spacr 0.1.76__py3-none-any.whl → 0.1.77__py3-none-any.whl

spacr/core.py

@@ -994,7 +994,7 @@ def apply_model_to_tar(tar_path, model_path, file_type='cell_png', image_size=22
     model = torch.load(model_path)
     
     dataset = TarImageDataset(tar_path, transform=transform)
-    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, n_jobs=n_jobs, pin_memory=True)
+    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, num_workers=n_jobs, pin_memory=True)
     
     model_name = os.path.splitext(os.path.basename(model_path))[0] 
     dataset_name = os.path.splitext(os.path.basename(tar_path))[0]  
@@ -1055,7 +1055,7 @@ def apply_model(src, model_path, image_size=224, batch_size=64, normalize=True,
     
     print(f'Loading dataset in {src} with {len(src)} images')
     dataset = NoClassDataset(data_dir=src, transform=transform, shuffle=True, load_to_memory=False)
-    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, n_jobs=n_jobs)
+    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, num_workers=n_jobs)
     print(f'Loaded {len(src)} images')
     
     result_loc = os.path.splitext(model_path)[0]+datetime.date.today().strftime('%y%m%d')+'_'+os.path.splitext(model_path)[1]+'_test_result.csv'
@@ -1404,10 +1404,10 @@ def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_
                 #val_dataset = augment_dataset(val_dataset, is_grayscale=(len(channels) == 1))
                 print(f'Data after augmentation: Train: {len(train_dataset)}')#, Validataion:{len(val_dataset)}')
 
-            train_loaders = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, n_jobs=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
-            val_loaders = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, n_jobs=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+            train_loaders = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+            val_loaders = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
         else:
-            train_loaders = DataLoader(data, batch_size=batch_size, shuffle=shuffle, n_jobs=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+            train_loaders = DataLoader(data, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
         
     elif train_mode == 'irm':
         data = MyDataset(data_dir, classes, transform=transform, shuffle=shuffle, pin_memory=pin_memory)
@@ -1436,13 +1436,13 @@ def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_
                     #val_dataset = augment_dataset(val_dataset, is_grayscale=(len(channels) == 1))
                     print(f'Data after augmentation: Train: {len(train_dataset)}')#, Validataion:{len(val_dataset)}')
 
-                train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, n_jobs=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
-                val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, n_jobs=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+                train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+                val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
 
                 train_loaders.append(train_loader)
                 val_loaders.append(val_loader)
             else:
-                train_loader = DataLoader(plate_data, batch_size=batch_size, shuffle=shuffle, n_jobs=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+                train_loader = DataLoader(plate_data, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
                 train_loaders.append(train_loader)
                 val_loaders.append(None)
     

{spacr-0.1.76.dist-info → spacr-0.1.77.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.76
+Version: 0.1.77
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.76.dist-info → spacr-0.1.77.dist-info}/RECORD

@@ -14,7 +14,7 @@ spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
 spacr/classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
 spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
-spacr/core.py,sha256=vDSqxiFUdQ0sCn5QRlFWYqR7CQCDaMGTD-xDOnikOfE,160176
+spacr/core.py,sha256=bm1cApGVTE218Ds3FqqWD5TsF5FF8kclHwPlvdOolzc,160216
 spacr/deep_spacr.py,sha256=ASBsN4JpHp_3S-91JUsB34IWTjTGPYI7jKV2qZnUR5M,37005
 spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
 spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
@@ -52,9 +52,9 @@ spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.1.76.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.76.dist-info/METADATA,sha256=SLaAcTSAOj_pyCLUshGwpwD0rt_XLRTE9p08sVbTalo,5050
-spacr-0.1.76.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.76.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.1.76.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.76.dist-info/RECORD,,
+spacr-0.1.77.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.1.77.dist-info/METADATA,sha256=FEEy3ZRedFlkX0jIEsC7MZ1qlDRCahOWGrtmzE7Mj3g,5050
+spacr-0.1.77.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.1.77.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.1.77.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.1.77.dist-info/RECORD,,