bytes track_lists/batch04_test_ATL07_A00.json | 1 - track_lists/batch05_NA_ATL10.txt | 331 - track_lists/batch05_test_ATL07_A00.h5 | Bin 8440152 -> 0 bytes track_lists/batch05_test_ATL07_A00.json | 9 - track_lists/batch06_ATL07_A00.h5 | Bin 8593954 -> 0 bytes track_lists/batch06_ATL07_A00.json | 333 - track_lists/batch07_drfab_A00.json | 5 - track_lists/batch08_2022_stormcases_A00.json | 3 - track_lists/batch_publish_ATL07.json | 11 - 20 files changed, 30106 deletions(-) delete mode 100644 track_lists/ATL10_tracks_complete.txt delete mode 100644 track_lists/Batch02_alex_tracks.json delete mode 100644 track_lists/alex_ATL07_filelist.txt delete mode 100644 track_lists/batch02_tracks.json delete mode 100644 track_lists/batch02_tracks_test.json delete mode 100644 track_lists/batch03_ATL03_A00.json delete mode 100644 track_lists/batch03_ATL07_filelist.txt delete mode 100644 track_lists/batch03_tracks_components.json delete mode 100644 track_lists/batch04_ATL10_A00.h5 delete mode 100644 track_lists/batch04_ATL10_A00.json delete mode 100644 track_lists/batch04_test_ATL07_A00.h5 delete mode 100644 track_lists/batch04_test_ATL07_A00.json delete mode 100644 track_lists/batch05_NA_ATL10.txt delete mode 100644 track_lists/batch05_test_ATL07_A00.h5 delete mode 100644 track_lists/batch05_test_ATL07_A00.json delete mode 100644 track_lists/batch06_ATL07_A00.h5 delete mode 100644 track_lists/batch06_ATL07_A00.json delete mode 100644 track_lists/batch07_drfab_A00.json delete mode 100644 track_lists/batch08_2022_stormcases_A00.json delete mode 100644 track_lists/batch_publish_ATL07.json diff --git a/track_lists/ATL10_tracks_complete.txt b/track_lists/ATL10_tracks_complete.txt deleted file mode 100644 index 1ca6e9b5..00000000 --- a/track_lists/ATL10_tracks_complete.txt +++ /dev/null @@ -1,28776 +0,0 @@ -https://n5eil01u.ecs.nsidc.org/DP7/ATLAS/ATL10.005/2021.12.22/ATL10-02_20211222220625_00101401_005_01.h5 -https://n5eil01u.ecs.nsidc.org/DP7/ATLAS/ATL10.005/2021.12.22/ATL10-01_20211222220625_00101401_005_01.h5 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"ATL07-01_20210228232220_10231001_004_01" -] diff --git a/track_lists/batch08_2022_stormcases_A00.json b/track_lists/batch08_2022_stormcases_A00.json deleted file mode 100644 index 664b1818..00000000 --- a/track_lists/batch08_2022_stormcases_A00.json +++ /dev/null @@ -1,3 +0,0 @@ -[ - "ATL07-01_20220123161656_04951401_005_01" -] diff --git a/track_lists/batch_publish_ATL07.json b/track_lists/batch_publish_ATL07.json deleted file mode 100644 index c2280fd9..00000000 --- a/track_lists/batch_publish_ATL07.json +++ /dev/null @@ -1,11 +0,0 @@ -[ -"ATL07-02_20190209140237_06590201_005_01", -"ATL07-02_20190213121958_07190201_005_01", -"ATL07-02_20190224012038_08800201_005_01", -"ATL07-02_20190502005851_05160301_005_01", -"ATL07-02_20190502040726_05180301_005_01", -"ATL07-02_20190210133657_06740201_005_01", -"ATL07-02_20190219063727_08070201_005_01", -"ATL07-02_20190208142818_06440201_005_01", -"ATL07-02_20190228213804_09540201_005_01" -] From 6a6d52a5f5d252b5f73e18ac62b5ed0e994efe6e Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Sun, 3 Mar 2024 18:22:27 -0500 Subject: [PATCH 19/51] changed to publish package on pypi and on prereleased type --- .github/workflows/publish_pypi.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index 36399a28..84b26647 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.github/workflows/publish_pypi.yml @@ -2,7 +2,7 @@ name: Publish Icesat2 to PyPI on: release: - types: [published] + types: [prereleased] jobs: build: @@ -33,4 +33,4 @@ jobs: uses: pypa/gh-action-pypi-publish@release/v1 with: packages_dir: dist - repository-url: https://test.pypi.org/legacy/ + repository-url: https://upload.pypi.org/legacy/ \ No newline at end of file From 99fdc59be80320439137a06f9b76d7ead99c108d Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Mon, 4 Mar 2024 22:12:06 +0000 Subject: [PATCH 20/51] add Dockerfile and devcontainer.json arguments to make install work --- .devcontainer/devcontainer.json | 26 ++++++++++++++++++++++++++ Dockerfile | 10 +++++++--- 2 files changed, 33 insertions(+), 3 deletions(-) create mode 100644 .devcontainer/devcontainer.json diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..8d96444e --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,26 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the +// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile +{ + "name": "Existing Dockerfile", + "build": { + // Sets the run context to one level up instead of the .devcontainer folder. + "context": "..", + // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename. + "dockerfile": "../Dockerfile" + } + + // Features to add to the dev container. More info: https://containers.dev/features. + // "features": {}, + + // Use 'forwardPorts' to make a list of ports inside the container available locally. + // "forwardPorts": [], + + // Uncomment the next line to run commands after the container is created. + // "postCreateCommand": "cat /etc/os-release", + + // Configure tool-specific properties. + // "customizations": {}, + + // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root. + // "remoteUser": "devcontainer" +} diff --git a/Dockerfile b/Dockerfile index 466445eb..ef57b371 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,11 +1,15 @@ # Use the official Python 3.11 image from the Docker Hub -FROM python:3.11 +FROM python:3.9 # Update the system and install the packages RUN apt-get update && apt-get install -y \ + git-lfs \ openmpi-bin \ openmpi-doc \ - libopenmpi-dev + libopenmpi-dev \ + gdal-bin \ + libgdal-dev + # Set the working directory to /app WORKDIR /app @@ -17,6 +21,6 @@ COPY . /app RUN mkdir -p /app/output # Install any needed packages specified in pyproject.toml -RUN pip install . +RUN pip install --editable ".[dev]" CMD ["/bin/bash"] \ No newline at end of file From 268377c698c5e5f1662991bc3de9032e9eaa4063 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Mon, 4 Mar 2024 22:44:45 +0000 Subject: [PATCH 21/51] =?UTF-8?q?add=20GDAL=20and=20LFS=20=E2=80=93=20make?= =?UTF-8?q?=20docker=20work?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Dockerfile => .devcontainer/Dockerfile | 2 +- .devcontainer/devcontainer.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename Dockerfile => .devcontainer/Dockerfile (96%) diff --git a/Dockerfile b/.devcontainer/Dockerfile similarity index 96% rename from Dockerfile rename to .devcontainer/Dockerfile index ef57b371..ccff69f5 100644 --- a/Dockerfile +++ b/.devcontainer/Dockerfile @@ -1,5 +1,5 @@ # Use the official Python 3.11 image from the Docker Hub -FROM python:3.9 +FROM python:3.11 # Update the system and install the packages RUN apt-get update && apt-get install -y \ diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 8d96444e..43a4a24b 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -6,7 +6,7 @@ // Sets the run context to one level up instead of the .devcontainer folder. "context": "..", // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename. - "dockerfile": "../Dockerfile" + "dockerfile": "Dockerfile" } // Features to add to the dev container. More info: https://containers.dev/features. From b09bad148d3afa8d5d2353b70d9f14963022207f Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Mon, 4 Mar 2024 17:55:03 -0500 Subject: [PATCH 22/51] feat: add dynamic versioning for PyPI --- pyproject.toml | 7 +++++-- src/icesat2_tracks/__init__.py | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 75b3b378..607ebab7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,8 @@ name = "icesat2-tracks" # Required # # For a discussion on single-sourcing the version, see # https://packaging.python.org/guides/single-sourcing-package-version/ -version = "0.0.0" # Required +# version = "0.0.0" # Required +dynamic = ["version"] # This is a one-line description or tagline of what your project does. This # corresponds to the "Summary" metadata field: @@ -190,5 +191,7 @@ where = ["src"] # https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support #requires = ["setuptools>=43.0.0", "wheel","hatchling"] #build-backend = "hatchling.build" -requires = ["setuptools>=43.0.0", "wheel"] +requires = ["setuptools>=43.0.0", "setuptools_scm>=8", "wheel"] build-backend = "setuptools.build_meta" + +[tool.setuptools_scm] \ No newline at end of file diff --git a/src/icesat2_tracks/__init__.py b/src/icesat2_tracks/__init__.py index 3aa0d7b3..f574b610 100644 --- a/src/icesat2_tracks/__init__.py +++ b/src/icesat2_tracks/__init__.py @@ -1 +1 @@ -__version__ = "0.0.0" \ No newline at end of file +"""Tools to analyse data from ICESat-2.""" \ No newline at end of file From bd83861158391e8a0122d9637beaefd3dc5c0754 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 09:24:16 -0500 Subject: [PATCH 23/51] Create dependabot.yml --- .github/dependabot.