diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml index 3ab1eb59..7b85a712 100644 --- a/.github/workflows/pr.yml +++ b/.github/workflows/pr.yml @@ -14,10 +14,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: "3.9" + python-version: "3.10" - name: Setup Dev Environment run: | pip install virtualenv diff --git a/docs/source/release_notes/index.md b/docs/source/release_notes/index.md index 84965f23..4602ac0a 100644 --- a/docs/source/release_notes/index.md +++ b/docs/source/release_notes/index.md @@ -10,6 +10,7 @@ ```{toctree} :maxdepth: 1 +v3.1.0 v3.0.0 ``` ## Version 2.0 diff --git a/notebooks/tutorials/03_segmentation_app.ipynb b/notebooks/tutorials/03_segmentation_app.ipynb index b7748590..7e83c79a 100644 --- a/notebooks/tutorials/03_segmentation_app.ipynb +++ b/notebooks/tutorials/03_segmentation_app.ipynb @@ -92,18 +92,16 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - ":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", - "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", + "/home/mqin/src/md-app-sdk/.test36/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", " import pkg_resources\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", - "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", + "/home/mqin/src/md-app-sdk/.test36/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", " import pkg_resources\n" ] } @@ -140,7 +138,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 2, "metadata": {}, "outputs": [ { @@ -372,7 +370,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 3, "metadata": {}, "outputs": [ { @@ -402,9 +400,18 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/mqin/src/md-app-sdk/.test36/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", + " import pkg_resources\n" + ] + } + ], "source": [ "import logging\n", "from numpy import uint8 # Needed if SaveImaged is enabled\n", @@ -463,7 +470,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -615,7 +622,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -736,120 +743,117 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "[2025-08-05 18:30:23,149] [INFO] (__main__.AISpleenSegApp) - Begin run\n", - "[info] [gxf_executor.cpp:379] Destroying context\n", "[info] [fragment.cpp:969] Loading extensions from configs...\n", - "[2025-08-05 18:30:23,158] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=[])\n", - "[2025-08-05 18:30:23,167] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", - "[2025-08-05 18:30:23,169] [INFO] (__main__.AISpleenSegApp) - App input and output path: dcm, output\n", + "[2025-09-04 18:15:51,418] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=[])\n", + "[2025-09-04 18:15:51,428] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", + "[2025-09-04 18:15:51,430] [INFO] (__main__.AISpleenSegApp) - App input and output path: dcm, output\n", "[info] [gxf_executor.cpp:344] Creating context\n", "[info] [gxf_executor.cpp:2508] Activating Graph...\n", "[info] [gxf_executor.cpp:2579] Running Graph...\n", "[info] [gxf_executor.cpp:2581] Waiting for completion...\n", "[info] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", - "[2025-08-05 18:30:23,190] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2025-08-05 18:30:23,710] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2025-08-05 18:30:23,711] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2025-09-04 18:15:51,680] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-09-04 18:15:51,992] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-09-04 18:15:51,994] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2025-08-05 18:30:23,712] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-08-05 18:30:23,713] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2025-08-05 18:30:23,714] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2025-08-05 18:30:23,715] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2025-08-05 18:30:23,715] [INFO] (root) - Series attribute Modality value: CT\n", - "[2025-08-05 18:30:23,716] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2025-08-05 18:30:23,717] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2025-08-05 18:30:23,718] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "[2025-08-05 18:30:23,719] [INFO] (root) - Series attribute ImageType value: None\n", - "[2025-08-05 18:30:23,720] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", - "[2025-08-05 18:30:23,721] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-08-05 18:30:23,722] [INFO] (root) - Series Selection finalized\n", - "[2025-08-05 18:30:23,722] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", - "[2025-08-05 18:30:23,723] [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", - "[2025-08-05 18:30:24,036] [INFO] (root) - Rescaled pixel data remains as of type float64.\n", - "[2025-08-05 18:30:24,040] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", - "[2025-08-05 18:30:24,041] [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", - "[2025-08-05 18:30:24,042] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", - "[2025-08-05 18:30:24,043] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", - "[2025-08-05 18:30:24,044] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", - "[2025-08-05 18:30:24,045] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", - "[2025-08-05 18:30:24,045] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", - "[2025-08-05 18:30:24,046] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", - "[2025-08-05 18:30:24,047] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", - "[2025-08-05 18:30:24,048] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", - "[2025-08-05 18:30:24,048] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", - "[2025-08-05 18:30:24,049] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", - "[2025-08-05 18:30:24,050] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", - "[2025-08-05 18:30:24,050] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "[2025-08-05 18:30:24,051] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2025-09-04 18:15:51,995] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-04 18:15:51,996] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-09-04 18:15:51,997] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-09-04 18:15:51,998] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-09-04 18:15:51,999] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-09-04 18:15:52,000] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-09-04 18:15:52,001] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-09-04 18:15:52,001] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-09-04 18:15:52,002] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-09-04 18:15:52,003] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-09-04 18:15:52,004] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-04 18:15:52,006] [INFO] (root) - Series Selection finalized\n", + "[2025-09-04 18:15:52,007] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-09-04 18:15:52,007] [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", + "[2025-09-04 18:15:52,617] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-09-04 18:15:52,619] [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", + "[2025-09-04 18:15:52,620] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-09-04 18:15:52,620] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-09-04 18:15:52,621] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-09-04 18:15:52,622] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-09-04 