feat(schema): Move more imaging data into imaging.yaml

Author: effigies

src/schema/rules/files/deriv/imaging.yaml

@@ -1,4 +1,9 @@
+# This document implements general imaging derivatives.
+#
+# The _volumetric rules cover supersets of files that would be covered by the
+# common derivatives spec, namely, the space and description entities.
 ---
+# Preprocessed and/or resampled volumes
 anat_parametric_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -17,6 +22,78 @@ anat_nonparametric_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.nonparametric.entities
 
+anat_defacemask_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.defacemask
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.defacemask.entities
+
+anat_mese_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.mese
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.mese.entities
+
+anat_megre_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.megre
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.megre.entities
+
+anat_multiflip_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.multiflip
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.multiflip.entities
+
+anat_multiinversion_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.multiinversion
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.multiinversion.entities
+
+anat_mp2rage_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.mp2rage
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.mp2rage.entities
+
+anat_vfamt_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.vfamt
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.vfamt.entities
+
+anat_mtr_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.anat.mtr
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.anat.mtr.entities
+
 dwi_dwi_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -62,6 +139,97 @@ func_phase_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.func.phase.entities
 
+fmap_fieldmaps_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.fieldmaps
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.fieldmaps.entities
+
+fmap_pepolar_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.pepolar
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.pepolar.entities
+
+fmap_pepolar_m0scan:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.pepolar_m0scan
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.pepolar.entities
+
+fmap_TB1DAM_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.TB1DAM
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.TB1DAM.entities
+
+fmap_TB1EPI_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.TB1EPI
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.TB1EPI.entities
+
+fmap_RFFieldMaps_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.RFFieldMaps
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.RFFieldMaps.entities
+
+fmap_TB1SRGE_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.TB1SRGE
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.TB1SRGE.entities
+
+fmap_parametric_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.fmap.parametric
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.fmap.parametric.entities
+
+perf_asl_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.perf.asl
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.perf.asl.entities
+
+pet_pet_volumetric:
+  $ref:
+    - meta.templates.deriv.volumetric
+    - rules.files.raw.pet.pet
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.raw.pet.pet.entities
+
+# Masks
 anat_parametric_mask:
   $ref:
     - meta.templates.deriv.mask
@@ -98,6 +266,7 @@ func_mask:
       - meta.templates.deriv.mask.entities
       - rules.files.raw.func.func.entities
 
+# Discrete and probabilistic segmentations
 anat_parametric_discrete_segmentation:
   $ref:
     - meta.templates.deriv.dseg

src/schema/rules/files/deriv/preprocessed_data.yaml

@@ -1,81 +1,8 @@
 # This document implements the common derivatives specification,
 # generally adding space and description entities to most raw data.
 #
-# Imaging files are omitted when it is redundant with the rules in
-# imaging.yaml
+# Imaging files are generally omitted, due to redundancy with imaging.yaml
 ---
-anat_defacemask_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.defacemask
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.defacemask.entities
-
-anat_megre_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.megre
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.megre.entities
-
-anat_mese_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.mese
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.mese.entities
-
-anat_multiflip_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.multiflip
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.multiflip.entities
-
-anat_multiinversion_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.multiinversion
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.multiinversion.entities
-
-anat_mp2rage_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.mp2rage
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.mp2rage.entities
-
-anat_vfamt_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.vfamt
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.vfamt.entities
-
-anat_mtr_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.anat.mtr
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.anat.mtr.entities
-
 beh_noncontinuous_common:
   $ref:
     - meta.templates.deriv.base
@@ -166,78 +93,6 @@ eeg_eeg_common:
       - meta.templates.deriv.spatial.entities
       - rules.files.raw.eeg.eeg.entities
 
-fmap_fieldmaps_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.fieldmaps
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.fieldmaps.entities
-
-fmap_pepolar_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.pepolar
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.pepolar.entities
-
-fmap_pepolar_m0scan:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.pepolar_m0scan
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.pepolar.entities
-
-fmap_TB1DAM_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.TB1DAM
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.TB1DAM.entities
-
-fmap_TB1EPI_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.TB1EPI
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.TB1EPI.entities
-
-fmap_RFFieldMaps_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.RFFieldMaps
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.RFFieldMaps.entities
-
-fmap_TB1SRGE_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.TB1SRGE
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.TB1SRGE.entities
-
-fmap_parametric_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.fmap.parametric
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.fmap.parametric.entities
-
 ieeg_ieeg_common:
   $ref:
     - meta.templates.deriv.spatial
@@ -301,24 +156,6 @@ micr_microscopy_common:
       - meta.templates.deriv.spatial.entities
       - rules.files.raw.micr.microscopy.entities
 
-perf_asl_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.perf.asl
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.perf.asl.entities
-
-pet_pet_common:
-  $ref:
-    - meta.templates.deriv.spatial
-    - rules.files.raw.pet.pet
-  entities:
-    $ref:
-      - meta.templates.deriv.spatial.entities
-      - rules.files.raw.pet.pet.entities
-
 pet_blood_common:
   $ref:
     - meta.templates.deriv.spatial