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Dev docs nilearn/nilearn@f132091 : [TEST] do not install latex for do…
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…c build (#4976)
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Expand Up @@ -69,7 +69,7 @@
},
"outputs": [],
"source": [
"print(\"Define and fit LSA\")\n\n# Transform the DataFrame for LSA\nlsa_events_df = events_df.copy()\nconditions = lsa_events_df[\"trial_type\"].unique()\ncondition_counter = {c: 0 for c in conditions}\nfor i_trial, trial in lsa_events_df.iterrows():\n trial_condition = trial[\"trial_type\"]\n condition_counter[trial_condition] += 1\n # We use a unique delimiter here (``__``) that shouldn't be in the\n # original condition names\n trial_name = f\"{trial_condition}__{condition_counter[trial_condition]:03d}\"\n lsa_events_df.loc[i_trial, \"trial_type\"] = trial_name\n\nlsa_glm = FirstLevelModel(**glm_parameters)\nlsa_glm.fit(fmri_file, lsa_events_df)\n\nfig, ax = plt.subplots(figsize=(10, 10))\nplot_design_matrix(lsa_glm.design_matrices_[0], axes=ax)\nshow()"
"print(\"Define and fit LSA\")\n\n# Transform the DataFrame for LSA\nlsa_events_df = events_df.copy()\nconditions = lsa_events_df[\"trial_type\"].unique()\ncondition_counter = dict.fromkeys(conditions, 0)\nfor i_trial, trial in lsa_events_df.iterrows():\n trial_condition = trial[\"trial_type\"]\n condition_counter[trial_condition] += 1\n # We use a unique delimiter here (``__``) that shouldn't be in the\n # original condition names\n trial_name = f\"{trial_condition}__{condition_counter[trial_condition]:03d}\"\n lsa_events_df.loc[i_trial, \"trial_type\"] = trial_name\n\nlsa_glm = FirstLevelModel(**glm_parameters)\nlsa_glm.fit(fmri_file, lsa_events_df)\n\nfig, ax = plt.subplots(figsize=(10, 10))\nplot_design_matrix(lsa_glm.design_matrices_[0], axes=ax)\nshow()"
]
},
{
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Expand Up @@ -126,7 +126,7 @@
# Transform the DataFrame for LSA
lsa_events_df = events_df.copy()
conditions = lsa_events_df["trial_type"].unique()
condition_counter = {c: 0 for c in conditions}
condition_counter = dict.fromkeys(conditions, 0)
for i_trial, trial in lsa_events_df.iterrows():
trial_condition = trial["trial_type"]
condition_counter[trial_condition] += 1
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Expand Up @@ -127,7 +127,7 @@ statistical map:
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f46afbf3970>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d86ba6310>
Expand Down Expand Up @@ -156,7 +156,7 @@ Visualizing works better with a threshold
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f46955d3fd0>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d872baaf0>
Expand Down Expand Up @@ -186,8 +186,7 @@ correspondence between rest and task
[get_dataset_dir] Dataset created in /home/runner/nilearn_data/smith_2009
[fetch_single_file] Downloading data from
https://www.fmrib.ox.ac.uk/datasets/brainmap+rsns/PNAS_Smith09_rsn10.nii.gz ...
[_chunk_report_] Downloaded 1802240 of 7565016 bytes (23.8%%, 3.3s remaining)
[fetch_single_file] ...done. (2 seconds, 0 min)
[fetch_single_file] ...done. (1 seconds, 0 min)
'/home/runner/nilearn_data/smith_2009/PNAS_Smith09_rsn10.nii.gz'
Expand Down Expand Up @@ -271,7 +270,7 @@ We can then plot it
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f46955a1340>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d87795eb0>
Expand Down Expand Up @@ -489,9 +488,9 @@ image.

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 22.619 seconds)
**Total running time of the script:** (0 minutes 24.752 seconds)

**Estimated memory usage:** 396 MB
**Estimated memory usage:** 393 MB


.. _sphx_glr_download_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py:
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240 changes: 120 additions & 120 deletions dev/_sources/auto_examples/00_tutorials/plot_decoding_tutorial.rst.txt

