enh: import base report-capable interfaces from niworkflows

This sidetracks #71 for interfaces with little discussion about whether
they can be consider core enough to be maintained within NiReports.

In addition, moves the SimpleBeforeAfter interface into the set of basic
interfaces, as it is very often used.

niworkflows/interfaces/reportlets/base.py → nireports/interfaces/reporting/base.py

@@ -21,15 +21,20 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """class mixin and utilities for enabling reports for nipype interfaces."""
-from nipype.interfaces.base import File, traits
+from pathlib import Path
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import File, traits, isdefined
 from nipype.interfaces.mixins import reporting
-from ... import NIWORKFLOWS_LOG
-from ...viz.utils import cuts_from_bbox, compose_view
+from nireports.reportlets.utils import cuts_from_bbox, compose_view
+
+_LOGGER = logging.getLogger("nipype.interface")
 
 
 class _SVGReportCapableInputSpec(reporting.ReportCapableInputSpec):
-    out_report = File(
-        "report.svg", usedefault=True, desc="filename for the visual report"
+    out_report = File("report.svg", usedefault=True, desc="filename for the visual report")
+    plot_params = traits.Dict(
+        traits.Str, value={}, usedefault=True, desc="pass parameters to plotter",
     )
     compress_report = traits.Enum(
         "auto",
@@ -58,9 +63,9 @@ def _generate_report(self):
         """Generate the visual report."""
         from nilearn.image import threshold_img, load_img
         from nilearn.masking import apply_mask, unmask
-        from niworkflows.viz.utils import plot_registration
+        from nireports.reportlets.mosaic import plot_registration
 
-        NIWORKFLOWS_LOG.info("Generating visual report")
+        _LOGGER.info("Generating visual report")
 
         fixed_image_nii = load_img(self._fixed_image)
         moving_image_nii = load_img(self._moving_image)
@@ -117,7 +122,7 @@ class SegmentationRC(reporting.ReportCapableInterface):
     """An abstract mixin to segmentation nipype interfaces."""
 
     def _generate_report(self):
-        from niworkflows.viz.utils import plot_segs
+        from nireports.reportlets.mosaic import plot_segs
 
         compose_view(
             plot_segs(
@@ -144,9 +149,9 @@ def _generate_report(self):
         """Generate the visual report."""
         from nilearn.image import threshold_img, load_img
         from nilearn.masking import apply_mask, unmask
-        from niworkflows.viz.utils import plot_registration
+        from nireports.reportlets.mosaic import plot_registration
 
-        NIWORKFLOWS_LOG.info("Generating visual report")
+        _LOGGER.info("Generating visual report")
 
         anat = load_img(self._anat_file)
         contour_nii = load_img(self._contour) if self._contour is not None else None
@@ -172,6 +177,7 @@ def _generate_report(self):
                 cuts=cuts,
                 contour=contour_nii,
                 compress=self.inputs.compress_report,
+                plot_params=self.inputs.plot_params,
             ),
             [],
             out_file=self._out_report,
@@ -189,9 +195,72 @@ class ReportingInterface(reporting.ReportCapableInterface):
     output_spec = reporting.ReportCapableOutputSpec
 
     def __init__(self, generate_report=True, **kwargs):
-        super(ReportingInterface, self).__init__(
-            generate_report=generate_report, **kwargs
-        )
+        super(ReportingInterface, self).__init__(generate_report=generate_report, **kwargs)
 
     def _run_interface(self, runtime):
         return runtime
+
+
+class _SimpleBeforeAfterInputSpecRPT(_SVGReportCapableInputSpec):
+    before = File(exists=True, mandatory=True, desc="file before")
+    after = File(exists=True, mandatory=True, desc="file after")
+    wm_seg = File(desc="reference white matter segmentation mask")
+    before_label = traits.Str("before", usedefault=True)
+    after_label = traits.Str("after", usedefault=True)
+    dismiss_affine = traits.Bool(False, usedefault=True, desc="rotate image(s) to cardinal axes")
+
+
+class SimpleBeforeAfterRPT(RegistrationRC, ReportingInterface):
+    input_spec = _SimpleBeforeAfterInputSpecRPT
+
+    def _post_run_hook(self, runtime):
+        """there is not inner interface to run"""
+        self._fixed_image_label = self.inputs.after_label
+        self._moving_image_label = self.inputs.before_label
+        self._fixed_image = self.inputs.after
+        self._moving_image = self.inputs.before
+        self._contour = self.inputs.wm_seg if isdefined(self.inputs.wm_seg) else None
+        self._dismiss_affine = self.inputs.dismiss_affine
+        _LOGGER.info(
+            "Report - setting before (%s) and after (%s) images",
+            self._fixed_image,
+            self._moving_image,
+        )
+
+        return super(SimpleBeforeAfterRPT, self)._post_run_hook(runtime)
+
+
+class _ResampleBeforeAfterInputSpecRPT(_SimpleBeforeAfterInputSpecRPT):
+    base = traits.Enum("before", "after", usedefault=True, mandatory=True)
+
+
+class ResampleBeforeAfterRPT(SimpleBeforeAfterRPT):
+    input_spec = _ResampleBeforeAfterInputSpecRPT
+
+    def _post_run_hook(self, runtime):
+        from nilearn import image as nli
+
+        self._fixed_image = self.inputs.after
+        self._moving_image = self.inputs.before
+        if self.inputs.base == "before":
+            resampled_after = nli.resample_to_img(self._fixed_image, self._moving_image)
+            fname = fname_presuffix(self._fixed_image, suffix="_resampled", newpath=runtime.cwd)
+            resampled_after.to_filename(fname)
+            self._fixed_image = fname
+        else:
+            resampled_before = nli.resample_to_img(self._moving_image, self._fixed_image)
+            fname = fname_presuffix(self._moving_image, suffix="_resampled", newpath=runtime.cwd)
+            resampled_before.to_filename(fname)
+            self._moving_image = fname
+        self._contour = self.inputs.wm_seg if isdefined(self.inputs.wm_seg) else None
+        _LOGGER.info(
+            "Report - setting before (%s) and after (%s) images",
+            self._fixed_image,
+            self._moving_image,
+        )
+
+        runtime = super(ResampleBeforeAfterRPT, self)._post_run_hook(runtime)
+        _LOGGER.info("Successfully created report (%s)", self._out_report)
+        Path(fname).unlink(missing_ok=True)
+
+        return runtime