celldetective 1.3.9.post1__py3-none-any.whl → 1.3.9.post3__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.3.9.post1"
+__version__ = "1.3.9.post3"

celldetective/extra_properties.py

@@ -29,6 +29,7 @@ from celldetective.utils import interpolate_nan, contour_of_instance_segmentatio
 import skimage.measure as skm
 from stardist import fill_label_holes
 from celldetective.segmentation import segment_frame_from_thresholds
+from sklearn.metrics import r2_score
 
 
 # def area_detected_in_ricm(regionmask, intensity_image, target_channel='adhesion_channel'):
@@ -65,7 +66,7 @@ from celldetective.segmentation import segment_frame_from_thresholds
 
 # 	return np.sum(lbl)
 
-def fraction_of_area_detected_in_ricm(regionmask, intensity_image, target_channel='adhesion_channel'):
+def fraction_of_area_detected_in_intensity(regionmask, intensity_image, target_channel='adhesion_channel'):
 
 	instructions = {
 		"thresholds": [
@@ -94,7 +95,7 @@ def fraction_of_area_detected_in_ricm(regionmask, intensity_image, target_channe
 	
 	return float(np.sum(lbl)) / float(np.sum(regionmask))
 
-def area_detected_in_ricm(regionmask, intensity_image, target_channel='adhesion_channel'):
+def area_detected_in_intensity(regionmask, intensity_image, target_channel='adhesion_channel'):
 
 	instructions = {
 		"thresholds": [
@@ -124,7 +125,7 @@ def area_detected_in_ricm(regionmask, intensity_image, target_channel='adhesion_
 	return float(np.sum(lbl))
 
 
-def area_dark(regionmask, intensity_image, target_channel='adhesion_channel', fill_holes=True): #, target_channel='adhesion_channel'
+def area_dark_intensity(regionmask, intensity_image, target_channel='adhesion_channel', fill_holes=True): #, target_channel='adhesion_channel'
 	
 	subregion = (intensity_image < 0.95)*regionmask # under one, under 0.8, under 0.6, whatever value!
 	if fill_holes:
@@ -135,7 +136,7 @@ def area_dark(regionmask, intensity_image, target_channel='adhesion_channel', fi
 	return float(np.sum(subregion))
 
 
-def fraction_of_area_dark(regionmask, intensity_image, target_channel='adhesion_channel', fill_holes=True): #, target_channel='adhesion_channel'
+def fraction_of_area_dark_intensity(regionmask, intensity_image, target_channel='adhesion_channel', fill_holes=True): #, target_channel='adhesion_channel'
 	
 	subregion = (intensity_image < 0.95)*regionmask # under one, under 0.8, under 0.6, whatever value!
 	if fill_holes:
@@ -182,60 +183,49 @@ def intensity_nanmean(regionmask, intensity_image):
 
 def intensity_centre_of_mass_displacement(regionmask, intensity_image):
 
-	intensity_image = interpolate_nan(intensity_image.copy())
+	if np.any(intensity_image!=intensity_image):
+		intensity_image = interpolate_nan(intensity_image.copy())
 
-	y, x = np.mgrid[:regionmask.shape[0], :regionmask.shape[1]]
-	xtemp = x.copy()
-	ytemp = y.copy()
-	intensity_weighted_center = center_of_mass(intensity_image, regionmask)
-	centroid_x = intensity_weighted_center[1]
-	centroid_y = intensity_weighted_center[0]
-
-	#centroid_x = np.sum(xtemp * intensity_image) / np.sum(intensity_image)
-	geometric_centroid_x = np.sum(xtemp * regionmask) / np.sum(regionmask)
-	geometric_centroid_y = np.sum(ytemp * regionmask) / np.sum(regionmask)
-	try:
-		distance = euclidean(np.array((geometric_centroid_y, geometric_centroid_x)), np.array((centroid_y, centroid_x)))
-	except:
-		distance = np.nan
+	if not np.all(intensity_image.flatten()==0):
+		
+		y, x = np.mgrid[:regionmask.shape[0], :regionmask.shape[1]]
+		xtemp = x.copy()
+		ytemp = y.copy()
 
-	delta_x = geometric_centroid_x - centroid_x
-	delta_y = geometric_centroid_y - centroid_y
-	direction_arctan = np.arctan2(delta_y, delta_x) * 180 / np.pi
-	if direction_arctan < 0:
-		direction_arctan += 360
+		intensity_image[intensity_image<=0.] = 0. #important to clip as negative intensities misbehave with center of mass
+		intensity_weighted_center = center_of_mass(intensity_image*regionmask, regionmask, 1)
+		centroid_x = intensity_weighted_center[1]
+		centroid_y = intensity_weighted_center[0]
 
-	return distance, direction_arctan, centroid_x - geometric_centroid_x, centroid_y - geometric_centroid_y
+		geometric_centroid_x = np.sum(xtemp * regionmask) / np.sum(regionmask)
+		geometric_centroid_y = np.sum(ytemp * regionmask) / np.sum(regionmask)
+		distance = np.sqrt((geometric_centroid_y - centroid_y)**2 + (geometric_centroid_x - centroid_x)**2)
 
-def intensity_radial_gradient(regionmask, intensity_image):
+		delta_x = geometric_centroid_x - centroid_x
+		delta_y = geometric_centroid_y - centroid_y
+		direction_arctan = np.arctan2(delta_y, delta_x) * 180 / np.pi
 
-	try:
-		warnings.filterwarnings('ignore', message="Polyfit may be poorly conditioned")
-		cell_mask = regionmask.copy()
-		intensity = intensity_image.copy()
-		y = intensity[cell_mask].flatten()
-		x = distance_transform_edt(cell_mask)
-		x = x[cell_mask].flatten()
-		params = np.polyfit(x, y, 1)
-		line = np.poly1d(params)
+		return distance, direction_arctan, centroid_x - geometric_centroid_x, centroid_y - geometric_centroid_y
 
-		return line.coefficients[0], line.coefficients[1]
-	except Exception as e:
-		print(e)
-		return np.nan, np.nan
+	else:
+		return np.nan, np.nan, np.nan, np.nan
 
 
 def intensity_centre_of_mass_displacement_edge(regionmask, intensity_image):
-	
-	intensity_image = interpolate_nan(intensity_image.copy())
-	edge_mask = contour_of_instance_segmentation(regionmask, 3)
 
-	if np.sum(edge_mask)>0:
+	if np.any(intensity_image!=intensity_image):
+		intensity_image = interpolate_nan(intensity_image.copy())
+
+	edge_mask = contour_of_instance_segmentation(regionmask, 3)
+	
+	if not np.all(intensity_image.flatten()==0) and np.sum(edge_mask)>0:
 		
 		y, x = np.mgrid[:edge_mask.shape[0], :edge_mask.shape[1]]
 		xtemp = x.copy()
 		ytemp = y.copy()
-		intensity_weighted_center = center_of_mass(intensity_image, edge_mask)
+		
+		intensity_image[intensity_image<=0.] = 0. #important to clip as negative intensities misbehave with center of mass
+		intensity_weighted_center = center_of_mass(intensity_image*edge_mask, edge_mask, 1)
 		centroid_x = intensity_weighted_center[1]
 		centroid_y = intensity_weighted_center[0]
 
@@ -243,17 +233,41 @@ def intensity_centre_of_mass_displacement_edge(regionmask, intensity_image):
 		geometric_centroid_x = np.sum(xtemp * regionmask) / np.sum(regionmask)
 		geometric_centroid_y = np.sum(ytemp * regionmask) / np.sum(regionmask)
 		
-		try:
-			distance = euclidean(np.array((geometric_centroid_y, geometric_centroid_x)), np.array((centroid_y, centroid_x)))
-		except:
-			distance = np.nan
+		distance = np.sqrt((geometric_centroid_y - centroid_y)**2 + (geometric_centroid_x - centroid_x)**2)
 
 		delta_x = geometric_centroid_x - centroid_x
 		delta_y = geometric_centroid_y - centroid_y
 		direction_arctan = np.arctan2(delta_y, delta_x) * 180 / np.pi
-		if direction_arctan < 0:
-			direction_arctan += 360
 
 		return distance, direction_arctan, centroid_x - geometric_centroid_x, centroid_y - geometric_centroid_y
 	else:
-		return np.nan, np.nan, np.nan, np.nan
+		return np.nan, np.nan, np.nan, np.nan
+
+
+def intensity_radial_gradient(regionmask, intensity_image):
+
+	"""
+	Determine if intensities are following a linear gradient from center to edge of the cell.
+	"""
+	
+	if np.any(intensity_image!=intensity_image):
+		intensity_image = interpolate_nan(intensity_image.copy())
+	
+	# try:
+	warnings.filterwarnings('ignore', message="Polyfit may be poorly conditioned")
+	
+	# intensities
+	y = intensity_image[regionmask].flatten()
+
+	# distance to edge
+	x = distance_transform_edt(regionmask.copy())
+	x = x[regionmask].flatten()
+	x = max(x) - x # origin at center of cells
+
+	params = np.polyfit(x, y, 1)
+	line = np.poly1d(params)
+	# coef > 0 --> more signal at edge than center, coef < 0 --> more signal at center than edge
+
+	r2 = r2_score(y, line(x))
+	
+	return line.coefficients[0], line.coefficients[1], r2

celldetective/gui/classifier_widget.py

@@ -365,7 +365,9 @@ class ClassifierWidget(QWidget, Styles):
 		except Exception as e:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText(f"The query could not be understood. No filtering was applied. {e}")
+			link = "https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html"
+			msg = "The query could not be understood. Please write a valid query following <a href='%s'>the documentation</a>. Wrap features in backticks (e.g. `feature` > 1) to facilitate query interpretation. " % link
+			msgBox.setText(msg)
 			msgBox.setWindowTitle("Warning")
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()

celldetective/gui/process_block.py

@@ -848,7 +848,7 @@ class ProcessPanel(QFrame, Styles):
 					if os.path.exists(os.sep.join([self.pos, 'output', 'tables', f'trajectories_{self.mode}.csv'])) and not self.parent_window.position_list.isMultipleSelection():
 						msgBox = QMessageBox()
 						msgBox.setIcon(QMessageBox.Question)
-						msgBox.setText("A trajectory set already exists. Previously annotated data for\nthis position will be lost. Do you want to proceed?")
+						msgBox.setText("A measurement table already exists. Previously annotated data for\nthis position will be lost. Do you want to proceed?")
 						msgBox.setWindowTitle("Info")
 						msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
 						returnValue = msgBox.exec()

celldetective/gui/processes/measure_cells.py

@@ -193,17 +193,20 @@ class MeasurementProcess(Process):
 		# Load trajectories, add centroid if not in trajectory
 		self.trajectories = self.pos+os.sep.join(['output','tables', self.table_name])
 		if os.path.exists(self.trajectories):
-			print('trajectory exists...')
+			print('Previous table detected...')
 			self.trajectories = pd.read_csv(self.trajectories)
 			if 'TRACK_ID' not in list(self.trajectories.columns):
+				print('Static measurements detected...')
 				self.do_iso_intensities = False
 				self.intensity_measurement_radii = None
 				if self.clear_previous:
-					print('No TRACK_ID... Clear previous measurements...')
+					print('Clear previous measurements...')
 					self.trajectories = None #remove_trajectory_measurements(trajectories, column_labels)
 					self.do_features = True
 					self.features += ['centroid']
+				self.column_labels.update({'track': 'ID'})
 			else:
+				print('Time series detected...')
 				if self.clear_previous:
 					print('TRACK_ID found... Clear previous measurements...')
 					self.trajectories = remove_trajectory_measurements(self.trajectories, self.column_labels)

celldetective/gui/thresholds_gui.py

@@ -1106,7 +1106,7 @@ class ThresholdNormalisation(ThresholdConfigWizard):
 			if len_movie_auto is not None:
 				self.len_movie = len_movie_auto
 			exp_config = self.exp_dir + "config.ini"
-			self.channel_names, self.channels = extract_experiment_channels(exp_config)
+			self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
 			self.channel_names = np.array(self.channel_names)
 			self.channels = np.array(self.channels)
 			self.nbr_channels = len(self.channels)

celldetective/io.py

@@ -210,19 +210,23 @@ def collect_experiment_metadata(pos_path=None, well_path=None):
 		pos_name = extract_position_name(pos_path)
 	else:
 		pos_name = 0
-	concentrations = get_experiment_concentrations(experiment, dtype=float)
-	cell_types = get_experiment_cell_types(experiment)
-	antibodies = get_experiment_antibodies(experiment)
-	pharmaceutical_agents = get_experiment_pharmaceutical_agents(experiment)
-	
-	dico = {"pos_path": pos_path, "position": pos_path, "pos_name": pos_name, "well_path": well_path, "well_name": well_name, "well_nbr": well_nbr, "experiment": experiment, "antibody": antibodies[idx], "concentration": concentrations[idx], "cell_type": cell_types[idx], "pharmaceutical_agent": pharmaceutical_agents[idx]}
+
+	dico = {"pos_path": pos_path, "position": pos_path, "pos_name": pos_name, "well_path": well_path, "well_name": well_name, "well_nbr": well_nbr, "experiment": experiment}
 
 	meta = get_experiment_metadata(experiment) # None or dict of metadata
 	if meta is not None:
 		keys = list(meta.keys())
 		for k in keys:
 			dico.update({k: meta[k]})
-	
+
+	labels = get_experiment_labels(experiment)
+	for k in list(labels.keys()):
+		values = labels[k]
+		try:
+			dico.update({k: values[idx]})
+		except Exception as e:
+			print(f"{e=}")
+
 	return dico
 
 
@@ -2498,24 +2502,34 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 		config = PurePath(expfolder, Path("config.ini"))
 		expfolder = str(expfolder)
 		exp_name = os.path.split(expfolder)[-1]
-		print(exp_name)
 
 		wells = get_experiment_wells(expfolder)
 		well_idx = list(wells).index(str(parent1)+os.sep)
-		ab = get_experiment_antibodies(expfolder)[well_idx]
-		conc = get_experiment_concentrations(expfolder)[well_idx]
-		ct = get_experiment_cell_types(expfolder)[well_idx]
-		pa = get_experiment_pharmaceutical_agents(expfolder)[well_idx]
 
+		label_info = get_experiment_labels(expfolder)
+		metadata_info = get_experiment_metadata(expfolder)
+
+		info = {}
+		for k in list(label_info.keys()):
+			values = label_info[k]
+			try:
+				info.update({k: values[well_idx]})
+			except Exception as e:
+				print(f"{e=}")
+
+		if metadata_info is not None:
+			keys = list(metadata_info.keys())
+			for k in keys:
+				info.update({k: metadata_info[k]})
 
 		spatial_calibration = float(ConfigSectionMap(config,"MovieSettings")["pxtoum"])
-		channel_names, channel_indices = extract_experiment_channels(config)
+		channel_names, channel_indices = extract_experiment_channels(expfolder)
 
 		annotation_folder = expfolder + os.sep + f'annotations_{population}' + os.sep
 		if not os.path.exists(annotation_folder):
 			os.mkdir(annotation_folder)
 
-		print('exporting!')
+		print('Exporting!')
 		t = viewer.dims.current_step[0]
 		labels_layer = viewer.layers['segmentation'].data[t]  # at current time
 
@@ -2578,11 +2592,14 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 
 				save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_roi_{xmin}_{xmax}_{ymin}_{ymax}_labelled.tif", lab, axes='YX')
 				save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_roi_{xmin}_{xmax}_{ymin}_{ymax}.tif", multichannel, axes='CYX')
-				info = {"spatial_calibration": spatial_calibration, "channels": list(channel_names), 'cell_type': ct, 'antibody': ab, 'concentration': conc, 'pharmaceutical_agent': pa}
+
+				info.update({"spatial_calibration": spatial_calibration, "channels": list(channel_names), 'frame': t})
+
 				info_name = annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_roi_{xmin}_{xmax}_{ymin}_{ymax}.json"
 				with open(info_name, 'w') as f:
 					json.dump(info, f, indent=4)
 
+
 		if fov_export:
 			frame = viewer.layers['Image'].data[t]
 			multichannel = [frame]
@@ -2595,11 +2612,14 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 			multichannel = np.array(multichannel)       
 			save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_labelled.tif", labels_layer, axes='YX')
 			save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}.tif", multichannel, axes='CYX')
-			info = {"spatial_calibration": spatial_calibration, "channels": list(channel_names), 'cell_type': ct, 'antibody': ab, 'concentration': conc, 'pharmaceutical_agent': pa}
+
+			info.update({"spatial_calibration": spatial_calibration, "channels": list(channel_names), 'frame': t})
+
 			info_name = annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}.json"
 			with open(info_name, 'w') as f:
 				json.dump(info, f, indent=4)
-			print('Done.')
+		
+		print('Done.')
 
 	@magicgui(call_button='Save the modified labels')
 	def save_widget():

celldetective/regionprops/_regionprops.py

@@ -101,12 +101,21 @@ class CustomRegionProps(RegionProperties):
 						arg_dict = dict(inspect.signature(func).parameters)
 						if self.channel_names is not None and 'target_channel' in arg_dict:
 							multichannel_list = [np.nan for i in range(self.image_intensity.shape[-1])]
+							len_output = 1
 							default_channel = arg_dict['target_channel']._default
+							
 							if default_channel in self.channel_names:
+								
 								idx = self.channel_names.index(default_channel)
-								multichannel_list[idx] = func(self.image, self.image_intensity[..., idx])
+								res = func(self.image, self.image_intensity[..., idx])
+								len_output = len(res)
+
+								multichannel_list = [[np.nan]*len_output for c in range(len(self.channel_names))]
+								multichannel_list[idx] = res
+
 							else:
 								print(f'Warning... Channel required by custom measurement ({default_channel}) could not be found in your data...')
+							
 							return np.stack(multichannel_list, axis=-1)
 						else:
 							multichannel_list = [

celldetective/scripts/measure_cells.py

@@ -59,7 +59,7 @@ movie_prefix = ConfigSectionMap(config,"MovieSettings")["movie_prefix"]
 spatial_calibration = float(ConfigSectionMap(config,"MovieSettings")["pxtoum"])
 time_calibration = float(ConfigSectionMap(config,"MovieSettings")["frametomin"])
 len_movie = float(ConfigSectionMap(config,"MovieSettings")["len_movie"])
-channel_names, channel_indices = extract_experiment_channels(config)
+channel_names, channel_indices = extract_experiment_channels(expfolder)
 nbr_channels = len(channel_names)
 
 # from tracking instructions, fetch btrack config, features, haralick, clean_traj, idea: fetch custom timeline?

celldetective/scripts/segment_cells_thresholds.py

@@ -72,7 +72,7 @@ threshold_instructions.update({'target_channel': channel_indices[0]})
 
 movie_prefix = ConfigSectionMap(config,"MovieSettings")["movie_prefix"]
 len_movie = float(ConfigSectionMap(config,"MovieSettings")["len_movie"])
-channel_names, channel_indices = extract_experiment_channels(config)
+channel_names, channel_indices = extract_experiment_channels(expfolder)
 threshold_instructions.update({'channel_names': channel_names})
 
 # Try to find the file

celldetective/scripts/track_cells.py

@@ -72,7 +72,7 @@ len_movie = float(ConfigSectionMap(config,"MovieSettings")["len_movie"])
 shape_x = int(ConfigSectionMap(config,"MovieSettings")["shape_x"])
 shape_y = int(ConfigSectionMap(config,"MovieSettings")["shape_y"])
 
-channel_names, channel_indices = extract_experiment_channels(config)
+channel_names, channel_indices = extract_experiment_channels(expfolder)
 nbr_channels = len(channel_names)
 
 # from tracking instructions, fetch btrack config, features, haralick, clean_traj, idea: fetch custom timeline?

celldetective/utils.py

@@ -1127,11 +1127,9 @@ def mask_edges(binary_mask, border_size):
 	return binary_mask
 
 def demangle_column_name(name):
-	if name.startswith("BACKTICK_QUOTED_STRING_") and not '_MINUS_' in name:
+	if name.startswith("BACKTICK_QUOTED_STRING_"):
 		# Unquote backtick-quoted string.
-		return name[len("BACKTICK_QUOTED_STRING_"):].replace("_DOT_", ".").replace("_SLASH_", "/")
-	elif name.startswith("BACKTICK_QUOTED_STRING_") and '_MINUS_' in name:
-		return name[len("BACKTICK_QUOTED_STRING_"):].replace("_DOT_", ".").replace("_SLASH_", "/").replace('_MINUS_','-')
+		return name[len("BACKTICK_QUOTED_STRING_"):].replace("_DOT_", ".").replace("_SLASH_", "/").replace('_MINUS_','-').replace('_PLUS_','+').replace('_PERCENT_','%').replace('_STAR_','*').replace('_LPAR_','(').replace('_RPAR_',')').replace('_AMPER_','&')
 	return name
 
 def extract_cols_from_query(query: str):
@@ -1250,124 +1248,103 @@ def rename_intensity_column(df, channels):
 	# Rename the intensity columns in the DataFrame based on the provided channel names.
 
 	"""
-
+		
 	channel_names = np.array(channels)
 	channel_indices = np.arange(len(channel_names),dtype=int)
+	intensity_cols = [s for s in list(df.columns) if 'intensity' in s]
+	
+	to_rename = {}
 
-	if np.any(['intensity' in c for c in list(df.columns)]):
-
-		intensity_indices = [s.startswith('intensity') for s in df.columns]
-		intensity_columns = df.columns[intensity_indices]
-
-		if len(channel_names) >= 1:
-			to_rename = {}
-			for k in range(len(intensity_columns)):
-
-				sections = np.array(re.split('-|_', intensity_columns[k]))
-				test_digit = np.array([s.isdigit() for s in sections])
-				index = int(sections[np.where(test_digit)[0]][-1])
+	for k in range(len(intensity_cols)):
+		
+		# identify if digit in section
+		sections = np.array(re.split('-|_', intensity_cols[k]))
+		test_digit = np.array([False for s in sections])
+		for j,s in enumerate(sections):
+			if s.isdigit():
+				if int(s)<len(channel_names):
+					test_digit[j] = True
+		print(f"{test_digit=}")
+			
+		if np.any(test_digit):
+			index = int(sections[np.where(test_digit)[0]][-1])
+		else:
+			print(f'No valid channel index found for {intensity_cols[k]}... Skipping the renaming for {intensity_cols[k]}...')
+			continue
+			
+		channel_name = channel_names[np.where(channel_indices==index)[0]][0]
+		new_name = np.delete(sections, np.where(test_digit)[0]) #np.where(test_digit)[0]
+		new_name = '_'.join(list(new_name))
+		new_name = new_name.replace('intensity', channel_name)
+		new_name = new_name.replace('-','_')
+		new_name = new_name.replace('_nanmean','_mean')
+		
+		to_rename.update({intensity_cols[k]: new_name})
+		
+		if 'centre' in intensity_cols[k]:
 
-				channel_name = channel_names[np.where(channel_indices==index)[0]][0]
-				new_name = np.delete(sections, np.where(test_digit)[0]) #np.where(test_digit)[0]
+			measure = np.array(re.split('-|_', new_name))
+			
+			if sections[-2] == "0":
+				new_name = np.delete(measure, -1)
 				new_name = '_'.join(list(new_name))
-				new_name = new_name.replace('intensity', channel_name)
-				new_name = new_name.replace('-','_')
-				new_name = new_name.replace('_nanmean','_mean')
-
-				to_rename.update({intensity_columns[k]: new_name})
-
-				if 'centre' in intensity_columns[k]:
-					# sections = np.array(re.split('-|_', intensity_columns[k]))
-					measure = np.array(re.split('-|_', new_name))
-					if sections[-2] == "0":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(new_name))
-						if 'edge' in intensity_columns[k]:
-							new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_displacement_in_px")
-						else:
-							new_name = new_name.replace('centre_of_mass', "centre_of_mass_displacement_in_px")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-					elif sections[-2] == "1":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(new_name))
-						if 'edge' in intensity_columns[k]:
-							new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_orientation")
-						else:
-							new_name = new_name.replace('centre_of_mass', "centre_of_mass_orientation")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-					elif sections[-2] == "2":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(new_name))
-						if 'edge' in intensity_columns[k]:
-							new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_x")
-						else:
-							new_name = new_name.replace('centre_of_mass', "centre_of_mass_x")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-					elif sections[-2] == "3":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(new_name))
-						if 'edge' in intensity_columns[k]:
-							new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_y")
-						else:
-							new_name = new_name.replace('centre_of_mass', "centre_of_mass_y")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-				if 'radial_gradient' in intensity_columns[k]:
-					# sections = np.array(re.split('-|_', intensity_columns[k]))
-					measure = np.array(re.split('-|_', new_name))
-					if sections[-2] == "0":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(measure))
-						new_name = new_name.replace('radial_gradient', "radial_gradient")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-					elif sections[-2] == "1":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(measure))
-						new_name = new_name.replace('radial_gradient', "radial_intercept")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-		else:
-			to_rename = {}
-			for k in range(len(intensity_columns)):
-				sections = np.array(re.split('_|-', intensity_columns[k]))
-				channel_name = channel_names[0]
-				test_digit = np.array([s.isdigit() for s in sections])
-				new_name = np.delete(sections, np.where(test_digit)[0])
+				if 'edge' in intensity_cols[k]:
+					new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_displacement_in_px")
+				else:
+					new_name = new_name.replace('centre_of_mass', "centre_of_mass_displacement_in_px")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
+			
+			elif sections[-2] == "1":
+				new_name = np.delete(measure, -1)
+				new_name = '_'.join(list(new_name))
+				if 'edge' in intensity_cols[k]:
+					new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_orientation")
+				else:
+					new_name = new_name.replace('centre_of_mass', "centre_of_mass_orientation")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
+				
+			elif sections[-2] == "2":
+				new_name = np.delete(measure, -1)
+				new_name = '_'.join(list(new_name))
+				if 'edge' in intensity_cols[k]:
+					new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_x")
+				else:
+					new_name = new_name.replace('centre_of_mass', "centre_of_mass_x")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
+			
+			elif sections[-2] == "3":
+				new_name = np.delete(measure, -1)
 				new_name = '_'.join(list(new_name))
-				new_name = new_name.replace('intensity', channel_name)
-				to_rename.update({intensity_columns[k]: new_name.replace('-','_')})
-				if 'centre' in intensity_columns[k]:
-					measure = np.array(re.split('-|_', new_name))
-					if sections[-2] == "0":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(new_name))
-						if 'edge' in intensity_columns[k]:
-							new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_displacement_in_px")
-						else:
-							new_name = new_name.replace('centre_of_mass', "centre_of_mass_displacement_in_px")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-					if sections[-2] == "1":
-						new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(new_name))
-						if 'edge' in intensity_columns[k]:
-							new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_orientation")
-						else:
-							new_name = new_name.replace('centre_of_mass', "centre_of_mass_orientation")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-				if 'radial_gradient' in intensity_columns[k]:
-					# sections = np.array(re.split('-|_', intensity_columns[k]))
-					measure = np.array(re.split('-|_', new_name))
-					if sections[-2] == "0":
-						#new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(measure))
-						new_name = new_name.replace('radial_gradient', "radial_gradient")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-					elif sections[-2] == "1":
-						#new_name = np.delete(measure, -1)
-						new_name = '_'.join(list(measure))
-						new_name = new_name.replace('radial_gradient', "radial_intercept")
-						to_rename.update({intensity_columns[k]: new_name.replace('-', '_')})
-
-		df = df.rename(columns=to_rename)
+				if 'edge' in intensity_cols[k]:
+					new_name = new_name.replace('centre_of_mass_displacement', "edge_centre_of_mass_y")
+				else:
+					new_name = new_name.replace('centre_of_mass', "centre_of_mass_y")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
+		
+		if 'radial_gradient' in intensity_cols[k]:
+			# sections = np.array(re.split('-|_', intensity_columns[k]))
+			measure = np.array(re.split('-|_', new_name))
+			
+			if sections[-2] == "0":
+				new_name = np.delete(measure, -1)
+				new_name = '_'.join(list(measure))
+				new_name = new_name.replace('radial_gradient', "radial_gradient")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
+			
+			elif sections[-2] == "1":
+				new_name = np.delete(measure, -1)
+				new_name = '_'.join(list(measure))
+				new_name = new_name.replace('radial_gradient', "radial_intercept")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
+	
+			elif sections[-2] == "2":
+				new_name = np.delete(measure, -1)
+				new_name = '_'.join(list(measure))
+				new_name = new_name.replace('radial_gradient', "radial_gradient_r2_score")
+				to_rename.update({intensity_cols[k]: new_name.replace('-', '_')})
 
+	df = df.rename(columns=to_rename)
+	
 	return df
 
 
@@ -2064,7 +2041,7 @@ def _get_img_num_per_channel(channels_indices, len_movie, nbr_channels):
 	>>> img_num_per_channel = _get_img_num_per_channel(channels_indices, len_movie, nbr_channels)
 	>>> print(img_num_per_channel)
 	# array([[ 1,  4,  7, 10, 13, 16, 19, 22, 25, 28],
-    #   [ 2,  5,  8, 11, 14, 17, 20, 23, 26, 29]])
+	#   [ 2,  5,  8, 11, 14, 17, 20, 23, 26, 29]])
 
 	"""
 
@@ -2152,9 +2129,9 @@ def _extract_channels_from_config(config):
 	>>> channels, indices = _extract_channels_from_config(config)
 	>>> print(channels)
 	# array(['brightfield_channel', 'adhesion_channel', 'fitc_channel',
-    #    'cy5_channel'], dtype='<U19')
-    >>> print(indices)
-    # array([0, 1, 2, 3])
+	#    'cy5_channel'], dtype='<U19')
+	>>> print(indices)
+	# array([0, 1, 2, 3])
 	"""
 
 	channel_names = []
@@ -2203,9 +2180,9 @@ def extract_experiment_channels(experiment):
 	>>> channels, indices = extract_experiment_channels(experiment)
 	>>> print(channels)
 	# array(['brightfield_channel', 'adhesion_channel', 'fitc_channel',
-    #    'cy5_channel'], dtype='<U19')
-    >>> print(indices)
-    # array([0, 1, 2, 3])
+	#    'cy5_channel'], dtype='<U19')
+	>>> print(indices)
+	# array([0, 1, 2, 3])
 	"""
 
 	config = get_config(experiment)

{celldetective-1.3.9.post1.dist-info → celldetective-1.3.9.post3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: celldetective
-Version: 1.3.9.post1
+Version: 1.3.9.post3
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.3.9.post1.dist-info → celldetective-1.3.9.post3.dist-info}/RECORD

@@ -1,10 +1,10 @@
 celldetective/__init__.py,sha256=bi3SGTMo6s2qQBsJAaKy-a4xaGcTQVW8zsqaiX5XKeY,139
 celldetective/__main__.py,sha256=bxTlSvbKhqn3LW_azd2baDCnDsgb37PAP9DfuAJ1_5M,1844
-celldetective/_version.py,sha256=inUx6HfMP-hKJVuc180XI7aE6ZP97KgQuKEq2PfuRJ4,28
+celldetective/_version.py,sha256=7LdGJtBuAQ99wkn-0aLzi5WGP1RCrguzXtOTqLyM6m8,28
 celldetective/events.py,sha256=UkjY_-THo6WviWWCLnDbma7jWOd_O9a60C4IOX2htG8,8254
-celldetective/extra_properties.py,sha256=PUs-lltSj_jSko_Gd-w483OxZW6oR3BAHQrw51DUxMg,8081
+celldetective/extra_properties.py,sha256=nP_EX2yxJuZRP283uYzN8km-_uOfW94u0zD_K2bIub8,8689
 celldetective/filters.py,sha256=6pl2IGPK2FH8KPWbjzQEbT4C-ruqE1fQ8NQNN7Euvy8,4433
-celldetective/io.py,sha256=HEy9KbidrPVbzzbC1kJcXR0TsvIxNgRiDk31ecdjxpE,121954
+celldetective/io.py,sha256=KDb1N7ccUAUXKE2NHo9TIC7A5u2A9wYieGteoa0ymN0,121754
 celldetective/measure.py,sha256=h1F08Vf7sy-20syMFZTUl1lHzE4h6cQvswJpwD9fcfE,58475
 celldetective/neighborhood.py,sha256=s-zVsfGnPlqs6HlDJCXRh21lLiPKbA_S1JC6uZvfG_0,56712
 celldetective/preprocessing.py,sha256=Wlt_PJua97CpMuWe_M65znUmz_yjYPqWIcs2ZK_RLgk,44109
@@ -12,7 +12,7 @@ celldetective/relative_measurements.py,sha256=-GWig0lC5UWAcJSPlo9Sp45khGj80fxuQf
 celldetective/segmentation.py,sha256=WApzoU1s3Ntvp0eIw_pRZXNwCA8LDKC9YoyR52tioz4,30943
 celldetective/signals.py,sha256=nMyyGUpla8D2sUYKY1zjbWsAueVPI_gUalY0KXfWteI,111595
 celldetective/tracking.py,sha256=VBJLd-1EeJarOVPBNEomhVBh9UYAMdSnH0tmUiUoTrY,40242
-celldetective/utils.py,sha256=RzC5yzuspnqF0_FG20mFTlrvPR2l5tpW0fyL32JccqY,106342
+celldetective/utils.py,sha256=0LENOCxNMuEmClLiyvo_jIO2as4i7a5bMk1NaXUhgVs,104430
 celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/InitWindow.py,sha256=TPKWYczhPHvPKWg654sXnE9xCEx6U-oWX0_OJgLTWbU,15044
@@ -20,7 +20,7 @@ celldetective/gui/__init__.py,sha256=2_r2xfOj4_2xj0yBkCTIfzlF94AHKm-j6Pvpd7DddQc
 celldetective/gui/about.py,sha256=FJZrj6C-p6uqp_3UaprKosuW-Sw9_HPNQAvFbis9Gdk,1749
 celldetective/gui/analyze_block.py,sha256=h0sp7Tk3hZFM8w0yTidwIjZX4WRI-lQF3JCFObrLCPo,2761
 celldetective/gui/btrack_options.py,sha256=F2wrhuaNSaBr6vNApI22XSjdI5Cl3q138qCYBk-FDu4,44684
-celldetective/gui/classifier_widget.py,sha256=nHWmaWXse2CxxRFmR4mA0JRADr5i0MsWldaqJQIQ-i8,19992
+celldetective/gui/classifier_widget.py,sha256=73h13QFtvYEy_jLl2DfSy9P3ERIOjWJAPn5mllYMPGc,20224
 celldetective/gui/configure_new_exp.py,sha256=N4SdL-4Xo0XbTAkCtt1ywr74HmHc5eaPlHGv1XgxAX0,20772
 celldetective/gui/control_panel.py,sha256=jFpedm03x6_jKabeadsNiigKnlh7sXCkulwe4gMCJaM,22042
 celldetective/gui/generic_signal_plot.py,sha256=Gv4KhA5vhbgVSj5jteE42T0aNCoQZtmIAUkEsMi6JNA,36309
@@ -31,7 +31,7 @@ celldetective/gui/measurement_options.py,sha256=sxtQPKSixVbrFcBC1XLLC4-h7ZHlgTLc
 celldetective/gui/neighborhood_options.py,sha256=FBNDvlzMPKp8s0Grxds90pCPHG1s27XrpMN0HV2gf0I,19839
 celldetective/gui/plot_measurements.py,sha256=n0pDUcYcsKlSMaUaBSVplGziuWp_7jKaeXdREs-MqyI,50848
 celldetective/gui/plot_signals_ui.py,sha256=7jCu-wLk_NDL4ThLZwhltODngre8iqPMUcEhJNNllo8,18189
-celldetective/gui/process_block.py,sha256=dH0zHIEouL8ApAD4uN7IR9dSl8X8QqE-hXL6U7HZHaM,71212
+celldetective/gui/process_block.py,sha256=rFmtrnYBohjNRqSTjxC86yDNnzcXE7w9eo9Vm0heh6A,71215
 celldetective/gui/retrain_segmentation_model_options.py,sha256=7iawDN4kwq56Z-dX9kQe9tLW8B3YMrIW_D85LMAAYwk,23906
 celldetective/gui/retrain_signal_model_options.py,sha256=GCa0WKKsgmH2CFDHAKxPGbHtCE19p1_bbcWNasyZw5o,22482
 celldetective/gui/seg_model_loader.py,sha256=b1BiHuAf_ZqroE4jSEVCo7ASQv-xyWMPWU799alpbNM,19727
@@ -41,7 +41,7 @@ celldetective/gui/signal_annotator_options.py,sha256=Tq20tybpelHFUqFCSemqH9es2Fq
 celldetective/gui/styles.py,sha256=SZy_ACkA6QB_4ANyY1V0m1QF66C0SVGssOrwW1Qt1Aw,5076
 celldetective/gui/survival_ui.py,sha256=Q-530cAK-SsKPr8sWFTbhGekB2CFLWd0SNjtV1Wr0oo,14202
 celldetective/gui/tableUI.py,sha256=Yz_pHk1ERXRb0QsBPrvLEwAGpvVlawgn1b6uzz5wL_0,58022
-celldetective/gui/thresholds_gui.py,sha256=O7NkeaPV1nnQdTbduXd3lMttWPBzKcJ-9jI5OMr8H-0,48808
+celldetective/gui/thresholds_gui.py,sha256=nxKYcEAGVdnQK0RM8pOu9MtYuBIYEvXiQCygzRjhv08,48810
 celldetective/gui/viewers.py,sha256=HDLB6j1FJwgKR6dQwzeHmcDvDMbDIYwD2svd-VZhJFE,47806