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50 changes: 10 additions & 40 deletions dev/_sources/auto_examples/00_tutorials/plot_nilearn_101.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ Let's quickly plot this file:
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f469533c8e0>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d873b1fd0>
Expand Down Expand Up @@ -125,7 +125,7 @@ Here we give as inputs the image filename and the smoothing value in mm
.. code-block:: none
<nibabel.nifti1.Nifti1Image object at 0x7f46953f5040>
<nibabel.nifti1.Nifti1Image object at 0x7f2d870c1430>
Expand Down Expand Up @@ -154,7 +154,7 @@ instance to look at it
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f46955ad370>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d87202ca0>
Expand Down Expand Up @@ -184,7 +184,7 @@ We could also pass it to the smoothing function
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f46afbc1eb0>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d86b8b580>
Expand Down Expand Up @@ -228,25 +228,9 @@ First let's fetch Haxby dataset for subject 1 and 2
[fetch_single_file] Downloading data from
http://data.pymvpa.org/datasets/haxby2001/subj1-2010.01.14.tar.gz ...
[_chunk_report_] Downloaded 17350656 of 314803244 bytes (5.5%%, 17.4s
[_chunk_report_] Downloaded 160612352 of 314803244 bytes (51.0%%, 1.0s
remaining)
[_chunk_report_] Downloaded 54288384 of 314803244 bytes (17.2%%, 9.8s
remaining)
[_chunk_report_] Downloaded 93011968 of 314803244 bytes (29.5%%, 7.3s
remaining)
[_chunk_report_] Downloaded 132554752 of 314803244 bytes (42.1%%, 5.6s
remaining)
[_chunk_report_] Downloaded 171368448 of 314803244 bytes (54.4%%, 4.3s
remaining)
[_chunk_report_] Downloaded 210788352 of 314803244 bytes (67.0%%, 3.0s
remaining)
[_chunk_report_] Downloaded 233324544 of 314803244 bytes (74.1%%, 2.5s
remaining)
[_chunk_report_] Downloaded 258310144 of 314803244 bytes (82.1%%, 1.8s
remaining)
[_chunk_report_] Downloaded 292855808 of 314803244 bytes (93.0%%, 0.7s
remaining)
[fetch_single_file] ...done. (10 seconds, 0 min)
[fetch_single_file] ...done. (2 seconds, 0 min)
[uncompress_file] Extracting data from
/home/runner/nilearn_data/haxby2001/b2fd65a88d22090da62c3fb828be840e/subj1-2010.
Expand All @@ -255,23 +239,9 @@ First let's fetch Haxby dataset for subject 1 and 2
[fetch_single_file] Downloading data from
http://data.pymvpa.org/datasets/haxby2001/subj2-2010.01.14.tar.gz ...
[_chunk_report_] Downloaded 22601728 of 291168628 bytes (7.8%%, 12.1s
remaining)
[_chunk_report_] Downloaded 60678144 of 291168628 bytes (20.8%%, 7.7s
remaining)
[_chunk_report_] Downloaded 99254272 of 291168628 bytes (34.1%%, 5.9s
remaining)
[_chunk_report_] Downloaded 138461184 of 291168628 bytes (47.6%%, 4.5s
remaining)
[_chunk_report_] Downloaded 173899776 of 291168628 bytes (59.7%%, 3.4s
remaining)
[_chunk_report_] Downloaded 212680704 of 291168628 bytes (73.0%%, 2.3s
remaining)
[_chunk_report_] Downloaded 251387904 of 291168628 bytes (86.3%%, 1.1s
remaining)
[_chunk_report_] Downloaded 289988608 of 291168628 bytes (99.6%%, 0.0s
[_chunk_report_] Downloaded 151470080 of 291168628 bytes (52.0%%, 0.9s
remaining)
[fetch_single_file] ...done. (8 seconds, 0 min)
[fetch_single_file] ...done. (2 seconds, 0 min)
[uncompress_file] Extracting data from
/home/runner/nilearn_data/haxby2001/b2fd65a88d22090da62c3fb828be840e/subj2-2010.
Expand Down Expand Up @@ -407,9 +377,9 @@ passed on to other nilearn tools, or saved to disk.

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 29.788 seconds)
**Total running time of the script:** (0 minutes 15.125 seconds)

**Estimated memory usage:** 299 MB
**Estimated memory usage:** 251 MB


.. _sphx_glr_download_auto_examples_00_tutorials_plot_nilearn_101.py:
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Expand Up @@ -67,16 +67,16 @@ A simple example of basic Python numerics and how to plot it.
.. code-block:: none
[<matplotlib.lines.Line2D object at 0x7f46b11f6d30>]
[<matplotlib.lines.Line2D object at 0x7f2d7d87cd30>]
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 0.192 seconds)
**Total running time of the script:** (0 minutes 0.196 seconds)

