FIX: reports were displaying incorrect plots; default contrast_matrix…

… plot to vertical

fitlins/interfaces/afni.py

@@ -260,14 +260,13 @@ def save_remlfit_results(self, maps, contrasts, runtime):
                 clean_vol_labels.append(x.rsplit('_', 1)[0])
             else:
                 clean_vol_labels.append(x)
-        for (name, weights, contrast_test) in contrasts:
+        for (name, weights, cont_ents, contrast_test) in contrasts:
             contrast_metadata.append(
                     {
-                        "name": name,
-                        "contrast": name,
+                        "name": self.inputs.spec['name'],
                         "level": self.inputs.spec['level'],
                         "stat": contrast_test,
-                        **self.inputs.spec['entities'],
+                        **cont_ents,
                     }
             )
 
@@ -309,7 +308,7 @@ def save_remlfit_results(self, maps, contrasts, runtime):
                     map_list.append(fname)
 
         # calculate effect variance
-        for (name, weights, contrast_type), effect_fname, stat_fname in zip(contrasts, effect_maps, stat_maps):
+        for (name, weights, contrast_entities, contrast_type), effect_fname, stat_fname in zip(contrasts, effect_maps, stat_maps):
             map_type = "effect_variance"
             effect_img = nb.load(effect_fname)
             effect = effect_img.get_fdata()
@@ -423,7 +422,7 @@ def get_afni_design_matrix(design, contrasts, stim_labels, t_r):
 
 def create_glt_test_info(design, contrasts):
 
-    labels, wts_arrays, test_vals = zip(*contrasts)
+    labels, wts_arrays, cont_ents, test_vals = zip(*contrasts)
 
     # Start defining a list containing the rows for the glt values in the
     # afni design matrix header:

fitlins/interfaces/bids.py

@@ -242,6 +242,7 @@ def _load_graph(self, runtime, graph, node=None, inputs=None, **filters):
                     'entities': spec.entities,
                     'level': spec.node.level,
                     'X': spec.X,
+                    'name': spec.node.name,
                     'model': spec.node.model,
                     # Metadata is only used in higher level models; save space
                     'metadata': spec.metadata if spec.node.level != "run" else None,
@@ -454,10 +455,11 @@ def _list_outputs(self):
             # In some instances, name/contrast could have the following
             # format (eg: gain.Range, gain.EqualIndifference).
             # This prevents issues when creating/searching files for the report
-            ents.update({k: str(v).replace('.', '_')
-                         for k, v in ents.items()
-                         if k in ("name", "contrast")})
-            ents = {k: snake_to_camel(str(v)) for k, v in ents.items()}
+            for k in ents:
+                if k in ("name", "contrast"):
+                    ents.update({k: str(ents[k]).replace('.', '_')})
+                    ents.update({k: str(ents[k]).replace('-', '_')})
+                    ents.update({k: snake_to_camel(str(ents[k]))})
 
             out_fname = os.path.join(
                 base_dir, layout.build_path(

fitlins/interfaces/nistats.py

@@ -43,7 +43,7 @@ def prepare_contrasts(contrasts, all_regressors):
         indices = sorter[np.searchsorted(all_regressors, conds, sorter=sorter)]
         weights[:, indices] = in_weights
 
-        out_contrasts.append((contrast_info['name'], weights, contrast_info['test']))
+        out_contrasts.append((contrast_info['name'], weights, contrast_info['entities'].copy(), contrast_info['test']))
 
     return out_contrasts
 
@@ -225,15 +225,14 @@ def _run_interface(self, runtime):
         zscore_maps = []
         pvalue_maps = []
         contrast_metadata = []
-        for name, weights, contrast_test in prepare_contrasts(
+        for name, weights, cont_ents, contrast_test in prepare_contrasts(
               spec['contrasts'], mat.columns):
             contrast_metadata.append(
                     {
-                        "name": name,
-                        "contrast": name,
+                        "name": spec['name'],
                         "level": spec['level'],
                         "stat": contrast_test,
-                        **out_ents,
+                        **cont_ents,
                     }
                 )
             if is_cifti:
@@ -353,13 +352,13 @@ def _run_interface(self, runtime):
                 model = level2.SecondLevelModel(smoothing_fwhm=smoothing_fwhm)
                 model.fit(filtered_effects, design_matrix=spec['X'])
 
-        for name, weights, contrast_test in contrasts:
+        for name, weights, cont_ents, contrast_test in contrasts:
             contrast_metadata.append(
                     {
-                        "name": name,
+                        "name": spec['name'],
                         "level": spec['level'],
                         "stat": contrast_test,
-                        **out_ents,
+                        **cont_ents,
                     }
                 )
 

fitlins/interfaces/visualizations.py

@@ -109,7 +109,7 @@ def _visualize(self, data, out_name):
 
 class ContrastMatrixPlotInputSpec(VisualizationInputSpec):
     contrast_info = traits.List(traits.Any)
-    orientation = traits.Enum('horizontal', 'vertical', usedefault=True,
+    orientation = traits.Enum('vertical', 'horizontal', usedefault=True,
                               desc='Display orientation of contrast matrix')
 
 

fitlins/viz/reports.py

@@ -71,36 +71,44 @@ def build_report_dict(deriv_dir, work_dir, graph):
         report_node = {'name': node, 'analyses': []}
         report['nodes'].append(report_node)
         for coll in colls:
-            ents = coll.entities.copy()
-            ents["level"] = coll.node.level
             contrasts = coll.contrasts
-            for key in ('datatype', 'desc', 'suffix', 'extension'):
-                ents.pop(key, None)
-            for key in graph.layout.get_entities(metadata=True):
-                ents.pop(key, None)
-
+
             analysis_dict = {
-                'entities': {
-                    key: val
-                    for key, val in ents.items()
-                    if key in ('subject', 'session', 'task', 'run') and val},
-                'contrasts': []
+                    'entities': {},
+                    'contrasts': []
             }
-            
+
             for contrast_info in contrasts:
                 glassbrain = []
-                if coll.node.level != 'run':
-                    cname = snake_to_camel((contrast_info.name).replace('.', '_'))
-                    ents["name"] = cname
-                    ents.pop("contrast", None)
+                cents = contrast_info.entities.copy()
+                cents["level"] = coll.node.level
+                cents["name"] = coll.node.name
+
+                contrasts = coll.contrasts
+                for key in ('datatype', 'desc', 'suffix', 'extension'):
+                    cents.pop(key, None)
+                for key in graph.layout.get_entities(metadata=True):
+                    cents.pop(key, None)
 
-                glassbrain = fl_layout.get(suffix='ortho', extension='png', **ents)
+                for k in cents:
+                    if k in ("name", "contrast"):
+                        cents.update({k: str(cents[k]).replace('.', '_')})
+                        cents.update({k: str(cents[k]).replace('-', '_')})
+                        cents.update({k: snake_to_camel(str(cents[k]))})
+
+                glassbrain = fl_layout.get(suffix='ortho', extension='png', **cents)
+
+                analysis_dict['entities'] = {
+                        key: val for key, val in cents.items()
+                        if key in ('subject', 'session', 'task', 'run') and val
+                }
 
                 analysis_dict['contrasts'].append(
                     {'name': displayify(contrast_info.name),
                      'glassbrain': glassbrain[0].path if glassbrain else None}
                 )
-
+
+            ents = coll.entities.copy()
             report_node['analyses'].append(analysis_dict)
             # Space doesn't apply to design/contrast matrices, or resolution
             for k in ['space', 'res']: