Fix up bugs.

Update cubids.py

Update cubids.py

Update cubids.py

Update cubids.py

Update cubids.py

Update schema.json

Remove prints.

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Update utils.py

Drop try/except.

Author: tsalo

cubids/cubids.py

@@ -1057,12 +1057,16 @@ def get_param_groups_from_entity_set(self, entity_set):
             raise Exception("Fieldmaps must be cached to find parameter groups.")
         key_entities = utils._entity_set_to_entities(entity_set)
         key_entities["extension"] = ".nii[.gz]*"
+        # Account for plus signs in entity values
+        key_entities = {k: v.replace("+", "\\+") for k, v in key_entities.items() if v is not None}
 
         matching_files = self.layout.get(
             return_type="file", scope="self", regex_search=True, **key_entities
         )
+        if not matching_files:
+            raise Exception(f"No files found for entity set: {key_entities}")
 
-        # ensure files who's entities contain key_entities but include other
+        # ensure files whose entities contain key_entities but include other
         # entities do not also get added to matching_files
         to_include = []
         for filepath in matching_files:
@@ -1256,14 +1260,12 @@ def get_param_groups_dataframes(self):
         labeled_files = []
         param_group_summaries = []
         for entity_set in entity_sets:
-            try:
-                (
-                    labeled_file_params,
-                    param_summary,
-                    modality,
-                ) = self.get_param_groups_from_entity_set(entity_set)
-            except Exception:
-                continue
+            (
+                labeled_file_params,
+                param_summary,
+                modality,
+            ) = self.get_param_groups_from_entity_set(entity_set)
+
             if labeled_file_params is None:
                 continue
             param_group_summaries.append(param_summary)

cubids/data/config.yml

@@ -311,6 +311,9 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
+    ImageOrientationPatientDICOM:
+      tolerance: 0.0001
+      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -350,6 +353,9 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
+    ImageOrientationPatientDICOM:
+      tolerance: 0.0001
+      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -389,6 +395,9 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
+    ImageOrientationPatientDICOM:
+      tolerance: 0.0001
+      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -428,6 +437,9 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
+    ImageOrientationPatientDICOM:
+      tolerance: 0.0001
+      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -479,6 +491,9 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
+    ImageOrientationPatientDICOM:
+      tolerance: 0.0001
+      suggest_variant_rename: yes
     LabelingDistance:
       tolerance: 0.1
       suggest_variant_rename: yes
@@ -535,6 +550,9 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
+    ImageOrientationPatientDICOM:
+      tolerance: 0.0001
+      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner: