From 01fce88d16fed229c6359334a7c83a6d718dd985 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 18:23:20 -0500
Subject: [PATCH 01/30] chore: replace print with logging in JONSWAP_gamma.py

---
 .../local_modules/JONSWAP_gamma.py            | 42 ++++++++++---------
 1 file changed, 22 insertions(+), 20 deletions(-)

diff --git a/src/icesat2_tracks/local_modules/JONSWAP_gamma.py b/src/icesat2_tracks/local_modules/JONSWAP_gamma.py
index 7c62f739..fe7a1793 100644
--- a/src/icesat2_tracks/local_modules/JONSWAP_gamma.py
+++ b/src/icesat2_tracks/local_modules/JONSWAP_gamma.py
@@ -1,3 +1,4 @@
+import logging
 import os
 from scipy.constants import g
 
@@ -16,6 +17,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
+_logger = logging.getLogger(__name__)
 
 # %%
 def normalize_time(time):
@@ -77,7 +79,7 @@ def gamma_time_normlized_amp_shifted(time, gammapar=2, loc=0.2, scale=0.1):
     """
     gamma_mod = gamma(gammapar, loc=loc[0, :], scale=scale).pdf(time[0, :])
     dloc = loc[0, :] - time[0, :][gamma_mod.argmax()]
-    # print(dloc)
+    # _logger.debug(dloc)
     gamma_mod = gamma(gammapar, loc=loc + dloc, scale=scale).pdf(time)
     return gamma_mod / gamma_mod.max()
 
@@ -140,7 +142,7 @@ def pierson_moskowitz_fetch_limit(f, X, U):
 
     alpha = 0.076 * (g * X / U**2) ** (-0.22)  # non-dimentional
     wp = 7.0 * np.pi * (g / U) * (g * X / U**2) ** (-0.33)
-    print("wp=" + str(wp))
+    _logger.debug("wp=%s", wp)
 
     sigma_p = 0.07
     sigma_pp = 0.09
@@ -173,8 +175,8 @@ def JONSWAP_default(f, X, U, gamma=3.3):
 
     alpha = 0.076 * (g * X / U**2) ** (-0.22)  # non-dimentional
     wp = 7.0 * np.pi * (g / U) * (g * X / U**2) ** (-0.33)
-    # print('wp='+str(wp))
-    # print('nu='+str(wp*U/(g)))
+    # _logger.debug('wp='+str(wp))
+    # _logger.debug('nu='+str(wp*U/(g)))
 
     sigma_p = 0.07
     sigma_pp = 0.09
@@ -257,7 +259,7 @@ def gamma_time_JONSWAP_default(
     # intersectf=intersect-intersect/slopet
     intersectF = -intersectT * slope_t
     pfreq = time * slope_t + intersectF
-    # print('intersect F=' + str(intersectF))
+    # _logger.debug('intersect F=' + str(intersectF))
 
     # intersectf=intersect#-intersect/slope
     slopeF = 1 / slope_t
@@ -265,13 +267,13 @@ def gamma_time_JONSWAP_default(
 
     # rint(pfreq.shape)
     tt, line = np.meshgrid(time, pfreq_forgamma)
-    # print(line)
-    # print(tt)
+    # _logger.debug(line)
+    # _logger.debug(tt)
     func_t = gamma_time_normlized_amp_shifted(
         tt, gammapar=tgammapar, loc=line, scale=tscale
     )
     # func_t_temp= (tamp*np.exp(- (time-t_center )**4 / tsigma ))
-    # print(func_t.shape)
+    # _logger.debug(func_t.shape)
 
     """ Define X(f_max and U) here """
 
@@ -338,7 +340,7 @@ def gamma_time_JONSWAP_nondim(
     # intersectf=intersect-intersect/slopet
     intersectF = -intersectT * slope_t
     pfreq = time * slope_t + intersectF
-    # print('intersect F=' + str(intersectF))
+    # _logger.debug('intersect F=' + str(intersectF))
 
     # intersectf=intersect#-intersect/slope
     slopeF = 1 / slope_t
@@ -346,13 +348,13 @@ def gamma_time_JONSWAP_nondim(
 
     # rint(pfreq.shape)
     tt, line = np.meshgrid(time, pfreq_forgamma)
-    # print(line)
-    # print(tt)
+    # _logger.debug(line)
+    # _logger.debug(tt)
     func_t = gamma_time_normlized_amp_shifted(
         tt, gammapar=tgammapar, loc=line, scale=tscale
     )
     # func_t_temp= (tamp*np.exp(- (time-t_center )**4 / tsigma ))
-    # print(func_t.shape)
+    # _logger.debug(func_t.shape)
 
     def X(f_max, U10):
         return 3.5**3.0 * g**2.0 / (U10 * f_max**3.0)
@@ -445,7 +447,7 @@ def residual_JONSWAP_default_gamma(
     # tt, tt= np.meshgrid(time, ff)
     model1d = model.reshape(model.shape[0] * model.shape[1])
     model1d[np.isnan(model1d)] = 0
-    # print(model1d)
+    # _logger.debug(model1d)
 
     if data is not None:
         if np.size(data.shape) != 1:
@@ -475,7 +477,7 @@ def residual_JONSWAP_default_gamma(
     if data is None:
         return model1d
     if weight is not None:
-        # print('use weight')
+        # _logger.debug('use weight')
         d = (model1d - data1d) * weight1d
         d[nan_track] = np.nan
         return d
@@ -557,7 +559,7 @@ def residual_JONSWAP_nondim_gamma(
     if data is None:
         return model1d
     if weight is not None:
-        # print('use weight')
+        # _logger.debug('use weight')
         d = (model1d - data1d) * weight1d
         d[nan_track] = np.nan
         return d
@@ -719,7 +721,7 @@ def Jm_regulizer(value_dict, prior):
 
     Jm = list()
     for k, I in prior.items():
-        # print(I)
+        # _logger.debug(I)
         if type(I["m_err"]) is float:
             Jm.append((I["m0"] - vd[k]) / I["m_err"])
         else:
@@ -770,7 +772,7 @@ def reg_func(p0, pi, p_err_unit):
             return (pi / p0 - 1) / ppercent
 
     for k, I in prior.items():
-        # print(I)
+        # _logger.debug(I)
         if type(I["m_err"]) is float:
             Jm.append(reg_func(I["m0"], vd[k], I["m_err"]))
             # Jm.append(    (I['m0']- vd[k] ) / I['m_err']    )
@@ -804,7 +806,7 @@ def reg_func(p0, pi, p_err_unit):
         vd[k] = I * np.random.rand()
 
     Jm = Jm_regulizer(vd, priors)
-    print(Jm)
+    _logger.debug(Jm)
 
 
 # %%
@@ -943,7 +945,7 @@ def cost(value_dict, time, f, data=None, weight=None, prior=False, eps=None):
 #     if prior is not None:
 #         Jm=Jm_regulizer(vdict, prior, alpha=5.0)
 #
-#     #print(Jm)
+#     #_logger.debug(Jm)
 #
 #     if data is None:
 #         return model1d
@@ -955,7 +957,7 @@ def cost(value_dict, time, f, data=None, weight=None, prior=False, eps=None):
 #     if (weight is not None) and (eps is None):
 #         d=(model1d - data1d)*weight
 #         d[nan_track]=np.nan
-#         #print(np.concatenate(( d,Jm )) )
+#         #_logger.debug(np.concatenate(( d,Jm )) )
 #         return np.concatenate(( d, Jm ))
 #
 #     if (eps is None) and (weight is None):

From 7430f57b315d023e0fe1fecfd90a946844974eaa Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 18:23:38 -0500
Subject: [PATCH 02/30] chore: replace print with logging in
 m3_colormanager_ph3.py

---
 .../local_modules/m_colormanager_ph3.py            | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/icesat2_tracks/local_modules/m_colormanager_ph3.py b/src/icesat2_tracks/local_modules/m_colormanager_ph3.py
index 6b7e4a5a..68424bba 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("%s %s", i['name'], i['data']['values'])
 
     return A
 
@@ -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:
@@ -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
 
 
@@ -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():
@@ -177,13 +177,13 @@ def colormaps(self,n, gamma=None):
 
         def show(self):
             for key in self.__dict__.keys():
-                _logger.debug(key)
+                _logger.debug("%s",key)
 
             _logger.debug('  rels dict:')
             for key in self.rels.keys():
-                _logger.debug('  '+key)
+                _logger.debug('  %s', key)
 
-            #print(self.__dict__)
+            #_logger.debug(self.__dict__)
         def plot(self):
             dd=self.__dict__.copy()
             dd_colors=dd['rels']

From 9da6708eb810d5b09f8dbbb603afbee6a0875d47 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 18:24:17 -0500
Subject: [PATCH 03/30] chore: replace print with logging in m_general_ph3.py

---
 .../local_modules/m_general_ph3.py            | 374 +++++++++---------
 1 file changed, 187 insertions(+), 187 deletions(-)

diff --git a/src/icesat2_tracks/local_modules/m_general_ph3.py b/src/icesat2_tracks/local_modules/m_general_ph3.py
index 6cb76fee..bbffdd15 100644
--- a/src/icesat2_tracks/local_modules/m_general_ph3.py
+++ b/src/icesat2_tracks/local_modules/m_general_ph3.py
@@ -57,8 +57,8 @@ def colormaps(self,n, gamma=None):
 
         def show(self):
             for key in self.__dict__.keys():
-                print(key)
-            #print(self.__dict__)
+                _logger.debug(key)
+            #_logger.debug(self.__dict__)
 
 
 # funny massage
@@ -124,13 +124,13 @@ def save(self,name=None,path=None, verbose=True):
                     os.makedirs(savepath)
                 #os.makedirs(savepath, exist_ok=True)
                 name=name if name is not None else datetime.date.today().strftime("%Y%m%d_%I%M%p")
-                #print(savepath)
-                #print(name)
+                #_logger.debug(savepath)
+                #_logger.debug(name)
                 extension='.pdf'
                 full_name= (os.path.join(savepath,name)) + extension
-                #print(full_name)
+                #_logger.debug(full_name)
                 self.fig.savefig(full_name, bbox_inches='tight', format='pdf', dpi=180)
-                _logger.info('save at: '+name)
+                _logger.info('save at: %s', name)
 
         def save_pup(self,name=None,path=None):
                 import datetime
@@ -142,13 +142,13 @@ def save_pup(self,name=None,path=None):
                     os.makedirs(savepath)
                 #os.makedirs(savepath, exist_ok=True)
                 name=name if name is not None else datetime.date.today().strftime("%Y%m%d_%I%M%p")
-                #print(savepath)
-                #print(name)
+                #_logger.debug(savepath)
+                #_logger.debug(name)
                 extension='.pdf'
                 full_name= (os.path.join(savepath,name)) + extension
-                #print(full_name)
+                #_logger.debug(full_name)
                 self.fig.savefig(full_name, bbox_inches='tight', format='pdf', dpi=300)
-                _logger.info('save at: ',full_name)
+                _logger.info('save at: %s',full_name)
 
         def save_light(self,name=None,path=None):
                 import datetime
@@ -158,13 +158,13 @@ def save_light(self,name=None,path=None):
                     os.makedirs(savepath)
                 #os.makedirs(savepath, exist_ok=True)
                 name=name if name is not None else datetime.date.today().strftime("%Y%m%d_%I%M%p")
-                #print(savepath)
-                #print(name)
+                #_logger.debug(savepath)
+                #_logger.debug(name)
                 extension='.png'
                 full_name= (os.path.join(savepath,name)) + extension
-                #print(full_name)
+                #_logger.debug(full_name)
                 self.fig.savefig(full_name, bbox_inches='tight', format='png', dpi=180)
-                _logger.info('save with: ',name)
+                _logger.info('save with: %s',name)
 
 class subplot_routines(figure_axis_xy):
         def __init__(self, ax):
@@ -297,7 +297,7 @@ def linear(self):
 
                 self.cs=plt.contourf(tt[:-2], self.fs[:],dd, self.clevs,cmap=self.cmap)
                 #self.cs=plt.pcolormesh(self.time[:-2], self.fs[:],dd,cmap=self.cmap,shading='gouraud')
-                print(self.clevs)
+                _logger.debug("%s", self.clevs)
                 plt.ylabel(('Power db(' + self.data_unit + '^2/' + self.sample_unit+ ')'))
                 plt.xlabel(('f  (' + self.sample_unit+ ')'))
                 self.cbar= plt.colorbar(self.cs,pad=0.01)#, Location='right')#
@@ -346,11 +346,11 @@ def power(self,  anomalie=False):
                 self.F.ax.set_yscale("log", nonposy='clip')
                 tt = self.time.astype(DT.datetime)
 
-                print(tt[:-1].shape, self.fs[:].shape,dd.T.shape)
+                _logger.debug("%s %s", tt[:-1].shape, self.fs[:].shape,dd.T.shape)
                 self.cs=plt.contourf(tt[:-1], self.fs[:],dd.T, self.clevs,cmap=self.cmap)
                 self.x=np.arange(0,tt[:-1].size)
                 #self.cs=plt.pcolormesh(self.time[:-2], self.fs[:],dd,cmap=self.cmap,shading='gouraud')
-                print(self.clevs)
+                _logger.debug("%s", self.clevs)
                 plt.xlabel('Time')
                 plt.ylabel(('f  (' + self.sample_unit+ ')'))
                 self.cbar= plt.colorbar(self.cs,pad=0.01)#, Location='right')#
@@ -437,13 +437,13 @@ def power_imshow(self, shading=None, downscale_fac=None, anomalie=False,
                         fsn_p=gen_log_space(self.fs.size,int(np.round(self.fs.size/downscale_fac)))
                         fsn_p_run=np.append(fsn_p,fsn_p[-1])
                         dd=dd.T
-                        #print(ddn.shape, fsn_p.shape)
+                        #_logger.debug(ddn.shape, fsn_p.shape)
                         for fr in np.arange(0,fsn_p.size,1):
-                            #print(np.mean(dd[fsn_p[fr]:fsn_p[fr+1], :],axis=0).shape)
+                            #_logger.debug(np.mean(dd[fsn_p[fr]:fsn_p[fr+1], :],axis=0).shape)
 
