Dev docs nilearn/nilearn@d642bb8 : [REF] refactor surface fixtures (#…

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nilearn · Dec 17, 2024 · 117a7b9 · 117a7b9
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diff --git a/dev/_images/sphx_glr_plot_haxby_different_estimators_thumb.png b/dev/_images/sphx_glr_plot_haxby_different_estimators_thumb.png
diff --git a/dev/_images/sphx_glr_plot_haxby_full_analysis_001.png b/dev/_images/sphx_glr_plot_haxby_full_analysis_001.png
diff --git a/dev/_images/sphx_glr_plot_haxby_full_analysis_thumb.png b/dev/_images/sphx_glr_plot_haxby_full_analysis_thumb.png
diff --git a/dev/_images/sphx_glr_plot_haxby_grid_search_001.png b/dev/_images/sphx_glr_plot_haxby_grid_search_001.png
diff --git a/dev/_images/sphx_glr_plot_haxby_grid_search_thumb.png b/dev/_images/sphx_glr_plot_haxby_grid_search_thumb.png
diff --git a/dev/_images/sphx_glr_plot_haxby_mass_univariate_002.png b/dev/_images/sphx_glr_plot_haxby_mass_univariate_002.png
diff --git a/dev/_images/sphx_glr_plot_haxby_searchlight_001.png b/dev/_images/sphx_glr_plot_haxby_searchlight_001.png
diff --git a/dev/_images/sphx_glr_plot_haxby_searchlight_thumb.png b/dev/_images/sphx_glr_plot_haxby_searchlight_thumb.png
diff --git a/dev/_images/sphx_glr_plot_localizer_mass_univariate_methods_001.png b/dev/_images/sphx_glr_plot_localizer_mass_univariate_methods_001.png
diff --git a/dev/_images/sphx_glr_plot_localizer_mass_univariate_methods_thumb.png b/dev/_images/sphx_glr_plot_localizer_mass_univariate_methods_thumb.png
diff --git a/dev/_images/sphx_glr_plot_oasis_vbm_004.png b/dev/_images/sphx_glr_plot_oasis_vbm_004.png
diff --git a/dev/_images/sphx_glr_plot_second_level_association_test_003.png b/dev/_images/sphx_glr_plot_second_level_association_test_003.png
diff --git a/dev/_images/sphx_glr_plot_second_level_one_sample_test_003.png b/dev/_images/sphx_glr_plot_second_level_one_sample_test_003.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_002.png b/dev/_images/sphx_glr_plot_simulated_data_002.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_003.png b/dev/_images/sphx_glr_plot_simulated_data_003.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_004.png b/dev/_images/sphx_glr_plot_simulated_data_004.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_006.png b/dev/_images/sphx_glr_plot_simulated_data_006.png
diff --git a/dev/_images/sphx_glr_plot_surface_image_and_maskers_003.png b/dev/_images/sphx_glr_plot_surface_image_and_maskers_003.png
diff --git a/dev/_sources/auto_examples/00_tutorials/plot_3d_and_4d_niimg.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_3d_and_4d_niimg.rst.txt
@@ -127,7 +127,7 @@ statistical map:
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c7b7f8460>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5c65fa220>
 
 
 
@@ -156,7 +156,7 @@ Visualizing works better with a threshold
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c611c6c40>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5ac1ca910>
 
 
 
@@ -186,7 +186,6 @@ 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 1777664 of 7565016 bytes (23.5%%,    3.4s remaining)
     [fetch_single_file]  ...done. (2 seconds, 0 min)
 
 
@@ -271,7 +270,7 @@ We can then plot it
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c6112e9a0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5ac19da60>
 
 
 
@@ -489,9 +488,9 @@ image.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 20.869 seconds)
+   **Total running time of the script:** (0 minutes 22.550 seconds)
 
-**Estimated memory usage:**  397 MB
+**Estimated memory usage:**  395 MB
 
 
 .. _sphx_glr_download_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py:

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_decoding_tutorial.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_decoding_tutorial.rst.txt
diff --git a/dev/_sources/auto_examples/00_tutorials/plot_nilearn_101.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_nilearn_101.rst.txt
@@ -77,7 +77,7 @@ Let's quickly plot this file:
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c611e8550>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5c5cebd30>
 
 
 
@@ -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 0x7f2c611a3b50>
+    <nibabel.nifti1.Nifti1Image object at 0x7ff5c7b5b1c0>
 
 
 
@@ -154,7 +154,7 @@ instance to look at it
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c611c4df0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5c5ceb520>
 
 
 
@@ -184,7 +184,7 @@ We could also pass it to the smoothing function
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c71af5550>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5a2d81130>
 
 
 
@@ -228,23 +228,13 @@ 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 15376384 of 314803244 bytes (4.9%%,   20.3s 
+    [_chunk_report_] Downloaded 75776000 of 314803244 bytes (24.1%%,    3.2s 
     remaining)
-    [_chunk_report_] Downloaded 52592640 of 314803244 bytes (16.7%%,   10.3s 
+    [_chunk_report_] Downloaded 172900352 of 314803244 bytes (54.9%%,    1.6s 
     remaining)
-    [_chunk_report_] Downloaded 91045888 of 314803244 bytes (28.9%%,    7.6s 
+    [_chunk_report_] Downloaded 270360576 of 314803244 bytes (85.9%%,    0.5s 
     remaining)
-    [_chunk_report_] Downloaded 129400832 of 314803244 bytes (41.1%%,    5.9s 
-    remaining)
-    [_chunk_report_] Downloaded 168304640 of 314803244 bytes (53.5%%,    4.4s 
-    remaining)
-    [_chunk_report_] Downloaded 206716928 of 314803244 bytes (65.7%%,    3.2s 
-    remaining)
-    [_chunk_report_] Downloaded 245497856 of 314803244 bytes (78.0%%,    2.0s 
-    remaining)
-    [_chunk_report_] Downloaded 284647424 of 314803244 bytes (90.4%%,    0.9s 
-    remaining)
-    [fetch_single_file]  ...done. (9 seconds, 0 min)
+    [fetch_single_file]  ...done. (4 seconds, 0 min)
 
     [uncompress_file] Extracting data from 
     /home/runner/nilearn_data/haxby2001/b2fd65a88d22090da62c3fb828be840e/subj1-2010.
@@ -253,23 +243,13 @@ 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 21831680 of 291168628 bytes (7.5%%,   12.6s 
-    remaining)
-    [_chunk_report_] Downloaded 55689216 of 291168628 bytes (19.1%%,    8.6s 
-    remaining)
-    [_chunk_report_] Downloaded 93863936 of 291168628 bytes (32.2%%,    6.4s 
-    remaining)
-    [_chunk_report_] Downloaded 132513792 of 291168628 bytes (45.5%%,    4.9s 
-    remaining)
-    [_chunk_report_] Downloaded 170582016 of 291168628 bytes (58.6%%,    3.6s 
-    remaining)
-    [_chunk_report_] Downloaded 208289792 of 291168628 bytes (71.5%%,    2.4s 
+    [_chunk_report_] Downloaded 76292096 of 291168628 bytes (26.2%%,    2.8s 
     remaining)
-    [_chunk_report_] Downloaded 246546432 of 291168628 bytes (84.7%%,    1.3s 
+    [_chunk_report_] Downloaded 173285376 of 291168628 bytes (59.5%%,    1.4s 
     remaining)
-    [_chunk_report_] Downloaded 284876800 of 291168628 bytes (97.8%%,    0.2s 
+    [_chunk_report_] Downloaded 271990784 of 291168628 bytes (93.4%%,    0.2s 
     remaining)
-    [fetch_single_file]  ...done. (8 seconds, 0 min)
+    [fetch_single_file]  ...done. (3 seconds, 0 min)
 
     [uncompress_file] Extracting data from 
     /home/runner/nilearn_data/haxby2001/b2fd65a88d22090da62c3fb828be840e/subj2-2010.
@@ -405,7 +385,7 @@ passed on to other nilearn tools, or saved to disk.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 28.615 seconds)
+   **Total running time of the script:** (0 minutes 17.983 seconds)
 
 **Estimated memory usage:**  299 MB
 

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_python_101.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_python_101.rst.txt
@@ -67,14 +67,14 @@ A simple example of basic Python numerics and how to plot it.
  .. code-block:: none
 
 
-    [<matplotlib.lines.Line2D object at 0x7f2c7cdf9970>]
+    [<matplotlib.lines.Line2D object at 0x7ff5c7bf9a30>]
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.190 seconds)
+   **Total running time of the script:** (0 minutes 0.193 seconds)
 
 **Estimated memory usage:**  110 MB
 

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_single_subject_single_run.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_single_subject_single_run.rst.txt
@@ -65,20 +65,35 @@ 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 1081344 of 30176409 bytes (3.6%%,   27.7s remaining)
-    [_chunk_report_] Downloaded 5799936 of 30176409 bytes (19.2%%,    8.6s 
+    [_chunk_report_] Downloaded 3440640 of 30176409 bytes (11.4%%,    8.2s 
     remaining)
-    [_chunk_report_] Downloaded 9895936 of 30176409 bytes (32.8%%,    6.3s 
+    [_chunk_report_] Downloaded 7864320 of 30176409 bytes (26.1%%,    6.1s 
     remaining)
-    [_chunk_report_] Downloaded 14237696 of 30176409 bytes (47.2%%,    4.6s 
+    [_chunk_report_] Downloaded 9830400 of 30176409 bytes (32.6%%,    6.5s 
     remaining)
-    [_chunk_report_] Downloaded 18718720 of 30176409 bytes (62.0%%,    3.1s 
+    [_chunk_report_] Downloaded 11788288 of 30176409 bytes (39.1%%,    6.5s 
     remaining)
-    [_chunk_report_] Downloaded 23273472 of 30176409 bytes (77.1%%,    1.8s 
+    [_chunk_report_] Downloaded 13918208 of 30176409 bytes (46.1%%,    6.1s 
     remaining)
-    [_chunk_report_] Downloaded 27860992 of 30176409 bytes (92.3%%,    0.6s 
+    [_chunk_report_] Downloaded 15982592 of 30176409 bytes (53.0%%,    5.5s 
     remaining)
-    [fetch_single_file]  ...done. (9 seconds, 0 min)
+    [_chunk_report_] Downloaded 18137088 of 30176409 bytes (60.1%%,    4.8s 
+    remaining)
+    [_chunk_report_] Downloaded 20037632 of 30176409 bytes (66.4%%,    4.2s 
+    remaining)
+    [_chunk_report_] Downloaded 21757952 of 30176409 bytes (72.1%%,    3.6s 
+    remaining)
+    [_chunk_report_] Downloaded 23674880 of 30176409 bytes (78.5%%,    2.8s 
+    remaining)
+    [_chunk_report_] Downloaded 25665536 of 30176409 bytes (85.1%%,    2.0s 
+    remaining)
+    [_chunk_report_] Downloaded 27033600 of 30176409 bytes (89.6%%,    1.4s 
+    remaining)
+    [_chunk_report_] Downloaded 28295168 of 30176409 bytes (93.8%%,    0.9s 
+    remaining)
+    [_chunk_report_] Downloaded 29614080 of 30176409 bytes (98.1%%,    0.3s 
+    remaining)
+    [fetch_single_file]  ...done. (16 seconds, 0 min)
 
     [uncompress_file] Extracting data from 
     /home/runner/nilearn_data/spm_auditory/MoAEpilot.bids.zip...
@@ -1256,9 +1271,9 @@ which makes it easier to represent it.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 25.564 seconds)
+   **Total running time of the script:** (0 minutes 32.654 seconds)
 
-**Estimated memory usage:**  733 MB
+**Estimated memory usage:**  738 MB
 
 
 .. _sphx_glr_download_auto_examples_00_tutorials_plot_single_subject_single_run.py:

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_surface_101.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_surface_101.rst.txt
@@ -1333,9 +1333,9 @@ See following examples for more details:
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.015 seconds)
+   **Total running time of the script:** (0 minutes 0.992 seconds)
 
-**Estimated memory usage:**  108 MB
+**Estimated memory usage:**  109 MB
 
 
 .. _sphx_glr_download_auto_examples_00_tutorials_plot_surface_101.py:

diff --git a/dev/_sources/auto_examples/00_tutorials/sg_execution_times.rst.txt b/dev/_sources/auto_examples/00_tutorials/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**01:55.098** total execution time for 6 files **from auto_examples/00_tutorials**:
+**01:51.930** total execution time for 6 files **from auto_examples/00_tutorials**:
 
 .. container::
 
@@ -33,20 +33,20 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_decoding_tutorial.py` (``plot_decoding_tutorial.py``)
-     - 00:38.844
-     - 1007.4
-   * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_nilearn_101.py` (``plot_nilearn_101.py``)
-     - 00:28.615
-     - 299.0
+     - 00:37.558
+     - 1008.5
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_single_subject_single_run.py` (``plot_single_subject_single_run.py``)
-     - 00:25.564
-     - 732.9
+     - 00:32.654
+     - 738.4
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py` (``plot_3d_and_4d_niimg.py``)
-     - 00:20.869
-     - 396.7
+     - 00:22.550
+     - 394.9
+   * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_nilearn_101.py` (``plot_nilearn_101.py``)
+     - 00:17.983
+     - 299.5
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_surface_101.py` (``plot_surface_101.py``)
-     - 00:01.015
-     - 107.6
+     - 00:00.992
+     - 109.2
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_python_101.py` (``plot_python_101.py``)
-     - 00:00.190
-     - 110.3
+     - 00:00.193
+     - 110.4
diff --git a/dev/_sources/auto_examples/01_plotting/plot_3d_map_to_surface_projection.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_3d_map_to_surface_projection.rst.txt
@@ -293,7 +293,7 @@ Plot 3D image for comparison
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.XSlicer object at 0x7f2c60b54f40>
+    <nilearn.plotting.displays._slicers.XSlicer object at 0x7ff5ab976910>
 
 
 
@@ -468,11 +468,25 @@ 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 15482880 of 34242788 bytes (45.2%%,    1.2s 
+    [_chunk_report_] Downloaded 4726784 of 34242788 bytes (13.8%%,    6.6s 
     remaining)
-    [_chunk_report_] Downloaded 29540352 of 34242788 bytes (86.3%%,    0.3s 
+    [_chunk_report_] Downloaded 7602176 of 34242788 bytes (22.2%%,    7.4s 
     remaining)
-    [fetch_single_file]  ...done. (4 seconds, 0 min)
+    [_chunk_report_] Downloaded 10993664 of 34242788 bytes (32.1%%,    6.6s 
+    remaining)
+    [_chunk_report_] Downloaded 14475264 of 34242788 bytes (42.3%%,    5.6s 
+    remaining)
+    [_chunk_report_] Downloaded 17793024 of 34242788 bytes (52.0%%,    4.8s 
+    remaining)
+    [_chunk_report_] Downloaded 21446656 of 34242788 bytes (62.6%%,    3.7s 
+    remaining)
+    [_chunk_report_] Downloaded 25894912 of 34242788 bytes (75.6%%,    2.3s 
+    remaining)
+    [_chunk_report_] Downloaded 30072832 of 34242788 bytes (87.8%%,    1.1s 
+    remaining)
+    [_chunk_report_] Downloaded 32694272 of 34242788 bytes (95.5%%,    0.4s 
+    remaining)
+    [fetch_single_file]  ...done. (13 seconds, 0 min)
 
     [uncompress_file] Extracting data from 
     /home/runner/nilearn_data/fsaverage/735bf0f211246c83396b5f21f706c224/download...
@@ -934,7 +948,7 @@ 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
@@ -1265,9 +1279,9 @@ Using nearest-neighbor interpolation with zero radius will achieve this.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 29.971 seconds)
+   **Total running time of the script:** (0 minutes 37.345 seconds)
 
-**Estimated memory usage:**  564 MB
+**Estimated memory usage:**  584 MB
 
 
 .. _sphx_glr_download_auto_examples_01_plotting_plot_3d_map_to_surface_projection.py:

diff --git a/dev/_sources/auto_examples/01_plotting/plot_atlas.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_atlas.rst.txt
@@ -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 17489920 of 25716861 bytes (68.0%%,    0.5s 
-    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
@@ -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...
@@ -107,7 +105,7 @@ Visualizing the Harvard-Oxford atlas
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c60a2f970>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5ac06e460>
 
 
 
@@ -137,7 +135,7 @@ Visualizing the Juelich atlas
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f2c60e5b100>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff5abe43340>
 
 
 
@@ -205,9 +203,9 @@ Visualizing the Juelich atlas with contours
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 59.849 seconds)
+   **Total running time of the script:** (1 minutes 2.969 seconds)
 
-**Estimated memory usage:**  162 MB
+**Estimated memory usage:**  108 MB
 
 
 .. _sphx_glr_download_auto_examples_01_plotting_plot_atlas.py:

diff --git a/dev/_sources/auto_examples/01_plotting/plot_carpet.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_carpet.rst.txt
@@ -208,9 +208,9 @@ Visualizing global patterns, separated by tissue type
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 6.087 seconds)
+   **Total running time of the script:** (0 minutes 6.018 seconds)
 
-**Estimated memory usage:**  1008 MB
+**Estimated memory usage:**  1108 MB
 
 
 .. _sphx_glr_download_auto_examples_01_plotting_plot_carpet.py: