celldetective 1.0.2.post1__py3-none-any.whl → 1.1.1__py3-none-any.whl

celldetective/scripts/analyze_signals.py

@@ -3,6 +3,7 @@ Copright © 2022 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 """
 
 import argparse
+import datetime
 import os
 import gc
 from art import tprint
@@ -45,6 +46,12 @@ else:
 	print('The trajectories table could not be found. Abort.')
 	os.abort()
 
+log=f'segmentation model: {model} \n'
+
+with open(pos+f'log_{mode}.json', 'a') as f:
+	f.write(f'{datetime.datetime.now()} SIGNAL ANALYSIS \n')
+	f.write(log)
+
 trajectories = analyze_signals(trajectories.copy(), model, interpolate_na=True, selected_signals=None, column_labels = column_labels, plot_outcome=True,output_dir=pos+'output/')
 trajectories = trajectories.sort_values(by=[column_labels['track'], column_labels['time']])
 trajectories.to_csv(pos+os.sep.join(['output','tables', table_name]), index=False)

celldetective/scripts/measure_cells.py

@@ -20,6 +20,7 @@ from natsort import natsorted
 from art import tprint
 from tifffile import imread
 import threading
+import datetime
 
 tprint("Measure")
 
@@ -195,6 +196,17 @@ if trajectories is None:
 	print('Use features as a substitute for the trajectory table.')
 	if 'label' not in features:
 		features.append('label')
+features_log=f'features: {features}'
+border_distances_log=f'border_distances: {border_distances}'
+haralick_options_log=f'haralick_options: {haralick_options}'
+background_correction_log=f'background_correction: {background_correction}'
+spot_detection_log=f'spot_detection: {spot_detection}'
+intensity_measurement_radii_log=f'intensity_measurement_radii: {intensity_measurement_radii}'
+isotropic_options_log=f'isotropic_operations: {isotropic_operations} \n'
+log='\n'.join([features_log,border_distances_log,haralick_options_log,background_correction_log,spot_detection_log,intensity_measurement_radii_log,isotropic_options_log])
+with open(pos + f'log_{mode}.json', 'a') as f:
+	f.write(f'{datetime.datetime.now()} MEASURE \n')
+	f.write(log+'\n')
 
 
 def measure_index(indices):

celldetective/scripts/segment_cells.py

@@ -3,6 +3,7 @@ Copright © 2022 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 """
 
 import argparse
+import datetime
 import os
 import json
 from stardist.models import StarDist2D
@@ -21,6 +22,9 @@ from art import tprint
 from scipy.ndimage import zoom
 import threading
 
+import matplotlib.pyplot as plt
+import time
+
 tprint("Segment")
 
 parser = argparse.ArgumentParser(description="Segment a movie in position with the selected model",
@@ -128,6 +132,10 @@ if os.path.exists(os.sep.join([pos,label_folder])):
 	rmtree(os.sep.join([pos,label_folder]))
 os.mkdir(os.sep.join([pos,label_folder]))
 print(f'Folder {os.sep.join([pos,label_folder])} successfully generated.')
+log=f'segmentation model: {modelname}\n'
+with open(pos+f'log_{mode}.json', 'a') as f:
+	f.write(f'{datetime.datetime.now()} SEGMENT \n')
+	f.write(log)
 
 
 # Loop over all frames and segment
@@ -154,10 +162,18 @@ def segment_index(indices):
 	for t in tqdm(indices,desc="frame"):
 		
 		# Load channels at time t
-		f = load_frames(img_num_channels[:,t], file, scale=scale, normalize_input=False)
-		f = normalize_per_channel([f], normalization_percentile_mode=normalization_percentile, normalization_values=normalization_values,
-									normalization_clipping=normalization_clip)
-		f = f[0]
+		values = []
+		percentiles = []
+		for k in range(len(normalization_percentile)):
+			if normalization_percentile[k]:
+				percentiles.append(normalization_values[k])
+				values.append(None)
+			else:
+				percentiles.append(None)
+				values.append(normalization_values[k])
+
+		f = load_frames(img_num_channels[:,t], file, scale=scale, normalize_input=True, normalize_kwargs={"percentiles": percentiles, 'values': values, 'clip': normalization_clip})
+
 		if np.any(img_num_channels[:,t]==-1):
 			f[:,:,np.where(img_num_channels[:,t]==-1)[0]] = 0.
 

