Hi,
I am working in Windows and I was able to install MONAILabel and run the exemplary server with the radiology app and the Task09_Spleen dataset.
I am able to see the images in 3D Slicer and everything seems normal.
When I draw some scribbles and click Update in the Scribbles tab, I get the following error:
Failed to post process label on MONAI Label Server using Histogram+GraphCut (see below)
The details of this error are as follows:
Traceback (most recent call last):
File “C:/Users/lukas/AppData/Local/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/MONAILabel/lib/Slicer-5.0/qt-scripted-modules/MONAILabel.py”, line 1867, in onUpdateScribbles
result_file, params = self.logic.infer(
File “C:/Users/lukas/AppData/Local/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/MONAILabel/lib/Slicer-5.0/qt-scripted-modules/MONAILabel.py”, line 2152, in infer
result_file, params = client.infer(model, image_in, params, label_in, file, session_id)
File “C:\Users\lukas\AppData\Local\NA-MIC\Slicer 5.0.3\NA-MIC\Extensions-30893\MONAILabel\lib\Slicer-5.0\qt-scripted-modules\MONAILabelLib\client.py”, line 192, in infer
raise MONAILabelException(
MONAILabelLib.client.MONAILabelException: (2, “Status: 500; Response: b’Internal Server Error’”)
The logs are included below:
[2022-08-30 06:45:27,691] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/lukas/radiology; studies: /home/lukas/Task09_Spleen/imagesTr; conf: {‘models’: ‘deepedit’}
[2022-08-30 06:45:27,752] [8015] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for MONAILabelApp Found: <class ‘main.MyApp’>
[2022-08-30 06:45:27,778] [8015] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation.Segmentation’>
[2022-08-30 06:45:27,779] [8015] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_3d.Deepgrow3D’>
[2022-08-30 06:45:27,790] [8015] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepedit.DeepEdit’>
[2022-08-30 06:45:27,792] [8015] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation_spleen.SegmentationSpleen’>
[2022-08-30 06:45:27,794] [8015] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_2d.Deepgrow2D’>
[2022-08-30 06:45:27,794] [8015] [MainThread] [INFO] (main:83) - +++ Adding Model: deepedit => lib.configs.deepedit.DeepEdit
[2022-08-30 06:45:27,794] [8015] [MainThread] [INFO] (monailabel.utils.others.generic:171) - Downloading resource: /home/lukas/radiology/model/pretrained_deepedit_dynunet.pt from https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_multilabel.pt
[2022-08-30 06:45:42,148] [8015] [MainThread] [INFO] (lib.configs.deepedit:144) - EPISTEMIC Enabled: 0; Samples: 5
[2022-08-30 06:45:42,149] [8015] [MainThread] [INFO] (lib.configs.deepedit:148) - TTA Enabled: 0; Samples: 5
[2022-08-30 06:45:42,150] [8015] [MainThread] [INFO] (main:87) - +++ Using Models: [‘deepedit’]
[2022-08-30 06:45:42,151] [8015] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /home/lukas/Task09_Spleen/imagesTr
[2022-08-30 06:45:42,151] [8015] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: [‘.nii.gz’, '.nii’, ‘.nrrd’, '.jpg’, ‘.png’, '.tif’, ‘.svs’, '.xml’]
[2022-08-30 06:45:42,153] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_63 => spleen_63.nii.gz
[2022-08-30 06:45:42,153] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_8 => spleen_8.nii.gz
[2022-08-30 06:45:42,153] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_20 => spleen_20.nii.gz
[2022-08-30 06:45:42,154] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_22 => spleen_22.nii.gz
[2022-08-30 06:45:42,154] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_25 => spleen_25.nii.gz
[2022-08-30 06:45:42,154] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_28 => spleen_28.nii.gz
[2022-08-30 06:45:42,154] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_56 => spleen_56.nii.gz
[2022-08-30 06:45:42,154] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_6 => spleen_6.nii.gz
[2022-08-30 06:45:42,155] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_40 => spleen_40.nii.gz
[2022-08-30 06:45:42,155] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_41 => spleen_41.nii.gz
[2022-08-30 06:45:42,155] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_33 => spleen_33.nii.gz
[2022-08-30 06:45:42,155] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_45 => spleen_45.nii.gz
[2022-08-30 06:45:42,155] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_31 => spleen_31.nii.gz
[2022-08-30 06:45:42,156] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_60 => spleen_60.nii.gz
[2022-08-30 06:45:42,156] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_3 => spleen_3.nii.gz
[2022-08-30 06:45:42,156] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_16 => spleen_16.nii.gz
[2022-08-30 06:45:42,156] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_52 => spleen_52.nii.gz
[2022-08-30 06:45:42,157] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_12 => spleen_12.nii.gz
