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examples: sort output of cells to ensure reproducibility on python3.5
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@fphammerle
fphammerle committed Feb 21, 2021
1 parent 7b966ee commit aafafa0
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2 changes: 1 addition & 1 deletion .github/workflows/python.yml
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Expand Up @@ -135,7 +135,7 @@ jobs:
strategy:
matrix:
python-version:
#- 3.5 TODO
- 3.5
- 3.6
- 3.7
#- 3.8 TODO
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57 changes: 29 additions & 28 deletions examples/ashs.ipynb
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Expand Up @@ -117,54 +117,54 @@
" <tr>\n",
" <th>0</th>\n",
" <td>CA1</td>\n",
" <td>678.903</td>\n",
" <td>678.901</td>\n",
" <td>bert</td>\n",
" <td>right</td>\n",
" <td>left</td>\n",
" <td>nogray</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CA2+3</td>\n",
" <td>123.458</td>\n",
" <th>3</th>\n",
" <td>CA1</td>\n",
" <td>678.903</td>\n",
" <td>bert</td>\n",
" <td>right</td>\n",
" <td>nogray</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>DG</td>\n",
" <td>901.236</td>\n",
" <th>5</th>\n",
" <td>CA2+3</td>\n",
" <td>123.457</td>\n",
" <td>bert</td>\n",
" <td>right</td>\n",
" <td>nogray</td>\n",
" <td>left</td>\n",
" <td>usegray</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <th>14</th>\n",
" <td>ERC</td>\n",
" <td>789.013</td>\n",
" <td>789.014</td>\n",
" <td>bert</td>\n",
" <td>right</td>\n",
" <td>nogray</td>\n",
" <td>left</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>PHC</td>\n",
" <td>2345.878</td>\n",
" <th>21</th>\n",
" <td>PRC</td>\n",
" <td>2345.679</td>\n",
" <td>bert</td>\n",
" <td>right</td>\n",
" <td>nogray</td>\n",
" <td>left</td>\n",
" <td>usegray</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" subfield volume_mm^3 subject hemisphere correction\n",
"0 CA1 678.903 bert right nogray\n",
"1 CA2+3 123.458 bert right nogray\n",
"2 DG 901.236 bert right nogray\n",
"3 ERC 789.013 bert right nogray\n",
"4 PHC 2345.878 bert right nogray"
" subfield volume_mm^3 subject hemisphere correction\n",
"0 CA1 678.901 bert left nogray\n",
"3 CA1 678.903 bert right nogray\n",
"5 CA2+3 123.457 bert left usegray\n",
"14 ERC 789.014 bert left None\n",
"21 PRC 2345.679 bert left usegray"
]
},
"execution_count": 4,
Expand All @@ -174,8 +174,9 @@
],
"source": [
"import pandas\n",
"volume_frame = pandas.concat([f.read_volumes_dataframe() for f in volume_files])\n",
"volume_frame.head()"
"volume_frame = pandas.concat(f.read_volumes_dataframe() for f in volume_files)\n",
"volume_frame.sort_values(by=['subfield', 'hemisphere', 'correction']) \\\n",
" .reset_index(drop=True).iloc[[0, 3, 5, 14, 21]]"
]
},
{
Expand Down Expand Up @@ -1158,7 +1159,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.5.10"
}
},
"nbformat": 4,
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57 changes: 29 additions & 28 deletions examples/compare_ashs_freesurfer_hipposf.ipynb
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Expand Up @@ -211,67 +211,67 @@
" <tr>\n",
" <th>7</th>\n",
" <td>Freesurfer</td>\n",
" <td>Hippocampal_tail</td>\n",
" <td>CA1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>Freesurfer</td>\n",
" <td>subiculum</td>\n",
" <td>CA3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>Freesurfer</td>\n",
" <td>CA1</td>\n",
" <td>CA4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>Freesurfer</td>\n",
" <td>hippocampal-fissure</td>\n",
" <td>GC-ML-DG</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>Freesurfer</td>\n",
" <td>presubiculum</td>\n",
" <td>HATA</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>Freesurfer</td>\n",
" <td>parasubiculum</td>\n",
" <td>Hippocampal_tail</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>Freesurfer</td>\n",
" <td>molecular_layer_HP</td>\n",
" <td>Whole_hippocampus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>Freesurfer</td>\n",
" <td>GC-ML-DG</td>\n",
" <td>fimbria</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>Freesurfer</td>\n",
" <td>CA3</td>\n",
" <td>hippocampal-fissure</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>Freesurfer</td>\n",
" <td>CA4</td>\n",
" <td>molecular_layer_HP</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>Freesurfer</td>\n",
" <td>fimbria</td>\n",
" <td>parasubiculum</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>Freesurfer</td>\n",
" <td>HATA</td>\n",
" <td>presubiculum</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>Freesurfer</td>\n",
" <td>Whole_hippocampus</td>\n",
" <td>subiculum</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
Expand All @@ -286,19 +286,19 @@
"4 ASHS PHC\n",
"5 ASHS PRC\n",
"6 ASHS SUB\n",
"7 Freesurfer Hippocampal_tail\n",
"8 Freesurfer subiculum\n",
"9 Freesurfer CA1\n",