                             ddn=np.vstack((ddn, np.mean(dd[fsn_p_run[fr]:fsn_p_run[fr+1], :],axis=0)))
                         ddn=np.delete(ddn, 0,0)
-                        #print(ddn.shape)
+                        #_logger.debug(ddn.shape)
                         dd2=ddn
                         fn=self.fs[fsn_p]
 
@@ -451,7 +451,7 @@ def power_imshow(self, shading=None, downscale_fac=None, anomalie=False,
                             tt=tt
                         else:
                             tt=tt[:-1]
-                        #print(dd2.shape, fn.shape, tt.shape)
+                        #_logger.debug(dd2.shape, fn.shape, tt.shape)
 
                 else:
                     if nopower is True:
@@ -462,18 +462,18 @@ def power_imshow(self, shading=None, downscale_fac=None, anomalie=False,
                     fn=self.fs
 
                 if isinstance(tt[0], np.datetime64):
-                    print('time axis is numpy.datetime64, converted to number for plotting')
+                    _logger.debug('time axis is numpy.datetime64, converted to number for plotting')
                     ttt=dates.date2num(tt.astype(DT.datetime))
-                    #print(ttt)
+                    #_logger.debug(ttt)
                 elif isinstance(tt[0], np.timedelta64):
-                    print('time axis is numpy.timedelta64, converted to number for plotting')
-                    #print(tt)
+                    _logger.debug('time axis is numpy.timedelta64, converted to number for plotting')
+                    #_logger.debug(tt)
                     ttt=tt
                 else:
-                    #print(type(tt[0]))
-                    #print(tt)
+                    #_logger.debug(type(tt[0]))
+                    #_logger.debug(tt)
 
-                    print('time axis is not converted')
+                    _logger.debug('time axis is not converted')
                     ttt=tt
 
                 MT.stats_format(dd2)
@@ -484,7 +484,7 @@ def power_imshow(self, shading=None, downscale_fac=None, anomalie=False,
 
                 #self.F.ax.set_yscale("log", nonposy='clip')
                 #self.cs=plt.pcolormesh(self.time[:-2], self.fs[:],dd,cmap=self.cmap,shading='gouraud')
-                #print(self.clevs)
+                #_logger.debug(self.clevs)
                 plt.ylabel(('f  (' + self.sample_unit+ ')'))
                 if cbar is True:
                     self.cbar= plt.colorbar(self.cs,pad=0.01)#, Location='right')#
@@ -594,13 +594,13 @@ def linear_imshow(self, shading=None, downscale_fac=None, anomalie=False, downsc
                         fsn_p=gen_log_space(self.fs.size,int(np.round(self.fs.size/downscale_fac)))
                         fsn_p_run=np.append(fsn_p,fsn_p[-1])
                         dd=dd.T
-                        #print(ddn.shape, fsn_p.shape)
+                        #_logger.debug(ddn.shape, fsn_p.shape)
                         for fr in np.arange(0,fsn_p.size,1):
-                            #print(np.mean(dd[fsn_p[fr]:fsn_p[fr+1], :],axis=0).shape)
+                            #_logger.debug(np.mean(dd[fsn_p[fr]:fsn_p[fr+1], :],axis=0).shape)
 
                             ddn=np.vstack((ddn, np.mean(dd[fsn_p_run[fr]:fsn_p_run[fr+1], :],axis=0)))
                         ddn=np.delete(ddn, 0,0)
-                        #print(ddn.shape)
+                        #_logger.debug(ddn.shape)
                         dd2=ddn
                         fn=self.fs[fsn_p]
 
@@ -608,7 +608,7 @@ def linear_imshow(self, shading=None, downscale_fac=None, anomalie=False, downsc
                             tt=tt
                         else:
                             tt=tt[:-1]
-                        #print(dd2.shape, fn.shape, tt.shape)
+                        #_logger.debug(dd2.shape, fn.shape, tt.shape)
 
                 else:
                     if nopower is True:
@@ -619,18 +619,18 @@ def linear_imshow(self, shading=None, downscale_fac=None, anomalie=False, downsc
                     fn=self.fs
 
                 if isinstance(tt[0], np.datetime64):
-                    print('numpy.datetime64')
+                    _logger.debug('numpy.datetime64')
                     ttt=dates.date2num(tt.astype(DT.datetime))
-                    #print(ttt)
+                    #_logger.debug(ttt)
                 elif isinstance(tt[0], np.timedelta64):
-                    print('numpy.timedelta64')
-                    #print(tt)
+                    _logger.debug('numpy.timedelta64')
+                    #_logger.debug(tt)
                     ttt=tt
                 else:
-                    #print(type(tt[0]))
-                    #print(tt)
+                    #_logger.debug(type(tt[0]))
+                    #_logger.debug(tt)
 
-                    print('something else')
+                    _logger.debug('something else')
                     ttt=tt
 
 
@@ -641,7 +641,7 @@ def linear_imshow(self, shading=None, downscale_fac=None, anomalie=False, downsc
 
                 #self.F.ax.set_yscale("log", nonposy='clip')
                 #self.cs=plt.pcolormesh(self.time[:-2], self.fs[:],dd,cmap=self.cmap,shading='gouraud')
-                #print(self.clevs)
+                #_logger.debug(self.clevs)
 
 
                 plt.ylabel(('f  (' + self.sample_unit+ ')'))
@@ -714,7 +714,7 @@ def __init__(self,f, thetas, data,unit=None, data_type='fraction' ,lims=None,  v
             self.min=np.nanmin(data[freq_sel_bool,:])#*0.5e-17
             self.max=np.nanmax(data[freq_sel_bool,:])
             if verbose:
-                print(str(self.min), str(self.max) )
+                _logger.debug(str(self.min), str(self.max) )
 
             self.ylabels=np.arange(10, 100, 20)
             self.data_type=data_type
@@ -837,11 +837,11 @@ def log_power(data):
 
 def echo_dt(a, as_string=False):
     string=str(a.astype('timedelta64[s]'))+'/'+str(a.astype('timedelta64[m]'))+'/'+str(a.astype('timedelta64[h]'))+'/'+str(a.astype('timedelta64[D]'))
-    #print(string)
+    #_logger.debug(string)
     if as_string:
         return string
     else:
-        print(string)
+        _logger.debug(string)
 
 def easy_dtstr(a):
     if a.astype('timedelta64[s]') < np.timedelta64(60,'s'):
@@ -879,13 +879,13 @@ def save_anyfig(fig,name=None,path=None):
                 if not os.path.exists(savepath):
                     os.makedirs(savepath)
                 name=name if name is not None else datetime.date.today().strftime("%Y%m%d_%I%M%p")
-                #print(savepath)
-                #print(name)
+                #_logger.debug(savepath)
+                #_logger.debug(name)
                 extension='.png'
                 full_name= (os.path.join(savepath,name)) + extension
-                #print(full_name)
+                #_logger.debug(full_name)
                 fig.savefig(full_name, bbox_inches='tight', format='png', dpi=180)
-                print('save at: ',full_name)
+                _logger.debug('save at: %s',full_name)
 #def downscale_2d(data,x,dx):
 #   s1,s2 =data.shape
 #   if s1 == x.size
@@ -893,50 +893,50 @@ def save_anyfig(fig,name=None,path=None):
 def read_cdo(file):
     cdo = Cdo()
     G=cdo.readCdf(file).variables
-    print(G.keys())
+    _logger.debug(G.keys())
     return G
 
 def build_timestamp(time, unit, start, verbose=True): #G.time,'h','1900-01-01' ):
     timestamp=np.datetime64(start)+time[:].astype('m8['+unit+']')
-    #print('timespan:', timestamp[0], '-', timestamp[-1])
+    #_logger.debug('timespan:', timestamp[0], '-', timestamp[-1])
     if verbose is True:
-        print(timestamp)
+        _logger.debug(timestamp)
     return timestamp
 
 def build_timestamp_v2(time, unit, start, verbose=True): #G.time,'h','1900-01-01' ):
     timestamp=np.datetime64(start)+time[:].astype('datetime64[s]')
-    #print('timespan:', timestamp[0], '-', timestamp[-1])
+    #_logger.debug('timespan:', timestamp[0], '-', timestamp[-1])
     if verbose is True:
-        print(timestamp)
+        _logger.debug(timestamp)
     return timestamp
 
 def cut_nparray(var, low, high, verbose=False):
     if low < high:
         if low < var[0]:
             if verbose:
-                print('out of lower limit!')
+                _logger.debug('out of lower limit!')
         if high > var[-1]:
             if verbose:
-                print('out of upper limit!')
-                print(high ,'>', var[-1])
+                _logger.debug('out of upper limit!')
+                _logger.debug("%s > %s", high, var[-1])
         return (var >=low) & (var <=high)
 
     elif high < low:
         if high < var[0]:
-            print('limits flipped, out of lower limit!')
+            _logger.debug('limits flipped, out of lower limit!')
         if low > var[-1]:
-            print('limits flipped, out of lower limit!')
+            _logger.debug('limits flipped, out of lower limit!')
 
         return (var >=high) & (var <=low)
 
     elif high == low:
         if verbose:
-            print('find nearest')
+            _logger.debug('find nearest')
         a=var-low
         return np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))
 
     else:
-        print('error')
+        _logger.debug('error')
         return
 
 def boxmean(data, lon , lat, xlim, ylim):#, data_index, G.lon[:], G.lat[:], [160, -140+360], [-50 , -70]):
@@ -957,30 +957,30 @@ def boxmean(data, lon , lat, xlim, ylim):#, data_index, G.lon[:], G.lat[:], [160
         ybool=(lat >=ylim[1]) & (lat <=ylim[0])
 
     if (xp == 0 and yp ==1):
-        #print('0,1')
+        #_logger.debug('0,1')
         datan=data[xbool,:,:][:,ybool,:].mean()
 
     elif (xp == 0 and yp ==2):
-        #print('0,2')
+        #_logger.debug('0,2')
         datan=data[xbool,:,:][:,:,ybool]
     elif (xp == 1 and yp ==0):
-        #print('1,0')
+        #_logger.debug('1,0')
         datan=data[:,xbool,:][ybool,:,:]
 
     elif (xp == 1 and yp ==2):
-        #print('1,2')
+        #_logger.debug('1,2')
         datan=data[:,xbool,:][:,:,ybool]
 
     elif (xp == 2 and yp ==0):
-        #print('2,0')
+        #_logger.debug('2,0')
         datan=data[:,:, xbool][ybool,:,:]
     elif (xp == 2 and yp ==1):
-        #print('2,1')
+        #_logger.debug('2,1')
         datan=data[:,:, xbool][:,ybool,:]
     else:
-        print('arrays have not the same shape')
+        _logger.debug('arrays have not the same shape')
 
-    print('new shape', datan.shape)
+    _logger.debug('new shape %s', datan.shape)
 
     return np.nanmean(np.nanmean(datan, axis=xp), axis=yp).squeeze() #, xbool , ybool
 
@@ -998,12 +998,12 @@ def detrend(data, od=None, x=None, plot=False, verbose=False):
 
 
     elif od > 0 :
-        if verbose: print('assume data is equal dist. You can define option x= if not.')
+        if verbose: _logger.debug('assume data is equal dist. You can define option x= if not.')
 
         d_org=data-np.nanmean(data)
         x=np.arange(0,d_org.size,1) if x is None else x
 
-        #print(np.isnan(x).sum(), np.isnan(d_org).sum())
+        #_logger.debug(np.isnan(x).sum(), np.isnan(d_org).sum())
         idx = np.isfinite(x) & np.isfinite(d_org)
         px=np.polyfit(x[idx], d_org[idx], od)
         dline=np.polyval( px, x)
@@ -1028,7 +1028,7 @@ def detrend(data, od=None, x=None, plot=False, verbose=False):
         stats['line']=dline
         stats['polynom order']=od
         stats['polyvals']=px
-    if verbose: print(stats)
+    if verbose: _logger.debug(stats)
     return d_detrend/np.nanstd(d_detrend) , stats
 
 def normalize(data):
@@ -1040,19 +1040,19 @@ def runningvar(var, m, tailcopy=False):
     m=int(m)
     s =var.shape
     if s[0] <= 2*m:
-        print('0 Dimension is smaller then averaging length')
+        _logger.debug('0 Dimension is smaller then averaging length')
         return
     rr=np.asarray(var)*np.nan
     var_range=np.arange(m,int(s[0])-m-1,1)
-#    print(var_range)
-#    print(np.isfinite(var))
-#    print(var_range[np.isfinite(var[m:int(s[0])-m-1])])
+#    _logger.debug(var_range)
+#    _logger.debug(np.isfinite(var))
+#    _logger.debug(var_range[np.isfinite(var[m:int(s[0])-m-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.nanvar(var[i-m:i+m])
 
     if tailcopy:
-#        print('tailcopy')
+#        _logger.debug('tailcopy')
         rr[0:m]=rr[m+1]
         rr[-m-1:-1]=rr[-m-2]
     return rr
@@ -1064,17 +1064,17 @@ def runningmean_wrap_around(var, m):
     m=int(m)
     s =var.shape
     if s[0] <= 2*m:
-        print('0 Dimension is smaller then averaging length')
+        _logger.debug('0 Dimension is smaller then averaging length')
         return
 
     rr=np.asarray(var)*np.nan
     var_range=np.arange(var.size)
-    #print(var_range[0], var_range[-1])
+    #_logger.debug(var_range[0], var_range[-1])
 
     for i in var_range:
-        #print(i, i-m, i+m)
-        #print(i, var.take(range(i-m, i+m ), mode='wrap'))
-        #print(i, var[i-m:i+m])
+        #_logger.debug(i, i-m, i+m)
+        #_logger.debug(i, var.take(range(i-m, i+m ), mode='wrap'))
+        #_logger.debug(i, var[i-m:i+m])
         #rm.append(var[i-m:i+m].mean())
         rr[int(i)]=np.nanmean(var.take(range(i-m, i+m ), mode='wrap'))
 
@@ -1084,20 +1084,20 @@ def runningmean(var, m, tailcopy=False):
     m=int(m)
     s =var.shape
     if s[0] <= 2*m:
-        print('0 Dimension is smaller then averaging length')
+        _logger.debug('0 Dimension is smaller then averaging length')
         return
     rr=np.asarray(var)*np.nan
-    #print(type(rr))
+    #_logger.debug(type(rr))
     var_range=np.arange(m,int(s[0])-m-1,1)
-#    print(var_range)
-#    print(np.isfinite(var))
-#    print(var_range[np.isfinite(var[m:int(s[0])-m-1])])
+#    _logger.debug(var_range)
+#    _logger.debug(np.isfinite(var))
+#    _logger.debug(var_range[np.isfinite(var[m:int(s[0])-m-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:
-#        print('tailcopy')
+#        _logger.debug('tailcopy')
         rr[0:m]=rr[m+1]
         rr[-m-1:-1]=rr[-m-2]
 
@@ -1142,14 +1142,14 @@ def find_max_ts(data_org, threshold=None, jump=None, smooth=True, spreed=None, p
 
     if smooth is True:
         data=runningmean(data,spreed)
-    #print(threshold is not None and threshold > np.nanmin(data))
+    #_logger.debug(threshold is not None and threshold > np.nanmin(data))
     #if threshold is not None and numpy.ndarray
 
     if threshold is not None and threshold > np.nanmin(data):
         data[np.isnan(data)]=0
         data[data<threshold]=0#np.nan
     else:
-        #print(type(data.astype('float64')))
+        #_logger.debug(type(data.astype('float64')))
         data[np.isnan(data)]=0
 
     index=np.where(np.diff(np.sign(np.gradient(data)))== -2)[0]+1
@@ -1162,7 +1162,7 @@ def find_max_ts(data_org, threshold=None, jump=None, smooth=True, spreed=None, p
 
         adjustment=data[i-1:i+2].argmax()-1
         if adjustment != 0:
-            #print(str(i) +' adjusted by ' + str(adjustment))
+            #_logger.debug(str(i) +' adjusted by ' + str(adjustment))
             index2.append(i+data[i-1:i+2].argmax()-1)
         else:
             index2.append(i)
@@ -1171,31 +1171,31 @@ def find_max_ts(data_org, threshold=None, jump=None, smooth=True, spreed=None, p
 
     if jump is None:
         if verbose:
-            print('index, data, edit ts (index)')
+            _logger.debug('index, data, edit ts (index)')
         return index, data, data[index]
     else:
         c=np.diff(index)
         b=[]
         i=0
         while i < index.size-1:
- #           print(i, index.size-2, c[i:])
+ #           _logger.debug(i, index.size-2, c[i:])
             if c[i] < jump:
                 if i >= index.size-2:
                     nc=1
                 elif sum(c[i:] >= jump) == 0:
                     nc=c[i:].size
                 else:
-#                    print(np.nonzero(c[i:] >= jump))
+#                    _logger.debug(np.nonzero(c[i:] >= jump))
                     nc=np.nonzero(c[i:] >= jump)[0][0]
                 b=np.append(b, np.round(np.mean(index[i:i+nc+1]))).astype(int)
- #               print(nc, index[i:i+nc+1], ' new', np.round(np.mean(index[i:i+nc+1])))
+ #               _logger.debug(nc, index[i:i+nc+1], ' new', np.round(np.mean(index[i:i+nc+1])))
                 i=i+nc+1
             else:
                 b=np.append(b, index[i]).astype(int)
-  #              print(' ', index[i], ' new', index[i])
+  #              _logger.debug(' ', index[i], ' new', index[i])
                 i=i+1
         if verbose:
-            print('index, edited ts, edit ts (index), org_index')
+            _logger.debug('index, edited ts, edit ts (index), org_index')
 
         return b, data, data[b], index
 
@@ -1204,7 +1204,7 @@ def spickes_to_nan(ts, nloop=None, spreed=1):
     i=0
     while i <= nloop:
         ts.max()
-        #print(np.where(ts == ts.max()))
+        #_logger.debug(np.where(ts == ts.max()))
         pa=np.where(ts == np.nanmax(ts))[0][0]
         ts[pa-spreed:pa+spreed]=np.NaN
         i=i+1
@@ -1217,37 +1217,37 @@ def spickes_to_mean(ts, nloop=None, spreed=1, gaussian=True):
     b=2*spreed
     gaus=signal.gaussian(b, std=b/10)
     while i <= nloop:
-        #print(i)
+        #_logger.debug(i)
         #ts.max()
-        #print(np.where(ts == ts.max()))
+        #_logger.debug(np.where(ts == ts.max()))
         tsabs=np.abs(ts)
         tmax=np.nanmax(tsabs)
-        #print(tsabs, tmax)
+        #_logger.debug(tsabs, tmax)
         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)
+            #_logger.debug(ts[pa-spreed:pa+spreed].shape)
             #print((gaus*(tmax-tsm)).shape)
-            #print(np.shape(gaus*(tmax-tsm)))
+            #_logger.debug(np.shape(gaus*(tmax-tsm)))
             le=int(pa-spreed)
             ue=int(pa+spreed)
 
             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)
+            #_logger.debug(ts[pa-spreed:pa+spreed].shape)
             #print((gaus*(tmax-tsm)).shape)
-            #print(np.shape(gaus*(tmax-tsm)))
-            #print(len(ts))
-            #print(pa+spreed)
+            #_logger.debug(np.shape(gaus*(tmax-tsm)))
+            #_logger.debug(len(ts))
+            #_logger.debug(pa+spreed)
             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)
+                #_logger.debug(le, ue)
                 ts[ le : ue ]=np.linspace(ts[le],ts[ue],len(ts[le:ue]))
 
         i=i+1
@@ -1257,7 +1257,7 @@ def spickes_to_mean(ts, nloop=None, spreed=1, gaussian=True):
 
 class composite_data:
         def __init__(self,var, index_weight=None):
-            #print(var.shape)
+            #_logger.debug(var.shape)
             self.composites=var
             self.comp_mean=np.nanmean(var, axis=0)
             self.comp_std=np.nanstd(var, axis=0)
@@ -1269,11 +1269,11 @@ def __init__(self,var, index_weight=None):
 
         def weight(self,index_weight):
             length=self.comp_mean.size
-            #print('composites ', self.composites.shape)
-            #print('index respeat',index_weight.shape,self.comp_mean.shape)
+            #_logger.debug('composites ', self.composites.shape)
+            #_logger.debug('index respeat',index_weight.shape,self.comp_mean.shape)
             weight_mat=np.repeat(index_weight,length).reshape((self.composites.shape))/index_weight.mean()
-            #print(weight_mat.shape)
-            #print(self.composites.shape)
+            #_logger.debug(weight_mat.shape)
+            #_logger.debug(self.composites.shape)
             self.comp_weighted_mean=np.nanmean(self.composites*weight_mat, axis=0)
             self.comp_weighted_norm=self.comp_weighted_mean/np.nanstd(self.comp_weighted_mean, axis=0)
 
@@ -1322,7 +1322,7 @@ def __init__(self,index, time=None, weigthing=False, span=None):
             self.weigthing=weigthing if weigthing is not False else None
             self.comp=dict()
             if time is None:
-                print('timeaxis is not defined. Make sure that both timeseries have the same timestamp')
+                _logger.debug('timeaxis is not defined. Make sure that both timeseries have the same timestamp')
                 self.time_index=None
             else:
                 self.time_index=time
@@ -1335,7 +1335,7 @@ def build_iter(self, dt=None, dt_unit=None):
         def corse_iter(self, dt, unit=None):
             '''build intereration aaxis and timestamps for corser resoltions'''
             #np.array(C.span)*dt_old
-            #print(type(self.dt), type(dt)
+            #_logger.debug(type(self.dt), type(dt)
 
             assert unit == self.iter.unit, "span units do not match! old unit=" + self.iter.unit +", new unit="+ unit
 
@@ -1343,41 +1343,41 @@ def corse_iter(self, dt, unit=None):
             # convert iter.dt in right unit
             dt_format=np.timedelta64(self.iter.dt,self.iter.unit ).astype('timedelta64['+unit+']').astype('float')
             span_new=np.array(self.span)*dt_format/dt
-            print('old span=',self.span )
-            print('new span=',span_new )
+            _logger.debug('old span= %s',self.span )
+            _logger.debug('new span= %s',span_new )
 
             for s in span_new:
                 span.append(int(np.floor(s)))
 
-            print(span)
+            _logger.debug(span)
             self.iter2=comp_iter(span, dt , unit=unit)
 
         def iter_info(self):
             self.iter_operate.__dict__
 
-            print('available iters')
+            _logger.debug('available iters')
             if self.iter is not None:
-                print('self.iter')
+                _logger.debug('self.iter')
                 self.iter.__dict__
             if self.iter2 is not None:
-                print('self.iter2')
+                _logger.debug('self.iter2')
                 self.iter2.__dict__
 
 
         def info(self):
-            print('index', self.index)
-            print('span', self.span)
-            print('weight', self.weigthing)
-            print('comp', self.comp.keys())
+            _logger.debug('index %s', self.index)
+            _logger.debug('span %s', self.span)
+            _logger.debug('weight %s', self.weigthing)
+            _logger.debug('comp %s', self.comp.keys())
 
         def transform_index_time(self, time_index, time_composite):
             """ find nearest time index of compostite time compared to index times"""
             index_composite=[]
             for i in self.index:
-                #print('old:',i, '   ',time_index[i])
+                #_logger.debug('old:',i, '   ',time_index[i])
                 t_diff=time_index[i]-time_composite
                 nindex=np.unravel_index(np.abs(t_diff).argmin(),t_diff.shape)
-                #print('new:',nindex,time_composite[nindex])#, t_diff[nindex[0]-5:nindex[0]+5])
+                #_logger.debug('new:',nindex,time_composite[nindex])#, t_diff[nindex[0]-5:nindex[0]+5])
                 index_composite=np.append(index_composite,nindex)
             return index_composite.astype(int)
 
@@ -1385,7 +1385,7 @@ def transform_index_time(self, time_index, time_composite):
         def compose_ts(self,ts,name, time=None):
             if time is not None:
                 if self.time_index is None:
-                    print('timeaxis of index TS is not defined!')
+                    _logger.debug('timeaxis of index TS is not defined!')
                     return
                 else:
                     iindex=self.transform_index_time(self.time_index, time)
@@ -1393,37 +1393,37 @@ def compose_ts(self,ts,name, time=None):
                 iindex=self.index
 
             span=self.iter_operate.span
-            print(iindex)
+            _logger.debug(iindex)
             if self.span != [0, 0]:
                 comp=np.empty((-span[0]+span[1]))#*np.NaN
                 self.length=comp.size
 
                 for i in iindex:
                     if i+span[0] < 0:
-                        print('i', i, 'span:', span[0], span[1] )
-                        print('left postion:', i+span[0])
+                        _logger.debug('i: %s span: %s %s', i, span[0], span[1] )
+                        _logger.debug('left postion: %s', i+span[0])
                         raise ValueError("composite span exceeds ts limits")
-                        #print('right postion:',i+self.span[1])
+                        #_logger.debug('right postion:',i+self.span[1])
                         return -1
                     elif i+span[1] > ts.size:
                         return -1
-                        print(i, span[0], span[1] )
-                        print('i', i, 'span:', span[0], span[1] )
-                        #print('left postion:', i+self.span[0])
-                        print('right postion:',i+span[1])
+                        _logger.debug(i, span[0], span[1] )
+                        _logger.debug('i: %s span: %s %s', i, span[0], span[1] )
+                        #_logger.debug('left postion:', i+self.span[0])
+                        _logger.debug('right postion: %s',i+span[1])
                         raise ValueError("composite span exceeds ts limits")
-                        #print('right postion:',i+self.span[1])
+                        #_logger.debug('right postion:',i+self.span[1])
                         return -1
 
                     #self.comp[i]=ts[i]
-                    print('comp', comp.shape)
-                    print('ts', ts[i+span[0]:i+span[1]].shape)
-                    #print('ltjergij')
-                    print(i, span[0], span[1] )
+                    _logger.debug('comp %s', comp.shape)
+                    _logger.debug('ts %s', ts[i+span[0]:i+span[1]].shape)
+                    #_logger.debug('ltjergij')
+                    _logger.debug("%s %s %s", i, span[0], span[1])
                     comp=np.vstack((comp,ts[i+span[0]:i+span[1]]))
                     #comp[:,i]=((comp,ts[i+self.span[0]:i+self.span[1]]))
-                    #print(ts[i])
-                    #print(comp)
+                    #_logger.debug(ts[i])
+                    #_logger.debug(comp)
                     #self.comp.append(ts[i])
 
                 comp=np.delete(comp,0,0)
@@ -1437,7 +1437,7 @@ def compose_ts(self,ts,name, time=None):
         def compose_2d(self,field, name, time=None):
             if time is not None:
                 if self.time_index is None:
-                    print('timeaxis of index TS is not defined!')
+                    _logger.debug('timeaxis of index TS is not defined!')
                     return
                 else:
                     iindex=self.transform_index_time(self.time_index, time)
@@ -1446,10 +1446,10 @@ def compose_2d(self,field, name, time=None):
             span=self.iter_operate.span
 
             if span != [0, 0]:
-                print(-span[0]+span[1],field.shape[1])
+                _logger.debug("%s %s", -span[0]+span[1],field.shape[1])
                 comp=np.empty((-span[0]+span[1],field.shape[1]))*np.NaN
                 self.length=-span[0]+span[1]
-               # print('comp shape',comp.shape)
+               # _logger.debug('comp shape',comp.shape)
                 for i in iindex:
                     if i+span[1] > field.shape[0]:
                         ff=field[i+span[0]:field.shape[0],:]
@@ -1463,10 +1463,10 @@ def compose_2d(self,field, name, time=None):
                         comp=np.vstack((comp,cc))
                     else:
                         comp=np.vstack((comp,field[i+span[0]:i+span[1],:]))
-                    #print(comp.shape)
+                    #_logger.debug(comp.shape)
 
-                #print('comp shape',comp.shape)
-                #print(iindex.size*self.length ,iindex.size, self.length,field.shape[1])
+                #_logger.debug('comp shape',comp.shape)
+                #_logger.debug(iindex.size*self.length ,iindex.size, self.length,field.shape[1])
                 comp=comp.reshape( iindex.size+1,self.length,field.shape[1])
                 #comp.shape
                 comp=np.delete(comp,0,0)
@@ -1475,7 +1475,7 @@ def compose_2d(self,field, name, time=None):
                 #b2_mean=b2.mean(axis=0)
                 self.comp[name]=comp1
             else:
-                print('no span defined')
+                _logger.debug('no span defined')
                 comp=field[iindex,:]
 
                 comp1=composite_data(comp, self.weigthing)
@@ -1485,7 +1485,7 @@ def compose_2d(self,field, name, time=None):
         def compose_field(self,field, name, time=None):
             if time is not None:
                 if self.time_index is None:
-                    print('timeaxis of index TS is not defined!')
+                    _logger.debug('timeaxis of index TS is not defined!')
                     return
                 else:
                     iindex=self.transform_index_time(self.time_index, time)
@@ -1493,18 +1493,18 @@ def compose_field(self,field, name, time=None):
                 iindex=self.index
 
             span=self.iter_operate.span
-            #print(field.shape)
-            #print('iindex', iindex)
+            #_logger.debug(field.shape)
+            #_logger.debug('iindex', iindex)
             if span != [0, 0]:
                 comp=np.empty((-span[0]+span[1],field.shape[1],field.shape[2]))*np.NaN
                 self.length=-span[0]+span[1]
-                #print(comp.shape)
+                #_logger.debug(comp.shape)
                 for i in iindex:
 
-                    #print(i+span[0],i+span[1])
+                    #_logger.debug(i+span[0],i+span[1])
                     comp=np.vstack((comp,field[i+span[0]:i+span[1],:,:]))
-                    #print(comp.shape)
-                #print(iindex)
+                    #_logger.debug(comp.shape)
+                #_logger.debug(iindex)
                 comp=comp.reshape( iindex.size+1,self.length,field.shape[1], field.shape[2])
                 #comp.shape
                 comp=np.delete(comp,0,0)
@@ -1513,7 +1513,7 @@ def compose_field(self,field, name, time=None):
                 #b2_mean=b2.mean(axis=0)
                 self.comp[name]=comp1
             else:
-                print('no span defined')
+                _logger.debug('no span defined')
                 comp=field[iindex,:,:]
 
                 comp1=composite_data(comp, self.weigthing)
@@ -1523,7 +1523,7 @@ def compose_field(self,field, name, time=None):
 def time_overlap(time1, time2):
 
     if (time1[0]-time2[0]).astype(int) > 0:
-        #print('time1 is first')
+        #_logger.debug('time1 is first')
         start=time1[0]
     else:
         start=time2[0]
@@ -1568,18 +1568,18 @@ def gen_log_space(limit, n):
 
 def linefit2Points(time_lin, f, data, f1, f2, f_delta=None,  plot=False):
     if isinstance(time_lin[0], np.datetime64):
-        print('type is numpy.datetime64', time_lin.shape)
+        _logger.debug('type is numpy.datetime64', time_lin.shape)
         time_lin=time_lin.astype('m8[s]').astype(int)
-        #print(ttt)
+        #_logger.debug(ttt)
 
     #if isinstance(time_delta, np.timedelta64):
     #        time_delta=time_delta.astype('m8[s]').astype(int)
-    #        #print(time_delta)
+    #        #_logger.debug(time_delta)
 
 
     if f.shape [0] != data.shape [0]:
-        print('ERROR: shapes are not correct')
-        print(f.shape, time_lin.shape, data.shape )
+        _logger.debug('ERROR: shapes are not correct')
+        _logger.debug("%s %s %s", f.shape, time_lin.shape, data.shape)
         return
 
     # find neerest discrete frequency
@@ -1587,14 +1587,14 @@ def linefit2Points(time_lin, f, data, f1, f2, f_delta=None,  plot=False):
     f1_approx=np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))
     a=f-f2
     f2_approx=np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))
-    #print(f2_approx)
+    #_logger.debug(f2_approx)
 
     # find postion of maximum at freqeuency band
     dd=np.squeeze(data[f1_approx,:])
     fin1=np.where(dd==dd.max())[0][0]
     dd=np.squeeze(data[f2_approx,:])
     fin2=np.where(dd==dd.max())[0][0]
-    #print(fin1,time_lin, time_lin.size)
+    #_logger.debug(fin1,time_lin, time_lin.size)
 
     # define as point in time
     x1=time_lin[fin1]
@@ -1615,7 +1615,7 @@ def linefit2Points(time_lin, f, data, f1, f2, f_delta=None,  plot=False):
     #fit simple line.
     p1, p2=np.polyfit([y1 , y2], [x1, x2], 1)
     limit_mid=np.polyval([p1, p2], f)
-    #print(p2, time_delta)
+    #_logger.debug(p2, time_delta)
     limit_line1=np.polyval([p1, p2], f-f_delta)
     limit_line2=np.polyval([p1, p2], f+f_delta)
 
@@ -1639,7 +1639,7 @@ def find_max_along_line(time_lin, f, data, f1, f2, f_delta=.05, spreed=10,  plot
 
     timestamp=time_lin
     if isinstance(time_lin[0], np.datetime64):
-        print('time is numpy.datetime64')
+        _logger.debug('time is numpy.datetime64')
         time_lin=time_lin.astype('m8[s]').astype(int)
 
     if mode is None:
@@ -1647,11 +1647,11 @@ def find_max_along_line(time_lin, f, data, f1, f2, f_delta=.05, spreed=10,  plot
     if mode is 'free_limits' or mode is 'upper_limit':
         if line_left[0] > time_lin[0]:
             f_start=0
-            print(' left line > time0')
-            print(line_left[0] , time_lin[0])
+            _logger.debug(' left line > time0')
+            _logger.debug("%s %s", line_left[0] , time_lin[0])
         else:
-            print(' left line < time')
-            print(line_left[0] , time_lin[0])
+            _logger.debug(' left line < time')
+            _logger.debug("%s %s", line_left[0] , time_lin[0])
             a=line_left-time_lin[0]
             f_start=np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))[0]+1
     else:
@@ -1659,22 +1659,22 @@ def find_max_along_line(time_lin, f, data, f1, f2, f_delta=.05, spreed=10,  plot
         a=f-f1
         f_start=np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))[0]
 
-    #print(f_start)
+    #_logger.debug(f_start)
     if mode == 'free_limits' or mode == 'lower_limit':
         if line_right[-1] > time_lin[-1]:
-            print(' right line > time window')
-            print( line_right[-1] ,time_lin[-1])
+            _logger.debug(' right line > time window')
+            _logger.debug("%s %s", line_right[-1] ,time_lin[-1])
             a=line_right-time_lin[-1]
             f_end=np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))[0]-1
         else:
-            print(' right line < time window')
-            print( line_right[-1] ,time_lin[-1])
+            _logger.debug(' right line < time window')
+            _logger.debug("%s %s", line_right[-1] ,time_lin[-1])
             f_end=time_lin.size-2
     else:
         a=f-f2
         f_end=np.unravel_index(np.abs(a).argmin(),np.transpose(a.shape))[0]
 
-    #print(f_end)
+    #_logger.debug(f_end)
 
     if plot:
         plt.figure()
@@ -1700,17 +1700,17 @@ def find_max_along_line(time_lin, f, data, f1, f2, f_delta=.05, spreed=10,  plot
 
     STR['left_limit']=line_left
     STR['right_limit']=line_right
-    #print(flin[f_start:f_end].shape)
+    #_logger.debug(flin[f_start:f_end].shape)
     for i in enumerate(flin[f_start:f_end]):
         ii=f_start+i[0]
-        #print(i[0])
-        #print('ii',ii , type(i[0]), type(i) )
-        #print(round(line_left[ii]), round(line_right[ii]))
+        #_logger.debug(i[0])
+        #_logger.debug('ii',ii , type(i[0]), type(i) )
+        #_logger.debug(round(line_left[ii]), round(line_right[ii]))
         cut=cut_nparray(time_lin, line_left[ii], line_right[ii], verbose=False)
-        #print( cut[:data.shape[1]].shape, data.shape)
+        #_logger.debug( cut[:data.shape[1]].shape, data.shape)
         #plt.plot(data[i, cut], Color='grey', alpha=0.5)
-        #print(type(data[ii, cut]), type(cut[0]), type(ii))
-        #print(data[ii, cut[:data.shape[1]]])
+        #_logger.debug(type(data[ii, cut]), type(cut[0]), type(ii))
+        #_logger.debug(data[ii, cut[:data.shape[1]]])
         out=find_max_ts(data[ii, cut[:data.shape[1]]], smooth=True, spreed=spreed, plot=plot, verbose=False)
         #STR['cut_pos'].append(np.where(np.diff(cut) == True)[0][0])
         STR['out'].append(out[0][0])
@@ -1797,15 +1797,15 @@ def RAMSAC_regression_bootstrap(time, freq, time_lin_arg=None, plot=False,  **kw
     #self.clevs=self.clevs if self.clevs is not None else clevels(dd)
     if time_lin_arg is not None:
         time_lin=time_lin_arg
-        print('time lin is set')
+        _logger.debug('time lin is set')
     else:
-        print('create linear time axis')
+        _logger.debug('create linear time axis')
         time_lin=np.linspace(time.min(), time.max(), freq.size)
 
     RAMS_predicted_line=time_lin*RAMS_slope+ RAMS_intercept
 
 
-    print(RAMS_slope, RAMS_intercept)
+    _logger.debug("%s %s", RAMS_slope, RAMS_intercept)
     RAMS_out=boot.ci((time, freq), simple_RAMSAC_regression_estimator, method='bca' , **kwargs)
 
     # Robustly fit linear model with RANSAC algorithm

From 2cefaf5b68a8efeb29d54c2f93f344399a6ad6fa Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 18:24:42 -0500
Subject: [PATCH 04/30] chore: replace print with logging in m_spectrum_ph3

---
 .../local_modules/m_spectrum_ph3.py           | 214 +++++++++---------
 1 file changed, 112 insertions(+), 102 deletions(-)

diff --git a/src/icesat2_tracks/local_modules/m_spectrum_ph3.py b/src/icesat2_tracks/local_modules/m_spectrum_ph3.py
index f904b63c..2dfaad17 100644
--- a/src/icesat2_tracks/local_modules/m_spectrum_ph3.py
+++ b/src/icesat2_tracks/local_modules/m_spectrum_ph3.py
@@ -1,3 +1,4 @@
+import logging
 
 import numpy as np
 from numpy import pi
@@ -12,6 +13,9 @@
 except ImportError:
     pass
 
+_logger = logging.getLogger(__name__)
+
+
 def calc_freq(self):
     """ calculate array of spectral variable (frequency or
             wavenumber) in cycles per unit of L """
@@ -71,18 +75,22 @@ def spicke_remover(data, nstd=20.0, spreed=500.0, max_loops=10.0 , verbose=False
         if  nstd* data.std() < np.max(np.abs(data2)):
             act_flag=True
             if verbose:
-                print('true: '+ str(nstd* datastd) +' < '+str( np.max(np.abs(data)) ) )
+                _logger.debug(
+                    'true: %s < %s',
+                    nstd * datastd,
+                    np.max(np.abs(data))
+                )
             data2=M.spickes_to_mean(data2, nloop=0, spreed=spreed, gaussian=False)
             looper_count+=1
         else:
             if verbose:
-                print('False: '+ str(nstd* datastd) +' > '+str( np.max(np.abs(data)) ) )
+                _logger.debug('False: %s > %s', nstd * datastd , np.max(np.abs(data)))
             peak_remove=False
 
         if looper_count > max_loops:
             peak_remove=False
             if verbose:
-                print('stoped by max#')
+                _logger.debug('stoped by max#')
 
 
     if verbose:
@@ -109,14 +117,14 @@ def __init__(self,data,dt, win_flag=1,pwelch=False, verbose=False):
 
         if win_flag:
             if verbose:
-                print('window')
+                _logger.debug('window')
             MT.write_log(self.hist, 'window')
             self.win_flag=win_flag
             self.phi=np.copy(self.data[:])
             self.phi*=win*np.sqrt(factor)
         else:
             if verbose:
-                print('no window')
+                _logger.debug('no window')
             MT.write_log(self.hist, 'no window')
             self.win_flag=0
             self.phi =np.copy(self.data[:])
@@ -141,11 +149,13 @@ def __init__(self,data,dt, win_flag=1,pwelch=False, verbose=False):
 
     def parceval(self):
 
-        print('Parcevals Theorem:')
-        print('variance of unweighted timeseries: ',self.data.var())
-        print('variance of weighted timeseries: ',self.phi.var() if self.win_flag is 1 else 'data not windowed')
-        print('variance of weighted timeseries: ',self.phi.var() )
-        print('variance of the Spectrum: ',self.var)
+        _logger.debug('Parcevals Theorem:')
+        _logger.debug('variance of unweighted timeseries: %s',self.data.var())
+        _logger.debug(
+            'variance of weighted timeseries: %s',
+            self.phi.var() if self.win_flag is 1 else 'data not windowed')
+        _logger.debug('variance of weighted timeseries: %s',self.phi.var() )
+        _logger.debug('variance of the Spectrum: %s',self.var)
 
 
 
@@ -165,7 +175,7 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
         if prewhite is None:
             data = np.array(data_org)    # field to be analyzed
         elif prewhite ==1:
-            print('prewhite =1')
+            _logger.debug('prewhite =1')
             data=np.gradient(np.array(data_org)  , axis=1)
         elif prewhite ==2:
             data=np.gradient(np.gradient(np.array(data_org), axis=1), axis=1)
@@ -182,7 +192,7 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
             M.echo_dt(L)
             L=L.item().total_seconds()
         #else:
-            #print('unknown L type')
+            #_logger.debug('unknown L type')
 
         ov=int(np.round(L/2)) if ov is None else ov
 
@@ -206,8 +216,8 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
 
         # exclude 0 freq.
         self.f=self.f[1:]
-        #print('fsize', self.f.size)
-        #print(data.size, L, ov, int(L-ov) )
+        #_logger.debug('fsize', self.f.size)
+        #_logger.debug(data.size, L, ov, int(L-ov) )
         nbin=int(np.floor(data_size/(L-ov)))-1
         self.nbin=nbin
         if save_chunks:
@@ -217,7 +227,7 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
         specs=np.empty([data_dim, int(nbin),self.f.size])
         self.mom_list=list()
         k=0
-        #print('iter range', np.arange(0,data.size,int(L-ov)))
+        #_logger.debug('iter range', np.arange(0,data.size,int(L-ov)))
         for i in np.arange(0,data_size-int(L-ov)+1,int(L-ov)):
 
             if (plot_chunks) and (i >= data_size-6*int(L-ov)):
@@ -226,18 +236,18 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
             self.phi=data[:,int(i):int(i+L)]
 
             #self.ii=np.append(self.ii,[i,i+L])
-            #print(self.phi.max())
+            #_logger.debug(self.phi.max())
 
-            #print(self.phi.mean())
-            #print(self.phi.shape)
-            #print('i',int(i), int(i+L))
-            #print(chunk.size, l)
+            #_logger.debug(self.phi.mean())
+            #_logger.debug(self.phi.shape)
+            #_logger.debug('i',int(i), int(i+L))
+            #_logger.debug(chunk.size, l)
             if int(i+L) <= data_size-1:
                 if save_chunks:
                     chunks[:, k,:]=self.phi
 
                 #normalizing
-                #print('normalizing')
+                #_logger.debug('normalizing')
                 #self.phi=signal.detrend(self.phi,axis=1)*win
                 #self.phi=(self.phi.T/np.std(self.phi, axis=1)).T
 
@@ -250,7 +260,7 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
                     plt.plot(self.phi)
 
                 X=self.calc_spectral_density()
-                #print(np.shape(X))
+                #_logger.debug(np.shape(X))
                 self.mom=self.calc_moments(X)
 
                 self.mom_list.append(self.mom)
@@ -262,17 +272,17 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
 
             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(data.size))
+                    _logger.debug('end of TS is reached')
+                    _logger.debug('last spec No: %s', last_k)
+                    _logger.debug('spec container: %s ', specs.shape)
+                    _logger.debug('last used Timestep: %s', last_used_TS)
+                    _logger.debug('length of TS %s', data.size)
 
             k+=1
 
-        #print('last k', last_k)
-        #print('len mom_list', len(self.mom_list)  )
-        #print('nbin', nbin)
+        #_logger.debug('last k', last_k)
+        #_logger.debug('len mom_list', len(self.mom_list)  )
+        #_logger.debug('nbin', nbin)
 
         if save_chunks:
             self.chunks=chunks
@@ -281,13 +291,13 @@ def __init__(self,data_org,dt, L=None, ov=None,window=None, save_chunks=False, p
         self.moments_stack=dict()
         self.moments_est=dict()
         for k in self.mom.keys():
-            #print(k)
+            #_logger.debug(k)
             stack=np.empty([nbin,self.f.size])
             for i in range(len(self.mom_list)):
                 #stack=np.vstack((stack,I[k])) #stack them
-                #print(i, k)
+                #_logger.debug(i, k)
                 stack[i,:]=self.mom_list[i][k] #stack them
-                #print(stack.shape)
+                #_logger.debug(stack.shape)
             #mom_est[k]=stack.mean(axis=0)
             #mean them and decide prewhitheing or nots
             if prewhite is None:
@@ -382,12 +392,12 @@ def cal_MEM(self, theta=None, flim=(0.01, .5)):
 
     #def parceval(self):
         ## method not checked jet
-    #    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() )
+    #    _logger.debug('Parcevals Theorem:')
+    #    _logger.debug('variance of unweighted timeseries: ',self.data.var())
+    #    _logger.debug('mean variance of timeseries chunks: ',self.chunks.var(axis=1).mean() if self.save_chunks is True else 'data not saved')
+        #_logger.debug('variance of weighted timeseries: ',self.phi.var() )
         #self.calc_var(self)
-    #    print('variance of the pwelch Spectrum: ',self.var)
+    #    _logger.debug('variance of the pwelch Spectrum: ',self.var)
 
     #def calc_var(self):
 
@@ -410,7 +420,7 @@ def __init__(self,data,dt,L=None, ov=None,window=None, save_chunks=False, plot_c
         if prewhite is None:
             self.data = data      # field to be analyzed
         elif prewhite ==1:
-            print('prewhite =1')
+            _logger.debug('prewhite =1')
             self.data=np.gradient(data)
         elif prewhite ==2:
             self.data=np.gradient(np.gradient(data))
@@ -425,7 +435,7 @@ def __init__(self,data,dt,L=None, ov=None,window=None, save_chunks=False, plot_c
             echo_dt(L)
             L=L.item().total_seconds()
         #else:
-            #print('unknown L type')
+            #_logger.debug('unknown L type')
 
         ov=int(np.round(L/2)) if ov is None else ov
 
@@ -445,9 +455,9 @@ def __init__(self,data,dt,L=None, ov=None,window=None, save_chunks=False, plot_c
             self.neven = True
         #calculate freq
         calc_freq(self)
-        #print(data.size, L, ov, int(L-ov) )
+        #_logger.debug(data.size, L, ov, int(L-ov) )
         nbin=int(np.floor(dsize/(L-ov)))
-        #print(nbin)
+        #_logger.debug(nbin)
         if periodogram:
             self.nbin=nbin
             self.dt_periodogram=L-ov
@@ -456,13 +466,13 @@ def __init__(self,data,dt,L=None, ov=None,window=None, save_chunks=False, plot_c
             chunks=np.empty([int(nbin),int(L)])
 
         specs=np.empty([int(nbin),self.f.size])
-        #print(chunks.shape)
+        #_logger.debug(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)))
+        #_logger.debug('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)):
@@ -471,12 +481,12 @@ def __init__(self,data,dt,L=None, ov=None,window=None, save_chunks=False, plot_c
             self.phi=data[int(i):int(i+L)]
 
             #self.ii=np.append(self.ii,[i,i+L])
-            #print(self.phi.max())
+            #_logger.debug(self.phi.max())
 
-            #print(self.phi.mean())
-            #print(self.phi.shape)
-            #print('i',int(i), int(i+L))
-            #print(chunk.size, l)
+            #_logger.debug(self.phi.mean())
+            #_logger.debug(self.phi.shape)
+            #_logger.debug('i',int(i), int(i+L))
+            #_logger.debug(chunk.size, l)
             if int(i+L) <= data.size-1:
                 if save_chunks:
                     chunks[k,:]=self.phi
@@ -496,11 +506,11 @@ def __init__(self,data,dt,L=None, ov=None,window=None, save_chunks=False, plot_c
                 del(self.spec)
             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')
+                    _logger.debug('end of TS is reached')
+                    _logger.debug('last spec No: '+str(last_k))
+                    _logger.debug('spec container: '+str(specs.shape))
+                    _logger.debug('last used Timestep: '+str(last_used_TS))
+                    _logger.debug('length of TS '+ str(dsize) +'ms')
 
             k+=1
 
@@ -529,12 +539,12 @@ def error(self, ci=0.95):
         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() )
+        _logger.debug('Parcevals Theorem:')
+        _logger.debug('variance of unweighted timeseries: ',self.data.var())
+        _logger.debug('mean variance of timeseries chunks: ',self.chunks.var(axis=1).mean() if self.save_chunks is True else 'data not saved')
+        #_logger.debug('variance of weighted timeseries: ',self.phi.var() )
         #self.calc_var(self)
-        print('variance of the pwelch Spectrum: ',self.var)
+        _logger.debug('variance of the pwelch Spectrum: ',self.var)
 
     def calc_var(self):
         """ Compute total variance from spectrum """
@@ -547,32 +557,32 @@ def __init__(self, data, dt, dt_unit=None, timestamp=None, L=None, ov=None, subL
         self.hist='Subsampled Spectogram'
         L=int(np.round(data.size/10)) if L is None else L
         if type(L) != int:
-            #print('Length = ')
+            #_logger.debug('Length = ')
             M.echo_dt(L)
             self.write_log('Length = '+ M.echo_dt(L, as_string=True))
             L=int(L.item().total_seconds())
         else:
-            print('unknown L type')
+            _logger.debug('unknown L type')
             self.write_log('Length = '+ 'unknown L type')
 
         subL=int(np.round(L/10)) if subL is None else subL
         if type(subL) != int:
-            #print('Subsample Length= ')
+            #_logger.debug('Subsample Length= ')
             #M.echo_dt(subL)
             self.write_log('Subsample Length= '+ M.echo_dt(subL, as_string=True))
             subL=int(subL.item().total_seconds())
         else:
-            #print('unknown subL type')
+            #_logger.debug('unknown subL type')
             self.write_log('Length = '+ 'unknown subL type')
 
         ov=int(np.round(L/2.0)) if ov is None else ov
         if type(ov) != int:
-            #print('overlab Length= ')
+            #_logger.debug('overlab Length= ')
             #M.echo_dt(ov)
             ov=int(ov.item().total_seconds())
         else:
             pass
-            #print('ov type:', type(ov))
+            #_logger.debug('ov type:', type(ov))
 
         self.n = subL
         if window is None:
@@ -604,21 +614,21 @@ def __init__(self, data, dt, dt_unit=None, timestamp=None, L=None, ov=None, subL
 
         n_specs=[]
         k=0
-        print('subL', subL)
-        print('L', L)
-        print(data_size_adjust)
-        #print(specs.shape, np.arange(0,data.size,int(L-ov)), np.arange(0,data.size-L,int(L-ov)).shape, )
-        #print(specs.shape,np.arange(0,data_size_adjust-int(L-ov)+1,int(L-ov)) )
+        _logger.debug('subL %s', subL)
+        _logger.debug('L %s', L)
+        _logger.debug("%s", data_size_adjust)
+        #_logger.debug(specs.shape, np.arange(0,data.size,int(L-ov)), np.arange(0,data.size-L,int(L-ov)).shape, )
+        #_logger.debug(specs.shape,np.arange(0,data_size_adjust-int(L-ov)+1,int(L-ov)) )
         for i in np.arange(0,data_size_adjust-int(L-ov)+1,int(L-ov)):
 
             phi=data[int(i):int(i+L)]
             #self.ii=np.append(self.ii,[i,i+L])
-            #print(self.phi.max())
+            #_logger.debug(self.phi.max())
 
-            #print(self.phi.mean())
-            #print(phi.shape)
-            #print('i',i, i+L, data.size, i+L <= data.size)
-            #print(chunk.size, l)
+            #_logger.debug(self.phi.mean())
+            #_logger.debug(phi.shape)
+            #_logger.debug('i',i, i+L, data.size, i+L <= data.size)
+            #_logger.debug(chunk.size, l)
             if i+L <= data.size:
 
                 if plot_chunks:
@@ -642,7 +652,7 @@ def __init__(self, data, dt, dt_unit=None, timestamp=None, L=None, ov=None, subL
                 del(self.spec_est)
             elif i+L > data.size:
                 phi=data[-L:]
-                #print('phi shape',phi.shape )
+                #_logger.debug('phi shape',phi.shape )
                 if plot_chunks:
                     plt.plot(phi)
                 if save_chunks:
@@ -663,8 +673,8 @@ def __init__(self, data, dt, dt_unit=None, timestamp=None, L=None, ov=None, subL
 
                 del(self.spec_est)
 
-            #print(k)
-            #print('------')
+            #_logger.debug(k)
+            #_logger.debug('------')
             k+=1
 
 
@@ -686,12 +696,12 @@ def __init__(self, data, dt, dt_unit=None, timestamp=None, L=None, ov=None, subL
             dt_unit='s'
             dt_timedelta=np.timedelta64(dt,dt_unit)
 
-        #print('sample resolution:')
+        #_logger.debug('sample resolution:')
         #M.echo_dt(dt_timedelta)
         self.write_log('basic sample resolution:'+ M.echo_dt(dt_timedelta, as_string=True))
 
         timeres=np.timedelta64(int(self.dt_periodogram), 's')
-        #print('time resolution:')
+        #_logger.debug('time resolution:')
         #M.echo_dt(timeres)
         self.write_log('Spectogram time res:'+ M.echo_dt(timeres, as_string=True))
 
@@ -702,21 +712,21 @@ def __init__(self, data, dt, dt_unit=None, timestamp=None, L=None, ov=None, subL
             start_time=timestamp[0]
             end_time=timestamp[-1]
 
-        #print('Periodogram starttime and endtime:')
-        #print(start_time)
-        #print(end_time)
+        #_logger.debug('Periodogram starttime and endtime:')
+        #_logger.debug(start_time)
+        #_logger.debug(end_time)
         self.write_log('Spectogram starttme:'+ str(start_time))
         self.write_log('            endtime:'+ str(end_time))
 
-        #print(type(start_time), type(L), type(end_time), type(dt_timedelta), print(timeres) )
+        #_logger.debug(type(start_time), type(L), type(end_time), type(dt_timedelta), _logger.debug(timeres) )
         time = np.arange(start_time+int(L/2), end_time+dt_timedelta, timeres)
-        #print(time)
+        #_logger.debug(time)
         if time.shape[0] != self.data.shape[0]:
             time=time[0:self.data.shape[0]]
         self.time=time
         self.timeres=timeres
         self.dt_unit=dt_unit
-        #print(self.time)
+        #_logger.debug(self.time)
         self.time_dict=create_timeaxis_collection(self.time)
         self.write_log('created timestamp collection')
 
@@ -726,24 +736,24 @@ def write_log(self, s, verbose=False):
         from m_tools_ph3 import write_log
         self.hist=write_log(self.hist, s, verbose=verbose)
     def log(self):
-        print('.hist variable')
-        print(self.hist)
+        _logger.debug('.hist variable')
+        _logger.debug("%s", self.hist)
     def power_anomalie(self, clim=None):
         dd=10*np.log10(self.data[:,:])
-        #print(dd)
+        #_logger.debug(dd)
         #if anomalie is True:
         #    dd_tmp=dd.mean(axis=0).repeat(self.time.size-1)
         #        dd=dd- dd_tmp.reshape(self.fs.size,self.time.size-1).T
 
         self.data_power_mean=np.nanmedian(dd, axis=0) if clim is None else 10*np.log10(clim)
         dd_tmp=self.data_power_mean.repeat(self.time.size)
-        print(self.data_power_mean.shape)
-        print(self.f.size,self.time.size)
+        _logger.debug("%s", self.data_power_mean.shape)
+        _logger.debug("%s %s", self.f.size,self.time.size)
         self.data_power_ano=dd- dd_tmp.reshape(self.f.size,self.time.size).T
 
     def anomalie(self, clim=None):
         #dd=
-        #print(dd)
+        #_logger.debug(dd)
         #if anomalie is True:
         #    dd_tmp=dd.mean(axis=0).repeat(self.time.size-1)
         #        dd=dd- dd_tmp.reshape(self.fs.size,self.time.size-1).T
@@ -765,10 +775,10 @@ def __init__(self,data,dt,dt_unit=None, timestamp=None,L=None, ov=None,window=No
             dt_unit='s'
             dt_timedelta=np.timedelta64(dt,dt_unit)
 
-        print('sample resolution:')
+        _logger.debug('sample resolution:')
         M.echo_dt(dt_timedelta)
         timeres=np.timedelta64(int(self.dt_periodogram), dt_unit)
-        print('time resolution:')
+        _logger.debug('time resolution:')
         M.echo_dt(timeres)
 
         if timestamp is None:
@@ -778,13 +788,13 @@ def __init__(self,data,dt,dt_unit=None, timestamp=None,L=None, ov=None,window=No
             start_time=timestamp[0]
             end_time=timestamp[-1]
 
-        print('Periodogram starttime and endtime:')
-        print(start_time)
-        print(end_time)
+        _logger.debug('Periodogram starttime and endtime:')
+        _logger.debug("%s", start_time)
+        _logger.debug("%s", end_time)
 
 
         time = np.arange(start_time+L/2, end_time+dt_timedelta, timeres)
-        #print(time)
+        #_logger.debug(time)
         if time.shape[0] != self.data.shape[0]:
             time=time[0:self.data.shape[0]]
         self.time=time
@@ -795,8 +805,8 @@ def __init__(self,data,dt,dt_unit=None, timestamp=None,L=None, ov=None,window=No
         #self.time=np.arange(,nin*)
     def save_data(self, path=None, S=None):
         P=save_data_periodogram(self , S=S)
-        print(P.meta)
-        print('constructed class for saving')
+        _logger.debug("%s", P.meta)
+        _logger.debug('constructed class for saving')
         save_file(P, path)
 
 
@@ -951,7 +961,7 @@ def peak_angle(data, freq,fpos,  max_jump=5, smooth_l=5):
     f_bool=M.cut_nparray(freq, fpos[0], fpos[-1])
     dregree_series=data[f_bool,:].mean(0)
     #plt.plot(dregree_series)
-    #print(dregree_series)
+    #_logger.debug(dregree_series)
 
     a=M.find_max_ts(dregree_series,smooth=True, spreed=smooth_l, plot=False, jump=max_jump,verbose=False)
     if len(a[0]) ==0:
@@ -966,7 +976,7 @@ def save_file( data, path):
     outfile=path
     f = open(outfile, 'wb')
     pickle.dump(data,f, pickle.HIGHEST_PROTOCOL)
-    print('saved to:',outfile)
+    _logger.debug('saved to: %s',outfile)
     f.close()
 
 ## ceasars funcitons

From 39babe5fbedfde71583a17cc6763157a431a5e0b Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 18:24:52 -0500
Subject: [PATCH 05/30] chore: replace print with logging in m_tools_ph3.py

---
 .../local_modules/m_tools_ph3.py              | 56 ++++++++++---------
 1 file changed, 31 insertions(+), 25 deletions(-)

diff --git a/src/icesat2_tracks/local_modules/m_tools_ph3.py b/src/icesat2_tracks/local_modules/m_tools_ph3.py
index 85122738..d459fe82 100644
--- a/src/icesat2_tracks/local_modules/m_tools_ph3.py
+++ b/src/icesat2_tracks/local_modules/m_tools_ph3.py
@@ -1,3 +1,5 @@
+import logging
+
 import matplotlib
 #matplotlib.use('Agg')
 import matplotlib.pyplot as plt
@@ -10,6 +12,8 @@
 #from matplotlib import dates
 #import datetime as DT
 
+_logger = logging.getLogger(__name__)
+
 
 def dt_form_timestamp(timestamp, unit=None):
     unit='h' if unit is None else unit
@@ -99,9 +103,9 @@ def fake_2d_data(verbose=True, timeaxis=False):
     z3= 1/(sigma * np.sqrt(2 * np.pi)) * np.exp( - (YY - mu)**2 / (2 * sigma**2) )
     z3=z3/z3.max()
     if verbose:
-        print('x' , x.shape)
-        print('y' , y.shape)
-        print('z' , z3.shape)
+        _logger.debug('x %s' , x.shape)
+        _logger.debug('y %s' , y.shape)
+        _logger.debug('z %s' , z3.shape)
 
         plt.contourf(x, y,z2/2+z3/2)
         plt.colorbar()
@@ -120,7 +124,7 @@ def pickle_save(name, path, data, verbose=True):
     with open(full_name, 'wb') as f2:
         pickle.dump(data, f2)
     if verbose:
-        print('save at: ',full_name)
+        _logger.debug('save at: %s',full_name)
 
 def pickle_load(name, path, verbose=True):
     #if not os.path.exists(path):
@@ -131,7 +135,7 @@ def pickle_load(name, path, verbose=True):
         data=pickle.load(f)
 
     if verbose:
-        print('load from: ',full_name)
+        _logger.debug('load from: %s',full_name)
     return data
 
 
@@ -144,7 +148,7 @@ def json_save(name, path, data, verbose=False, return_name=False):
     with open(full_name, 'w') as outfile:
         json.dump(data, outfile, indent=2)
     if verbose:
-        print('save at: ',full_name)
+        _logger.debug('save at: %s',full_name)
     if return_name:
         return full_name_root
     else:
@@ -170,7 +174,7 @@ def default(self, obj):
     with open(full_name, 'w') as outfile:
         json.dump(data, outfile, cls=CustomJSONizer, indent=2)
     if verbose:
-        print('save at: ',full_name)
+        _logger.debug('save at: %s',full_name)
     if return_name:
         return full_name_root
     else:
@@ -184,7 +188,7 @@ def json_load(name, path, verbose=False):
     with open(full_name, 'r') as ifile:
         data=json.load(ifile)
     if verbose:
-        print('loaded from: ',full_name)
+        _logger.debug('loaded from: %s', full_name)
     return data
 
 def h5_load(name, path, verbose=False):
@@ -201,7 +205,7 @@ def h5_load_v2(name, path, verbose=False):
 
     h5f = h5py.File(path + name + '.h5','r')
     if verbose:
-        print(h5f.keys())
+        _logger.debug("%s", h5f.keys())
 
     data_dict=dict()
     for k, I in h5f.iteritems():
@@ -229,7 +233,7 @@ def h5_save(name, path, data_dict, verbose=False, mode='w'):
     store.close()
 
     if verbose:
-        print('saved at: ' +full_name)
+        _logger.debug('saved at: %s', full_name)
 
 
 
@@ -251,7 +255,7 @@ def h5_save(name, path, data_dict, verbose=False, mode='w'):
     store.close()
 
     if verbose:
-        print('saved at: ' +full_name)
+        _logger.debug('saved at: %s', full_name)
 
 
 def load_pandas_table_dict(name , save_path):
@@ -262,8 +266,8 @@ def load_pandas_table_dict(name , save_path):
 
     return_dict=dict()
     with HDFStore(save_path+'/'+name+'.h5') as store:
-        #print(store)
-        #print(store.keys())
+        #_logger.debug(store)
+        #_logger.debug(store.keys())
         for k in store.keys():
             return_dict[k[1:]]=store.get(k)
 
@@ -296,9 +300,9 @@ def write_log(hist, string, verbose=False, short=True , date=True):
         message='\n '.ljust(2)+' '+string
 
     if verbose== True:
-        print(message)
+        _logger.debug(message)
     elif verbose == 'all':
-        print(hist+message)
+        _logger.debug(hist+message)
     return hist+message
 
 def add_line_var(ss, name, var):
@@ -320,9 +324,9 @@ def write_variables_log(hist, var_list, locals, verbose=False, date=False):
         message='\n '.ljust(5)+' '+stringg
 
     if verbose== True:
-        print(message)
+        _logger.debug(message)
     elif verbose == 'all':
-        print(hist+message)
+        _logger.debug(hist+message)
     return hist+message
 
 
@@ -333,7 +337,7 @@ def save_log_txt(name, path, hist,verbose=False):
     with open(full_name, 'w') as ifile:
         ifile.write(str(hist))
     if verbose:
-        print('saved at: ',full_name)
+        _logger.debug('saved at: %s',full_name)
 
 def load_log_txt(name, path):
     import glob
@@ -345,7 +349,7 @@ def load_log_txt(name, path):
 
 def shape(a):
 	for i in a:
-		print(i.shape)
+		_logger.debug(i.shape)
 
 def find_O(a, case='round'):
     if case=='round':
@@ -368,11 +372,13 @@ def find_O(a, case='round'):
         raise Warning('no propper case')
 
 def stats(a):
-	print('shape' , a.shape)
-	print('Nans',np.sum(np.isnan(a)))
-	print('max' , np.nanmax(a))
-	print('min' ,np.nanmin(a))
-	print('mean' ,np.nanmean(a))
+	_logger.debug('shape %s' , a.shape)
+	_logger.debug('Nans %s',np.sum(np.isnan(a)))
+	_logger.debug('max %s' , np.nanmax(a))
+	_logger.debug('min %s' ,np.nanmin(a))
+	_logger.debug('mean %s' ,np.nanmean(a))
 
 def stats_format(a, name=None):
-	print('Name:', str(name),'   Shape:' , a.shape ,'   NaNs:',np.sum(np.isnan(a)),' max:', np.nanmax(a),' min', np.nanmin(a),' mean:', np.nanmean(a))
+	_logger.debug('Name: %s   Shape: %s   NaNs: %s    max: %s    min: %s    mean: %s',
+                  str(name), a.shape , np.sum(np.isnan(a)), np.nanmax(a),
+                  np.nanmin(a), np.nanmean(a))

From 5d220d354ca5fe762eb94d0b67d7893c4880d41e Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 16:44:34 -0400
Subject: [PATCH 06/30] fix: update formatting in logging

---
 src/icesat2waves/local_modules/m_general_ph3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 750523b6..31cc322f 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1392,9 +1392,9 @@ def compose_ts(self, ts, name, time=None):
                     return -1
 
                 _logger.debug('comp %s', comp.shape)
-                _logger.debug('ts %s', ts[i+span[0]:i+span[1]].shape)
+                _logger.debug('ts %s', ts[i + span[0]:i + span[1]].shape)
                 _logger.debug("%s %s %s", i, span[0], span[1])
-                comp=np.vstack((comp,ts[i+span[0]:i+span[1]]))
+                comp = np.vstack((comp, ts[i + span[0]:i + span[1]]))
 
             comp = np.delete(comp, 0, 0)
             comp1 = CompositeData(comp, self.weigthing)

From 397c3005724b366f414155c883df5dcd0affb47a Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 17:44:53 -0400
Subject: [PATCH 07/30] fix: reformat debugs from prints

---
 src/icesat2waves/local_modules/m_tools_ph3.py | 23 ++++++++++++-------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py
index 9b2c2203..d99848db 100644
--- a/src/icesat2waves/local_modules/m_tools_ph3.py
+++ b/src/icesat2waves/local_modules/m_tools_ph3.py
@@ -313,13 +313,20 @@ def find_O(a, case="round"):
 
 
 def stats(a):
-	_logger.debug("shape %s" , a.shape)
-	_logger.debug("Nans %s",np.sum(np.isnan(a)))
-	_logger.debug("max %s" , np.nanmax(a))
-	_logger.debug("min %s" ,np.nanmin(a))
-	_logger.debug("mean %s" ,np.nanmean(a))
+    _logger.debug(
+        f"shape: %s\n"
+        f"Nans: %s\n"
+        f"max: %s\n"
+        f"min: %s\n"
+        f"mean: %s"
+    , a.shape, np.sum(np.isnan(a)), np.nanmax(a), np.nanmin(a), np.nanmean(a))
+
 
 def stats_format(a, name=None):
-	_logger.debug("Name: %s   Shape: %s   NaNs: %s    max: %s    min: %s    mean: %s",
-                  str(name), a.shape , np.sum(np.isnan(a)), np.nanmax(a),
-                  np.nanmin(a), np.nanmean(a))
+    _logger.debug("Name: %s\n"
+                  "   Shape: %s\n"
+                  "   NaNs: %s\n"
+                  "   max: %s\n"
+                  "   min: %s\n"
+                  "   mean: %s",
+                  name, a.shape, np.sum(np.isnan(a)), np.nanmax(a), np.nanmin(a), np.nanmean(a))

From 044db609c949a3fe0fdf06bc1f825ab7fb3cb762 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 17:54:36 -0400
Subject: [PATCH 08/30] revert change to boot.ci call

---
 src/icesat2waves/local_modules/m_general_ph3.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 31cc322f..cf709d1d 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1748,7 +1748,8 @@ def RAMSAC_regression_bootstrap(time, freq, time_lin_arg=None, plot=False, **kwa
     RAMS_predicted_line = time_lin * RAMS_slope + RAMS_intercept
 
     _logger.debug("%s %s", RAMS_slope, RAMS_intercept)
-    RAMS_out=boot.ci((time, freq), simple_RAMSAC_regression_estimator, method="bca", **kwargs
+    RAMS_out = boot.ci(
+        (time, freq), simple_RAMSAC_regression_estimator, method="bca", **kwargs
     )
 
     slope = np.append(RAMS_slope, RAMS_out[:, 0])

From 59112946875e2e7fd1cbbdd940a9e5b854a7468b Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 17:56:28 -0400
Subject: [PATCH 09/30] fix: replace evaluated strings

---
 src/icesat2waves/local_modules/m_spectrum_ph3.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_spectrum_ph3.py b/src/icesat2waves/local_modules/m_spectrum_ph3.py
index 2872ee35..737cd4b4 100644
--- a/src/icesat2waves/local_modules/m_spectrum_ph3.py
+++ b/src/icesat2waves/local_modules/m_spectrum_ph3.py
@@ -470,10 +470,10 @@ def __init__(
             else:
                 if plot_chunks:
                     _logger.debug("end of TS is reached")
-                    _logger.debug("last spec No: " + str(last_k))
-                    _logger.debug("spec container: " + str(specs.shape))
-                    _logger.debug("last used Timestep: " + str(last_used_TS))
-                    _logger.debug("length of TS " + str(dsize) + "ms")
+                    _logger.debug("last spec No: %s", last_k)
+                    _logger.debug("spec container: %s", specs.shape)
+                    _logger.debug("last used Timestep: %s", last_used_TS)
+                    _logger.debug("length of TS %s ms", dsize)
 
             k += 1
 

From 063c21e58c9dd8e18070faeea744fbed9a134abb Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 17:58:16 -0400
Subject: [PATCH 10/30] chore: remove unused from __future__ import

---
 src/icesat2waves/local_modules/m_colormanager_ph3.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_colormanager_ph3.py b/src/icesat2waves/local_modules/m_colormanager_ph3.py
index 2fa4d5f7..6e35e456 100644
--- a/src/icesat2waves/local_modules/m_colormanager_ph3.py
+++ b/src/icesat2waves/local_modules/m_colormanager_ph3.py
@@ -1,5 +1,4 @@
 from __future__ import unicode_literals
-from __future__ import print_function
 from __future__ import division
 
 from matplotlib.colors import LinearSegmentedColormap

From f33a6fb2ecf1ebb390a4456af8a8f73ba3f83f57 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 18:09:00 -0400
Subject: [PATCH 11/30] make updates from PR review

add more context to debug messages

Co-Authored-By: Carlos Paniagua <68481491+cpaniaguam@users.noreply.github.com>
---
 .../local_modules/m_general_ph3.py            | 33 ++++++++++---------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index cf709d1d..640350a7 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -53,8 +53,8 @@ def colormaps(self, n, gamma=None):
         )
 
     def show(self):
-        for key in self.__dict__.keys():
-            _logger.debug(key)
+        for key, value in self.__dict__.items():
+            _logger.debug("Key: %s, Value: %s", key, value)
 
 
 class FigureAxisXY:
@@ -296,7 +296,7 @@ def linear(self):
         self.F.ax.set_yscale("log", nonposy="clip")
         tt = self.time.astype(DT.datetime)
         self.cs = plt.contourf(tt[:-2], self.fs[:], dd, self.clevs, cmap=self.cmap)
-        _logger.debug("%s", self.clevs)
+        _logger.debug("clevels: %s", self.clevs)
         plt.ylabel(f"Power db({self.data_unit}^2/{self.sample_unit})")
         plt.xlabel(f"f  ({self.sample_unit})")
         self.cbar = plt.colorbar(self.cs, pad=0.01)
@@ -341,10 +341,11 @@ def power(self, anomalie=False):
         self.F.ax.set_yscale("log", nonposy="clip")
         tt = self.time.astype(DT.datetime)
 
-        _logger.debug("%s %s", tt[:-1].shape, self.fs[:].shape,dd.T.shape)
+        _logger.debug("Shape of tt: %s, Shape of fs: %s, Shape of dd.T: %s",
+                      tt[:-1].shape, self.fs[:].shape, dd.T.shape)
         self.cs = plt.contourf(tt[:-1], self.fs[:], dd.T, self.clevs, cmap=self.cmap)
         self.x = np.arange(0, tt[:-1].size)
-        _logger.debug("%s", self.clevs)
+        _logger.debug("clevels: %s", self.clevs)
         plt.xlabel("Time")
         plt.ylabel(f"f  ({self.sample_unit})")
         self.cbar = plt.colorbar(self.cs, pad=0.01)
@@ -702,7 +703,7 @@ def __init__(
         self.min = np.nanmin(data[freq_sel_bool, :])
         self.max = np.nanmax(data[freq_sel_bool, :])
         if verbose:
-            _logger.debug(str(self.min), str(self.max))
+            _logger.debug("min: %s, max: %s", self.min, self.max)
 
         self.ylabels = np.arange(10, 100, 20)
         self.data_type = data_type
@@ -886,21 +887,21 @@ def save_anyfig(fig, name=None, path=None):
 def read_cdo(file):
     cdo = Cdo()
     G = cdo.readCdf(file).variables
-    _logger.debug(G.keys())
+    _logger.debug("keys in G: %s", list(G.keys()))
     return G
 
 
 def build_timestamp(time, unit, start, verbose=True):
     timestamp = np.datetime64(start) + time[:].astype("m8[" + unit + "]")
     if verbose:
-        _logger.debug(timestamp)
+        _logger.debug("timestamp: %s", timestamp)
     return timestamp
 
 
 def build_timestamp_v2(time, unit, start, verbose=True):
     timestamp = np.datetime64(start) + time[:].astype("datetime64[s]")
     if verbose:
-        _logger.debug(timestamp)
+        _logger.debug("timestamp: %s", timestamp)
     return timestamp
 
 
@@ -912,7 +913,7 @@ def cut_nparray(var, low, high, verbose=False):
         if high > var[-1]:
             if verbose:
                 _logger.debug('out of upper limit!')
-                _logger.debug("%s > %s", high, var[-1])
+                _logger.debug("high: %s, last var: %s", high, var[-1])
         return (var >= low) & (var <= high)
 
     elif high < low:
@@ -1014,7 +1015,7 @@ def detrend(data, od=None, x=None, plot=False, verbose=False):
         stats["polynom order"] = od
         stats["polyvals"] = px
     if verbose:
-        _logger.debug(stats)
+        _logger.debug("stats: %s", stats)
     return d_detrend / np.nanstd(d_detrend), stats
 
 
@@ -1331,7 +1332,7 @@ def corse_iter(self, dt, unit=None):
         for s in span_new:
             span.append(int(np.floor(s)))
 
-        _logger.debug(span)
+        _logger.debug("span: %s", span)
         self.iter2 = CompIter(span, dt, unit=unit)
 
     def iter_info(self):
@@ -1371,7 +1372,7 @@ def compose_ts(self, ts, name, time=None):
             iindex = self.index
 
         span = self.iter_operate.span
-        _logger.debug(iindex)
+        _logger.debug("iindex: %s", iindex)
         if self.span != [0, 0]:
             comp = np.empty((-span[0] + span[1]))
             self.length = comp.size
@@ -1385,7 +1386,7 @@ def compose_ts(self, ts, name, time=None):
                     return -1
                 elif i + span[1] > ts.size:
                     return -1
-                    _logger.debug(i, span[0], span[1])
+                    _logger.debug("%s %s %s", i, span[0], span[1])
                     _logger.debug('i: %s span: %s %s', i, span[0], span[1])
                     _logger.debug('right postion: %s',i+span[1])
                     raise ValueError("composite span exceeds ts limits")
@@ -1529,8 +1530,8 @@ def linefit2Points(time_lin, f, data, f1, f2, f_delta=None, plot=False):
         time_lin = time_lin.astype("m8[s]").astype(int)
 
     if f.shape[0] != data.shape[0]:
-        _logger.debug("ERROR: shapes are not correct")
-        _logger.debug("%s %s %s", f.shape, time_lin.shape, data.shape)
+        _logger.error("ERROR: shapes are not correct")
+        _logger.error("%s %s %s", f.shape, time_lin.shape, data.shape)
         return
 
     # find neerest discrete frequency

From 277bca8d549cdfa3cb9f34fd06c445016abb936c Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 18:15:07 -0400
Subject: [PATCH 12/30] Added more context

Co-Authored-By: Carlos Paniagua <68481491+cpaniaguam@users.noreply.github.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 640350a7..a6f30335 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1531,7 +1531,7 @@ def linefit2Points(time_lin, f, data, f1, f2, f_delta=None, plot=False):
 
     if f.shape[0] != data.shape[0]:
         _logger.error("ERROR: shapes are not correct")
-        _logger.error("%s %s %s", f.shape, time_lin.shape, data.shape)
+        _logger.error("f: %s; time_lin: %s; data: %s", f.shape, time_lin.shape, data.shape)
         return
 
     # find neerest discrete frequency
@@ -1616,7 +1616,7 @@ def find_max_along_line(
     if mode == "free_limits" or mode == "lower_limit":
         if line_right[-1] > time_lin[-1]:
             _logger.debug(" right line > time window")
-            _logger.debug("%s %s",line_right[-1], time_lin[-1])
+            _logger.debug("line_right[-1]: %s, time_lin[-1]: %s", line_right[-1], time_lin[-1])
             a = line_right - time_lin[-1]
             f_end = np.unravel_index(np.abs(a).argmin(), np.transpose(a.shape))[0] - 1
         else:
@@ -1748,7 +1748,7 @@ def RAMSAC_regression_bootstrap(time, freq, time_lin_arg=None, plot=False, **kwa
 
     RAMS_predicted_line = time_lin * RAMS_slope + RAMS_intercept
 
-    _logger.debug("%s %s", RAMS_slope, RAMS_intercept)
+    _logger.debug("RAMS_slope: %s RAMS_intercept: %s", RAMS_slope, RAMS_intercept)
     RAMS_out = boot.ci(
         (time, freq), simple_RAMSAC_regression_estimator, method="bca", **kwargs
     )

From c3dcebd59835162c045e90a36551ada0ad0cc1fe Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 18:18:12 -0400
Subject: [PATCH 13/30] Updates from PR review

Co-Authored-By: Carlos Paniagua <68481491+cpaniaguam@users.noreply.github.com>
---
 src/icesat2waves/local_modules/m_spectrum_ph3.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_spectrum_ph3.py b/src/icesat2waves/local_modules/m_spectrum_ph3.py
index 737cd4b4..668ee3f3 100644
--- a/src/icesat2waves/local_modules/m_spectrum_ph3.py
+++ b/src/icesat2waves/local_modules/m_spectrum_ph3.py
@@ -586,7 +586,7 @@ def __init__(
         k = 0
         _logger.debug('subL %s', subL)
         _logger.debug('L %s', L)
-        _logger.debug("%s", data_size_adjust)
+        _logger.debug("data_size_adjust: %s", data_size_adjust)
 
         for i in np.arange(0, data_size_adjust - int(L - ov) + 1, int(L - ov)):
 
@@ -703,8 +703,7 @@ def write_log(self, s, verbose=False):
         self.hist = MT.write_log(self.hist, s, verbose=verbose)
 
     def log(self):
-        _logger.debug(".hist variable")
-        _logger.debug("%s", self.hist)
+        _logger.debug(".hist variable: %s", self.hist)
     def power_anomalie(self, clim=None):
         dd = 10 * np.log10(self.data[:, :])
 
@@ -773,7 +772,7 @@ def __init__(
 
     def save_data(self, path=None, S=None):
         P = SaveDataPeriodogram(self, S=S)
-        _logger.debug("%s", P.meta)
+        _logger.debug("P.meta: %s", P.meta)
         _logger.debug("constructed class for saving")
         save_file(P, path)
 

From 0399770be36ae0f2ffc8e6f86e83090f457b68d7 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 18:20:04 -0400
Subject: [PATCH 14/30] Updates from PR review

Co-Authored-By: Carlos Paniagua <68481491+cpaniaguam@users.noreply.github.com>
---
 src/icesat2waves/local_modules/m_tools_ph3.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py
index d99848db..11b570a7 100644
--- a/src/icesat2waves/local_modules/m_tools_ph3.py
+++ b/src/icesat2waves/local_modules/m_tools_ph3.py
@@ -193,7 +193,7 @@ def h5_load_v2(name, path, verbose=False):
 
     with h5py.File(path + name + '.h5','r') as h5f:
         if verbose:
-            _logger.debug("%s", h5f.keys())
+            _logger.debug("%s h5f keys: %s", name, h5f.keys())
 
         data_dict = {k: v[:] for k, v in h5f.items()}
 
@@ -246,7 +246,7 @@ def write_log(hist, string, verbose=False, short=True, date=True):
     message = f"\n{now} {string}" if date else f"\n  {string}"
 
     if verbose in [True, 'all']:
-        _logger.debug("%s", hist + message if verbose == 'all' else message)
+        _logger.debug("hist message: %s", hist + message if verbose == 'all' else message)
 
     return hist + message
 
@@ -288,7 +288,7 @@ def load_log_txt(hist_file, path):
 
 def shape(a):
     for i in a:
-        _logger.debug(i.shape)
+        _logger.debug("shape of %s: %s", i, i.shape)
 
 
 def find_O(a, case="round"):

From b9360dee6e2afe27e724d28c9838ee339a95cf30 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Wed, 13 Mar 2024 18:21:13 -0400
Subject: [PATCH 15/30] Updates from PR review

Co-Authored-By: Carlos Paniagua <68481491+cpaniaguam@users.noreply.github.com>
---
 src/icesat2waves/local_modules/m_spectrum_ph3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_spectrum_ph3.py b/src/icesat2waves/local_modules/m_spectrum_ph3.py
index 668ee3f3..36099aaf 100644
--- a/src/icesat2waves/local_modules/m_spectrum_ph3.py
+++ b/src/icesat2waves/local_modules/m_spectrum_ph3.py
@@ -711,8 +711,8 @@ def power_anomalie(self, clim=None):
             np.nanmedian(dd, axis=0) if clim is None else 10 * np.log10(clim)
         )
         dd_tmp = self.data_power_mean.repeat(self.time.size)
-        _logger.debug("%s", self.data_power_mean.shape)
-        _logger.debug("%s %s", self.f.size, self.time.size)
+        _logger.debug("data power mean shape: %s", self.data_power_mean.shape)
+        _logger.debug("f size: %s, time size: %s", self.f.size, self.time.size)
         self.data_power_ano = dd - dd_tmp.reshape(self.f.size, self.time.size).T
 
     def anomalie(self, clim=None):

From 278af162cb2a9502f92958ddb308431e36db5635 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 10:51:02 -0400
Subject: [PATCH 16/30] Update src/icesat2waves/local_modules/m_general_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index a6f30335..2061ce48 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -965,7 +965,7 @@ def boxmean(data, lon, lat, xlim, ylim):
         case (2, 1):
             datan = data[:, :, xbool][:, ybool, :]
         case _:
-            _logger.debug('arrays have not the same shape')
+            _logger.debug('arrays do not have the same shape')
 
 
     _logger.debug("new shape %s", datan.shape)

From 4417d8afdf425350377f558b38a19a8f9fb5a85b Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 10:51:02 -0400
Subject: [PATCH 17/30] chore: add more context to debugger

---
 src/icesat2waves/local_modules/jonswap_gamma.py | 2 +-
 src/icesat2waves/local_modules/m_general_ph3.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icesat2waves/local_modules/jonswap_gamma.py b/src/icesat2waves/local_modules/jonswap_gamma.py
index 540ac361..07d6861b 100644
--- a/src/icesat2waves/local_modules/jonswap_gamma.py
+++ b/src/icesat2waves/local_modules/jonswap_gamma.py
@@ -731,7 +731,7 @@ def reg_func(p0, pi, p_err_unit):
         vd[k] = I * np.random.rand()
 
     Jm = Jm_regulizer(vd, priors)
-    _logger.debug(Jm)
+    _logger.debug("Jm from regulizer: %s", Jm)
 
 
 
diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index a6f30335..2061ce48 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -965,7 +965,7 @@ def boxmean(data, lon, lat, xlim, ylim):
         case (2, 1):
             datan = data[:, :, xbool][:, ybool, :]
         case _:
-            _logger.debug('arrays have not the same shape')
+            _logger.debug('arrays do not have the same shape')
 
 
     _logger.debug("new shape %s", datan.shape)

From d2cdb6b980d1d85b399f52ea3980be94fda3bba6 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 11:00:16 -0400
Subject: [PATCH 18/30] chore: add more context to debugger

---
 src/icesat2waves/local_modules/m_general_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 2061ce48..7d3735c7 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -931,7 +931,7 @@ def cut_nparray(var, low, high, verbose=False):
         return np.unravel_index(np.abs(a).argmin(), np.transpose(a.shape))
 
     else:
-        _logger.debug("error")
+        _logger.warning("error in cut_nparray()")
         return
 
 

From f67c66c3a31316a9bff45b256967e03d2ad0907c Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 11:17:22 -0400
Subject: [PATCH 19/30] chore: add more context to debugger

---
 src/icesat2waves/local_modules/m_general_ph3.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 7d3735c7..d1db48d2 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1598,6 +1598,9 @@ def find_max_along_line(
 
     if mode is None:
         mode = "free_limits"
+
+    _logger.debug("find_max_along_line with %s", mode)
+
     if mode in ["free_limits", "upper_limit"]:
         if line_left[0] > time_lin[0]:
             f_start = 0

From 7799236a478c57328a0288a777e1b356f300b24e Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 11:24:00 -0400
Subject: [PATCH 20/30] chore: reordered and deduplicated logging calls

---
 src/icesat2waves/local_modules/m_general_ph3.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index d1db48d2..bc11a3d1 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1602,13 +1602,12 @@ def find_max_along_line(
     _logger.debug("find_max_along_line with %s", mode)
 
     if mode in ["free_limits", "upper_limit"]:
+        _logger.debug("line_left[0]: %s, time_lin[0]: %s", line_left[0], time_lin[0])
         if line_left[0] > time_lin[0]:
-            f_start = 0
             _logger.debug(" left line > time0")
-            _logger.debug("%s %s", line_left[0], time_lin[0])
+            f_start = 0
         else:
-            _logger.debug(" left line < time")
-            _logger.debug("%s %s", line_left[0], time_lin[0])
+            _logger.debug(" left line < time0")
             a = line_left - time_lin[0]
             f_start = np.unravel_index(np.abs(a).argmin(), np.transpose(a.shape))[0] + 1
     else:
@@ -1617,14 +1616,13 @@ def find_max_along_line(
         f_start = np.unravel_index(np.abs(a).argmin(), np.transpose(a.shape))[0]
 
     if mode == "free_limits" or mode == "lower_limit":
+        _logger.debug("line_right[-1]: %s, time_lin[-1]: %s", line_right[-1], time_lin[-1])
         if line_right[-1] > time_lin[-1]:
             _logger.debug(" right line > time window")
-            _logger.debug("line_right[-1]: %s, time_lin[-1]: %s", line_right[-1], time_lin[-1])
             a = line_right - time_lin[-1]
             f_end = np.unravel_index(np.abs(a).argmin(), np.transpose(a.shape))[0] - 1
         else:
             _logger.debug(" right line < time window")
-            _logger.debug("%s %s",line_right[-1], time_lin[-1])
             f_end = time_lin.size - 2
     else:
         a = f - f2

From 01cc0419ea92702c5b83663e6ea76d724e7ff992 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 11:27:13 -0400
Subject: [PATCH 21/30] chore: add more logging context

---
 src/icesat2waves/local_modules/m_tools_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py
index 11b570a7..afd0d736 100644
--- a/src/icesat2waves/local_modules/m_tools_ph3.py
+++ b/src/icesat2waves/local_modules/m_tools_ph3.py
@@ -265,7 +265,7 @@ def write_variables_log(hist, var_list, locals, verbose=False, date=False):
     message = f"\n{now} {stringg}" if date else f"\n{' '.ljust(5)} {stringg}"
 
     if verbose in [True, 'all']:
-        _logger.debug("%s", hist + message if verbose == 'all' else message)
+        _logger.debug("write_variables_log: %s", hist + message if verbose == 'all' else message)
 
 
 def save_log_txt(name, path, hist, verbose=False):

From 63a00d01ab1e68ec6904cb69f26111e35fe25291 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Fri, 15 Mar 2024 11:30:07 -0400
Subject: [PATCH 22/30] Update
 src/icesat2waves/local_modules/m_colormanager_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_colormanager_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_colormanager_ph3.py b/src/icesat2waves/local_modules/m_colormanager_ph3.py
index 6e35e456..9bb03267 100644
--- a/src/icesat2waves/local_modules/m_colormanager_ph3.py
+++ b/src/icesat2waves/local_modules/m_colormanager_ph3.py
@@ -172,7 +172,7 @@ def colormaps(self,n, gamma=None):
 
         def show(self):
             for key in self.__dict__.keys():
-                _logger.debug("%s",key)
+                _logger.debug("key: %s", key)
 
             _logger.debug('  rels dict keys:')
             for key in self.rels.keys():

From 07d2190772d7bcf5e3c0ecd0000c4f5765b1aefd Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 18 Mar 2024 18:02:07 +0100
Subject: [PATCH 23/30] Update src/icesat2waves/local_modules/m_tools_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_tools_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py
index afd0d736..5ea7468a 100644
--- a/src/icesat2waves/local_modules/m_tools_ph3.py
+++ b/src/icesat2waves/local_modules/m_tools_ph3.py
@@ -288,7 +288,7 @@ def load_log_txt(hist_file, path):
 
 def shape(a):
     for i in a:
-        _logger.debug("shape of %s: %s", i, i.shape)
+        _logger.debug("shape of i=%s: %s", i, i.shape)
 
 
 def find_O(a, case="round"):

From f514e3c7db1503ce5a6c7956ab221fa0cf25187b Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 18 Mar 2024 18:02:37 +0100
Subject: [PATCH 24/30] Update src/icesat2waves/local_modules/m_general_ph3.py

Co-authored-by: Camilo Diaz <k.diaz99@gmail.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index bc11a3d1..5253e5db 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1372,7 +1372,7 @@ def compose_ts(self, ts, name, time=None):
             iindex = self.index
 
         span = self.iter_operate.span
-        _logger.debug("iindex: %s", iindex)
+        _logger.debug("index: %s", iindex)
         if self.span != [0, 0]:
             comp = np.empty((-span[0] + span[1]))
             self.length = comp.size

From d4b31bc4b2984264341f3abacec22e86ed6ca6ca Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 18 Mar 2024 18:15:12 +0100
Subject: [PATCH 25/30] update debugging calls with iter.

Co-Authored-By: Carlos Paniagua <68481491+cpaniaguam@users.noreply.github.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index bc11a3d1..0b0cff24 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1340,10 +1340,10 @@ def iter_info(self):
 
         _logger.debug("available iters")
         if self.iter is not None:
-            _logger.debug("self.iter")
+            _logger.debug("self.iter: %s", self.iter)
             self.iter.__dict__
         if self.iter2 is not None:
-            _logger.debug("self.iter2")
+            _logger.debug("self.iter2: %s", self.iter2)
             self.iter2.__dict__
 
     def info(self):

From e105dde18cdd093d74d3ef3ec3caa424b1030473 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Tue, 19 Mar 2024 14:42:58 +0100
Subject: [PATCH 26/30] Update src/icesat2waves/local_modules/m_general_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 3eb32ede..3eabdfc6 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1386,7 +1386,6 @@ def compose_ts(self, ts, name, time=None):
                     return -1
                 elif i + span[1] > ts.size:
                     return -1
-                    _logger.debug("%s %s %s", i, span[0], span[1])
                     _logger.debug('i: %s span: %s %s', i, span[0], span[1])
                     _logger.debug('right postion: %s',i+span[1])
                     raise ValueError("composite span exceeds ts limits")

From fa7b492c85294d79a28fd7573cf63b2d4467ddf2 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Tue, 19 Mar 2024 14:43:30 +0100
Subject: [PATCH 27/30] Update src/icesat2waves/local_modules/m_tools_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_tools_ph3.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py
index 5ea7468a..d597f01c 100644
--- a/src/icesat2waves/local_modules/m_tools_ph3.py
+++ b/src/icesat2waves/local_modules/m_tools_ph3.py
@@ -314,12 +314,14 @@ def find_O(a, case="round"):
 
 def stats(a):
     _logger.debug(
-        f"shape: %s\n"
-        f"Nans: %s\n"
-        f"max: %s\n"
-        f"min: %s\n"
-        f"mean: %s"
-    , a.shape, np.sum(np.isnan(a)), np.nanmax(a), np.nanmin(a), np.nanmean(a))
+        "shape: %s\nNans: %s\nmax: %s\nmin: %s\nmean: %s",
+        a.shape,
+        np.sum(np.isnan(a)),
+        np.nanmax(a),
+        np.nanmin(a),
+        np.nanmean(a)
+    )
+
 
 
 def stats_format(a, name=None):

From c80198dd5ab83a56097fab6376aa3d39488b0713 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Tue, 19 Mar 2024 14:44:13 +0100
Subject: [PATCH 28/30] Update src/icesat2waves/local_modules/m_tools_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_tools_ph3.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/icesat2waves/local_modules/m_tools_ph3.py b/src/icesat2waves/local_modules/m_tools_ph3.py
index d597f01c..23b911fc 100644
--- a/src/icesat2waves/local_modules/m_tools_ph3.py
+++ b/src/icesat2waves/local_modules/m_tools_ph3.py
@@ -325,10 +325,12 @@ def stats(a):
 
 
 def stats_format(a, name=None):
-    _logger.debug("Name: %s\n"
-                  "   Shape: %s\n"
-                  "   NaNs: %s\n"
-                  "   max: %s\n"
-                  "   min: %s\n"
-                  "   mean: %s",
-                  name, a.shape, np.sum(np.isnan(a)), np.nanmax(a), np.nanmin(a), np.nanmean(a))
+    _logger.debug(
+        "Name: %s\n"
+        "   Shape: %s\n"
+        "   NaNs: %s\n"
+        "   max: %s\n"
+        "   min: %s\n"
+        "   mean: %s",
+        name, a.shape, np.sum(np.isnan(a)), np.nanmax(a), np.nanmin(a), np.nanmean(a)
+    )

From 52c73202d83765b0007790e5869a01fd1073be58 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Tue, 19 Mar 2024 14:44:26 +0100
Subject: [PATCH 29/30] Update src/icesat2waves/local_modules/m_general_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index 3eabdfc6..fd24c934 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1393,7 +1393,7 @@ def compose_ts(self, ts, name, time=None):
 
                 _logger.debug('comp %s', comp.shape)
                 _logger.debug('ts %s', ts[i + span[0]:i + span[1]].shape)
-                _logger.debug("%s %s %s", i, span[0], span[1])
+                _logger.debug('i: %s span: %s %s', i, span[0], span[1])
                 comp = np.vstack((comp, ts[i + span[0]:i + span[1]]))
 
             comp = np.delete(comp, 0, 0)

From ece4f27ee82fd7eaad1a889f330be4cbfc0f32b5 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Tue, 19 Mar 2024 14:44:43 +0100
Subject: [PATCH 30/30] Update src/icesat2waves/local_modules/m_general_ph3.py

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
---
 src/icesat2waves/local_modules/m_general_ph3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icesat2waves/local_modules/m_general_ph3.py b/src/icesat2waves/local_modules/m_general_ph3.py
index fd24c934..ce6381fa 100644
--- a/src/icesat2waves/local_modules/m_general_ph3.py
+++ b/src/icesat2waves/local_modules/m_general_ph3.py
@@ -1415,7 +1415,7 @@ def compose_2d(self, field, name, time=None):
         span = self.iter_operate.span
 
         if span != [0, 0]:
-            _logger.debug("%s %s", -span[0]+span[1],field.shape[1])
+            _logger.debug("span range: %s, field shape: %s", -span[0]+span[1],field.shape[1])
             comp = np.empty((-span[0] + span[1], field.shape[1])) * np.NaN
             self.length = -span[0] + span[1]
             for i in iindex: