diff --git a/examples/apps/ai_remote_infer_app/spleen_seg_operator.py b/examples/apps/ai_remote_infer_app/spleen_seg_operator.py index 814feebb..197cd58f 100644 --- a/examples/apps/ai_remote_infer_app/spleen_seg_operator.py +++ b/examples/apps/ai_remote_infer_app/spleen_seg_operator.py @@ -127,7 +127,7 @@ def pre_process(self, img_reader, out_dir: str = "./input_images") -> Compose: resample=False, output_ext=".nii", ), - Orientationd(keys=my_key, axcodes="RAS"), + Orientationd(keys=my_key, axcodes="LPS"), Spacingd(keys=my_key, pixdim=[1.5, 1.5, 2.9], mode=["bilinear"]), ScaleIntensityRanged(keys=my_key, a_min=-57, a_max=164, b_min=0.0, b_max=1.0, clip=True), EnsureTyped(keys=my_key), diff --git a/examples/apps/ai_unetr_seg_app/unetr_seg_operator.py b/examples/apps/ai_unetr_seg_app/unetr_seg_operator.py index dbbb2b30..d31f5c2c 100644 --- a/examples/apps/ai_unetr_seg_app/unetr_seg_operator.py +++ b/examples/apps/ai_unetr_seg_app/unetr_seg_operator.py @@ -143,7 +143,7 @@ def pre_process(self, img_reader, out_dir: str = "./input_images") -> Compose: output_ext=".nii", ), Spacingd(keys=my_key, pixdim=(1.5, 1.5, 2.0), mode=("bilinear")), - Orientationd(keys=my_key, axcodes="RAS"), + Orientationd(keys=my_key, axcodes="LPS"), ScaleIntensityRanged(my_key, a_min=-175, a_max=250, b_min=0.0, b_max=1.0, clip=True), CropForegroundd(my_key, source_key=my_key), ] diff --git a/examples/apps/cchmc_ped_abd_ct_seg_app/abdomen_seg_operator.py b/examples/apps/cchmc_ped_abd_ct_seg_app/abdomen_seg_operator.py index 2f412f14..6dabfe5e 100644 --- a/examples/apps/cchmc_ped_abd_ct_seg_app/abdomen_seg_operator.py +++ b/examples/apps/cchmc_ped_abd_ct_seg_app/abdomen_seg_operator.py @@ -226,7 +226,7 @@ def pre_process(self, img_reader) -> Compose: # img_reader: specialized InMemImageReader, derived from MONAI ImageReader LoadImaged(keys=my_key, reader=img_reader), EnsureChannelFirstd(keys=my_key), - Orientationd(keys=my_key, axcodes="RAS"), + Orientationd(keys=my_key, axcodes="LPS"), Spacingd(keys=my_key, pixdim=[1.5, 1.5, 3.0], mode=["bilinear"]), ScaleIntensityRanged(keys=my_key, a_min=-250, a_max=400, b_min=0.0, b_max=1.0, clip=True), CropForegroundd(keys=my_key, source_key=my_key, mode="minimum"), diff --git a/notebooks/tutorials/03_segmentation_app.ipynb b/notebooks/tutorials/03_segmentation_app.ipynb index b4d9aed8..1933f47a 100644 --- a/notebooks/tutorials/03_segmentation_app.ipynb +++ b/notebooks/tutorials/03_segmentation_app.ipynb @@ -92,23 +92,21 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "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", - "/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", + "/home/mqin/src/md-app-sdk/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": [ "# Install MONAI and other necessary image processing packages for the application\n", - "!python -c \"import monai\" || pip install --upgrade -q \"monai<=1.5.0\"\n", + "!python -c \"import monai\" || pip install --upgrade -q \"monai\"\n", "!python -c \"import torch\" || pip install -q \"torch>=1.10.2\"\n", "!python -c \"import numpy\" || pip install -q \"numpy>=1.21\"\n", "!python -c \"import nibabel\" || pip install -q \"nibabel>=3.2.1\"\n", @@ -407,7 +405,7 @@ "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", + "/home/mqin/src/md-app-sdk/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" ] } @@ -569,7 +567,7 @@ " resample=False,\n", " output_ext=\".nii\",\n", " ),\n", - " Orientationd(keys=my_key, axcodes=\"RAS\"),\n", + " Orientationd(keys=my_key, axcodes=\"LPS\"),\n", " Spacingd(keys=my_key, pixdim=[1.5, 1.5, 2.9], mode=[\"bilinear\"]),\n", " ScaleIntensityRanged(keys=my_key, a_min=-57, a_max=164, b_min=0.0, b_max=1.0, clip=True),\n", " EnsureTyped(keys=my_key),\n", @@ -751,109 +749,116 @@ "output_type": "stream", "text": [ "[info] [fragment.cpp:969] Loading extensions from configs...\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", + "[2025-09-29 23:44:21,073] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=[])\n", + "[2025-09-29 23:44:21,081] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", + "[2025-09-29 23:44:21,082] [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", - "[2025-09-04 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", + "[2025-09-29 23:44:21,243] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-09-29 23:44:21,732] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-09-29 23:44:21,733] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\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", + "[2025-09-29 23:44:21,734] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-29 23:44:21,734] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-09-29 23:44:21,735] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-09-29 23:44:21,736] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-09-29 23:44:21,737] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-09-29 23:44:21,737] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-09-29 23:44:21,738] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-09-29 23:44:21,739] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-09-29 23:44:21,739] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-09-29 23:44:21,740] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-09-29 23:44:21,741] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-29 23:44:21,741] [INFO] (root) - Series Selection finalized\n", + "[2025-09-29 23:44:21,742] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-09-29 23:44:21,743] [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", + "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/utils/deprecate_utils.py:321: FutureWarning: monai.transforms.spatial.dictionary Orientationd.__init__:labels: Current default value of argument `labels=(('L', 'R'), ('P', 'A'), ('I', 'S'))` was changed in version None from `labels=(('L', 'R'), ('P', 'A'), ('I', 'S'))` to `labels=None`. Default value changed to None meaning that the transform now uses the 'space' of a meta-tensor, if applicable, to determine appropriate axis labels.\n", + " warn_deprecated(argname, msg, warning_category)\n", + "[2025-09-29 23:44:22,119] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-09-29 23:44:22,121] [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", + "[2025-09-29 23:44:22,122] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-09-29 23:44:22,123] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-09-29 23:44:22,124] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-09-29 23:44:22,125] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-09-29 23:44:22,126] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-09-29 23:44:22,126] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-09-29 23:44:22,127] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-09-29 23:44:22,128] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-09-29 23:44:22,129] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-09-29 23:44:22,129] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-09-29 23:44:22,130] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-09-29 23:44:22,130] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2025-09-29 23:44:22,131] [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", - "[2025-09-04 18:15:52,632] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-09-29 23:44:22,132] [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", - "[2025-09-04 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" + "[2025-09-29 23:44:22,133] [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", + "[2025-09-29 23:44:22,133] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-09-29 23:44:22,134] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-09-29 23:44:22,134] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-09-29 23:44:22,135] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-09-29 23:44:22,135] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-09-29 23:44:22,140] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "[2025-09-29 23:44:22,141] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - space: LPS, type \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "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" + "2025-09-29 23:44:22,776 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": [ - "[2025-09-04 18:15:55,072] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n" + "[2025-09-29 23:44:24,436] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/inferers/utils.py:226: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)\n", + " win_data = torch.cat([inputs[win_slice] for win_slice in unravel_slice]).to(sw_device)\n", + "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/inferers/utils.py:370: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)\n", + " out[idx_zm] += p\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "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" + "2025-09-29 