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Merge branch 'auth_fix' of github.com:individual-brain-charting/api i…
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@man-shu
man-shu committed Oct 5, 2023
2 parents c5fa689 + c7131d4 commit 29b65f0
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126 changes: 68 additions & 58 deletions examples/get_data.ipynb
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"text": [
"[siibra:INFO] Version: 0.4a47\n",
"[siibra:WARNING] This is a development release. Use at your own risk.\n",
"[siibra:INFO] Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python.\n"
"[siibra:INFO] Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python.\n",
"[siibra:INFO] Clearing siibra cache at /home/himanshu/.cache/siibra.retrieval\n"
]
}
],
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"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Found 12 files for subjects ['08'] and tasks ['Discount'].\n"
]
},
{
"data": {
"text/html": [
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"cell_type": "markdown",
"metadata": {},
"source": [
"Now before we download these files, we need to authenticate with EBRAINS. This will return a link that takes you to EBRAINS login page and stores an access token locally.\n",
"\n"
"Now we are ready to download the few selected maps that we filtered.\n",
"\n",
"The following will save the requested maps under\n",
"``ibc_data/resulting_smooth_maps/sub-08/task-Discount`` \n",
"(or whatever subject you chose). And will also create a local CSV file ``ibc_data/downloaded_volume_maps.csv`` to track the downloaded files. This will contain local file paths and the time they were downloaded at, and is updated everytime you download new files.\n"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Found 12 files to download.\n",
"***\n",
"To continue, please go to https://iam.ebrains.eu/auth/realms/hbp/device?user_code=LGDW-XTRE\n",
"***\n",
"To continue, please go to https://iam.ebrains.eu/auth/realms/hbp/device?user_code=UFKZ-XXQU\n",
"***\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[siibra:INFO] 139625 objects found for dataset ad04f919-7dcc-48d9-864a-d7b62af3d49d returned.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ebrains token successfuly set.\n"
]
}
],
"source": [
"ibc.authenticate()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we are ready to download the few selected maps that we filtered.\n",
"\n",
"The following will save the requested maps under\n",
"``ibc_data/resulting_smooth_maps/sub-08/task-Discount`` \n",
"(or whatever subject you chose). And will also create a local CSV file ``ibc_data/downloaded_volume_maps.csv`` to track the downloaded files. This will contain local file paths and the time they were downloaded at, and is updated everytime you download new files.\n"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[siibra:INFO] 139625 objects found for dataset ad04f919-7dcc-48d9-864a-d7b62af3d49d returned.\n",
"12it [00:01, 11.22it/s]\n"
"\n",
"Overall Progress: 0%|\u001b[32m \u001b[0m| 0/12 [00:00<?, ?it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 17%|\u001b[32m██████████████████████████████████████████▌ \u001b[0m| 2/12 [00:00<00:00, 12.46it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 33%|\u001b[32m█████████████████████████████████████████████████████████████████████████████████████ \u001b[0m| 4/12 [00:00<00:00, 12.26it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 50%|\u001b[32m███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ \u001b[0m| 6/12 [00:00<00:00, 11.73it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 67%|\u001b[32m██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ \u001b[0m| 8/12 [00:00<00:00, 11.80it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 83%|\u001b[32m███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ \u001b[0m| 10/12 [00:00<00:00, 11.94it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 100%|\u001b[32m██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████\u001b[0m| 12/12 [00:01<00:00, 11.97it/s]\u001b[0m\u001b[A\n"
]
},
{
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" <tr>\n",
" <th>0</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.588770</td>\n",
" <td>2023-10-05 17:23:53.472528</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.765652</td>\n",
" <td>2023-10-05 17:23:53.628380</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.772669</td>\n",
" <td>2023-10-05 17:23:53.634523</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.944780</td>\n",
" <td>2023-10-05 17:23:53.793226</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.949580</td>\n",
" <td>2023-10-05 17:23:53.799418</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.116007</td>\n",
" <td>2023-10-05 17:23:53.972341</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.121902</td>\n",
" <td>2023-10-05 17:23:53.979429</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.298023</td>\n",
" <td>2023-10-05 17:23:54.140314</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.302662</td>\n",
" <td>2023-10-05 17:23:54.146809</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.471236</td>\n",
" <td>2023-10-05 17:23:54.304385</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.476903</td>\n",
" <td>2023-10-05 17:23:54.310566</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.651207</td>\n",
" <td>2023-10-05 17:23:54.468429</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
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"11 ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-... \n",
"\n",
" downloaded_on \n",
"0 2023-09-18 17:37:15.588770 \n",
"1 2023-09-18 17:37:15.765652 \n",
"2 2023-09-18 17:37:15.772669 \n",
"3 2023-09-18 17:37:15.944780 \n",
"4 2023-09-18 17:37:15.949580 \n",
"5 2023-09-18 17:37:16.116007 \n",
"6 2023-09-18 17:37:16.121902 \n",
"7 2023-09-18 17:37:16.298023 \n",
"8 2023-09-18 17:37:16.302662 \n",
"9 2023-09-18 17:37:16.471236 \n",
"10 2023-09-18 17:37:16.476903 \n",
"11 2023-09-18 17:37:16.651207 "
"0 2023-10-05 17:23:53.472528 \n",
"1 2023-10-05 17:23:53.628380 \n",
"2 2023-10-05 17:23:53.634523 \n",
"3 2023-10-05 17:23:53.793226 \n",
"4 2023-10-05 17:23:53.799418 \n",
"5 2023-10-05 17:23:53.972341 \n",
"6 2023-10-05 17:23:53.979429 \n",
"7 2023-10-05 17:23:54.140314 \n",
"8 2023-10-05 17:23:54.146809 \n",
"9 2023-10-05 17:23:54.304385 \n",
"10 2023-10-05 17:23:54.310566 \n",
"11 2023-10-05 17:23:54.468429 "
]
},
"execution_count": 7,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
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},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<nilearn.plotting.displays._slicers.OrthoSlicer at 0x7f341bf5fb80>"
"<nilearn.plotting.displays._slicers.OrthoSlicer at 0x7f7bdd436bb0>"
]
},
"execution_count": 8,
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
},
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