celldetective 1.1.1.post1__py3-none-any.whl → 1.1.1.post4__py3-none-any.whl

celldetective/segmentation.py

@@ -20,6 +20,7 @@ from skimage.segmentation import watershed
 from skimage.feature import peak_local_max
 from skimage.measure import regionprops_table
 from skimage.exposure import match_histograms
+from scipy.ndimage import zoom
 import pandas as pd
 import subprocess
 
@@ -27,7 +28,7 @@ import subprocess
 abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],'celldetective'])
 
 def segment(stack, model_name, channels=None, spatial_calibration=None, view_on_napari=False,
-			use_gpu=True, time_flat_normalization=False, time_flat_percentiles=(0.0,99.99)):
+			use_gpu=True, channel_axis=-1):
 	
 	"""
 	
@@ -85,7 +86,10 @@ def segment(stack, model_name, channels=None, spatial_calibration=None, view_on_
 	if not use_gpu:
 		os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
 	else:
-		os.environ['CUDA_VISIBLE_DEVICES'] = '0'		
+		os.environ['CUDA_VISIBLE_DEVICES'] = '0'
+
+	if channel_axis != -1:
+		stack = np.moveaxis(stack, channel_axis, -1)
 
 	if channels is not None:
 		assert len(channels)==stack.shape[-1],f'The channel names provided do not match with the expected number of channels in the stack: {stack.shape[-1]}.'
@@ -96,48 +100,83 @@ def segment(stack, model_name, channels=None, spatial_calibration=None, view_on_
 	required_spatial_calibration = input_config['spatial_calibration']
 	model_type = input_config['model_type']
 
-	if 'normalize' in input_config:
-		normalize = input_config['normalize']
-	else:
-		normalize = True
+	normalization_percentile = input_config['normalization_percentile']
+	normalization_clip = input_config['normalization_clip']
+	normalization_values = input_config['normalization_values']
 
 	if model_type=='cellpose':
 		diameter = input_config['diameter']
-		if diameter!=30:
-			required_spatial_calibration = None
+		# if diameter!=30:
+		# 	required_spatial_calibration = None
 		cellprob_threshold = input_config['cellprob_threshold']
 		flow_threshold = input_config['flow_threshold']
 
 	scale = _estimate_scale_factor(spatial_calibration, required_spatial_calibration)
 
 	if model_type=='stardist':
+
 		model = StarDist2D(None, name=model_name, basedir=Path(model_path).parent)
-		print(f"StarDist model {model_name} successfully loaded")
+		model.config.use_gpu = use_gpu
+		model.use_gpu = use_gpu
+		print(f"StarDist model {model_name} successfully loaded.")
+		scale_model = scale
 
 	elif model_type=='cellpose':
-		model = CellposeModel(gpu=use_gpu, pretrained_model=model_path+model_path.split('/')[-2], diam_mean=30.0)
+		
+		import torch
+		if not use_gpu:
+			device = torch.device("cpu")
+		else:
+			device = torch.device("cuda")
+
+		model = CellposeModel(gpu=use_gpu, device=device, pretrained_model=model_path+model_path.split('/')[-2], model_type=None, nchan=len(required_channels))
 		if scale is None:
 			scale_model = model.diam_mean / model.diam_labels
 		else:
 			scale_model = scale * model.diam_mean / model.diam_labels
+		print(f"Diam mean: {model.diam_mean}; Diam labels: {model.diam_labels}; Final rescaling: {scale_model}...")
+		print(f'Cellpose model {model_name} successfully loaded.')
 
 	labels = []
-	if (time_flat_normalization)*normalize:
-		normalization_values = get_stack_normalization_values(stack[:,:,:,channel_indices], percentiles=time_flat_percentiles)
-	else:
-		normalization_values = [None]*len(channel_indices)
 
 	for t in tqdm(range(len(stack)),desc="frame"):
 
 		# normalize
-		frame = stack[t,:,:,np.array(channel_indices)]
-		if np.argmin(frame.shape)!=(frame.ndim-1):
-			frame = np.moveaxis(frame,np.argmin(frame.shape),-1)
-		if normalize:
-			frame = normalize_multichannel(frame, values=normalization_values)
-
-		if scale is not None:
-			frame = [ndi.zoom(frame[:,:,c].copy(), [scale_model,scale_model], order=3, prefilter=False) for c in range(frame.shape[-1])]
+		channel_indices = np.array(channel_indices)
+		none_channel_indices = np.where(channel_indices==None)[0]
+		channel_indices[channel_indices==None] = 0
+		print(channel_indices)
+
+		frame = stack[t,:,:,channel_indices.astype(int)].astype(float)
+		if frame.ndim==2:
+			frame = frame[:,:,np.newaxis]
+		if frame.ndim==3 and np.array(frame.shape).argmin()==0:
+			frame = np.moveaxis(frame,0,-1)
+		template = frame.copy()
+
+		values = []
+		percentiles = []
+		for k in range(len(normalization_percentile)):
+			if normalization_percentile[k]:
+				percentiles.append(normalization_values[k])
+				values.append(None)
+			else:
+				percentiles.append(None)
+				values.append(normalization_values[k])
+
+		frame = normalize_multichannel(frame, **{"percentiles": percentiles, 'values': values, 'clip': normalization_clip})
+		
+		if scale_model is not None:
+			frame = [zoom(frame[:,:,c].copy(), [scale_model,scale_model], order=3, prefilter=False) for c in range(frame.shape[-1])]
+			frame = np.moveaxis(frame,0,-1)
+		
+		for k in range(frame.shape[2]):
+			unique_values = np.unique(frame[:,:,k])
+			if len(unique_values)==1:
+				frame[0,0,k] += 1
+		
+		frame = np.moveaxis([interpolate_nan(frame[:,:,c].copy()) for c in range(frame.shape[-1])],0,-1)
+		frame[:,:,none_channel_indices] = 0.
 
 		if model_type=="stardist":
 
@@ -145,16 +184,15 @@ def segment(stack, model_name, channels=None, spatial_calibration=None, view_on_
 			Y_pred = Y_pred.astype(np.uint16)
 
 		elif model_type=="cellpose":
-
-			Y_pred, _, _ = model.eval(frame, diameter = diameter, cellprob_threshold=cellprob_threshold, flow_threshold=flow_threshold, channels=None, normalize=False)
+			
+			img = np.moveaxis(frame, -1, 0)
+			Y_pred, _, _ = model.eval(img, diameter = diameter, cellprob_threshold=cellprob_threshold, flow_threshold=flow_threshold, channels=None, normalize=False)
 			Y_pred = Y_pred.astype(np.uint16)
 
-		if scale is not None:
-			Y_pred = ndi.zoom(Y_pred, [1./scale_model,1./scale_model],order=0)
-
-
 		if Y_pred.shape != stack[0].shape[:2]:
-			Y_pred = resize(Y_pred, stack[0].shape, order=0)
+			Y_pred = zoom(Y_pred, [1./scale_model,1./scale_model],order=0)
+		if Y_pred.shape != template.shape[:2]:
+			Y_pred = resize(Y_pred, template.shape[:2], order=0)
 
 		labels.append(Y_pred)
 

celldetective/utils.py

@@ -23,6 +23,7 @@ from tqdm import tqdm
 import shutil
 import tempfile
 from scipy.interpolate import griddata
+import re
 
 
 def derivative(x, timeline, window, mode='bi'):
@@ -430,6 +431,31 @@ def mask_edges(binary_mask, border_size):
 	return binary_mask
 