23:44:25,454 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": [ - "[2025-09-04 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", + "[2025-09-29 23:44:26,921] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-09-29 23:44:26,923] [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", + "[2025-09-29 23:44:27,049] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-09-29 23:44:27,089] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-09-29 23:44:27,095] [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", " check_person_name(patient_name)\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", + "[2025-09-29 23:44:28,454] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-29 23:44:28,455] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-09-29 23:44:28,456] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-29 23:44:28,457] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-09-29 23:44:28,458] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-09-29 23:44:28,459] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-29 23:44:28,460] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-09-29 23:44:28,460] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-09-29 23:44:28,461] [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", - "[2025-09-04 18:15:59,132] [INFO] (__main__.AISpleenSegApp) - End run\n" + "[2025-09-29 23:44:28,569] [INFO] (__main__.AISpleenSegApp) - End run\n" ] } ], @@ -1032,7 +1037,7 @@ " resample=False,\n", " output_ext=\".nii\",\n", " ),\n", - " Orientationd(keys=my_key, axcodes=\"RAS\"),\n", + " Orientationd(keys=my_key, axcodes=\"LPS\"),\n", " Spacingd(keys=my_key, pixdim=[1.5, 1.5, 2.9], mode=[\"bilinear\"]),\n", " ScaleIntensityRanged(keys=my_key, a_min=-57, a_max=164, b_min=0.0, b_max=1.0, clip=True),\n", " EnsureTyped(keys=my_key),\n", @@ -1292,88 +1297,95 @@ "name": "stdout", "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", + "/home/mqin/src/md-app-sdk/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", - "[2025-09-04 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", + "[2025-09-29 23:44:32,617] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, triton_server_netloc=None, argv=['my_app'])\n", + "[2025-09-29 23:44:32,620] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=), triton_server_netloc=\n", + "[2025-09-29 23:44:32,620] [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", - "[2025-09-04 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", + "[2025-09-29 23:44:32,742] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\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", + "[2025-09-29 23:44:33,040] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Series Selection finalized\n", + "[2025-09-29 23:44:33,040] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-09-29 23:44:33,040] [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", + "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/utils/deprecate_utils.py:321: FutureWarning: monai.transforms.spatial.dictionary Orientationd.__init__:labels: Current default value of argument `labels=(('L', 'R'), ('P', 'A'), ('I', 'S'))` was changed in version None from `labels=(('L', 'R'), ('P', 'A'), ('I', 'S'))` to `labels=None`. Default value changed to None meaning that the transform now uses the 'space' of a meta-tensor, if applicable, to determine appropriate axis labels.\n", + " warn_deprecated(argname, msg, warning_category)\n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-09-29 23:44:33,404] [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", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2025-09-29 23:44:33,404] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2025-09-29 23:44:33,405] [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", - "[2025-09-04 18:16:04,993] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2025-09-29 23:44:33,405] [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", - "[2025-09-04 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", + "[2025-09-29 23:44:33,405] [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", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "[2025-09-29 23:44:33,405] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - space: LPS, type \n", + "2025-09-29 23:44:34,044 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", + "[2025-09-29 23:44:35,794] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/inferers/utils.py:226: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)\n", + " win_data = torch.cat([inputs[win_slice] for win_slice in unravel_slice]).to(sw_device)\n", + "/home/mqin/src/md-app-sdk/.venv/lib/python3.10/site-packages/monai/inferers/utils.py:370: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)\n", + " out[idx_zm] += p\n", + "2025-09-29 23:44:36,872 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", + "[2025-09-29 23:44:38,317] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-09-29 23:44:38,318] [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", + "[2025-09-29 23:44:38,443] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-09-29 23:44:38,482] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", + "[2025-09-29 23:44:38,487] [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", " check_person_name(patient_name)\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", + "[2025-09-29 23:44:39,777] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-29 23:44:39,777] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-09-29 23:44:39,777] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-29 23:44:39,777] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-09-29 23:44:39,778] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-09-29 23:44:39,778] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2025-09-29 23:44:39,778] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-09-29 23:44:39,778] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-09-29 23:44:39,778] [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", - "[2025-09-04 18:16:11,344] [INFO] (app.AISpleenSegApp) - End run\n", + "[2025-09-29 23:44:39,872] [INFO] (app.AISpleenSegApp) - End run\n", "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:379] Destroying context\n" ] } @@ -1393,7 +1405,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.76468060613059000496618284304659134.dcm\n", + "1.2.826.0.1.3680043.10.511.3.29717756681998834683338751730398576.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", @@ -1493,23 +1505,23 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[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", + "[2025-09-29 23:44:41,781] [INFO] (common) - Downloading CLI manifest file...\n", + "[2025-09-29 23:44:41,978] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2025-09-29 23:44:41,980] [INFO] (packager.parameters) - Application: /home/mqin/src/md-app-sdk/notebooks/tutorials/my_app\n", + "[2025-09-29 23:44:41,981] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2025-09-29 23:44:41,981] [INFO] (packager) - Scanning for models in /home/mqin/src/md-app-sdk/notebooks/tutorials/models...\n", + "[2025-09-29 23:44:41,981] [DEBUG] (packager) - Model model=/home/mqin/src/md-app-sdk/notebooks/tutorials/models/model added.\n", + "[2025-09-29 23:44:41,981] [INFO] (packager) - Reading application configuration from /home/mqin/src/md-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", + "[2025-09-29 23:44:41,985] [INFO] (packager) - Generating app.json...\n", + "[2025-09-29 23:44:41,985] [INFO] (packager) - Generating pkg.json...\n", + "[2025-09-29 23:44:41,989] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1544,7 +1556,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2025-09-04 18:26:44,605] [DEBUG] (common) - \n", + "[2025-09-29 23:44:41,989] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1564,18 +1576,18 @@ "}\n", "================ End pkg.json ================\n", " \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", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - ================ Begin requirements.txt ================\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - highdicom>=0.18.2\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - monai>=1.0\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - nibabel>=3.2.1\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - numpy>=1.21.6\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - pydicom>=2.3.0\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - setuptools>=59.5.0 # for pkg_resources\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - SimpleITK>=2.0.0\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - torch>=1.12.0\n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - \n", + "[2025-09-29 23:44:42,011] [DEBUG] (packager.builder) - ================ End requirements.txt ==================\n", + "[2025-09-29 23:44:42,012] [DEBUG] (packager.builder) - \n", "========== Begin Build Parameters ==========\n", "{'add_hosts': None,\n", " 'additional_lib_paths': '',\n", @@ -1619,25 +1631,25 @@ " 'working_dir': PosixPath('/var/holoscan')}\n", "=========== End Build Parameters ===========\n", "\n", - "[2025-09-04 18:26:44,630] [DEBUG] (packager.builder) - \n", + "[2025-09-29 23:44:42,012] [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", " 'cuda_deb_arch': 'x86_64',\n", " 'custom_base_image': False,\n", " 'custom_holoscan_sdk': False,\n", - " 'custom_monai_deploy_sdk': True,\n", + " 'custom_monai_deploy_sdk': False,\n", " 'gpu_type': 'dgpu',\n", " 'holoscan_deb_arch': 'amd64',\n", " 'holoscan_sdk_file': '3.5.0',\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+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", + " 'monai_deploy_sdk_file': None,\n", + " 'monai_deploy_sdk_filename': None,\n", " 'tag': 'my_app:1.0',\n", " 'target_arch': 'x86_64'}\n", "=========== End Platform Parameters ===========\n", "\n", - "[2025-09-04 18:26:44,650] [DEBUG] (packager.builder) - \n", + "[2025-09-29 23:44:42,029] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "ARG GPU_TYPE=dgpu\n", @@ -1776,9 +1788,10 @@ "\n", "\n", "# Install MONAI Deploy App SDK\n", - "# Copy user-specified MONAI Deploy SDK file\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", + "# Install MONAI Deploy from PyPI org\n", + "RUN pip install monai-deploy-app-sdk==1.0.0\n", + "\n", "\n", "COPY ./models /opt/holoscan/models\n", "\n", @@ -1794,9 +1807,9 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\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", + "[2025-09-29 23:44:42,728] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2025-09-29 23:44:42,729] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2025-09-29 23:44:42,729] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", @@ -1805,7 +1818,7 @@ " 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+28.g7da6e97.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: N/A\n", " gRPC Health Probe: N/A\n", " SDK Version: 3.5.0\n", " SDK: monai-deploy\n", @@ -1815,367 +1828,264 @@ "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 4.94kB done\n", + "#1 transferring dockerfile: 4.76kB done\n", "#1 DONE 0.1s\n", "\n", - "#2 [auth] nvidia/cuda:pull token for nvcr.io\n", - "#2 DONE 0.0s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", + "#2 ...\n", "\n", - "#3 [internal] load metadata for nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", - "#3 DONE 0.8s\n", + "#3 [auth] nvidia/cuda:pull token for nvcr.io\n", + "#3 DONE 0.0s\n", + "\n", + "#2 [internal] load metadata for nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", + "#2 DONE 0.5s\n", "\n", "#4 [internal] load .dockerignore\n", "#4 transferring context: 1.80kB done\n", "#4 DONE 0.1s\n", "\n", - "#5 [internal] load build context\n", - "#5 DONE 0.0s\n", + "#5 importing cache manifest from nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", + "#5 ...\n", "\n", - "#6 importing cache manifest from local:2981386072432009811\n", - "#6 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", + "#6 [internal] load build context\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 0.0s done\n", + "#7 importing cache manifest from local:1788272027054474049\n", + "#7 inferred cache manifest type: application/vnd.oci.image.index.v1+json 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 0.3s\n", + "#5 importing cache manifest from nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04\n", + "#5 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", + "#5 DONE 0.4s\n", + "\n", + "#8 [base 1/2] FROM nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04@sha256:ebef3c171eeef0298e4eb2e4be843105edf3b8b0ac45e0b43acee358e8046867\n", + "#8 resolve nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04@sha256:ebef3c171eeef0298e4eb2e4be843105edf3b8b0ac45e0b43acee358e8046867 0.1s done\n", + "#8 DONE 0.1s\n", "\n", - "#5 [internal] load build context\n", - "#5 transferring context: 19.57MB 0.2s done\n", - "#5 DONE 0.3s\n", + "#6 [internal] load build context\n", + "#6 transferring context: 19.43MB 0.1s done\n", + "#6 DONE 0.2s\n", "\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 [release 1/20] 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", "#9 CACHED\n", "\n", - "#10 [release 13/21] RUN pip install --upgrade pip\n", + "#10 [release 7/20] WORKDIR /var/holoscan\n", "#10 CACHED\n", "\n", - "#11 [release 9/21] RUN chmod +x /var/holoscan/tools\n", + "#11 [release 10/20] RUN rm -rf /usr/lib/python3.12/EXTERNALLY-MANAGED\n", "#11 CACHED\n", "\n", - "#12 [release 8/21] COPY ./tools /var/holoscan/tools\n", + "#12 [release 11/20] WORKDIR /var/holoscan\n", "#12 CACHED\n", "\n", - "#13 [release 11/21] WORKDIR /var/holoscan\n", + "#13 [release 6/20] RUN chown -R holoscan /var/holoscan && chown -R holoscan /var/holoscan/input && chown -R holoscan /var/holoscan/output\n", "#13 CACHED\n", "\n", - "#14 [release 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", + "#14 [release 5/20] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#14 CACHED\n", "\n", - "#15 [release 7/21] WORKDIR /var/holoscan\n", + "#15 [release 2/20] 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", "#15 CACHED\n", "\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 [release 9/20] RUN chmod +x /var/holoscan/tools\n", "#16 CACHED\n", "\n", - "#17 [release 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#17 [release 3/20] RUN if id \"ubuntu\" >/dev/null 2>&1; then touch /var/mail/ubuntu && chown ubuntu /var/mail/ubuntu && userdel -r ubuntu; fi\n", "#17 CACHED\n", "\n", - "#18 [release 10/21] RUN rm -rf /usr/lib/python3.12/EXTERNALLY-MANAGED\n", + "#18 [release 8/20] COPY ./tools /var/holoscan/tools\n", "#18 CACHED\n", "\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 [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", "#19 CACHED\n", "\n", - "#20 [release 12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#20 [release 4/20] RUN groupadd -f -g 1000 holoscan\n", "#20 CACHED\n", "\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 [release 12/20] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#21 CACHED\n", "\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 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 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 79.6s done\n", - "#23 CACHED\n", - "\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 tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.315 Downloading tritonclient-2.60.0-py3-none-manylinux1_x86_64.whl.metadata (2.8 kB)\n", - "#25 1.377 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.381 Downloading typeguard-4.4.4-py3-none-any.whl.metadata (3.3 kB)\n", - "#25 1.390 Requirement already satisfied: pip>22.0.2 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (25.2)\n", - "#25 1.429 Collecting cupy-cuda12x<14.0,>=12.2 (from holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.438 Downloading cupy_cuda12x-13.6.0-cp312-cp312-manylinux2014_x86_64.whl.metadata (2.4 kB)\n", - "#25 1.491 Collecting cloudpickle<4.0,>=3.0 (from holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.497 Downloading cloudpickle-3.1.1-py3-none-any.whl.metadata (7.1 kB)\n", - "#25 1.508 Requirement already satisfied: pillow>=11.2 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (11.3.0)\n", - "#25 1.595 Collecting wheel-axle-runtime<1.0 (from holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.607 Downloading wheel_axle_runtime-0.0.7-py3-none-any.whl.metadata (8.3 kB)\n", - "#25 1.682 Collecting fastrlock>=0.5 (from cupy-cuda12x<14.0,>=12.2->holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.688 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 1.696 Requirement already satisfied: Jinja2<4.0.0,>=3.1.6 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (3.1.6)\n", - "#25 1.696 Requirement already satisfied: packaging<26.0,>=25.0 in /home/holoscan/.local/lib/python3.12/site-packages (from holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (25.0)\n", - "#25 1.826 Collecting psutil<8.0,>=7.0.0 (from holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.830 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 1.928 Collecting python-on-whales>=0.77.0 (from holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 1.938 Downloading python_on_whales-0.78.0-py3-none-any.whl.metadata (18 kB)\n", - "#25 2.029 Collecting pyyaml<7.0,>=6.0 (from holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.033 Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)\n", - "#25 2.108 Collecting requests<3.0,>=2.32 (from holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.112 Downloading requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)\n", - "#25 2.130 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~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (3.0.2)\n", - "#25 2.263 Collecting charset_normalizer<4,>=2 (from requests<3.0,>=2.32->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.268 Downloading charset_normalizer-3.4.