**Estimated memory usage:** 110 MB
**Estimated memory usage:** 111 MB


.. _sphx_glr_download_auto_examples_00_tutorials_plot_python_101.py:
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Expand Up @@ -65,22 +65,19 @@ Retrieving the data
[fetch_spm_auditory] Data absent, downloading...
[fetch_single_file] Downloading data from
https://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip ...
[_chunk_report_] Downloaded 1351680 of 30176409 bytes (4.5%%, 22.7s remaining)
[_chunk_report_] Downloaded 6619136 of 30176409 bytes (21.9%%, 7.4s
[_chunk_report_] Downloaded 3268608 of 30176409 bytes (10.8%%, 8.2s
remaining)
[_chunk_report_] Downloaded 10125312 of 30176409 bytes (33.6%%, 6.2s
[_chunk_report_] Downloaded 7561216 of 30176409 bytes (25.1%%, 6.0s
remaining)
[_chunk_report_] Downloaded 13852672 of 30176409 bytes (45.9%%, 4.9s
[_chunk_report_] Downloaded 12181504 of 30176409 bytes (40.4%%, 4.5s
remaining)
[_chunk_report_] Downloaded 17719296 of 30176409 bytes (58.7%%, 3.6s
[_chunk_report_] Downloaded 16965632 of 30176409 bytes (56.2%%, 3.1s
remaining)
[_chunk_report_] Downloaded 21635072 of 30176409 bytes (71.7%%, 2.4s
[_chunk_report_] Downloaded 21831680 of 30176409 bytes (72.3%%, 1.9s
remaining)
[_chunk_report_] Downloaded 25255936 of 30176409 bytes (83.7%%, 1.4s
[_chunk_report_] Downloaded 26689536 of 30176409 bytes (88.4%%, 0.8s
remaining)
[_chunk_report_] Downloaded 29048832 of 30176409 bytes (96.3%%, 0.3s
remaining)
[fetch_single_file] ...done. (10 seconds, 0 min)
[fetch_single_file] ...done. (9 seconds, 0 min)
[uncompress_file] Extracting data from
/home/runner/nilearn_data/spm_auditory/MoAEpilot.bids.zip...
Expand Down Expand Up @@ -1258,9 +1255,9 @@ which makes it easier to represent it.

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 27.766 seconds)
**Total running time of the script:** (0 minutes 28.514 seconds)

**Estimated memory usage:** 764 MB
**Estimated memory usage:** 740 MB


.. _sphx_glr_download_auto_examples_00_tutorials_plot_single_subject_single_run.py:
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Original file line number Diff line number Diff line change
Expand Up @@ -1333,9 +1333,9 @@ See following examples for more details:

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 0.999 seconds)
**Total running time of the script:** (0 minutes 1.188 seconds)

**Estimated memory usage:** 108 MB
**Estimated memory usage:** 109 MB


.. _sphx_glr_download_auto_examples_00_tutorials_plot_surface_101.py:
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28 changes: 14 additions & 14 deletions dev/_sources/auto_examples/00_tutorials/sg_execution_times.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**02:00.781** total execution time for 6 files **from auto_examples/00_tutorials**:
**01:51.219** total execution time for 6 files **from auto_examples/00_tutorials**:

.. container::

Expand All @@ -33,20 +33,20 @@ Computation times
- Time
- Mem (MB)
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_decoding_tutorial.py` (``plot_decoding_tutorial.py``)
- 00:39.417
- 1009.8
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_nilearn_101.py` (``plot_nilearn_101.py``)
- 00:29.788
- 299.3
- 00:41.444
- 1061.8
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_single_subject_single_run.py` (``plot_single_subject_single_run.py``)
- 00:27.766
- 763.6
- 00:28.514
- 739.6
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py` (``plot_3d_and_4d_niimg.py``)
- 00:22.619
- 396.5
- 00:24.752
- 392.7
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_nilearn_101.py` (``plot_nilearn_101.py``)
- 00:15.125
- 250.9
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_surface_101.py` (``plot_surface_101.py``)
- 00:00.999
- 107.7
- 00:01.188
- 109.5
* - :ref:`sphx_glr_auto_examples_00_tutorials_plot_python_101.py` (``plot_python_101.py``)
- 00:00.192
- 110.3
- 00:00.196
- 111.5
Original file line number Diff line number Diff line change
Expand Up @@ -293,7 +293,7 @@ Plot 3D image for comparison
.. code-block:: none


<nilearn.plotting.displays._slicers.XSlicer object at 0x7f4694c49160>
<nilearn.plotting.displays._slicers.XSlicer object at 0x7f2d62cbad90>



Expand Down Expand Up @@ -468,13 +468,9 @@ but finer visualizations.

[get_dataset_dir] Dataset created in /home/runner/nilearn_data/fsaverage
[fetch_single_file] Downloading data from https://osf.io/svf8k/download ...
[_chunk_report_] Downloaded 4022272 of 34242788 bytes (11.7%%, 7.5s
[_chunk_report_] Downloaded 16875520 of 34242788 bytes (49.3%%, 1.0s
remaining)
[_chunk_report_] Downloaded 18989056 of 34242788 bytes (55.5%%, 1.6s
remaining)
[_chunk_report_] Downloaded 33792000 of 34242788 bytes (98.7%%, 0.0s
remaining)
[fetch_single_file] ...done. (5 seconds, 0 min)
[fetch_single_file] ...done. (4 seconds, 0 min)

[uncompress_file] Extracting data from
/home/runner/nilearn_data/fsaverage/735bf0f211246c83396b5f21f706c224/download...
Expand Down Expand Up @@ -936,7 +932,7 @@ Using nearest-neighbor interpolation with zero radius will achieve this.
[get_dataset_dir] Dataset created in /home/runner/nilearn_data/destrieux_2009
[fetch_single_file] Downloading data from
https://www.nitrc.org/frs/download.php/11942/destrieux2009.tgz ...
[fetch_single_file] ...done. (1 seconds, 0 min)
[fetch_single_file] ...done. (0 seconds, 0 min)

[uncompress_file] Extracting data from
/home/runner/nilearn_data/destrieux_2009/2a2e5a5707983d509d9319c692c867ab/destri
Expand Down Expand Up @@ -1267,9 +1263,9 @@ Using nearest-neighbor interpolation with zero radius will achieve this.

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 30.654 seconds)
**Total running time of the script:** (0 minutes 29.457 seconds)

**Estimated memory usage:** 548 MB
**Estimated memory usage:** 551 MB


.. _sphx_glr_download_auto_examples_01_plotting_plot_3d_map_to_surface_projection.py:
Expand Down
14 changes: 6 additions & 8 deletions dev/_sources/auto_examples/01_plotting/plot_atlas.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -55,9 +55,7 @@ Retrieving the atlas data
[get_dataset_dir] Dataset created in /home/runner/nilearn_data/fsl
[fetch_single_file] Downloading data from
https://www.nitrc.org/frs/download.php/9902/HarvardOxford.tgz ...
[_chunk_report_] Downloaded 20406272 of 25716861 bytes (79.3%%, 0.3s
remaining)
[fetch_single_file] ...done. (2 seconds, 0 min)
[fetch_single_file] ...done. (1 seconds, 0 min)
[uncompress_file] Extracting data from
/home/runner/nilearn_data/fsl/5c734f16e50cc772ef593cab9bb3137b/HarvardOxford.tgz
Expand All @@ -67,7 +65,7 @@ Retrieving the atlas data
[get_dataset_dir] Dataset found in /home/runner/nilearn_data/fsl
[fetch_single_file] Downloading data from
https://www.nitrc.org/frs/download.php/12096/Juelich.tgz ...
[fetch_single_file] ...done. (1 seconds, 0 min)
[fetch_single_file] ...done. (0 seconds, 0 min)
[uncompress_file] Extracting data from
/home/runner/nilearn_data/fsl/7e62e7e7fcc4d6e1428b6b2cb48f7a7c/Juelich.tgz...
Expand Down Expand Up @@ -107,7 +105,7 @@ Visualizing the Harvard-Oxford atlas
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f4694b799a0>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d7d914280>
Expand Down Expand Up @@ -137,7 +135,7 @@ Visualizing the Juelich atlas
.. code-block:: none
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f46afbf11f0>
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2d86fcb3d0>
Expand Down Expand Up @@ -205,9 +203,9 @@ Visualizing the Juelich atlas with contours

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (1 minutes 2.528 seconds)
**Total running time of the script:** (1 minutes 6.116 seconds)

**Estimated memory usage:** 108 MB
**Estimated memory usage:** 164 MB


.. _sphx_glr_download_auto_examples_01_plotting_plot_atlas.py:
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4 changes: 2 additions & 2 deletions dev/_sources/auto_examples/01_plotting/plot_carpet.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -208,9 +208,9 @@ Visualizing global patterns, separated by tissue type
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 6.205 seconds)
**Total running time of the script:** (0 minutes 6.537 seconds)

**Estimated memory usage:** 1006 MB
**Estimated memory usage:** 1014 MB


.. _sphx_glr_download_auto_examples_01_plotting_plot_carpet.py:
Expand Down
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