[SCHEMA] BEP017

src/schema/objects/columns.yaml

@@ -296,6 +296,11 @@ material:
   description: |
     Material of the electrode (for example, `Tin`, `Ag/AgCl`, `Gold`).
   type: string
+matrix_index:
+  name: index
+  display_name: Matrix Index
+  description: Todo
+  type: integer
 metabolite_parent_fraction:
   name: metabolite_parent_fraction
   display_name: Metabolite parent fraction
@@ -339,6 +344,16 @@ name__segmentations:
   description: |
     The unique label name.
   type: string
+node_file:
+  name: node_file
+  display_name: Node Filename
+  description: Todo
+  type: uri
+node_index:
+  name: node_index
+  display_name: Node Index
+  description: Todo
+  type: number
 notch:
   name: notch
   display_name: Notch frequencies

src/schema/objects/entities.yaml

@@ -152,6 +152,15 @@ label:
     This entity is only applicable to derivative data.
   type: string
   format: label
+measure:
+  name: meas
+  display_name: Measure
+  description: |
+    Todo
+
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
 modality:
   name: mod
   display_name: Corresponding Modality

src/schema/objects/extensions.yaml

@@ -63,16 +63,28 @@ con:
     Raw continuous data from a KIT/Yokogawa/Ricoh MEG system.
 
     Successor to the `.sqd` extension for raw continuous data.
-dat:
-  value: .dat
-  display_name: MEG Fine-Calibration Format
-  description: |
-    A fine-calibration file used for Neuromag/Elekta/MEGIN MEG recording hardware.
 CTF:
   value: .ds/
   display_name: CTF MEG Dataset Directory
   description: |
     A directory for MEG data, typically containing a `.meg4` file for the data and a `.res4` file for the resources.
+dat:
+  value: .dat
+  display_name: MEG Fine-Calibration Format
+  description: |
+    A fine-calibration file used for Neuromag/Elekta/MEGIN MEG recording hardware.
+dense_h5:
+  value: .dense.h5
+  display_name: Dense H5
+  description: Todo
+dense_tsv:
+  value: .dense.tsv
+  display_name: Dense TSV
+  description: Todo
+dense_zarr:
+  value: .dense.zarr
+  display_name: Dense Zarr
+  description: Todo
 dlabelnii:
   value: .dlabel.nii
   display_name: CIFTI-2 Dense Label File
@@ -244,6 +256,18 @@ snirf:
   display_name: Shared Near Infrared Spectroscopy Format
   description: |
     HDF5 file organized according to the [SNIRF specification](https://github.com/fNIRS/snirf)
+sparse_h5:
+  value: .sparse.h5
+  display_name: Sparse H5
+  description: Todo
+sparse_tsv:
+  value: .sparse.tsv
+  display_name: Sparse TSV
+  description: Todo
+sparse_zarr:
+  value: .sparse.zarr
+  display_name: Sparse Zarr
+  description: Todo
 sqd:
   value: .sqd
   display_name: SQD
@@ -302,6 +326,10 @@ vmrk:
     A text marker file in the
     [BrainVision Core Data Format](https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/).
     These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
+zarr:
+  value: .zarr
+  display_name: zarr
+  description: Todo
 Any:
   value: .*
   display_name: Any Extension

src/schema/objects/metadata.yaml

@@ -198,6 +198,13 @@ Authors:
   type: array
   items:
     type: string
+Axes:
+  name: Axes
+  display_name: Axes
+  description: Todo
+  type: array
+  items:
+    type: object
 B0FieldIdentifier:
   name: B0FieldIdentifier
   display_name: B0 Field Identifier
@@ -709,6 +716,11 @@ DigitizedLandmarks:
     `true` or `false` value indicating whether anatomical landmark points
     (fiducials) are contained within this recording.
   type: boolean
+Directed:
+  name: Directed
+  display_name: Directed Graph
+  type: boolean
+  description: todo
 DispersionConstant:
   name: DispersionConstant
   display_name: Dispersion Constant
@@ -2192,13 +2204,25 @@ NIRSCoordinateProcessingDescription:
     Has any post-processing (such as projection) been done on the optode
     positions (for example, `"surface_projection"`, `"n/a"`).
   type: string
+NodeFiles:
+  name: NodeFiles
+  display_name: Node Files
+  descripiton: Todo
+  type: array
+  items:
+    type uri
 NonlinearGradientCorrection:
   name: NonlinearGradientCorrection
   display_name: Nonlinear Gradient Correction
   description: |
     Boolean stating if the image saved has been corrected for gradient
     nonlinearities by the scanner sequence.
   type: boolean
+NonNegative:
+  name: NonNegative
+  display_name: Non Negative
+  description: Todo
+  type: boolean
 NumberOfVolumesDiscardedByScanner:
   name: NumberOfVolumesDiscardedByScanner
   display_name: Number Of Volumes Discarded By Scanner
@@ -2679,6 +2703,11 @@ ReferencesAndLinks:
   items:
     type: string
   type: array
+RelationshipMeasure:
+  name: RelationshipMeasure
+  display_name: Relationship Measure
+  descrption: Todo
+  type: string
 RepetitionTime:
   name: RepetitionTime
   display_name: Repetition Time
@@ -3120,6 +3149,12 @@ SliceTiming:
     type: number
     minimum: 0
     unit: s
+Software:
+  name: Software
+  display_name: Software
+  description: todo
+  type: string
+  format: uri
 SoftwareFilters:
   name: SoftwareFilters
   display_name: Software Filters
@@ -3583,6 +3618,11 @@ Units:
     (see [Units](SPEC_ROOT/common-principles.md#units)).
   type: string
   format: unit
+ValidDiagonal:
+  name: ValidDiagonal
+  display_name: Valid Diagonal
+  description: Todo
+  type: boolean
 VascularCrushing:
   name: VascularCrushing
   display_name: Vascular Crushing
@@ -3649,6 +3689,11 @@ WaterSuppressionTechnique:
   description: |
     The name of the pulse sequence used for water suppression (for example, `"CHESS"`, `"VAPOR"`).
   type: string
+Weighted:
+  name: Weighted
+  display_name: Weighted Matrix
+  description: Todo
+  type: boolean
 WholeBloodAvail:
   name: WholeBloodAvail
   display_name: Whole Blood Avail

src/schema/objects/suffixes.yaml

@@ -697,6 +697,10 @@ nirs:
   value: nirs
   display_name: Near Infrared Spectroscopy
   description: Data associated with a Shared Near Infrared Spectroscopy Format file.
+nodeindices:
+  value: nodeindices
+  display_name: Node Indices
+  description: Todo
 noRF:
   value: noRF
   display_name: No Radio Frequency Excitation Scan
@@ -780,6 +784,10 @@ probseg:
     A probabilistic segmentation.
 
     This suffix may only be used in derivative datasets.
+relmat:
+  value: relmat
+  display_name: Relationship Matrix
+  description: Todo
 sbref:
   value: sbref
   display_name: Single-band reference image

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

@@ -0,0 +1,30 @@
+---
+relmat:
+  entities:
+    measure: optional
+  datatypes:
+    - any
+  extensions:
+    - .json
+    - .tsv
+    - .h5
+    - .zarr
+    - .sparse.tsv
+    - .sparse.h5
+    - .sparse.zarr
+    - .dense.tsv
+    - .dense.h5
+    - .dense.zarr
+  suffixes:
+    - relmat
+
+nodeindicies:
+  entities:
+    measure: optional
+  suffixes:
+    - nodeindicies
+  datatypes:
+    - any
+  extensions:
+    - .json
+    - .tsv

src/schema/rules/sidecars/derivatives/relmat.yaml

@@ -0,0 +1,24 @@
+Relmat:
+  selectors:
+    - suffix == "relmat"
+  fields:
+    Directed: required
+    RelationshipMeasure: required
+    Software: required
+    ValidDiagonal: required
+    Weighted: required
+    Axes: recommended
+    NodeFiles: recommended
+    NonNegative: recommended
+    AdditionalMatrixDimensions: optional
+    AdditionalMatrixDimensionDescription: optional
+    AdditionalMatrixDimensionsUnits: optional
+    Description: optional
+    MeasureDescription: optional
+    MeasurePoint: optional
+    MeasureUnits: optional
+    NodeIndicesFile: optional
+    Serialization:
+      level: optional
+      level_addendum: required if `StorageFormat` is "UpperTriangular" or "LowerTriangular"
+    Sources: optional

src/schema/rules/tabular_data/derivatives/relmat.yaml

@@ -0,0 +1,14 @@
+---
+NodeIndices:
+  selectors:
+    suffix == "nodeindices"
+  columns:
+    matrix_index: required
+    node_file: required
+    node_index: required
+  additional_columns: allowed
+  initial_columns:
+    - matrix_index
+    - node_file
+    - node_index
+  index_columns: [matrix_index]