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..dfd0e308 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,10 @@ +# Set update schedule for GitHub Actions + +version: 2 +updates: + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "weekly" From 619c8f0f5fbbe85fe1f531fab10764f0c678a925 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 09:25:13 -0500 Subject: [PATCH 24/51] Update dependabot.yml --- .github/dependabot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index dfd0e308..674f488a 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -7,4 +7,4 @@ updates: directory: "/" schedule: # Check for updates to GitHub Actions every week - interval: "weekly" + interval: "monthly" From 78c286047e7b4762e09ebbbbb5e74646080148ee Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:36:18 -0500 Subject: [PATCH 25/51] Update .github/dependabot.yml Co-authored-by: Carlos Paniagua --- .github/dependabot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 674f488a..88b50625 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -6,5 +6,5 @@ updates: - package-ecosystem: "github-actions" directory: "/" schedule: - # Check for updates to GitHub Actions every week + # Check for updates to GitHub Actions every month interval: "monthly" From 8e91491d940baa169afd0002aba86bad6824e8c5 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:38:15 -0500 Subject: [PATCH 26/51] Update src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py Co-authored-by: Camilo Diaz --- src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py b/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py index 21b9213b..ce16fa49 100644 --- a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py +++ b/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py @@ -131,7 +131,7 @@ def run_B01_SL_load_single_file( save_path_json = Path(workdir, batch_key, "A01b_ID") save_path_json.mkdir(parents=True, exist_ok=True) - ATL03_track_name = "ATL03_" + track_name + ".h5" + ATL03_track_name = f"ATL03_{track_name}.h5" # Configure SL Session icesat2.init("slideruleearth.io") From aaab734c96a75cf3c40e75915c630589fde8b23d Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:38:35 -0500 Subject: [PATCH 27/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 6b7e4a5a..0244d758 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -181,7 +181,7 @@ def show(self): _logger.debug(' rels dict:') for key in self.rels.keys(): - _logger.debug(' '+key) + _logger.debug(" %s", key) #print(self.__dict__) def plot(self): From f9779d5779cb385d05f66e46f9c6ca14f7ab8c3d Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:38:44 -0500 Subject: [PATCH 28/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 0244d758..9206275b 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -179,7 +179,7 @@ def show(self): for key in self.__dict__.keys(): _logger.debug(key) - _logger.debug(' rels dict:') + _logger.debug(' rels dict keys:') for key in self.rels.keys(): _logger.debug(" %s", key) From a044c61abea026614e3cdb95b93f3002e14d20d4 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:38:59 -0500 Subject: [PATCH 29/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 9206275b..6e2f8df3 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -65,7 +65,7 @@ def __init__(self, path=None, name=None): # setattr(self.colors, k, v) except: _logger.debug('fail load theme, fall back to default theme') - _logger.debug(path+'mhell_colortheme17') + _logger.debug("path: %s", path+'mhell_colortheme17')) self.default_colors() else: From 4cc2da5e8d8c32d32d17660f7f862c2f5afcb032 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:39:18 -0500 Subject: [PATCH 30/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 6e2f8df3..19fe156e 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -45,7 +45,7 @@ def json_load(name, path): with open(full_name, 'r') as ifile: data=json.load(ifile) - _logger.debug('loaded from: {full_name}') + _logger.debug('loaded from: %s', full_name) return data From cd12cd5ee7239e98ee82f18f9b79b8d5a4a40a57 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:39:39 -0500 Subject: [PATCH 31/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 19fe156e..74a8bec5 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -32,7 +32,7 @@ def json_save(name, path, data, return_name=False): full_name= (os.path.join(full_name_root+ '.json')) with open(full_name, 'w') as outfile: json.dump(data, outfile) - _logger.debug(f'save at: {full_name}') + _logger.debug('save at %s:', full_name) if return_name: return full_name_root else: From 3cc72fe240f44fa94be3a0164f5478d653446434 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:39:51 -0500 Subject: [PATCH 32/51] Update src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py Co-authored-by: Camilo Diaz --- src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py b/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py index ce16fa49..367452da 100644 --- a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py +++ b/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py @@ -250,7 +250,7 @@ def run_B01_SL_load_single_file( _logger.info("write A01b .json") DD = {"case_ID": ID_name, "tracks": {}} - DD["tracks"]["ATL03"] = "ATL10-" + track_name + DD["tracks"]["ATL03"] = f"ATL10-{track_name}" start_pos = abs(table_data.lats).argmin() end_pos = abs(table_data.lats).argmax() From fd26f772d0a7bc05d347563440b60ecd1274fdb3 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:40:09 -0500 Subject: [PATCH 33/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 74a8bec5..ee086b1e 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -19,7 +19,7 @@ def ase_to_json(path): A=swatch.parse(path) for i in A[0]['swatches']: - _logger.debug(i['name'] + ' ' + str(i['data']['values'])) + _logger.debug("swatch name: %s, swatch values: %s", i['name'], i['data']['values']) return A From 6ebff19bfa037ab07be6f3301af3580c5c2906cb Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:40:18 -0500 Subject: [PATCH 34/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py Co-authored-by: Carlos Paniagua --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index ee086b1e..8e821d4d 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -55,7 +55,7 @@ class color: def __init__(self, path=None, name=None): self.white=(1,1,1) if (path is not None) & (name is not None): - _logger.debug('color theme: '+name) + _logger.debug("color theme: %s", name) try: theme=json_load(name, path) for k, v in theme.items(): From a8494579643bbe793ab302123ce8ed965ccd8574 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:41:52 -0500 Subject: [PATCH 35/51] Apply suggestions from code review --- src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py b/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py index 367452da..fe464254 100644 --- a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py +++ b/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py @@ -161,10 +161,9 @@ def run_B01_SL_load_single_file( } maximum_height = 30 # (meters) maximum height past dem_h correction - _logger.info("STARTS") _logger.info("Fetching ATL03 data from sliderule") gdf = icesat2.atl06p(params_yapc, resources=[ATL03_track_name]) - _logger.info("ENDS") + _logger.info("Finished fetching ATL03 data from sliderule") gdf = sct.correct_and_remove_height(gdf, maximum_height) cdict = dict() From 39b145f932892bc33084c856937bfc36db618810 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Tue, 5 Mar 2024 14:45:10 -0500 Subject: [PATCH 36/51] Update src/icesat2_tracks/local_modules/m_colormanager_ph3.py --- src/icesat2_tracks/local_modules/m_colormanager_ph3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py index 8e821d4d..dc2adaa4 100644 --- a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py +++ b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py @@ -65,7 +65,7 @@ def __init__(self, path=None, name=None): # setattr(self.colors, k, v) except: _logger.debug('fail load theme, fall back to default theme') - _logger.debug("path: %s", path+'mhell_colortheme17')) + _logger.debug("path: %s", path+'mhell_colortheme17') self.default_colors() else: From e17cccc45da5abdbe3640c35034222d61afbe50e Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Tue, 5 Mar 2024 15:11:03 -0500 Subject: [PATCH 37/51] removing url parameter in Publish to PyPI action. Applied new name of package to icesat2waves --- .github/workflows/publish_pypi.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index 84b26647..35f3d536 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.github/workflows/publish_pypi.yml @@ -1,8 +1,8 @@ -name: Publish Icesat2 to PyPI +name: Publish icesat2waves to PyPI on: release: - types: [prereleased] + types: [published] jobs: build: @@ -32,5 +32,4 @@ jobs: - name: Publish to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - packages_dir: dist - repository-url: https://upload.pypi.org/legacy/ \ No newline at end of file + packages_dir: dist \ No newline at end of file From bb7461522d87bc90da99b6be7568b3737ab29d16 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 5 Mar 2024 20:32:54 +0000 Subject: [PATCH 38/51] chore(deps): bump actions/checkout from 2 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/publish_pypi.yml | 2 +- .github/workflows/python_ci.yml | 2 +- .github/workflows/test_icesat2_tracks_pipeline.yml | 2 +- .github/workflows/test_test_suite.