18:15:52,623] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-09-04 18:15:52,624] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-09-04 18:15:52,625] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-09-04 18:15:52,625] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-09-04 18:15:52,626] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-09-04 18:15:52,627] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-09-04 18:15:52,628] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-09-04 18:15:52,629] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2025-09-04 18:15:52,631] [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", - "[2025-08-05 18:30:24,053] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-09-04 18:15:52,632] [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", - "[2025-08-05 18:30:24,053] [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", - "[2025-08-05 18:30:24,054] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", - "[2025-08-05 18:30:24,058] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", - "[2025-08-05 18:30:24,059] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", - "[2025-08-05 18:30:24,060] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", - "[2025-08-05 18:30:24,062] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", - "[2025-08-05 18:30:24,062] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n" + "[2025-09-04 18:15:52,633] [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", + "[2025-09-04 18:15:52,635] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-09-04 18:15:52,636] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-09-04 18:15:52,636] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-09-04 18:15:52,637] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-09-04 18:15:52,638] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-09-04 18:15:52,638] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "2025-08-05 18:30:24,892 INFO image_writer.py:197 - writing: /home/mqin/src/md-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" + "2025-09-04 18:15:53,325 INFO image_writer.py:197 - writing: /home/mqin/src/md-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": [ - "[2025-08-05 18:30:26,562] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n" + "[2025-09-04 18:15:55,072] [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": [ - "2025-08-05 18:30:27,125 INFO image_writer.py:197 - writing: /home/mqin/src/md-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" + "2025-09-04 18:15:56,145 INFO image_writer.py:197 - writing: /home/mqin/src/md-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": [ - "[2025-08-05 18:30:28,601] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", - "[2025-08-05 18:30:28,603] [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", - "[2025-08-05 18:30:28,731] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", - "[2025-08-05 18:30:28,770] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", - "[2025-08-05 18:30:28,775] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", - "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/highdicom/base.py:165: 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", + "[2025-09-04 18:15:57,644] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-09-04 18:15:57,647] [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", + "[2025-09-04 18:15:57,774] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-09-04 18:15:57,812] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-09-04 18:15:57,817] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "/home/mqin/src/md-app-sdk/.test36/lib/python3.10/site-packages/highdicom/base.py:165: 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", - "[2025-08-05 18:30:29,715] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-08-05 18:30:29,717] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2025-08-05 18:30:29,718] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-08-05 18:30:29,719] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2025-08-05 18:30:29,720] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2025-08-05 18:30:29,721] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-08-05 18:30:29,721] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2025-08-05 18:30:29,722] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2025-08-05 18:30:29,723] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2025-09-04 18:15:59,022] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-04 18:15:59,023] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-09-04 18:15:59,024] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-04 18:15:59,025] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-09-04 18:15:59,026] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-09-04 18:15:59,027] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-04 18:15:59,028] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-09-04 18:15:59,029] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-09-04 18:15:59,029] [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:2588] Deactivating Graph...\n", "[info] [gxf_executor.cpp:2597] Graph execution finished.\n", - "[2025-08-05 18:30:29,829] [INFO] (__main__.AISpleenSegApp) - End run\n" + "[2025-09-04 18:15:59,132] [INFO] (__main__.AISpleenSegApp) - End run\n" ] } ], @@ -882,7 +886,7 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -899,7 +903,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -1075,7 +1079,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -1232,7 +1236,7 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -1253,7 +1257,7 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": 12, "metadata": {}, "outputs": [ { @@ -1281,97 +1285,95 @@ }, { "cell_type": "code", - "execution_count": 33, + "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - ":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", - "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", + "/home/mqin/src/md-app-sdk/.test36/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", " import pkg_resources\n", "[\u001b[32minfo\u001b[m] [fragment.cpp:969] Loading extensions from configs...\n", - "[2025-08-05 18:30:34,733] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['my_app'])\n", - "[2025-08-05 18:30:34,735] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", - "[2025-08-05 18:30:34,735] [INFO] (app.AISpleenSegApp) - App input and output path: dcm, output\n", + "[2025-09-04 18:16:03,964] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['my_app'])\n", + "[2025-09-04 18:16:03,967] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", + "[2025-09-04 18:16:03,967] [INFO] (app.AISpleenSegApp) - App input and output path: dcm, output\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:344] Creating context\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2508] Activating Graph...\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2579] Running Graph...\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2581] Waiting for completion...