celldetective 1.3.7.post1__py3-none-any.whl → 1.3.7.post2__py3-none-any.whl

celldetective/signals.py

@@ -325,9 +325,6 @@ def analyze_signals_at_position(pos, model, mode, use_gpu=True, return_table=Fal
 
 def analyze_pair_signals_at_position(pos, model, use_gpu=True):
 	
-	"""
-
-	"""
 
 	pos = pos.replace('\\','/')
 	pos = rf"{pos}"
@@ -364,199 +361,8 @@ 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)
-
-#     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,
 						model_path=None, plot_outcome=False, output_dir=None, column_labels = {'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}):
-	"""
-	"""
 
 	model_path = locate_signal_model(model, path=model_path, pairs=True)
 	print(f'Looking for model in {model_path}...')
@@ -832,6 +638,7 @@ class SignalDetectionModel(object):
 		-----
 		- The models are expected to be saved in .h5 format with the filenames "classifier.h5" and "regressor.h5".
 		- The configuration file is expected to be named "config_input.json" and located in the same directory as the models.
+		
 		"""
 
 		if self.pretrained.endswith(os.sep):
@@ -893,6 +700,7 @@ class SignalDetectionModel(object):
 		-----
 		- The models are created using a custom ResNet architecture defined elsewhere in the codebase.
 		- The models are stored in the `model_class` and `model_reg` attributes of the class.
+		
 		"""
 
 		self.model_class = ResNetModelCurrent(n_channels=self.n_channels,
@@ -925,6 +733,7 @@ class SignalDetectionModel(object):
 		-----
 		- This method should be called before any TensorFlow/Keras operations that might allocate GPU memory.
 		- If no GPUs are detected, the method will pass silently.
+		
 		"""
 
 		try:
@@ -987,6 +796,7 @@ class SignalDetectionModel(object):
 		Notes
 		-----
 		- The method automatically splits the dataset into training, validation, and test sets according to the specified splits.
+		
 		"""
 
 		if not hasattr(self, 'normalization_percentile'):
@@ -1049,6 +859,7 @@ class SignalDetectionModel(object):
 		-----
 		- This method provides an alternative way to train the model when data is already loaded into memory, offering
 		  flexibility for data preprocessing steps outside this class.
+		
 		"""
 
 		self.normalize = normalize
@@ -1179,6 +990,7 @@ class SignalDetectionModel(object):
 		-----
 		- The method processes the input signals according to the specified options to ensure compatibility with the model's
 		  input requirements.
+		
 		"""
 
 		self.x = np.copy(x)
@@ -1240,6 +1052,7 @@ class SignalDetectionModel(object):
 		-----
 		- The method processes the input signals according to the specified options and uses the regression model to
 		  predict times at which a particular event of interest occurs.
+		
 		"""
 
 		self.x = np.copy(x)
@@ -1290,6 +1103,7 @@ class SignalDetectionModel(object):
 		-----
 		- This method is useful for preparing signals that have gaps or missing time points before further processing
 		  or model training.
+		
 		"""
 
 		for i in range(len(x_set)):
@@ -1317,6 +1131,7 @@ class SignalDetectionModel(object):
 		- The classifier model predicts the class of each signal, such as live, dead, or miscellaneous.
 		- Training parameters such as epochs, batch size, and learning rate are specified during class instantiation.
 		- Model performance metrics and training history are saved for analysis.
+		
 		"""
 
 		# if pretrained model
@@ -1461,6 +1276,7 @@ class SignalDetectionModel(object):
 		- The regressor model estimates the time at which an event of interest occurs within each signal.
 		- Only signals predicted to have an event by the classifier model are used for regressor training.
 		- Model performance metrics and training history are saved for analysis.
+		
 		"""
 
 
@@ -1545,6 +1361,7 @@ class SignalDetectionModel(object):
 		-----
 		- Plots include loss and accuracy metrics over epochs for the classifier, and loss metrics for the regressor.
 		- The plots are saved as image files in the model's output directory.
+		
 		"""
 
 		if mode=="regressor":
@@ -1589,6 +1406,7 @@ class SignalDetectionModel(object):
 		-----
 		- Evaluation is performed on both test and validation datasets, if available.
 		- Regression plots and performance metrics are saved in the model's output directory.
+		
 		"""
 
 
@@ -1641,6 +1459,7 @@ class SignalDetectionModel(object):
 		-----
 		- Callbacks include learning rate reduction on plateau, early stopping, model checkpointing, and TensorBoard logging.
 		- The list of callbacks is stored in the class attribute `cb` and used during model training.
+		
 		"""
 		
 		self.cb = []
@@ -1698,6 +1517,7 @@ class SignalDetectionModel(object):
 		-----
 		- Signal annotations are expected to be stored in .npy format and contain required channels and event information.
 		- The method applies specified normalization and interpolation options to prepare the signals for model training.
+		
 		"""
 
 		
@@ -1781,6 +1601,7 @@ class SignalDetectionModel(object):
 		-----
 		- Augmentation strategies include random time shifting and signal modifications to simulate variations in real data.
 		- The augmented dataset is used for training the classifier and regressor models to improve generalization.
+		
 		"""
 
 		
@@ -1902,89 +1723,6 @@ class SignalDetectionModel(object):
 		return signals_recast, times_of_interest
 
 
-	# def load_and_normalize(self, subset):
-		
-	# 	"""
-	# 	Loads a subset of signal data from an annotation file and applies normalization.
-
-	# 	Parameters
-	# 	----------
-	# 	subset : str
-	# 		The file path to the .npy annotation file containing signal data for a subset of observations.
-
-	# 	Notes
-	# 	-----
-	# 	- The method extracts required signal channels from the annotation file and applies specified normalization
-	# 	  and interpolation steps.
-	# 	- Preprocessed signals are added to the global dataset for model training.
-	# 	"""
-			
-	# 	set_k = np.load(subset,allow_pickle=True)
-	# 	### here do a mapping between channel option and existing signals
-
-	# 	required_signals = self.channel_option
-	# 	available_signals = list(set_k[0].keys())
-
-	# 	selected_signals = []
-	# 	for s in required_signals:
-	# 		pattern_test = [s in a for a in available_signals]
-	# 		if np.any(pattern_test):
-	# 			valid_columns = np.array(available_signals)[np.array(pattern_test)]
-	# 			if len(valid_columns)==1:
-	# 				selected_signals.append(valid_columns[0])
-	# 			else:
-	# 				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])
-	# 		else:
-	# 			return None	
-		
-
-	# 	key_to_check = selected_signals[0] #self.channel_option[0]
-	# 	signal_lengths = [len(l[key_to_check]) for l in set_k]
-	# 	max_length = np.amax(signal_lengths)
-
-	# 	fluo = np.zeros((len(set_k),max_length,self.n_channels))
-	# 	classes = np.zeros(len(set_k))
-	# 	times_of_interest = np.zeros(len(set_k))
-		
-	# 	for k in range(len(set_k)):
-			
-	# 		for i in range(self.n_channels):
-	# 			try:
-	# 				# take into account timeline for accurate time regression
-	# 				timeline = set_k[k]['FRAME'].astype(int)
-	# 				fluo[k,timeline,i] = set_k[k][selected_signals[i]]
-	# 			except:
-	# 				print(f"Attribute {selected_signals[i]} matched to {self.channel_option[i]} not found in annotation...")
-	# 				pass
-
-	# 		classes[k] = set_k[k]["class"]
-	# 		times_of_interest[k] = set_k[k]["time_of_interest"]
-
-	# 	# Correct absurd times of interest
-	# 	times_of_interest[np.nonzero(classes)] = -1
-	# 	times_of_interest[(times_of_interest<=0.0)] = -1
-
-	# 	# Attempt per-set normalization
-	# 	fluo = pad_to_model_length(fluo, self.model_signal_length)
-	# 	if self.normalize:
-	# 		fluo = normalize_signal_set(fluo, self.channel_option, normalization_percentile=self.normalization_percentile, 
-	# 									normalization_values=self.normalization_values, normalization_clip=self.normalization_clip,
-	# 									)
-			
-	# 	# Trivial normalization for time of interest
-	# 	times_of_interest /= self.model_signal_length
-		
-	# 	# Add to global dataset
-	# 	self.x_set.extend(fluo)
-	# 	self.y_time_set.extend(times_of_interest)
-	# 	self.y_class_set.extend(classes)
-
 def _interpret_normalization_parameters(n_channels, normalization_percentile, normalization_values, normalization_clip):
 	
