celldetective 1.1.1.post1__py3-none-any.whl → 1.1.1.post3__py3-none-any.whl

celldetective/scripts/segment_cells.py

@@ -148,6 +148,7 @@ def segment_index(indices):
 		model.config.use_gpu = use_gpu
 		model.use_gpu = use_gpu
 		print(f"StarDist model {modelname} successfully loaded.")
+		scale_model = scale
 
 	elif model_type=='cellpose':
 

celldetective/scripts/train_segmentation_model.py

@@ -60,17 +60,10 @@ batch_size = training_instructions['batch_size']
 
 # Load dataset
 print(f'Datasets: {datasets}')
-X,Y = load_image_dataset(datasets, target_channels, train_spatial_calibration=spatial_calibration,
+X,Y,filenames = load_image_dataset(datasets, target_channels, train_spatial_calibration=spatial_calibration,
 						mask_suffix='labelled')
 print('Dataset loaded...')
 
-# Normalize images
-# X = normalize_per_channel(X,
-# 						  normalization_percentile_mode=normalization_percentile, 
-# 						  normalization_values=normalization_values, 
-# 						  normalization_clipping=normalization_clip
-# 						  )
-
 values = []
 percentiles = []
 for k in range(len(normalization_percentile)):
@@ -88,17 +81,6 @@ for k in range(len(X)):
 	x_interp = np.moveaxis([interpolate_nan(x[:,:,c].copy()) for c in range(x.shape[-1])],0,-1)
 	X[k] = x_interp
 
-# for x in X[:10]:
-# 	plt.imshow(x[:,:,0])
-# 	plt.colorbar()
-# 	plt.pause(2)
-# 	plt.close()
-
-# 	plt.imshow(x[:,:,1])
-# 	plt.colorbar()
-# 	plt.pause(2)
-# 	plt.close()
-
 Y = [fill_label_holes(y) for y in tqdm(Y)]
 
 assert len(X) > 1, "not enough training data"
@@ -107,7 +89,11 @@ ind = rng.permutation(len(X))
 n_val = max(1, int(round(validation_split * len(ind))))
 ind_train, ind_val = ind[:-n_val], ind[-n_val:]
 X_val, Y_val = [X[i] for i in ind_val]  , [Y[i] for i in ind_val]
-X_trn, Y_trn = [X[i] for i in ind_train], [Y[i] for i in ind_train] 
+X_trn, Y_trn = [X[i] for i in ind_train], [Y[i] for i in ind_train]
+
+files_train = [filenames[i] for i in ind_train]
+files_val = [filenames[i] for i in ind_val]
+
 print('number of images: %3d' % len(X))
 print('- training:       %3d' % len(X_trn))
 print('- validation:     %3d' % len(X_val))
@@ -134,7 +120,10 @@ if model_type=='cellpose':
 	import torch
 	
 	if not use_gpu:
+		print('Using CPU for training...')
 		device = torch.device("cpu")
+	else:
+		print('Using GPU for training...')
 		
 	logger, log_file = logger_setup()
 	print(f'Pretrained model: ',pretrained)
@@ -163,7 +152,7 @@ if model_type=='cellpose':
 	config_inputs = {"channels": target_channels, "diameter": standard_diameter, 'cellprob_threshold': 0., 'flow_threshold': 0.4,
 	'normalization_percentile': normalization_percentile, 'normalization_clip': normalization_clip,
 	'normalization_values': normalization_values, 'model_type': 'cellpose',
-	'spatial_calibration': input_spatial_calibration}
+	'spatial_calibration': input_spatial_calibration, 'dataset': {'train': files_train, 'validation': files_val}}
 	json_input_config = json.dumps(config_inputs, indent=4)
 	with open(os.sep.join([target_directory, model_name, "config_input.json"]), "w") as outfile:
 		outfile.write(json_input_config)
@@ -234,7 +223,7 @@ elif model_type=='stardist':
 
 	config_inputs = {"channels": target_channels, 'normalization_percentile': normalization_percentile,
 	'normalization_clip': normalization_clip, 'normalization_values': normalization_values, 
-	'model_type': 'stardist', 'spatial_calibration': spatial_calibration}
+	'model_type': 'stardist', 'spatial_calibration': spatial_calibration, 'dataset': {'train': files_train, 'validation': files_val}}
 
 	json_input_config = json.dumps(config_inputs, indent=4)
 	with open(os.sep.join([target_directory, model_name, "config_input.json"]), "w") as outfile:

celldetective/utils.py

@@ -2046,7 +2046,7 @@ 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 +2101,10 @@ 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.post3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.1.1.post1
+Version: 1.1.1.post3
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.1.1.post1.dist-info → celldetective-1.1.1.post3.dist-info}/RECORD

@@ -6,11 +6,11 @@ celldetective/filters.py,sha256=b0qKwHor1fvNA_dHovP17nQz8EsW5YlyhT2TJnayn08,3615
 celldetective/io.py,sha256=ptaX4GadWuf0zOQ3ZWSLCzihEID-YAalPfxW1nqvgIU,80889
 celldetective/measure.py,sha256=HDQZfSRx3daOCV5Snu1paYU5JYkwu8engO2qZqhTAUo,48089
 celldetective/neighborhood.py,sha256=QCuhesMHGyr3c3ys9wWcNR1HM6CHdHe51R8upoolgPw,49514
-celldetective/preprocessing.py,sha256=psCs4CAI7gG3YlKvxkXKnpClFL4SjWm5TToXq2ZwL-s,37137
+celldetective/preprocessing.py,sha256=dpor6ry6RChzd-rdH98SQc0zvLZv95YZB5KIGym1mEY,37388
 celldetective/segmentation.py,sha256=Hu4-lOJ4UhPw2o0Hn_NPOCHsa6Iwsw5A3PR6X3Tzbb8,29196
 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=f0VvWv5ZgndZiWsFFDs0O6tJlRXkRtPW0xEKM_R90yo,77581
 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
@@ -22,22 +22,22 @@ celldetective/gui/configure_new_exp.py,sha256=ANJ-Zn4sjBphtj_aoJu6m1PFEKyv9gxeh9
 celldetective/gui/control_panel.py,sha256=wcDqe4XaDJRMmPmWKJpxd0D9V4_DrdRGnEH6D7B_IK0,17557
 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=sHTWXsKdRoHYYrPELEW7djNetevcQ-RKW9aQQ2FvWoc,37644
 celldetective/gui/measurement_options.py,sha256=i0CdAfupHJAqhOT7RsufEK919sAzQnFBkQO4IAMYZL0,47704
 celldetective/gui/neighborhood_options.py,sha256=sdKxVRliZtuKSpcPfnFxqkW4V8rN2tzjhDxOPVmElyE,20191
 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_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=7QSvkvVpglcluLxqhKjehmYDwHoyZs0R7uLcJK_9fhs,34268
 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
@@ -76,9 +76,9 @@ tests/test_segmentation.py,sha256=-3b7o_fUVMYxfVwX5VHFqRF0dDXObSTtylf5XQGcq1A,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-1.1.1.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.post3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.1.1.post3.dist-info/METADATA,sha256=r2-IaTUiO4VxRyIFdQJbsYx_MJltOPt76Emkf8XqAtk,12418
+celldetective-1.1.1.post3.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
+celldetective-1.1.1.post3.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.1.1.post3.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.1.1.post3.dist-info/RECORD,,

{celldetective-1.1.1.post1.dist-info → celldetective-1.1.1.post3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.1)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any