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Dec 13, 2021
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Remove developer names/aliases from notebooks and documentation #225

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14 changes: 7 additions & 7 deletions notebooks/tutorials/03_segmentation_app.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_update_1203.zip\n",
"To: ~/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_update_1203.zip\n",
"104MB [00:10, 10.3MB/s] \n",
"Archive: ai_spleen_seg_data_updated_1203.zip\n",
" creating: dcm/\n",
Expand Down Expand Up @@ -958,7 +958,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"file written: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/1.2.826.0.1.3680043.2.1125.1/1.2.826.0.1.3680043.2.1125.1_seg.nii.gz.\n",
"file written: ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/1.2.826.0.1.3680043.2.1125.1/1.2.826.0.1.3680043.2.1125.1_seg.nii.gz.\n",
"Output Seg image numpy array shaped: (515, 440, 440)\n",
"Output Seg image pixel max value: 1\n",
"\u001b[34mDone performing execution of operator SpleenSegOperator\n",
Expand All @@ -972,7 +972,7 @@
"output_type": "stream",
"text": [
"[2021-11-24 15:29:20,287] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-11-24 15:29:22,188] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-11-24 15:29:22,188] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-11-24 15:29:22,346] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - File saved.\n"
]
},
Expand Down Expand Up @@ -1351,7 +1351,7 @@
"StudyDescription: spleen, type <class 'str'>\n",
"AccessionNumber: 1, type <class 'str'>\n",
"selection_name: CT Series, type <class 'str'>\n",
"file written: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/1.2.826.0.1.3680043.2.1125.1/1.2.826.0.1.3680043.2.1125.1_seg.nii.gz.\n",
"file written: ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/1.2.826.0.1.3680043.2.1125.1/1.2.826.0.1.3680043.2.1125.1_seg.nii.gz.\n",
"Output Seg image numpy array shaped: (515, 440, 440)\n",
"Output Seg image pixel max value: 1\n",
"\u001b[34mDone performing execution of operator SpleenSegOperator\n",
Expand All @@ -1362,7 +1362,7 @@
"[2021-11-24 15:29:55,905] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Number of slices in the numpy image: 515\n",
"[2021-11-24 15:29:55,905] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Labels of the segments: ['Spleen']\n",
"[2021-11-24 15:29:57,442] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-11-24 15:29:59,170] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-11-24 15:29:59,170] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-11-24 15:29:59,323] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - File saved.\n",
"\u001b[34mDone performing execution of operator DICOMSegmentationWriterOperator\n",
"\u001b[39m\n"
Expand Down Expand Up @@ -1444,7 +1444,7 @@
"StudyDescription: spleen, type <class 'str'>\n",
"AccessionNumber: 1, type <class 'str'>\n",
"selection_name: CT Series, type <class 'str'>\n",
"file written: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/1.2.826.0.1.3680043.2.1125.1/1.2.826.0.1.3680043.2.1125.1_seg.nii.gz.\n",
"file written: ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/1.2.826.0.1.3680043.2.1125.1/1.2.826.0.1.3680043.2.1125.1_seg.nii.gz.\n",
"Output Seg image numpy array shaped: (515, 440, 440)\n",
"Output Seg image pixel max value: 1\n",
"\u001b[34mDone performing execution of operator SpleenSegOperator\n",
Expand All @@ -1455,7 +1455,7 @@
"[2021-11-24 15:31:34,476] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Number of slices in the numpy image: 515\n",
"[2021-11-24 15:31:34,476] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Labels of the segments: ['Spleen']\n",
"[2021-11-24 15:31:36,032] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-11-24 15:31:37,810] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-11-24 15:31:37,810] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-11-24 15:31:37,964] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - File saved.\n",
"\u001b[34mDone performing execution of operator DICOMSegmentationWriterOperator\n",
"\u001b[39m\n"
Expand Down
12 changes: 6 additions & 6 deletions notebooks/tutorials/04_mis_tutorial.ipynb
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Expand Up @@ -162,7 +162,7 @@
"remote: Total 274 (delta 127), reused 213 (delta 90), pack-reused 0\u001b[K\n",
"Receiving objects: 100% (274/274), 79.20 KiB | 705.00 KiB/s, done.\n",
"Resolving deltas: 100% (127/127), done.\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/monai-deploy-app-server/components/inference-service\n",
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can we replace /home/<user> with ~ ?

"~/src/monai-deploy-app-sdk/notebooks/tutorials/monai-deploy-app-server/components/inference-service\n",
"\n",
"Step 1/12 : FROM python:3.9-slim-buster\n",
" ---> edd87973afe0\n",
Expand Down Expand Up @@ -201,7 +201,7 @@
" ---> a6834eb5a23b\n",
"Successfully built a6834eb5a23b\n",
"Successfully tagged monai/inference-service:0.1\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials\n"
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can we replace /home/ with ~ ?

