Skip to content

Commit 3b06f9b

Browse files
MMelQinMMelQin
committed
Made sure to use the App SDK in dev and the latest Holoscan build (post RC1)
Signed-off-by: M Q <mingmelvinq@nvidia.com>
1 parent fa7f913 commit 3b06f9b

File tree

1 file changed

+29
-67
lines changed

1 file changed

+29
-67
lines changed

‎notebooks/tutorials/06_monai_bundle_app.ipynb

Lines changed: 29 additions & 67 deletions
Original file line numberDiff line numberDiff line change
@@ -96,49 +96,7 @@
9696
"cell_type": "code",
9797
"execution_count": 1,
9898
"metadata": {},
99-
"outputs": [
100-
{
101-
"name": "stdout",
102-
"output_type": "stream",
103-
"text": [
104-
"Traceback (most recent call last):\n",
105-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/module.py\", line 210, in load_submodules\n",
106-
" mod = import_module(name)\n",
107-
" File \"/usr/lib/python3.8/importlib/__init__.py\", line 127, in import_module\n",
108-
" return _bootstrap._gcd_import(name[level:], package, level)\n",
109-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/deploy/__init__.py\", line 23, in <module>\n",
110-
" from . import _version, cli, core, exceptions, resources, utils\n",
111-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/deploy/core/__init__.py\", line 28, in <module>\n",
112-
" from holoscan.core import *\n",
113-
"ModuleNotFoundError: No module named 'holoscan'\n",
114-
"\n",
115-
"The above exception was the direct cause of the following exception:\n",
116-
"\n",
117-
"Traceback (most recent call last):\n",
118-
" File \"<string>\", line 1, in <module>\n",
119-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/__init__.py\", line 58, in <module>\n",
120-
" load_submodules(sys.modules[__name__], False, exclude_pattern=excludes)\n",
121-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/module.py\", line 220, in load_submodules\n",
122-
" raise type(e)(f\"{e}\\n{msg}\").with_traceback(e.__traceback__) from e # raise with modified message\n",
123-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/module.py\", line 210, in load_submodules\n",
124-
" mod = import_module(name)\n",
125-
" File \"/usr/lib/python3.8/importlib/__init__.py\", line 127, in import_module\n",
126-
" return _bootstrap._gcd_import(name[level:], package, level)\n",
127-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/deploy/__init__.py\", line 23, in <module>\n",
128-
" from . import _version, cli, core, exceptions, resources, utils\n",
129-
" File \"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/deploy/core/__init__.py\", line 28, in <module>\n",
130-
" from holoscan.core import *\n",
131-
"ModuleNotFoundError: No module named 'holoscan'\n",
132-
"\n",
133-
"Multiple versions of MONAI may have been installed?\n",
134-
"Please see the installation guide: https://docs.monai.io/en/stable/installation.html\n",
135-
"\n",
136-
"Traceback (most recent call last):\n",
137-
" File \"<string>\", line 1, in <module>\n",
138-
"ModuleNotFoundError: No module named 'holoscan'\n"
139-
]
140-
}
141-
],
99+
"outputs": [],
142100
"source": [
143101
"# Install MONAI and other necessary image processing packages for the application\n",
144102
"!python -c \"import monai\" || pip install --upgrade -q \"monai\"\n",
@@ -151,7 +109,7 @@
151109
"\n",
152110
"# Install MONAI Deploy App SDK package\n",
153111
"!python -c \"import holoscan\" || pip install --upgrade -q \"holoscan>=0.5.0\"\n",
154-
"!python -c \"import monai.deploy\" || pip install --upgrade -q \"monai-deploy-app-sdk\""
112+
"!python -c \"import monai.deploy\" || pip install -q \"monai-deploy-app-sdk\""
155113
]
156114
},
157115
{
@@ -191,9 +149,9 @@
191149
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages (from requests[socks]->gdown) (1.7.1)\n",
192150
"Downloading...\n",
193151
"From (uriginal): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ\n",
194-
"From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=ae4af86a-4eaa-42ff-bf19-1801b6ae866a\n",
152+
"From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=ad392e53-43ed-43b4-b993-a6d4516ae786\n",
195153
"To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_bundle_data.zip\n",
196-
"100%|██████████████████████████████████████| 79.4M/79.4M [00:01<00:00, 49.6MB/s]\n",
154+
"100%|██████████████████████████████████████| 79.4M/79.4M [00:01<00:00, 72.9MB/s]\n",
197155
"Archive: ai_spleen_seg_bundle_data.zip\n",
198156
" inflating: dcm/1-001.dcm \n",
199157
" inflating: dcm/1-002.dcm \n",
@@ -692,22 +650,22 @@
692650
"name": "stdout",
693651
"output_type": "stream",
694652
"text": [
695-
"\u001b[0m2023-07-17 11:53:36.055 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
696-
"\u001b[0m2023-07-17 11:53:36.418 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 8 entities\u001b[0m\n"
653+
"\u001b[0m2023-07-17 12:12:27.610 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
654+
"\u001b[0m2023-07-17 12:12:27.699 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 8 entities\u001b[0m\n"
697655
]
698656
},
699657
{
700658
"name": "stderr",
701659
"output_type": "stream",
702660
"text": [
703-
"[2023-07-17 11:53:36.372] [holoscan] [info] [gxf_executor.cpp:100] Loading extensions from configs...\n",
661+
"[2023-07-17 12:12:27.664] [holoscan] [info] [gxf_executor.cpp:100] Loading extensions from configs...\n",
704662
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:321: FutureWarning: monai.transforms.io.dictionary LoadImaged.__init__:image_only: Current default value of argument `image_only=False` has been deprecated since version 1.1. It will be changed to `image_only=True` in version 1.3.\n",
705663
" warn_deprecated(argname, msg, warning_category)\n",
706664
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:321: FutureWarning: monai.transforms.io.dictionary SaveImaged.__init__:resample: Current default value of argument `resample=True` has been deprecated since version 1.1. It will be changed to `resample=False` in version 1.3.\n",
707665
" warn_deprecated(argname, msg, warning_category)\n",
708-
"[2023-07-17 11:53:36.417] [holoscan] [info] [gxf_executor.cpp:291] Activating Graph...\n",
709-
"[2023-07-17 11:53:36.418] [holoscan] [info] [gxf_executor.cpp:293] Running Graph...\n",
710-
"[2023-07-17 11:53:36.418] [holoscan] [info] [gxf_executor.cpp:295] Waiting for completion...\n",
666+
"[2023-07-17 12:12:27.697] [holoscan] [info] [gxf_executor.cpp:291] Activating Graph...\n",
667+
"[2023-07-17 12:12:27.698] [holoscan] [info] [gxf_executor.cpp:293] Running Graph...\n",
668+
"[2023-07-17 12:12:27.698] [holoscan] [info] [gxf_executor.cpp:295] Waiting for completion...\n",
711669
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/highdicom/valuerep.py:54: 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 http://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",
712670
" warnings.warn(\n",
713671
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/pydicom/valuerep.py:443: UserWarning: A value of type 'int64' cannot be assigned to a tag with VR UL.\n",
@@ -720,15 +678,15 @@
720678
"name": "stdout",
721679
"output_type": "stream",
722680
"text": [
723-
"\u001b[0m2023-07-17 11:53:55.412 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
724-
"\u001b[0m2023-07-17 11:53:55.413 INFO gxf/std/greedy_scheduler.cpp@367: Scheduler finished.\u001b[0m\n"
681+
"\u001b[0m2023-07-17 12:12:46.525 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
682+
"\u001b[0m2023-07-17 12:12:46.525 INFO gxf/std/greedy_scheduler.cpp@367: Scheduler finished.\u001b[0m\n"
725683
]
726684
},
727685
{
728686
"name": "stderr",
729687
"output_type": "stream",
730688
"text": [
731-
"[2023-07-17 11:53:55.413] [holoscan] [info] [gxf_executor.cpp:297] Deactivating Graph...\n"
689+
"[2023-07-17 12:12:46.525] [holoscan] [info] [gxf_executor.cpp:297] Deactivating Graph...\n"
732690
]
733691
}
734692
],
@@ -779,7 +737,7 @@
779737
"name": "stdout",
780738
"output_type": "stream",
781739
"text": [
782-
"Writing my_app/app.py\n"
740+
"Overwriting my_app/app.py\n"
783741
]
784742
}
785743
],
@@ -977,7 +935,7 @@
977935
"name": "stdout",
978936
"output_type": "stream",
979937
"text": [
980-
"Writing my_app/__main__.py\n"
938+
"Overwriting my_app/__main__.py\n"
981939
]
982940
}
983941
],
@@ -998,7 +956,7 @@
998956
"name": "stdout",
999957
"output_type": "stream",
1000958
"text": [
1001-
"app.py\t__main__.py\n"
959+
"app.py\t__main__.py __pycache__\n"
1002960
]
1003961
}
1004962
],
@@ -1023,25 +981,25 @@
1023981
"name": "stdout",
1024982
"output_type": "stream",
1025983
"text": [
1026-
"\u001b[0m2023-07-17 11:54:01.521 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
