misc

bigfish/detection/__init__.py

@@ -3,8 +3,8 @@
 # License: BSD 3 clause
 
 """
-The bigfish.detection module includes function to detect RNA spot in 2-d and
-3-d.
+The bigfish.detection subpackage includes function to detect RNA spot in 2-d
+and 3-d.
 """
 
 from .utils import get_sigma

bigfish/detection/cluster_decomposition.py

@@ -20,10 +20,11 @@
 from skimage.measure import label
 
 
-# ### Main function ###
-
 # TODO add parameter to detect more or less clusters
 # TODO add parameter to fit more or less spots in a cluster
+
+# ### Main function ###
+
 def decompose_cluster(image, spots, voxel_size_z=None, voxel_size_yx=100,
                       psf_z=None, psf_yx=200):
     """Detect potential regions with clustered spots and fit as many reference

bigfish/detection/tests/test_cluster_decomposition.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.cluster_decomposition submodule.
+Unitary tests for bigfish.stack.cluster_decomposition module.
 """
 
 # TODO test bigfish.detection.decompose_cluster

bigfish/detection/tests/test_foci_detection.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.foci_detection submodule.
+Unitary tests for bigfish.stack.foci_detection module.
 """
 
 # TODO test bigfish.detection.detect_foci

bigfish/detection/tests/test_spot_detection.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.spot_detection submodule.
+Unitary tests for bigfish.stack.spot_detection module.
 """
 
 # TODO test bigfish.detection.spot_detector

bigfish/detection/tests/test_utils.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.utils submodule.
+Unitary tests for bigfish.stack.utils module.
 """
 
 # TODO test bigfish.utils.get_sigma

bigfish/detection/utils.py

@@ -3,16 +3,16 @@
 # License: BSD 3 clause
 
 """
-Utility functions for bigfish.stack submodule.
+Utility functions for bigfish.stack subpackage.
 """
 
 import bigfish.stack as stack
 import numpy as np
 
+
 # TODO add function to calibrate psf
 # TODO add function to compute signal-to-noise ratio
 
-
 # ### Signal-to-Noise ratio ###
 
 def compute_snr(image, sigma, minimum_distance=1,

bigfish/plot/__init__.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-The bigfish.plot module includes functions to plot images and results.
+The bigfish.plot subpackage includes functions to plot images and results.
 """
 
 from .plot_images import plot_yx

bigfish/plot/plot_classification.py

@@ -1,8 +1,11 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
 Functions to plot results from classification model.
 """
+
 import matplotlib.pyplot as plt
 import numpy as np
 

bigfish/plot/plot_images.py

@@ -10,11 +10,11 @@
 
 import bigfish.stack as stack
 
+from .utils import save_plot, get_minmax_values
+
 import matplotlib.pyplot as plt
 import numpy as np
 
-from .utils import save_plot, get_minmax_values
-
 from skimage.segmentation import find_boundaries
 from matplotlib.colors import ListedColormap
 from matplotlib.patches import RegularPolygon

bigfish/plot/utils.py

@@ -1,7 +1,9 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
-Utility functions for bigfish.plot submodule.
+Utility functions for bigfish.plot subpackage.
 """
 
 import matplotlib.pyplot as plt

bigfish/segmentation/__init__.py

@@ -3,8 +3,8 @@
 # License: BSD 3 clause
 
 """
-The bigfish.segmentation module includes functions to segment or label nuclei
-and cells.
+The bigfish.segmentation subpackage includes functions to segment or label
+nuclei and cells.
 """
 
 from .utils import label_instances

bigfish/segmentation/test/test_cell_segmentation.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.segmentation.cell_segmentation submodule.
+Unitary tests for bigfish.segmentation.cell_segmentation module.
 """
 
 

bigfish/segmentation/test/test_nuc_segmentation.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.segmentation.nuc_segmentation submodule.
+Unitary tests for bigfish.segmentation.nuc_segmentation module.
 """
 
 

bigfish/segmentation/test/test_utils.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.segmentation.utils submodule.
+Unitary tests for bigfish.segmentation.utils module.
 """
 
 

bigfish/segmentation/utils.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Utility functions for nuclei and cytoplasm segmentation.
+Utility functions for bigfish.segmentation subpackage.
 """
 
 import bigfish.stack as stack

bigfish/stack/__init__.py

@@ -3,8 +3,8 @@
 # License: BSD 3 clause
 
 """
-The bigfish.stack module includes functions to read data, preprocess them and
-build stack of images.
+The bigfish.stack subpackage includes functions to read data, preprocess them
+and build stack of images.
 """
 
 from .utils import check_array

bigfish/stack/filter.py

@@ -2,7 +2,7 @@
 # Author: Arthur Imbert <[email protected]>
 # License: BSD 3 clause
 
-"""Filter functions."""
+"""Filtering functions."""
 
 import numpy as np
 

bigfish/stack/postprocess.py

@@ -17,10 +17,10 @@
 from skimage.measure import regionprops, find_contours
 from skimage.draw import polygon_perimeter
 
+
 # TODO extract cell-RNAs matrix
 # TODO sum up extraction results in a (csv) file
 
-
 # ### Transcription sites ###
 
 def identify_transcription_site(nuc_mask, foci):

bigfish/stack/preprocess.py

@@ -27,10 +27,10 @@
 from skimage import img_as_uint
 from skimage.exposure import rescale_intensity
 
+
 # TODO only read in memory one or several channels (and not the entire image)
 # TODO allow new keys to define a recipe
 
-
 # ### Building stack ###
 
 def build_stacks(data_map, input_dimension=None, sanity_check=False,

bigfish/stack/tests/test_augmentation.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.augmentation submodule.
+Unitary tests for bigfish.stack.augmentation module.
 """
 
 import pytest

bigfish/stack/tests/test_filter.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.filter submodule.
+Unitary tests for bigfish.stack.filter module.
 """
 
 import pytest

bigfish/stack/tests/test_io.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.io submodule.
+Unitary tests for bigfish.stack.io module.
 """
 
 import os

bigfish/stack/tests/test_postprocess.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.postprocess submodule.
+Unitary tests for bigfish.stack.postprocess module.
 """
 
 # TODO add test bigfish.stack.identify_transcription_site

bigfish/stack/tests/test_preprocess.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.preprocess submodule.
+Unitary tests for bigfish.stack.preprocess module.
 """
 
 import os

bigfish/stack/tests/test_projection.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.projection submodule.
+Unitary tests for bigfish.stack.projection module.
 """
 
 import pytest

bigfish/stack/tests/test_utils.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Unitary tests for bigfish.stack.utils submodule.
+Unitary tests for bigfish.stack.utils module.
 """
 
 import os

bigfish/stack/utils.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Utility functions for bigfish.stack submodule.
+Utility functions for bigfish.stack subpackage.
 """
 
 import os

data/__init__.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-The bigfish.data module includes functions to load data.
+The bigfish.data subpackage includes functions to load data.
 """
 
 from .utils import check_input_data

data/utils.py

@@ -3,7 +3,7 @@
 # License: BSD 3 clause
 
 """
-Utility functions for bigfish.data submodule.
+Utility functions for bigfish.data subpackage.
 """
 
 import os
@@ -29,6 +29,7 @@ def check_input_data(input_directory):
     -------
     input_directory : str
         Path of the input data directory.
+
     """
     # check if input dapi image exists
     path = os.path.join(input_directory, filename_input_dapi)