 
+def extract_cols_from_query(query: str):
+	
+	# Track variables in a dictionary to be used as a dictionary of globals. From: https://stackoverflow.com/questions/64576913/extract-pandas-dataframe-column-names-from-query-string
+	
+	variables = {}
+
+	while True:
+		try:
+			# Try creating a Expr object with the query string and dictionary of globals.
+			# This will raise an error as long as the dictionary of globals is incomplete.
+			env = pd.core.computation.scope.ensure_scope(level=0, global_dict=variables)
+			pd.core.computation.eval.Expr(query, env=env)
+
+			# Exit the loop when evaluation is successful.
+			break
+		except pd.errors.UndefinedVariableError as e:
+			# This relies on the format defined here: https://github.com/pandas-dev/pandas/blob/965ceca9fd796940050d6fc817707bba1c4f9bff/pandas/errors/__init__.py#L401
+			name = re.findall("name '(.+?)' is not defined", str(e))[0]
+
+			# Add the name to the globals dictionary with a dummy value.
+			variables[name] = None
+
+	return list(variables.keys())
+
+
 def create_patch_mask(h, w, center=None, radius=None):
 
 	"""
@@ -1058,20 +1084,33 @@ def _extract_channel_indices(channels, required_channels):
 	# [0, 1]
 	"""
 
-	if channels is not None:
-		channel_indices = []
-		for ch in required_channels:
-			
+	channel_indices = []
+	for c in required_channels:
+		if c!='None' and c is not None:
 			try:
-				idx = channels.index(ch)
-			except ValueError:
-				print('Mismatch between the channels required by the model and the provided channels.')
-				return None
+				ch_idx = channels.index(c)
+				channel_indices.append(ch_idx)
+			except Exception as e:
+				print(f"Error {e}. The channel required by the model is not available in your data... Check the configuration file.")
+				channels = None
+				break
+		else:
+			channel_indices.append(None)
 
-			channel_indices.append(idx)
-		channel_indices = np.array(channel_indices)
-	else:
-		channel_indices = np.arange(len(required_channels))
+	# if channels is not None:
+	# 	channel_indices = []
+	# 	for ch in required_channels:
+			
+	# 		try:
+	# 			idx = channels.index(ch)
+	# 		except ValueError:
+	# 			print('Mismatch between the channels required by the model and the provided channels.')
+	# 			return None
+
+	# 		channel_indices.append(idx)
+	# 	channel_indices = np.array(channel_indices)
+	# else:
+	# 	channel_indices = np.arange(len(required_channels))
 
 	return channel_indices
 
@@ -2046,7 +2085,7 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 		
 	assert isinstance(channels, list),'Please provide a list of channels. Abort.'
 
-	X = []; Y = [];
+	X = []; Y = []; files = [];
 
 	for ds in datasets:
 		print(f'Loading data from dataset {ds}...')
@@ -2101,9 +2140,10 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 					
 			X.append(image)
 			Y.append(mask)
+			files.append(im)
 
 	assert len(X)==len(Y),'The number of images does not match with the number of masks... Abort.'
-	return X,Y
+	return X,Y,files
 
 
 def download_url_to_file(url, dst, progress=True):

{celldetective-1.1.1.post1.dist-info → celldetective-1.1.1.post4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.1.1.post1
+Version: 1.1.1.post4
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.1.1.post1.dist-info → celldetective-1.1.1.post4.dist-info}/RECORD

@@ -1,43 +1,43 @@
 celldetective/__init__.py,sha256=FEZpJKcskBH2IginYzeqPWoR1lVGuyYCXhv7Hnlkoo8,49
-celldetective/__main__.py,sha256=XFAkq_2cBEkWAVXDGSNFagoQBglyl0Y-GOO3KFc8UqM,13888
+celldetective/__main__.py,sha256=TQzL_FLAeEF1YIyRZXMiai40xXy21roPPV23ig4jwG0,14494
 celldetective/events.py,sha256=s2pWnR3Z1fcB15sET5WsF2Pi6v6qv16hks_m3WiklNs,3658
 celldetective/extra_properties.py,sha256=ZdWV046RR8jrQPYxLSVVb1cXkWYxfrrLj2tXfc358cU,4179
 celldetective/filters.py,sha256=b0qKwHor1fvNA_dHovP17nQz8EsW5YlyhT2TJnayn08,3615
-celldetective/io.py,sha256=ptaX4GadWuf0zOQ3ZWSLCzihEID-YAalPfxW1nqvgIU,80889
+celldetective/io.py,sha256=_ivq2zE5ffHadZ-YOWSSX5J1GTlEohg6WPvC3xEBZvQ,82819
 celldetective/measure.py,sha256=HDQZfSRx3daOCV5Snu1paYU5JYkwu8engO2qZqhTAUo,48089
-celldetective/neighborhood.py,sha256=QCuhesMHGyr3c3ys9wWcNR1HM6CHdHe51R8upoolgPw,49514
-celldetective/preprocessing.py,sha256=psCs4CAI7gG3YlKvxkXKnpClFL4SjWm5TToXq2ZwL-s,37137
-celldetective/segmentation.py,sha256=Hu4-lOJ4UhPw2o0Hn_NPOCHsa6Iwsw5A3PR6X3Tzbb8,29196
+celldetective/neighborhood.py,sha256=Jl9VujKYZ9R2pcqmPt5HyeCy5LieNal-oCsD8b7uIWQ,51182
+celldetective/preprocessing.py,sha256=TKOJTc5o4rSgXqtYeZz-0ox062dD494VMiie3L-9aV4,38305
+celldetective/segmentation.py,sha256=L2VJKmOewC1CNZPiWCO6yUfxt78u9k1NHPr2qTyTaBM,30458
 celldetective/signals.py,sha256=P7eiDZGGIAYCFBKjGCBi8gMBvJYywxlxZNzyGgw-26Y,102783
 celldetective/tracking.py,sha256=A0mhdF4uq4m8OX1-rhtuhG69rlh_6Pb34Aebu7hIeKM,37601
-celldetective/utils.py,sha256=00jBr_Ur6wX3xeFQzwgpFv9XDhnt_VCh-e2usFdrfo4,77543
+celldetective/utils.py,sha256=ahHZkLr6ceUDY5sN6uOcGzqKaLjpOIdB_kjhXj_gggA,79003
 celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/__init__.py,sha256=y2dvrUdJi17QMgPjl8WN3XFHYzJpu2ul4_8y7MQV1Bk,941
 celldetective/gui/about.py,sha256=i-y54Opb10pKTVNUEcJC-D6Cbiqud2EJ3ZLayXqhdqc,1715
 celldetective/gui/analyze_block.py,sha256=WD3JQQylx_dVozFCvNqrOyR6LcNHV7R1_gGh7XqOVeI,25423
 celldetective/gui/btrack_options.py,sha256=eQEf63yTUsPCN-d1LqgAMmUQpfv2FH85FqnOSaR-9Q8,35575
-celldetective/gui/classifier_widget.py,sha256=52a3kOfU3uMEzUYMIOHGqiy-Q5itMEvcG-3JYrO34I8,16918
+celldetective/gui/classifier_widget.py,sha256=PNg72YlFvKjGdlARaquvY4ALpNV7KZps9LJqAemSUqc,17225
 celldetective/gui/configure_new_exp.py,sha256=ANJ-Zn4sjBphtj_aoJu6m1PFEKyv9gxeh9XqS6xOGjk,18969
-celldetective/gui/control_panel.py,sha256=wcDqe4XaDJRMmPmWKJpxd0D9V4_DrdRGnEH6D7B_IK0,17557
+celldetective/gui/control_panel.py,sha256=srpQMxMA8ZOuxqfzRgFZl0OtV1H9bgf2nt20A7vtFps,18101
 celldetective/gui/gui_utils.py,sha256=PidFfdc8XASeIzZO5pfKgwqe4vROG7-KpYMcBZ42jdw,22673
 celldetective/gui/json_readers.py,sha256=fTrNrlxv9NCae8ZJexBEHxI3yCLRqt6F0Yo1OeDycfA,3686
-celldetective/gui/layouts.py,sha256=gC24lyA48hzOo2oabYF1vXTFh5r7WcQFVkqjAXXo5g0,26997
+celldetective/gui/layouts.py,sha256=MCmGOjZFoL2a24Gu6WH9UgOnI6ZbGNqWxEEf1QMVqqQ,37678
 celldetective/gui/measurement_options.py,sha256=i0CdAfupHJAqhOT7RsufEK919sAzQnFBkQO4IAMYZL0,47704
-celldetective/gui/neighborhood_options.py,sha256=sdKxVRliZtuKSpcPfnFxqkW4V8rN2tzjhDxOPVmElyE,20191
+celldetective/gui/neighborhood_options.py,sha256=sASKSSRl4Fwu0NwLaH-xX0SCvGRiyRA5JuNA288lP8o,20436
 celldetective/gui/plot_measurements.py,sha256=xUoGxV6uXcen-t4yWtAmcGTUayICI-FxTVKPrWMNlfg,51799
 celldetective/gui/plot_signals_ui.py,sha256=TwWU2u3_mkRNsM8er0kI_kwr5EoZ29YEzlr0cQzyW4A,43732
 celldetective/gui/process_block.py,sha256=7n9glZ1ojEi1bObqwIj4giNhrteT69X1EPMQ1hK63aU,53565
-celldetective/gui/retrain_segmentation_model_options.py,sha256=-rkuUzI_vFFlZC3LAAYEELoJUKcz6PmkpCrxKZindhg,27218
-celldetective/gui/retrain_signal_model_options.py,sha256=uHZy3FGsGMHfZL_nYnuFiXF57XaAMVzjYxVF2OXhYnY,24184
+celldetective/gui/retrain_segmentation_model_options.py,sha256=VixtKZTjoJFJy8X6aDbAf0zgK46aXj3I6oPP_92yqhA,22457
+celldetective/gui/retrain_signal_model_options.py,sha256=gdK1ITuaTPNvnQWXYuUBcP_pH5cvaEEns5XejjTi_Eo,17854
 celldetective/gui/seg_model_loader.py,sha256=uKp8oab-4QdTGqb-tb6bOD-FLD_154GOvgWFYz97BwY,17350
-celldetective/gui/signal_annotator.py,sha256=4ymMpo_GjSBsJSRkyNKrWRLy0EFXHINbFtp9ykDqfGE,84864
+celldetective/gui/signal_annotator.py,sha256=yHsVCu6Nm8_7bxXfvBfx-xymH9bXBpnQ4TUih1d66cM,86791
 celldetective/gui/signal_annotator_options.py,sha256=-Q7f8eCwniqbgLJqMCa91Wc-V3VHAZidwt7LPd4Z5yU,10879
 celldetective/gui/styles.py,sha256=Vw4wr6MQ4iBwhOY-ZWAxFDZZ3CNohmEnuPPazwhJaho,4129
 celldetective/gui/survival_ui.py,sha256=2JGLC5m6D_gVLwnBAM7uEvuCKw1Cli8nM9i5s7TIpGg,33612
-celldetective/gui/tableUI.py,sha256=QRYlXc7751Ka5qbUHSGbE_nXTiiezAVfEWXiRKRmuRM,32188
+celldetective/gui/tableUI.py,sha256=jkvXkLv2GLimApClvwtwAgpYJi8cpLKBM7MEBdbejbE,34572
 celldetective/gui/thresholds_gui.py,sha256=b8SkG4DlfxBRjacKTe1NSNkq7rJm8lnSLifH-mg846k,49529
-celldetective/gui/viewers.py,sha256=G8uNb0U_4tJiZkcAWX9BbCSBIUbF4tjedZD-5o4WKxY,27734
+celldetective/gui/viewers.py,sha256=buBholjAieaVVb6YinVhxPshEHxBEU3er_N0UrkwAew,27734
 celldetective/icons/logo-large.png,sha256=FXSwV3u6zEKcfpuSn4unnqB0oUnN9cHqQ9BCKWytrpg,36631
 celldetective/icons/logo.png,sha256=wV2OS8_dU5Td5cgdPbCOU3JpMpTwNuYLnfVcnQX0tJA,2437
 celldetective/icons/signals_icon.png,sha256=vEiKoqWTtN0-uJgVqtAlwCuP-f4QeWYOlO3sdp2tg2w,3969
@@ -60,10 +60,10 @@ celldetective/models/tracking_configs/ricm.json,sha256=L-vmwCR1f89U-qnH2Ms0cBfPF
 celldetective/models/tracking_configs/ricm2.json,sha256=DDjJ6ScYcDWvlsy7ujPID8v8H28vcNcMuZmNR8XmGxo,2718
 celldetective/scripts/analyze_signals.py,sha256=23TXGNw-j5xT3ss4mXlnKdBgFLnQ50JUEQOC6_H7Q_0,2203
 celldetective/scripts/measure_cells.py,sha256=4uRG6Dg0WsO-N8ZaBJ4loWOvX6FdHaCblIFXq6Dtirc,11000
-celldetective/scripts/segment_cells.py,sha256=OSP52sPPHyhfXEjiXXdezkDY4MiFXLBWTb2_umRBD-M,8269