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (36 kB)\n", - "#25 2.333 Collecting idna<4,>=2.5 (from requests<3.0,>=2.32->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.337 Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)\n", - "#25 2.422 Collecting urllib3<3,>=1.21.1 (from requests<3.0,>=2.32->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.425 Downloading urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)\n", - "#25 2.501 Collecting certifi>=2017.4.17 (from requests<3.0,>=2.32->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.506 Downloading certifi-2025.8.3-py3-none-any.whl.metadata (2.4 kB)\n", - "#25 2.535 Requirement already satisfied: filelock in /home/holoscan/.local/lib/python3.12/site-packages (from wheel-axle-runtime<1.0->holoscan~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (3.18.0)\n", - "#25 2.708 Collecting pydantic!=2.0.*,<3,>=2 (from python-on-whales>=0.77.0->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.712 Downloading pydantic-2.11.7-py3-none-any.whl.metadata (67 kB)\n", - "#25 2.731 Requirement already satisfied: typing-extensions in /home/holoscan/.local/lib/python3.12/site-packages (from python-on-whales>=0.77.0->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty) (4.14.1)\n", - "#25 2.770 Collecting annotated-types>=0.6.0 (from pydantic!=2.0.*,<3,>=2->python-on-whales>=0.77.0->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 2.777 Downloading annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)\n", - "#25 3.462 Collecting pydantic-core==2.33.2 (from pydantic!=2.0.*,<3,>=2->python-on-whales>=0.77.0->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 3.466 Downloading pydantic_core-2.33.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB)\n", - "#25 3.522 Collecting typing-inspection>=0.4.0 (from pydantic!=2.0.*,<3,>=2->python-on-whales>=0.77.0->holoscan-cli~=3.5.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 3.530 Downloading typing_inspection-0.4.1-py3-none-any.whl.metadata (2.6 kB)\n", - "#25 3.683 Collecting python-rapidjson>=0.9.1 (from tritonclient>=2.53.0->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 3.688 Downloading python_rapidjson-1.21-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (23 kB)\n", - "#25 4.293 Collecting aiohttp<4.0.0,>=3.8.1 (from tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 4.297 Downloading aiohttp-3.12.15-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)\n", - "#25 4.378 Collecting cuda-python (from tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 4.384 Downloading cuda_python-13.0.1-py3-none-any.whl.metadata (4.7 kB)\n", - "#25 4.539 Collecting geventhttpclient>=2.3.3 (from tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 4.544 Downloading geventhttpclient-2.3.4-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (8.4 kB)\n", - "#25 5.137 Collecting grpcio<1.68,>=1.63.0 (from tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 5.151 Downloading grpcio-1.67.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)\n", - "#25 5.373 Collecting protobuf<6.0dev,>=5.26.1 (from tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 5.379 Downloading protobuf-5.29.5-cp38-abi3-manylinux2014_x86_64.whl.metadata (592 bytes)\n", - "#25 5.444 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 5.463 Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)\n", - "#25 5.508 Collecting aiosignal>=1.4.0 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 5.517 Downloading aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)\n", - "#25 5.584 Collecting attrs>=17.3.0 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 5.608 Downloading attrs-25.3.0-py3-none-any.whl.metadata (10 kB)\n", - "#25 5.755 Collecting frozenlist>=1.1.1 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 5.797 Downloading frozenlist-1.7.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)\n", - "#25 6.183 Collecting multidict<7.0,>=4.5 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 6.187 Downloading multidict-6.6.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)\n", - "#25 6.286 Collecting propcache>=0.2.0 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 6.291 Downloading propcache-0.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)\n", - "#25 6.593 Collecting yarl<2.0,>=1.17.0 (from aiohttp<4.0.0,>=3.8.1->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 6.597 Downloading yarl-1.20.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB)\n", - "#25 6.776 Collecting gevent (from geventhttpclient>=2.3.3->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 6.782 Downloading gevent-25.8.2-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (14 kB)\n", - "#25 6.891 Collecting brotli (from geventhttpclient>=2.3.3->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 6.895 Downloading Brotli-1.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB)\n", - "#25 6.963 Collecting cuda-bindings~=13.0.1 (from cuda-python->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 6.969 Downloading cuda_bindings-13.0.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)\n", - "#25 7.031 Collecting cuda-pathfinder~=1.1 (from cuda-python->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 7.040 Downloading cuda_pathfinder-1.2.1-py3-none-any.whl.metadata (3.1 kB)\n", - "#25 7.230 Collecting greenlet>=3.2.2 (from gevent->geventhttpclient>=2.3.3->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 7.233 Downloading greenlet-3.2.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (4.1 kB)\n", - "#25 7.291 Collecting zope.event (from gevent->geventhttpclient>=2.3.3->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 7.300 Downloading zope_event-5.1.1-py3-none-any.whl.metadata (5.0 kB)\n", - "#25 7.443 Collecting zope.interface (from gevent->geventhttpclient>=2.3.3->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 7.458 Downloading zope.interface-7.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (44 kB)\n", - "#25 7.756 Collecting setuptools>=75.8.2 (from zope.event->gevent->geventhttpclient>=2.3.3->tritonclient[all]>=2.53.0->monai-deploy-app-sdk==1.0.0+28.g7da6e97.dirty)\n", - "#25 7.761 Downloading setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)\n", - "#25 7.806 Downloading holoscan-3.5.0-cp312-cp312-manylinux_2_35_x86_64.whl (40.6 MB)\n", - "#25 8.582 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.6/40.6 MB 52.3 MB/s 0:00:00\n", - "#25 8.587 Downloading cloudpickle-3.1.1-py3-none-any.whl (20 kB)\n", - "#25 8.609 Downloading cupy_cuda12x-13.6.0-cp312-cp312-manylinux2014_x86_64.whl (112.9 MB)\n", - "#25 10.41 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 112.9/112.9 MB 62.8 MB/s 0:00:01\n", - "#25 10.48 Downloading holoscan_cli-3.5.0-py3-none-any.whl (73 kB)\n", - "#25 10.51 Downloading psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (277 kB)\n", - "#25 10.53 Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (767 kB)\n", - "#25 10.57 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 767.5/767.5 kB 19.3 MB/s 0:00:00\n", - "#25 10.57 Downloading requests-2.32.5-py3-none-any.whl (64 kB)\n", - "#25 10.60 Downloading charset_normalizer-3.4.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (151 kB)\n", - "#25 10.62 Downloading idna-3.10-py3-none-any.whl (70 kB)\n", - "#25 10.65 Downloading urllib3-2.5.0-py3-none-any.whl (129 kB)\n", - "#25 10.67 Downloading wheel_axle_runtime-0.0.7-py3-none-any.whl (14 kB)\n", - "#25 10.69 Downloading certifi-2025.8.3-py3-none-any.whl (161 kB)\n", - "#25 10.72 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", - "#25 10.74 Downloading 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 aiohttp-3.12.15-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB)\n", - "#25 11.34 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 39.6 MB/s 0:00:00\n", - "#25 11.35 Downloading grpcio-1.67.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.9 MB)\n", - "#25 11.57 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.9/5.9 MB 26.0 MB/s 0:00:00\n", - "#25 11.58 Downloading multidict-6.6.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (256 kB)\n", - "#25 11.61 Downloading protobuf-5.29.5-cp38-abi3-manylinux2014_x86_64.whl (319 kB)\n", - "#25 11.63 Downloading yarl-1.20.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (355 kB)\n", - "#25 11.66 Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)\n", - "#25 11.68 Downloading aiosignal-1.4.0-py3-none-any.whl (7.5 kB)\n", - "#25 11.70 Downloading attrs-25.3.0-py3-none-any.whl (63 kB)\n", - "#25 11.73 Downloading frozenlist-1.7.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (241 kB)\n", - "#25 11.76 Downloading geventhttpclient-2.3.4-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (114 kB)\n", - "#25 11.78 Downloading propcache-0.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (224 kB)\n", - "#25 11.80 Downloading typeguard-4.4.4-py3-none-any.whl (34 kB)\n", - "#25 11.83 Downloading typing_inspection-0.4.1-py3-none-any.whl (14 kB)\n", - "#25 11.85 Downloading Brotli-1.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.9 MB)\n", - "#25 11.91 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.9/2.9 MB 47.0 MB/s 0:00:00\n", - "#25 11.93 Downloading cuda_python-13.0.1-py3-none-any.whl (7.6 kB)\n", - "#25 11.96 Downloading cuda_bindings-13.0.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.3 MB)\n", - "#25 12.21 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.3/12.3 MB 49.6 MB/s 0:00:00\n", - "#25 12.22 Downloading cuda_pathfinder-1.2.1-py3-none-any.whl (22 kB)\n", - "#25 12.24 Downloading gevent-25.8.2-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (2.1 MB)\n", - "#25 12.28 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 44.7 MB/s 0:00:00\n", - "#25 12.30 Downloading greenlet-3.2.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (607 kB)\n", - "#25 12.32 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 607.6/607.6 kB 15.9 MB/s 0:00:00\n", - "#25 12.33 Downloading zope_event-5.1.1-py3-none-any.whl (7.0 kB)\n", - "#25 12.36 Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB)\n", - "#25 12.39 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 30.2 MB/s 0:00:00\n", - "#25 12.41 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 13.04 Installing collected packages: fastrlock, 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-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", - "\n", - "#27 [release 18/21] COPY ./map/app.json /etc/holoscan/app.json\n", - "#27 DONE 0.1s\n", - "\n", - "#28 [release 19/21] COPY ./app.config /var/holoscan/app.yaml\n", - "#28 DONE 0.1s\n", - "\n", - "#29 [release 20/21] COPY ./map/pkg.json /etc/holoscan/pkg.json\n", - "#29 DONE 0.1s\n", - "\n", - "#30 [release 21/21] COPY ./app /opt/holoscan/app\n", - "#30 DONE 0.1s\n", - "\n", - "#31 exporting to docker image format\n", - "#31 exporting layers\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 fffcb65df949 32.77kB / 137.08kB\n", - "#32 loading layer 2178ec0bf8a1 557.06kB / 419.44MB\n", - "#32 loading layer 2178ec0bf8a1 159.32MB / 419.44MB 2.1s\n", - "#32 loading layer 2178ec0bf8a1 233.96MB / 419.44MB 4.3s\n", - "#32 loading layer 2178ec0bf8a1 344.26MB / 419.44MB 8.4s\n", - "#32 loading layer 2178ec0bf8a1 379.36MB / 419.44MB 10.4s\n", - "#32 loading layer 2178ec0bf8a1 419.44MB / 419.44MB 12.6s\n", - "#32 loading layer 4d2c412f9127 196.61kB / 17.81MB\n", - "#32 loading layer f8150b55fcf2 489B / 489B\n", - "#32 loading layer 1f280f035fad 316B / 316B\n", - "#32 loading layer 715c9abab80b 303B / 303B\n", - "#32 loading layer 7b32e5073096 3.91kB / 3.91kB\n", - "#32 loading layer 7b32e5073096 3.91kB / 3.91kB 0.6s done\n", - "#32 loading layer fffcb65df949 137.08kB / 137.08kB 14.0s done\n", - "#32 loading layer 2178ec0bf8a1 419.44MB / 419.44MB 13.8s done\n", - "#32 loading layer 4d2c412f9127 17.81MB / 17.81MB 1.1s done\n", - "#32 loading layer f8150b55fcf2 489B / 489B 0.8s done\n", - "#32 loading layer 1f280f035fad 316B / 316B 0.7s done\n", - "#32 loading layer 715c9abab80b 303B / 303B 0.7s done\n", - "#32 DONE 14.0s\n", - "\n", - "#31 exporting to docker image format\n", - "#31 sending tarball 52.3s done\n", - "#31 DONE 76.2s\n", - "\n", - "#33 exporting cache to client directory\n", - "#33 preparing build cache for export\n", - "#33 writing layer sha256:0485e1ad7d46995100cf1b77f4ca14706112dd0c6ec89a4b27417fb530d97bc1\n", - "#33 writing layer sha256:0485e1ad7d46995100cf1b77f4ca14706112dd0c6ec89a4b27417fb530d97bc1 done\n", - "#33 writing layer sha256:05ec76e31584ec109785cc7045bd88df0240411233c2fcdad66b621c662034c0 done\n", - "#33 writing layer sha256:071ee33ea2913f8a44d367ce1fac3948d244a01a0e58677d20e3d1b11881f63a done\n", - "#33 writing layer sha256:398182656c471d6ecca3c2d6d30e97193b40ffc8028a94515093960322f3d64e done\n", - "#33 writing layer sha256:3a0580ebaa42b1bf4000a30bc41f7eb7515781cacf3decd4477a0cc5a8ab1c6b 0.0s done\n", - "#33 writing layer sha256:3d6ab8c799cda2f4c6a6277b0e24dd2231c5de83b0316968b7cce81156bb8be0 done\n", - "#33 writing layer sha256:412478cd44c10aeead18c6d42d36b15001877642f4898482ae43e9d64943816c\n", - "#33 writing layer sha256:412478cd44c10aeead18c6d42d36b15001877642f4898482ae43e9d64943816c 0.4s done\n", - "#33 writing layer sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1\n", - "#33 writing layer sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 done\n", - "#33 writing layer sha256:545a3ada5b6bc612a11c13a659775d67eeda5a61615e7f49c76ecd24adcad626 done\n", - "#33 writing layer sha256:55beb86aff885ea504c9f3229987dd7d44ac9f79c50673fec06a77f351a8d370 0.0s done\n", - "#33 writing layer sha256:5a7813e071bfadf18aaa6ca8318be4824a9b6297b3240f2cc84c1db6f4113040 done\n", - "#33 writing layer sha256:65398c5cd3c9452772de9b83589458c4c36ad14755dc157ad9948b6957c22d2c 0.0s done\n", - "#33 writing layer sha256:670825eb703e30d051d7c75ca2435361313a82247e9efbbb35022bd79ba7acdc done\n", - "#33 writing layer sha256:7209097bfb98d6f8b422984480f1fddead5ea62f8900ff6b6548e060b71aca76 done\n", - "#33 writing layer sha256:73389fbd088f5ed5d9fd258baced59de092978b4f483920ea6d074522a105119 done\n", - "#33 writing layer sha256:882067111f43dcefcfb9978ba194a78f79bf241e8fda47517aa249574d08d23e done\n", - "#33 writing layer sha256:8a4d2334f6482fc11525d35c7cac493392668299e692ce7a4c81a3ffa8cec81d 0.0s done\n", - "#33 writing layer sha256:9bcf3fca67a2ec66412c29446355d00fd60dc631766810af7e14fa9f68122f89 0.0s done\n", - "#33 writing layer sha256:9d7b7f0b8d0d1b0dc0d04230b9af8705ef56d7881728bc8439d94f34e2b346fa\n", - "#33 writing layer sha256:9d7b7f0b8d0d1b0dc0d04230b9af8705ef56d7881728bc8439d94f34e2b346fa done\n", - "#33 writing layer sha256:a102f36d092c0e9e0bef8c97854f606af9156aa36ab408e6fa4b88e27124a7e6 done\n", - "#33 writing layer sha256:a7e0585aa1334f827ee888d93df571cf5ca476e64f9d6fc41514d685358b50a1 done\n", - "#33 writing layer sha256:b8641f6fe7613397c5a2b24da0b0a541c2511ef1e0347be3cb2139ff622a0f2c done\n", - "#33 writing layer sha256:c5b0ebd4c7a351c4b972af1cfebad9e226e1f3e151dada98a607f838751c4bfa done\n", - "#33 writing layer sha256:cbb9175a9bc5f6553f8c0c5025ea9521898b8a3956ee24798dc35c24c6185053 done\n", - "#33 writing layer sha256:cd8285169945900d649da229211c6cc1c69607bd85875e5afa9b01f051815aa1 done\n", - "#33 writing layer sha256:cde14b3f73510edb711cb4c12549cb989f8979805cb15be6701a93315d22cc34 done\n", - "#33 writing layer sha256:d14c0c9ac374a3716bbffda1b99c321e0da9112a55c52b6092fbb69c06c4f08c done\n", - "#33 writing layer sha256:d1db3e659f189f3ff72fe162270a2d87d36dc187a10dca62d5b63a2561c2ab01\n", - "#33 writing layer sha256:d1db3e659f189f3ff72fe162270a2d87d36dc187a10dca62d5b63a2561c2ab01 6.7s done\n", - "#33 writing layer sha256:d960bf65a541a1e0a07996511018156f53db3892491a48235285d7b949718940\n", - "#33 preparing build cache for export 7.5s done\n", - "#33 writing layer sha256:d960bf65a541a1e0a07996511018156f53db3892491a48235285d7b949718940 done\n", - "#33 writing layer sha256:dc8ef917f4d947ac946de58bbd3e597df3eccf6d3114660dc1d10ac65d4c9292 done\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", + "#22 [release 13/20] RUN pip install --upgrade pip\n", + "#22 0.820 Defaulting to user installation because normal site-packages is not writeable\n", + "#22 0.889 Requirement already satisfied: pip in /usr/lib/python3/dist-packages (24.0)\n", + "#22 1.093 Collecting pip\n", + "#22 1.158 Downloading pip-25.2-py3-none-any.whl.metadata (4.7 kB)\n", + "#22 1.192 Downloading pip-25.2-py3-none-any.whl (1.8 MB)\n", + "#22 1.273 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 23.4 MB/s eta 0:00:00\n", + "#22 1.306 Installing collected packages: pip\n", + "#22 2.113 Successfully installed pip-25.2\n", + "#22 DONE 3.1s\n", + "\n", + "#23 [release 14/20] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", + "#23 0.669 Collecting highdicom>=0.18.2 (from -r /tmp/requirements.txt (line 1))\n", + "#23 0.707 Downloading highdicom-0.26.1-py3-none-any.whl.metadata (5.8 kB)\n", + "#23 0.741 Collecting monai>=1.0 (from -r /tmp/requirements.txt (line 2))\n", + "#23 0.747 Downloading monai-1.5.1-py3-none-any.whl.metadata (13 kB)\n", + "#23 0.789 Collecting nibabel>=3.2.1 (from -r /tmp/requirements.txt (line 3))\n", + "#23 0.793 Downloading nibabel-5.3.2-py3-none-any.whl.metadata (9.1 kB)\n", + "#23 0.977 Collecting numpy>=1.21.6 (from -r /tmp/requirements.txt (line 4))\n", + "#23 0.980 Downloading numpy-2.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)\n", + "#23 1.014 Collecting pydicom>=2.3.0 (from -r /tmp/requirements.txt (line 5))\n", + "#23 1.019 Downloading pydicom-3.0.1-py3-none-any.whl.metadata (9.4 kB)\n", + "#23 1.026 Requirement already satisfied: setuptools>=59.5.0 in /usr/lib/python3/dist-packages (from -r /tmp/requirements.txt (line 6)) (68.1.2)\n", + "#23 1.055 Collecting SimpleITK>=2.0.0 (from -r /tmp/requirements.txt (line 7))\n", + "#23 1.062 Downloading simpleitk-2.5.2-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.2 kB)\n", + "#23 1.107 Collecting torch>=1.12.0 (from -r /tmp/requirements.txt (line 8))\n", + "#23 1.110 Downloading torch-2.8.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (30 kB)\n", + "#23 1.257 Collecting pillow>=8.3 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 1))\n", + "#23 1.260 Downloading pillow-11.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)\n", + "#23 1.361 Collecting pyjpegls>=1.0.0 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 1))\n", + "#23 1.366 Downloading pyjpegls-1.5.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.5 kB)\n", + "#23 1.391 Collecting typing-extensions>=4.0.0 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 1))\n", + "#23 1.395 Downloading typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)\n", + "#23 1.433 Collecting packaging>=20 (from nibabel>=3.2.1->-r /tmp/requirements.txt (line 3))\n", + "#23 1.436 Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB)\n", + "#23 1.456 Collecting filelock (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.460 Downloading filelock-3.19.1-py3-none-any.whl.metadata (2.1 kB)\n", + "#23 1.477 Collecting sympy>=1.13.3 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.480 Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)\n", + "#23 1.496 Collecting networkx (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.499 Downloading networkx-3.5-py3-none-any.whl.metadata (6.3 kB)\n", + "#23 1.513 Collecting jinja2 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.517 Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)\n", + "#23 1.533 Collecting fsspec (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.536 Downloading fsspec-2025.9.0-py3-none-any.whl.metadata (10 kB)\n", + "#23 1.564 Collecting nvidia-cuda-nvrtc-cu12==12.8.93 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.567 Downloading nvidia_cuda_nvrtc_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.576 Collecting nvidia-cuda-runtime-cu12==12.8.90 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.579 Downloading nvidia_cuda_runtime_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.590 Collecting nvidia-cuda-cupti-cu12==12.8.90 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.593 Downloading nvidia_cuda_cupti_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.605 Collecting nvidia-cudnn-cu12==9.10.2.21 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.609 Downloading nvidia_cudnn_cu12-9.10.2.21-py3-none-manylinux_2_27_x86_64.whl.metadata (1.8 kB)\n", + "#23 1.619 Collecting nvidia-cublas-cu12==12.8.4.1 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.622 Downloading nvidia_cublas_cu12-12.8.4.1-py3-none-manylinux_2_27_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.632 Collecting nvidia-cufft-cu12==11.3.3.83 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.635 Downloading nvidia_cufft_cu12-11.3.3.83-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.646 Collecting nvidia-curand-cu12==10.3.9.90 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.649 Downloading nvidia_curand_cu12-10.3.9.90-py3-none-manylinux_2_27_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.659 Collecting nvidia-cusolver-cu12==11.7.3.90 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.663 Downloading nvidia_cusolver_cu12-11.7.3.90-py3-none-manylinux_2_27_x86_64.whl.metadata (1.8 kB)\n", + "#23 1.672 Collecting nvidia-cusparse-cu12==12.5.8.93 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.675 Downloading nvidia_cusparse_cu12-12.5.8.93-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.8 kB)\n", + "#23 1.682 Collecting nvidia-cusparselt-cu12==0.7.1 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.686 Downloading nvidia_cusparselt_cu12-0.7.1-py3-none-manylinux2014_x86_64.whl.metadata (7.0 kB)\n", + "#23 1.694 Collecting nvidia-nccl-cu12==2.27.3 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.699 Downloading nvidia_nccl_cu12-2.27.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.0 kB)\n", + "#23 1.711 Collecting nvidia-nvtx-cu12==12.8.90 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.714 Downloading nvidia_nvtx_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.8 kB)\n", + "#23 1.725 Collecting nvidia-nvjitlink-cu12==12.8.93 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.727 Downloading nvidia_nvjitlink_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.734 Collecting nvidia-cufile-cu12==1.13.1.3 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.738 Downloading nvidia_cufile_cu12-1.13.1.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.747 Collecting triton==3.4.0 (from torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.750 Downloading triton-3.4.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.7 kB)\n", + "#23 1.780 Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.784 Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)\n", + "#23 1.836 Collecting MarkupSafe>=2.0 (from jinja2->torch>=1.12.0->-r /tmp/requirements.txt (line 8))\n", + "#23 1.839 Downloading markupsafe-3.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)\n", + "#23 1.848 Downloading highdicom-0.26.1-py3-none-any.whl (1.1 MB)\n", + "#23 1.861 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 120.6 MB/s 0:00:00\n", + "#23 1.866 Downloading monai-1.5.1-py3-none-any.whl (2.7 MB)\n", + "#23 1.904 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 84.9 MB/s 0:00:00\n", + "#23 1.910 Downloading numpy-2.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)\n", + "#23 2.063 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.6/16.6 MB 111.2 MB/s 0:00:00\n", + "#23 2.069 Downloading nibabel-5.3.2-py3-none-any.whl (3.3 MB)\n", + "#23 2.100 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 119.8 MB/s 0:00:00\n", + "#23 2.106 Downloading pydicom-3.0.1-py3-none-any.whl (2.4 MB)\n", + "#23 2.129 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 117.9 MB/s 0:00:00\n", + "#23 2.134 Downloading simpleitk-2.5.2-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (52.6 MB)\n", + "#23 2.801 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.6/52.6 MB 79.2 MB/s 0:00:00\n", + "#23 2.808 Downloading torch-2.8.0-cp312-cp312-manylinux_2_28_x86_64.whl (887.9 MB)\n", + "#23 14.04 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 887.9/887.9 MB 72.2 MB/s 0:00:11\n", + "#23 14.04 Downloading nvidia_cublas_cu12-12.8.4.1-py3-none-manylinux_2_27_x86_64.whl (594.3 MB)\n", + "#23 19.72 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 594.3/594.3 MB 112.0 MB/s 0:00:05\n", + "#23 19.72 Downloading nvidia_cuda_cupti_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (10.2 MB)\n", + "#23 19.84 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.2/10.2 MB 88.5 MB/s 0:00:00\n", + "#23 19.85 Downloading nvidia_cuda_nvrtc_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (88.0 MB)\n", + "#23 20.65 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.0/88.0 MB 110.7 MB/s 0:00:00\n", + "#23 20.65 Downloading nvidia_cuda_runtime_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (954 kB)\n", + "#23 20.67 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 954.8/954.8 kB 115.9 MB/s 0:00:00\n", + "#23 20.67 Downloading nvidia_cudnn_cu12-9.10.2.21-py3-none-manylinux_2_27_x86_64.whl (706.8 MB)\n", + "#23 28.45 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 706.8/706.8 MB 93.5 MB/s 0:00:07\n", + "#23 28.46 Downloading nvidia_cufft_cu12-11.3.3.83-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (193.1 MB)\n", + "#23 30.82 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 193.1/193.1 MB 82.1 MB/s 0:00:02\n", + "#23 30.82 Downloading nvidia_cufile_cu12-1.13.1.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.2 MB)\n", + "#23 30.84 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 119.4 MB/s 0:00:00\n", + "#23 30.85 Downloading nvidia_curand_cu12-10.3.9.90-py3-none-manylinux_2_27_x86_64.whl (63.6 MB)\n", + "#23 31.50 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.6/63.6 MB 99.8 MB/s 0:00:00\n", + "#23 31.50 Downloading nvidia_cusolver_cu12-11.7.3.90-py3-none-manylinux_2_27_x86_64.whl (267.5 MB)\n", + "#23 34.93 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 267.5/267.5 MB 77.6 MB/s 0:00:03\n", + "#23 34.93 Downloading nvidia_cusparse_cu12-12.5.8.93-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (288.2 MB)\n", + "#23 38.45 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 MB 79.5 MB/s 0:00:03\n", + "#23 38.46 Downloading nvidia_cusparselt_cu12-0.7.1-py3-none-manylinux2014_x86_64.whl (287.2 MB)\n", + "#23 41.73 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 287.2/287.2 MB 88.3 MB/s 0:00:03\n", + "#23 41.73 Downloading nvidia_nccl_cu12-2.27.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (322.4 MB)\n", + "#23 45.81 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 322.4/322.4 MB 78.4 MB/s 0:00:04\n", + "#23 45.82 Downloading nvidia_nvjitlink_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (39.3 MB)\n", + "#23 46.21 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.3/39.3 MB 104.3 MB/s 0:00:00\n", + "#23 46.22 Downloading nvidia_nvtx_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (89 kB)\n", + "#23 46.23 Downloading triton-3.4.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (155.6 MB)\n", + "#23 48.05 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.6/155.6 MB 85.2 MB/s 0:00:01\n", + "#23 48.06 Downloading packaging-25.0-py3-none-any.whl (66 kB)\n", + "#23 48.07 Downloading pillow-11.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)\n", + "#23 48.14 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.6/6.6 MB 101.2 MB/s 0:00:00\n", + "#23 48.23 Downloading pyjpegls-1.5.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.7 MB)\n", + "#23 48.33 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 26.4 MB/s 0:00:00\n", + "#23 48.33 Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)\n", + "#23 48.47 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 44.4 MB/s 0:00:00\n", + "#23 48.48 Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)\n", + "#23 48.49 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 139.8 MB/s 0:00:00\n", + "#23 48.49 Downloading typing_extensions-4.15.0-py3-none-any.whl (44 kB)\n", + "#23 48.49 Downloading filelock-3.19.1-py3-none-any.whl (15 kB)\n", + "#23 48.50 Downloading fsspec-2025.9.0-py3-none-any.whl (199 kB)\n", + "#23 48.50 Downloading jinja2-3.1.6-py3-none-any.whl (134 kB)\n", + "#23 48.51 Downloading markupsafe-3.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)\n", + "#23 48.51 Downloading networkx-3.5-py3-none-any.whl (2.0 MB)\n", + "#23 48.53 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 116.8 MB/s 0:00:00\n", + "#23 57.28 Installing collected packages: SimpleITK, nvidia-cusparselt-cu12, mpmath, typing-extensions, triton, sympy, pydicom, pillow, packaging, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufile-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, MarkupSafe, fsspec, filelock, pyjpegls, nvidia-cusparse-cu12, nvidia-cufft-cu12, nvidia-cudnn-cu12, nibabel, jinja2, nvidia-cusolver-cu12, highdicom, torch, monai\n", + "#23 121.2 \n", + "#23 121.2 Successfully installed MarkupSafe-3.0.3 SimpleITK-2.5.2 filelock-3.19.1 fsspec-2025.9.0 highdicom-0.26.1 jinja2-3.1.6 monai-1.5.1 mpmath-1.3.0 networkx-3.5 nibabel-5.3.2 numpy-2.3.3 nvidia-cublas-cu12-12.8.4.1 nvidia-cuda-cupti-cu12-12.8.90 nvidia-cuda-nvrtc-cu12-12.8.93 nvidia-cuda-runtime-cu12-12.8.90 nvidia-cudnn-cu12-9.10.2.21 nvidia-cufft-cu12-11.3.3.83 nvidia-cufile-cu12-1.13.1.3 nvidia-curand-cu12-10.3.9.90 nvidia-cusolver-cu12-11.7.3.90 nvidia-cusparse-cu12-12.5.8.93 nvidia-cusparselt-cu12-0.7.1 nvidia-nccl-cu12-2.27.3 nvidia-nvjitlink-cu12-12.8.93 nvidia-nvtx-cu12-12.8.90 packaging-25.0 pillow-11.3.0 pydicom-3.0.1 pyjpegls-1.5.1 sympy-1.14.0 torch-2.8.0 triton-3.4.0 typing-extensions-4.15.0\n", + "#23 DONE 122.6s\n", + "\n", + "#24 [release 15/20] RUN pip install monai-deploy-app-sdk==1.0.0\n", + "#24 0.781 Defaulting to user installation because normal site-packages is not writeable\n", + "#24 1.033 Collecting monai-deploy-app-sdk==1.0.0\n", + "#24 1.150 Downloading monai_deploy_app_sdk-1.0.0-py3-none-any.whl.metadata (7.6 kB)\n", + "#24 1.175 Requirement already satisfied: numpy>=1.21.6 in /home/holoscan/.local/lib/python3.12/site-packages (from monai-deploy-app-sdk==1.0.0) (2.3.3)\n", + "#24 1.297 INFO: pip is looking at multiple versions of monai-deploy-app-sdk to determine which version is compatible with other requirements. This could take a while.\n", + "#24 1.298 ERROR: Could not find a version that satisfies the requirement holoscan~=1.0 (from monai-deploy-app-sdk) (from versions: 0.0.0.post1, 2.6.0, 2.7.0, 2.8.0, 2.9.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0, 3.4.0, 3.5.0, 3.6.0)\n", + "#24 1.447 ERROR: No matching distribution found for holoscan~=1.0\n", + "#24 ERROR: process \"/bin/sh -c pip install monai-deploy-app-sdk==1.0.0\" did not complete successfully: exit code: 1\n", + "------\n", + " > [release 15/20] RUN pip install monai-deploy-app-sdk==1.0.0:\n", + "0.781 Defaulting to user installation because normal site-packages is not writeable\n", + "1.033 Collecting monai-deploy-app-sdk==1.0.0\n", + "1.150 Downloading monai_deploy_app_sdk-1.0.0-py3-none-any.whl.metadata (7.6 kB)\n", + "1.175 Requirement already satisfied: numpy>=1.21.6 in /home/holoscan/.local/lib/python3.12/site-packages (from monai-deploy-app-sdk==1.0.0) (2.3.3)\n", + "1.297 INFO: pip is looking at multiple versions of monai-deploy-app-sdk to determine which version is compatible with other requirements. This could take a while.\n", + "1.298 ERROR: Could not find a version that satisfies the requirement holoscan~=1.0 (from monai-deploy-app-sdk) (from versions: 0.0.0.post1, 2.6.0, 2.7.0, 2.8.0, 2.9.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0, 3.4.0, 3.5.0, 3.6.0)\n", + "1.447 ERROR: No matching distribution found for holoscan~=1.0\n", + "------\n", + "Dockerfile:140\n", + "--------------------\n", + " 138 | \n", + " 139 | # Install MONAI Deploy from PyPI org\n", + " 140 | >>> RUN pip install monai-deploy-app-sdk==1.0.0\n", + " 141 | \n", + " 142 | \n", + "--------------------\n", + "ERROR: failed to build: failed to solve: process \"/bin/sh -c pip install monai-deploy-app-sdk==1.0.0\" did not complete successfully: exit code: 1\n", + "The command executed was `/usr/bin/docker buildx build --progress plain --build-arg UID=1000 --build-arg GID=1000 --build-arg UNAME=holoscan --build-arg GPU_TYPE=dgpu --builder holoscan_app_builder --pull --load --file /tmp/holoscan_tmptsbybsaz/Dockerfile --cache-from type=local,src=/home/mqin/.holoscan_build_cache --cache-from type=registry,ref=nvcr.io/nvidia/cuda:12.8.1-runtime-ubuntu24.04 --cache-to type=local,dest=/home/mqin/.holoscan_build_cache --platform linux/amd64 --tag my_app-x64-workstation-dgpu-linux-amd64:1.0 /tmp/holoscan_tmptsbybsaz`.\n", + "It returned with code 1\n", + "The content of stdout is ''\n", + "The content of stderr can be found above the stacktrace (it wasn't captured).\n", + "[2025-09-29 23:46:52,256] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", - " Status: Succeeded\n", - " Docker Tag: my_app-x64-workstation-dgpu-linux-amd64:1.0\n", - " Tarball: None\n" + " Status: Failure\n", + " Error: Error building image: see Docker output for additional details.\n", + " \n" ] } ], @@ -2196,14 +2106,14 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "my_app-x64-workstation-dgpu-linux-amd64 1.0 497a1c32b76e 5 minutes ago 10.3GB\n" + "my_app-x64-workstation-dgpu-linux-amd64 1.0 497a1c32b76e 3 weeks ago 10.3GB\n" ] } ], @@ -2222,7 +2132,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 19, "metadata": {}, "outputs": [ { @@ -2231,23 +2141,23 @@ "text": [ "output\n", "dcm\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", + "[2025-09-29 23:46:53,770] [INFO] (runner) - Checking dependencies...\n", + "[2025-09-29 23:46:53,770] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2025-09-04 18:34:36,446] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2025-09-29 23:46:53,771] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2025-09-04 18:34:36,447] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2025-09-29 23:46:53,771] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\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", + "[2025-09-29 23:46:53,899] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "Successfully copied 2.56kB to /tmp/tmp_tzi5rwl/app.json\n", + "Successfully copied 2.05kB to /tmp/tmp_tzi5rwl/pkg.json\n", + "c6b784bef1f56095b133293927d341b883a932b2d894367ea2b0e065d1221f4b\n", + "[2025-09-29 23:46:54,265] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2025-09-04 18:34:36,907] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2025-09-29 23:46:54,265] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\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", + "[2025-09-29 23:46:54,667] [INFO] (common) - Launching container (4d77d0dd21f3) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: bold_kowalevski\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -2257,7 +2167,7 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2025-09-05 01:34:38 [INFO] Launching application python3 /opt/holoscan/app ...\n", + "2025-09-30 06:46:55 [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 +2177,11 @@ "\n", "[info] [gxf_executor.cpp:344] Creating context\n", "\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", + "[2025-09-30 06:47:02,343] [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", - "[2025-09-05 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", + "[2025-09-30 06:47:02,349] [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", - "[2025-09-05 01:34:43,650] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", + "[2025-09-30 06:47:02,349] [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", @@ -2281,71 +2191,71 @@ "\n", "[info] [greedy_scheduler.cpp:191] Scheduling 5 entities\n", "\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", + "[2025-09-30 06:47:02,513] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", "\n", - "[2025-09-05 01:34:44,749] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2025-09-30 06:47:02,915] [INFO] (root) - Finding series for Selection named: CT Series\n", "\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", + "[2025-09-30 06:47:02,915] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", "\n", " # of series: 1\n", "\n", - "[2025-09-05 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", + "[2025-09-30 06:47:02,915] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2025-09-30 06:47:02,915] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute Modality value: CT\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Series attribute Modality value: CT\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Series attribute ImageType value: None\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Series attribute ImageType value: None\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Instance level attribute ImageType value: [\"['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']\"]\n", "\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", + "[2025-09-30 06:47:02,916] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Series Selection finalized\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Series Selection finalized\n", "\n", - "[2025-09-05 01:34:44,750] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", + "[2025-09-30 06:47:02,916] [INFO] (root) - Series Description of selected DICOM Series for inference: ABD/PANC 3.0 B31f\n", "\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", + "[2025-09-30 06:47:02,916] [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", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", "\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", + "[2025-09-30 06:47:03,267] [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", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", "\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", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", "\n", - "[2025-09-05 01:34:45,116] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", "\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", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", "\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", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", "\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", + "[2025-09-30 06:47:03,267] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", "\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", + "[2025-09-30 06:47:03,268] [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", @@ -2353,7 +2263,7 @@ "\n", " [ 0. 0. 0. 1. ]], type \n", "\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", + "[2025-09-30 06:47:03,268] [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", @@ -2361,57 +2271,57 @@ "\n", " [ 0. 0. 0. 1. ]], type \n", "\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", + "[2025-09-30 06:47:03,268] [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", - "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2025-09-30 06:47:03,268] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", "\n", - "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2025-09-30 06:47:03,268] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", "\n", - "[2025-09-05 01:34:45,117] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2025-09-30 06:47:03,268] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", "\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", + "[2025-09-30 06:47:03,268] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", "\n", - "[2025-09-05 01:34:45,118] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2025-09-30 06:47:03,268] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", "\n", - "[2025-09-05 01:34:45,118] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "[2025-09-30 06:47:03,268] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", "\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", + "2025-09-30 06:47:04,033 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", - "[2025-09-05 01:34:47,592] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", + "[2025-09-30 06:47:05,849] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Input of shape: torch.Size([1, 1, 270, 270, 106])\n", "\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", + "2025-09-30 06:47:07,676 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", - "[2025-09-05 01:34:51,014] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", + "[2025-09-30 06:47:09,109] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform length/batch size of output: 1\n", "\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", + "[2025-09-30 06:47:09,113] [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", - "[2025-09-05 01:34:51,151] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", + "[2025-09-30 06:47:09,251] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Post transform pred of shape: (1, 512, 512, 204)\n", "\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", + "[2025-09-30 06:47:09,289] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array of type shape: (204, 512, 512)\n", "\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", + "[2025-09-30 06:47:09,293] [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", - "[2025-09-05 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", + "[2025-09-30 06:47:10,455] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2025-09-30 06:47:10,455] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", "\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", + "[2025-09-30 06:47:10,455] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2025-09-30 06:47:10,455] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", "\n", - "[2025-09-05 01:34:52,342] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2025-09-30 06:47:10,456] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", "\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", + "[2025-09-30 06:47:10,456] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2025-09-30 06:47:10,456] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", "\n", - "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2025-09-30 06:47:10,456] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", "\n", - "[2025-09-05 01:34:52,343] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2025-09-30 06:47:10,456] [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", @@ -2421,13 +2331,13 @@ "\n", "[info] [gxf_executor.cpp:2597] Graph execution finished.\n", "\n", - "[2025-09-05 01:34:52,422] [INFO] (app.AISpleenSegApp) - End run\n", + "[2025-09-30 06:47:10,539] [INFO] (app.AISpleenSegApp) - End run\n", "\n", "[info] [gxf_executor.cpp:379] Destroying context\n", "\n", - "2025-09-05 01:34:54 [INFO] Application exited with 0.\n", + "2025-09-30 06:47:11 [INFO] Application exited with 0.\n", "\n", - "[2025-09-04 18:34:54,814] [INFO] (common) - Container 'objective_lalande'(3a29b7f7e4ec) exited with code 0.\n" + "[2025-09-29 23:47:12,577] [INFO] (common) - Container 'bold_kowalevski'(4d77d0dd21f3) exited with code 0.\n" ] } ], @@ -2441,7 +2351,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 20, "metadata": {}, "outputs": [ { @@ -2449,7 +2359,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.88991892166852090760434123092314736.dcm\n", + "1.2.826.0.1.3680043.10.511.3.2703228368843626345529444779803874.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", @@ -2468,7 +2378,7 @@ ], "metadata": { "kernelspec": { - "display_name": ".test36", + "display_name": ".venv", "language": "python", "name": "python3" }, diff --git a/platforms/nuance_pin/app/inference.py b/platforms/nuance_pin/app/inference.py index 1d805e39..908f16a2 100644 --- a/platforms/nuance_pin/app/inference.py +++ b/platforms/nuance_pin/app/inference.py @@ -181,7 +181,7 @@ def pre_process(self, img_reader) -> Compose: Spacingd(keys=image_key, pixdim=(0.703125, 0.703125, 1.25)), Orientationd( keys=image_key, - axcodes="RAS", + axcodes="LPS", ), EnsureChannelFirstd(keys=image_key), ScaleIntensityRanged(image_key, a_min=-1024.0, a_max=300.0, b_min=0.0, b_max=1.0, clip=True),