 celldetective/gui/workers.py,sha256=P4qUMXuCtGcggGmJr3VitAPSfRG30wkJ1B0pfcdGbKg,4225
 celldetective/gui/help/DL-segmentation-strategy.json,sha256=PZD9xXjrwbX3TiudHJPuvcyZD28o4k-fVgeTd7dBKzI,1583
@@ -56,7 +56,7 @@ celldetective/gui/help/propagate-classification.json,sha256=F7Ir1mtgRVTXWLN7n3ny
 celldetective/gui/help/track-postprocessing.json,sha256=VaGd8EEkA33OL-EI3NXWZ8yHeWWyUeImDF5yAjsVYGA,3990
 celldetective/gui/help/tracking.json,sha256=yIAoOToqCSQ_XF4gwEZCcyXcvQ3mROju263ZPDvlUyY,776
 celldetective/gui/processes/downloader.py,sha256=SuMTuM82QOZBqLfj36I14fhZ2k3NmLp0PBcGUHxnpXI,3287
-celldetective/gui/processes/measure_cells.py,sha256=MLkVLLuUtVVgwQB9a9N8eZ5TzF-Xtuhzb5wtcFRa1lU,12846
+celldetective/gui/processes/measure_cells.py,sha256=7JPNkUCZ-w8v7yW-jwghH70Auk-IMOjlsnZlfr1Qjp0,12966
 celldetective/gui/processes/segment_cells.py,sha256=49Bh3nejkrxlLNhlP3Y_6-flkBOhkqFMQmrc2qDj7Dk,11320
 celldetective/gui/processes/track_cells.py,sha256=y8ohHAMcGtAjrJOP1WqvDfy_K85LbmdXoN7CA7BYpaY,9942
 celldetective/gui/processes/train_segmentation_model.py,sha256=bvcPG19hBjhNY9hd6Ch5_wk2FOJYQg97Azoz4RKeP-0,10776
@@ -99,14 +99,14 @@ celldetective/models/tracking_configs/no_z_motion.json,sha256=b4RWOJ0w6Y2e0vJYwK
 celldetective/models/tracking_configs/ricm.json,sha256=L-vmwCR1f89U-qnH2Ms0cBfPFR_dxIWoe2ccH8V-QBA,2727
 celldetective/models/tracking_configs/ricm2.json,sha256=DDjJ6ScYcDWvlsy7ujPID8v8H28vcNcMuZmNR8XmGxo,2718
 celldetective/regionprops/__init__.py,sha256=ohe9vC7j4lnpKnGXidVo1PVfoQfC8TqCuHTNo8rXmdg,44
-celldetective/regionprops/_regionprops.py,sha256=K1yHZDdLe81N9w73XMmRVLVsaMXJ3IE5VLP8ui6QsL4,9855
+celldetective/regionprops/_regionprops.py,sha256=5pxet-E2Eg6bSs7n0xjknDPQr15G14nUAqPRfDffzz0,10042
 celldetective/regionprops/props.json,sha256=sCwACmbh0n-JAw9eve9yV85REukoMBJLsRjxCwTRMm8,2424
 celldetective/scripts/analyze_signals.py,sha256=YE05wZujl2hQFWkvqATBcCx-cAd_V3RxnvKoh0SB7To,2194
-celldetective/scripts/measure_cells.py,sha256=GvuHrSb3S-JnUjBaACx84BhUd_vUrwEHiSgDV9BoXXE,11766
+celldetective/scripts/measure_cells.py,sha256=edZ9xlUsLg1TI_yudp7bd04B_oqdHk9Ee4mSDe8G86w,11769
 celldetective/scripts/measure_relative.py,sha256=wI7ibgWCsh5NVfcYum9LK0khL7cwKyCxwHFaXG4oWjM,3698
 celldetective/scripts/segment_cells.py,sha256=AZfHqig0WBMkAh9ho7JHmjM9vMO-EiPVviTHJcDj5Mw,6954
-celldetective/scripts/segment_cells_thresholds.py,sha256=lsW5hsHenNPiyIwZuZHipeCN2Wer69VcLko5rS96GAU,5118
-celldetective/scripts/track_cells.py,sha256=_OPfn9BsbvdpAU4dg36SXmOTx_BkDkZL4N05X0_Tig4,8795
+celldetective/scripts/segment_cells_thresholds.py,sha256=J_QW53ndopSeq-uelBa2oTUCC2wG_FFCahEnn7PYpUE,5121
+celldetective/scripts/track_cells.py,sha256=3I83-rkaShSzBSvYH0OVzjcgHeIohCxumA5W-lHg5Rw,8798
 celldetective/scripts/train_segmentation_model.py,sha256=XExaGg8kkdirgN206J0mwiWtqeRE076-Ld2b89tReAI,9229
 celldetective/scripts/train_signal_model.py,sha256=D643wKVYg-LWHF2VU9FWKSuazXrpCpQK0YjGqoIimD0,3167
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -121,9 +121,9 @@ tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,34
 tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
 tests/test_tracking.py,sha256=8hebWSqEIuttD1ABn-6dKCT7EXKRR7-4RwyFWi1WPFo,8800
 tests/test_utils.py,sha256=NKRCAC1d89aBK5cWjTb7-pInYow901RrT-uBlIdz4KI,3692
-celldetective-1.3.9.post1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-celldetective-1.3.9.post1.dist-info/METADATA,sha256=BoHCKyoqbyXNoavOGrxdZI9_7D9Uc-MX-KRQ65s7pO0,10753
-celldetective-1.3.9.post1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-celldetective-1.3.9.post1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.3.9.post1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.3.9.post1.dist-info/RECORD,,
+celldetective-1.3.9.post3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.3.9.post3.dist-info/METADATA,sha256=IH5Ea7-lEKV8k_kgSYxLmxN9mB_IcncHnRExw5HSN5w,10753
+celldetective-1.3.9.post3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+celldetective-1.3.9.post3.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.3.9.post3.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.3.9.post3.dist-info/RECORD,,