Merge branch 'main' into doc/add-usecase

CHANGES.rst

@@ -1,3 +1,15 @@
+23.2.2 (August 19, 2024)
+========================
+Bug-fix release in the 23.2.x series.
+
+CHANGES
+-------
+
+**Full Changelog**: https://github.com/nipreps/nireports/compare/23.2.1...23.2.2
+
+* ENH: Support PNGs and JPGs in reportlets (#126)
+
+
 23.2.1 (May 07, 2024)
 =====================
 Bug-fix release in the 23.2.x series.

nireports/assembler/data/rating-widget/bootstrap.yml

@@ -7,7 +7,7 @@ defaults:
   endpoint: "https://localhost:8000/"
   access_token: <secret_token>
 settings:
-  style: 'width: 30%; top: 100px; left: 65%;'
+  style: 'width: 30%; top: 100px; left: 65%; max-height: 85%; overflow-y: auto;'
   navbar_label: Rating widget
   mintime: 10
 components:

nireports/assembler/report.py

@@ -96,7 +96,7 @@ class Report:
        ...     dirs_exist_ok=True,
        ... )
        >>> REPORT_BASELINE_LENGTH = 41770
-       >>> RATING_WIDGET_LENGTH = 83308
+       >>> RATING_WIDGET_LENGTH = 83343
 
 
     Examples

nireports/assembler/reportlet.py

@@ -33,22 +33,21 @@
 from nireports.assembler import data
 from nireports.assembler.misc import dict2html, read_crashfile
 
-SVG_SNIPPET = [
-    """\
+IMG_SNIPPET = """\
 <div class="reportlet">
-<object class="svg-reportlet" type="image/svg+xml" data="./{name}" style="{style}">
-Problem loading figure {name}. If the link below works, please try \
-reloading the report in your browser.</object>
+<img class="{ext}-reportlet" src="./{name}" style="{style}" />
 </div>
 <small>Get figure file: <a href="./{name}" target="_blank">{name}</a></small>
-""",
-    """\
+"""
+
+SVG_SNIPPET = """\
 <div class="reportlet">
-<img class="svg-reportlet" src="./{name}" style="{style}" />
+<object class="{ext}-reportlet" type="image/{ext}+xml" data="./{name}" style="{style}">
+Problem loading figure {name}. If the link below works, please try \
+reloading the report in your browser.</object>
 </div>
 <small>Get figure file: <a href="./{name}" target="_blank">{name}</a></small>
-""",
-]
+"""
 
 METADATA_ACCORDION_BLOCK = """\
 <div class="accordion accordion-flush" id="{metadata_id}">
@@ -265,10 +264,36 @@ def __init__(self, layout, config=None, out_dir=None, bids_filters=None, metadat
                     style = {"width": "100%"} if is_static else {}
                     style.update(config.get("style", {}))
 
-                    contents = SVG_SNIPPET[is_static].format(
+                    snippet = IMG_SNIPPET if is_static else SVG_SNIPPET
+                    contents = snippet.format(
+                        ext=ext[1:],
                         name=html_anchor,
                         style="; ".join(f"{k}: {v}" for k, v in style.items()),
                     )
+                elif ext in (".png", ".jpg", ".jpeg"):
+                    entities = dict(bidsfile.entities)
+                    if desc_text:
+                        desc_text = desc_text.format(**entities)
+
+                    try:
+                        html_anchor = src.relative_to(out_dir)
+                    except ValueError:
+                        html_anchor = src.relative_to(Path(layout.root))
+                        dst = out_dir / html_anchor
+                        dst.parent.mkdir(parents=True, exist_ok=True)
+                        copyfile(src, dst, copy=True, use_hardlink=True)
+
+                    style = {"width": "100%"}
+                    style.update(config.get("style", {}))
+
+                    snippet = IMG_SNIPPET
+                    contents = snippet.format(
+                        ext=ext[1:],
+                        name=html_anchor,
+                        style="; ".join(f"{k}: {v}" for k, v in style.items()),
+                    )
+                else:
+                    raise RuntimeError(f"Unsupported file extension: {ext}")
 
                 if contents:
                     self.components.append((contents, desc_text))

nireports/conftest.py

@@ -41,6 +41,14 @@
 test_workdir = os.getenv("TEST_WORK_DIR")
 
 
+@pytest.fixture(scope="session", autouse=True)
+def legacy_printoptions():
+    from packaging.version import Version
+
+    if Version(np.__version__) >= Version("1.22"):
+        np.set_printoptions(legacy="1.21")
+
+
 @pytest.fixture(autouse=True)
 def expand_namespace(doctest_namespace):
     doctest_namespace["PY_VERSION"] = version_info

nireports/interfaces/__init__.py

@@ -24,11 +24,16 @@
 
 from nireports.interfaces.fmri import FMRISummary
 from nireports.interfaces.mosaic import PlotContours, PlotMosaic, PlotSpikes
-from nireports.interfaces.nuisance import CompCorVariancePlot, ConfoundsCorrelationPlot
+from nireports.interfaces.nuisance import (
+    CompCorVariancePlot,
+    ConfoundsCorrelationPlot,
+    RaincloudPlot,
+)
 
 __all__ = (
     "CompCorVariancePlot",
     "ConfoundsCorrelationPlot",
+    "RaincloudPlot",
     "FMRISummary",
     "PlotContours",
     "PlotMosaic",

nireports/interfaces/nuisance.py

@@ -32,7 +32,7 @@
 )
 from nipype.utils.filemanip import fname_presuffix
 
-from nireports.reportlets.nuisance import confounds_correlation_plot
+from nireports.reportlets.nuisance import confounds_correlation_plot, plot_raincloud
 from nireports.reportlets.xca import compcor_variance_plot
 
 
@@ -142,3 +142,109 @@ def _run_interface(self, runtime):
             ignore_initial_volumes=self.inputs.ignore_initial_volumes,
         )
         return runtime
+
+
+class _RaincloudPlotInputSpec(BaseInterfaceInputSpec):
+    data_file = File(exists=True, mandatory=True, desc="File containing the data")
+    out_file = traits.Either(None, File, value=None, usedefault=True, desc="Path to save plot")
+    group_name = traits.Str(
+        "group_name",
+        mandatory=True,
+        desc="Group name of interest",
+    )
+    feature = traits.Str(
+        "feature",
+        mandatory=True,
+        desc="Feature of interest",
+    )
+    palette = traits.Str(
+        "Set2",
+        usedefault=True,
+        desc="Color palette name",
+    )
+    orient = traits.Str(
+        "v",
+        usedefault=True,
+        desc="Orientation",
+    )
+    density = traits.Bool(
+        True,
+        usedefault=True,
+        desc="``True`` to plot the density",
+    )
+    upper_limit_value = traits.Float(
+        None,
+        usedefault=True,
+        desc="Upper limit value over which any value in the data will be styled "
+        "with a different style",
+    )
+    upper_limit_color = traits.Str(
+        "gray",
+        usedefault=True,
+        desc="Lower limit value under which any value in the data will be styled "
+        "with a different style",
+    )
+    lower_limit_value = traits.Float(
+        None,
+        usedefault=True,
+        desc="",
+    )
+    lower_limit_color = traits.Str(
+        "gray",
+        usedefault=True,
+        desc="Color name to represent values under ``lower_limit_value``",
+    )
+    limit_offset = traits.Float(
+        None,
+        usedefault=True,
+        desc="Offset to plot the values over/under the upper/lower limit values",
+    )
+    mark_nans = traits.Bool(
+        True,
+        usedefault=True,
+        desc="``True`` to plot NaNs as dots. ``nans_values`` must be provided if True",
+    )
+    nans_value = traits.Float(
+        None,
+        usedefault=True,
+        desc="Value to use for NaN values`",
+    )
+    nans_color = traits.Str(
+        "black",
+        usedefault=True,
+        desc="Color name to represent NaN values",
+    )
+
+
+class _RaincloudPlotOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc="Path to saved plot")
+
+
+class RaincloudPlot(SimpleInterface):
+    """Plot a raincloud of values."""
+
+    input_spec = _RaincloudPlotInputSpec
+    output_spec = _RaincloudPlotOutputSpec
+
+    def _run_interface(self, runtime, **kwargs):
+        if self.inputs.out_file is None:
+            self._results["out_file"] = fname_presuffix(
+                self.inputs.data_file,
+                suffix="_raincloud.svg",
+                use_ext=False,
+                newpath=runtime.cwd,
+            )
+        else:
+            self._results["out_file"] = self.inputs.out_file
+        plot_raincloud(
+            data_file=self.inputs.data_file,
+            group_name=self.inputs.group_name,
+            feature=self.inputs.feature,
+            palette=self.inputs.palette,
+            orient=self.inputs.orient,
+            density=self.inputs.density,
+            mark_nans=self.inputs.mark_nans,
+            output_file=self._results["out_file"],
+            **kwargs,
+        )
+        return runtime