"~/src/monai-deploy-app-sdk/notebooks/tutorials\n"
]
}
],
Expand Down Expand Up @@ -230,7 +230,7 @@
"text": [
"Downloading...\n",
"From: https://drive.google.com/uc?id=12uNO1tyqZh1oFkZH41Osliey7TRm-BBG\n",
"To: /home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/charts.zip\n",
Copy link

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can we replace /home/ with ~ ?

"To: ~/src/monai-deploy-app-sdk/notebooks/tutorials/charts.zip\n",
"100%|██████████████████████████████████████| 9.18k/9.18k [00:00<00:00, 10.9MB/s]\n",
"Archive: charts.zip\n",
" inflating: charts/templates/monaiinferenceservice-deployment.yaml \n",
Expand Down Expand Up @@ -260,8 +260,8 @@
"\n",
"| Parameter | Value Description |\n",
"| ----------- | ----------- |\n",
"| `images.monaiInferenceServiceTag` | MONAI Inference Service image name (`pritishnahar/monai-deploy`) |\n",
"| `images.monaiInferenceService` | MONAI Inference Service image tag (`inference-service-0.1`) |\n",
"| `images.monaiInferenceService` | MONAI Inference Service image name (`monai/inference-service`) |\n",
"| `images.monaiInferenceServiceTag` | MONAI Inference Service image tag (`0.1`) |\n",
"| `payloadService.hostVolumePath` | Path to a local directory which will serve as a shared volume for payloads between MIS and its pods |\n",
"| `map.urn` | Name:Tag of MAP image built with MONAI application packager |\n",
"| `map.entrypoint` | Application entrypoint which can obtained from `app.json` |\n",
Expand Down Expand Up @@ -453,7 +453,7 @@
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gupta/miniconda3/envs/monairsna/lib/python3.6/site-packages (from requests[socks]->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
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we should standardize this path so that it copy/pasted it just works.

"To: ~/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
"100%|████████████████████████████████████████| 104M/104M [00:20<00:00, 4.97MB/s]\n",
"Archive: ai_spleen_seg_data_updated_1203.zip\n",
" inflating: dcm/IMG0001.dcm \n",
Expand Down
26 changes: 13 additions & 13 deletions notebooks/tutorials/05_full_tutorial.ipynb
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Expand Up @@ -129,7 +129,7 @@
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
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can we replace /home/<user> with ~ ?

we should also standardize the path we use. I recommend using ~/src/monai-deploy-app-sdk/.

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~/src/ only works if that directory is created in advance.

We can also use a variable the repopath, eg: export MONAIREPO=${PWD}

"To: ~/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
"104MB [00:10, 10.3MB/s] \n",
"Archive: ai_spleen_seg_data_update_1203.zip\n",
" creating: dcm/\n",
Expand Down Expand Up @@ -905,7 +905,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"file written: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/Img_in_context/Img_in_context_seg.nii.gz.\n",
"file written: ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/Img_in_context/Img_in_context_seg.nii.gz.\n",
"Output Seg image numpy array shaped: (515, 440, 440)\n",
"Output Seg image pixel max value: 1\n",
"\u001b[34mDone performing execution of operator SpleenSegOperator\n",
Expand All @@ -919,7 +919,7 @@
"output_type": "stream",
"text": [
"[2021-09-23 02:20:19,972] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-09-23 02:20:21,118] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
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can we replace /home/<user> with ~ ?

"[2021-09-23 02:20:21,118] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-09-23 02:20:21,397] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - File saved.\n"
]
},
Expand Down Expand Up @@ -1257,7 +1257,7 @@
"\u001b[39m\n",
"\u001b[34mGoing to initiate execution of operator SpleenSegOperator\u001b[39m\n",
"\u001b[32mExecuting operator SpleenSegOperator \u001b[33m(Process ID: 5326, Operator ID: a46c7abc-1f90-4009-80d2-0804b23221db)\u001b[39m\n",
"file written: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/Img_in_context/Img_in_context_seg.nii.gz.\n",
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can we replace /home/<user> with ~ ?

"file written: ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/Img_in_context/Img_in_context_seg.nii.gz.\n",
"Output Seg image numpy array shaped: (515, 440, 440)\n",
"Output Seg image pixel max value: 1\n",
"\u001b[34mDone performing execution of operator SpleenSegOperator\n",
Expand All @@ -1268,7 +1268,7 @@
"[2021-09-23 02:20:31,260] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Number of slices in the numpy image: 515\n",
"[2021-09-23 02:20:31,260] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Labels of the segments: ['Spleen']\n",
"[2021-09-23 02:20:33,355] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-09-23 02:20:34,659] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
Copy link

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can we replace /home/<user> with ~ ?

