Merge pull request #89 from effigies/enh/plotting_improvements

ENH: Plotting improvements
poldracklab · Jan 22, 2019 · c7cc798 · c7cc798
2 parents 890f48d + 0bc7995
commit c7cc798
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Showing 2 changed files with 15 additions and 1 deletion.
diff --git a/fitlins/interfaces/visualizations.py b/fitlins/interfaces/visualizations.py
@@ -6,7 +6,7 @@
 
 from nipype.interfaces.base import (
     SimpleInterface, BaseInterfaceInputSpec, TraitedSpec,
-    File, traits
+    File, traits, isdefined
     )
 from nipype.utils.filemanip import fname_presuffix, split_filename
 
@@ -99,9 +99,20 @@ def _visualize(self, data, out_name):
         plot_and_save(out_name, plot_contrast_matrix, contrast_matrix,
                       ornt=self.inputs.orientation)
 
+class GlassBrainPlotInputSpec(VisualizationInputSpec):
+    threshold = traits.Enum('auto', None, traits.Float(), usedefault=True)
+    vmax = traits.Float()
+    colormap = traits.Str('bwr_r', usedefault=True)
 
 class GlassBrainPlot(Visualization):
+    input_spec = GlassBrainPlotInputSpec
+
     def _visualize(self, data, out_name):
+        vmax = self.inputs.vmax
+        if not isdefined(vmax):
+            vmax = None
         nlp.plot_glass_brain(data, colorbar=True, plot_abs=False,
                              display_mode='lyrz', axes=None,
+                             vmax=vmax, threshold=self.inputs.threshold,
+                             cmap=self.inputs.colormap,
                              output_file=out_name)
diff --git a/fitlins/workflows/base.py b/fitlins/workflows/base.py
@@ -149,6 +149,8 @@ def init_fitlins_wf(bids_dir, derivatives, out_dir, space, desc=None,
 
         level = 'l{:d}'.format(ix + 1)
 
+        # TODO: No longer used at higher level, suggesting we can simply return
+        # entities from loader as a single list
         select_entities = pe.Node(
             niu.Select(index=ix),
             name='select_{}_entities'.format(level),
@@ -193,6 +195,7 @@ def init_fitlins_wf(bids_dir, derivatives, out_dir, space, desc=None,
             name='ds_{}_contrast_plots'.format(level))
 
         if ix == 0:
+            plot_contrasts.inputs.vmax = 20
             wf.connect([
                 (loader, select_entities, [('entities', 'inlist')]),
                 (select_entities, getter,  [('out', 'entities')]),