Merge pull request #57 from oesteban/enh/plotting-transparent

ENH: Transparency on fieldmap plots!

sdcflows/interfaces/reportlets.py

@@ -1,21 +1,30 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Interfaces to generate speciality reportlets."""
+import numpy as np
 from nilearn.image import threshold_img, load_img
 from niworkflows import NIWORKFLOWS_LOG
 from niworkflows.viz.utils import cuts_from_bbox, compose_view
-from nipype.interfaces.base import File, isdefined
+from nipype.interfaces.base import File, isdefined, traits
 from nipype.interfaces.mixins import reporting
 
 from ..viz.utils import plot_registration, coolwarm_transparent
 
 
 class _FieldmapReportletInputSpec(reporting.ReportCapableInputSpec):
     reference = File(exists=True, mandatory=True, desc='input reference')
+    moving = File(exists=True, desc='input moving')
     fieldmap = File(exists=True, mandatory=True, desc='input fieldmap')
+    max_alpha = traits.Float(0.7, usedefault=True, desc='maximum alpha channel')
     mask = File(exists=True, desc='brain mask')
     out_report = File('report.svg', usedefault=True,
                       desc='filename for the visual report')
+    show = traits.Enum(1, 0, 'both', usedefault=True,
+                       desc='where the fieldmap should be shown')
+    reference_label = traits.Str('Reference', usedefault=True,
+                                 desc='a label name for the reference mosaic')
+    moving_label = traits.Str('Fieldmap (Hz)', usedefault=True,
+                              desc='a label name for the reference mosaic')
 
 
 class FieldmapReportlet(reporting.ReportCapableInterface):
@@ -37,30 +46,51 @@ def _generate_report(self):
         """Generate a reportlet."""
         NIWORKFLOWS_LOG.info('Generating visual report')
 
-        refnii = load_img(self.inputs.reference)
+        movnii = refnii = load_img(self.inputs.reference)
         fmapnii = load_img(self.inputs.fieldmap)
-        contour_nii = load_img(self.inputs.mask) if isdefined(self.inputs.mask) else None
-        mask_nii = threshold_img(refnii, 1e-3)
+
+        if isdefined(self.inputs.moving):
+            movnii = load_img(self.inputs.moving)
+
+        contour_nii = mask_nii = None
+        if isdefined(self.inputs.mask):
+            contour_nii = load_img(self.inputs.mask)
+            maskdata = contour_nii.get_fdata() > 0
+        else:
+            mask_nii = threshold_img(refnii, 1e-3)
+            maskdata = mask_nii.get_fdata() > 0
         cuts = cuts_from_bbox(contour_nii or mask_nii, cuts=self._n_cuts)
         fmapdata = fmapnii.get_fdata()
-        vmax = max(fmapdata.max(), abs(fmapdata.min()))
+        vmax = max(abs(np.percentile(fmapdata[maskdata], 99.8)),
+                   abs(np.percentile(fmapdata[maskdata], 0.2)))
+
+        fmap_overlay = [{
+            'overlay': fmapnii,
+            'overlay_params': {
+                'cmap': coolwarm_transparent(max_alpha=self.inputs.max_alpha),
+                'vmax': vmax,
+                'vmin': -vmax,
+            }
+        }] * 2
+
+        if self.inputs.show != 'both':
+            fmap_overlay[not self.inputs.show] = {}
 
         # Call composer
         compose_view(
-            plot_registration(refnii, 'fixed-image',
+            plot_registration(movnii, 'moving-image',
                               estimate_brightness=True,
                               cuts=cuts,
-                              label='reference',
+                              label=self.inputs.moving_label,
                               contour=contour_nii,
-                              compress=False),
-            plot_registration(fmapnii, 'moving-image',
+                              compress=False,
+                              **fmap_overlay[1]),
+            plot_registration(refnii, 'fixed-image',
                               estimate_brightness=True,
                               cuts=cuts,
-                              label='fieldmap (Hz)',
+                              label=self.inputs.reference_label,
                               contour=contour_nii,
                               compress=False,
-                              plot_params={'cmap': coolwarm_transparent(),
-                                           'vmax': vmax,
-                                           'vmin': -vmax}),
+                              **fmap_overlay[0]),
             out_file=self._out_report
         )

sdcflows/viz/utils.py

@@ -6,7 +6,7 @@
 def plot_registration(anat_nii, div_id, plot_params=None,
                       order=('z', 'x', 'y'), cuts=None,
                       estimate_brightness=False, label=None, contour=None,
-                      compress='auto'):
+                      compress='auto', overlay=None, overlay_params=None):
     """
     Plot the foreground and background views.
 
@@ -15,6 +15,7 @@ def plot_registration(anat_nii, div_id, plot_params=None,
     from uuid import uuid4
 
     from lxml import etree
+    import matplotlib.pyplot as plt
     from nilearn.plotting import plot_anat
     from svgutils.transform import SVGFigure
     from niworkflows.viz.utils import robust_set_limits, extract_svg, SVGNS
@@ -41,6 +42,15 @@ def plot_registration(anat_nii, div_id, plot_params=None,
 
         # Generate nilearn figure
         display = plot_anat(anat_nii, **plot_params)
+        if overlay is not None:
+            _overlay_params = {
+                'vmin': overlay.get_fdata().min(),
+                'vmax': overlay.get_fdata().max(),
+                'cmap': plt.cm.gray,
+                'interpolation': 'nearest',
+            }
+            _overlay_params.update(overlay_params)
+            display.add_overlay(overlay, **_overlay_params)
         if contour is not None:
             display.add_contours(contour, colors='g', levels=[0.5],
                                  linewidths=0.5)
@@ -60,7 +70,7 @@ def plot_registration(anat_nii, div_id, plot_params=None,
     return out_files
 
 
-def coolwarm_transparent():
+def coolwarm_transparent(max_alpha=0.7, opaque_perc=30, transparent_perc=8):
     """Modify the coolwarm color scale to have full transparency around the middle."""
     import numpy as np
     import matplotlib.pylab as pl
@@ -72,9 +82,15 @@ def coolwarm_transparent():
     # Get the colormap colors
     my_cmap = cmap(np.arange(cmap.N))
 
+    _20perc = (cmap.N * opaque_perc) // 100
+    midpoint = cmap.N // 2 + 1
+    _10perc = (cmap.N * transparent_perc) // 100
     # Set alpha
-    alpha = np.ones(cmap.N)
-    alpha[128:160] = np.linspace(0, 1, len(alpha[128:160]))
-    alpha[96:128] = np.linspace(1, 0, len(alpha[96:128]))
+    alpha = np.ones(cmap.N) * max_alpha
+    alpha[midpoint - _10perc:midpoint + _10perc] = 0
+    alpha[_20perc:midpoint - _10perc - 1] = np.linspace(
+        max_alpha, 0, len(alpha[_20perc:midpoint - _10perc - 1]))
+    alpha[midpoint + _10perc:-_20perc] = np.linspace(
+        0, max_alpha, len(alpha[midpoint + _10perc:-_20perc]))
     my_cmap[:, -1] = alpha
     return ListedColormap(my_cmap)

sdcflows/workflows/tests/test_pepolar.py

@@ -157,7 +157,7 @@ def test_pepolar_wf1(bids_layouts, output_path, dataset, workdir):
             wf.inputs.inputnode.in_reference_brain = boldref.path
             wf.inputs.inputnode.in_reference = boldref.path
 
-        rep = pe.Node(FieldmapReportlet(), 'simple_report')
+        rep = pe.Node(FieldmapReportlet(reference_label='EPI Reference'), 'simple_report')
         rep.interface._always_run = True
         dsink = pe.Node(DerivativesDataSink(
             base_directory=str(output_path), keep_dtype=True,

sdcflows/workflows/tests/test_phdiff.py

@@ -31,7 +31,7 @@ def test_workflow(bids_layouts, tmpdir, output_path, dataset, workdir):
 
     if output_path:
         from ...interfaces.reportlets import FieldmapReportlet
-        rep = pe.Node(FieldmapReportlet(), 'simple_report')
+        rep = pe.Node(FieldmapReportlet(reference_label='Magnitude'), 'simple_report')
         rep.interface._always_run = True
 
         dsink = pe.Node(DerivativesDataSink(