[2022-08-30 06:45:42,157] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_19 => spleen_19.nii.gz
[2022-08-30 06:45:42,157] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_26 => spleen_26.nii.gz
[2022-08-30 06:45:42,157] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_47 => spleen_47.nii.gz
[2022-08-30 06:45:42,157] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_32 => spleen_32.nii.gz
[2022-08-30 06:45:42,158] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_29 => spleen_29.nii.gz
[2022-08-30 06:45:42,158] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_14 => spleen_14.nii.gz
[2022-08-30 06:45:42,158] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_17 => spleen_17.nii.gz
[2022-08-30 06:45:42,158] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_49 => spleen_49.nii.gz
[2022-08-30 06:45:42,158] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_21 => spleen_21.nii.gz
[2022-08-30 06:45:42,159] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_38 => spleen_38.nii.gz
[2022-08-30 06:45:42,159] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_59 => spleen_59.nii.gz
[2022-08-30 06:45:42,159] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_10 => spleen_10.nii.gz
[2022-08-30 06:45:42,159] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_13 => spleen_13.nii.gz
[2022-08-30 06:45:42,159] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_2 => spleen_2.nii.gz
[2022-08-30 06:45:42,160] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_44 => spleen_44.nii.gz
[2022-08-30 06:45:42,160] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_61 => spleen_61.nii.gz
[2022-08-30 06:45:42,160] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_62 => spleen_62.nii.gz
[2022-08-30 06:45:42,160] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_53 => spleen_53.nii.gz
[2022-08-30 06:45:42,160] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_9 => spleen_9.nii.gz
[2022-08-30 06:45:42,161] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_24 => spleen_24.nii.gz
[2022-08-30 06:45:42,161] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_18 => spleen_18.nii.gz
[2022-08-30 06:45:42,161] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_27 => spleen_27.nii.gz
[2022-08-30 06:45:42,161] [8015] [MainThread] [INFO] (monailabel.datastore.local:557) - Adding New Image: spleen_46 => spleen_46.nii.gz
[2022-08-30 06:45:42,163] [8015] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 41
[2022-08-30 06:45:42,165] [8015] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-08-30 06:45:42,166] [8015] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit => <lib.infers.deepedit.DeepEdit object at 0x7f9a7410ac50>
[2022-08-30 06:45:42,166] [8015] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit_seg => <lib.infers.deepedit.DeepEdit object at 0x7f9a630226d0>
[2022-08-30 06:45:42,167] [8015] [MainThread] [INFO] (main:161) - +++ Adding Trainer:: deepedit => <lib.trainers.deepedit.DeepEdit object at 0x7f9a63022850>
[2022-08-30 06:45:42,167] [8015] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/lukas/.cache/monailabel/sessions
[2022-08-30 06:45:42,167] [8015] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-08-30 06:45:42,167] [8015] [MainThread] [INFO] (monailabel.interfaces.app:460) - App Init - completed
[2022-08-30 06:45:42,168] [8015] [MainThread] [INFO] (timeloop:60) - Starting Timeloop…
[2022-08-30 06:45:42,168] [8015] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7f9a74059950>
[2022-08-30 06:45:42,168] [8015] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-08-30 06:47:34,447] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘random’, ‘client_id’: ‘user-xyz’}
[2022-08-30 06:47:34,449] [8015] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: [‘spleen_63’, ‘spleen_8’, ‘spleen_20’, ‘spleen_22’, ‘spleen_25’, ‘spleen_28’, ‘spleen_56’, ‘spleen_6’, ‘spleen_40’, ‘spleen_41’, ‘spleen_33’, ‘spleen_45’, ‘spleen_31’, ‘spleen_60’, ‘spleen_3’, ‘spleen_16’, ‘spleen_52’, ‘spleen_12’, ‘spleen_19’, ‘spleen_26’, ‘spleen_47’, ‘spleen_32’, ‘spleen_29’, ‘spleen_14’, ‘spleen_17’, ‘spleen_49’, ‘spleen_21’, ‘spleen_38’, ‘spleen_59’, ‘spleen_10’, ‘spleen_13’, ‘spleen_2’, ‘spleen_44’, ‘spleen_61’, ‘spleen_62’, ‘spleen_53’, ‘spleen_9’, ‘spleen_24’, ‘spleen_18’, ‘spleen_27’, ‘spleen_46’]; Weight: [1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054, 1661842054]
[2022-08-30 06:47:34,450] [8015] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_41
[2022-08-30 06:47:34,454] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_41’, ‘ts’: 1661841942, ‘name’: ‘spleen_41.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_41.nii.gz’}
[2022-08-30 06:50:17,167] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘first’, ‘client_id’: ‘user-xyz’}
[2022-08-30 06:50:17,167] [8015] [MainThread] [INFO] (lib.activelearning.first:36) - First: Selected Image: spleen_10
[2022-08-30 06:50:17,171] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_10’, ‘ts’: 1661841942, ‘name’: ‘spleen_10.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_10.nii.gz’}
[2022-08-30 06:50:30,760] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘first’, ‘client_id’: ‘user-xyz’}
[2022-08-30 06:50:30,760] [8015] [MainThread] [INFO] (lib.activelearning.first:36) - First: Selected Image: spleen_10
[2022-08-30 06:50:30,763] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_10’, ‘ts’: 1661841942, ‘name’: ‘spleen_10.nii.gz’, ‘strategy’: {‘first’: {‘ts’: 1661842230, ‘client_id’: ‘user-xyz’}}, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_10.nii.gz’}
[2022-08-30 06:50:36,629] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘first’, ‘client_id’: ‘user-xyz’}
[2022-08-30 06:50:36,630] [8015] [MainThread] [INFO] (lib.activelearning.first:36) - First: Selected Image: spleen_10
[2022-08-30 06:50:36,633] [8015] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_10’, ‘ts’: 1661841942, ‘name’: ‘spleen_10.nii.gz’, ‘strategy’: {‘first’: {‘ts’: 1661842236, ‘client_id’: ‘user-xyz’}}, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_10.nii.gz’}
[2022-08-30 06:52:46,679] [8015] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {‘model’: ‘Histogram+GraphCut’, ‘image’: ‘spleen_10’, ‘label’: ‘/tmp/tmp1j82ejpz.nii.gz’, ‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘roi’: , ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’}
[2022-08-30 06:52:46,680] [8015] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:265) - Infer Request (final): {‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘model’: ‘Histogram+GraphCut’, ‘image’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_10.nii.gz’, ‘label’: ‘/tmp/tmp1j82ejpz.nii.gz’, ‘roi’: , ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’, ‘description’: ‘A post processing step with histogram-based GraphCut for Generic segmentation’, ‘device’: ‘cpu’}
[2022-08-30 06:52:46,682] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - PRE - Run Transform(s)
[2022-08-30 06:52:46,682] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - PRE - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’]
[2022-08-30 06:52:47,495] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (LoadImaged): Time: 0.8118; image: (512, 512, 55)(torch.float32); label: (512, 512, 55)(torch.float32)
[2022-08-30 06:52:47,617] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (EnsureChannelFirstd): Time: 0.1213; image: (1, 512, 512, 55)(torch.float32); label: (1, 512, 512, 55)(torch.float32)
[2022-08-30 06:52:47,617] [8015] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 06:52:47,617] [8015] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 06:52:47,623] [8015] [MainThread] [INFO] (monailabel.scribbles.transforms:111) - Scribbles: (1, 512, 512, 55)
[2022-08-30 06:52:47,623] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (AddBackgroundScribblesFromROId): Time: 0.0063; image: (1, 512, 512, 55)(torch.float32); label: (1, 512, 512, 55)(float32)
[2022-08-30 06:52:48,808] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (Spacingd): Time: 1.1842; image: (1, 201, 201, 55)(torch.float32); label: (1, 205, 205, 12)(torch.float32)
[2022-08-30 06:52:48,852] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (ScaleIntensityRanged): Time: 0.0432; image: (1, 201, 201, 55)(torch.float32); label: (1, 205, 205, 12)(torch.float32)
[2022-08-30 06:52:48,853] [8015] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:400) - Inferer:: cpu => Compose => {‘transforms’: (<monailabel.scribbles.transforms.MakeLikelihoodFromScribblesHistogramd object at 0x7f9a60f396d0>,), ‘map_items’: True, ‘unpack_items’: False, ‘log_stats’: False, ‘R’: RandomState(MT19937) at 0x7F9AAD53D8D0}
[2022-08-30 06:52:48,853] [8015] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:352) - Infer model path: None
[2022-08-30 06:52:48,853] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - INF - Run Inferer(s)
[2022-08-30 06:52:48,854] [8015] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - INF - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’, ‘image_meta_dict’, ‘label_meta_dict’, ‘latencies’]
[2022-08-30 06:52:48,854] [8015] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 06:52:48,854] [8015] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 06:58:29,521] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/lukas/radiology; studies: /home/lukas/Task09_Spleen/imagesTr; conf: {‘models’: ‘deepedit’}
[2022-08-30 06:58:29,525] [15129] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for MONAILabelApp Found: <class ‘main.MyApp’>
[2022-08-30 06:58:29,529] [15129] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation.Segmentation’>
[2022-08-30 06:58:29,530] [15129] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_3d.Deepgrow3D’>
[2022-08-30 06:58:29,532] [15129] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepedit.DeepEdit’>
