ENH: Add interface for diagnostic plotting of intermediate steps

cmtklib/report.py

@@ -0,0 +1,95 @@
+# Copyright (C) 2009-2021, Ecole Polytechnique Federale de Lausanne (EPFL) and
+# Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, and CMP3 contributors
+# All rights reserved.
+#
+#  This software is distributed under the open-source license Modified BSD.
+
+"""Module that defines Nipype interfaces for visual diagnostic plots."""
+
+from nipype.interfaces.base import BaseInterface, TraitedSpec, File, traits, Directory, CommandLine, BaseInterfaceInputSpec
+import numpy as np
+import matplotlib.pyplot as plt
+import nilearn.plotting as nplt
+
+class overlayAnatDiffQC_InputSpec(BaseInterfaceInputSpec):
+    anat_file = File(exists=True)
+    dwi_fa_file = File(exists=True)
+    out_anat_dwi_plot = File(exists=False)
+
+
+class overlayAnatDiffQC_OutputSpec(TraitedSpec):
+    out_anat_dwi_plot = File(exists=True)
+
+
+class overlayAnatDiffQC(BaseInterface):
+    """Produce an anatomical T1 image with diffusion FA overlay
+
+    .. note::
+        Note used.
+    """
+    input_spec = overlayAnatDiffQC_InputSpec
+    output_spec = overlayAnatDiffQC_OutputSpec
+    title = "Anatomical T1 image with diffusion FA overlay"
+
+    def _run_interface(self,runtime):
+        nplt.plot_anat(self.inputs.anat_file,
+                       title=title,
+                       display_mode='ortho', dim=0, draw_cross=False, annotate=False)
+        display.add_overlay(self.inputs.dwi_fa_file)
+        display.savefig(self.inputs.out_anat_dwi_plot)
+        display.close()
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        nplt.plot_anat(self.inputs.anat_file,
+                       title=title,
+                       display_mode='ortho', dim=0, draw_cross=False, annotate=False)
+        display.add_overlay(self.inputs.dwi_fa_file)
+        display.savefig(self.inputs.out_anat_dwi_plot)
+        display.close()
+
+        outputs["out_anat_dwi_plot"] = self.inputs.out_anat_dwi_plot
+        return outputs
+
+class carpetPlot_InputSpec(BaseInterfaceInputSpec):
+    timeseries_npy = File(exists=True)
+    out_carpet_plot = File(exists=False)
+
+
+class carpetPlot_OutputSpec(TraitedSpec):
+    out_carpet_plot = File(exists=True)
+
+
+class carpetPlot(BaseInterface):
+    """Produce a carpet plot for artifact correction.
+
+    .. note::
+        Note used.
+    """
+    input_spec = carpetPlot_InputSpec
+    output_spec = carpetPlot_OutputSpec
+
+    def _carpet_plot(self):
+        timeseries = np.load(self.inputs.timeseries_npy)
+        figsize = (10, 10)
+        figure = plt.figure(figsize=figsize)
+        axes = figure.add_subplot(1, 1, 1)
+        axes.set_xlabel("ROI")
+        axes.set_ylabel("Time sample")
+        m = axes.imshow(timeseries, interpolation = "nearest", cmap = "magma")
+        plt.colorbar(m, shrink = 0.1)
+
+        plt.savefig(self.inputs.out_carpet_plot)
+        plt.close()
+
+    def _run_interface(self,runtime):
+        self._carpet_plot()
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        self._carpet_plot()
+
+        outputs["out_carpet_plot"] = self.inputs.out_carpet_plot
+        return outputs