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index 36399a28..f57b13bf 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.github/workflows/publish_pypi.yml @@ -13,7 +13,7 @@ jobs: id-token: write steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v2 diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index 8bc33900..1459c4c6 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -15,7 +15,7 @@ jobs: - name: install mpi macos if: matrix.os == 'macos-latest' run: brew install open-mpi - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: setup python uses: actions/setup-python@v4 with: diff --git a/.github/workflows/test_icesat2_tracks_pipeline.yml b/.github/workflows/test_icesat2_tracks_pipeline.yml index 736a96c2..1a2c883a 100644 --- a/.github/workflows/test_icesat2_tracks_pipeline.yml +++ b/.github/workflows/test_icesat2_tracks_pipeline.yml @@ -13,7 +13,7 @@ jobs: steps: - name: install mpi run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: setup python uses: actions/setup-python@v4 with: diff --git a/.github/workflows/test_test_suite.yml b/.github/workflows/test_test_suite.yml index 3ab9c0f3..ba19f179 100644 --- a/.github/workflows/test_test_suite.yml +++ b/.github/workflows/test_test_suite.yml @@ -13,7 +13,7 @@ jobs: steps: - name: install mpi run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: lfs: true - name: setup python From cdcbd40d5710adb633b04cdf12d4e797e805de5c Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Tue, 5 Mar 2024 16:09:23 -0500 Subject: [PATCH 39/51] Adding some changes missed in the last commit --- .../ICEsat2_SI_tools/angle_optimizer.py | 2 +- .../ICEsat2_SI_tools/filter_regrid.py | 13 +++++++------ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py index b7cfbfd8..497e835a 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py @@ -125,7 +125,7 @@ def likelyhood_func( tot_var = z_error**2 + z_model**2 def simple_log_panelty(x, x0, sigma): - return -np.power((x - x0) / sigma, 2.0) / 2.0 + return -((x - x0) / sigma) ** 2.0 / 2.0 # try ot get prior if prior is not None: diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py index 50c60b79..9b3b5954 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py @@ -3,6 +3,7 @@ import pandas as pd import matplotlib as plt + def process_single_stencil_set( stancil_set, T2, key_var, key_x_coord, stancil_width, calc_stencil_stats ): @@ -72,9 +73,9 @@ def track_pole_ward_file(hdf5_file, product="ALT03"): ";last lat =" + str(abs(T_lat[T_time.argmax()])), ) - _lhs = abs(T_lat[T_time.argmax()]) + _lhs = abs(T_lat[T_time.argmax()]) _rhs = abs(T_lat[T_time.argmin()]) - return _lhs > _rhs + return _lhs > _rhs def track_type(T): @@ -83,7 +84,7 @@ def track_type(T): T is a pandas table """ - max_lat = T["lats"].iloc[T["delta_time"].argmax()] + max_lat = T["lats"].iloc[T["delta_time"].argmax()] min_lat = T["lats"].iloc[T["delta_time"].argmin()] delta_lat = max_lat - min_lat return delta_lat < 0 @@ -414,10 +415,10 @@ def calc_stencil_stats(istencil): Tmedian = T2[i_mask].median() - Tmedian[key + "_weighted_mean"] = np.nan - Tmedian[key + "_mode"] = np.nan + Tmedian[f"{key}_weighted_mean"] = np.nan + Tmedian[f"{key}_mode"] = np.nan Tmedian["N_photos"] = Nphoton - Tmedian[key + "_std"] = np.nan + Tmedian[f"{key}_std"] = np.nan return istencil[1], Tmedian From 7d5e579a4d8364a80debb4d6a492ada80c05c089 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Tue, 5 Mar 2024 16:38:19 -0500 Subject: [PATCH 40/51] more missed changes in previous commits --- .../ICEsat2_SI_tools/spectral_estimates.py | 28 +++++++++---------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 9759b3c5..145087cb 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -20,7 +20,7 @@ def is_not_even(number): # basic functions def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): """ - returns all need chunk boudaries and center position given L, and ov + returns all need chunk boundaries and center position given L, and ov inputs: L desired length of window, dsize size of the data @@ -39,10 +39,7 @@ def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] ) - if iter_flag is True: - return iter(position_stancil.T.tolist()) - else: - return position_stancil + return iter(position_stancil.T.tolist()) if iter_flag else position_stancil def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag=True): @@ -257,10 +254,7 @@ def calc_freq_LS( neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx df = dx / 50 - if neven: - f = df * np.arange(df, N + 1) - else: - f = df * np.arange(df, N) + f = df * np.arange(df, N + 1) if neven else df * np.arange(df, N) return f, df @@ -453,11 +447,15 @@ def calc_spectrum_apply(stancil): # repack data, create xarray self.spec_name = "power_spec" if name is None else name - G = dict() - for xi, I in D_specs.items(): - G[xi] = xr.DataArray( - I, dims=["k"], coords={"k": self.k, "x": xi}, name=self.spec_name - ) + G = { + xi: xr.DataArray( + I, + dims=["k"], + coords={"k": self.k, "x": xi * self.dx}, + name=self.spec_name, + ) + for xi, I in D_specs.items() + } self.G = xr.concat(G.values(), dim="x").T if self.G.k[0] == 0: @@ -468,7 +466,7 @@ def calc_spectrum_apply(stancil): return self.G - # cal variance + def calc_var(self): """Compute total variance from spectragram""" # do not consider zeroth frequency From 8bbbb499e11c2d69befa06f4def1bd6e80325d26 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 5 Mar 2024 21:43:37 +0000 Subject: [PATCH 41/51] chore(deps): bump actions/setup-python from 2 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/publish_pypi.yml | 2 +- .github/workflows/python_ci.yml | 2 +- .github/workflows/test_icesat2_tracks_pipeline.yml | 2 +- .github/workflows/test_test_suite.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index 4bd1f7da..56d8facf 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.github/workflows/publish_pypi.yml @@ -16,7 +16,7 @@ jobs: uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: 3.11 diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index 1459c4c6..8923bff4 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -17,7 +17,7 @@ jobs: run: brew install open-mpi - uses: actions/checkout@v4 - name: setup python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.version }} # install the python version needed cache: "pip" diff --git a/.github/workflows/test_icesat2_tracks_pipeline.yml b/.github/workflows/test_icesat2_tracks_pipeline.yml index 1a2c883a..150f2bbe 100644 --- a/.github/workflows/test_icesat2_tracks_pipeline.yml +++ b/.github/workflows/test_icesat2_tracks_pipeline.yml @@ -15,7 +15,7 @@ jobs: run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev - uses: actions/checkout@v4 - name: setup python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.version }} # install the python version needed cache: "pip" diff --git a/.github/workflows/test_test_suite.yml b/.github/workflows/test_test_suite.yml index ba19f179..674211a6 100644 --- a/.github/workflows/test_test_suite.yml +++ b/.github/workflows/test_test_suite.yml @@ -17,7 +17,7 @@ jobs: with: lfs: true - name: setup python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.version }} # install the python version needed cache: "pip" From 5ecfe893267436198c8c86cca1afeaa9cddcdbad Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Tue, 5 Mar 2024 16:50:41 -0500 Subject: [PATCH 42/51] added table of contents in readme --- README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/README.md b/README.md index c0a2c488..2590eee5 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,16 @@ # ICESAT2 Track Analysis +- [ICESAT2 Track Analysis](#icesat2-track-analysis) + - [Installation for Developers](#installation-for-developers) + - [Installing on Oscar (Deprecated)](#installing-on-oscar-deprecated) + - [Conda Configuration (Deprecated)](#conda-configuration-deprecated) + - [`.condarc`](#condarc) + - [`pkgs_dirs`](#pkgs_dirs) + - [`envs_dirs`](#envs_dirs) + - [Environment Variables](#environment-variables) + - [Command line interface](#command-line-interface) + - [Sample workflow](#sample-workflow) + ## Installation for Developers Prerequisites: From 7fad6550574e3fb11a224e523b46109ed41afcb1 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Tue, 5 Mar 2024 18:33:50 -0500 Subject: [PATCH 43/51] removed deprecated sections from readme --- README.md | 157 ------------------------------------------------------ 1 file changed, 157 deletions(-) diff --git a/README.md b/README.md index 2590eee5..083700d9 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,6 @@ - [ICESAT2 Track Analysis](#icesat2-track-analysis) - [Installation for Developers](#installation-for-developers) - - [Installing on Oscar (Deprecated)](#installing-on-oscar-deprecated) - - [Conda Configuration (Deprecated)](#conda-configuration-deprecated) - - [`.condarc`](#condarc) - - [`pkgs_dirs`](#pkgs_dirs) - - [`envs_dirs`](#envs_dirs) - - [Environment Variables](#environment-variables) - [Command line interface](#command-line-interface) - [Sample workflow](#sample-workflow) @@ -66,157 +60,6 @@ Installation: python -c "import icesat2_tracks; print(icesat2_tracks.__version__)" ``` -## Installing on Oscar (Deprecated) - -If any of these commands fail, check the conda configuration (listed below) before retrying for possible fixes. - -Load a conda module. - -```shell -module load miniconda/23.1.0 -``` - -Follow any prompts from the module load command, like running the following line: -```shell -source /gpfs/runtime/opt/miniconda/23.1.0/etc/profile.d/conda.sh -``` - -Create a new environment using: -```shell -conda create --name "2021-icesat2-tracks" -``` - -Activate the environment using: -```shell -conda activate "2021-icesat2-tracks" -``` - -Install or update the packages in the environment with those listed in the `environment.yml` file using: -```shell -conda env update --file environment.yml -``` - -(You can create and install dependencies in the environment in a single command using: -```shell -conda env create --name "2021-icesat2-tracks" --file environment.yml -``` -... but this has more steps and is thus more likely to fail. Since the installation step takes a long period of time, it is recommended to use the separate commands instead.) - -## Conda Configuration (Deprecated) - -Conda draws its configuration from multiple places, and will behave differently when the configuration is different, even when using the same `environment.yml` file. - -#### `.condarc` - -The `.condarc` file in your home directory sets your conda configuration. If the file doesn't exist, you can create it with: -```shell -touch ~/.condarc -``` - -#### `pkgs_dirs` - -`pkgs_dirs` is the location where conda downloads package files from registries like `anaconda.org`. - -If you use the defaults, when trying to install packages you may get a warning like: -``` -WARNING conda.lock:touch(51): Failed to create lock, do not run conda in parallel processes [errno 13] -... -ERROR Could not open file /gpfs/runtime/opt/miniconda/4.12.0/pkgs/cache/b63425f9.json -``` - -In this case, you might be trying to download packages to the global directory `/gpfs/runtime/opt/miniconda/4.12.0/pkgs` where you have no write-permissions, rather than your home directory where you have write-permissions. - -View the conda configuration: -```shell -conda config --show -``` - -Check that the `pkgs_dirs` setting points to a location in your home directory: -```yaml -pkgs_dirs: - - /users/username/anaconda/pkg -``` - -If it doesn't, update this using: -```shell -conda config --add pkgs_dirs ~/anaconda/pkg -``` - -(Use `--remove` instead of `--add` to remove an entry.) - -#### `envs_dirs` - -`envs_dirs` is the location where there is a separate directory per environment containing the installed packages. - -View the conda configuration: -```shell -conda config --show -``` - -Check that the `envs_dirs` setting to a location in your home directory: -```yaml -envs_dirs: - - /users/username/anaconda/envs -``` - -... and update this using: -```shell -conda config --add envs_dirs ~/anaconda/envs -``` - -(Use `--remove` instead of `--add` to remove an entry.) - -Always re-check the configuration after running the `conda config` command. - -#### Environment Variables - -Note that modules (like `miniconda/23.1.0`) set environment variables like `CONDA_ENVS_PATH` which override the conda config. - -You might view the conda config and see the following entries: -```yaml -envs_dirs: - - /users/username/anaconda - - /users/username/anaconda/envs -``` - -If you try to run -```shell -conda config --remove envs_dirs ~/anaconda -``` -... you'll get a warning: -``` -'envs_dirs': '/users/username/anaconda' is not in the 'envs_dirs' key of the config file -``` - -... and find that the value is still there when you rerun `conda config --show`: -```yaml -envs_dirs: - - /users/username/anaconda # <-- still here! - - /users/username/anaconda/envs -``` - -The value might have been silently set by the `module load` command using an environment variable. - -Check for environment variables by running: -```shell -$ printenv | grep ^CONDA_ -CONDA_SHLVL=0 -CONDA_EXE=/gpfs/runtime/opt/miniconda/23.1.0/bin/conda -CONDA_ENVS_PATH=~/anaconda # <- this is the offending variable -CONDA_PYTHON_EXE=/gpfs/runtime/opt/miniconda/23.1.0/bin/python -``` - -To unset a value like `CONDA_ENVS_PATH` use: -```shell -unset CONDA_ENVS_PATH -``` - -... then check that rerun `conda config --show` no longer shows the has modified the conda config to match the values you wanted: -```yaml -envs_dirs: - - /users/username/anaconda/envs -``` - ## Command line interface The `icesat2waves` package comes with a command-line interface (CLI) that facilitates interaction with the package directly from your terminal. This can be particularly useful for scripting and automation. You can access the help documentation for the CLI by running the following command: From b9d963cd06eee896c8a2e3a121cd310640934480 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Wed, 6 Mar 2024 10:28:40 -0500 Subject: [PATCH 44/51] fixed bug in spectral_estimates.py --- src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 145087cb..fd619cd1 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -451,7 +451,7 @@ def calc_spectrum_apply(stancil): xi: xr.DataArray( I, dims=["k"], - coords={"k": self.k, "x": xi * self.dx}, + coords={"k": self.k, "x": xi }, name=self.spec_name, ) for xi, I in D_specs.items() From 290c3860551ad05a93712e64d0e73887871ca903 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 7 Mar 2024 12:11:22 -0500 Subject: [PATCH 45/51] applied suggested changed in review --- .../ICEsat2_SI_tools/spectral_estimates.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index fd619cd1..7aef0a5d 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -220,7 +220,7 @@ def calc_freq_LS( minimum_frequency, maximum_frequency only used for LS_auto """ - if method is "fftX2": + if method == "fftX2": neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx df = 1.0 / ((N - 1) * dx) / 2 @@ -406,19 +406,20 @@ def __init__(self, x_grid, data, Lpoints, ov=None, window=None): """ self.Lpoints = Lpoints + #when not defined in create_chunk_boundaries then L/2 self.ov = int(Lpoints / 2) if ov is None else ov self.data = data # create subsample k - self.k, self.dk = calc_freq_fft(x_grid, Lpoints) + self.k, self.dk = calc_freq_fft(x_grid, Lpoints) # return 1/ unit of frid points # to get the waveumber units (2 pi/ lambda), multiply by 2 pi self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi # create window self.win = create_window(Lpoints) - def cal_spectrogram(self, data=None, name=None): + def cal_spectrogram(self, data=None, name="power_spec"): """ defines apply function and calculated all sub-sample sprectra using map """ @@ -446,7 +447,7 @@ def calc_spectrum_apply(stancil): self.N_stancils = len(chunk_positions) # repack data, create xarray - self.spec_name = "power_spec" if name is None else name + self.spec_name = name G = { xi: xr.DataArray( I, @@ -565,7 +566,7 @@ def __init__( self.k, self.dk = self.k[::kjumps], self.dk * kjumps self.win = None - def cal_spectrogram(self, x=None, data=None, name=None, dx=1): + def cal_spectrogram(self, x=None, data=None, name="power_spec", dx=1): """ defines apply function and calculated all sub-sample sprectra using map dx nominal resolution of the data resolutionif not set, dx= 1 @@ -576,7 +577,7 @@ def cal_spectrogram(self, x=None, data=None, name=None, dx=1): L, dk = self.L, self.dk win = self.win self.dx = dx - + # init Lomb scargle object with noise as nummy data () self.LS = LombScargle(X[0:L], np.random.randn(L) * 0.001, fit_mean=True) def calc_spectrum_apply(stancil): @@ -601,7 +602,7 @@ def calc_spectrum_apply(stancil): self.N_stancils = len(chunk_positions) # repack data, create xarray - self.spec_name = "power_spec" if name is None else name + self.spec_name = name G = dict() for xi, I in D_specs.items(): G[xi] = xr.DataArray( From c60d0d7287e86cd14c92ea7550520add8799cccb Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 7 Mar 2024 12:14:32 -0500 Subject: [PATCH 46/51] file spectral_estimates.py formatted --- .../ICEsat2_SI_tools/spectral_estimates.py | 23 ++++++++++--------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 7aef0a5d..829426fa 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -406,13 +406,15 @@ def __init__(self, x_grid, data, Lpoints, ov=None, window=None): """ self.Lpoints = Lpoints - #when not defined in create_chunk_boundaries then L/2 + # when not defined in create_chunk_boundaries then L/2 self.ov = int(Lpoints / 2) if ov is None else ov self.data = data # create subsample k - self.k, self.dk = calc_freq_fft(x_grid, Lpoints) # return 1/ unit of frid points + self.k, self.dk = calc_freq_fft( + x_grid, Lpoints + ) # return 1/ unit of frid points # to get the waveumber units (2 pi/ lambda), multiply by 2 pi self.k, self.dk = self.k * 2 * np.pi, self.dk * 2 * np.pi @@ -449,14 +451,14 @@ def calc_spectrum_apply(stancil): # repack data, create xarray self.spec_name = name G = { - xi: xr.DataArray( - I, - dims=["k"], - coords={"k": self.k, "x": xi }, - name=self.spec_name, - ) - for xi, I in D_specs.items() - } + xi: xr.DataArray( + I, + dims=["k"], + coords={"k": self.k, "x": xi}, + name=self.spec_name, + ) + for xi, I in D_specs.items() + } self.G = xr.concat(G.values(), dim="x").T if self.G.k[0] == 0: @@ -467,7 +469,6 @@ def calc_spectrum_apply(stancil): return self.G - def calc_var(self): """Compute total variance from spectragram""" # do not consider zeroth frequency From 356d9f2001bcc10fb3cbf24448e552b3b5c73655 Mon Sep 17 00:00:00 2001 From: Camilo Diaz Date: Thu, 7 Mar 2024 13:19:07 -0500 Subject: [PATCH 47/51] added some code refactoring --- .../ICEsat2_SI_tools/spectral_estimates.py | 31 +++++-------------- 1 file changed, 7 insertions(+), 24 deletions(-) diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py index 829426fa..ed772575 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py +++ b/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py @@ -44,7 +44,7 @@ def create_chunk_boundaries(L, dsize, ov=None, iter_flag=True): def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag=True): """ - returns all need chunk boudaries and center position given L, and ov + returns all need chunk boundaries and center position given L, and ov inputs: L desired length of window in units of the x axis of the data, data_limits (x_min, x_max) tuple with the beginning and end the the derived window stancils @@ -65,11 +65,8 @@ def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag position_stancil = np.vstack( [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] ) - - if iter_flag is True: - return iter(position_stancil.T.tolist()) - else: - return position_stancil + + return iter(position_stancil.T.tolist()) if iter_flag else position_stancil def Z_to_power(Z, df, N): @@ -174,11 +171,7 @@ def calc_freq_fft(x_grid, N): dx = np.round(np.median(np.diff(x_grid)), 1) df = 1.0 / ((N - 1) * dx) - - if neven: - f = df * np.arange(N / 2 + 1) - else: - f = df * np.arange((N - 1) / 2.0 + 1) + f = df * np.arange(N / 2 + 1) if neven else df * np.arange((N - 1) / 2.0 + 1) return f, df @@ -192,11 +185,7 @@ def calc_freq_fft_given_dx(dx, N): neven = is_not_even(N) df = 1.0 / ((N - 1) * dx) - - if neven: - f = df * np.arange(N / 2 + 1) - else: - f = df * np.arange((N - 1) / 2.0 + 1) + f = df * np.arange(N / 2 + 1) if neven else df * np.arange((N - 1) / 2.0 + 1) return f, df @@ -224,19 +213,13 @@ def calc_freq_LS( neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx df = 1.0 / ((N - 1) * dx) / 2 - if neven: - f = df * np.arange(df, N + 1) - else: - f = df * np.arange(df, (N - 1) + 1) + f = df * np.arange(df, N + 1) if neven else df * np.arange(df, N) elif method is "fft": neven = is_not_even(N) dx = np.diff(x).mean() if dx is None else dx df = 1.0 / ((N - 1) * dx) - if neven: - f = df * np.arange(N / 2 + 1) - else: - f = df * np.arange((N - 1) / 2.0 + 1) + f = df * np.arange(N / 2 + 1) if neven else df * np.arange((N - 1) / 2.0 + 1) elif method is "LS_auto": From 8adf818901a4d078a12f6a62012688611f8ca00c Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Thu, 7 Mar 2024 20:27:10 +0000 Subject: [PATCH 48/51] chore: rename as per PEP 8 --- README.md | 4 ++-- pyproject.toml | 18 +++++++++--------- .../__init__.py | 0 .../analysis_db/A02c_IOWAGA_thredds_prior.py | 18 +++++++++--------- .../analysis_db/B01_SL_load_single_file.py | 14 +++++++------- .../analysis_db/B02_make_spectra_gFT.py | 18 +++++++++--------- .../analysis_db/B03_plot_spectra_ov.py | 12 ++++++------ .../analysis_db/B04_angle.py | 14 +++++++------- .../analysis_db/B05_define_angle.py | 14 +++++++------- .../analysis_db/B06_correct_separate_var.py | 12 ++++++------ .../analysis_db/__init__.py | 0 src/{icesat2_tracks => icesat2waves}/app.py | 16 ++++++++-------- .../clitools.py | 0 .../config/__init__.py | 0 .../config/color_def.ai | 0 .../config/color_def.ase | Bin .../config/color_def.json | 0 .../config/config.json | 0 .../config/generate_colors.py | 2 +- .../config/startup.py} | 4 ++-- .../local_modules/__init__.py | 0 .../local_modules/jonswap_gamma.py} | 0 .../local_modules/m_colormanager_ph3.py | 0 .../local_modules/m_general_ph3.py | 0 .../local_modules/m_spectrum_ph3.py | 2 +- .../local_modules/m_tools_ph3.py | 0 .../tools}/__init__.py | 0 .../tools}/angle_optimizer.py | 0 .../tools}/beam_stats.py | 4 ++-- .../tools}/convert_GPS_time.py | 0 .../tools}/convert_julian.py | 0 .../tools}/filter_regrid.py | 0 .../tools}/generalized_FT.py | 4 ++-- .../tools}/iotools.py | 4 ++-- .../tools}/lanczos.py | 0 .../tools}/read_ground_tracks.py | 0 .../tools}/sliderule_converter_tools.py | 0 .../tools}/spectral_estimates.py | 0 .../tools}/spicke_remover.py | 0 .../tools}/wave_tools.py | 0 tests/test_steps.py | 2 +- 41 files changed, 81 insertions(+), 81 deletions(-) rename src/{icesat2_tracks => icesat2waves}/__init__.py (100%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/A02c_IOWAGA_thredds_prior.py (97%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/B01_SL_load_single_file.py (96%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/B02_make_spectra_gFT.py (97%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/B03_plot_spectra_ov.py (98%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/B04_angle.py (98%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/B05_define_angle.py (97%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/B06_correct_separate_var.py (98%) rename src/{icesat2_tracks => icesat2waves}/analysis_db/__init__.py (100%) rename src/{icesat2_tracks => icesat2waves}/app.py (89%) rename src/{icesat2_tracks => icesat2waves}/clitools.py (100%) rename src/{icesat2_tracks => icesat2waves}/config/__init__.py (100%) rename src/{icesat2_tracks => icesat2waves}/config/color_def.ai (100%) rename src/{icesat2_tracks => icesat2waves}/config/color_def.ase (100%) rename src/{icesat2_tracks => icesat2waves}/config/color_def.json (100%) rename src/{icesat2_tracks => icesat2waves}/config/config.json (100%) rename src/{icesat2_tracks => icesat2waves}/config/generate_colors.py (94%) rename src/{icesat2_tracks/config/IceSAT2_startup.py => icesat2waves/config/startup.py} (96%) rename src/{icesat2_tracks => icesat2waves}/local_modules/__init__.py (100%) rename src/{icesat2_tracks/local_modules/JONSWAP_gamma.py => icesat2waves/local_modules/jonswap_gamma.py} (100%) rename src/{icesat2_tracks => icesat2waves}/local_modules/m_colormanager_ph3.py (100%) rename src/{icesat2_tracks => icesat2waves}/local_modules/m_general_ph3.py (100%) rename src/{icesat2_tracks => icesat2waves}/local_modules/m_spectrum_ph3.py (99%) rename src/{icesat2_tracks => icesat2waves}/local_modules/m_tools_ph3.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/__init__.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/angle_optimizer.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/beam_stats.py (98%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/convert_GPS_time.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/convert_julian.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/filter_regrid.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/generalized_FT.py (99%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/iotools.py (99%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/lanczos.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/read_ground_tracks.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/sliderule_converter_tools.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/spectral_estimates.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/spicke_remover.py (100%) rename src/{icesat2_tracks/ICEsat2_SI_tools => icesat2waves/tools}/wave_tools.py (100%) diff --git a/README.md b/README.md index 083700d9..c0844480 100644 --- a/README.md +++ b/README.md @@ -55,9 +55,9 @@ Installation: > pip install --upgrade --editable ".[dev]" > ``` -- Check the module `icesat2_tracks` is available by loading the module: +- Check the module `icesat2waves` is available by loading the module: ```shell - python -c "import icesat2_tracks; print(icesat2_tracks.__version__)" + python -c "import icesat2waves; print(icesat2waves.__version__)" ``` ## Command line interface diff --git a/pyproject.toml b/pyproject.toml index 607ebab7..dd57f910 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -165,14 +165,14 @@ test = [ # which executes the function `main` from this package when invoked. [project.scripts] # Optional #TODO: ADD ANY SCRIPTS WE WANT TO HAVE -load-file = "icesat2_tracks.analysis_db.B01_SL_load_single_file:load_file_app" -make-spectra = "icesat2_tracks.analysis_db.B02_make_spectra_gFT:make_spectra_app" -plot-spectra = "icesat2_tracks.analysis_db.B03_plot_spectra_ov:plot_spectra" -make-iowaga-threads-prior = "icesat2_tracks.analysis_db.A02c_IOWAGA_thredds_prior:make_iowaga_threads_prior_app" -make-b04-angle = "icesat2_tracks.analysis_db.B04_angle:make_b04_angle_app" -define-angle = "icesat2_tracks.analysis_db.B05_define_angle:define_angle_app" -correct-separate = "icesat2_tracks.analysis_db.B06_correct_separate_var:correct_separate_app" -icesat2waves = "icesat2_tracks.app:app" +load-file = "icesat2waves.analysis_db.B01_SL_load_single_file:load_file_app" +make-spectra = "icesat2waves.analysis_db.B02_make_spectra_gFT:make_spectra_app" +plot-spectra = "icesat2waves.analysis_db.B03_plot_spectra_ov:plot_spectra" +make-iowaga-threads-prior = "icesat2waves.analysis_db.A02c_IOWAGA_thredds_prior:make_iowaga_threads_prior_app" +make-b04-angle = "icesat2waves.analysis_db.B04_angle:make_b04_angle_app" +define-angle = "icesat2waves.analysis_db.B05_define_angle:define_angle_app" +correct-separate = "icesat2waves.analysis_db.B06_correct_separate_var:correct_separate_app" +icesat2waves = "icesat2waves.app:app" # This is configuration specific to the `setuptools` build backend. @@ -181,7 +181,7 @@ icesat2waves = "icesat2_tracks.app:app" # If there are data files included in your packages that need to be # installed, specify them here. # TODO: ADD ANY DATA FILES WE WANT TO HAVE -package-data = {"icesat2_tracks" = ["config/*.json"]} +package-data = {"icesat2waves" = ["config/*.json"]} [tool.setuptools.packages.find] where = ["src"] diff --git a/src/icesat2_tracks/__init__.py b/src/icesat2waves/__init__.py similarity index 100% rename from src/icesat2_tracks/__init__.py rename to src/icesat2waves/__init__.py diff --git a/src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py b/src/icesat2waves/analysis_db/A02c_IOWAGA_thredds_prior.py similarity index 97% rename from src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py rename to src/icesat2waves/analysis_db/A02c_IOWAGA_thredds_prior.py index b8d45404..3137531f 100644 --- a/src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py +++ b/src/icesat2waves/analysis_db/A02c_IOWAGA_thredds_prior.py @@ -13,15 +13,15 @@ from siphon.catalog import TDSCatalog import typer -from icesat2_tracks.config.IceSAT2_startup import mconfig -import icesat2_tracks.ICEsat2_SI_tools.iotools as io -import icesat2_tracks.ICEsat2_SI_tools.wave_tools as waves -import icesat2_tracks.local_modules.m_tools_ph3 as MT -import icesat2_tracks.local_modules.m_general_ph3 as M -from icesat2_tracks.config.IceSAT2_startup import color_schemes -from icesat2_tracks.config.IceSAT2_startup import font_for_print - -from icesat2_tracks.clitools import ( +from icesat2waves.config.startup import mconfig +import icesat2waves.tools.iotools as io +import icesat2waves.tools.wave_tools as waves +import icesat2waves.local_modules.m_tools_ph3 as MT +import icesat2waves.local_modules.m_general_ph3 as M +from icesat2waves.config.startup import color_schemes +from icesat2waves.config.startup import font_for_print + +from icesat2waves.clitools import ( echo, validate_batch_key, validate_output_dir, diff --git a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py b/src/icesat2waves/analysis_db/B01_SL_load_single_file.py similarity index 96% rename from src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py rename to src/icesat2waves/analysis_db/B01_SL_load_single_file.py index 756ca3a8..fbbb0f6b 100644 --- a/src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py +++ b/src/icesat2waves/analysis_db/B01_SL_load_single_file.py @@ -16,19 +16,19 @@ SettingWithCopyWarning, ) # TODO: remove when warnings are handled -from icesat2_tracks.config.IceSAT2_startup import ( +from icesat2waves.config.startup import ( mconfig, color_schemes, font_for_pres, plt, ) -import icesat2_tracks.ICEsat2_SI_tools.sliderule_converter_tools as sct -import icesat2_tracks.ICEsat2_SI_tools.iotools as io -import icesat2_tracks.ICEsat2_SI_tools.beam_stats as beam_stats -import icesat2_tracks.local_modules.m_tools_ph3 as MT -from icesat2_tracks.local_modules import m_general_ph3 as M +import icesat2waves.tools.sliderule_converter_tools as sct +import icesat2waves.tools.iotools as io +import icesat2waves.tools.beam_stats as beam_stats +import icesat2waves.local_modules.m_tools_ph3 as MT +from icesat2waves.local_modules import m_general_ph3 as M -from icesat2_tracks.clitools import ( +from icesat2waves.clitools import ( validate_track_name, validate_batch_key, validate_output_dir, diff --git a/src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py b/src/icesat2waves/analysis_db/B02_make_spectra_gFT.py similarity index 97% rename from src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py rename to src/icesat2waves/analysis_db/B02_make_spectra_gFT.py index fca302da..99012270 100644 --- a/src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py +++ b/src/icesat2waves/analysis_db/B02_make_spectra_gFT.py @@ -20,15 +20,15 @@ from matplotlib import pyplot as plt import typer -import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT -import icesat2_tracks.ICEsat2_SI_tools.iotools as io -import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec -import icesat2_tracks.local_modules.m_general_ph3 as M -import icesat2_tracks.local_modules.m_spectrum_ph3 as spicke_remover -import icesat2_tracks.local_modules.m_tools_ph3 as MT -from icesat2_tracks.config.IceSAT2_startup import mconfig - -from icesat2_tracks.clitools import ( +import icesat2waves.tools.generalized_FT as gFT +import icesat2waves.tools.iotools as io +import icesat2waves.tools.spectral_estimates as spec +import icesat2waves.local_modules.m_general_ph3 as M +import icesat2waves.local_modules.m_spectrum_ph3 as spicke_remover +import icesat2waves.local_modules.m_tools_ph3 as MT +from icesat2waves.config.startup import mconfig + +from icesat2waves.clitools import ( echo, validate_batch_key, validate_output_dir, diff --git a/src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py b/src/icesat2waves/analysis_db/B03_plot_spectra_ov.py similarity index 98% rename from src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py rename to src/icesat2waves/analysis_db/B03_plot_spectra_ov.py index 4dcd197f..92bb5b16 100644 --- a/src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py +++ b/src/icesat2waves/analysis_db/B03_plot_spectra_ov.py @@ -11,18 +11,18 @@ from matplotlib.gridspec import GridSpec import typer -import icesat2_tracks.ICEsat2_SI_tools.iotools as io -import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT -import icesat2_tracks.local_modules.m_tools_ph3 as MT -from icesat2_tracks.local_modules import m_general_ph3 as M -from icesat2_tracks.config.IceSAT2_startup import ( +import icesat2waves.tools.iotools as io +import icesat2waves.tools.generalized_FT as gFT +import icesat2waves.local_modules.m_tools_ph3 as MT +from icesat2waves.local_modules import m_general_ph3 as M +from icesat2waves.config.startup import ( mconfig, color_schemes, plt, font_for_print, ) -from icesat2_tracks.clitools import ( +from icesat2waves.clitools import ( echo, validate_batch_key, validate_output_dir, diff --git a/src/icesat2_tracks/analysis_db/B04_angle.py b/src/icesat2waves/analysis_db/B04_angle.py similarity index 98% rename from src/icesat2_tracks/analysis_db/B04_angle.py rename to src/icesat2waves/analysis_db/B04_angle.py index 6c85ec8a..16b33e10 100644 --- a/src/icesat2_tracks/analysis_db/B04_angle.py +++ b/src/icesat2waves/analysis_db/B04_angle.py @@ -6,7 +6,7 @@ import itertools -from icesat2_tracks.config.IceSAT2_startup import ( +from icesat2waves.config.startup import ( mconfig, color_schemes, font_for_print, @@ -15,7 +15,7 @@ import h5py -import icesat2_tracks.ICEsat2_SI_tools.iotools as io +import icesat2waves.tools.iotools as io import xarray as xr import numpy as np from scipy.constants import g @@ -25,11 +25,11 @@ import matplotlib.pyplot as plt from numba import jit # maybe for later optimizations? # noqa: F401 -from icesat2_tracks.ICEsat2_SI_tools import angle_optimizer +from icesat2waves.tools import angle_optimizer -import icesat2_tracks.local_modules.m_tools_ph3 as MT -import icesat2_tracks.local_modules.m_general_ph3 as M -from icesat2_tracks.ICEsat2_SI_tools import angle_optimizer +import icesat2waves.local_modules.m_tools_ph3 as MT +import icesat2waves.local_modules.m_general_ph3 as M +from icesat2waves.tools import angle_optimizer import pandas as pd @@ -38,7 +38,7 @@ from typer import Option -from icesat2_tracks.clitools import ( +from icesat2waves.clitools import ( validate_batch_key, validate_output_dir, suppress_stdout, diff --git a/src/icesat2_tracks/analysis_db/B05_define_angle.py b/src/icesat2waves/analysis_db/B05_define_angle.py similarity index 97% rename from src/icesat2_tracks/analysis_db/B05_define_angle.py rename to src/icesat2waves/analysis_db/B05_define_angle.py index 1ca15f87..aae612ff 100644 --- a/src/icesat2_tracks/analysis_db/B05_define_angle.py +++ b/src/icesat2waves/analysis_db/B05_define_angle.py @@ -9,26 +9,26 @@ from matplotlib import pyplot as plt from typer import Option -from icesat2_tracks.config.IceSAT2_startup import ( +from icesat2waves.config.startup import ( mconfig, color_schemes, font_for_print, ) -from icesat2_tracks.ICEsat2_SI_tools.iotools import init_from_input, ID_to_str -import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec +from icesat2waves.tools.iotools import init_from_input, ID_to_str +import icesat2waves.tools.spectral_estimates as spec import xarray as xr import numpy as np import time -import icesat2_tracks.ICEsat2_SI_tools.lanczos as lanczos -import icesat2_tracks.local_modules.m_tools_ph3 as MT -import icesat2_tracks.local_modules.m_general_ph3 as M +import icesat2waves.tools.lanczos as lanczos +import icesat2waves.local_modules.m_tools_ph3 as MT +import icesat2waves.local_modules.m_general_ph3 as M from matplotlib.gridspec import GridSpec from scipy.ndimage import label -from icesat2_tracks.clitools import ( +from icesat2waves.clitools import ( validate_batch_key, validate_output_dir, suppress_stdout, diff --git a/src/icesat2_tracks/analysis_db/B06_correct_separate_var.py b/src/icesat2waves/analysis_db/B06_correct_separate_var.py similarity index 98% rename from src/icesat2_tracks/analysis_db/B06_correct_separate_var.py rename to src/icesat2waves/analysis_db/B06_correct_separate_var.py index fe84d31b..bf18e560 100644 --- a/src/icesat2_tracks/analysis_db/B06_correct_separate_var.py +++ b/src/icesat2waves/analysis_db/B06_correct_separate_var.py @@ -8,12 +8,12 @@ import h5py from pathlib import Path -import icesat2_tracks.ICEsat2_SI_tools.iotools as io -import icesat2_tracks.local_modules.m_tools_ph3 as MT -from icesat2_tracks.local_modules import m_general_ph3 as M +import icesat2waves.tools.iotools as io +import icesat2waves.local_modules.m_tools_ph3 as MT +from icesat2waves.local_modules import m_general_ph3 as M import time import copy -import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT +import icesat2waves.tools.generalized_FT as gFT import pandas as pd import xarray as xr import numpy as np @@ -22,7 +22,7 @@ import piecewise_regression import typer -from icesat2_tracks.config.IceSAT2_startup import ( +from icesat2waves.config.startup import ( mconfig, color_schemes, font_for_pres, @@ -31,7 +31,7 @@ fig_sizes, ) -from icesat2_tracks.clitools import ( +from icesat2waves.clitools import ( echo, validate_batch_key, validate_output_dir, diff --git a/src/icesat2_tracks/analysis_db/__init__.py b/src/icesat2waves/analysis_db/__init__.py similarity index 100% rename from src/icesat2_tracks/analysis_db/__init__.py rename to src/icesat2waves/analysis_db/__init__.py diff --git a/src/icesat2_tracks/app.py b/src/icesat2waves/app.py similarity index 89% rename from src/icesat2_tracks/app.py rename to src/icesat2waves/app.py index 8c98a282..342a4a4f 100644 --- a/src/icesat2_tracks/app.py +++ b/src/icesat2waves/app.py @@ -3,33 +3,33 @@ Main CLI for icesat2waves. """ from typer import Typer, Option -from icesat2_tracks.analysis_db.B01_SL_load_single_file import ( +from icesat2waves.analysis_db.B01_SL_load_single_file import ( run_B01_SL_load_single_file as _loadfile, ) -from icesat2_tracks.analysis_db.B02_make_spectra_gFT import ( +from icesat2waves.analysis_db.B02_make_spectra_gFT import ( run_B02_make_spectra_gFT as _makespectra, ) -from icesat2_tracks.analysis_db.B03_plot_spectra_ov import ( +from icesat2waves.analysis_db.B03_plot_spectra_ov import ( run_B03_plot_spectra_ov as _plotspectra, ) -from icesat2_tracks.analysis_db.A02c_IOWAGA_thredds_prior import ( +from icesat2waves.analysis_db.A02c_IOWAGA_thredds_prior import ( run_A02c_IOWAGA_thredds_prior as _threddsprior, ) -from icesat2_tracks.analysis_db.B04_angle import run_B04_angle as _run_B04_angle +from icesat2waves.analysis_db.B04_angle import run_B04_angle as _run_B04_angle -from icesat2_tracks.analysis_db.B05_define_angle import define_angle as _define_angle +from icesat2waves.analysis_db.B05_define_angle import define_angle as _define_angle -from icesat2_tracks.analysis_db.B06_correct_separate_var import ( +from icesat2waves.analysis_db.B06_correct_separate_var import ( run_B06_correct_separate_var as _run_correct_separate_var, ) -from icesat2_tracks.clitools import ( +from icesat2waves.clitools import ( validate_track_name, validate_batch_key, validate_output_dir, diff --git a/src/icesat2_tracks/clitools.py b/src/icesat2waves/clitools.py similarity index 100% rename from src/icesat2_tracks/clitools.py rename to src/icesat2waves/clitools.py diff --git a/src/icesat2_tracks/config/__init__.py b/src/icesat2waves/config/__init__.py similarity index 100% rename from src/icesat2_tracks/config/__init__.py rename to src/icesat2waves/config/__init__.py diff --git a/src/icesat2_tracks/config/color_def.ai b/src/icesat2waves/config/color_def.ai similarity index 100% rename from src/icesat2_tracks/config/color_def.ai rename to src/icesat2waves/config/color_def.ai diff --git a/src/icesat2_tracks/config/color_def.ase b/src/icesat2waves/config/color_def.ase similarity index 100% rename from src/icesat2_tracks/config/color_def.ase rename to src/icesat2waves/config/color_def.ase diff --git a/src/icesat2_tracks/config/color_def.json b/src/icesat2waves/config/color_def.json similarity index 100% rename from src/icesat2_tracks/config/color_def.json rename to src/icesat2waves/config/color_def.json diff --git a/src/icesat2_tracks/config/config.json b/src/icesat2waves/config/config.json similarity index 100% rename from src/icesat2_tracks/config/config.json rename to src/icesat2waves/config/config.json diff --git a/src/icesat2_tracks/config/generate_colors.py b/src/icesat2waves/config/generate_colors.py similarity index 94% rename from src/icesat2_tracks/config/generate_colors.py rename to src/icesat2waves/config/generate_colors.py index b6a792b6..0eb653dd 100644 --- a/src/icesat2_tracks/config/generate_colors.py +++ b/src/icesat2waves/config/generate_colors.py @@ -1,5 +1,5 @@ #%matplotlib inline -from icesat2_tracks.local_modules import m_colormanager_ph3 as M_color +from icesat2waves.local_modules import m_colormanager_ph3 as M_color mconfig['paths'] path=mconfig['paths']['config'] diff --git a/src/icesat2_tracks/config/IceSAT2_startup.py b/src/icesat2waves/config/startup.py similarity index 96% rename from src/icesat2_tracks/config/IceSAT2_startup.py rename to src/icesat2waves/config/startup.py index d1e27938..60564f11 100644 --- a/src/icesat2_tracks/config/IceSAT2_startup.py +++ b/src/icesat2waves/config/startup.py @@ -4,8 +4,8 @@ import matplotlib.pyplot as plt -from icesat2_tracks.local_modules import m_colormanager_ph3 as M_color -from icesat2_tracks.local_modules import m_tools_ph3 as MT +from icesat2waves.local_modules import m_colormanager_ph3 as M_color +from icesat2waves.local_modules import m_tools_ph3 as MT ## Read folders and configuration paths config_dir_path = os.path.dirname(__file__) diff --git a/src/icesat2_tracks/local_modules/__init__.py b/src/icesat2waves/local_modules/__init__.py similarity index 100% rename from src/icesat2_tracks/local_modules/__init__.py rename to src/icesat2waves/local_modules/__init__.py diff --git a/src/icesat2_tracks/local_modules/JONSWAP_gamma.py b/src/icesat2waves/local_modules/jonswap_gamma.py similarity index 100% rename from src/icesat2_tracks/local_modules/JONSWAP_gamma.py rename to src/icesat2waves/local_modules/jonswap_gamma.py diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2waves/local_modules/m_colormanager_ph3.py similarity index 100% rename from src/icesat2_tracks/local_modules/m_colormanager_ph3.py rename to src/icesat2waves/local_modules/m_colormanager_ph3.py diff --git a/src/icesat2_tracks/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py similarity index 100% rename from src/icesat2_tracks/local_modules/m_general_ph3.py rename to src/icesat2waves/local_modules/m_general_ph3.py diff --git a/src/icesat2_tracks/local_modules/m_spectrum_ph3.py b/src/icesat2waves/local_modules/m_spectrum_ph3.py similarity index 99% rename from src/icesat2_tracks/local_modules/m_spectrum_ph3.py rename to src/icesat2waves/local_modules/m_spectrum_ph3.py index f904b63c..0c997959 100644 --- a/src/icesat2_tracks/local_modules/m_spectrum_ph3.py +++ b/src/icesat2waves/local_modules/m_spectrum_ph3.py @@ -4,7 +4,7 @@ from scipy.special import gammainc from scipy import signal import matplotlib.pyplot as plt -from icesat2_tracks.local_modules import m_general_ph3 as M +from icesat2waves.local_modules import m_general_ph3 as M try: import mkl diff --git a/src/icesat2_tracks/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py similarity index 100% rename from src/icesat2_tracks/local_modules/m_tools_ph3.py rename to src/icesat2waves/local_modules/m_tools_ph3.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/__init__.py b/src/icesat2waves/tools/__init__.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/__init__.py rename to src/icesat2waves/tools/__init__.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py b/src/icesat2waves/tools/angle_optimizer.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/angle_optimizer.py rename to src/icesat2waves/tools/angle_optimizer.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py b/src/icesat2waves/tools/beam_stats.py similarity index 98% rename from src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py rename to src/icesat2waves/tools/beam_stats.py index 3f815e15..096b170c 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/beam_stats.py +++ b/src/icesat2waves/tools/beam_stats.py @@ -1,7 +1,7 @@ import numpy as np import pandas as pd -import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec -import icesat2_tracks.ICEsat2_SI_tools.iotools as io_local +import icesat2waves.tools.spectral_estimates as spec +import icesat2waves.tools.iotools as io_local import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py b/src/icesat2waves/tools/convert_GPS_time.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/convert_GPS_time.py rename to src/icesat2waves/tools/convert_GPS_time.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/convert_julian.py b/src/icesat2waves/tools/convert_julian.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/convert_julian.py rename to src/icesat2waves/tools/convert_julian.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py b/src/icesat2waves/tools/filter_regrid.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/filter_regrid.py rename to src/icesat2waves/tools/filter_regrid.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py b/src/icesat2waves/tools/generalized_FT.py similarity index 99% rename from src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py rename to src/icesat2waves/tools/generalized_FT.py index abec0dbc..9bfd0aaf 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/generalized_FT.py +++ b/src/icesat2waves/tools/generalized_FT.py @@ -10,8 +10,8 @@ from scipy.signal import detrend import lmfit as LM -from icesat2_tracks.ICEsat2_SI_tools import lanczos, spectral_estimates as spec -import icesat2_tracks.local_modules.JONSWAP_gamma as spectal_models +from icesat2waves.tools import lanczos, spectral_estimates as spec +import icesat2waves.local_modules.jonswap_gamma as spectal_models def rebin(data, dk): diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py b/src/icesat2waves/tools/iotools.py similarity index 99% rename from src/icesat2_tracks/ICEsat2_SI_tools/iotools.py rename to src/icesat2waves/tools/iotools.py index 45444490..05faae5e 100644 --- a/src/icesat2_tracks/ICEsat2_SI_tools/iotools.py +++ b/src/icesat2waves/tools/iotools.py @@ -12,9 +12,9 @@ import pandas as pd import h5py from sliderule import icesat2 -from icesat2_tracks.ICEsat2_SI_tools import sliderule_converter_tools as sct +from icesat2waves.tools import sliderule_converter_tools as sct import icesat2_toolkit.utilities -import icesat2_tracks.ICEsat2_SI_tools.convert_GPS_time as cGPS +import icesat2waves.tools.convert_GPS_time as cGPS def init_from_input(arguments): diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py b/src/icesat2waves/tools/lanczos.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/lanczos.py rename to src/icesat2waves/tools/lanczos.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py b/src/icesat2waves/tools/read_ground_tracks.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/read_ground_tracks.py rename to src/icesat2waves/tools/read_ground_tracks.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py b/src/icesat2waves/tools/sliderule_converter_tools.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/sliderule_converter_tools.py rename to src/icesat2waves/tools/sliderule_converter_tools.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py b/src/icesat2waves/tools/spectral_estimates.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/spectral_estimates.py rename to src/icesat2waves/tools/spectral_estimates.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py b/src/icesat2waves/tools/spicke_remover.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/spicke_remover.py rename to src/icesat2waves/tools/spicke_remover.py diff --git a/src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py b/src/icesat2waves/tools/wave_tools.py similarity index 100% rename from src/icesat2_tracks/ICEsat2_SI_tools/wave_tools.py rename to src/icesat2waves/tools/wave_tools.py diff --git a/tests/test_steps.py b/tests/test_steps.py index d477d202..c7d8faca 100644 --- a/tests/test_steps.py +++ b/tests/test_steps.py @@ -102,7 +102,7 @@ def create_script(script_name, track_name="SH_20190502_05180312"): "--verbose", "--output-dir", ] - base_path = "src/icesat2_tracks/analysis_db/" + base_path = "src/icesat2waves/analysis_db/" return head + [f"{base_path}{script_name}.py"] + tail From 6d826253affe46d25c5424a88a1203fd1269942c Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Thu, 7 Mar 2024 16:48:09 -0500 Subject: [PATCH 49/51] chore: update pyproject.toml icesat2-tracks => icesat2waves min python ver => 3.10 TODO: rename repo --- pyproject.toml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index dd57f910..b318f6e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ # There are some restrictions on what makes a valid project name # specification here: # https://packaging.python.org/specifications/core-metadata/#name -name = "icesat2-tracks" # Required +name = "icesat2waves" # Required # Versions should comply with PEP 440: # https://www.python.org/dev/peps/pep-0440/ @@ -39,7 +39,7 @@ readme = "README.md" # Optional # 'Programming Language' classifiers above, 'pip install' will check this # and refuse to install the project if the version does not match. See # https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires -requires-python = ">=3.9" +requires-python = ">=3.10" # This is either text indicating the license for the distribution, or a file # that contains the license @@ -92,7 +92,6 @@ classifiers = [ # Optional # Specify the Python versions you support here. In particular, ensure # that you indicate you support Python 3. These classifiers are *not* # checked by "pip install". See instead "python_requires" below. - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3 :: Only", @@ -138,7 +137,7 @@ dependencies = [ # Optional dev = [ "check-manifest", "black", - "icesat2-tracks[test]" + "icesat2waves[test]" ] test = [ "coverage", @@ -157,9 +156,9 @@ test = [ # maintainers, and where to support the project financially. The key is # what's used to render the link text on PyPI. [project.urls] # Optional -"Homepage" = "https://github.com/brown-ccv/icesat2-tracks" -"Bug Reports" = "https://github.com/brown-ccv/icesat2-tracks/issues" -"Source" = "https://github.com/brown-ccv/icesat2-tracks" +"Homepage" = "https://github.com/brown-ccv/icesat2waves" +"Bug Reports" = "https://github.com/brown-ccv/icesat2waves/issues" +"Source" = "https://github.com/brown-ccv/icesat2waves" # The following would provide a command line executable called `sample` # which executes the function `main` from this package when invoked. @@ -194,4 +193,4 @@ where = ["src"] requires = ["setuptools>=43.0.0", "setuptools_scm>=8", "wheel"] build-backend = "setuptools.build_meta" -[tool.setuptools_scm] \ No newline at end of file +[tool.setuptools_scm] From 99e31f4ee020ae5bc61405dda15bfa4fa032e4ba Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Fri, 8 Mar 2024 13:32:18 -0500 Subject: [PATCH 50/51] fix: icesat2_tracks => icesat2waves in spectral_estimates.py --- src/icesat2waves/tools/spectral_estimates.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/icesat2waves/tools/spectral_estimates.py b/src/icesat2waves/tools/spectral_estimates.py index ed772575..1a8574dc 100644 --- a/src/icesat2waves/tools/spectral_estimates.py +++ b/src/icesat2waves/tools/spectral_estimates.py @@ -8,7 +8,7 @@ import pandas as pd from scipy import signal import lmfit as LM -import icesat2_tracks.local_modules.m_general_ph3 as M +import icesat2waves.local_modules.m_general_ph3 as M from matplotlib.gridspec import GridSpec import matplotlib.pyplot as plt @@ -65,7 +65,7 @@ def create_chunk_boundaries_unit_lengths(L_unit, data_limits, ov=None, iter_flag position_stancil = np.vstack( [xleft[0:max_size], xcenter_pos[0:max_size], xright[0:max_size]] ) - + return iter(position_stancil.T.tolist()) if iter_flag else position_stancil From 40d9116bb12820ed554f8d7c345eff66572bab63 Mon Sep 17 00:00:00 2001 From: Carlos Paniagua Date: Fri, 8 Mar 2024 18:25:30 -0500 Subject: [PATCH 51/51] fix: update README.md with python 3.10 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c0844480..0a6b1701 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Prerequisites: - A POSIX-compatible system (Linux or macOS) -- Python 3.9 (run `python --version` to check that your version of python is correct) +- Python 3.10 (run `python --version` to check that your version of python is correct) - MPI (e.g. from `brew install open-mpi` on macOS) - HDF5 (e.g. from `brew install hdf5` on macOS)