WIP: Refactor

Author: jhlegarreta

nireports/interfaces/nuisance.py

@@ -260,25 +260,26 @@ def _run_interface(self, runtime, **kwargs):
 
 
 class _MotionPlotInputSpec(BaseInterfaceInputSpec):
-    original_pet = File(
+    uncorr_file = File(
         exists=True,
         mandatory=True,
-        desc="Original (uncorrected) PET series in native PET space",
+        desc="Original (uncorrected) volume in native space",
     )
-    corrected_pet = File(
+    corr_file = File(
         exists=True,
         mandatory=True,
         desc=(
-            "Motion-corrected PET series derived by applying the estimated motion "
-            "transforms to the original data in native PET space"
+            "Motion-corrected volume derived by applying the estimated motion "
+            "transforms to the original data in native space"
         ),
     )
     fd_file = File(exists=True, desc="Confounds file containing framewise displacement")
     duration = traits.Float(0.2, usedefault=True, desc="Frame duration for the GIF (seconds)")
+    out_file = traits.Either(None, File, value=None, usedefault=True, desc="Path to save plot")
 
 
 class _MotionPlotOutputSpec(TraitedSpec):
-    svg_file = File(exists=True, desc="Animated before/after motion correction SVG")
+    out_file = File(exists=True, desc="Path to saved plot")
 
 
 class MotionPlot(SimpleInterface):
@@ -295,25 +296,34 @@ class MotionPlot(SimpleInterface):
     output_spec = _MotionPlotOutputSpec
 
     def _run_interface(self, runtime):
-        runtime.cwd = Path(runtime.cwd)
-
-        svg_file = runtime.cwd / "pet_motion_hmc.svg"
-        svg_file.parent.mkdir(parents=True, exist_ok=True)
 
         fd_values = None
         if isdefined(self.inputs.fd_file):
             fd_values = load_framewise_displacement(self.inputs.fd_file)
 
+        if self.inputs.out_file is None:
+            self._results["out_file"] = fname_presuffix(
+                self.inputs.corr_file,
+                suffix="_hmc.svg",
+                use_ext=False,
+                newpath=runtime.cwd,
+            )
+        else:
+            self._results["out_file"] = self.inputs.out_file
+
         # ToDo
-        # Does not make sense to assign to an input parameter
-        svg_file = plot_motion(
-            load_api(self.inputs.original_pet, SpatialImage),
-            load_api(self.inputs.corrected_pet, SpatialImage),
-            svg_file,
+        # Contrary to the other plot functions, IMO it makes most sense that
+        # we pass the actual data to the plot functions rather than the files.
+        # Same goes for passing output_fle vs the function returning the fig
+        svg_content = plot_motion(
+            load_api(self.inputs.uncorr_file, SpatialImage),
+            load_api(self.inputs.corr_file, SpatialImage),
             self.inputs.duration,
-            fd_values=fd_values,
+            fd_values,
         )
 
-        self._results["svg_file"] = str(svg_file)
+        out_file = Path(self._results["out_file"])
+        out_file.write_text(svg_content, encoding="utf-8")
+        self._results["out_file"] = str(out_file)
 
         return runtime