From 9a7dd8264f7b26f6991fb725f9c716de7da6ba93 Mon Sep 17 00:00:00 2001 From: Stephen Aylward Date: Sat, 14 Dec 2024 23:04:06 -0500 Subject: [PATCH] Added to README, fixed copyright, exclude from runner --- README.md | 4 ++ nvidia_nims/vista_3d_remote_nim.ipynb | 56 ++++++++++++++++++++------- runner.sh | 2 + 3 files changed, 47 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 7e7ca7aaf..0d3822f48 100644 --- a/README.md +++ b/README.md @@ -302,6 +302,10 @@ This tutorial shows several visualization approaches for 3D image during transfo #### [Auto3DSeg](./auto3dseg/) This folder shows how to run the comprehensive Auto3DSeg pipeline with minimal inputs and customize the Auto3Dseg modules to meet different user requirements. +#### **NVIDIA NIMs** +#### [Vista3D Remote NIM](nvidia_nims/vista_3d_remove_num.ipynb) +This tutorial illustrates sending an image to the Vista3D NIM running on NVIDIA's AI Enterprise / GPU Cloud servers. Results are saved to disk and viewed using pyvista. Registration to generate an API Key is required at [build.nvidia.com](https://build.nvidia.com). Registration and key generation is free and provides free credits for processing images. + #### **Self-Supervised Learning** ##### [self_supervised_pretraining](self_supervised_pretraining/vit_unetr_ssl/ssl_train.ipynb) This tutorial shows how to construct a training workflow of self-supervised learning where unlabeled data is utilized. The tutorial shows how to train a model on TCIA dataset of unlabeled Covid-19 cases. diff --git a/nvidia_nims/vista_3d_remote_nim.ipynb b/nvidia_nims/vista_3d_remote_nim.ipynb index 1c2c35aff..af5eadd77 100644 --- a/nvidia_nims/vista_3d_remote_nim.ipynb +++ b/nvidia_nims/vista_3d_remote_nim.ipynb @@ -5,18 +5,17 @@ "id": "7b50dffd", "metadata": {}, "source": [ - "```\n", - "Copyright (c) MONAI Consortium\n", - "Licensed under the Apache License, Version 2.0 (the \"License\");\n", - "you may not use this file except in compliance with the License.\n", - "You may obtain a copy of the License at\n", - " http://www.apache.org/licenses/LICENSE-2.0\n", - "Unless required by applicable law or agreed to in writing, software\n", - "distributed under the License is distributed on an \"AS IS\" BASIS,\n", - "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n", - "See the License for the specific language governing permissions and\n", - "limitations under the License.\n", - "```\n", + "\n", + "Copyright (c) MONAI Consortium \n", + "Licensed under the Apache License, Version 2.0 (the \"License\"); \n", + "you may not use this file except in compliance with the License. \n", + "You may obtain a copy of the License at \n", + "    http://www.apache.org/licenses/LICENSE-2.0 \n", + "Unless required by applicable law or agreed to in writing, software \n", + "distributed under the License is distributed on an \"AS IS\" BASIS, \n", + "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. \n", + "See the License for the specific language governing permissions and \n", + "limitations under the License. \n", "\n", "# Calling Vista-3D NIM on NVAIE\n", "\n", @@ -67,7 +66,7 @@ "id": "1f78537f", "metadata": {}, "source": [ - "## Setup the python environment\n", + "## Setup environment\n", "\n", "- `itk`: used to support a variety of image file formats and to convert images for viewing via pyvista.\n", " - Learn more at https://github.com/InsightSoftwareConsortium/ITK\n", @@ -92,7 +91,7 @@ "id": "24ff5fb5", "metadata": {}, "source": [ - "## Setup the imports" + "## Setup imports" ] }, { @@ -251,7 +250,10 @@ "metadata": {}, "outputs": [], "source": [ - "ngc_api_key = os.environ[\"NGC_API_KEY\"]" + "ngc_api_key = os.environ[\"NGC_API_KEY\"]\n", + "\n", + "if ngc_api_key == \"\":\n", + " raise ValueError(\"Please set the NGC_API_KEY environment variable.\")" ] }, { @@ -307,6 +309,30 @@ "WARNING: The input image should have 1.5 mm isotropic spacing. Performance will be degraded.\n", " The input image has spacing: itkVectorD3 ([0.902344, 0.902344, 5])\n" ] + }, + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[7], line 5\u001b[0m\n\u001b[0;32m 2\u001b[0m input_image \u001b[38;5;241m=\u001b[39m itk\u001b[38;5;241m.