[DOC] display all masker reports in the doc

.github/codespell_ignore_words.txt

@@ -9,4 +9,5 @@ mapp
 nin
 serie
 fwe
+fo
 coo

.gitignore

@@ -38,6 +38,9 @@ build
 dist/
 nilearn/_version.py
 
+# notebooks
+.ipynb_checkpoints
+
 # virtual environment
 env/
 venv/

doc/changes/latest.rst

@@ -25,7 +25,7 @@ Enhancements
 Changes
 -------
 
-- :bdg-primary:`Doc` Render several examples of GLM reports as part of the documentation (:gh:`4267` by `Rémi Gau`_).
+- :bdg-primary:`Doc` Render examples of GLM and masker reports as part of the documentation (:gh:`4267` and :gh:`4295` by `Rémi Gau`_).
 - :bdg-dark:`Code` Improve colorbar size and labels in mosaic display (:gh:`4284` by `Rémi Gau`_).
 - :bdg-primary:`Doc` Render the description of the templates, atlases and datasets of the :mod:`nilearn.datasets` as part of the documentation (:gh:`4232` by `Rémi Gau`_).
 - :bdg-dark:`Code` Change the colormap to ``gray`` for the background image in the :class:`nilearn.maskers.NiftiSpheresMasker` (:gh:`4269` by `Rémi Gau`_).

doc/modules/generated_reports/masker_reports_examples.rst

@@ -5,10 +5,50 @@
 Examples masker reports
 =======================
 
+Nifti masker
+------------
+
+.. raw:: html
+   :file: nifti_masker.html
+
+.. raw:: html
+   :file: multi_nifti_masker.html
+
+.. raw:: html
+   :file: multi_nifti_masker_fitted.html
+
+
+Nifti labels masker
+-------------------
+
+.. raw:: html
+   :file: nifti_labels_masker_fitted.html
+
+.. raw:: html
+   :file: nifti_labels_masker_atlas.html
+
+.. raw:: html
+   :file: multi_nifti_labels_masker_atlas.html
+
+.. raw:: html
+   :file: multi_nifti_labels_masker_fitted.html
+
+Nifti maps masker
+-----------------
+
+.. raw:: html
+   :file: nifti_maps_masker.html
+
+.. raw:: html
+   :file: multi_nifti_maps_masker_atlas.html
+
+.. raw:: html
+   :file: multi_nifti_maps_masker_fitted.html
+
 Nifti sphere masker
 -------------------
 
 Adapted from :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_adhd_dmn.py`
 
 .. raw:: html
-   :file: flm_adhd_dmn_sphere_masker.html
+   :file: nifti_sphere_masker.html

doc/visual_testing/reporter_visual_inspection_suite.py

@@ -21,7 +21,15 @@
 from nilearn.glm.second_level import SecondLevelModel
 from nilearn.image import mean_img, resample_to_img
 from nilearn.interfaces.fsl import get_design_from_fslmat
-from nilearn.maskers import NiftiSpheresMasker
+from nilearn.maskers import (
+    MultiNiftiLabelsMasker,
+    MultiNiftiMapsMasker,
+    MultiNiftiMasker,
+    NiftiLabelsMasker,
+    NiftiMapsMasker,
+    NiftiMasker,
+    NiftiSpheresMasker,
+)
 from nilearn.reporting import make_glm_report
 
 REPORTS_DIR = Path(__file__).parent.parent / "modules" / "generated_reports"
@@ -35,9 +43,8 @@ def report_flm_adhd_dmn():
     t_r = 2.0
     slice_time_ref = 0.0
     n_scans = 176
-    pcc_coords = (0, -53, 26)
 
-    adhd_dataset = datasets.fetch_adhd(n_subjects=1)
+    pcc_coords = (0, -53, 26)
 
     seed_masker = NiftiSpheresMasker(
         [pcc_coords],
@@ -48,13 +55,13 @@ def report_flm_adhd_dmn():
         high_pass=0.01,
         t_r=t_r,
         memory="nilearn_cache",
-        memory_level=1,
-        verbose=0,
     )
 
+    adhd_dataset = datasets.fetch_adhd(n_subjects=1)
     seed_time_series = seed_masker.fit_transform(adhd_dataset.func[0])
-    report = seed_masker.generate_report()
-    report.save_as_html(REPORTS_DIR / "flm_adhd_dmn_sphere_masker.html")
+
+    masker_report = seed_masker.generate_report()
+    masker_report.save_as_html(REPORTS_DIR / "nifti_sphere_masker.html")
 
     frametimes = np.linspace(0, (n_scans - 1) * t_r, n_scans)
 
@@ -72,7 +79,7 @@ def report_flm_adhd_dmn():
         run_imgs=adhd_dataset.func[0], design_matrices=design_matrix
     )
 
-    report = make_glm_report(
+    glm_report = make_glm_report(
         first_level_model,
         contrasts=contrasts,
         title="ADHD DMN Report",
@@ -83,9 +90,9 @@ def report_flm_adhd_dmn():
         plot_type="glass",
         report_dims=(1200, "a"),
     )
+    glm_report.save_as_html(REPORTS_DIR / "flm_adhd_dmn.html")
 
-    report.save_as_html(REPORTS_DIR / "flm_adhd_dmn.html")
-    report.get_iframe()
+    return masker_report, glm_report
 
 
 # %%
@@ -181,7 +188,7 @@ def report_flm_bids_features():
     )
 
     report.save_as_html(REPORTS_DIR / "flm_bids_features.html")
-    report.get_iframe()
+    return report
 
 
 # %%
@@ -216,9 +223,8 @@ def report_flm_fiac():
         bg_img=mean_img_,
         height_control="fdr",
     )
-
     report.save_as_html(REPORTS_DIR / "flm_fiac.html")
-    report.get_iframe()
+    return report
 
 
 # %%
@@ -269,16 +275,173 @@ def report_slm_oasis():
         height_control=None,
         plot_type="glass",
     )
-
     report.save_as_html(REPORTS_DIR / "slm_oasis.html")
-    report.get_iframe()
+    return report
+
+
+# %%
+# Adapted from examples/03_connectivity/plot_probabilistic_atlas_extraction.py
+def report_nifti_maps_masker():
+
+    atlas = datasets.fetch_atlas_msdl()
+    atlas_filename = atlas["maps"]
+
+    data = datasets.fetch_development_fmri(n_subjects=1)
+
+    masker = NiftiMapsMasker(
+        maps_img=atlas_filename,
+        standardize="zscore_sample",
+        standardize_confounds="zscore_sample",
+        memory="nilearn_cache",
+        cmap="grey",
+    )
+    masker.fit(data.func[0])
+
+    report = masker.generate_report(displayed_maps=[2, 6, 7, 16, 21])
+    report.save_as_html(REPORTS_DIR / "nifti_maps_masker.html")
+    return report
+
+
+#  %%
+# Adapted from examples/06_manipulating_images/plot_nifti_labels_simple.py
+def report_nifti_labels_masker():
+
+    atlas = datasets.fetch_atlas_schaefer_2018()
+
+    atlas.labels = np.insert(atlas.labels, 0, "Background")
+
+    masker = NiftiLabelsMasker(
+        atlas.maps,
+        labels=atlas.labels,
+        standardize="zscore_sample",
+    )
+    masker.fit()
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "nifti_labels_masker_atlas.html")
+
+    data = datasets.fetch_development_fmri(n_subjects=1)
+    masker.fit(data.func[0])
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "nifti_labels_masker_fitted.html")
+    return report
+
+
+#  %%
+# Adapted from examples/06_manipulating_images/plot_nifti_simple.py
+def report_nifti_masker():
+
+    masker = NiftiMasker(
+        standardize="zscore_sample",
+        mask_strategy="epi",
+        memory="nilearn_cache",
+        memory_level=2,
+        smoothing_fwhm=8,
+        cmap="grey",
+    )
+
+    data = datasets.fetch_development_fmri(n_subjects=1)
+    masker.fit(data.func[0])
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "nifti_masker.html")
+    return report
+
+
+def report_multi_nifti_masker():
+
+    data = datasets.fetch_miyawaki2008()
+
+    masker = MultiNiftiMasker(
+        mask_img=data.mask,
+        detrend=True,
+        standardize="zscore_sample",
+        n_jobs=2,
+        cmap="grey",
+    )
+    masker.fit()
+    empty_report = masker.generate_report()
+    empty_report.save_as_html(REPORTS_DIR / "multi_nifti_masker.html")
+
+    fmri_random_runs_filenames = data.func[12:]
+    masker.fit(fmri_random_runs_filenames)
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "multi_nifti_masker_fitted.html")
+    return empty_report, report
+
+
+#  %%
+#  Adapted from examples/03_connectivity/plot_atlas_comparison.py
+def report_multi_nifti_labels_masker():
+
+    yeo = datasets.fetch_atlas_yeo_2011()
+
+    data = datasets.fetch_development_fmri(n_subjects=2)
+
+    masker = MultiNiftiLabelsMasker(
+        labels_img=yeo["thick_17"],
+        standardize="zscore_sample",
+        standardize_confounds="zscore_sample",
+        memory="nilearn_cache",
+        n_jobs=2,
+    )
+
+    masker.fit()
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "multi_nifti_labels_masker_atlas.html")
+
+    _ = masker.fit_transform(data.func, confounds=data.confounds)
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "multi_nifti_labels_masker_fitted.html")
+    return report
+
+
+#  %%
+#  Adapted from examples/03_connectivity/plot_atlas_comparison.py
+def report_multi_nifti_maps_masker():
+
+    difumo = datasets.fetch_atlas_difumo(
+        dimension=64, resolution_mm=2, legacy_format=False
+    )
+
+    data = datasets.fetch_development_fmri(n_subjects=2)
+
+    masker = MultiNiftiMapsMasker(
+        maps_img=difumo.maps,
+        standardize="zscore_sample",
+        standardize_confounds="zscore_sample",
+        memory="nilearn_cache",
+        n_jobs=2,
+    )
+
+    masker.fit()
+    empty_report = masker.generate_report()
+    empty_report.save_as_html(
+        REPORTS_DIR / "multi_nifti_maps_masker_atlas.html"
+    )
+
+    _ = masker.fit_transform(data.func, confounds=data.confounds)
+    report = masker.generate_report()
+    report.save_as_html(REPORTS_DIR / "multi_nifti_maps_masker_fitted.html")
+
+    return empty_report, report
 
 
 # %%
 if __name__ == "__main__":
 
-    print("\nGenerating GLM reports templates\n")
+    print("\nGenerating masker reports templates\n")
+    t0 = time.time()
+
+    report_nifti_masker()
+    report_nifti_maps_masker()
+    report_nifti_labels_masker()
+    report_multi_nifti_masker()
+    report_multi_nifti_labels_masker()
+    report_multi_nifti_maps_masker()
 
+    t1 = time.time()
+    print(f"\nTook: {(t1 - t0)} seconds\n")
+
+    print("\nGenerating GLM reports templates\n")
     t0 = time.time()
 
     report_flm_adhd_dmn()
@@ -287,5 +450,4 @@ def report_slm_oasis():
     report_slm_oasis()
 
     t1 = time.time()
-
-    print(f"\nRun took: {(t1 - t0)} seconds\n")
+    print(f"\nTook: {(t1 - t0)} seconds\n")