"[2021-09-23 02:20:34,659] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-09-23 02:20:34,846] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - File saved.\n",
"\u001b[34mDone performing execution of operator DICOMSegmentationWriterOperator\n",
"\u001b[39m\n"
Expand Down Expand Up @@ -1309,7 +1309,7 @@
"\u001b[39m\n",
"\u001b[34mGoing to initiate execution of operator SpleenSegOperator\u001b[39m\n",
"\u001b[32mExecuting operator SpleenSegOperator \u001b[33m(Process ID: 5905, Operator ID: 33da2642-2729-46ea-afe0-632e2a1ae5fc)\u001b[39m\n",
"file written: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/Img_in_context/Img_in_context_seg.nii.gz.\n",
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can we replace /home/<user> with ~ ?

"file written: ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/prediction_output/Img_in_context/Img_in_context_seg.nii.gz.\n",
"Output Seg image numpy array shaped: (515, 440, 440)\n",
"Output Seg image pixel max value: 1\n",
"\u001b[34mDone performing execution of operator SpleenSegOperator\n",
Expand All @@ -1320,7 +1320,7 @@
"[2021-09-23 02:20:44,984] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Number of slices in the numpy image: 515\n",
"[2021-09-23 02:20:44,984] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Labels of the segments: ['Spleen']\n",
"[2021-09-23 02:20:47,101] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-09-23 02:20:48,312] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
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can we replace /home/<user> with ~ ?

"[2021-09-23 02:20:48,312] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file ~/src/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
"[2021-09-23 02:20:48,513] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - File saved.\n",
"\u001b[34mDone performing execution of operator DICOMSegmentationWriterOperator\n",
"\u001b[39m\n"
Expand Down Expand Up @@ -1683,7 +1683,7 @@
"remote: Total 274 (delta 127), reused 213 (delta 90), pack-reused 0\u001b[K\n",
"Receiving objects: 100% (274/274), 79.20 KiB | 705.00 KiB/s, done.\n",
"Resolving deltas: 100% (127/127), done.\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/monai-deploy-app-server/components/inference-service\n",
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can we replace /home/<user> with ~ ?

"~/src/monai-deploy-app-sdk/notebooks/tutorials/monai-deploy-app-server/components/inference-service\n",
"\n",
"Step 1/12 : FROM python:3.9-slim-buster\n",
" ---> edd87973afe0\n",
Expand Down Expand Up @@ -1722,7 +1722,7 @@
" ---> a6834eb5a23b\n",
"Successfully built a6834eb5a23b\n",
"Successfully tagged monai/inference-service:0.1\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials\n"
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can we replace /home/<user> with ~ ?

"~/src/monai-deploy-app-sdk/notebooks/tutorials\n"
]
}
],
Expand Down Expand Up @@ -1751,7 +1751,7 @@
"text": [
"Downloading...\n",
"From: https://drive.google.com/uc?id=12uNO1tyqZh1oFkZH41Osliey7TRm-BBG\n",
"To: /home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/charts.zip\n",
Copy link

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can we replace /home/<user> with ~ ?

"To: ~/src/monai-deploy-app-sdk/notebooks/tutorials/charts.zip\n",
"100%|██████████████████████████████████████| 9.18k/9.18k [00:00<00:00, 10.9MB/s]\n",
"Archive: charts.zip\n",
" inflating: charts/templates/monaiinferenceservice-deployment.yaml \n",
Expand Down Expand Up @@ -1781,8 +1781,8 @@
"\n",
"| Parameter | Value Description |\n",
"| ----------- | ----------- |\n",
"| `images.monaiInferenceServiceTag` | MONAI Inference Service image name (`pritishnahar/monai-deploy`) |\n",
"| `images.monaiInferenceService` | MONAI Inference Service image tag (`inference-service-0.1`) |\n",
"| `images.monaiInferenceService` | MONAI Inference Service image name (`monai/inference-service`) |\n",
"| `images.monaiInferenceServiceTag` | MONAI Inference Service image tag (`0.1`) |\n",
"| `payloadService.hostVolumePath` | Path to a local directory which will serve as a shared volume for payloads between MIS and its pods |\n",
"| `map.urn` | Name:Tag of MAP image built with MONAI application packager |\n",
"| `map.entrypoint` | Application entrypoint which can obtained from `app.json` |\n",
Expand Down Expand Up @@ -2042,7 +2042,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/home/kavink/.local/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.\n",
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can we replace /home/<user> with ~ ?

"~/.local/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.\n",
" warn(\"Fetchers from the nilearn.datasets module will be \"\n"
]
},
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