[ENH] State of the schema sprint

src/04-modality-specific-files/02-magnetoencephalography.md

@@ -284,7 +284,7 @@ and a guide for using macros can be found at
 {{ MACROS___make_columns_table(
    {
       "name__channels": "REQUIRED",
-      "type__channels": "REQUIRED",
+      "type__meg_channels": "REQUIRED",
       "units": "REQUIRED",
    }
 ) }}

src/04-modality-specific-files/03-electroencephalography.md

@@ -252,7 +252,7 @@ and a guide for using macros can be found at
 {{ MACROS___make_columns_table(
    {
       "name__channels": "REQUIRED",
-      "type__channels": "REQUIRED",
+      "type__eeg_channels": "REQUIRED",
       "units": "REQUIRED",
    }
 ) }}

src/04-modality-specific-files/04-intracranial-electroencephalography.md

@@ -276,7 +276,7 @@ and a guide for using macros can be found at
       "name__channels": ("REQUIRED", "When a corresponding electrode is specified in `_electrodes.tsv`, "
                          "the name of that electrode MAY be specified here and the reference electrode "
                          "name MAY be provided in the `reference` column."),
-      "type__channels": "REQUIRED",
+      "type__ieeg_channels": "REQUIRED",
       "units": "REQUIRED",
       "low_cutoff": "REQUIRED",
       "high_cutoff": "REQUIRED",

src/schema/README.md

@@ -1,9 +1,9 @@
 # BIDS-schema
 
-Portions of the BIDS specification are defined using YAML files, in order to
+Portions of the BIDS specification are defined using YAML files in order to
 make the specification machine-readable.
 
-Currently, the portions of the specification that rely on this schema are
+Currently the portions of the specification that rely on this schema are
 the entity tables, entity definitions, filename templates, and metadata tables.
 Any changes to the specification should be mirrored in the schema.
 
@@ -73,7 +73,7 @@ For objects with `snake_case` names, two underscores must be used.
 There should also be a comment near the object definition in the YAML file describing the nature of the different objects.
 
 For example, the TSV column `"reference"` means different things when used for EEG data, as compared to iEEG data.
-As such, there are two definitions in `columns.yaml` for the `"reference"` column: `"reference__eeg"` and `"reference_ieeg"`.
+As such, there are two definitions in `columns.yaml` for the `"reference"` column: `"reference__eeg"` and `"reference__ieeg"`.
 
 ```yaml
 # reference column for channels.tsv files for EEG data

src/schema/SCHEMA_VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

src/schema/meta/context.yaml

@@ -0,0 +1,260 @@
+#
+# The context provides the namespaces available to rules.
+# These namespaces are used by selectors to define the scope of application
+# for a rule, as well as assertions, to determine whether the rule is satisfied.
+#
+# Not all components of the context will be defined; for example a NIfTI header
+# will only be defined when examining a NIfTI file.
+#
+# The dataset namespace is constructed once and is available when visiting all
+# files.
+#
+# The subject namespace is constructed once per subject, and is available when
+# visiting all files within that subject.
+#
+# All other (current) namespaces are defined on individual files.
+# Sidecar metadata and file associations are built according to the inheritance
+# principle.
+#
+---
+context:
+    type: object
+    properties:
+        dataset:
+            description: "Properties and contents of the entire dataset"
+            type: object
+            properties:
+                dataset_description:
+                    description: "Contents of /dataset_description.json"
+                    type: object
+                files:
+                    description: "List of all files in dataset"
+                    type: array
+                tree:
+                    description: "Tree view of all files in dataset"
+                    type: object
+                ignored:
+                    description: "Set of ignored files"
+                    type: array
+                modalities:
+                    description: "Modalities present in the dataset"
+                    type: array
+                subjects:
+                    description: "Collections of subjects in dataset"
+                    type: object
+                    properties:
+                        sub_dirs:
+                            description: "Subjects as determined by sub-*/ directories"
+                            type: array
+                            items:
+                                type: string
+                        participant_id:
+                            description: "The participant_id column of participants.tsv"
+                            type: array
+                            items:
+                                type: string
+                        phenotype:
+                            description: "The union of participant_id columns in phenotype files"
+                            type: array
+                            items:
+                                type: string
+        subject:
+            description: "Properties and contents of the current subject"
+            type: object
+            properties:
+                sessions:
+                    description: "Collections of sessions in subject"
+                    type: object
+                    properties:
+                        ses_dirs:
+                            description: "Sessions as determined by ses-*/ directories"
+                            type: array
+                            items:
+                                type: string
+                        session_id:
+                            description: "The session_id column of sessions.tsv"
+                            type: array
+                            items:
+                                type: string
+                        phenotype:
+                            description: "The union of session_id columns in phenotype files"
+                            type: array
+                            items:
+                                type: string
+
+        # Properties of the current file
+        path:
+            description: "Path of the current file"
+            type: string
+        entities:
+            description: "Entities parsed from the current filename"
+            type: object
+        datatype:
+            description: "Datatype of current file, for examples, anat"
+            type: string
+        suffix:
+            description: "Suffix of current file"
+            type: string
+        extension:
+            description: "Extension of current file including initial dot"
+            type: string
+        modality:
+            description: "Modality of current file, for examples, MRI"
+            type: string
+
+        sidecar:
+            description: "Sidecar metadata constructed via the inheritance principle"
+            type: object
+        associations:
+            # Note that this is not intended to be an exhaustive list of associated files
+            # or to expose every attribute of those files. It is specifically those files
+            # and attributes for which a rule needs to be applied from an originating file.
+            description: |
+                Associated files, indexed by suffix, selected according to the inheritance principle
+            type: object
+            properties:
+                events:
+                    description: "Events file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated events file"
+                            type: string
+                        onset:
+                            description: "Contents of the onset column"
+                            type: array
+                            items:
+                                type: string
+                aslcontext:
+                    description: "ASL context file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated aslcontext file"
+                            type: string
+                        n_rows:
+                            description: "Number of rows in aslcontext.tsv"
+                            type: integer
+                        volume_type:
+                            description: "Contents of the volume_type column"
+                            type: array
+                            items:
+                                type: string
+                m0scan:
+                    description: "M0 scan file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated M0 scan file"
+                            type: string
+                magnitude:
+                    description: "Magnitude image file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated magnitude file"
+                            type: string
+                magnitude1:
+                    description: "Magnitude1 image file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated magnitude1 file"
+                            type: string
+                bval:
+                    description: "B value file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated bval file"
+                            type: string
+                        n_cols:
+                            description: "Number of columns in bval file"
+                            type: integer
+                bvec:
+                    description: "B vector file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated bvec file"
+                            type: string
+                        n_cols:
+                            description: "Number of columns in bvec file"
+                            type: integer
+
+        # The following properties are populated if the current file is of an appropriate type
+        columns:
+            description: "TSV columns, indexed by column header, values are arrays with column contents"
+            type: object
+            additionalProperties:
+                type: array
+        json:
+            description: "Contents of the current JSON file"
+            type: object
+        nifti_header:
+            name: "NIfTI Header"
+            description: "Parsed contents of NIfTI header referenced elsewhere in schema."
+            type: object
+            properties:
+                dim_info:
+                    name: "Dimension Information"
+                    description: "Metadata about dimensions data."
+                    type: object
+                    properties:
+                        freq:
+                            name: "Frequency"
+                            description: "These fields encode which spatial dimension (1, 2, or 3)."
+                            type: integer
+                        phase:
+                            name: "Phase"
+                            description: "Corresponds to which acquisition dimension for MRI data."
+                            type: integer
+                        slice:
+                            name: "Slice"
+                            description: "Slice dimensions."
+                            type: integer
+                dim:
+                    name: "Data Dimensions"
+                    description: "Data seq dimensions."
+                    type: array
+                    minItems: 8
+                    maxItems: 8
+                    items:
+                        type: integer
+                pixdim:
+                    name: "Pixel Dimension"
+                    description: "Grid spacings (unit per dimension)."
+                    type: array
+                    minItems: 8
+                    maxItems: 8
+                    items:
+                        type: number
+                xyzt_units:
+                    name: "XYZT Units"
+                    description: "Units of pixdim[1..4]"
+                    xyz:
+                        name: "XYZ Units"
+                        description: "String representing the unit of voxel spacing."
+                        type: string
+                        enum:
+                        - "unknown"
+                        - "meter"
+                        - "mm"
+                        - "um"
+                    t:
+                        name: "Time Unit"
+                        description: "String representing the unit of inter-volume intervals."
+                        type: string
+                        enum:
+                        - "unknown"
+                        - "sec"
+                        - "msec"
+                        - "usec"
+                qform_code:
+                    name: "qform code"
+                    description: "Use of the quaternion fields."
+                    type: integer
+                sform_code:
+                    name: "sform code"
+                    description: "Use of the affine fields."
+                    type: integer

src/schema/objects/columns.yaml

@@ -466,7 +466,31 @@ trigger:
     continuous measurement of the scanner trigger signal
   type: number
 # type column in channels.tsv files
-type__channels:
+type__eeg_channels:
+  name: type
+  description: |
+    Type of channel; MUST use the channel types listed below.
+    Note that the type MUST be in upper-case.
+  type: string
+  enum:
+  - AUDIO
+  - EEG
+  - EOG
+  - ECG
+  - EMG
+  - EYEGAZE
+  - GSR
+  - HEOG
+  - MISC
+  - PPG
+  - PUPIL
+  - REF
+  - RESP
+  - SYSCLOCK
+  - TEMP
+  - TRIG
+  - VEOG
+type__meg_channels:
   name: type
   description: |
     Type of channel; MUST use the channel types listed below.
@@ -501,6 +525,33 @@ type__channels:
   - HLU
   - FITERR
   - OTHER
+type__ieeg_channels:
+  name: type
+  description: |
+    Type of channel; MUST use the channel types listed below.
+    Note that the type MUST be in upper-case.
+  type: string
+  enum:
+  - EEG
+  - ECOG
+  - SEEG
+  - DBS
+  - VEOG
+  - HEOG
+  - EOG
+  - ECG
+  - EMG
+  - TRIG
+  - AUDIO
+  - PD
+  - EYEGAZE
+  - PUPIL
+  - MISC
+  - SYSCLOCK
+  - ADC
+  - DAC
+  - REF
+  - OTHER
 # type column for electrodes.tsv files
 type__electrodes:
   name: type