 	"""
@@ -2028,6 +1766,7 @@ def _interpret_normalization_parameters(n_channels, normalization_percentile, no
 	>>> params = _interpret_normalization_parameters(n_channels, normalization_percentile, normalization_values, normalization_clip)
 	>>> print(params)
 	# ([True, True], [[0.1, 99.9], [0.1, 99.9]], [False, False])
+
 	"""
 
 
@@ -2101,6 +1840,7 @@ def normalize_signal_set(signal_set, channel_option, percentile_alive=[0.01,99.9
 	>>> channel_option = ['alive', 'dead']
 	>>> normalized_signals = normalize_signal_set(signal_set, channel_option)
 	# Normalizes the signal set based on the default percentile values for 'alive' and 'dead' channels.
+
 	"""
 
 	# Check normalization params are ok
@@ -2584,6 +2324,7 @@ def ResNetModelCurrent(n_channels, n_slices, depth=2, use_pooling=True, n_classe
 	--------
 	>>> model = ResNetModelCurrent(n_channels=1, n_slices=2, depth=2, use_pooling=True, n_classes=3, dropout_rate=0.1, dense_collection=512, header="classifier", model_signal_length=128)
 	# Creates a ResNet model configured for classification with 3 classes.
+
 	"""
 
 	if header=="classifier":
@@ -2652,6 +2393,7 @@ def train_signal_model(config):
 	>>> config_path = '/path/to/training_config.json'
 	>>> train_signal_model(config_path)
 	# This will execute the 'train_signal_model.py' script using the parameters specified in 'training_config.json'.
+
 	"""
 
 	config = config.replace('\\','/')
@@ -2698,6 +2440,7 @@ def T_MSD(x,y,dt):
 	>>> T_MSD(x, y, dt)
 	([6.0, 9.0, 4.666666666666667, 1.6666666666666667],
 	 array([1., 2., 3., 4.]))
+
 	"""
 
 	msd = []
@@ -2735,6 +2478,7 @@ def linear_msd(t, m):
 	>>> m = 2.0
 	>>> linear_msd(t, m)
 	array([2., 4., 6., 8.])
+
 	"""
 
 	return m*t
@@ -2766,6 +2510,7 @@ def alpha_msd(t, m, alpha):
 	>>> alpha = 0.5
 	>>> alpha_msd(t, m, alpha)
 	array([2.        , 4.        , 6.        , 8.        ])
+
 	"""
 
 	return m*t**alpha
@@ -2820,6 +2565,7 @@ def sliding_msd(x, y, timeline, window, mode='bi', n_points_migration=7,  n_poin
 	>>> timeline = np.array([0, 1, 2, 3, 4, 5, 6])
 	>>> window = 3
 	>>> s_msd, s_alpha = sliding_msd(x, y, timeline, window, n_points_migration=2, n_points_transport=3)
+
 	"""
 
 	assert window > n_points_migration,'Please set a window larger than the number of fit points...'
@@ -2956,6 +2702,7 @@ def sliding_msd_drift(x, y, timeline, window, mode='bi', n_points_migration=7,
 	>>> window = 11
 	>>> diffusion, velocity = sliding_msd_drift(x, y, timeline, window, mode='bi')
 	# Calculates the diffusion coefficient and drift velocity using a bidirectional sliding window.
+
 	"""
 
 	assert window > n_points_migration,'Please set a window larger than the number of fit points...'
@@ -3007,7 +2754,7 @@ def columnwise_mean(matrix, min_nbr_values = 1):
 	"""
 	Calculate the column-wise mean and standard deviation of non-NaN elements in the input matrix.
 
-	Parameters:
+	Parameters
 	----------
 	matrix : numpy.ndarray
 		The input matrix for which column-wise mean and standard deviation are calculated.
@@ -3015,7 +2762,7 @@ def columnwise_mean(matrix, min_nbr_values = 1):
 		The minimum number of non-NaN values required in a column to calculate mean and standard deviation.
 		Default is 8.
 
-	Returns:
+	Returns
 	-------
 	mean_line : numpy.ndarray
 		An array containing the column-wise mean of non-NaN elements. Elements with fewer than `min_nbr_values` non-NaN
@@ -3024,11 +2771,12 @@ def columnwise_mean(matrix, min_nbr_values = 1):
 		An array containing the column-wise standard deviation of non-NaN elements. Elements with fewer than `min_nbr_values`
 		non-NaN values are replaced with NaN.
 
-	Notes:
-	------
+	Notes
+	-----
 	1. This function calculates the mean and standard deviation of non-NaN elements in each column of the input matrix.
 	2. Columns with fewer than `min_nbr_values` non-zero elements will have NaN as the mean and standard deviation.
 	3. NaN values in the input matrix are ignored during calculation.
+
 	"""
 
 	mean_line = np.zeros(matrix.shape[1])
@@ -3050,7 +2798,7 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	"""
 	Calculate the mean and standard deviation of a specified signal for tracks of a given class in the input DataFrame.
 
-	Parameters:
+	Parameters
 	----------
 	df : pandas.DataFrame
 		Input DataFrame containing tracking data.
@@ -3063,7 +2811,7 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	class_value : int, optional
 		Value representing the class of interest. Default is 0.
 
-	Returns:
+	Returns
 	-------
 	mean_signal : numpy.ndarray
 		An array containing the mean signal values for tracks of the specified class. Tracks with class not equal to
@@ -3074,12 +2822,13 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	actual_timeline : numpy.ndarray
 		An array representing the time points corresponding to the mean signal values.
 
-	Notes:
-	------
+	Notes
+	-----
 	1. This function calculates the mean and standard deviation of the specified signal for tracks of a given class.
 	2. Tracks with class not equal to `class_value` are excluded from the calculation.
 	3. Tracks with missing or NaN values in the specified signal are ignored during calculation.
 	4. Tracks are aligned based on their 'FRAME' values and the specified `time_col` (if provided).
+	
 	"""
 
 	assert signal_name in list(df.columns),"The signal you want to plot is not one of the measured features."
@@ -3142,11 +2891,11 @@ def mean_signal(df, signal_name, class_col, time_col=None, class_value=[0], retu
 	else:
 		return mean_signal, std_signal, actual_timeline
 
-if __name__ == "__main__":
+# if __name__ == "__main__":
 
-	# model = MultiScaleResNetModel(3, n_classes = 3, dropout_rate=0, dense_collection=1024, header="classifier", model_signal_length = 128)
-	# print(model.summary())
-	model = ResNetModelCurrent(1, 2, depth=2, use_pooling=True, n_classes = 3, dropout_rate=0.1, dense_collection=512,
-					   header="classifier", model_signal_length = 128)
-	print(model.summary())
-	#plot_model(model, to_file='test.png', show_shapes=True)
+# 	# model = MultiScaleResNetModel(3, n_classes = 3, dropout_rate=0, dense_collection=1024, header="classifier", model_signal_length = 128)
+# 	# print(model.summary())
+# 	model = ResNetModelCurrent(1, 2, depth=2, use_pooling=True, n_classes = 3, dropout_rate=0.1, dense_collection=512,
+# 					   header="classifier", model_signal_length = 128)
+# 	print(model.summary())
+# 	#plot_model(model, to_file='test.png', show_shapes=True)

celldetective/tracking.py

@@ -937,18 +937,6 @@ def track_at_position(pos, mode, return_tracks=False, view_on_napari=False, thre
 		return df
 	else:
 		return None	
-	
-	# # if return_labels or view_on_napari:
-	# # 	labels = locate_labels(pos, population=mode)
-	# # if view_on_napari:
-	# # 	if stack_prefix is None:
-	# # 		stack_prefix = ''
-	# # 	stack = locate_stack(pos, prefix=stack_prefix)
-	# # 	_view_on_napari(tracks=None, stack=stack, labels=labels)
-	# # if return_labels:
-	# # 	return labels
-	# # else:
-	# return None
 
 def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}):
 	
@@ -972,27 +960,33 @@ def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_la
 
 	column_labels : dict, optional
 		A dictionary mapping logical column names to actual column names in `tab`. Keys include:
-		- `'track'`: The column indicating the track ID (default: `"TRACK_ID"`).
-		- `'time'`: The column indicating the frame/time (default: `"FRAME"`).
-		- `'x'`: The column indicating the X-coordinate (default: `"POSITION_X"`).
-		- `'y'`: The column indicating the Y-coordinate (default: `"POSITION_Y"`).
+		
+			- `'track'`: The column indicating the track ID (default: `"TRACK_ID"`).
+			- `'time'`: The column indicating the frame/time (default: `"FRAME"`).
+			- `'x'`: The column indicating the X-coordinate (default: `"POSITION_X"`).
+			- `'y'`: The column indicating the Y-coordinate (default: `"POSITION_Y"`).
 
 	Returns
 	-------
 	pandas.DataFrame
 		The input DataFrame `df` with two additional columns:
-		- `'class_firstdetection'`: A class assigned based on detection status:
-			- `0`: Valid detection not near the edge and not at the initial frame.
-			- `2`: Detection near the edge, at the initial frame, or no detection available.
-		- `'t_firstdetection'`: The adjusted first detection time (in frame units):
-			- `-1`: Indicates no valid detection or detection near the edge.
-			- A float value representing the adjusted first detection time otherwise.
+		
+			- `'class_firstdetection'`: A class assigned based on detection status:
+			
+				- `0`: Valid detection not near the edge and not at the initial frame.
+				- `2`: Detection near the edge, at the initial frame, or no detection available.
+		
+			- `'t_firstdetection'`: The adjusted first detection time (in frame units):
+			
+				- `-1`: Indicates no valid detection or detection near the edge.
+				- A float value representing the adjusted first detection time otherwise.
 
 	Notes
 	-----
 	- The function assumes that tracks are grouped and sorted by track ID and frame.
 	- Detections near the edge or at the initial frame (frame 0) are considered invalid and assigned special values.
 	- If `img_shape` is not provided, edge checks are skipped.
+
 	"""
 
 	df = df.sort_values(by=[column_labels['track'],column_labels['time']])

{celldetective-1.3.7.post1.dist-info → celldetective-1.3.7.post2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: celldetective
-Version: 1.3.7.post1
+Version: 1.3.7.post2
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -30,6 +30,7 @@ Requires-Dist: setuptools
 Requires-Dist: scipy
 Requires-Dist: seaborn
 Requires-Dist: opencv-python-headless==4.7.0.72
+Requires-Dist: PyQt5
 Requires-Dist: liblapack
 Requires-Dist: gputools
 Requires-Dist: lmfit
@@ -43,6 +44,14 @@ Requires-Dist: h5py
 Requires-Dist: cliffs_delta
 Requires-Dist: requests
 Requires-Dist: trackpy
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 # Celldetective