Merge branch 'main' into 2405

.pre-commit-config.yaml

@@ -50,7 +50,7 @@ repos:
     -   id: flynt
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.1
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
@@ -62,7 +62,7 @@ repos:
     -   id: rst-inline-touching-normal
 
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.1.1
+    rev: 24.2.0
     hooks:
     -   id: black
         args: [--config, pyproject.toml]

doc/changes/latest.rst

@@ -8,7 +8,9 @@
 Fixes
 -----
 
-- :bdg-dark:`Code` Fix errant warning when using ``stat_type`` in :func:`nilearn.glm.compute_contrast` (:gh:`4257` by `Eric Larson`_)
+- :bdg-dark:`Code` Fix errant warning when using ``stat_type`` in :func:`nilearn.glm.compute_contrast` (:gh:`4257` by `Eric Larson`_).
+- :bdg-dark:`Code` Fix when thresholding is applied to images by GLM reports (:gh:`4258` by `Rémi Gau`_).
+- :bdg-dark:`Code` Make sure that :class:`nilearn.maskers.NiftiSpheresMasker` reports displays properly when it contains only 1 sphere (:gh:`4269` by `Rémi Gau`_).
 
 Enhancements
 ------------
@@ -17,3 +19,4 @@ Changes
 -------
 
 - :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`_).

nilearn/maskers/nifti_spheres_masker.py

@@ -333,13 +333,13 @@ def __init__(
         # Parameters for reporting
         self.reports = reports
         self.report_id = -1
-        self._report_content = dict()
-        self._report_content["description"] = (
-            "This reports shows the regions "
-            "defined by the spheres of the masker."
-        )
-        self._report_content["warning_message"] = None
-
+        self._report_content = {
+            "description": (
+                "This reports shows the regions defined "
+                "by the spheres of the masker."
+            ),
+            "warning_message": None,
+        }
         self.verbose = verbose
 
     def generate_report(self, displayed_spheres="all"):
@@ -506,7 +506,9 @@ def _reporting(self):
             )
             regions_summary["relative size (in %)"].append("not implemented")
             if idx in spheres_to_be_displayed:
-                display = plotting.plot_img(img, cut_coords=positions[idx])
+                display = plotting.plot_img(
+                    img, cut_coords=positions[idx], cmap="gray"
+                )
                 display.add_markers(
                     marker_coords=[positions[idx]],
                     marker_color="g",

nilearn/reporting/data/README.txt → nilearn/reporting/data/README.md

@@ -1,4 +1,3 @@
 This directory contains files required for nilearn reporting.
 
 html/                        : templates for HTML files
-css/                         : styling sheets

nilearn/reporting/data/html/report_body_template.html

@@ -140,7 +140,7 @@
   font-size: 12pt;
   font-weight: 200;
   border-radius: 6px;
-  padding: 5px;css=resource_path.joinpath('css'),
+  padding: 5px;
 
   margin-left: 3pt;
 

nilearn/reporting/data/html/report_body_template_niftilabelsmasker.html

@@ -140,8 +140,7 @@
   font-size: 12pt;
   font-weight: 200;
   border-radius: 6px;
-  padding: 5px;css=resource_path.joinpath('css'),
-
+  padding: 5px;
   margin-left: 3pt;
 
   /* Position the tooltip text - see examples below! */

nilearn/reporting/data/html/report_body_template_niftimapsmasker.html

@@ -141,8 +141,7 @@
   font-size: 12pt;
   font-weight: 200;
   border-radius: 6px;
-  padding: 5px;css=resource_path.joinpath('css'),
-
+  padding: 5px;
   margin-left: 3pt;
 
   /* Position the tooltip text - see examples below! */

nilearn/reporting/data/html/report_body_template_niftispheresmasker.html

@@ -141,8 +141,7 @@
   font-size: 12pt;
   font-weight: 200;
   border-radius: 6px;
-  padding: 5px;css=resource_path.joinpath('css'),
-
+  padding: 5px;
   margin-left: 3pt;
 
   /* Position the tooltip text - see examples below! */

nilearn/reporting/glm_reporter.py

@@ -227,8 +227,7 @@ def make_glm_report(
             mask_img = model.masker_.mask_img_
 
     mask_plot_html_code = _mask_to_svg(
-        mask_img=mask_img,
-        bg_img=bg_img,
+        mask_img=mask_img, bg_img=bg_img, cut_coords=cut_coords
     )
     all_components = _make_stat_maps_contrast_clusters(
         stat_img=statistical_maps,
@@ -635,7 +634,7 @@ def _resize_plot_inches(plot, width_change=0, height_change=0):
     return plot
 
 
-def _mask_to_svg(mask_img, bg_img):
+def _mask_to_svg(mask_img, bg_img, cut_coords=None):
     """Plot cuts of an mask image and creates SVG code of it.
 
     Parameters
@@ -662,6 +661,7 @@ def _mask_to_svg(mask_img, bg_img):
             bg_img=bg_img,
             display_mode="z",
             cmap="Set1",
+            cut_coords=cut_coords,
         )
         mask_plot_svg = _plot_to_svg(plt.gcf())
         # prevents sphinx-gallery & jupyter from scraping & inserting plots
@@ -769,30 +769,40 @@ def _make_stat_maps_contrast_clusters(
         components_template_text = html_template_obj.read()
     for contrast_name, stat_map_img in stat_img.items():
         component_text_ = string.Template(components_template_text)
-        thresholded_stat_map, threshold = threshold_stats_img(
+
+        # Only use threshold_stats_img to adjust the threshold
+        # that we will pass to  _clustering_params_to_dataframe
+        # and _stat_map_to_svg
+        # Necessary to avoid :
+        # https://github.com/nilearn/nilearn/issues/4192
+        thresholded_img, threshold = threshold_stats_img(
             stat_img=stat_map_img,
             threshold=threshold,
             alpha=alpha,
             cluster_threshold=cluster_threshold,
             height_control=height_control,
         )
+
         table_details = _clustering_params_to_dataframe(
             threshold,
             cluster_threshold,
             min_distance,
             height_control,
             alpha,
         )
+
         stat_map_svg = _stat_map_to_svg(
-            stat_img=thresholded_stat_map,
+            stat_img=thresholded_img,
+            threshold=threshold,
             bg_img=bg_img,
             cut_coords=cut_coords,
             display_mode=display_mode,
             plot_type=plot_type,
             table_details=table_details,
         )
+
         cluster_table = get_clusters_table(
-            stat_map_img,
+            thresholded_img,
             stat_threshold=threshold,
             cluster_threshold=cluster_threshold,
             min_distance=min_distance,
@@ -897,6 +907,7 @@ def _clustering_params_to_dataframe(
 @fill_doc
 def _stat_map_to_svg(
     stat_img,
+    threshold,
     bg_img,
     cut_coords,
     display_mode,
@@ -913,6 +924,9 @@ def _stat_map_to_svg(
        to be plotted as slices or glass brain.
        Does not perform any thresholding.
 
+    threshold : float
+       Desired threshold in z-scale.
+
     bg_img : Niimg-like object
         Only used when plot_type is 'slice'.
         See :ref:`extracting_data`.
@@ -971,6 +985,7 @@ def _stat_map_to_svg(
             colorbar=True,
             cmap=cmap,
             symmetric_cbar=symmetric_cbar,
+            threshold=threshold,
         )
     elif plot_type == "glass":
         stat_map_plot = plot_glass_brain(
@@ -980,6 +995,7 @@ def _stat_map_to_svg(
             plot_abs=False,
             symmetric_cbar=True,
             cmap=cmap,
+            threshold=threshold,
         )
     else:
         raise ValueError(

nilearn/reporting/html_report.py

@@ -7,6 +7,7 @@
 from string import Template
 
 from nilearn.externals import tempita
+from nilearn.maskers import NiftiSpheresMasker
 from nilearn.plotting.html_document import HTMLDocument
 from nilearn.reporting.utils import figure_to_svg_base64
 
@@ -163,6 +164,9 @@ def _define_overlay(estimator):
     if len(displays) == 1:  # set overlay to None
         overlay, image = None, displays[0]
 
+    elif isinstance(estimator, NiftiSpheresMasker):
+        overlay, image = None, displays
+
     elif len(displays) == 2:
         overlay, image = displays[0], displays[1]
 

nilearn/reporting/tests/test_glm_reporter.py

@@ -234,6 +234,7 @@ def test_stat_map_to_svg_slice_z(img_3d_mni, cut_coords):
         display_mode="ortho",
         plot_type="slice",
         table_details=table_details,
+        threshold=2.76,
     )
 
 
@@ -247,6 +248,7 @@ def test_stat_map_to_svg_glass_z(img_3d_mni, cut_coords):
         display_mode="z",
         plot_type="glass",
         table_details=table_details,
+        threshold=2.76,
     )
 
 
@@ -264,6 +266,7 @@ def test_stat_map_to_svg_invalid_plot_type(img_3d_mni, cut_coords):
             display_mode="z",
             plot_type="junk",
             table_details={"junk": 0},
+            threshold=2.76,
         )
 
 

nilearn/reporting/tests/test_html_report.py

@@ -323,6 +323,21 @@ def test_nifti_spheres_masker_report_displayed_spheres_list_more_than_seeds():
         masker.generate_report(displayed_spheres=displayed_spheres)
 
 
+def test_nifti_spheres_masker_report_1_sphere():
+    """Check the report for sphere actually works for one sphere.
+
+    See https://github.com/nilearn/nilearn/issues/4268
+    """
+    report = NiftiSpheresMasker([(1, 1, 1)]).fit().generate_report()
+
+    empty_div = """
+                    <img id="map1" class="pure-img" width="100%"
+                        src="data:image/svg+xml;base64,D"
+                        style="display:none;" alt="image"/>"""
+
+    assert empty_div not in report.body
+
+
 def test_nifti_labels_masker_report_smoke_test(labels, labels_img):
     """Smoke test."""
     labels_img_floats = new_img_like(