1027-
"[2023-07-17 11:54:01.571] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:100] Loading extensions from configs...\n",
984+
"\u001b[0m2023-07-17 12:12:52.436 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
985+
"[2023-07-17 12:12:52.486] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:100] Loading extensions from configs...\n",
1028986
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:321: FutureWarning: monai.transforms.io.dictionary LoadImaged.__init__:image_only: Current default value of argument `image_only=False` has been deprecated since version 1.1. It will be changed to `image_only=True` in version 1.3.\n",
1029987
" warn_deprecated(argname, msg, warning_category)\n",
1030988
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:321: FutureWarning: monai.transforms.io.dictionary SaveImaged.__init__:resample: Current default value of argument `resample=True` has been deprecated since version 1.1. It will be changed to `resample=False` in version 1.3.\n",
1031989
" warn_deprecated(argname, msg, warning_category)\n",
1032-
"[2023-07-17 11:54:01.603] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:291] Activating Graph...\n",
1033-
"[2023-07-17 11:54:01.605] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:293] Running Graph...\n",
1034-
"[2023-07-17 11:54:01.605] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:295] Waiting for completion...\n",
1035-
"\u001b[0m2023-07-17 11:54:01.605 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 8 entities\u001b[0m\n",
990+
"[2023-07-17 12:12:52.517] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:291] Activating Graph...\n",
991+
"[2023-07-17 12:12:52.519] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:293] Running Graph...\n",
992+
"[2023-07-17 12:12:52.519] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:295] Waiting for completion...\n",
993+
"\u001b[0m2023-07-17 12:12:52.519 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 8 entities\u001b[0m\n",
1036994
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/highdicom/valuerep.py:54: 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 http://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",
1037995
" warnings.warn(\n",
1038996
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/pydicom/valuerep.py:443: UserWarning: A value of type 'int64' cannot be assigned to a tag with VR UL.\n",
1039997
" warnings.warn(msg)\n",
1040998
"/home/mqin/src/monai-deploy-app-sdk/.venv05/lib/python3.8/site-packages/pydicom/valuerep.py:443: UserWarning: A value of type 'int64' cannot be assigned to a tag with VR US.\n",
1041999
" warnings.warn(msg)\n",
1042-
"\u001b[0m2023-07-17 11:54:21.240 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
1043-
"\u001b[0m2023-07-17 11:54:21.240 INFO gxf/std/greedy_scheduler.cpp@367: Scheduler finished.\u001b[0m\n",
1044-
"[2023-07-17 11:54:21.240] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:297] Deactivating Graph...\n"
1000+
"\u001b[0m2023-07-17 12:13:10.185 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
1001+
"\u001b[0m2023-07-17 12:13:10.186 INFO gxf/std/greedy_scheduler.cpp@367: Scheduler finished.\u001b[0m\n",
1002+
"[2023-07-17 12:13:10.186] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:297] Deactivating Graph...\n"
10451003
]
10461004
}
10471005
],
@@ -1059,7 +1017,9 @@
10591017
"output_type": "stream",
10601018
"text": [
10611019
"1.2.826.0.1.3680043.10.511.3.11565767286231630615882468443894896.dcm\n",
1020+
"1.2.826.0.1.3680043.10.511.3.22789238752634624953083456478280376.dcm\n",
10621021
"1.2.826.0.1.3680043.10.511.3.94716163589988006822094645064927186.dcm\n",
1022+
"1.2.826.0.1.3680043.10.511.3.96729054302193257237773310971953370.dcm\n",
10631023
"final_output.png\n",
10641024
"stl\n"
10651025
]
@@ -1167,7 +1127,9 @@
11671127
"output_type": "stream",
11681128
"text": [
11691129
"1.2.826.0.1.3680043.10.511.3.11565767286231630615882468443894896.dcm\n",
1130+
"1.2.826.0.1.3680043.10.511.3.22789238752634624953083456478280376.dcm\n",
11701131
"1.2.826.0.1.3680043.10.511.3.94716163589988006822094645064927186.dcm\n",
1132+
"1.2.826.0.1.3680043.10.511.3.96729054302193257237773310971953370.dcm\n",
11711133
"final_output.png\n",
11721134
"stl\n"
11731135
]

0 commit comments

Comments
 (0)