\n", "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", - "[2025-08-05 18:30:34,808] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2025-08-05 18:30:35,273] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2025-08-05 18:30:35,273] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2025-09-04 18:16:04,102] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2025-08-05 18:30:35,273] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-08-05 18:30:35,273] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2025-08-05 18:30:35,273] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Series attribute Modality value: CT\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Series attribute ImageType value: None\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Series Selection finalized\n", - "[2025-08-05 18:30:35,274] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", - "[2025-08-05 18:30:35,274] [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", - "[2025-08-05 18:30:35,587] [INFO] (root) - Rescaled pixel data remains as of type float64.\n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", - "[2025-08-05 18:30:35,592] [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", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", - "[2025-08-05 18:30:35,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-09-04 18:16:04,612] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-09-04 18:16:04,613] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-09-04 18:16:04,613] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-09-04 18:16:04,613] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-09-04 18:16:04,613] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-04 18:16:04,613] [INFO] (root) - Series Selection finalized\n", + "[2025-09-04 18:16:04,613] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-09-04 18:16:04,613] [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", + "[2025-09-04 18:16:04,992] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-09-04 18:16:04,992] [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", + "[2025-09-04 18:16:04,992] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2025-09-04 18:16:04,993] [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", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-09-04 18:16:04,993] [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", - "[2025-08-05 18:30:35,593] [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", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", - "[2025-08-05 18:30:35,593] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", - "2025-08-05 18:30:36,450 INFO image_writer.py:197 - writing: /home/mqin/src/md-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", - "[2025-08-05 18:30:38,155] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", - "2025-08-05 18:30:39,290 INFO image_writer.py:197 - writing: /home/mqin/src/md-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", - "[2025-08-05 18:30:40,732] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", - "[2025-08-05 18:30:40,735] [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", - "[2025-08-05 18:30:40,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", - "[2025-08-05 18:30:40,922] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", - "[2025-08-05 18:30:40,927] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", - "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/highdicom/base.py:165: 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", + "[2025-09-04 18:16:04,993] [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", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "2025-09-04 18:16:05,646 INFO image_writer.py:197 - writing: /home/mqin/src/md-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", + "[2025-09-04 18:16:07,370] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "2025-09-04 18:16:08,424 INFO image_writer.py:197 - writing: /home/mqin/src/md-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", + "[2025-09-04 18:16:09,889] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-09-04 18:16:09,890] [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", + "[2025-09-04 18:16:10,015] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-09-04 18:16:10,051] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-09-04 18:16:10,056] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "/home/mqin/src/md-app-sdk/.test36/lib/python3.10/site-packages/highdicom/base.py:165: 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", - "[2025-08-05 18:30:42,109] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-08-05 18:30:42,109] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2025-08-05 18:30:42,109] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-08-05 18:30:42,109] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2025-08-05 18:30:42,110] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2025-08-05 18:30:42,110] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2025-08-05 18:30:42,110] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2025-08-05 18:30:42,110] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2025-08-05 18:30:42,110] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2025-09-04 18:16:11,242] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-04 18:16:11,242] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-09-04 18:16:11,243] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-04 18:16:11,243] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-09-04 18:16:11,243] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-09-04 18:16:11,243] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-04 18:16:11,243] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-09-04 18:16:11,243] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-09-04 18:16:11,243] [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:2588] Deactivating Graph...\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:2597] Graph execution finished.\n", - "[2025-08-05 18:30:42,199] [INFO] (app.AISpleenSegApp) - End run\n", + "[2025-09-04 18:16:11,344] [INFO] (app.AISpleenSegApp) - End run\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:379] Destroying context\n" ] } @@ -1383,7 +1385,7 @@ }, { "cell_type": "code", - "execution_count": 34, + "execution_count": 14, "metadata": {}, "outputs": [ { @@ -1391,7 +1393,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.76406040679624919123643745655891328.dcm\n", + "1.2.826.0.1.3680043.10.511.3.76468060613059000496618284304659134.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", @@ -1425,7 +1427,7 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": 15, "metadata": {}, "outputs": [ { @@ -1455,7 +1457,7 @@ }, { "cell_type": "code", - "execution_count": 36, + "execution_count": 16, "metadata": {}, "outputs": [ { @@ -1498,16 +1500,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2025-08-05 18:30:44,294] [INFO] (common) - Downloading CLI manifest file...\n", - "[2025-08-05 18:30:44,482] [DEBUG] (common) - Validating CLI manifest file...\n", - "[2025-08-05 18:30:44,482] [INFO] (packager.parameters) - Application: /home/mqin/src/md-app-sdk/notebooks/tutorials/my_app\n", - "[2025-08-05 18:30:44,482] [INFO] (packager.parameters) - Detected application type: Python Module\n", - "[2025-08-05 18:30:44,483] [INFO] (packager) - Scanning for models in /home/mqin/src/md-app-sdk/notebooks/tutorials/models...\n", - "[2025-08-05 18:30:44,483] [DEBUG] (packager) - Model model=/home/mqin/src/md-app-sdk/notebooks/tutorials/models/model added.\n", - "[2025-08-05 18:30:44,483] [INFO] (packager) - Reading application configuration from /home/mqin/src/md-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", - "[2025-08-05 18:30:44,487] [INFO] (packager) - Generating app.json...\n", - "[2025-08-05 18:30:44,488] [INFO] (packager) - Generating pkg.json...\n", - "[2025-08-05 18:30:44,493] [DEBUG] (common) - \n", + "[2025-09-04 18:26:44,384] [INFO] (common) - Downloading CLI manifest file...\n", + "[2025-09-04 18:26:44,590] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2025-09-04 18:26:44,592] [INFO] (packager.parameters) - Application: /home/mqin/src/md-app-sdk/notebooks/tutorials/my_app\n", + "[2025-09-04 18:26:44,593] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2025-09-04 18:26:44,593] [INFO] (packager) - Scanning for models in /home/mqin/src/md-app-sdk/notebooks/tutorials/models...\n", + "[2025-09-04 18:26:44,593] [DEBUG] (packager) - Model model=/home/mqin/src/md-app-sdk/notebooks/tutorials/models/model added.\n", + "[2025-09-04 18:26:44,593] [INFO] (packager) - Reading application configuration from /home/mqin/src/md-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", + "[2025-09-04 18:26:44,600] [INFO] (packager) - Generating app.json...\n", + "[2025-09-04 18:26:44,600] [INFO] (packager) - Generating pkg.json...\n", + "[2025-09-04 18:26:44,605] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1542,7 +1544,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2025-08-05 18:30:44,493] [DEBUG] (common) - \n", + "[2025-09-04 18:26:44,605] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1562,18 +1564,18 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - ================ Begin requirements.txt ================\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - highdicom>=0.18.2\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - monai>=1.0\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - nibabel>=3.2.1\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - numpy>=1.21.6\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - pydicom>=2.3.0\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - setuptools>=59.5.0 # for pkg_resources\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - SimpleITK>=2.0.0\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - torch>=1.12.0\n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - \n", - "[2025-08-05 18:30:44,519] [DEBUG] (packager.builder) - ================ End requirements.txt ==================\n", - "[2025-08-05 18:30:44,520] [DEBUG] (packager.builder) - \n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - ================ Begin requirements.txt ================\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - highdicom>=0.18.2\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - monai>=1.0\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - nibabel>=3.2.1\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - numpy>=1.21.6\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - pydicom>=2.3.0\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - setuptools>=59.5.0 # for pkg_resources\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - SimpleITK>=2.0.0\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - torch>=1.12.0\n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - \n", + "[2025-09-04 18:26:44,628] [DEBUG] (packager.builder) - ================ End requirements.txt ==================\n", + "[2025-09-04 18:26:44,629] [DEBUG] (packager.builder) - \n", "========== Begin Build Parameters ==========\n", "{'add_hosts': None,\n", " 'additional_lib_paths': '',\n", @@ -1617,7 +1619,7 @@ " 'working_dir': PosixPath('/var/holoscan')}\n", "=========== End Build Parameters ===========\n", "\n", - "[2025-08-05 18:30:44,520] [DEBUG] (packager.builder) - \n", + "[2025-09-04 18:26:44,630] [DEBUG] (packager.builder) - \n", "========== Begin Platform Parameters ==========\n", "{'base_image': 'nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04',\n", " 'build_image': None,\n", @@ -1629,13 +1631,13 @@ " 'holoscan_deb_arch': 'amd64',\n", " 'holoscan_sdk_file': '3.5.0',\n", " 'holoscan_sdk_filename': '3.5.0',\n", - " 'monai_deploy_sdk_file': PosixPath('/home/mqin/src/md-app-sdk/dist/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl'),\n", - " 'monai_deploy_sdk_filename': 'monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl',\n", + " 'monai_deploy_sdk_file': PosixPath('/home/mqin/src/md-app-sdk/dist/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl'),\n", + " 'monai_deploy_sdk_filename': 'monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl',\n", " 'tag': 'my_app:1.0',\n", " 'target_arch': 'x86_64'}\n", "=========== End Platform Parameters ===========\n", "\n", - "[2025-08-05 18:30:44,541] [DEBUG] (packager.builder) - \n", + "[2025-09-04 18:26:44,650] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "ARG GPU_TYPE=dgpu\n", @@ -1775,8 +1777,8 @@ "\n", "# Install MONAI Deploy App SDK\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl /tmp/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl\n", + "COPY ./monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl\n", "\n", "COPY ./models /opt/holoscan/models\n", "\n", @@ -1792,9 +1794,9 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2025-08-05 18:30:45,203] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2025-08-05 18:30:45,204] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", - "[2025-08-05 18:30:45,204] [INFO] (packager.builder) - \n", + "[2025-09-04 18:26:45,258] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2025-09-04 18:26:45,258] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2025-09-04 18:26:45,258] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", @@ -1803,7 +1805,7 @@ " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: 3.5.0\n", - " MONAI Deploy App SDK Package: /home/mqin/src/md-app-sdk/dist/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/md-app-sdk/dist/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", " SDK Version: 3.5.0\n", " SDK: monai-deploy\n", @@ -1813,17 +1815,14 @@ "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 4.92kB done\n", + "#1 transferring dockerfile: 4.94kB done\n", "#1 DONE 0.1s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", - "#2 ...\n", - "\n", - "#3 [auth] nvidia/cuda:pull token for nvcr.io\n", - "#3 DONE 0.0s\n", + "#2 [auth] nvidia/cuda:pull token for nvcr.io\n", + "#2 DONE 0.0s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", - "#2 DONE 0.8s\n", + "#3 [internal] load metadata for nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", + "#3 DONE 0.8s\n", "\n", "#4 [internal] load .dockerignore\n", "#4 transferring context: 1.80kB done\n", @@ -1832,250 +1831,253 @@ "#5 [internal] load build context\n", "#5 DONE 0.0s\n", "\n", - "#6 importing cache manifest from local:15722606582337824522\n", + "#6 importing cache manifest from local:2981386072432009811\n", "#6 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#6 DONE 0.0s\n", "\n", "#7 [base 1/2] FROM nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04@sha256:ebef3c171eeef0298e4eb2e4be843105edf3b8b0ac45e0b43acee358e8046867\n", - "#7 resolve nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04@sha256:ebef3c171eeef0298e4eb2e4be843105edf3b8b0ac45e0b43acee358e8046867 0.1s done\n", - "#7 DONE 0.1s\n", + "#7 resolve nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04@sha256:ebef3c171eeef0298e4eb2e4be843105edf3b8b0ac45e0b43acee358e8046867 0.0s done\n", + "#7 DONE 0.0s\n", "\n", "#8 importing cache manifest from nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", "#8 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#8 DONE 0.4s\n", + "#8 DONE 0.3s\n", "\n", "#5 [internal] load build context\n", - "#5 transferring context: 19.56MB 0.2s done\n", + "#5 transferring context: 19.57MB 0.2s done\n", "#5 DONE 0.3s\n", "\n", - "#9 [release 12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#9 [release 3/21] RUN if id \"ubuntu\" >/dev/null 2>&1; then touch /var/mail/ubuntu && chown ubuntu /var/mail/ubuntu && userdel -r ubuntu; fi\n", "#9 CACHED\n", "\n", - "#10 [release 6/21] RUN chown -R holoscan /var/holoscan && chown -R holoscan /var/holoscan/input && chown -R holoscan /var/holoscan/output\n", + "#10 [release 13/21] RUN pip install --upgrade pip\n", "#10 CACHED\n", "\n", - "#11 [release 7/21] WORKDIR /var/holoscan\n", + "#11 [release 9/21] RUN chmod +x /var/holoscan/tools\n", "#11 CACHED\n", "\n", "#12 [release 8/21] COPY ./tools /var/holoscan/tools\n", "#12 CACHED\n", "\n", - "#13 [release 3/21] RUN if id \"ubuntu\" >/dev/null 2>&1; then touch /var/mail/ubuntu && chown ubuntu /var/mail/ubuntu && userdel -r ubuntu; fi\n", + "#13 [release 11/21] WORKDIR /var/holoscan\n", "#13 CACHED\n", "\n", - "#14 [release 13/21] RUN pip install --upgrade pip\n", + "#14 [release 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#14 CACHED\n", "\n", - "#15 [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", + "#15 [release 7/21] WORKDIR /var/holoscan\n", "#15 CACHED\n", "\n", - "#16 [release 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#16 [release 2/21] RUN apt update && apt-get install -y --no-install-recommends --no-install-suggests python3-minimal=3.12.3-* libpython3-stdlib=3.12.3-* python3=3.12.3-* python3-venv=3.12.3-* python3-pip=24.0+dfsg-* && rm -rf /var/lib/apt/lists/*\n", "#16 CACHED\n", "\n", - "#17 [release 10/21] RUN rm -rf /usr/lib/python3.12/EXTERNALLY-MANAGED\n", + "#17 [release 4/21] RUN groupadd -f -g 1000 holoscan\n", "#17 CACHED\n", "\n", - "#18 [release 11/21] WORKDIR /var/holoscan\n", + "#18 [release 10/21] RUN rm -rf /usr/lib/python3.12/EXTERNALLY-MANAGED\n", "#18 CACHED\n", "\n", - "#19 [release 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", + "#19 [release 1/21] 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", "#19 CACHED\n", "\n", - "#20 [release 2/21] RUN apt update && apt-get install -y --no-install-recommends --no-install-suggests python3-minimal=3.12.3-* libpython3-stdlib=3.12.3-* python3=3.12.3-* python3-venv=3.12.3-* python3-pip=24.0+dfsg-* && rm -rf /var/lib/apt/lists/*\n", + "#20 [release 12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#20 CACHED\n", "\n", - "#21 [release 9/21] RUN chmod +x /var/holoscan/tools\n", + "#21 [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", "#21 CACHED\n", "\n", - "#22 [release 1/21] 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", + "#22 [release 6/21] RUN chown -R holoscan /var/holoscan && chown -R holoscan /var/holoscan/input && chown -R holoscan /var/holoscan/output\n", "#22 CACHED\n", "\n", "#23 [release 14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", - "#23 extracting sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1\n", - "#23 extracting sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 0.0s done\n", + "#23 sha256:cd8285169945900d649da229211c6cc1c69607bd85875e5afa9b01f051815aa1 252B / 252B done\n", "#23 extracting sha256:cd8285169945900d649da229211c6cc1c69607bd85875e5afa9b01f051815aa1\n", "#23 extracting sha256:cd8285169945900d649da229211c6cc1c69607bd85875e5afa9b01f051815aa1 0.0s done\n", + "#23 sha256:d960bf65a541a1e0a07996511018156f53db3892491a48235285d7b949718940 5.33MB / 5.33MB 0.1s done\n", "#23 extracting sha256:d960bf65a541a1e0a07996511018156f53db3892491a48235285d7b949718940\n", "#23 extracting sha256:d960bf65a541a1e0a07996511018156f53db3892491a48235285d7b949718940 0.6s done\n", "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 8.39MB / 3.21GB 0.2s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 175.11MB / 3.21GB 2.7s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 337.64MB / 3.21GB 5.3s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 503.32MB / 3.21GB 7.8s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 667.94MB / 3.21GB 10.4s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 831.52MB / 3.21GB 12.9s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 996.53MB / 3.21GB 15.6s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.17GB / 3.21GB 18.3s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.33GB / 3.21GB 21.2s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.49GB / 3.21GB 24.3s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.65GB / 3.21GB 27.5s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.82GB / 3.21GB 30.2s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.98GB / 3.21GB 32.7s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.15GB / 3.21GB 35.7s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.31GB / 3.21GB 38.3s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.48GB / 3.21GB 41.0s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.64GB / 3.21GB 43.4s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.81GB / 3.21GB 45.9s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.97GB / 3.21GB 48.5s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 3.15GB / 3.21GB 51.2s\n", - "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 3.21GB / 3.21GB 55.1s done\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 173.02MB / 3.21GB 2.7s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 334.50MB / 3.21GB 5.0s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 500.17MB / 3.21GB 7.4s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 671.09MB / 3.21GB 9.9s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 841.70MB / 3.21GB 12.5s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.01GB / 3.21GB 15.0s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.18GB / 3.21GB 17.6s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.34GB / 3.21GB 20.7s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.51GB / 3.21GB 23.9s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.67GB / 3.21GB 26.4s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 1.83GB / 3.21GB 29.0s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.00GB / 3.21GB 31.5s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.16GB / 3.21GB 34.1s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.33GB / 3.21GB 37.1s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.50GB / 3.21GB 39.9s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.67GB / 3.21GB 42.5s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.83GB / 3.21GB 45.0s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 2.99GB / 3.21GB 47.4s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 3.16GB / 3.21GB 50.1s\n", + "#23 sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 3.21GB / 3.21GB 54.9s done\n", "#23 extracting sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc\n", - "#23 extracting sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 77.8s done\n", + "#23 extracting sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc 79.6s done\n", "#23 CACHED\n", "\n", - "#24 [release 15/21] COPY ./monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl /tmp/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl\n", - "#24 DONE 3.8s\n", - "\n", - "#25 [release 16/21] RUN pip install /tmp/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl\n", - "#25 0.807 Defaulting to user installation because normal site-packages is not writeable\n", - "#25 0.961 Processing /tmp/monai_deploy_app_sdk-1.0.0+34.gfb1c2c6-py3-none-any.whl\n", - "#25 0.972 Requirement already satisfied: numpy>=1.21.6 in /home/holoscan/.local/lib/python3.12/site-packages (from monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (2.3.2)\n", - "#25 1.172 Collecting holoscan~=3.0 (from monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.304 Downloading holoscan-3.5.0-cp312-cp312-manylinux_2_35_x86_64.whl.metadata (6.5 kB)\n", - "#25 1.368 Collecting holoscan-cli~=3.0 (from monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.383 Downloading holoscan_cli-3.5.0-py3-none-any.whl.metadata (4.0 kB)\n", - "#25 1.455 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.469 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", - "#25 1.554 Collecting tritonclient>=2.53.0 (from tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.566 Downloading tritonclient-2.59.0-py3-none-manylinux1_x86_64.whl.metadata (2.8 kB)\n", - "#25 1.646 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.658 Downloading typeguard-4.4.4-py3-none-any.whl.metadata (3.3 kB)\n", - "#25 1.685 Requirement already satisfied: pip>22.0.2 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (25.2)\n", - "#25 1.752 Collecting cupy-cuda12x<14.0,>=12.2 (from holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.764 Downloading cupy_cuda12x-13.5.1-cp312-cp312-manylinux2014_x86_64.whl.metadata (2.4 kB)\n", - "#25 1.834 Collecting cloudpickle<4.0,>=3.0 (from holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.849 Downloading cloudpickle-3.1.1-py3-none-any.whl.metadata (7.1 kB)\n", - "#25 1.877 Requirement already satisfied: pillow>=11.2 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (11.3.0)\n", - "#25 1.983 Collecting wheel-axle-runtime<1.0 (from holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 1.998 Downloading wheel_axle_runtime-0.0.6-py3-none-any.whl.metadata (8.1 kB)\n", - "#25 2.088 Collecting fastrlock>=0.5 (from cupy-cuda12x<14.0,>=12.2->holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.100 Downloading fastrlock-0.8.3-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_28_x86_64.whl.metadata (7.7 kB)\n", - "#25 2.125 Requirement already satisfied: Jinja2<4.0.0,>=3.1.6 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (3.1.6)\n", - "#25 2.127 Requirement already satisfied: packaging<26.0,>=25.0 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (25.0)\n", - "#25 2.254 Collecting psutil<8.0,>=7.0.0 (from holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.265 Downloading psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB)\n", - "#25 2.354 Collecting python-on-whales>=0.77.0 (from holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.366 Downloading python_on_whales-0.78.0-py3-none-any.whl.metadata (18 kB)\n", - "#25 2.488 Collecting pyyaml<7.0,>=6.0 (from holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.500 Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)\n", - "#25 2.588 Collecting requests<3.0,>=2.32 (from holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.599 Downloading requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)\n", - "#25 2.631 Requirement already satisfied: MarkupSafe>=2.0 in /home/holoscan/.local/lib/python3.12/site-packages (from Jinja2<4.0.0,>=3.1.6->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (3.0.2)\n", - "#25 2.756 Collecting charset_normalizer<4,>=2 (from requests<3.0,>=2.32->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.767 Downloading charset_normalizer-3.4.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)\n", - "#25 2.841 Collecting idna<4,>=2.5 (from requests<3.0,>=2.32->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.855 Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)\n", - "#25 2.942 Collecting urllib3<3,>=1.21.1 (from requests<3.0,>=2.32->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 2.955 Downloading urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)\n", - "#25 3.034 Collecting certifi>=2017.4.17 (from requests<3.0,>=2.32->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 3.046 Downloading certifi-2025.8.3-py3-none-any.whl.metadata (2.4 kB)\n", - "#25 3.080 Requirement already satisfied: filelock in /home/holoscan/.local/lib/python3.12/site-packages (from wheel-axle-runtime<1.0->holoscan~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (3.18.0)\n", - "#25 3.232 Collecting pydantic!=2.0.*,<3,>=2 (from python-on-whales>=0.77.0->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6)\n", - "#25 3.243 Downloading pydantic-2.11.7-py3-none-any.whl.metadata (67 kB)\n", - "#25 3.284 Requirement already satisfied: typing-extensions in /home/holoscan/.local/lib/python3.12/site-packages (from python-on-whales>=0.77.0->holoscan-cli~=3.0->monai-deploy-app-sdk==1.0.0+34.gfb1c2c6) (4.14.1)\n", - "#25 3.323 Collecting annotated-types>=0.6.0 (from 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- "#25 17.10 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 19.5 MB/s 0:00:00\n", - "#25 17.12 Downloading zope.interface-7.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (264 kB)\n", - "#25 17.76 Installing collected packages: fastrlock, cuda-bindings, brotli, wheel-axle-runtime, urllib3, typing-inspection, typeguard, setuptools, pyyaml, python-rapidjson, pydantic-core, psutil, protobuf, propcache, multidict, idna, grpcio, greenlet, frozenlist, cupy-cuda12x, cuda-python, colorama, cloudpickle, charset_normalizer, certifi, attrs, annotated-types, aiohappyeyeballs, zope.interface, zope.event, yarl, tritonclient, requests, pydantic, holoscan, aiosignal, python-on-whales, gevent, aiohttp, holoscan-cli, geventhttpclient, monai-deploy-app-sdk\n", - "#25 24.83 \n", - "#25 24.84 Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0 annotated-types-0.7.0 attrs-25.3.0 brotli-1.1.0 certifi-2025.8.3 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-3.5.0 holoscan-cli-3.5.0 idna-3.10 monai-deploy-app-sdk-1.0.0+34.gfb1c2c6 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-0.78.0 python-rapidjson-1.21 pyyaml-6.0.2 requests-2.32.4 setuptools-80.9.0 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-5.1.1 zope.interface-7.2\n", - "#25 DONE 28.1s\n", + "#24 [release 15/21] COPY ./monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl\n", + "#24 DONE 5.1s\n", + "\n", + "#25 [release 16/21] RUN pip install /tmp/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl\n", + "#25 0.717 Defaulting to user installation because normal site-packages is not writeable\n", + "#25 0.792 Processing /tmp/monai_deploy_app_sdk-1.0.0+28.g7da6e97.dirty-py3-none-any.whl\n", + "#25 0.804 Requirement already satisfied: numpy>=1.21.6 in /home/holoscan/.local/lib/python3.12/site-packages (from monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (2.3.2)\n", + "#25 0.938 Collecting holoscan~=3.5.0 (from monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", + "#25 0.984 Downloading holoscan-3.5.0-cp312-cp312-manylinux_2_35_x86_64.whl.metadata (6.5 kB)\n", + "#25 1.087 Collecting holoscan-cli~=3.5.0 (from monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", + "#25 1.158 Downloading holoscan_cli-3.5.0-py3-none-any.whl.metadata (4.0 kB)\n", + "#25 1.226 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", + "#25 1.233 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", + "#25 1.309 Collecting tritonclient>=2.53.0 (from 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fastrlock-0.8.3-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_28_x86_64.whl (53 kB)\n", + "#25 10.77 Downloading python_on_whales-0.78.0-py3-none-any.whl (118 kB)\n", + "#25 10.80 Downloading pydantic-2.11.7-py3-none-any.whl (444 kB)\n", + "#25 10.83 Downloading pydantic_core-2.33.