Merge branch 'depends'

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)
 
 
 <img src="imgs/overview.png" />

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
 
 

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

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)

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,

blinx/utils.py

@@ -1,6 +1,5 @@
 import jax.numpy as jnp
 import numpy as np
-import scipy.signal
 
 
 def find_maximum(matrix):

pyproject.toml

@@ -15,7 +15,7 @@ authors = [
     { name = 'Alex Hillsley', email = '[email protected]' },
 ]
 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]