From e83bdf9b3704835f5ca91d8d355e14599227d557 Mon Sep 17 00:00:00 2001 From: ahillsley Date: Mon, 17 Jun 2024 13:56:01 -0400 Subject: [PATCH 1/3] fix typos in the Readme --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6b7b3e0..7748757 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,4 @@ -blinx -== +# blinx - **[Introduction](#introduction)** - **[Installation](#installation)** @@ -13,7 +12,7 @@ when only their combined intensity can be measured, as reported in ***A Bayesian Method to Count the Number of Molecules within a Diffraction Limited Spot*** [pre-print](https://www.biorxiv.org/content/10.1101/2024.04.18.590066v2) now available on BioRxiv. -Experiments associated with the pre-print can be found in [blix_experiments](https://github.com/funkelab/blinx_experiments) +Experiments associated with the pre-print can be found in [blinx_experiments](https://github.com/funkelab/blinx_experiments) From 02a965728a5f54f9cb16549f5bdca46e2c0f8af1 Mon Sep 17 00:00:00 2001 From: ahillsley Date: Mon, 17 Jun 2024 13:59:56 -0400 Subject: [PATCH 2/3] remove unused dependencies --- blinx/estimate.py | 2 +- blinx/fluorescence_model.py | 2 -- blinx/parameters.py | 2 -- blinx/trace_model.py | 2 +- blinx/utils.py | 1 - 5 files changed, 2 insertions(+), 7 deletions(-) diff --git a/blinx/estimate.py b/blinx/estimate.py index cf24eac..c943d68 100644 --- a/blinx/estimate.py +++ b/blinx/estimate.py @@ -11,7 +11,7 @@ # FIXME: post_process should be renamed and find a new home from .post_process import post_process as find_most_likely_y -from .trace_model import get_trace_log_likelihood, log_p_x_parameters +from .trace_model import log_p_x_parameters from .utils import find_maximum diff --git a/blinx/fluorescence_model.py b/blinx/fluorescence_model.py index 3b15ec4..2693a35 100644 --- a/blinx/fluorescence_model.py +++ b/blinx/fluorescence_model.py @@ -2,8 +2,6 @@ import jax.numpy as jnp from jax import random -from .constants import eps - def p_x_given_z( x_left, x_right, z, r_e, r_bg, mean_ro, sigma_ro, gain, hyper_parameters diff --git a/blinx/parameters.py b/blinx/parameters.py index 4e7eb9d..936d195 100644 --- a/blinx/parameters.py +++ b/blinx/parameters.py @@ -2,8 +2,6 @@ import jax.numpy as jnp from jax.tree_util import register_pytree_node_class -from .fluorescence_model import p_norm - def inv_sigmoid(p): return -jax.lax.log(1.0 / p - 1.0) diff --git a/blinx/trace_model.py b/blinx/trace_model.py index f6208e3..dddeeb4 100644 --- a/blinx/trace_model.py +++ b/blinx/trace_model.py @@ -6,7 +6,7 @@ from jax import random from scipy.special import comb -from .fluorescence_model import p_x_given_z, sample_x_given_z, p_norm +from .fluorescence_model import p_x_given_z, sample_x_given_z from .markov_chain import ( get_measurement_log_likelihood, get_steady_state, diff --git a/blinx/utils.py b/blinx/utils.py index cd1dd71..f0e9713 100644 --- a/blinx/utils.py +++ b/blinx/utils.py @@ -1,6 +1,5 @@ import jax.numpy as jnp import numpy as np -import scipy.signal def find_maximum(matrix): From 5c25569c1c28cb51f785dabdb60653aaa5e0f83e Mon Sep 17 00:00:00 2001 From: ahillsley Date: Mon, 17 Jun 2024 14:00:12 -0400 Subject: [PATCH 3/3] update dependencies --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8bd355f..afb68c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ authors = [ { name = 'Alex Hillsley', email = 'hillsleya@janelia.hhmi.org' }, ] dynamic = ["version"] -dependencies = ["numpy", "scipy", "jax", "jaxlib", "optax", "scikit-image", "tqdm"] +dependencies = ["numpy", "scipy", "jax", "jaxlib", "optax", "scikit-image", "tqdm", "pandas", "h5py"] [project.optional-dependencies] dev = ["pre-commit", "pytest", "pytest-cov", "ruff", "twine", "build"] @@ -27,7 +27,6 @@ docs = [ "tomli", "jupyter_sphinx", "plotly", - "pandas" ] [project.urls]