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.0 MB)\n", + "#25 10.88 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 42.2 MB/s 0:00:00\n", + "#25 10.89 Downloading annotated_types-0.7.0-py3-none-any.whl (13 kB)\n", + "#25 10.91 Downloading tritonclient-2.60.0-py3-none-manylinux1_x86_64.whl (14.5 MB)\n", + "#25 11.24 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.5/14.5 MB 43.7 MB/s 0:00:00\n", + "#25 11.25 Downloading python_rapidjson-1.21-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (1.7 MB)\n", + "#25 11.29 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 42.0 MB/s 0:00:00\n", + "#25 11.30 Downloading 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setuptools, pyyaml, python-rapidjson, pydantic-core, psutil, protobuf, propcache, multidict, idna, grpcio, greenlet, frozenlist, cupy-cuda12x, cuda-pathfinder, colorama, cloudpickle, charset_normalizer, certifi, attrs, annotated-types, aiohappyeyeballs, zope.interface, zope.event, yarl, tritonclient, requests, pydantic, holoscan, cuda-bindings, aiosignal, python-on-whales, gevent, cuda-python, aiohttp, holoscan-cli, geventhttpclient, monai-deploy-app-sdk\n", + "#25 19.81 \n", + "#25 19.83 Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0 annotated-types-0.7.0 attrs-25.3.0 brotli-1.1.0 certifi-2025.8.3 charset_normalizer-3.4.3 cloudpickle-3.1.1 colorama-0.4.6 cuda-bindings-13.0.1 cuda-pathfinder-1.2.1 cuda-python-13.0.1 cupy-cuda12x-13.6.0 fastrlock-0.8.3 frozenlist-1.7.0 gevent-25.8.2 geventhttpclient-2.3.4 greenlet-3.2.4 grpcio-1.67.1 holoscan-3.5.0 holoscan-cli-3.5.0 idna-3.10 monai-deploy-app-sdk-1.0.0+28.g7da6e97.dirty multidict-6.6.4 propcache-0.3.2 protobuf-5.29.5 psutil-7.0.0 pydantic-2.11.7 pydantic-core-2.33.2 python-on-whales-0.78.0 python-rapidjson-1.21 pyyaml-6.0.2 requests-2.32.5 setuptools-80.9.0 tritonclient-2.60.0 typeguard-4.4.4 typing-inspection-0.4.1 urllib3-2.5.0 wheel-axle-runtime-0.0.7 yarl-1.20.1 zope.event-5.1.1 zope.interface-7.2\n", + "#25 DONE 22.5s\n", "\n", "#26 [release 17/21] COPY ./models /opt/holoscan/models\n", "#26 DONE 0.3s\n", @@ -2094,81 +2096,81 @@ "\n", "#31 exporting to docker image format\n", "#31 exporting layers\n", - "#31 exporting layers 23.4s done\n", - "#31 exporting manifest sha256:534c562a2a833d9d95932f80639e8dc25b129ffa6be1620ca13381d26879982c 0.0s done\n", - "#31 exporting config sha256:39cb7966781dad88ff8a6b10b70a8c4d314bef750b76a77eaf7deacbfde96431 0.0s done\n", + "#31 exporting layers 23.8s done\n", + "#31 exporting manifest sha256:c84f5839d0f153c8c8ccb63fb388504efc344bdd258170f786a6d1f5c6362684 0.0s done\n", + "#31 exporting config sha256:497a1c32b76eb5306ff23ddf131918f3a974545926f8554c88bc8f27eb940901 0.0s done\n", "#31 sending tarball\n", "#31 ...\n", "\n", "#32 importing to docker\n", - "#32 loading layer 66fc9d898acc 32.77kB / 127.61kB\n", - "#32 loading layer e7aaa0be9f22 557.06kB / 419.28MB\n", - "#32 loading layer e7aaa0be9f22 154.86MB / 419.28MB 2.1s\n", - "#32 loading layer e7aaa0be9f22 233.41MB / 419.28MB 4.2s\n", - "#32 loading layer e7aaa0be9f22 347.60MB / 419.28MB 8.3s\n", - "#32 loading layer e7aaa0be9f22 393.84MB / 419.28MB 10.3s\n", - "#32 loading layer 7d9308adb028 196.61kB / 17.81MB\n", - "#32 loading layer 043ca3b87c84 487B / 487B\n", - "#32 loading layer 1f47903e113c 314B / 314B\n", - "#32 loading layer d101894c3f31 303B / 303B\n", - "#32 loading layer ed38daddfc73 3.91kB / 3.91kB\n", - "#32 loading layer 66fc9d898acc 127.61kB / 127.61kB 13.9s done\n", - "#32 loading layer e7aaa0be9f22 419.28MB / 419.28MB 13.8s done\n", - "#32 loading layer 7d9308adb028 17.81MB / 17.81MB 1.5s done\n", - "#32 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sha256:b2b5707b6ca1f27538514dc4f44445111eaeec6eb663c9634759ce215300867d 0.2s done\n", - "#33 preparing build cache for export 8.9s done\n", - "#33 writing cache manifest sha256:8222f20f991cb48573389c1e3bd2a3ba6e09bc7337a06df5d95eec9f5b93c9af 0.1s done\n", - "#33 DONE 8.9s\n", - "[2025-08-05 18:35:10,577] [INFO] (packager) - Build Summary:\n", + "#33 writing config sha256:061f191f21483bb3aa13ddb45f68ab226d8c391e968deee9958cee6c322ae657 0.0s done\n", + "#33 writing cache manifest sha256:137f69559021d1407b62487b53f678be33062feb5a494364e4b6e92e9afa3587 0.0s done\n", + "#33 DONE 7.5s\n", + "[2025-09-04 18:30:55,707] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -2194,14 +2196,14 @@ }, { "cell_type": "code", - "execution_count": 38, + "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "my_app-x64-workstation-dgpu-linux-amd64 1.0 39cb7966781d About a minute ago 10.2GB\n" + "my_app-x64-workstation-dgpu-linux-amd64 1.0 497a1c32b76e 5 minutes ago 10.3GB\n" ] } ], @@ -2220,7 +2222,7 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": 23, "metadata": {}, "outputs": [ { @@ -2229,23 +2231,23 @@ "text": [ "output\n", "dcm\n", - "[2025-08-05 18:35:14,890] [INFO] (runner) - Checking dependencies...\n", - "[2025-08-05 18:35:14,890] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2025-09-04 18:34:36,446] [INFO] (runner) - Checking dependencies...\n", + "[2025-09-04 18:34:36,446] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2025-08-05 18:35:14,890] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2025-09-04 18:34:36,446] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2025-08-05 18:35:14,891] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2025-09-04 18:34:36,447] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2025-08-05 18:35:14,977] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "Successfully copied 2.56kB to /tmp/tmpwth005_4/app.json\n", - "Successfully copied 2.05kB to /tmp/tmpwth005_4/pkg.json\n", - "9170531a0c9ecb52ca9beaeedb778e152610255adad1afb9575f82ad53e67619\n", - "[2025-08-05 18:35:15,310] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2025-09-04 18:34:36,561] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "Successfully copied 2.56kB to /tmp/tmp_pisicq0/app.json\n", + "Successfully copied 2.05kB to /tmp/tmp_pisicq0/pkg.json\n", + "1ab9a6ec3fba694aaccb00d92e2aec287057363d660b193928dbb243af76dd01\n", + "[2025-09-04 18:34:36,906] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2025-08-05 18:35:15,311] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2025-09-04 18:34:36,907] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2025-08-05 18:35:15,704] [INFO] (common) - Launching container (f6da9764c3b4) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: amazing_borg\n", + "[2025-09-04 18:34:37,269] [INFO] (common) - Launching container (3a29b7f7e4ec) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: objective_lalande\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -2255,9 +2257,7 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2025-08-06 01:35:16 [INFO] Launching application python3 /opt/holoscan/app ...\n", - "\n", - ":1297: 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", + "2025-09-05 01:34:38 [INFO] Launching application python3 /opt/holoscan/app ...\n", "\n", "/home/holoscan/.local/lib/python3.12/site-packages/monai/deploy/utils/importutil.py:20: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n", "\n", @@ -2267,11 +2267,11 @@ "\n", "[info] [gxf_executor.cpp:344] Creating context\n", "\n", - "[2025-08-06 01:35:21,790] [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", + "[2025-09-05 01:34:43,648] [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", - "[2025-08-06 01:35:21,791] [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", + "[2025-09-05 01:34:43,650] [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", - "[2025-08-06 01:35:21,791] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", + "[2025-09-05 01:34:43,650] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", "\n", "[info] [gxf_executor.cpp:2508] Activating Graph...\n", "\n", @@ -2281,73 +2281,71 @@ "\n", "[info] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", "\n", - "[2025-08-06 01:35:21,886] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-09-05 01:34:43,835] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-09-05 01:34:44,749] [INFO] (root) - Finding series for Selection named: CT Series\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2025-09-05 01:34:44,749] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", "\n", " # of series: 1\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-05 01:34:44,749] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute Modality value: CT\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", "\n", - "[2025-08-06 01:35:22,660] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute ImageType value: None\n", "\n", - "[2025-08-06 01:35:22,661] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", "\n", - "[2025-08-06 01:35:22,661] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-08-06 01:35:22,661] [INFO] (root) - Series Selection finalized\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Series Selection finalized\n", "\n", - "[2025-08-06 01:35:22,661] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-09-05 01:34:44,750] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", "\n", - "[2025-08-06 01:35:22,661] [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", + "[2025-09-05 01:34:44,750] [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", - "[2025-08-06 01:35:22,950] [INFO] (root) - Rescaled pixel data remains as of type float64.\n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", "\n", - "[2025-08-06 01:35:22,953] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-09-05 01:34:45,116] [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", "\n", - "[2025-08-06 01:35:22,953] [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", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", "\n", - "[2025-08-06 01:35:22,953] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", "\n", - "[2025-08-06 01:35:22,953] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", "\n", - "[2025-08-06 01:35:22,953] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", "\n", - "[2025-08-06 01:35:22,953] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", "\n", - "[2025-08-06 01:35:22,953] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", "\n", " [ 0. 0.7890625 0. -398.60547 ]\n", "\n", @@ -2355,7 +2353,7 @@ "\n", " [ 0. 0. 0. 1. ]], type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-09-05 01:34:45,117] [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", @@ -2363,57 +2361,57 @@ "\n", " [ 0. 0. 0. 1. ]], type \n", "\n", - "[2025-08-06 01:35:22,954] [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", + "[2025-09-05 01:34:45,117] [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", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", "\n", - "[2025-08-06 01:35:22,954] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-09-05 01:34:45,118] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", "\n", - "[2025-08-06 01:35:22,955] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-09-05 01:34:45,118] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", "\n", - "[2025-08-06 01:35:22,955] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "[2025-09-05 01:34:45,118] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", "\n", - "2025-08-06 01:35:23,791 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", + "2025-09-05 01:34:45,821 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", "\n", - "[2025-08-06 01:35:25,472] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "[2025-09-05 01:34:47,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", "\n", - "2025-08-06 01:35:26,513 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", + "2025-09-05 01:34:49,524 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", "\n", - "[2025-08-06 01:35:27,964] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-09-05 01:34:51,014] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", "\n", - "[2025-08-06 01:35:27,967] [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", + "[2025-09-05 01:34:51,019] [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", "\n", - "[2025-08-06 01:35:28,095] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-09-05 01:34:51,151] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", "\n", - "[2025-08-06 01:35:28,136] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-09-05 01:34:51,189] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", "\n", - "[2025-08-06 01:35:28,140] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[2025-09-05 01:34:51,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", "\n", "/home/holoscan/.local/lib/python3.12/site-packages/highdicom/base.py:165: 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", "\n", " check_person_name(patient_name)\n", "\n", - "[2025-08-06 01:35:29,253] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2025-08-06 01:35:29,253] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", "\n", - "[2025-08-06 01:35:29,254] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\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", "\n", @@ -2423,13 +2421,13 @@ "\n", "[info] [gxf_executor.cpp:2597] Graph execution finished.\n", "\n", - "[2025-08-06 01:35:29,334] [INFO] (app.AISpleenSegApp) - End run\n", + "[2025-09-05 01:34:52,422] [INFO] (app.AISpleenSegApp) - End run\n", "\n", "[info] [gxf_executor.cpp:379] Destroying context\n", "\n", - "2025-08-06 01:35:30 [INFO] Application exited with 0.\n", + "2025-09-05 01:34:54 [INFO] Application exited with 0.\n", "\n", - "[2025-08-05 18:35:31,410] [INFO] (common) - Container 'amazing_borg'(f6da9764c3b4) exited with code 0.\n" + "[2025-09-04 18:34:54,814] [INFO] (common) - Container 'objective_lalande'(3a29b7f7e4ec) exited with code 0.\n" ] } ], @@ -2443,7 +2441,7 @@ }, { "cell_type": "code", - "execution_count": 40, + "execution_count": 24, "metadata": {}, "outputs": [ { @@ -2451,7 +2449,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.28812684571814926223695349363943565.dcm\n", + "1.2.826.0.1.3680043.10.511.3.88991892166852090760434123092314736.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", @@ -2470,7 +2468,7 @@ ], "metadata": { "kernelspec": { - "display_name": ".venv", + "display_name": ".test36", "language": "python", "name": "python3" }, diff --git a/pyproject.toml b/pyproject.toml index 10fcfc02..953b3eda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta" [tool.black] line-length = 120 -target-version = ['py38', 'py39', 'py310', 'py311', 'py312'] +target-version = ['py39', 'py310', 'py311', 'py312', 'py313'] include = '\.pyi?$' exclude = ''' ( diff --git a/requirements.txt b/requirements.txt index ff677186..365bc447 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ -holoscan~=3.0 -holoscan-cli~=3.0 +holoscan<=3.5.0 +holoscan-cli<=3.5.0 numpy>=1.21.6 colorama>=0.4.1 tritonclient[all]>=2.53.0 diff --git a/setup.cfg b/setup.cfg index e8966435..6413b321 100644 --- a/setup.cfg +++ b/setup.cfg @@ -24,8 +24,8 @@ python_requires = >=3.9, <3.14 # cucim install_requires = numpy>=1.21.6 - holoscan~=3.0 - holoscan-cli~=3.0 + holoscan<=3.5.0 + holoscan-cli<=3.5.0 colorama>=0.4.1 tritonclient[all]>=2.53.0 typeguard>=3.0.0