+celldetective/scripts/segment_cells.py,sha256=55hM3JbMoW5TB43uENgtvADL8BziI17B3GjG4axsj6s,8291
 celldetective/scripts/segment_cells_thresholds.py,sha256=GbWXa6xoO8s4PinJPZIxAuosw4vpzyJ7FiFYpSURojk,4998
 celldetective/scripts/track_cells.py,sha256=AaNiYEW4osYKKR2kbdVLOUnQEBbcZIA-D0mkhcxPWTY,7985
-celldetective/scripts/train_segmentation_model.py,sha256=UY493QK7_FhS9uHYl2eeEYx7t0kw1jhvc0YMY12YZpI,8614
+celldetective/scripts/train_segmentation_model.py,sha256=rw5LD70PrE_SCBvaFt0ri1uSa-YI5DM5exH_BGVlw5Y,8515
 celldetective/scripts/train_signal_model.py,sha256=9-dmPCLKJ9ypjsV9AwFd-Sb6B6YaHS0QGT218H5hUPo,1861
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
@@ -72,13 +72,13 @@ tests/test_io.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
 tests/test_measure.py,sha256=FEUAs1rVHylvIvubCb0bJDNGZLVmkgXNgI3NaGQ1dA8,4542
 tests/test_neighborhood.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
 tests/test_preprocessing.py,sha256=FI-Wk-kc4wWmOQg_NLCUIZC1oti396wr5cC-BauBai0,1436
-tests/test_segmentation.py,sha256=-3b7o_fUVMYxfVwX5VHFqRF0dDXObSTtylf5XQGcq1A,3493
+tests/test_segmentation.py,sha256=_HB8CCq-Ci6amf0xAmDIUuwtBUU_EGpgqLvcvSHrGug,3427
 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-1.1.1.post1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-celldetective-1.1.1.post1.dist-info/METADATA,sha256=MItn6uMJhqWHbN0urj8068yO8xcUoc9c3kUsYTVre10,12418
-celldetective-1.1.1.post1.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
-celldetective-1.1.1.post1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.1.1.post1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.1.1.post1.dist-info/RECORD,,
+celldetective-1.1.1.post4.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.1.1.post4.dist-info/METADATA,sha256=hN7LbHEXIAV9Saz6XZZIxWnhbVQmvbJ9QRFwJ00PHLo,12418
+celldetective-1.1.1.post4.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+celldetective-1.1.1.post4.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.1.1.post4.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.1.1.post4.dist-info/RECORD,,

{celldetective-1.1.1.post1.dist-info → celldetective-1.1.1.post4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.1)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tests/test_segmentation.py

@@ -44,7 +44,7 @@ class TestDLMCF7Segmentation(unittest.TestCase):
 	def test_correct_segmentation_with_transferred_model(self):
 		
 		labels = segment(self.stack, "MCF7_h_versatile", channels=self.channels, spatial_calibration=self.spatial_calibration, view_on_napari=False,
-			use_gpu=True, time_flat_normalization=False, time_flat_percentiles=(0.0,99.99))
+			use_gpu=True)
 		np.testing.assert_array_equal(labels[0], labels[1])
 
 		self.binary_label_true = self.label_true.copy().astype(float)