\u001b[39mimread(input_image_filename)\n\u001b[0;32m 4\u001b[0m \u001b[38;5;66;03m# run the model using the api key and input image\u001b[39;00m\n\u001b[1;32m----> 5\u001b[0m output_image \u001b[38;5;241m=\u001b[39m \u001b[43mnvaie_vista3d_nim\u001b[49m\u001b[43m(\u001b[49m\u001b[43mngc_api_key\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43minput_image\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 7\u001b[0m \u001b[38;5;66;03m# save the results to \"output_image.mha\"\u001b[39;00m\n\u001b[0;32m 8\u001b[0m itk\u001b[38;5;241m.\u001b[39mimwrite(output_image, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m./output_image.mha\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "Cell \u001b[1;32mIn[4], line 24\u001b[0m, in \u001b[0;36mnvaie_vista3d_nim\u001b[1;34m(api_key, input_image)\u001b[0m\n\u001b[0;32m 21\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m The input image has Hounsfield Units in the range:\u001b[39m\u001b[38;5;124m\"\u001b[39m, [minv, maxv])\n\u001b[0;32m 23\u001b[0m \u001b[38;5;66;03m# Post the image to file.io and get the link\u001b[39;00m\n\u001b[1;32m---> 24\u001b[0m input_image_url \u001b[38;5;241m=\u001b[39m \u001b[43mpost_image_to_fileio\u001b[49m\u001b[43m(\u001b[49m\u001b[43minput_image\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 26\u001b[0m \u001b[38;5;66;03m# Define the header and payload for the API call\u001b[39;00m\n\u001b[0;32m 27\u001b[0m header \u001b[38;5;241m=\u001b[39m {\n\u001b[0;32m 28\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAuthorization\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mBearer \u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m+\u001b[39m api_key,\n\u001b[0;32m 29\u001b[0m }\n", + "Cell \u001b[1;32mIn[3], line 12\u001b[0m, in \u001b[0;36mpost_image_to_fileio\u001b[1;34m(input_image)\u001b[0m\n\u001b[0;32m 10\u001b[0m \u001b[38;5;66;03m# Upload the file\u001b[39;00m\n\u001b[0;32m 11\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(tmp_filename), \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrb\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m---> 12\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[43mrequests\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpost\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mhttps://file.io/\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfiles\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m{\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mfile\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mf\u001b[49m\u001b[43m}\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 13\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m res\u001b[38;5;241m.\u001b[39mstatus_code \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m200\u001b[39m:\n\u001b[0;32m 14\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCannot upload file. The response \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mres\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\requests\\api.py:115\u001b[0m, in \u001b[0;36mpost\u001b[1;34m(url, data, json, **kwargs)\u001b[0m\n\u001b[0;32m 103\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mpost\u001b[39m(url, data\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, json\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m 104\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124;03m\"\"\"Sends a POST request.\u001b[39;00m\n\u001b[0;32m 105\u001b[0m \n\u001b[0;32m 106\u001b[0m \u001b[38;5;124;03m :param url: URL for the new :class:`Request` object.\u001b[39;00m\n\u001b[1;32m (...)\u001b[0m\n\u001b[0;32m 112\u001b[0m \u001b[38;5;124;03m :rtype: requests.Response\u001b[39;00m\n\u001b[0;32m 113\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[1;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m request(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpost\u001b[39m\u001b[38;5;124m\"\u001b[39m, url, data\u001b[38;5;241m=\u001b[39mdata, json\u001b[38;5;241m=\u001b[39mjson, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\requests\\api.py:59\u001b[0m, in \u001b[0;36mrequest\u001b[1;34m(method, url, **kwargs)\u001b[0m\n\u001b[0;32m 55\u001b[0m \u001b[38;5;66;03m# By using the 'with' statement we are sure the session is closed, thus we\u001b[39;00m\n\u001b[0;32m 56\u001b[0m \u001b[38;5;66;03m# avoid leaving sockets open which can trigger a ResourceWarning in some\u001b[39;00m\n\u001b[0;32m 57\u001b[0m \u001b[38;5;66;03m# cases, and look like a memory leak in others.\u001b[39;00m\n\u001b[0;32m 58\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m sessions\u001b[38;5;241m.\u001b[39mSession() \u001b[38;5;28;01mas\u001b[39;00m session:\n\u001b[1;32m---> 59\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m session\u001b[38;5;241m.\u001b[39mrequest(method\u001b[38;5;241m=\u001b[39mmethod, url\u001b[38;5;241m=\u001b[39murl, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\requests\\sessions.py:589\u001b[0m, in \u001b[0;36mSession.request\u001b[1;34m(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)\u001b[0m\n\u001b[0;32m 584\u001b[0m send_kwargs \u001b[38;5;241m=\u001b[39m {\n\u001b[0;32m 585\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtimeout\u001b[39m\u001b[38;5;124m\"\u001b[39m: timeout,\n\u001b[0;32m 586\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mallow_redirects\u001b[39m\u001b[38;5;124m\"\u001b[39m: allow_redirects,\n\u001b[0;32m 587\u001b[0m }\n\u001b[0;32m 588\u001b[0m send_kwargs\u001b[38;5;241m.\u001b[39mupdate(settings)\n\u001b[1;32m--> 589\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msend(prep, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msend_kwargs)\n\u001b[0;32m 591\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m resp\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\requests\\sessions.py:703\u001b[0m, in \u001b[0;36mSession.send\u001b[1;34m(self, request, **kwargs)\u001b[0m\n\u001b[0;32m 700\u001b[0m start \u001b[38;5;241m=\u001b[39m preferred_clock()\n\u001b[0;32m 702\u001b[0m \u001b[38;5;66;03m# Send the request\u001b[39;00m\n\u001b[1;32m--> 703\u001b[0m r \u001b[38;5;241m=\u001b[39m adapter\u001b[38;5;241m.\u001b[39msend(request, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[0;32m 705\u001b[0m \u001b[38;5;66;03m# Total elapsed time of the request (approximately)\u001b[39;00m\n\u001b[0;32m 706\u001b[0m elapsed \u001b[38;5;241m=\u001b[39m preferred_clock() \u001b[38;5;241m-\u001b[39m start\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\requests\\adapters.py:667\u001b[0m, in \u001b[0;36mHTTPAdapter.send\u001b[1;34m(self, request, stream, timeout, verify, cert, proxies)\u001b[0m\n\u001b[0;32m 664\u001b[0m timeout \u001b[38;5;241m=\u001b[39m TimeoutSauce(connect\u001b[38;5;241m=\u001b[39mtimeout, read\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[0;32m 666\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m--> 667\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43murlopen\u001b[49m\u001b[43m(\u001b[49m\n\u001b[0;32m 668\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 669\u001b[0m \u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 670\u001b[0m \u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbody\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 671\u001b[0m \u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 672\u001b[0m \u001b[43m \u001b[49m\u001b[43mredirect\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[0;32m 673\u001b[0m \u001b[43m \u001b[49m\u001b[43massert_same_host\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[0;32m 674\u001b[0m \u001b[43m \u001b[49m\u001b[43mpreload_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[0;32m 675\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[0;32m 676\u001b[0m \u001b[43m \u001b[49m\u001b[43mretries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmax_retries\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 677\u001b[0m \u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 678\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunked\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunked\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 679\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 681\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (ProtocolError, \u001b[38;5;167;01mOSError\u001b[39;00m) \u001b[38;5;28;01mas\u001b[39;00m err:\n\u001b[0;32m 682\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mConnectionError\u001b[39;00m(err, request\u001b[38;5;241m=\u001b[39mrequest)\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\urllib3\\connectionpool.py:789\u001b[0m, in \u001b[0;36mHTTPConnectionPool.urlopen\u001b[1;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)\u001b[0m\n\u001b[0;32m 786\u001b[0m response_conn \u001b[38;5;241m=\u001b[39m conn \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m release_conn \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m 788\u001b[0m \u001b[38;5;66;03m# Make the request on the HTTPConnection object\u001b[39;00m\n\u001b[1;32m--> 789\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_make_request(\n\u001b[0;32m 790\u001b[0m conn,\n\u001b[0;32m 791\u001b[0m method,\n\u001b[0;32m 792\u001b[0m url,\n\u001b[0;32m 793\u001b[0m timeout\u001b[38;5;241m=\u001b[39mtimeout_obj,\n\u001b[0;32m 794\u001b[0m body\u001b[38;5;241m=\u001b[39mbody,\n\u001b[0;32m 795\u001b[0m headers\u001b[38;5;241m=\u001b[39mheaders,\n\u001b[0;32m 796\u001b[0m chunked\u001b[38;5;241m=\u001b[39mchunked,\n\u001b[0;32m 797\u001b[0m retries\u001b[38;5;241m=\u001b[39mretries,\n\u001b[0;32m 798\u001b[0m response_conn\u001b[38;5;241m=\u001b[39mresponse_conn,\n\u001b[0;32m 799\u001b[0m preload_content\u001b[38;5;241m=\u001b[39mpreload_content,\n\u001b[0;32m 800\u001b[0m decode_content\u001b[38;5;241m=\u001b[39mdecode_content,\n\u001b[0;32m 801\u001b[0m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mresponse_kw,\n\u001b[0;32m 802\u001b[0m )\n\u001b[0;32m 804\u001b[0m \u001b[38;5;66;03m# Everything went great!\u001b[39;00m\n\u001b[0;32m 805\u001b[0m clean_exit \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\urllib3\\connectionpool.py:495\u001b[0m, in \u001b[0;36mHTTPConnectionPool._make_request\u001b[1;34m(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)\u001b[0m\n\u001b[0;32m 492\u001b[0m \u001b[38;5;66;03m# conn.request() calls http.client.*.request, not the method in\u001b[39;00m\n\u001b[0;32m 493\u001b[0m \u001b[38;5;66;03m# urllib3.request. It also calls makefile (recv) on the socket.\u001b[39;00m\n\u001b[0;32m 494\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m--> 495\u001b[0m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\n\u001b[0;32m 496\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 497\u001b[0m \u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 498\u001b[0m \u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbody\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 499\u001b[0m \u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 500\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunked\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunked\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 501\u001b[0m \u001b[43m \u001b[49m\u001b[43mpreload_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpreload_content\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 502\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdecode_content\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 503\u001b[0m \u001b[43m \u001b[49m\u001b[43menforce_content_length\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43menforce_content_length\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m 504\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 506\u001b[0m \u001b[38;5;66;03m# We are swallowing BrokenPipeError (errno.EPIPE) since the server is\u001b[39;00m\n\u001b[0;32m 507\u001b[0m \u001b[38;5;66;03m# legitimately able to close the connection after sending a valid response.\u001b[39;00m\n\u001b[0;32m 508\u001b[0m \u001b[38;5;66;03m# With this behaviour, the received response is still readable.\u001b[39;00m\n\u001b[0;32m 509\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBrokenPipeError\u001b[39;00m:\n", + "File \u001b[1;32mc:\\src\\MONAI\\tutorials\\nvidia_nims\\venv\\lib\\site-packages\\urllib3\\connection.py:455\u001b[0m, in \u001b[0;36mHTTPConnection.request\u001b[1;34m(self, method, url, body, headers, chunked, preload_content, decode_content, enforce_content_length)\u001b[0m\n\u001b[0;32m 453\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msend(\u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m%x\u001b[39;00m\u001b[38;5;130;01m\\r\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m%\u001b[39m\u001b[38;5;124mb\u001b[39m\u001b[38;5;130;01m\\r\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m%\u001b[39m (\u001b[38;5;28mlen\u001b[39m(chunk), chunk))\n\u001b[0;32m 454\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m--> 455\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[43mchunk\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 457\u001b[0m \u001b[38;5;66;03m# Regardless of whether we have a body or not, if we're in\u001b[39;00m\n\u001b[0;32m 458\u001b[0m \u001b[38;5;66;03m# chunked mode we want to send an explicit empty chunk.\u001b[39;00m\n\u001b[0;32m 459\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m chunked:\n", + "File \u001b[1;32m~\\AppData\\Local\\Programs\\Python\\Python310\\lib\\http\\client.py:999\u001b[0m, in \u001b[0;36mHTTPConnection.send\u001b[1;34m(self, data)\u001b[0m\n\u001b[0;32m 997\u001b[0m sys\u001b[38;5;241m.\u001b[39maudit(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mhttp.client.send\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28mself\u001b[39m, data)\n\u001b[0;32m 998\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m--> 999\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msock\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msendall\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 1000\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[0;32m 1001\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(data, collections\u001b[38;5;241m.\u001b[39mabc\u001b[38;5;241m.\u001b[39mIterable):\n", + "File \u001b[1;32m~\\AppData\\Local\\Programs\\Python\\Python310\\lib\\ssl.py:1237\u001b[0m, in \u001b[0;36mSSLSocket.sendall\u001b[1;34m(self, data, flags)\u001b[0m\n\u001b[0;32m 1235\u001b[0m amount \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlen\u001b[39m(byte_view)\n\u001b[0;32m 1236\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m count \u001b[38;5;241m<\u001b[39m amount:\n\u001b[1;32m-> 1237\u001b[0m v \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbyte_view\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcount\u001b[49m\u001b[43m:\u001b[49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 1238\u001b[0m count \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m v\n\u001b[0;32m 1239\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "File \u001b[1;32m~\\AppData\\Local\\Programs\\Python\\Python310\\lib\\ssl.py:1206\u001b[0m, in \u001b[0;36mSSLSocket.send\u001b[1;34m(self, data, flags)\u001b[0m\n\u001b[0;32m 1202\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m flags \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m 1203\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[0;32m 1204\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnon-zero flags not allowed in calls to send() on \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m%\u001b[39m\n\u001b[0;32m 1205\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__class__\u001b[39m)\n\u001b[1;32m-> 1206\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sslobj\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwrite\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 1207\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m 1208\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28msuper\u001b[39m()\u001b[38;5;241m.\u001b[39msend(data, flags)\n", + "\u001b[1;31mKeyboardInterrupt\u001b[0m: " + ] } ], "source": [ diff --git a/runner.sh b/runner.sh index 07c9c07d7..888b92ba8 100755 --- a/runner.sh +++ b/runner.sh @@ -82,6 +82,7 @@ doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" mask_augmentation_e doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" maisi_inference_tutorial.ipynb) doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" realism_diversity_metrics.ipynb) doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" omniverse_integration.ipynb) +doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" vista_3d_remote_nim.ipynb) # Execution of the notebook in these folders / with the filename cannot be automated skip_run_papermill=() @@ -129,6 +130,7 @@ skip_run_papermill=("${skip_run_papermill[@]}" .*nuclick_infer.ipynb*) # https: skip_run_papermill=("${skip_run_papermill[@]}" .*unet_segmentation_3d_ignite_clearml.ipynb*) # https://github.com/Project-MONAI/tutorials/issues/1555 skip_run_papermill=("${skip_run_papermill[@]}" .*vista_2d_tutorial_monai.ipynb*) skip_run_papermill=("${skip_run_papermill[@]}" .*learn2reg_oasis_unpaired_brain_mr.ipynb*) +skip_run_papermill=("${skip_run_papermill[@]}" .*vista_3d_remote_nim.ipynb*) # output formatting 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