refactor stack and detection

bigfish/detection/__init__.py

@@ -1,32 +1,68 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 The bigfish.detection module includes function to detect RNA spot in 2-d and
 3-d.
 """
 
-from .spot_detection import (
-    log_lm, local_maximum_detection, spots_thresholding, compute_snr,
-    from_threshold_to_snr, get_sigma, log_cc, get_cc)
-from .cluster_decomposition import (
-    gaussian_3d, precompute_erf, build_reference_spot_3d,
-    initialize_spot_parameter_3d, objective_function, fit_gaussian_3d,
-    simulate_fitted_gaussian_3d, fit_gaussian_mixture, filter_clusters,
-    decompose_clusters, run_decomposition)
-from .foci_detection import (
-    convert_spot_coordinates, cluster_spots, extract_foci)
-
-
-_spots = ["log_lm", "local_maximum_detection", "spots_thresholding",
-          "compute_snr", "from_threshold_to_snr", "get_sigma", "log_cc",
-          "get_cc", "filter_cc"]
-
-_clusters = ["gaussian_3d", "precompute_erf", "build_reference_spot_3d",
-             "initialize_spot_parameter_3d", "objective_function",
-             "fit_gaussian_3d", "simulate_fitted_gaussian_3d",
-             "fit_gaussian_mixture", "filter_clusters", "decompose_clusters",
-             "run_decomposition"]
-
-_foci = ["convert_spot_coordinates", "cluster_spots", "extract_foci"]
+from .spot_detection import log_lm
+from .spot_detection import local_maximum_detection
+from .spot_detection import spots_thresholding
+from .spot_detection import compute_snr
+from .spot_detection import from_threshold_to_snr
+from .spot_detection import get_sigma
+from .spot_detection import log_cc
+from .spot_detection import get_cc
+from .spot_detection import log_lm
+from .spot_detection import log_lm
+from .spot_detection import log_lm
+
+from .cluster_decomposition import gaussian_3d
+from .cluster_decomposition import precompute_erf
+from .cluster_decomposition import build_reference_spot_3d
+from .cluster_decomposition import initialize_spot_parameter_3d
+from .cluster_decomposition import objective_function
+from .cluster_decomposition import fit_gaussian_3d
+from .cluster_decomposition import simulate_fitted_gaussian_3d
+from .cluster_decomposition import fit_gaussian_mixture
+from .cluster_decomposition import filter_clusters
+from .cluster_decomposition import decompose_clusters
+from .cluster_decomposition import run_decomposition
+
+from .foci_detection import convert_spot_coordinates
+from .foci_detection import cluster_spots
+from .foci_detection import extract_foci
+
+
+_spots = [
+    "log_lm",
+    "local_maximum_detection",
+    "spots_thresholding",
+    "compute_snr",
+    "from_threshold_to_snr",
+    "get_sigma",
+    "log_cc",
+    "get_cc",
+    "filter_cc"]
+
+_clusters = [
+    "gaussian_3d",
+    "precompute_erf",
+    "build_reference_spot_3d",
+    "initialize_spot_parameter_3d",
+    "objective_function",
+    "fit_gaussian_3d",
+    "simulate_fitted_gaussian_3d",
+    "fit_gaussian_mixture",
+    "filter_clusters",
+    "decompose_clusters",
+    "run_decomposition"]
+
+_foci = [
+    "convert_spot_coordinates",
+    "cluster_spots",
+    "extract_foci"]
 
 __all__ = _spots + _clusters + _foci

bigfish/detection/cluster_decomposition.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 Functions to fit gaussian functions to the detected RNA spots, especially in

bigfish/detection/foci_detection.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 Functions to fit gaussian functions to the detected RNA spots, especially in

bigfish/detection/spot_detection.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 Class and functions to detect RNA spots in 2-d and 3-d.
@@ -15,6 +17,7 @@
 # TODO complete documentation methods
 # TODO add sanity check functions
 # TODO improve documentation with optional output
+# TODO add function to calibrate psf
 
 # ### LoG detection ###
 
@@ -96,6 +99,7 @@ def local_maximum_detection(image, minimum_distance):
     stack.check_parameter(minimum_distance=(float, int))
 
     # compute the kernel size (centered around our pixel because it is uneven)
+    # TODO use tuple with a different size for each axis
     kernel_size = int(2 * minimum_distance + 1)
 
     # apply maximum filter to the original image

bigfish/detection/tests/test_spot_detection.py

@@ -0,0 +1,17 @@
+# -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
+
+"""
+Unitary tests for bigfish.stack.filter submodule.
+"""
+
+import pytest
+
+import numpy as np
+import bigfish.stack as stack
+
+from bigfish.stack.filter import _define_kernel
+
+from numpy.testing import assert_array_equal
+from numpy.testing import assert_allclose

bigfish/stack/__init__.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 The bigfish.stack module includes functions to read data, preprocess them and

bigfish/stack/augmentation.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 Functions to augment the data (images or coordinates).

bigfish/stack/filter.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """Filter functions."""
 

bigfish/stack/illumination.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """Illumination correction functions."""
 

bigfish/stack/postprocess.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 Functions used to format and clean any intermediate results loaded in or

bigfish/stack/projection.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """2-d projection functions."""