celldetective 1.3.0.post1__py3-none-any.whl → 1.3.2__py3-none-any.whl

celldetective/signals.py

@@ -17,6 +17,7 @@ from sklearn.metrics import confusion_matrix, classification_report
 from sklearn.metrics import jaccard_score, balanced_accuracy_score, precision_score, recall_score
 from scipy.interpolate import interp1d
 from scipy.ndimage import shift
+from sklearn.metrics import ConfusionMatrixDisplay
 
 from celldetective.io import locate_signal_model, get_position_pickle, get_position_table
 from celldetective.tracking import clean_trajectories, interpolate_nan_properties
@@ -149,7 +150,7 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 	assert os.path.exists(model_config_path),f'Model configuration could not be located in folder {model_path}... Abort.'
 
 	available_signals = list(trajectories.columns)
-	print('The available_signals are : ',available_signals)
+	#print('The available_signals are : ',available_signals)
 
 	f = open(model_config_path)
 	config = json.load(f)
@@ -167,22 +168,11 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 		selected_signals = []
 		for s in required_signals:
 			pattern_test = [s in a or s==a for a in available_signals]
-			print(f'Pattern test for signal {s}: ', pattern_test)
+			#print(f'Pattern test for signal {s}: ', pattern_test)
 			assert np.any(pattern_test),f'No signal matches with the requirements of the model {required_signals}. Please pass the signals manually with the argument selected_signals or add measurements. Abort.'
-			valid_columns = np.array(available_signals)[np.array(pattern_test)]
-			if len(valid_columns)==1:
-				selected_signals.append(valid_columns[0])
-			else:
-				#print(test_number_of_nan(trajectories, valid_columns))
-				print(f'Found several candidate signals: {valid_columns}')
-				for vc in natsorted(valid_columns):
-					if 'circle' in vc:
-						selected_signals.append(vc)
-						break
-				else:
-					selected_signals.append(valid_columns[0])
-				# do something more complicated in case of one to many columns
-				#pass
+			valid_columns = natsorted(np.array(available_signals)[np.array(pattern_test)])
+			print(f"Selecting the first time series among: {valid_columns} for input requirement {s}...")
+			selected_signals.append(valid_columns[0])
 	else:
 		assert len(selected_signals)==len(required_signals),f'Mismatch between the number of required signals {required_signals} and the provided signals {selected_signals}... Abort.'
 
@@ -202,13 +192,7 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 			signals[i,frames,j] = signal
 			signals[i,max(frames):,j] = signal[-1]
 
-	# for i in range(5):
-	# 	print('pre model')
-	# 	plt.plot(signals[i,:,0])
-	# 	plt.show()
-
 	model = SignalDetectionModel(pretrained=complete_path)
-	print('signal shape: ', signals.shape)
 
 	classes = model.predict_class(signals)
 	times_recast = model.predict_time_of_interest(signals)
@@ -378,194 +362,193 @@ def analyze_pair_signals_at_position(pos, model, use_gpu=True):
 	return None		
 
 
-def analyze_signals(trajectories, model, interpolate_na=True,
-                    selected_signals=None,
-                    model_path=None,
-                    column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'},
-                    plot_outcome=False, output_dir=None):
-    """
-	Analyzes signals from trajectory data using a specified signal detection model and configuration.
-
-	This function preprocesses trajectory data, selects specified signals, and applies a pretrained signal detection
-	model to predict classes and times of interest for each trajectory. It supports custom column labeling, interpolation
-	of missing values, and plotting of analysis outcomes.
-
-	Parameters
-	----------
-	trajectories : pandas.DataFrame
-		DataFrame containing trajectory data with columns for track ID, frame, position, and signals.
-	model : str
-		The name of the signal detection model to be used for analysis.
-	interpolate_na : bool, optional
-		Whether to interpolate missing values in the trajectories (default is True).
-	selected_signals : list of str, optional
-		A list of column names from `trajectories` representing the signals to be analyzed. If None, signals will
-		be automatically selected based on the model configuration (default is None).
-	column_labels : dict, optional
-		A dictionary mapping the default column names ('track', 'time', 'x', 'y') to the corresponding column names
-		in `trajectories` (default is {'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}).
-	plot_outcome : bool, optional
-		If True, generates and saves a plot of the signal analysis outcome (default is False).
-	output_dir : str, optional
-		The directory where the outcome plot will be saved. Required if `plot_outcome` is True (default is None).
-
-	Returns
-	-------
-	pandas.DataFrame
-		The input `trajectories` DataFrame with additional columns for predicted classes, times of interest, and
-		corresponding colors based on status and class.
-
-	Raises
-	------
-	AssertionError
-		If the model or its configuration file cannot be located.
-
-	Notes
-	-----
-	- The function relies on an external model configuration file (`config_input.json`) located in the model's directory.
-	- Signal selection and preprocessing are based on the requirements specified in the model's configuration.
-
-	"""
-
-    model_path = locate_signal_model(model, path=model_path)
-    complete_path = model_path  # +model
-    complete_path = rf"{complete_path}"
-    model_config_path = os.sep.join([complete_path, 'config_input.json'])
-    model_config_path = rf"{model_config_path}"
-    assert os.path.exists(complete_path), f'Model {model} could not be located in folder {model_path}... Abort.'
-    assert os.path.exists(
-        model_config_path), f'Model configuration could not be located in folder {model_path}... Abort.'
-
-    available_signals = list(trajectories.columns)
-    print('The available_signals are : ', available_signals)
-
-    f = open(model_config_path)
-    config = json.load(f)
-    required_signals = config["channels"]
-
-    try:
-        label = config['label']
-        if label == '':
-            label = None
-    except:
-        label = None
-
-    if selected_signals is None:
-        selected_signals = []
-        for s in required_signals:
-            pattern_test = [s in a or s == a for a in available_signals]
-            print(f'Pattern test for signal {s}: ', pattern_test)
-            assert np.any(
-                pattern_test), f'No signal matches with the requirements of the model {required_signals}. Please pass the signals manually with the argument selected_signals or add measurements. Abort.'
-            valid_columns = np.array(available_signals)[np.array(pattern_test)]
-            if len(valid_columns) == 1:
-                selected_signals.append(valid_columns[0])
-            else:
-                # print(test_number_of_nan(trajectories, valid_columns))
-                print(f'Found several candidate signals: {valid_columns}')
-                for vc in natsorted(valid_columns):
-                    if 'circle' in vc:
-                        selected_signals.append(vc)
-                        break
-                else:
-                    selected_signals.append(valid_columns[0])
-        # do something more complicated in case of one to many columns
-        # pass
-    else:
-        assert len(selected_signals) == len(
-            required_signals), f'Mismatch between the number of required signals {required_signals} and the provided signals {selected_signals}... Abort.'
-
-    print(f'The following channels will be passed to the model: {selected_signals}')
-    trajectories_clean = clean_trajectories(trajectories, interpolate_na=interpolate_na,
-                                            interpolate_position_gaps=interpolate_na, column_labels=column_labels)
-
-    max_signal_size = int(trajectories_clean[column_labels['time']].max()) + 2
-    tracks = trajectories_clean[column_labels['track']].unique()
-    signals = np.zeros((len(tracks), max_signal_size, len(selected_signals)))
-
-    for i, (tid, group) in enumerate(trajectories_clean.groupby(column_labels['track'])):
-        frames = group[column_labels['time']].to_numpy().astype(int)
-        for j, col in enumerate(selected_signals):
-            signal = group[col].to_numpy()
-            signals[i, frames, j] = signal
-            signals[i, max(frames):, j] = signal[-1]
-
-    # for i in range(5):
-    # 	print('pre model')
-    # 	plt.plot(signals[i,:,0])
-    # 	plt.show()
-
-    model = SignalDetectionModel(pretrained=complete_path)
-    print('signal shape: ', signals.shape)
-
-    classes = model.predict_class(signals)
-    times_recast = model.predict_time_of_interest(signals)
-
-    if label is None:
-        class_col = 'class'
-        time_col = 't0'
-        status_col = 'status'
-    else:
-        class_col = 'class_' + label
-        time_col = 't_' + label
-        status_col = 'status_' + label
-
-    for i, (tid, group) in enumerate(trajectories.groupby(column_labels['track'])):
-        indices = group.index
-        trajectories.loc[indices, class_col] = classes[i]
-        trajectories.loc[indices, time_col] = times_recast[i]
-    print('Done.')
-
-    for tid, group in trajectories.groupby(column_labels['track']):
-
-        indices = group.index
-        t0 = group[time_col].to_numpy()[0]
-        cclass = group[class_col].to_numpy()[0]
-        timeline = group[column_labels['time']].to_numpy()
-        status = np.zeros_like(timeline)
-        if t0 > 0:
-            status[timeline >= t0] = 1.
-        if cclass == 2:
-            status[:] = 2
-        if cclass > 2:
-            status[:] = 42
-        status_color = [color_from_status(s) for s in status]
-        class_color = [color_from_class(cclass) for i in range(len(status))]
-
-        trajectories.loc[indices, status_col] = status
-        trajectories.loc[indices, 'status_color'] = status_color
-        trajectories.loc[indices, 'class_color'] = class_color
-
-    if plot_outcome:
-        fig, ax = plt.subplots(1, len(selected_signals), figsize=(10, 5))
-        for i, s in enumerate(selected_signals):
-            for k, (tid, group) in enumerate(trajectories.groupby(column_labels['track'])):
-                cclass = group[class_col].to_numpy()[0]
-                t0 = group[time_col].to_numpy()[0]
-                timeline = group[column_labels['time']].to_numpy()
-                if cclass == 0:
-                    if len(selected_signals) > 1:
-                        ax[i].plot(timeline - t0, group[s].to_numpy(), c='tab:blue', alpha=0.1)
-                    else:
-                        ax.plot(timeline - t0, group[s].to_numpy(), c='tab:blue', alpha=0.1)
-        if len(selected_signals) > 1:
-            for a, s in zip(ax, selected_signals):
-                a.set_title(s)
-                a.set_xlabel(r'time - t$_0$ [frame]')
-                a.spines['top'].set_visible(False)
-                a.spines['right'].set_visible(False)
-        else:
-            ax.set_title(s)
-            ax.set_xlabel(r'time - t$_0$ [frame]')
-            ax.spines['top'].set_visible(False)
-            ax.spines['right'].set_visible(False)
-        plt.tight_layout()
-        if output_dir is not None:
-            plt.savefig(output_dir + 'signal_collapse.png', bbox_inches='tight', dpi=300)
-        plt.pause(3)
-        plt.close()
-
-    return trajectories
+# def analyze_signals(trajectories, model, interpolate_na=True,
+#                     selected_signals=None,
+#                     model_path=None,
+#                     column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'},
+#                     plot_outcome=False, output_dir=None):
+#     """
+# 	Analyzes signals from trajectory data using a specified signal detection model and configuration.
+
+# 	This function preprocesses trajectory data, selects specified signals, and applies a pretrained signal detection
+# 	model to predict classes and times of interest for each trajectory. It supports custom column labeling, interpolation
+# 	of missing values, and plotting of analysis outcomes.
+
+# 	Parameters
+# 	----------
+# 	trajectories : pandas.DataFrame
+# 		DataFrame containing trajectory data with columns for track ID, frame, position, and signals.
+# 	model : str
+# 		The name of the signal detection model to be used for analysis.
+# 	interpolate_na : bool, optional
+# 		Whether to interpolate missing values in the trajectories (default is True).
+# 	selected_signals : list of str, optional
+# 		A list of column names from `trajectories` representing the signals to be analyzed. If None, signals will
+# 		be automatically selected based on the model configuration (default is None).
+# 	column_labels : dict, optional
+# 		A dictionary mapping the default column names ('track', 'time', 'x', 'y') to the corresponding column names
+# 		in `trajectories` (default is {'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}).
+# 	plot_outcome : bool, optional
+# 		If True, generates and saves a plot of the signal analysis outcome (default is False).
+# 	output_dir : str, optional
+# 		The directory where the outcome plot will be saved. Required if `plot_outcome` is True (default is None).
+
+# 	Returns
+# 	-------
+# 	pandas.DataFrame
+# 		The input `trajectories` DataFrame with additional columns for predicted classes, times of interest, and
+# 		corresponding colors based on status and class.
+
+# 	Raises
+# 	------
+# 	AssertionError
+# 		If the model or its configuration file cannot be located.
+
+# 	Notes
+# 	-----
+# 	- The function relies on an external model configuration file (`config_input.json`) located in the model's directory.
+# 	- Signal selection and preprocessing are based on the requirements specified in the model's configuration.
+
+# 	"""
+
+#     model_path = locate_signal_model(model, path=model_path)
+#     complete_path = model_path  # +model
+#     complete_path = rf"{complete_path}"
+#     model_config_path = os.sep.join([complete_path, 'config_input.json'])
+#     model_config_path = rf"{model_config_path}"
+#     assert os.path.exists(complete_path), f'Model {model} could not be located in folder {model_path}... Abort.'
+#     assert os.path.exists(
+#         model_config_path), f'Model configuration could not be located in folder {model_path}... Abort.'
+
+#     available_signals = list(trajectories.columns)
+
+#     f = open(model_config_path)
+#     config = json.load(f)
+#     required_signals = config["channels"]
+
+#     try:
+#         label = config['label']
+#         if label == '':
+#             label = None
+#     except:
+#         label = None
+
+#     if selected_signals is None:
+#         selected_signals = []
+#         for s in required_signals:
+#             pattern_test = [s in a or s == a for a in available_signals]
+#             #print(f'Pattern test for signal {s}: ', pattern_test)
+#             assert np.any(
+#                 pattern_test), f'No signal matches with the requirements of the model {required_signals}. Please pass the signals manually with the argument selected_signals or add measurements. Abort.'
+#             valid_columns = np.array(available_signals)[np.array(pattern_test)]
+#             if len(valid_columns) == 1:
+#                 selected_signals.append(valid_columns[0])
+#             else:
+#                 # print(test_number_of_nan(trajectories, valid_columns))
+#                 print(f'Found several candidate signals: {valid_columns}')
+#                 for vc in natsorted(valid_columns):
+#                     if 'circle' in vc:
+#                         selected_signals.append(vc)
+#                         break
+#                 else:
+#                     selected_signals.append(valid_columns[0])
+#         # do something more complicated in case of one to many columns
+#         # pass
+#     else:
+#         assert len(selected_signals) == len(
+#             required_signals), f'Mismatch between the number of required signals {required_signals} and the provided signals {selected_signals}... Abort.'
+
+#     print(f'The following channels will be passed to the model: {selected_signals}')
+#     trajectories_clean = clean_trajectories(trajectories, interpolate_na=interpolate_na,
+#                                             interpolate_position_gaps=interpolate_na, column_labels=column_labels)
+
+#     max_signal_size = int(trajectories_clean[column_labels['time']].max()) + 2
+#     tracks = trajectories_clean[column_labels['track']].unique()
+#     signals = np.zeros((len(tracks), max_signal_size, len(selected_signals)))
+
+#     for i, (tid, group) in enumerate(trajectories_clean.groupby(column_labels['track'])):
+#         frames = group[column_labels['time']].to_numpy().astype(int)
+#         for j, col in enumerate(selected_signals):
+#             signal = group[col].to_numpy()
+#             signals[i, frames, j] = signal
+#             signals[i, max(frames):, j] = signal[-1]
+
+#     # for i in range(5):
+#     # 	print('pre model')
+#     # 	plt.plot(signals[i,:,0])
+#     # 	plt.show()
+
+#     model = SignalDetectionModel(pretrained=complete_path)
+#     print('signal shape: ', signals.shape)
+
+#     classes = model.predict_class(signals)
+#     times_recast = model.predict_time_of_interest(signals)
+
+#     if label is None:
+#         class_col = 'class'
+#         time_col = 't0'
+#         status_col = 'status'
+#     else:
+#         class_col = 'class_' + label
+#         time_col = 't_' + label
+#         status_col = 'status_' + label
+
+#     for i, (tid, group) in enumerate(trajectories.groupby(column_labels['track'])):
+#         indices = group.index
+#         trajectories.loc[indices, class_col] = classes[i]
+#         trajectories.loc[indices, time_col] = times_recast[i]
+#     print('Done.')
+
+#     for tid, group in trajectories.groupby(column_labels['track']):
+
+#         indices = group.index
+#         t0 = group[time_col].to_numpy()[0]
+#         cclass = group[class_col].to_numpy()[0]
+#         timeline = group[column_labels['time']].to_numpy()
+#         status = np.zeros_like(timeline)
+#         if t0 > 0:
+#             status[timeline >= t0] = 1.
+#         if cclass == 2:
+#             status[:] = 2
+#         if cclass > 2:
+#             status[:] = 42
+#         status_color = [color_from_status(s) for s in status]
+#         class_color = [color_from_class(cclass) for i in range(len(status))]
+
+#         trajectories.loc[indices, status_col] = status
+#         trajectories.loc[indices, 'status_color'] = status_color
+#         trajectories.loc[indices, 'class_color'] = class_color
+
+#     if plot_outcome:
+#         fig, ax = plt.subplots(1, len(selected_signals), figsize=(10, 5))
+#         for i, s in enumerate(selected_signals):
+#             for k, (tid, group) in enumerate(trajectories.groupby(column_labels['track'])):
+#                 cclass = group[class_col].to_numpy()[0]
+#                 t0 = group[time_col].to_numpy()[0]
+#                 timeline = group[column_labels['time']].to_numpy()
+#                 if cclass == 0:
+#                     if len(selected_signals) > 1:
+#                         ax[i].plot(timeline - t0, group[s].to_numpy(), c='tab:blue', alpha=0.1)
+#                     else:
+#                         ax.plot(timeline - t0, group[s].to_numpy(), c='tab:blue', alpha=0.1)
+#         if len(selected_signals) > 1:
+#             for a, s in zip(ax, selected_signals):
+#                 a.set_title(s)
+#                 a.set_xlabel(r'time - t$_0$ [frame]')
+#                 a.spines['top'].set_visible(False)
+#                 a.spines['right'].set_visible(False)
+#         else:
+#             ax.set_title(s)
+#             ax.set_xlabel(r'time - t$_0$ [frame]')
+#             ax.spines['top'].set_visible(False)
+#             ax.spines['right'].set_visible(False)
+#         plt.tight_layout()
+#         if output_dir is not None:
+#             plt.savefig(output_dir + 'signal_collapse.png', bbox_inches='tight', dpi=300)
+#         plt.pause(3)
+#         plt.close()
+
+#     return trajectories
 
 
 def analyze_pair_signals(trajectories_pairs,trajectories_reference,trajectories_neighbors, model, interpolate_na=True, selected_signals=None,
@@ -1405,7 +1388,10 @@ class SignalDetectionModel(object):
 
 			if self.show_plots:
 				try:
-					plot_confusion_matrix(results, ["dead","alive","miscellaneous"], output_dir=self.model_folder+os.sep, title=title)
+					ConfusionMatrixDisplay.from_predictions(ground_truth, predictions, cmap="Blues", normalize="pred", display_labels=["event","no event","left censored"])
+					plt.savefig(os.sep.join([self.model_folder,"test_confusion_matrix.png"]),bbox_inches='tight',dpi=300)
+					plt.pause(3)
+					plt.close()
 				except Exception as e:
 					print(e)
 					pass
@@ -1434,8 +1420,12 @@ class SignalDetectionModel(object):
 
 			if self.show_plots:
 				try:
-					plot_confusion_matrix(results, ["dead","alive","miscellaneous"], output_dir=self.model_folder+os.sep, title=title)
-				except:
+					ConfusionMatrixDisplay.from_predictions(ground_truth, predictions, cmap="Blues", normalize="pred", display_labels=["event","no event","left censored"])
+					plt.savefig(os.sep.join([self.model_folder,"validation_confusion_matrix.png"]),bbox_inches='tight',dpi=300)
+					plt.pause(3)
+					plt.close()
+				except Exception as e:
+					print(e)
 					pass
 			print("Validation set: ",classification_report(ground_truth,predictions))
 
@@ -3077,9 +3067,13 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	assert signal_name in list(df.columns),"The signal you want to plot is not one of the measured features."
 	if isinstance(class_value,int):
 		class_value = [class_value]
+	elif class_value is None or class_col is None:
+		class_col = 'class_temp'
+		df['class_temp'] = 1
+		class_value = [1]
 
 	if forced_max_duration is None:
-		max_duration = ceil(np.amax(df.groupby(['position','TRACK_ID']).size().values))
+		max_duration = int(df['FRAME'].max())+1 #ceil(np.amax(df.groupby(['position','TRACK_ID']).size().values))
 	else:
 		max_duration = forced_max_duration
 	
@@ -3115,9 +3109,12 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 		else:
 			signal = track_group[signal_name].to_numpy()
 
+		if ref_time <=0:
+			ref_time = 0
+
 		timeline = track_group['FRAME'].unique().astype(int)
 		timeline_shifted = timeline - ref_time + max_duration
-		signal_matrix[trackid,timeline_shifted] = signal
+		signal_matrix[trackid,timeline_shifted.astype(int)] = signal
 		trackid+=1
 	
 	mean_signal, std_signal = columnwise_mean(signal_matrix, min_nbr_values=min_nbr_values)

celldetective/tracking.py

@@ -609,7 +609,7 @@ def interpolate_time_gaps(trajectories, column_labels={'track': "TRACK_ID", 'tim
 
 	trajectories[column_labels['time']] = pd.to_datetime(trajectories[column_labels['time']], unit='s')
 	trajectories.set_index(column_labels['track'], inplace=True)
-	trajectories = trajectories.groupby(column_labels['track'], group_keys=True).apply(lambda x: x.set_index(column_labels['time']).resample('1S').asfreq()).reset_index()
+	trajectories = trajectories.groupby(column_labels['track'], group_keys=True).apply(lambda x: x.set_index(column_labels['time']).resample('1s').asfreq()).reset_index()
 	trajectories[[column_labels['x'], column_labels['y']]] = trajectories.groupby(column_labels['track'], group_keys=False)[[column_labels['x'], column_labels['y']]].apply(lambda x: x.interpolate(method='linear'))
 	trajectories.reset_index(drop=True, inplace=True)
 	trajectories[column_labels['time']] = trajectories[column_labels['time']].astype('int64').astype(float) / 10**9
@@ -679,7 +679,11 @@ def extrapolate_tracks(trajectories, post=False, pre=False, column_labels={'trac
 			extrapolated_positions = pd.DataFrame({column_labels['x']: last_known_position[0][1], column_labels['y']: last_known_position[0][2]}, index=np.arange(last_known_position[0][0] + 1, max_time + 1))
 			track_data = extrapolated_frames.join(extrapolated_positions, how="inner", on=column_labels['time'])
 			track_data[column_labels['track']] = track_id
-			df_extrapolated = pd.concat([df_extrapolated, track_data])
+
+			if len(df_extrapolated)==0:
+				df_extrapolated = track_data
+			elif len(track_data)!=0:
+				df_extrapolated = pd.concat([df_extrapolated, track_data])
 
 
 		# concatenate the original dataframe and the extrapolated dataframe
@@ -960,7 +964,7 @@ def write_first_detection_class(tab, column_labels={'track': "TRACK_ID", 'time':
 			if np.any(detection==detection):
 				t_first = timeline[detection==detection][0]
 				cclass = 0
-				if t_first==0:
+				if t_first<=0:
 					t_first = -1
 					cclass = 2
 				else:

celldetective/utils.py

@@ -1,3 +1,4 @@
+
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
@@ -29,6 +30,21 @@ from skimage.morphology import disk
 from scipy.stats import ks_2samp
 from cliffs_delta import cliffs_delta
 
+def safe_log(array):
+
+	if isinstance(array,int) or isinstance(array,float):
+		if value<=0.:
+			return np.nan
+		else:
+			return np.log10(value)
+	else:
+		if isinstance(array, list):
+			array = np.array(array)
+		output_array = np.zeros_like(array).astype(float)
+		output_array[:] = np.nan
+		output_array[array==array] = np.log10(array[array==array])
+		return output_array
+
 def contour_of_instance_segmentation(label, distance):
 
 	"""
@@ -2347,12 +2363,12 @@ def download_zenodo_file(file, output_dir):
 	if len(file_to_rename)>0 and not file_to_rename[0].endswith(os.sep) and not file.startswith('demo'):
 		os.rename(file_to_rename[0], os.sep.join([output_dir,file,file]))
 
-	if file.startswith('db_'):
-		os.rename(os.sep.join([output_dir,file.replace('db_','')]), os.sep.join([output_dir,file]))
-	if file=='db-si-NucPI':
-		os.rename(os.sep.join([output_dir,'db2-NucPI']), os.sep.join([output_dir,file]))
-	if file=='db-si-NucCondensation':
-		os.rename(os.sep.join([output_dir,'db1-NucCondensation']), os.sep.join([output_dir,file]))
+	#if file.startswith('db_'):
+	#	os.rename(os.sep.join([output_dir,file.replace('db_','')]), os.sep.join([output_dir,file]))
+	#if file=='db-si-NucPI':
+	#	os.rename(os.sep.join([output_dir,'db2-NucPI']), os.sep.join([output_dir,file]))
+	#if file=='db-si-NucCondensation':
+	#	os.rename(os.sep.join([output_dir,'db1-NucCondensation']), os.sep.join([output_dir,file]))
 
 	os.remove(path_to_zip_file)
 

{celldetective-1.3.0.post1.dist-info → celldetective-1.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.0.post1
+Version: 1.3.2
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -68,7 +68,7 @@ analysis on multimodal time lapse microscopy images.
 
 ## Overview
 
-![Pipeline](https://github.com/remyeltorro/celldetective/raw/main/docs/source/_static/celldetective-blocks.png)
+![Pipeline](https://github.com/celldetective/celldetective/raw/main/docs/source/_static/celldetective-blocks.png)
 
 
 Celldetective was designed to analyze time-lapse microscopy images in difficult situations: mixed cell populations that are only separable through multimodal information. This software provides a toolkit for the analysis of cell population interactions. 
@@ -87,7 +87,7 @@ Instead of reinventing the wheel and out of respect for the amazing work done by
 
 **Target Audience**: The software is targeted to scientists who are interested in quantifying dynamically (or not) cell populations from microscopy images. Experimental scientists who produce such images can also analyze their data, thanks to the graphical interface, that completely removes the need for coding, and the many helper functions that guide the user in the analysis steps. Finally, the modular structure of Celldetective welcomes users with a partial need. 
 
-![Signal analysis](https://github.com/remyeltorro/celldetective/raw/main/docs/source/_static/signal-annotator.gif)
+![Signal analysis](https://github.com/celldetective/celldetective/raw/main/docs/source/_static/signal-annotator.gif)
 
 
 # System requirements