diff --git a/notebooks/tutorials/03_segmentation_app.ipynb b/notebooks/tutorials/03_segmentation_app.ipynb index 57886cc8..5a17c7e1 100644 --- a/notebooks/tutorials/03_segmentation_app.ipynb +++ b/notebooks/tutorials/03_segmentation_app.ipynb @@ -731,112 +731,110 @@ "output_type": "stream", "text": [ "[info] [fragment.cpp:705] Loading extensions from configs...\n", - "[2025-04-22 10:06:42,869] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=[])\n", - "[2025-04-22 10:06:42,879] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", - "[2025-04-22 10:06:42,880] [INFO] (__main__.AISpleenSegApp) - App input and output path: dcm, output\n", + "[2025-07-11 15:20:01,635] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=[])\n", + "[2025-07-11 15:20:01,642] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", + "[2025-07-11 15:20:01,643] [INFO] (__main__.AISpleenSegApp) - App input and output path: dcm, output\n", "[info] [gxf_executor.cpp:265] Creating context\n", "[info] [gxf_executor.cpp:2396] Activating Graph...\n", "[info] [gxf_executor.cpp:2426] Running Graph...\n", "[info] [gxf_executor.cpp:2428] Waiting for completion...\n", "[info] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", - "[2025-04-22 10:06:42,916] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2025-04-22 10:06:43,413] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2025-04-22 10:06:43,414] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2025-07-11 15:20:01,732] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-07-11 15:20:02,256] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-07-11 15:20:02,257] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2025-04-22 10:06:43,416] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-04-22 10:06:43,417] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2025-04-22 10:06:43,418] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2025-04-22 10:06:43,420] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2025-04-22 10:06:43,421] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2025-04-22 10:06:43,422] [INFO] (root) - Series attribute Modality value: CT\n", - "[2025-04-22 10:06:43,426] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2025-04-22 10:06:43,427] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2025-04-22 10:06:43,429] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2025-04-22 10:06:43,430] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2025-04-22 10:06:43,432] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "[2025-04-22 10:06:43,434] [INFO] (root) - Series attribute ImageType value: None\n", - "[2025-04-22 10:06:43,436] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-04-22 10:06:43,437] [INFO] (root) - Series Selection finalized.\n", - "[2025-04-22 10:06:43,438] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", - "[2025-04-22 10:06:43,438] [INFO] (root) - Series Instance UID of selected DICOM Series for inference: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-04-22 10:06:43,669] [INFO] (root) - Casting to float32\n", - "[2025-04-22 10:06:43,735] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", - "[2025-04-22 10:06:43,737] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", - "[2025-04-22 10:06:43,737] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", - "[2025-04-22 10:06:43,738] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", - "[2025-04-22 10:06:43,739] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", - "[2025-04-22 10:06:43,739] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", - "[2025-04-22 10:06:43,740] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", - "[2025-04-22 10:06:43,740] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", - "[2025-04-22 10:06:43,741] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", - "[2025-04-22 10:06:43,742] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", - "[2025-04-22 10:06:43,743] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", - "[2025-04-22 10:06:43,744] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", - "[2025-04-22 10:06:43,745] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", - "[2025-04-22 10:06:43,746] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "[2025-04-22 10:06:43,747] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2025-07-11 15:20:02,258] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 15:20:02,259] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-07-11 15:20:02,259] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-07-11 15:20:02,260] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-07-11 15:20:02,261] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-07-11 15:20:02,262] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-07-11 15:20:02,264] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-07-11 15:20:02,266] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-07-11 15:20:02,267] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-07-11 15:20:02,268] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-07-11 15:20:02,268] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 15:20:02,269] [INFO] (root) - Series Selection finalized\n", + "[2025-07-11 15:20:02,270] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-07-11 15:20:02,270] [INFO] (root) - Series Instance UID of selected DICOM Series for inference: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 15:20:02,504] [INFO] (root) - Casting to float32\n", + "[2025-07-11 15:20:02,565] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-07-11 15:20:02,566] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", + "[2025-07-11 15:20:02,567] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-07-11 15:20:02,568] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-07-11 15:20:02,568] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-07-11 15:20:02,569] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-07-11 15:20:02,570] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-07-11 15:20:02,570] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-07-11 15:20:02,571] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-07-11 15:20:02,571] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-07-11 15:20:02,572] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-07-11 15:20:02,573] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-07-11 15:20:02,574] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-07-11 15:20:02,574] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2025-07-11 15:20:02,575] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", " [ 0. 0.7890625 0. -398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2025-04-22 10:06:43,749] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-07-11 15:20:02,576] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", " [ -0. -0.7890625 -0. 398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2025-04-22 10:06:43,750] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", - "[2025-04-22 10:06:43,751] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", - "[2025-04-22 10:06:43,754] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", - "[2025-04-22 10:06:43,755] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", - "[2025-04-22 10:06:43,756] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", - "[2025-04-22 10:06:43,757] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", - "[2025-04-22 10:06:43,758] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n" + "[2025-07-11 15:20:02,577] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", + "[2025-07-11 15:20:02,577] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-07-11 15:20:02,578] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-07-11 15:20:02,579] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-07-11 15:20:02,579] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-07-11 15:20:02,581] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-07-11 15:20:02,582] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "2025-04-22 10:06:44,648 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n" + "2025-07-11 15:20:03,373 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "[2025-04-22 10:06:46,578] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n" + "[2025-07-11 15:20:05,444] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "2025-04-22 10:06:47,732 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n" + "2025-07-11 15:20:07,158 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "[2025-04-22 10:06:49,272] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", - "[2025-04-22 10:06:49,277] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pixel spacings for pred: tensor([0.7891, 0.7891, 1.5000], dtype=torch.float64)\n", - "[2025-04-22 10:06:49,408] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", - "[2025-04-22 10:06:49,448] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", - "[2025-04-22 10:06:49,453] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[2025-07-11 15:20:08,749] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-07-11 15:20:08,757] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pixel spacings for pred: tensor([0.7891, 0.7891, 1.5000], dtype=torch.float64)\n", + "[2025-07-11 15:20:08,893] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-07-11 15:20:08,937] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-07-11 15:20:08,944] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/base.py:163: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " check_person_name(patient_name)\n", - "[2025-04-22 10:06:50,720] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-04-22 10:06:50,721] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2025-04-22 10:06:50,722] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-04-22 10:06:50,723] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2025-04-22 10:06:50,725] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2025-04-22 10:06:50,726] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-04-22 10:06:50,727] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2025-04-22 10:06:50,728] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2025-04-22 10:06:50,730] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2025-07-11 15:20:10,281] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-07-11 15:20:10,282] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-07-11 15:20:10,283] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-07-11 15:20:10,284] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-07-11 15:20:10,285] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-07-11 15:20:10,286] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-07-11 15:20:10,286] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-07-11 15:20:10,287] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-07-11 15:20:10,288] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", "[info] [greedy_scheduler.cpp:372] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", "[info] [greedy_scheduler.cpp:401] Scheduler finished.\n", "[info] [gxf_executor.cpp:2431] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:2439] Graph execution finished.\n", - "[2025-04-22 10:06:50,833] [INFO] (__main__.AISpleenSegApp) - End run\n" + "[2025-07-11 15:20:10,404] [INFO] (__main__.AISpleenSegApp) - End run\n", + "[info] [gxf_executor.cpp:2439] Graph execution finished.\n" ] } ], @@ -1276,88 +1274,86 @@ "output_type": "stream", "text": [ "[\u001b[32minfo\u001b[m] [fragment.cpp:705] Loading extensions from configs...\n", - "[2025-04-22 10:06:55,953] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['my_app'])\n", - "[2025-04-22 10:06:55,955] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", - "[2025-04-22 10:06:55,955] [INFO] (app.AISpleenSegApp) - App input and output path: dcm, output\n", + "[2025-07-11 15:20:15,982] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['my_app'])\n", + "[2025-07-11 15:20:15,985] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", + "[2025-07-11 15:20:15,985] [INFO] (app.AISpleenSegApp) - App input and output path: dcm, output\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:265] Creating context\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2396] Activating Graph...\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2426] Running Graph...\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2428] Waiting for completion...\n", "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", - "[2025-04-22 10:06:55,974] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2025-04-22 10:06:56,476] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2025-07-11 15:20:16,009] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-07-11 15:20:16,530] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-07-11 15:20:16,530] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute Modality value: CT\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series attribute ImageType value: None\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series Selection finalized.\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", - "[2025-04-22 10:06:56,477] [INFO] (root) - Series Instance UID of selected DICOM Series for inference: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-04-22 10:06:56,909] [INFO] (root) - Casting to float32\n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2025-07-11 15:20:16,530] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 15:20:16,530] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-07-11 15:20:16,530] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Series Selection finalized\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-07-11 15:20:16,531] [INFO] (root) - Series Instance UID of selected DICOM Series for inference: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 15:20:16,790] [INFO] (root) - Casting to float32\n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-07-11 15:20:16,950] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", " [ 0. 0.7890625 0. -398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", " [ -0. -0.7890625 -0. 398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", - "[2025-04-22 10:06:57,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", - "2025-04-22 10:06:57,920 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", - "[2025-04-22 10:06:59,901] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", - "2025-04-22 10:07:00,973 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", - "[2025-04-22 10:07:02,569] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", - "[2025-04-22 10:07:02,570] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pixel spacings for pred: tensor([0.7891, 0.7891, 1.5000], dtype=torch.float64)\n", - "[2025-04-22 10:07:02,697] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", - "[2025-04-22 10:07:02,820] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", - "[2025-04-22 10:07:02,825] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-07-11 15:20:16,951] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "2025-07-11 15:20:17,904 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", + "[2025-07-11 15:20:19,936] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "2025-07-11 15:20:21,146 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", + "[2025-07-11 15:20:22,648] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-07-11 15:20:22,650] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pixel spacings for pred: tensor([0.7891, 0.7891, 1.5000], dtype=torch.float64)\n", + "[2025-07-11 15:20:22,778] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-07-11 15:20:22,816] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-07-11 15:20:22,820] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/base.py:163: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " check_person_name(patient_name)\n", - "[2025-04-22 10:07:04,062] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-04-22 10:07:04,062] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2025-04-22 10:07:04,062] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-04-22 10:07:04,062] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2025-04-22 10:07:04,063] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2025-04-22 10:07:04,063] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-04-22 10:07:04,063] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2025-04-22 10:07:04,063] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2025-04-22 10:07:04,063] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2025-07-11 15:20:24,091] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-07-11 15:20:24,092] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-07-11 15:20:24,093] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:372] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:401] Scheduler finished.\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2431] Deactivating Graph...\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2439] Graph execution finished.\n", - "[2025-04-22 10:07:04,175] [INFO] (app.AISpleenSegApp) - End run\n", + "[2025-07-11 15:20:24,186] [INFO] (app.AISpleenSegApp) - End run\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:295] Destroying context\n" ] } @@ -1377,7 +1373,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.17902633705887989912813743024111302.dcm\n", + "1.2.826.0.1.3680043.10.511.3.29040833486441853728344499723748304.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", @@ -1484,16 +1480,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2025-04-22 10:07:06,268] [INFO] (common) - Downloading CLI manifest file...\n", - "[2025-04-22 10:07:06,478] [DEBUG] (common) - Validating CLI manifest file...\n", - "[2025-04-22 10:07:06,478] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", - "[2025-04-22 10:07:06,478] [INFO] (packager.parameters) - Detected application type: Python Module\n", - "[2025-04-22 10:07:06,478] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", - "[2025-04-22 10:07:06,478] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", - "[2025-04-22 10:07:06,478] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", - "[2025-04-22 10:07:06,480] [INFO] (packager) - Generating app.json...\n", - "[2025-04-22 10:07:06,481] [INFO] (packager) - Generating pkg.json...\n", - "[2025-04-22 10:07:06,483] [DEBUG] (common) - \n", + "[2025-07-11 15:20:26,536] [INFO] (common) - Downloading CLI manifest file...\n", + "[2025-07-11 15:20:26,719] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2025-07-11 15:20:26,720] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", + "[2025-07-11 15:20:26,720] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2025-07-11 15:20:26,720] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", + "[2025-07-11 15:20:26,720] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", + "[2025-07-11 15:20:26,721] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", + "[2025-07-11 15:20:26,724] [INFO] (packager) - Generating app.json...\n", + "[2025-07-11 15:20:26,725] [INFO] (packager) - Generating pkg.json...\n", + "[2025-07-11 15:20:26,730] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1521,14 +1517,14 @@ " },\n", " \"readiness\": null,\n", " \"sdk\": \"monai-deploy\",\n", - " \"sdkVersion\": \"0.5.1\",\n", + " \"sdkVersion\": \"3.0.0\",\n", " \"timeout\": 0,\n", " \"version\": 1.0,\n", " \"workingDirectory\": \"/var/holoscan\"\n", "}\n", "================ End app.json ================\n", " \n", - "[2025-04-22 10:07:06,484] [DEBUG] (common) - \n", + "[2025-07-11 15:20:26,730] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1548,7 +1544,7 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2025-04-22 10:07:06,504] [DEBUG] (packager.builder) - \n", + "[2025-07-11 15:20:26,756] [DEBUG] (packager.builder) - \n", "========== Begin Build Parameters ==========\n", "{'additional_lib_paths': '',\n", " 'app_config_file_path': PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml'),\n", @@ -1573,7 +1569,7 @@ " 'logs_dir': PosixPath('/var/holoscan/logs'),\n", " 'models': {'model': PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model')},\n", " 'models_dir': PosixPath('/opt/holoscan/models'),\n", - " 'monai_deploy_app_sdk_version': '0.5.1',\n", + " 'monai_deploy_app_sdk_version': '3.0.0',\n", " 'no_cache': False,\n", " 'output_dir': 'output/',\n", " 'pip_packages': None,\n", @@ -1590,25 +1586,25 @@ " 'working_dir': PosixPath('/var/holoscan')}\n", "=========== End Build Parameters ===========\n", "\n", - "[2025-04-22 10:07:06,504] [DEBUG] (packager.builder) - \n", + "[2025-07-11 15:20:26,757] [DEBUG] (packager.builder) - \n", "========== Begin Platform Parameters ==========\n", "{'base_image': 'nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04',\n", " 'build_image': None,\n", " 'cuda_deb_arch': 'x86_64',\n", " 'custom_base_image': False,\n", " 'custom_holoscan_sdk': False,\n", - " 'custom_monai_deploy_sdk': True,\n", + " 'custom_monai_deploy_sdk': False,\n", " 'gpu_type': 'dgpu',\n", " 'holoscan_deb_arch': 'amd64',\n", " 'holoscan_sdk_file': '3.1.0',\n", " 'holoscan_sdk_filename': '3.1.0',\n", - " 'monai_deploy_sdk_file': PosixPath('/home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl'),\n", - " 'monai_deploy_sdk_filename': 'monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl',\n", + " 'monai_deploy_sdk_file': None,\n", + " 'monai_deploy_sdk_filename': None,\n", " 'tag': 'my_app:1.0',\n", " 'target_arch': 'x86_64'}\n", "=========== End Platform Parameters ===========\n", "\n", - "[2025-04-22 10:07:06,521] [DEBUG] (packager.builder) - \n", + "[2025-07-11 15:20:26,777] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "ARG GPU_TYPE=dgpu\n", @@ -1674,7 +1670,7 @@ "LABEL org.opencontainers.image.version=\"1.0\"\n", "LABEL org.nvidia.holoscan=\"3.1.0\"\n", "\n", - "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", + "LABEL org.monai.deploy.app-sdk=\"3.0.0\"\n", "\n", "ENV HOLOSCAN_INPUT_PATH=/var/holoscan/input\n", "ENV HOLOSCAN_OUTPUT_PATH=/var/holoscan/output\n", @@ -1744,9 +1740,10 @@ "\n", "\n", "# Install MONAI Deploy App SDK\n", - "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl\n", + "\n", + "# Install MONAI Deploy from PyPI org\n", + "RUN pip install monai-deploy-app-sdk==3.0.0\n", + "\n", "\n", "COPY ./models /opt/holoscan/models\n", "\n", @@ -1761,7 +1758,7 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2025-04-22 10:07:06,522] [INFO] (packager.builder) - \n", + "[2025-07-11 15:20:26,777] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", @@ -1770,26 +1767,29 @@ " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: 3.1.0\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: N/A\n", " gRPC Health Probe: N/A\n", " SDK Version: 3.1.0\n", " SDK: monai-deploy\n", " Tag: my_app-x64-workstation-dgpu-linux-amd64:1.0\n", " Included features/dependencies: N/A\n", " \n", - "[2025-04-22 10:07:06,841] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2025-04-22 10:07:06,841] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2025-07-11 15:20:27,472] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2025-07-11 15:20:27,473] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 4.74kB done\n", + "#1 transferring dockerfile: 4.56kB done\n", "#1 DONE 0.1s\n", "\n", - "#2 [auth] nvidia/cuda:pull token for nvcr.io\n", - "#2 DONE 0.0s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04\n", + "#2 ...\n", + "\n", + "#3 [auth] nvidia/cuda:pull token for nvcr.io\n", + "#3 DONE 0.0s\n", "\n", - "#3 [internal] load metadata for nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04\n", - "#3 DONE 0.4s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04\n", + "#2 DONE 0.6s\n", "\n", "#4 [internal] load .dockerignore\n", "#4 transferring context: 1.80kB done\n", @@ -1801,491 +1801,477 @@ "#6 [internal] load build context\n", "#6 DONE 0.0s\n", "\n", - "#7 importing cache manifest from local:9106061615573359344\n", + "#7 importing cache manifest from local:16206736018656734975\n", "#7 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#7 DONE 0.0s\n", "\n", "#8 [base 1/2] FROM nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04@sha256:22fc009e5cea0b8b91d94c99fdd419d2366810b5ea835e47b8343bc15800c186\n", - "#8 resolve nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04@sha256:22fc009e5cea0b8b91d94c99fdd419d2366810b5ea835e47b8343bc15800c186 0.1s done\n", + "#8 resolve nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04@sha256:22fc009e5cea0b8b91d94c99fdd419d2366810b5ea835e47b8343bc15800c186 0.0s done\n", "#8 DONE 0.1s\n", "\n", "#5 importing cache manifest from nvcr.io/nvidia/cuda:12.6.0-runtime-ubuntu22.04\n", "#5 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#5 DONE 0.3s\n", + "#5 DONE 0.6s\n", "\n", "#6 [internal] load build context\n", - "#6 transferring context: 19.58MB 0.1s done\n", - "#6 DONE 0.3s\n", + "#6 transferring context: 19.43MB 0.1s done\n", + "#6 DONE 0.2s\n", "\n", - "#9 [release 4/19] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", + "#9 [base 2/2] RUN apt-get update && apt-get install -y --no-install-recommends --no-install-suggests curl jq && rm -rf /var/lib/apt/lists/*\n", "#9 CACHED\n", "\n", - "#10 [release 5/19] RUN chown -R holoscan /var/holoscan && chown -R holoscan /var/holoscan/input && chown -R holoscan /var/holoscan/output\n", + "#10 [release 1/18] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#10 CACHED\n", "\n", - "#11 [release 2/19] RUN apt update && apt-get install -y --no-install-recommends --no-install-suggests python3-minimal=3.10.6-1~22.04 libpython3-stdlib=3.10.6-1~22.04 python3=3.10.6-1~22.04 python3-venv=3.10.6-1~22.04 python3-pip=22.0.2+dfsg-* && rm -rf /var/lib/apt/lists/*\n", + "#11 [release 5/18] RUN chown -R holoscan /var/holoscan && chown -R holoscan /var/holoscan/input && chown -R holoscan /var/holoscan/output\n", "#11 CACHED\n", "\n", - "#12 [release 3/19] RUN groupadd -f -g 1000 holoscan\n", + "#12 [release 3/18] RUN groupadd -f -g 1000 holoscan\n", "#12 CACHED\n", "\n", - "#13 [base 2/2] RUN apt-get update && apt-get install -y --no-install-recommends --no-install-suggests curl jq && rm -rf /var/lib/apt/lists/*\n", + "#13 [release 6/18] WORKDIR /var/holoscan\n", "#13 CACHED\n", "\n", - "#14 [release 1/19] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", + "#14 [release 7/18] COPY ./tools /var/holoscan/tools\n", "#14 CACHED\n", "\n", - "#15 [release 6/19] WORKDIR /var/holoscan\n", + "#15 [release 4/18] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#15 CACHED\n", "\n", - "#16 [release 7/19] COPY ./tools /var/holoscan/tools\n", + "#16 [release 8/18] RUN chmod +x /var/holoscan/tools\n", "#16 CACHED\n", "\n", - "#17 [release 8/19] RUN chmod +x /var/holoscan/tools\n", + "#17 [release 2/18] RUN apt update && apt-get install -y --no-install-recommends --no-install-suggests python3-minimal=3.10.6-1~22.04 libpython3-stdlib=3.10.6-1~22.04 python3=3.10.6-1~22.04 python3-venv=3.10.6-1~22.04 python3-pip=22.0.2+dfsg-* && rm -rf /var/lib/apt/lists/*\n", "#17 CACHED\n", "\n", - "#18 [release 9/19] WORKDIR /var/holoscan\n", + "#18 [release 9/18] WORKDIR /var/holoscan\n", "#18 CACHED\n", "\n", - "#19 [release 10/19] COPY ./pip/requirements.txt /tmp/requirements.txt\n", - "#19 DONE 1.4s\n", - "\n", - "#20 [release 11/19] RUN pip install --upgrade pip\n", - "#20 0.781 Defaulting to user installation because normal site-packages is not writeable\n", - "#20 0.831 Requirement already satisfied: pip in /usr/lib/python3/dist-packages (22.0.2)\n", - "#20 0.968 Collecting pip\n", - "#20 1.063 Downloading pip-25.0.1-py3-none-any.whl (1.8 MB)\n", - "#20 1.220 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 12.3 MB/s eta 0:00:00\n", - "#20 1.247 Installing collected packages: pip\n", - "#20 1.992 Successfully installed pip-25.0.1\n", - "#20 DONE 2.2s\n", - "\n", - "#21 [release 12/19] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", - "#21 0.752 Collecting highdicom>=0.18.2 (from -r /tmp/requirements.txt (line 1))\n", - "#21 0.790 Downloading highdicom-0.25.1-py3-none-any.whl.metadata (5.0 kB)\n", - "#21 0.829 Collecting monai>=1.0 (from -r /tmp/requirements.txt (line 2))\n", - "#21 0.842 Downloading monai-1.4.0-py3-none-any.whl.metadata (11 kB)\n", - "#21 0.945 Collecting nibabel>=3.2.1 (from -r /tmp/requirements.txt (line 3))\n", - "#21 0.956 Downloading nibabel-5.3.2-py3-none-any.whl.metadata (9.1 kB)\n", - "#21 1.134 Collecting numpy>=1.21.6 (from -r /tmp/requirements.txt (line 4))\n", - "#21 1.144 Downloading numpy-2.2.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)\n", - "#21 1.183 Collecting pydicom>=2.3.0 (from -r /tmp/requirements.txt (line 5))\n", - "#21 1.195 Downloading pydicom-3.0.1-py3-none-any.whl.metadata (9.4 kB)\n", - "#21 1.203 Requirement already satisfied: setuptools>=59.5.0 in /usr/lib/python3/dist-packages (from -r /tmp/requirements.txt (line 6)) (59.6.0)\n", - "#21 1.236 Collecting SimpleITK>=2.0.0 (from -r /tmp/requirements.txt (line 7))\n", - "#21 1.247 Downloading SimpleITK-2.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)\n", - 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nvidia-nccl-cu12-2.21.5 nvidia-nvjitlink-cu12-12.4.127 nvidia-nvtx-cu12-12.4.127 packaging-25.0 pillow-11.2.1 pydicom-3.0.1 pyjpegls-1.4.0 sympy-1.13.1 torch-2.6.0 triton-3.2.0 typing-extensions-4.13.2\n", - "#21 DONE 98.6s\n", - "\n", - "#22 [release 13/19] COPY ./monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl\n", - "#22 DONE 0.3s\n", - "\n", - "#23 [release 14/19] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl\n", - "#23 0.726 Defaulting to user installation because normal site-packages is not writeable\n", - "#23 0.853 Processing /tmp/monai_deploy_app_sdk-0.5.1+37.g96f7e31.dirty-py3-none-any.whl\n", - "#23 0.864 Requirement already satisfied: numpy>=1.21.6 in /home/holoscan/.local/lib/python3.10/site-packages (from monai-deploy-app-sdk==0.5.1+37.g96f7e31.dirty) (1.26.4)\n", - "#23 1.007 Collecting holoscan~=3.0 (from monai-deploy-app-sdk==0.5.1+37.g96f7e31.dirty)\n", 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markdown-it-py>=2.2.0->rich>=10.11.0->typer>=0.4.1->python-on-whales<0.61.0,>=0.60.1->holoscan-cli~=3.0->monai-deploy-app-sdk==0.5.1+37.g96f7e31.dirty)\n", - "#23 7.271 Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)\n", - "#23 7.320 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", - "#23 7.349 Downloading holoscan-3.1.0-cp310-cp310-manylinux_2_35_x86_64.whl (39.8 MB)\n", - "#23 8.075 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.8/39.8 MB 55.3 MB/s eta 0:00:00\n", - "#23 8.089 Downloading holoscan_cli-3.1.0-py3-none-any.whl (72 kB)\n", - "#23 8.123 Downloading tritonclient-2.56.0-py3-none-manylinux1_x86_64.whl (14.4 MB)\n", - "#23 8.397 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.4/14.4 MB 53.1 MB/s eta 0:00:00\n", - "#23 8.411 Downloading typeguard-4.4.2-py3-none-any.whl (35 kB)\n", - "#23 8.442 Downloading aiohttp-3.11.18-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)\n", - "#23 8.495 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 29.5 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cuda-bindings, brotli, zope.interface, zope.event, wheel-axle-runtime, urllib3, typeguard, tqdm, shellingham, pyyaml, python-rapidjson, pygments, pydantic, psutil, protobuf, propcache, packaging, multidict, mdurl, idna, grpcio, greenlet, frozenlist, cupy-cuda12x, cuda-python, colorama, cloudpickle, click, charset-normalizer, certifi, attrs, async-timeout, aiohappyeyeballs, yarl, tritonclient, requests, markdown-it-py, holoscan, gevent, aiosignal, rich, geventhttpclient, aiohttp, typer, python-on-whales, holoscan-cli, monai-deploy-app-sdk\n", - "#23 14.78 Attempting uninstall: packaging\n", - "#23 14.78 Found existing installation: packaging 25.0\n", - "#23 14.79 Uninstalling packaging-25.0:\n", - "#23 14.81 Successfully uninstalled packaging-25.0\n", - "#23 19.62 Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.11.18 aiosignal-1.3.2 async-timeout-5.0.1 attrs-25.3.0 brotli-1.1.0 certifi-2025.1.31 charset-normalizer-3.4.1 click-8.1.8 cloudpickle-3.1.1 colorama-0.4.6 cuda-bindings-12.8.0 cuda-python-12.8.0 cupy-cuda12x-13.4.1 fastrlock-0.8.3 frozenlist-1.6.0 gevent-25.4.1 geventhttpclient-2.3.3 greenlet-3.2.1 grpcio-1.67.1 holoscan-3.1.0 holoscan-cli-3.1.0 idna-3.10 markdown-it-py-3.0.0 mdurl-0.1.2 monai-deploy-app-sdk-0.5.1+37.g96f7e31.dirty multidict-6.4.3 packaging-23.2 propcache-0.3.1 protobuf-5.29.4 psutil-6.1.1 pydantic-1.10.21 pygments-2.19.1 python-on-whales-0.60.1 python-rapidjson-1.20 pyyaml-6.0.2 requests-2.32.3 rich-14.0.0 shellingham-1.5.4 tqdm-4.67.1 tritonclient-2.56.0 typeguard-4.4.2 typer-0.15.2 urllib3-2.4.0 wheel-axle-runtime-0.0.6 yarl-1.20.0 zope.event-5.0 zope.interface-7.2\n", - "#23 DONE 21.6s\n", - "\n", - "#24 [release 15/19] COPY ./models /opt/holoscan/models\n", - "#24 DONE 0.3s\n", - "\n", - "#25 [release 16/19] COPY ./map/app.json /etc/holoscan/app.json\n", + "#19 [release 10/18] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#19 DONE 1.5s\n", + "\n", + "#20 [release 11/18] RUN pip install --upgrade pip\n", + "#20 0.960 Defaulting to user installation because normal site-packages is not writeable\n", + "#20 1.001 Requirement already satisfied: pip in /usr/lib/python3/dist-packages (22.0.2)\n", + "#20 1.179 Collecting pip\n", + "#20 1.259 Downloading pip-25.1.1-py3-none-any.whl (1.8 MB)\n", + "#20 1.400 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 13.5 MB/s eta 0:00:00\n", + "#20 1.428 Installing collected packages: pip\n", + "#20 2.161 Successfully installed pip-25.1.1\n", + "#20 DONE 2.4s\n", + "\n", + "#21 [release 12/18] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", + "#21 0.683 Collecting highdicom>=0.18.2 (from -r /tmp/requirements.txt (line 1))\n", + "#21 0.769 Downloading highdicom-0.26.0-py3-none-any.whl.metadata (5.8 kB)\n", + "#21 0.798 Collecting monai>=1.0 (from -r /tmp/requirements.txt (line 2))\n", + "#21 0.804 Downloading monai-1.5.0-py3-none-any.whl.metadata (13 kB)\n", + "#21 0.885 Collecting nibabel>=3.2.1 (from -r /tmp/requirements.txt (line 3))\n", + "#21 0.890 Downloading nibabel-5.3.2-py3-none-any.whl.metadata (9.1 kB)\n", + "#21 1.067 Collecting numpy>=1.21.6 (from -r /tmp/requirements.txt (line 4))\n", + "#21 1.071 Downloading numpy-2.2.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)\n", + "#21 1.086 Collecting pydicom>=2.3.0 (from -r /tmp/requirements.txt (line 5))\n", + "#21 1.091 Downloading pydicom-3.0.1-py3-none-any.whl.metadata (9.4 kB)\n", + "#21 1.096 Requirement already satisfied: setuptools>=59.5.0 in /usr/lib/python3/dist-packages (from -r /tmp/requirements.txt (line 6)) (59.6.0)\n", + "#21 1.131 Collecting SimpleITK>=2.0.0 (from -r /tmp/requirements.txt (line 7))\n", + "#21 1.135 Downloading simpleitk-2.5.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.2 kB)\n", + "#21 1.176 Collecting torch>=1.12.0 (from -r /tmp/requirements.txt (line 8))\n", + "#21 1.180 Downloading torch-2.7.1-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (29 kB)\n", + "#21 1.395 Collecting pillow>=8.3 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 1))\n", + "#21 1.398 Downloading pillow-11.3.0-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)\n", + "#21 1.507 Collecting pyjpegls>=1.0.0 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 1))\n", + "#21 1.574 Downloading pyjpegls-1.5.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.5 kB)\n", + "#21 1.603 Collecting typing-extensions>=4.0.0 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 1))\n", + "#21 1.606 Downloading typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB)\n", + "#21 1.623 Collecting torch>=1.12.0 (from -r /tmp/requirements.txt (line 8))\n", + "#21 1.628 Downloading torch-2.6.0-cp310-cp310-manylinux1_x86_64.whl.metadata (28 kB)\n", + "#21 1.649 Collecting filelock (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#21 1.652 Downloading filelock-3.18.0-py3-none-any.whl.metadata (2.9 kB)\n", + "#21 1.676 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"#22 13.31 Installing collected packages: fastrlock, cuda-bindings, brotli, zope.interface, zope.event, wheel-axle-runtime, urllib3, typing-inspection, typeguard, pyyaml, python-rapidjson, pydantic-core, psutil, protobuf, propcache, multidict, idna, grpcio, greenlet, frozenlist, cupy-cuda12x, cuda-python, colorama, cloudpickle, charset_normalizer, certifi, attrs, async-timeout, annotated-types, aiohappyeyeballs, yarl, tritonclient, requests, pydantic, holoscan, gevent, aiosignal, python-on-whales, geventhttpclient, aiohttp, holoscan-cli, monai-deploy-app-sdk\n", + "#22 19.39 \n", + "#22 19.41 Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.14 aiosignal-1.4.0 annotated-types-0.7.0 async-timeout-5.0.1 attrs-25.3.0 brotli-1.1.0 certifi-2025.7.9 charset_normalizer-3.4.2 cloudpickle-3.1.1 colorama-0.4.6 cuda-bindings-12.9.0 cuda-python-12.9.0 cupy-cuda12x-13.5.1 fastrlock-0.8.3 frozenlist-1.7.0 gevent-25.5.1 geventhttpclient-2.3.4 greenlet-3.2.3 grpcio-1.67.1 holoscan-3.4.0 holoscan-cli-3.4.1 idna-3.10 monai-deploy-app-sdk-3.0.0 multidict-6.6.3 propcache-0.3.2 protobuf-5.29.5 psutil-7.0.0 pydantic-2.11.7 pydantic-core-2.33.2 python-on-whales-0.77.0 python-rapidjson-1.21 pyyaml-6.0.2 requests-2.32.4 tritonclient-2.59.0 typeguard-4.4.4 typing-inspection-0.4.1 urllib3-2.5.0 wheel-axle-runtime-0.0.6 yarl-1.20.1 zope.event-5.1 zope.interface-7.2\n", + "#22 DONE 23.1s\n", + "\n", + "#23 [release 14/18] COPY ./models /opt/holoscan/models\n", + "#23 DONE 0.3s\n", + "\n", + "#24 [release 15/18] COPY ./map/app.json /etc/holoscan/app.json\n", + "#24 DONE 0.1s\n", + "\n", + "#25 [release 16/18] COPY ./app.config /var/holoscan/app.yaml\n", "#25 DONE 0.1s\n", "\n", - "#26 [release 17/19] COPY ./app.config /var/holoscan/app.yaml\n", + "#26 [release 17/18] COPY ./map/pkg.json /etc/holoscan/pkg.json\n", "#26 DONE 0.1s\n", "\n", - "#27 [release 18/19] COPY ./map/pkg.json /etc/holoscan/pkg.json\n", + "#27 [release 18/18] COPY ./app /opt/holoscan/app\n", "#27 DONE 0.1s\n", "\n", - "#28 [release 19/19] COPY ./app /opt/holoscan/app\n", - "#28 DONE 0.1s\n", - "\n", - "#29 exporting to docker image format\n", - "#29 exporting layers\n", - "#29 exporting layers 175.3s done\n", - "#29 exporting manifest sha256:f63297f6525a89f74b13e561b30821ab4985a18db4b815eb995ac1aed030557b 0.0s done\n", - "#29 exporting config sha256:7266e968de607504eff9dfbb7c4e0c00adf190678ce9232099aab9c0d2d1cb24 0.0s done\n", - "#29 sending tarball\n", - "#29 ...\n", - "\n", - "#30 importing to docker\n", - "#30 loading layer 481caafed616 251B / 251B\n", - "#30 loading layer e39cf4d7d38e 65.54kB / 5.09MB\n", - "#30 loading layer 3795307a2740 557.06kB / 3.20GB\n", - "#30 loading layer 3795307a2740 130.91MB / 3.20GB 6.2s\n", - "#30 loading layer 3795307a2740 278.53MB / 3.20GB 12.4s\n", - "#30 loading layer 3795307a2740 483.52MB / 3.20GB 16.5s\n", - "#30 loading layer 3795307a2740 677.94MB / 3.20GB 20.7s\n", - "#30 loading layer 3795307a2740 851.18MB / 3.20GB 24.8s\n", - "#30 loading layer 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3.20GB 50.6s\n", + "#29 loading layer 99bc88294797 2.29GB / 3.20GB 56.9s\n", + "#29 loading layer 99bc88294797 2.47GB / 3.20GB 61.0s\n", + "#29 loading layer 99bc88294797 2.68GB / 3.20GB 65.2s\n", + "#29 loading layer 99bc88294797 2.85GB / 3.20GB 71.3s\n", + "#29 loading layer 99bc88294797 3.05GB / 3.20GB 77.5s\n", + "#29 loading layer d84cc5762b51 557.06kB / 410.12MB\n", + "#29 loading layer d84cc5762b51 100.83MB / 410.12MB 2.0s\n", + "#29 loading layer d84cc5762b51 223.38MB / 410.12MB 4.1s\n", + "#29 loading layer d84cc5762b51 247.33MB / 410.12MB 6.1s\n", + "#29 loading layer d84cc5762b51 302.48MB / 410.12MB 8.2s\n", + "#29 loading layer d84cc5762b51 362.09MB / 410.12MB 10.2s\n", + "#29 loading layer d84cc5762b51 408.32MB / 410.12MB 12.3s\n", + "#29 loading layer c1e31f779dbf 196.61kB / 17.81MB\n", + "#29 loading layer eb5ad4842001 493B / 493B\n", + "#29 loading layer 075e208c93ac 317B / 317B\n", + "#29 loading layer bb00143b58ab 303B / 303B\n", + "#29 loading layer 64cc6b44b6fe 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64cc6b44b6fe 3.91kB / 3.91kB 0.4s done\n", + "#29 DONE 100.2s\n", + "\n", + "#28 exporting to docker image format\n", + "#28 sending tarball 147.7s done\n", + "#28 DONE 342.2s\n", + "\n", + "#30 exporting cache to client directory\n", + "#30 preparing build cache for export\n", + "#30 writing layer sha256:15c8a513e955106bfa02942e4ee77e1ac1ee964cb95bf340e31a584686d1e78a\n", + "#30 writing layer sha256:15c8a513e955106bfa02942e4ee77e1ac1ee964cb95bf340e31a584686d1e78a 55.3s done\n", + "#30 writing layer sha256:1a0d52c93099897b518eb6cc6cd0fa3d52ff733e8606b4d8c92675ba9e7101ff\n", + "#30 writing layer sha256:1a0d52c93099897b518eb6cc6cd0fa3d52ff733e8606b4d8c92675ba9e7101ff done\n", + "#30 writing layer sha256:234b866f57e0c5d555af2d87a1857a17ec4ac7e70d2dc6c31ff0a072a4607f24 done\n", + "#30 writing layer sha256:255905badeaa82f032e1043580eed8b745c19cd4a2cb7183883ee5a30f851d6d done\n", + "#30 writing layer sha256:29092a460bd4fea986f5f68c5730aba3596e946c0812871200c3f08ae0093ea7\n", + "#30 writing 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sha256:d0b9db5eaf93e490f07bab8abb1ac5475febcf822c25f2e1d1c82ff4273a7d0d done\n", + "#30 writing layer sha256:d339273dfb7fc3b7fd896d3610d360ab9a09ab33a818093cb73b4be7639b6e99 done\n", + "#30 writing layer sha256:da44fb0aa6d6f7c651c7eec8e11510c9c048b066b2ba36b261cefea12ff5ee3e done\n", + "#30 writing layer sha256:de9360c47fdf1792b18703fc5fccd579fbdb1c46e901d8c1cfea7a6ea8e892dc 0.0s done\n", + "#30 writing layer sha256:e8ce2bfcc12c342fb3dadd099e0b43db4e695df829a70ee5bdddfcb1d805a92d 0.0s done\n", + "#30 writing layer sha256:efc9014e2a4cb1e133b80bb4f047e9141e98685eb95b8d2471a8e35b86643e31 done\n", + "#30 writing layer sha256:f3af93a430a247328c59fb2228f6fa43a0ce742b03464db94acf7c45311e31cd done\n", + "#30 writing layer sha256:f88a79707e66de747f83afd283fa0e8184378c1ec86836d4fe0d44435a44b21a 0.0s done\n", + "#30 writing config sha256:5ab3cef90f0fa799a119bd8024d89614827d64032fba855bb0610e8533988f8c 0.0s done\n", + "#30 preparing build cache for export 63.9s done\n", + "#30 writing cache manifest sha256:d57e0a4769d58a968994fb8bd0e41d16eb55a9a7e7572e5ee1e2217768470dac 0.0s done\n", + "#30 DONE 63.9s\n", + "[2025-07-11 15:29:41,498] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -2318,7 +2304,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "my_app-x64-workstation-dgpu-linux-amd64 1.0 7266e968de60 6 minutes ago 9.07GB\n" + "my_app-x64-workstation-dgpu-linux-amd64 1.0 e4c5cdbe1596 6 minutes ago 9.09GB\n" ] } ], @@ -2346,23 +2332,23 @@ "text": [ "output\n", "dcm\n", - "[2025-04-22 10:15:26,072] [INFO] (runner) - Checking dependencies...\n", - "[2025-04-22 10:15:26,072] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2025-07-11 15:29:43,510] [INFO] (runner) - Checking dependencies...\n", + "[2025-07-11 15:29:43,510] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2025-04-22 10:15:26,074] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2025-07-11 15:29:43,511] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2025-04-22 10:15:26,074] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2025-07-11 15:29:43,511] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2025-04-22 10:15:26,152] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "Successfully copied 2.56kB to /tmp/tmpxd644i6e/app.json\n", - "Successfully copied 2.05kB to /tmp/tmpxd644i6e/pkg.json\n", - "3e8dc45282382e26bf37bf8ab8bafbfe8a12c219cfb364cc1a38bc3c645bcbf8\n", - "[2025-04-22 10:15:26,569] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2025-07-11 15:29:43,596] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "Successfully copied 2.56kB to /tmp/tmpq66wvfuq/app.json\n", + "Successfully copied 2.05kB to /tmp/tmpq66wvfuq/pkg.json\n", + "4611f2dd75358632a4a0c39a51d8fb2e0d232b19ebb584fc5d66d737eddc426c\n", + "[2025-07-11 15:29:43,961] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2025-04-22 10:15:26,579] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2025-07-11 15:29:43,963] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2025-04-22 10:15:27,009] [INFO] (common) - Launching container (81398038b14f) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: youthful_pare\n", + "[2025-07-11 15:29:44,372] [INFO] (common) - Launching container (b54fdddf6a0d) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: gifted_visvesvaraya\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -2372,177 +2358,135 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2025-04-22 17:15:27 [INFO] Launching application python3 /opt/holoscan/app ...\n", + "2025-07-11 22:29:45 [INFO] Launching application python3 /opt/holoscan/app ...\n", "\n", - "[info] [fragment.cpp:705] Loading extensions from configs...\n", + ":1184: FutureWarning: The cuda.cudart module is deprecated and will be removed in a future release, please switch to use the cuda.bindings.runtime module instead.\n", "\n", - "[info] [gxf_executor.cpp:265] Creating context\n", + "[info] [fragment.cpp:778] Loading extensions from configs...\n", "\n", - "[2025-04-22 17:15:33,511] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['/opt/holoscan/app'])\n", + "[info] [gxf_executor.cpp:329] Creating context\n", "\n", - "[2025-04-22 17:15:33,514] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan), triton_server_netloc=\n", + "[2025-07-11 22:29:52,205] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['/opt/holoscan/app'])\n", "\n", - "[2025-04-22 17:15:33,514] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", + "[2025-07-11 22:29:52,210] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan), triton_server_netloc=\n", "\n", - "[info] [gxf_executor.cpp:2396] Activating Graph...\n", + "[2025-07-11 22:29:52,210] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", "\n", - "[info] [gxf_executor.cpp:2426] Running Graph...\n", + "[info] [gxf_executor.cpp:2415] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:2428] Waiting for completion...\n", + "[info] [gxf_executor.cpp:2484] Running Graph...\n", + "\n", + "[info] [gxf_executor.cpp:2486] Waiting for completion...\n", "\n", "[info] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", "\n", - "[2025-04-22 17:15:33,524] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-07-11 22:29:52,241] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", "\n", - "[2025-04-22 17:15:33,962] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-07-11 22:29:53,177] [INFO] (root) - Finding series for Selection named: CT Series\n", "\n", - "[2025-04-22 17:15:33,962] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2025-07-11 22:29:53,177] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", "\n", " # of series: 1\n", "\n", - "[2025-04-22 17:15:33,962] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "\n", - "[2025-04-22 17:15:33,962] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "\n", - "[2025-04-22 17:15:33,962] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "\n", - "[2025-04-22 17:15:33,962] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series attribute Modality value: CT\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series attribute ImageType value: None\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series Selection finalized.\n", - "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-07-11 22:29:53,177] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-04-22 17:15:33,963] [INFO] (root) - Series Instance UID of selected DICOM Series for inference: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-07-11 22:29:53,177] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", "\n", - "[2025-04-22 17:15:34,270] [INFO] (root) - Casting to float32\n", + "[2025-07-11 22:29:53,177] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-07-11 22:29:53,177] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series attribute Modality value: CT\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series attribute ImageType value: None\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series Selection finalized.\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-07-11 22:29:53,178] [INFO] (root) - Series Instance UID of selected DICOM Series for inference: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[error] [gxf_wrapper.cpp:118] Exception occurred for operator: 'series_to_vol_op' - TypeError: can_cast() does not support Python ints, floats, and complex because the result used to depend on the value.\n", "\n", - "[2025-04-22 17:15:34,406] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "This change was part of adopting NEP 50, we may explicitly allow them again in the future.\n", "\n", - " [ 0. 0.7890625 0. -398.60547 ]\n", - "\n", - " [ 0. 0. 1.5 -383. ]\n", - "\n", - " [ 0. 0. 0. 1. ]], type \n", - "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", - "\n", - " [ -0. -0.7890625 -0. 398.60547 ]\n", - "\n", - " [ 0. 0. 1.5 -383. ]\n", - "\n", - " [ 0. 0. 0. 1. ]], type \n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "At:\n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + " /home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/dicom_series_to_volume_operator.py(163): generate_voxel_data\n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + " /home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/dicom_series_to_volume_operator.py(83): convert_to_image\n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + " /home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/dicom_series_to_volume_operator.py(60): compute\n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", "\n", - "[2025-04-22 17:15:34,407] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", "\n", - "2025-04-22 17:15:35,292 INFO image_writer.py:197 - writing: /var/holoscan/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", + "[error] [entity_executor.cpp:596] Failed to tick codelet series_to_vol_op in entity: series_to_vol_op code: GXF_FAILURE\n", "\n", - "[2025-04-22 17:15:37,261] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "[warning] [greedy_scheduler.cpp:243] Error while executing entity 21 named 'series_to_vol_op': GXF_FAILURE\n", "\n", - "2025-04-22 17:15:39,032 INFO image_writer.py:197 - writing: /var/holoscan/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", + "[info] [greedy_scheduler.cpp:401] Scheduler finished.\n", "\n", - "[2025-04-22 17:15:40,582] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[error] [program.cpp:580] wait failed. Deactivating...\n", "\n", - "[2025-04-22 17:15:40,587] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pixel spacings for pred: tensor([0.7891, 0.7891, 1.5000], dtype=torch.float64)\n", + "[error] [runtime.cpp:1649] Graph wait failed with error: GXF_FAILURE\n", "\n", - "[2025-04-22 17:15:40,719] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[warning] [gxf_executor.cpp:2487] GXF call GxfGraphWait(context) in line 2487 of file /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp failed with 'GXF_FAILURE' (1)\n", "\n", - "[2025-04-22 17:15:40,758] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[info] [gxf_executor.cpp:2498] Graph execution finished.\n", "\n", - "[2025-04-22 17:15:40,763] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[error] [gxf_executor.cpp:2506] Graph execution error: GXF_FAILURE\n", "\n", - "/home/holoscan/.local/lib/python3.10/site-packages/highdicom/base.py:163: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", + "Traceback (most recent call last):\n", "\n", - " check_person_name(patient_name)\n", + " File \"/usr/lib/python3.10/runpy.py\", line 196, in _run_module_as_main\n", "\n", - "[2025-04-22 17:15:41,997] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + " return _run_code(code, main_globals, None,\n", "\n", - "[2025-04-22 17:15:41,997] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + " File \"/usr/lib/python3.10/runpy.py\", line 86, in _run_code\n", "\n", - "[2025-04-22 17:15:41,997] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + " exec(code, run_globals)\n", "\n", - "[2025-04-22 17:15:41,997] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + " File \"/opt/holoscan/app/__main__.py\", line 4, in \n", "\n", - "[2025-04-22 17:15:41,998] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + " AISpleenSegApp().run()\n", "\n", - "[2025-04-22 17:15:41,998] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + " File \"/opt/holoscan/app/app.py\", line 26, in run\n", "\n", - "[2025-04-22 17:15:41,998] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + " super().run(*args, **kwargs)\n", "\n", - "[2025-04-22 17:15:41,998] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/dicom_series_to_volume_operator.py\", line 60, in compute\n", "\n", - "[2025-04-22 17:15:41,999] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + " image = self.convert_to_image(study_selected_series_list)\n", "\n", - "[info] [greedy_scheduler.cpp:372] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", + " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/dicom_series_to_volume_operator.py\", line 83, in convert_to_image\n", "\n", - "[info] [greedy_scheduler.cpp:401] Scheduler finished.\n", + " voxel_data = self.generate_voxel_data(dicom_series)\n", "\n", - "[info] [gxf_executor.cpp:2431] Deactivating Graph...\n", + " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/dicom_series_to_volume_operator.py\", line 163, in generate_voxel_data\n", "\n", - "[info] [gxf_executor.cpp:2439] Graph execution finished.\n", + " and np.can_cast(intercept, np.uint16, casting=\"safe\")\n", "\n", - "[2025-04-22 17:15:42,103] [INFO] (app.AISpleenSegApp) - End run\n", + "TypeError: can_cast() does not support Python ints, floats, and complex because the result used to depend on the value.\n", "\n", - "[info] [gxf_executor.cpp:295] Destroying context\n", + "This change was part of adopting NEP 50, we may explicitly allow them again in the future.\n", "\n", - "[2025-04-22 10:15:44,346] [INFO] (common) - Container 'youthful_pare'(81398038b14f) exited.\n" + "[2025-07-11 15:29:54,807] [INFO] (common) - Container 'gifted_visvesvaraya'(b54fdddf6a0d) exited.\n" ] } ], @@ -2564,15 +2508,9 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.89222091780069825813597121405605044.dcm\n", "saved_images_folder\n", "\n", - "output/saved_images_folder:\n", - "1.3.6.1.4.1.14519.5.2.1.7085.2626\n", - "\n", - "output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626:\n", - "1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", - "1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n" + "output/saved_images_folder:\n" ] } ],