celldetective/scripts/track_cells.py

@@ -3,6 +3,7 @@ Copright © 2022 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 """
 
 import argparse
+import datetime
 import os
 import json
 from celldetective.io import auto_load_number_of_frames, load_frames, interpret_tracking_configuration
@@ -139,6 +140,16 @@ img_num_channels = _get_img_num_per_channel(channel_indices, len_movie, nbr_chan
 #######################################
 
 timestep_dataframes = []
+features_log=f'features: {features}'
+mask_channels_log=f'mask_channels: {mask_channels}'
+haralick_option_log=f'haralick_options: {haralick_options}'
+post_processing_option_log=f'post_processing_options: {post_processing_options}'
+log_list=[features_log, mask_channels_log, haralick_option_log, post_processing_option_log]
+log='\n'.join(log_list)
+
+with open(pos+f'log_{mode}.json', 'a') as f:
+	f.write(f'{datetime.datetime.now()} TRACK \n')
+	f.write(log+"\n")
 
 def measure_index(indices):
 	for t in tqdm(indices,desc="frame"):

celldetective/scripts/train_segmentation_model.py

@@ -11,28 +11,15 @@ from tqdm import tqdm
 import numpy as np
 import random
 
-from celldetective.utils import load_image_dataset, normalize_per_channel, augmenter
+from celldetective.utils import load_image_dataset, normalize_per_channel, augmenter, interpolate_nan
+from celldetective.io import normalize_multichannel
 from stardist import fill_label_holes
 from art import tprint
 import matplotlib.pyplot as plt
 
-def interpolate_nan(array_like):
-	array = array_like.copy()
-	
-	isnan_array = ~np.isnan(array)
-	
-	xp = isnan_array.ravel().nonzero()[0]
-	
-	fp = array[~np.isnan(array)]
-	x = np.isnan(array).ravel().nonzero()[0]
-	
-	array[np.isnan(array)] = np.interp(x, xp, fp)
-	
-	return array
 
 tprint("Train")
 
-
 parser = argparse.ArgumentParser(description="Train a signal model from instructions.",
 								formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 parser.add_argument('-c',"--config", required=True,help="Training instructions")
@@ -78,25 +65,39 @@ X,Y = load_image_dataset(datasets, target_channels, train_spatial_calibration=sp
 print('Dataset loaded...')
 
 # Normalize images
-X = normalize_per_channel(X,
-						  normalization_percentile_mode=normalization_percentile, 
-						  normalization_values=normalization_values, 
-						  normalization_clipping=normalization_clip
-						  )
-
-for x in X:
-	plt.imshow(x[:,:,0])
-	plt.xlim(0,1004)
-	plt.ylim(0,1002)
-	plt.colorbar()
-	plt.pause(2)
-	plt.close()
-	print(x.shape)
-	interp = interpolate_nan(x)
-	print(interp.shape)
-	print(np.any(np.isnan(x).flatten()))
-	print(np.any(np.isnan(interp).flatten()))
-
+# X = normalize_per_channel(X,
+# 						  normalization_percentile_mode=normalization_percentile, 
+# 						  normalization_values=normalization_values, 
+# 						  normalization_clipping=normalization_clip
+# 						  )
+
+values = []
+percentiles = []
+for k in range(len(normalization_percentile)):
+	if normalization_percentile[k]:
+		percentiles.append(normalization_values[k])
+		values.append(None)
+	else:
+		percentiles.append(None)
+		values.append(normalization_values[k])
+
+X = [normalize_multichannel(x, **{"percentiles": percentiles, 'values': values, 'clip': normalization_clip}) for x in X]
+
+for k in range(len(X)):
+	x = X[k].copy()
+	x_interp = np.moveaxis([interpolate_nan(x[:,:,c].copy()) for c in range(x.shape[-1])],0,-1)
+	X[k] = x_interp
+
+# for x in X[:10]:
+# 	plt.imshow(x[:,:,0])
+# 	plt.colorbar()
+# 	plt.pause(2)
+# 	plt.close()
+
+# 	plt.imshow(x[:,:,1])
+# 	plt.colorbar()
+# 	plt.pause(2)
+# 	plt.close()
 