"10 Freesurfer hippocampal-fissure\n",
"11 Freesurfer presubiculum\n",
"12 Freesurfer parasubiculum\n",
"13 Freesurfer molecular_layer_HP\n",
"14 Freesurfer GC-ML-DG\n",
"15 Freesurfer CA3\n",
"16 Freesurfer CA4\n",
"17 Freesurfer fimbria\n",
"18 Freesurfer HATA\n",
"19 Freesurfer Whole_hippocampus"
"7 Freesurfer CA1\n",
"8 Freesurfer CA3\n",
"9 Freesurfer CA4\n",
"10 Freesurfer GC-ML-DG\n",
"11 Freesurfer HATA\n",
"12 Freesurfer Hippocampal_tail\n",
"13 Freesurfer Whole_hippocampus\n",
"14 Freesurfer fimbria\n",
"15 Freesurfer hippocampal-fissure\n",
"16 Freesurfer molecular_layer_HP\n",
"17 Freesurfer parasubiculum\n",
"18 Freesurfer presubiculum\n",
"19 Freesurfer subiculum"
]
},
"execution_count": 3,
Expand All @@ -307,7 +307,8 @@
}
],
"source": [
"volume_frame[['source_type', 'subfield']].drop_duplicates().reset_index(drop=True)"
"volume_frame[['source_type', 'subfield']].drop_duplicates() \\\n",
" .sort_values(by=['source_type', 'subfield']).reset_index(drop=True)"
]
},
{
Expand Down Expand Up @@ -1299,7 +1300,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.5.10"
}
},
"nbformat": 4,
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63 changes: 37 additions & 26 deletions examples/freesurfer_hipposf.ipynb
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Expand Up @@ -25,7 +25,7 @@
{
"data": {
"text/plain": [
"['lh.hippoSfVolumes-T1.v10.txt', 'lh.hippoSfVolumes-T1-T2.v10.txt']"
"['lh.hippoSfVolumes-T1-T2.v10.txt', 'lh.hippoSfVolumes-T1.v10.txt']"
]
},
"execution_count": 2,
Expand All @@ -39,7 +39,7 @@
"\n",
"volume_files = list(filter(lambda f: f.subject == SUBJECT, \n",
" HippocampalSubfieldsVolumeFile.find(SUBJECTS_DIR)))\n",
"[os.path.basename(f.absolute_path) for f in volume_files]"
"sorted(os.path.basename(f.absolute_path) for f in volume_files)"
]
},
{
Expand Down Expand Up @@ -79,44 +79,53 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>Hippocampal_tail</td>\n",
" <td>123.456789</td>\n",
" <td>CA1</td>\n",
" <td>44.567891</td>\n",
" <td>bert</td>\n",
" <td>left</td>\n",
" <td>True</td>\n",
" <td>None</td>\n",
" <td>T2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>subiculum</td>\n",
" <td>234.567891</td>\n",
" <td>CA1</td>\n",
" <td>34.567891</td>\n",
" <td>bert</td>\n",
" <td>left</td>\n",
" <td>True</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>CA1</td>\n",
" <td>34.567891</td>\n",
" <th>3</th>\n",
" <td>CA3</td>\n",
" <td>678.912345</td>\n",
" <td>bert</td>\n",
" <td>left</td>\n",
" <td>True</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>hippocampal-fissure</td>\n",
" <td>345.678912</td>\n",
" <th>5</th>\n",
" <td>CA4</td>\n",
" <td>789.123456</td>\n",
" <td>bert</td>\n",
" <td>left</td>\n",
" <td>True</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>presubiculum</td>\n",
" <td>456.789123</td>\n",
" <th>8</th>\n",
" <td>HATA</td>\n",
" <td>91.244567</td>\n",
" <td>bert</td>\n",
" <td>left</td>\n",
" <td>True</td>\n",
" <td>T2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>Whole_hippocampus</td>\n",
" <td>1234.567899</td>\n",
" <td>bert</td>\n",
" <td>left</td>\n",
" <td>True</td>\n",
Expand All @@ -127,12 +136,13 @@
"</div>"
],
"text/plain": [
" subfield volume_mm^3 subject hemisphere T1_input analysis_id\n",
"0 Hippocampal_tail 123.456789 bert left True None\n",
"1 subiculum 234.567891 bert left True None\n",
"2 CA1 34.567891 bert left True None\n",
"3 hippocampal-fissure 345.678912 bert left True None\n",
"4 presubiculum 456.789123 bert left True None"
" subfield volume_mm^3 subject hemisphere T1_input analysis_id\n",
"0 CA1 44.567891 bert left True T2\n",
"1 CA1 34.567891 bert left True None\n",
"3 CA3 678.912345 bert left True None\n",
"5 CA4 789.123456 bert left True None\n",
"8 HATA 91.244567 bert left True T2\n",
"13 Whole_hippocampus 1234.567899 bert left True None"
]
},
"execution_count": 3,
Expand All @@ -143,7 +153,8 @@
"source": [
"import pandas\n",
"volume_frame = pandas.concat([f.read_volumes_dataframe() for f in volume_files])\n",
"volume_frame.head()"
"volume_frame.sort_values(by=['subfield', 'analysis_id']) \\\n",
" .reset_index(drop=True).iloc[[0, 1, 3, 5, 8, 13]]"
]
},
{
Expand Down Expand Up @@ -223,8 +234,8 @@
" return ' & '.join(filter(None, mri_sequences))\n",
"\n",
"volume_frame['segmentation_mode'] = volume_frame.apply(generate_mode_label, axis=1)\n",
"volume_frame.to_csv('freesurfer_hipposf_volumes_{}.csv'.format(SUBJECT),\n",
" index=False)\n",
"volume_frame.sort_values(by=['subfield', 'segmentation_mode']) \\\n",
" .to_csv('freesurfer_hipposf_volumes_{}.csv'.format(SUBJECT), index=False)\n",
"volume_frame['segmentation_mode'].value_counts().sort_index()"
]
},
Expand Down Expand Up @@ -2016,7 +2027,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.5.10"
}
},
"nbformat": 4,
Expand Down

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