[2022-08-30 06:58:29,532] [15129] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation_spleen.SegmentationSpleen’>
[2022-08-30 06:58:29,533] [15129] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_2d.Deepgrow2D’>
[2022-08-30 06:58:29,533] [15129] [MainThread] [INFO] (main:83) - +++ Adding Model: deepedit => lib.configs.deepedit.DeepEdit
[2022-08-30 06:58:30,511] [15129] [MainThread] [INFO] (lib.configs.deepedit:144) - EPISTEMIC Enabled: 0; Samples: 5
[2022-08-30 06:58:30,511] [15129] [MainThread] [INFO] (lib.configs.deepedit:148) - TTA Enabled: 0; Samples: 5
[2022-08-30 06:58:30,511] [15129] [MainThread] [INFO] (main:87) - +++ Using Models: [‘deepedit’]
[2022-08-30 06:58:30,512] [15129] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /home/lukas/Task09_Spleen/imagesTr
[2022-08-30 06:58:30,512] [15129] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: [‘.nii.gz’, '.nii’, ‘.nrrd’, '.jpg’, ‘.png’, '.tif’, ‘.svs’, '.xml’]
[2022-08-30 06:58:30,518] [15129] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-08-30 06:58:30,518] [15129] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-08-30 06:58:30,519] [15129] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit => <lib.infers.deepedit.DeepEdit object at 0x7fc616be5610>
[2022-08-30 06:58:30,519] [15129] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit_seg => <lib.infers.deepedit.DeepEdit object at 0x7fc61d7ae650>
[2022-08-30 06:58:30,519] [15129] [MainThread] [INFO] (main:161) - +++ Adding Trainer:: deepedit => <lib.trainers.deepedit.DeepEdit object at 0x7fc6101b7190>
[2022-08-30 06:58:30,520] [15129] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/lukas/.cache/monailabel/sessions
[2022-08-30 06:58:30,520] [15129] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-08-30 06:58:30,520] [15129] [MainThread] [INFO] (monailabel.interfaces.app:460) - App Init - completed
[2022-08-30 06:58:30,520] [15129] [MainThread] [INFO] (timeloop:60) - Starting Timeloop…
[2022-08-30 06:58:30,520] [15129] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7fc6119b27a0>
[2022-08-30 06:58:30,521] [15129] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-08-30 06:59:05,474] [15129] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘random’, ‘client_id’: ‘user-xyz’}
[2022-08-30 06:59:05,478] [15129] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: [‘spleen_63’, ‘spleen_8’, ‘spleen_20’, ‘spleen_22’, ‘spleen_25’, ‘spleen_28’, ‘spleen_56’, ‘spleen_6’, ‘spleen_40’, ‘spleen_41’, ‘spleen_33’, ‘spleen_45’, ‘spleen_31’, ‘spleen_60’, ‘spleen_3’, ‘spleen_16’, ‘spleen_52’, ‘spleen_12’, ‘spleen_19’, ‘spleen_26’, ‘spleen_47’, ‘spleen_32’, ‘spleen_29’, ‘spleen_14’, ‘spleen_17’, ‘spleen_49’, ‘spleen_21’, ‘spleen_38’, ‘spleen_59’, ‘spleen_10’, ‘spleen_13’, ‘spleen_2’, ‘spleen_44’, ‘spleen_61’, ‘spleen_62’, ‘spleen_53’, ‘spleen_9’, ‘spleen_24’, ‘spleen_18’, ‘spleen_27’, ‘spleen_46’]; Weight: [1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 691, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745, 1661842745]
[2022-08-30 06:59:05,478] [15129] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_16
[2022-08-30 06:59:05,484] [15129] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_16’, ‘ts’: 1661841942, ‘name’: ‘spleen_16.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_16.nii.gz’}
[2022-08-30 07:00:29,907] [15129] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {‘model’: ‘Histogram+GraphCut’, ‘image’: ‘spleen_16’, ‘label’: ‘/tmp/tmpr6wyzmqn.nii.gz’, ‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘roi’: [88, 190, 254, 431, 25, 39], ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:00:29,908] [15129] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:265) - Infer Request (final): {‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘model’: ‘Histogram+GraphCut’, ‘image’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_16.nii.gz’, ‘label’: ‘/tmp/tmpr6wyzmqn.nii.gz’, ‘roi’: [88, 190, 254, 431, 25, 39], ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’, ‘description’: ‘A post processing step with histogram-based GraphCut for Generic segmentation’, ‘device’: ‘cpu’}
[2022-08-30 07:00:29,910] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - PRE - Run Transform(s)
[2022-08-30 07:00:29,910] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - PRE - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’]
[2022-08-30 07:00:30,815] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (LoadImaged): Time: 0.9036; image: (512, 512, 61)(torch.float32); label: (512, 512, 61)(torch.float32)
[2022-08-30 07:00:30,816] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (EnsureChannelFirstd): Time: 0.0005; image: (1, 512, 512, 61)(torch.float32); label: (1, 512, 512, 61)(torch.float32)
[2022-08-30 07:00:30,816] [15129] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 07:00:30,816] [15129] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 07:00:30,816] [15129] [MainThread] [INFO] (monailabel.scribbles.transforms:111) - Scribbles: (1, 512, 512, 61)
[2022-08-30 07:00:30,873] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (AddBackgroundScribblesFromROId): Time: 0.0568; image: (1, 512, 512, 61)(torch.float32); label: (1, 512, 512, 61)(float32)
[2022-08-30 07:00:31,192] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (Spacingd): Time: 0.3187; image: (1, 163, 163, 97)(torch.float32); label: (1, 205, 205, 13)(torch.float32)
[2022-08-30 07:00:31,203] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (ScaleIntensityRanged): Time: 0.0101; image: (1, 163, 163, 97)(torch.float32); label: (1, 205, 205, 13)(torch.float32)
[2022-08-30 07:00:31,205] [15129] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:400) - Inferer:: cpu => Compose => {‘transforms’: (<monailabel.scribbles.transforms.MakeLikelihoodFromScribblesHistogramd object at 0x7fc61d6a1150>,), ‘map_items’: True, ‘unpack_items’: False, ‘log_stats’: False, ‘R’: RandomState(MT19937) at 0x7FC61D6AB490}
[2022-08-30 07:00:31,205] [15129] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:352) - Infer model path: None
[2022-08-30 07:00:31,205] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - INF - Run Inferer(s)
[2022-08-30 07:00:31,205] [15129] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - INF - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’, ‘image_meta_dict’, ‘label_meta_dict’, ‘latencies’]
[2022-08-30 07:00:31,206] [15129] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 07:00:31,207] [15129] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 07:05:59,582] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/lukas/radiology; studies: /home/lukas/Task09_Spleen/imagesTr; conf: {‘models’: ‘deepedit’}
[2022-08-30 07:05:59,586] [19017] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for MONAILabelApp Found: <class ‘main.MyApp’>
[2022-08-30 07:05:59,591] [19017] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation.Segmentation’>
[2022-08-30 07:05:59,591] [19017] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_3d.Deepgrow3D’>
[2022-08-30 07:05:59,593] [19017] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepedit.DeepEdit’>
[2022-08-30 07:05:59,594] [19017] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation_spleen.SegmentationSpleen’>
[2022-08-30 07:05:59,594] [19017] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_2d.Deepgrow2D’>
[2022-08-30 07:05:59,595] [19017] [MainThread] [INFO] (main:83) - +++ Adding Model: deepedit => lib.configs.deepedit.DeepEdit
[2022-08-30 07:06:00,586] [19017] [MainThread] [INFO] (lib.configs.deepedit:144) - EPISTEMIC Enabled: 0; Samples: 5
[2022-08-30 07:06:00,587] [19017] [MainThread] [INFO] (lib.configs.deepedit:148) - TTA Enabled: 0; Samples: 5
[2022-08-30 07:06:00,587] [19017] [MainThread] [INFO] (main:87) - +++ Using Models: [‘deepedit’]
[2022-08-30 07:06:00,587] [19017] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /home/lukas/Task09_Spleen/imagesTr
[2022-08-30 07:06:00,587] [19017] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: [‘.nii.gz’, '.nii’, ‘.nrrd’, '.jpg’, ‘.png’, '.tif’, ‘.svs’, '.xml’]
[2022-08-30 07:06:00,593] [19017] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-08-30 07:06:00,593] [19017] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-08-30 07:06:00,595] [19017] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit => <lib.infers.deepedit.DeepEdit object at 0x7f39ef5a46d0>
[2022-08-30 07:06:00,595] [19017] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit_seg => <lib.infers.deepedit.DeepEdit object at 0x7f39e53b4190>
[2022-08-30 07:06:00,595] [19017] [MainThread] [INFO] (main:161) - +++ Adding Trainer:: deepedit => <lib.trainers.deepedit.DeepEdit object at 0x7f39e53b42d0>
[2022-08-30 07:06:00,595] [19017] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/lukas/.cache/monailabel/sessions
[2022-08-30 07:06:00,595] [19017] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-08-30 07:06:00,595] [19017] [MainThread] [INFO] (monailabel.interfaces.app:460) - App Init - completed
[2022-08-30 07:06:00,596] [19017] [MainThread] [INFO] (timeloop:60) - Starting Timeloop…
[2022-08-30 07:06:00,596] [19017] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7f39e576d320>
[2022-08-30 07:06:00,596] [19017] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-08-30 07:06:25,853] [19017] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘random’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:06:25,855] [19017] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: [‘spleen_63’, ‘spleen_8’, ‘spleen_20’, ‘spleen_22’, ‘spleen_25’, ‘spleen_28’, ‘spleen_56’, ‘spleen_6’, ‘spleen_40’, ‘spleen_41’, ‘spleen_33’, ‘spleen_45’, ‘spleen_31’, ‘spleen_60’, ‘spleen_3’, ‘spleen_16’, ‘spleen_52’, ‘spleen_12’, ‘spleen_19’, ‘spleen_26’, ‘spleen_47’, ‘spleen_32’, ‘spleen_29’, ‘spleen_14’, ‘spleen_17’, ‘spleen_49’, ‘spleen_21’, ‘spleen_38’, ‘spleen_59’, ‘spleen_10’, ‘spleen_13’, ‘spleen_2’, ‘spleen_44’, ‘spleen_61’, ‘spleen_62’, ‘spleen_53’, ‘spleen_9’, ‘spleen_24’, ‘spleen_18’, ‘spleen_27’, ‘spleen_46’]; Weight: [1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1131, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 440, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185, 1661843185]
[2022-08-30 07:06:25,855] [19017] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_27
[2022-08-30 07:06:25,860] [19017] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_27’, ‘ts’: 1661841942, ‘name’: ‘spleen_27.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_27.nii.gz’}
[2022-08-30 07:06:39,936] [19017] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘random’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:06:39,938] [19017] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: [‘spleen_63’, ‘spleen_8’, ‘spleen_20’, ‘spleen_22’, ‘spleen_25’, ‘spleen_28’, ‘spleen_56’, ‘spleen_6’, ‘spleen_40’, ‘spleen_41’, ‘spleen_33’, ‘spleen_45’, ‘spleen_31’, ‘spleen_60’, ‘spleen_3’, ‘spleen_16’, ‘spleen_52’, ‘spleen_12’, ‘spleen_19’, ‘spleen_26’, ‘spleen_47’, ‘spleen_32’, ‘spleen_29’, ‘spleen_14’, ‘spleen_17’, ‘spleen_49’, ‘spleen_21’, ‘spleen_38’, ‘spleen_59’, ‘spleen_10’, ‘spleen_13’, ‘spleen_2’, ‘spleen_44’, ‘spleen_61’, ‘spleen_62’, ‘spleen_53’, ‘spleen_9’, ‘spleen_24’, ‘spleen_18’, ‘spleen_27’, ‘spleen_46’]; Weight: [1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1145, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 454, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 1661843199, 14, 1661843199]
[2022-08-30 07:06:39,938] [19017] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_49
[2022-08-30 07:06:39,941] [19017] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_49’, ‘ts’: 1661841942, ‘name’: ‘spleen_49.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_49.nii.gz’}
[2022-08-30 07:07:42,923] [19017] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {‘model’: ‘Histogram+GraphCut’, ‘image’: ‘spleen_49’, ‘label’: ‘/tmp/tmp2n85sm6p.nii.gz’, ‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘roi’: [24, 137, 124, 306, 6, 53], ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:07:42,924] [19017] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:265) - Infer Request (final): {‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘model’: ‘Histogram+GraphCut’, ‘image’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_49.nii.gz’, ‘label’: ‘/tmp/tmp2n85sm6p.nii.gz’, ‘roi’: [24, 137, 124, 306, 6, 53], ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’, ‘description’: ‘A post processing step with histogram-based GraphCut for Generic segmentation’, ‘device’: ‘cpu’}
[2022-08-30 07:07:42,926] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - PRE - Run Transform(s)
[2022-08-30 07:07:42,926] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - PRE - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’]
[2022-08-30 07:07:43,825] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (LoadImaged): Time: 0.8985; image: (512, 512, 61)(torch.float32); label: (512, 512, 61)(torch.float32)
[2022-08-30 07:07:43,827] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (EnsureChannelFirstd): Time: 0.0007; image: (1, 512, 512, 61)(torch.float32); label: (1, 512, 512, 61)(torch.float32)
[2022-08-30 07:07:43,827] [19017] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 07:07:43,827] [19017] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 07:07:43,828] [19017] [MainThread] [INFO] (monailabel.scribbles.transforms:111) - Scribbles: (1, 512, 512, 61)
[2022-08-30 07:07:43,889] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (AddBackgroundScribblesFromROId): Time: 0.0618; image: (1, 512, 512, 61)(torch.float32); label: (1, 512, 512, 61)(float32)
[2022-08-30 07:07:44,233] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (Spacingd): Time: 0.3435; image: (1, 175, 175, 49)(torch.float32); label: (1, 205, 205, 13)(torch.float32)
[2022-08-30 07:07:44,238] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (ScaleIntensityRanged): Time: 0.0042; image: (1, 175, 175, 49)(torch.float32); label: (1, 205, 205, 13)(torch.float32)
[2022-08-30 07:07:44,239] [19017] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:400) - Inferer:: cpu => Compose => {‘transforms’: (<monailabel.scribbles.transforms.MakeLikelihoodFromScribblesHistogramd object at 0x7f39e42f2090>,), ‘map_items’: True, ‘unpack_items’: False, ‘log_stats’: False, ‘R’: RandomState(MT19937) at 0x7F39F28B6380}
[2022-08-30 07:07:44,239] [19017] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:352) - Infer model path: None
[2022-08-30 07:07:44,239] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - INF - Run Inferer(s)
[2022-08-30 07:07:44,239] [19017] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - INF - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’, ‘image_meta_dict’, ‘label_meta_dict’, ‘latencies’]
[2022-08-30 07:07:44,240] [19017] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 07:07:44,240] [19017] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 07:16:57,278] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/lukas/radiology; studies: /home/lukas/Task09_Spleen/imagesTr; conf: {‘models’: ‘deepedit’}
[2022-08-30 07:16:57,282] [25061] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for MONAILabelApp Found: <class ‘main.MyApp’>
[2022-08-30 07:16:57,286] [25061] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation.Segmentation’>
[2022-08-30 07:16:57,287] [25061] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_3d.Deepgrow3D’>
[2022-08-30 07:16:57,289] [25061] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepedit.DeepEdit’>
[2022-08-30 07:16:57,290] [25061] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.segmentation_spleen.SegmentationSpleen’>
[2022-08-30 07:16:57,290] [25061] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class ‘lib.configs.deepgrow_2d.Deepgrow2D’>
[2022-08-30 07:16:57,290] [25061] [MainThread] [INFO] (main:83) - +++ Adding Model: deepedit => lib.configs.deepedit.DeepEdit
[2022-08-30 07:16:58,278] [25061] [MainThread] [INFO] (lib.configs.deepedit:144) - EPISTEMIC Enabled: 0; Samples: 5
[2022-08-30 07:16:58,279] [25061] [MainThread] [INFO] (lib.configs.deepedit:148) - TTA Enabled: 0; Samples: 5
[2022-08-30 07:16:58,279] [25061] [MainThread] [INFO] (main:87) - +++ Using Models: [‘deepedit’]
[2022-08-30 07:16:58,279] [25061] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /home/lukas/Task09_Spleen/imagesTr
[2022-08-30 07:16:58,279] [25061] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: [‘.nii.gz’, '.nii’, ‘.nrrd’, '.jpg’, ‘.png’, '.tif’, ‘.svs’, '.xml’]
[2022-08-30 07:16:58,285] [25061] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-08-30 07:16:58,285] [25061] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-08-30 07:16:58,287] [25061] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit => <lib.infers.deepedit.DeepEdit object at 0x7fa70d2d1610>
[2022-08-30 07:16:58,287] [25061] [MainThread] [INFO] (main:112) - +++ Adding Inferer:: deepedit_seg => <lib.infers.deepedit.DeepEdit object at 0x7fa7045f91d0>
[2022-08-30 07:16:58,287] [25061] [MainThread] [INFO] (main:161) - +++ Adding Trainer:: deepedit => <lib.trainers.deepedit.DeepEdit object at 0x7fa7045f9310>
[2022-08-30 07:16:58,287] [25061] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/lukas/.cache/monailabel/sessions
[2022-08-30 07:16:58,288] [25061] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-08-30 07:16:58,288] [25061] [MainThread] [INFO] (monailabel.interfaces.app:460) - App Init - completed
[2022-08-30 07:16:58,288] [25061] [MainThread] [INFO] (timeloop:60) - Starting Timeloop…
[2022-08-30 07:16:58,288] [25061] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7fa7049b2320>
[2022-08-30 07:16:58,289] [25061] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-08-30 07:17:32,947] [25061] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘random’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:17:32,949] [25061] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: [‘spleen_63’, ‘spleen_8’, ‘spleen_20’, ‘spleen_22’, ‘spleen_25’, ‘spleen_28’, ‘spleen_56’, ‘spleen_6’, ‘spleen_40’, ‘spleen_41’, ‘spleen_33’, ‘spleen_45’, ‘spleen_31’, ‘spleen_60’, ‘spleen_3’, ‘spleen_16’, ‘spleen_52’, ‘spleen_12’, ‘spleen_19’, ‘spleen_26’, ‘spleen_47’, ‘spleen_32’, ‘spleen_29’, ‘spleen_14’, ‘spleen_17’, ‘spleen_49’, ‘spleen_21’, ‘spleen_38’, ‘spleen_59’, ‘spleen_10’, ‘spleen_13’, ‘spleen_2’, ‘spleen_44’, ‘spleen_61’, ‘spleen_62’, ‘spleen_53’, ‘spleen_9’, ‘spleen_24’, ‘spleen_18’, ‘spleen_27’, ‘spleen_46’]; Weight: [1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1798, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1107, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 653, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 1661843852, 667, 1661843852]
[2022-08-30 07:17:32,949] [25061] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_26
[2022-08-30 07:17:32,953] [25061] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_26’, ‘ts’: 1661841942, ‘name’: ‘spleen_26.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_26.nii.gz’}
