[BEP038] Schema refactor

src/metaschema.json

@@ -378,18 +378,6 @@
               "required": ["core", "tables"],
               "additionalProperties": false
             },
-            "atlas": {
-              "type": "object",
-              "patternProperties": {
-                "^[a-z_]+$": {
-                  "type": "object",
-                  "patternProperties": {
-                    "^[a-zA-Z0-9_]+$": { "$ref": "#/definitions/suffixRule" }
-                  }
-                }
-              },
-              "additionalProperties": false
-            },
             "deriv": {
               "type": "object",
               "patternProperties": {
@@ -431,10 +419,9 @@
             "^derivatives$": {
               "type": "object",
               "properties": {
-                "common_derivatives": { "$ref": "#/definitions/json" },
-                "atlas": { "$ref": "#/definitions/json" }
+                "common_derivatives": { "$ref": "#/definitions/json" }
               },
-              "required": ["common_derivatives", "atlas"],
+              "required": ["common_derivatives"],
               "additionalProperties": false
             },
             "^(?!derivatives$)[a-z_]+$": {

src/schema/README.md

@@ -167,21 +167,23 @@ references (the cases in which they are used will be presented later):
     (which are in turn references to individual values), and the references inside `GeneticLevel.anyOf` indicate that there may be a single
     such value or a list of values.
 
-1.  In [`rules.files.deriv.preprocessed_data`][preprocessed_data]:
+1.  In [`rules.files.deriv.imaging`](./rules/files/deriv/imaging.yaml):
     ```YAML
-    anat_nonparametric_common:
-      $ref: rules.files.raw.anat.nonparametric
+    anat_parametric_volumetric:
+      $ref: rules.files.raw.anat.parametric
       entities:
-        $ref: rules.files.raw.anat.nonparametric.entities
-        space: optional
-        description: optional
+        $ref:
+          - meta.templates.deriv.volumetric.entities
+          - rules.files.raw.anat.parametric.entities
     ```
     Here, the derivative datatype rule starts by copying the raw datatype rule
     `rules.files.raw.anat.nonparametric`.
     It then *overrides* the `entities` portion of that rule with a new object.
-    To *extend* the original `entities`, it again begins
-    by referencing `rules.files.raw.anat.nonparametric.entities`,
-    and adding the new entities `space` and `description`.
+    To *extend* the original `entities`, it composes
+    `meta.templates.deriv.volumetric.entities`
+    and `rules.files.raw.anat.nonparametric.entities`.
+    When multiple references are aggregated, the first reference takes
+    precedence.
 
 ### Expressions
 
@@ -1071,5 +1073,4 @@ ensuring consistency across the entire schema directory. Validation of the schem
 incorporated into the CI, so any changes that are inconsistent will be flagged before
 inclusion.
 
-[preprocessed_data]: https://github.com/bids-standard/bids-specification/tree/master/src/schema/rules/files/deriv/preprocessed_data.yaml
 [tabular files]: https://bids-specification.readthedocs.io/en/stable/common-principles.html#tabular-files

src/schema/meta/templates.yaml

@@ -6,25 +6,145 @@
 #
 # filerule:
 #   entities:
-#     $ref: meta.templates.raw_base_entities
+#     $ref: meta.templates.raw.base.entities
 #     task: optional
 #     ...
 #   datatypes:
 #     ...
-raw_base_entities:
-  subject: required
-  session: optional
+
+raw:
+  base:
+    entities:
+      subject: required
+      session: optional
+
+  recording:
+    entities:
+      $ref: meta.templates.raw.base.entities
+      acquisition: optional
+      run: optional
+
+  task:
+    entities:
+      $ref: meta.templates.raw.recording.entities
+      task: required
+
+  mri:
+    entities:
+      $ref: meta.templates.raw.recording.entities
+      ceagent: optional
+      reconstruction: optional
+      chunk: optional
+
+  epi:
+    entities:
+      $ref: meta.templates.raw.mri.entities
+      direction: optional
+      part: optional
+
+# Entities that apply to most derivative files
+#     $ref: meta.templates.deriv.base.entities
+#     task: optional
+#     ...
+#   datatypes:
+#     ...
+deriv:
+  base:
+    selectors:
+      - dataset.dataset_description.DatasetType == 'derivative'
+    entities:
+      subject: optional
+      session: optional
+      description: optional
+
+  spatial:
+    $ref: meta.templates.deriv.base
+    entities:
+      $ref: meta.templates.deriv.base.entities
+      space: optional
+
+  # Imaging derivatives
+  volumetric:
+    $ref: meta.templates.deriv.spatial
+    extensions:
+      - .nii.gz
+      - .nii
+      - .json
+    entities:
+      $ref: meta.templates.deriv.spatial.entities
+      resolution: optional
+
+  surface:
+    $ref: meta.templates.deriv.spatial
+    entities:
+      $ref: meta.templates.deriv.spatial.entities
+      hemisphere: optional
+      density: optional
+
+  mask:
+    $ref: meta.templates.deriv.volumetric
+    suffixes:
+      - mask
+    entities:
+      $ref: meta.templates.deriv.volumetric.entities
+      label: optional
+
+  dseg:
+    $ref: meta.templates.deriv.volumetric
+    extensions:
+      - .nii.gz
+      - .nii
+      - .tsv
+      - .json
+    suffixes:
+      - dseg
+    entities:
+      $ref: meta.templates.deriv.volumetric.entities
+      cohort: optional
+      atlas: optional
+      segmentation: optional
+      scale: optional
+
+  probseg:
+    $ref: meta.templates.deriv.volumetric
+    extensions:
+      - .nii.gz
+      - .nii
+      - .json
+    suffixes:
+      - probseg
+    entities:
+      $ref: meta.templates.deriv.volumetric.entities
+      cohort: optional
+      atlas: optional
+      segmentation: optional
+      scale: optional
+      label: optional
+
+  dseg_surface:
+    $ref: meta.templates.deriv.surface
+    extensions:
+      - .label.gii
+      - .dlabel.nii
+      - .tsv
+      - .json
+    suffixes:
+      - dseg
+    entities:
+      $ref: meta.templates.deriv.surface.entities
+      cohort: optional
+      atlas: optional
+      segmentation: optional
+      scale: optional
 
 # Entities that apply to most atlas files
 # Include thus:
 #
 # filerule:
 #   entities:
-#     $ref: meta.templates.atlas_base_entities
-#     task: optional
-#     ...
-#   datatypes:
-#     ...
-atlas_base_entities:
-  template: required
-  cohort: optional
+#     $ref: meta.templates.atlas.base.entities
+atlas:
+  base:
+    entities:
+      template: required
+      cohort: optional

src/schema/objects/suffixes.yaml

@@ -578,6 +578,15 @@ defacemask:
   description: |
     A binary mask that was used to remove facial features from an anatomical MRI
     image.
+description:
+  value: description
+  display_name: Description file
+  description: |
+    A JSON file describing the entities that occur in the filename.
+
+    At present, this is used for atlas descriptions.
+
+    This file MUST be located at the root of the dataset.
 descriptions:
   value: descriptions
   display_name: Description Entity Definitions