 Y = [fill_label_holes(y) for y in tqdm(Y)]
 

celldetective/segmentation.py

@@ -13,7 +13,8 @@ from cellpose.models import CellposeModel
 from skimage.transform import resize
 from celldetective.io import _view_on_napari, locate_labels, locate_stack, _view_on_napari
 from celldetective.filters import * #rework this to give a name
-from celldetective.utils import rename_intensity_column
+from celldetective.utils import rename_intensity_column, mask_edges, estimate_unreliable_edge
+from stardist import fill_label_holes
 import scipy.ndimage as ndi
 from skimage.segmentation import watershed
 from skimage.feature import peak_local_max
@@ -132,7 +133,7 @@ def segment(stack, model_name, channels=None, spatial_calibration=None, view_on_
 			frame = normalize_multichannel(frame, values=normalization_values)
 
 		if scale is not None:
-			frame = ndi.zoom(frame, [scale,scale,1], order=3)		
+			frame = [ndi.zoom(frame[:,:,c].copy(), [scale,scale], order=3, prefilter=False) for c in range(frame.shape[-1])]
 
 		if model_type=="stardist":
 
@@ -273,7 +274,8 @@ def segment_frame_from_thresholds(frame, target_channel=0, thresholds=None, equa
 		img = match_histograms(img, equalize_reference)
 	img_mc = frame.copy()
 	img = filter_image(img, filters=filters)
-	binary_image = threshold_image(img, thresholds[0], thresholds[1])
+	edge = estimate_unreliable_edge(filters)
+	binary_image = threshold_image(img, thresholds[0], thresholds[1], fill_holes=True, edge_exclusion=edge)
 	coords,distance = identify_markers_from_binary(binary_image, marker_min_distance, footprint_size=marker_footprint_size, footprint=marker_footprint, return_edt=True)
 	instance_seg = apply_watershed(binary_image, coords, distance)
 	instance_seg = filter_on_property(instance_seg, intensity_image=img_mc, queries=feature_queries, channel_names=channel_names)
@@ -357,7 +359,7 @@ def filter_on_property(labels, intensity_image=None, queries=None, channel_names
 	return labels
 
 
-def apply_watershed(binary_image, coords, distance):
+def apply_watershed(binary_image, coords, distance, fill_holes=True):
 
 	"""
 	Applies the watershed algorithm to segment objects in a binary image using given markers and distance map.
@@ -404,7 +406,8 @@ def apply_watershed(binary_image, coords, distance):
 	mask[tuple(coords.T)] = True
 	markers, _ = ndi.label(mask)
 	labels = watershed(-distance, markers, mask=binary_image)
-
+	if fill_holes:
+		labels = fill_label_holes(labels)
 	return labels
 
 def identify_markers_from_binary(binary_image, min_distance, footprint_size=20, footprint=None, return_edt=False):
@@ -457,7 +460,7 @@ def identify_markers_from_binary(binary_image, min_distance, footprint_size=20,
 		return coords
 
 
-def threshold_image(img, min_threshold, max_threshold, foreground_value=255., fill_holes=True):
+def threshold_image(img, min_threshold, max_threshold, foreground_value=255., fill_holes=True, edge_exclusion=None):
 
 	"""
 	
@@ -496,10 +499,12 @@ def threshold_image(img, min_threshold, max_threshold, foreground_value=255., fi
 
 	"""
 
-
-	binary = (img>=min_threshold)*(img<=max_threshold) * foreground_value
+	binary = np.zeros_like(img).astype(bool)
+	binary[img==img] = (img[img==img]>=min_threshold)*(img[img==img]<=max_threshold) * foreground_value
+	if isinstance(edge_exclusion, (int,np.int_)):
+		binary = mask_edges(binary, edge_exclusion)
 	if fill_holes:
-		binary = ndi.binary_fill_holes(binary)
+		binary = ndi.binary_fill_holes(binary.astype(int))
 	return binary
 
 def filter_image(img, filters=None):