[2022-08-30 07:17:47,731] [25061] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {‘strategy’: ‘random’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:17:47,732] [25061] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: [‘spleen_63’, ‘spleen_8’, ‘spleen_20’, ‘spleen_22’, ‘spleen_25’, ‘spleen_28’, ‘spleen_56’, ‘spleen_6’, ‘spleen_40’, ‘spleen_41’, ‘spleen_33’, ‘spleen_45’, ‘spleen_31’, ‘spleen_60’, ‘spleen_3’, ‘spleen_16’, ‘spleen_52’, ‘spleen_12’, ‘spleen_19’, ‘spleen_26’, ‘spleen_47’, ‘spleen_32’, ‘spleen_29’, ‘spleen_14’, ‘spleen_17’, ‘spleen_49’, ‘spleen_21’, ‘spleen_38’, ‘spleen_59’, ‘spleen_10’, ‘spleen_13’, ‘spleen_2’, ‘spleen_44’, ‘spleen_61’, ‘spleen_62’, ‘spleen_53’, ‘spleen_9’, ‘spleen_24’, ‘spleen_18’, ‘spleen_27’, ‘spleen_46’]; Weight: [1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1813, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1122, 1661843867, 1661843867, 1661843867, 15, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 668, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 1661843867, 682, 1661843867]
[2022-08-30 07:17:47,733] [25061] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_14
[2022-08-30 07:17:47,736] [25061] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {‘id’: ‘spleen_14’, ‘ts’: 1661841942, ‘name’: ‘spleen_14.nii.gz’, ‘path’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_14.nii.gz’}
[2022-08-30 07:18:21,299] [25061] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {‘model’: ‘Histogram+GraphCut’, ‘image’: ‘spleen_14’, ‘label’: ‘/tmp/tmp4nz9wtc4.nii.gz’, ‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘roi’: , ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’}
[2022-08-30 07:18:21,299] [25061] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:265) - Infer Request (final): {‘num_bins’: 64, ‘lamda’: 1.0, ‘sigma’: 0.1, ‘model’: ‘Histogram+GraphCut’, ‘image’: ‘/home/lukas/Task09_Spleen/imagesTr/spleen_14.nii.gz’, ‘label’: ‘/tmp/tmp4nz9wtc4.nii.gz’, ‘roi’: , ‘label_info’: [{‘name’: ‘background’, ‘id’: 1}, {‘name’: ‘spleen’, ‘id’: 2}, {‘name’: ‘right kidney’, ‘id’: 3}, {‘name’: ‘left kidney’, ‘id’: 4}, {‘name’: ‘liver’, ‘id’: 5}, {‘name’: ‘stomach’, ‘id’: 6}, {‘name’: ‘aorta’, ‘id’: 7}, {‘name’: ‘inferior vena cava’, ‘id’: 8}, {‘name’: ‘background_scribbles’, ‘id’: 9}, {‘name’: ‘foreground_scribbles’, ‘id’: 10}], ‘selected_label_name’: ‘spleen’, ‘result_extension’: ‘.nrrd’, ‘result_dtype’: ‘uint8’, ‘client_id’: ‘user-xyz’, ‘description’: ‘A post processing step with histogram-based GraphCut for Generic segmentation’, ‘device’: ‘cpu’}
[2022-08-30 07:18:21,302] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - PRE - Run Transform(s)
[2022-08-30 07:18:21,303] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - PRE - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’]
[2022-08-30 07:18:22,043] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (LoadImaged): Time: 0.7396; image: (512, 512, 54)(torch.float32); label: (512, 512, 54)(torch.float32)
[2022-08-30 07:18:22,044] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (EnsureChannelFirstd): Time: 0.0005; image: (1, 512, 512, 54)(torch.float32); label: (1, 512, 512, 54)(torch.float32)
[2022-08-30 07:18:22,044] [25061] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 07:18:22,044] [25061] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
[2022-08-30 07:18:22,045] [25061] [MainThread] [INFO] (monailabel.scribbles.transforms:111) - Scribbles: (1, 512, 512, 54)
[2022-08-30 07:18:22,045] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (AddBackgroundScribblesFromROId): Time: 0.0006; image: (1, 512, 512, 54)(torch.float32); label: (1, 512, 512, 54)(float32)
[2022-08-30 07:18:22,334] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (Spacingd): Time: 0.2885; image: (1, 175, 175, 54)(torch.float32); label: (1, 205, 205, 12)(torch.float32)
[2022-08-30 07:18:22,339] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:108) - PRE - Transform (ScaleIntensityRanged): Time: 0.0049; image: (1, 175, 175, 54)(torch.float32); label: (1, 205, 205, 12)(torch.float32)
[2022-08-30 07:18:22,341] [25061] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:400) - Inferer:: cpu => Compose => {‘transforms’: (<monailabel.scribbles.transforms.MakeLikelihoodFromScribblesHistogramd object at 0x7fa701d37690>,), ‘map_items’: True, ‘unpack_items’: False, ‘log_stats’: False, ‘R’: RandomState(MT19937) at 0x7FA711AFB380}
[2022-08-30 07:18:22,341] [25061] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:352) - Infer model path: None
[2022-08-30 07:18:22,342] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - INF - Run Inferer(s)
[2022-08-30 07:18:22,342] [25061] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - INF - Input Keys: [‘num_bins’, ‘lamda’, ‘sigma’, ‘model’, ‘image’, ‘label’, ‘roi’, ‘label_info’, ‘selected_label_name’, ‘result_extension’, ‘result_dtype’, ‘client_id’, ‘description’, ‘device’, ‘image_path’, ‘image_meta_dict’, ‘label_meta_dict’, ‘latencies’]
[2022-08-30 07:18:22,343] [25061] [MainThread] [INFO] (root:74) - Loading background scribbles labels from: background_scribbles with index: 9
[2022-08-30 07:18:22,343] [25061] [MainThread] [INFO] (root:79) - Loading foreground scribbles labels from: foreground_scribbles with index: 10
I have a numpy version that is 1.21.6 and the SimpleCRF package is installed.
Any ideas on how to fix this?
Thank you in advance!
Lukas