diff --git a/src/metaschema.json b/src/metaschema.json index 020ddfadf4..49d0f8cab7 100644 --- a/src/metaschema.json +++ b/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_]+$": { diff --git a/src/schema/README.md b/src/schema/README.md index 3505ea1b04..4d53a38c74 100644 --- a/src/schema/README.md +++ b/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 diff --git a/src/schema/meta/templates.yaml b/src/schema/meta/templates.yaml index 2c2618f04e..11689c6e0a 100644 --- a/src/schema/meta/templates.yaml +++ b/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 diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index 1e2825ced2..0592acf140 100644 --- a/src/schema/objects/suffixes.yaml +++ b/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 diff --git a/src/schema/rules/files/atlas/anat.yaml b/src/schema/rules/files/atlas/anat.yaml deleted file mode 100644 index bcfe29c0b1..0000000000 --- a/src/schema/rules/files/atlas/anat.yaml +++ /dev/null @@ -1,210 +0,0 @@ ---- -nonparametric: - suffixes: - - T1w - - T2w - - PDw - - T2starw - - FLAIR - - inplaneT1 - - inplaneT2 - - PDT2 - - angio - - T2star # deprecated - - FLASH # deprecated - - PD # deprecated - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: optional - part: optional - chunk: optional - -parametric: - suffixes: - - T1map - - T2map - - T2starmap - - R1map - - R2map - - R2starmap - - PDmap - - MTRmap - - MTsat - - UNIT1 - - T1rho - - MWFmap - - MTVmap - - Chimap - - S0map - - M0map - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - chunk: optional - -defacemask: - suffixes: - - defacemask - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - modality: optional - chunk: optional - -multiecho: - suffixes: - - MESE - - MEGRE - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: required - part: optional - chunk: optional - -multiflip: - suffixes: - - VFA - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: optional - flip: required - part: optional - chunk: optional - -multiinversion: - suffixes: - - IRT1 - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - inversion: required - part: optional - chunk: optional - -mp2rage: - suffixes: - - MP2RAGE - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: optional - flip: optional - inversion: required - part: optional - chunk: optional - -vfamt: - suffixes: - - MPM - - MTS - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: optional - flip: required - mtransfer: required - part: optional - chunk: optional - -mtr: - suffixes: - - MTR - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - anat - entities: - $ref: meta.templates.atlas_base_entities - task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - mtransfer: required - part: optional - chunk: optional diff --git a/src/schema/rules/files/atlas/derivatives.yaml b/src/schema/rules/files/atlas/derivatives.yaml deleted file mode 100644 index 3c6eef8595..0000000000 --- a/src/schema/rules/files/atlas/derivatives.yaml +++ /dev/null @@ -1,260 +0,0 @@ ---- -anat_parametric_volumetric: - $ref: rules.files.atlas.anat.parametric - entities: - $ref: rules.files.atlas.anat.parametric.entities - space: optional - resolution: optional - density: optional - description: optional - -anat_nonparametric_volumetric: - $ref: rules.files.atlas.anat.nonparametric - entities: - $ref: rules.files.atlas.anat.nonparametric.entities - space: optional - resolution: optional - density: optional - description: optional - -dwi_volumetric: - $ref: rules.files.atlas.dwi.dwi - entities: - $ref: rules.files.atlas.dwi.dwi.entities - space: optional - resolution: optional - density: optional - description: optional - -func_volumetric: - $ref: rules.files.atlas.func.func - entities: - $ref: rules.files.atlas.func.func.entities - space: optional - resolution: optional - density: optional - description: optional - -anat_parametric_mask: - $ref: rules.files.atlas.anat.parametric - suffixes: - - mask - entities: - $ref: rules.files.atlas.anat.parametric.entities - space: optional - resolution: optional - density: optional - label: optional - description: optional - -anat_nonparametric_mask: - $ref: rules.files.atlas.anat.nonparametric - suffixes: - - mask - entities: - $ref: rules.files.atlas.anat.nonparametric.entities - space: optional - resolution: optional - density: optional - label: optional - description: optional - -dwi_mask: - $ref: rules.files.atlas.dwi.dwi - suffixes: - - mask - entities: - $ref: rules.files.atlas.dwi.dwi.entities - space: optional - resolution: optional - density: optional - label: optional - description: optional - -func_mask: - $ref: rules.files.atlas.func.func - suffixes: - - mask - entities: - $ref: rules.files.atlas.func.func.entities - space: optional - resolution: optional - density: optional - label: optional - description: optional - -anat_parametric_discrete_segmentation: - $ref: rules.files.atlas.anat.parametric - suffixes: - - dseg - entities: - $ref: rules.files.atlas.anat.parametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - - .tsv - -anat_nonparametric_discrete_segmentation: - $ref: rules.files.atlas.anat.nonparametric - suffixes: - - dseg - entities: - $ref: rules.files.atlas.anat.nonparametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - - .tsv - -func_discrete_segmentation: - $ref: rules.files.atlas.func.func - suffixes: - - dseg - entities: - $ref: rules.files.atlas.func.func.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional - -dwi_discrete_segmentation: - $ref: rules.files.atlas.dwi.dwi - suffixes: - - dseg - entities: - $ref: rules.files.atlas.dwi.dwi.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional - -anat_parametric_probabilistic_segmentation: - $ref: rules.files.atlas.anat.parametric - suffixes: - - probseg - entities: - $ref: rules.files.atlas.anat.parametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - label: optional - description: optional - -anat_nonparametric_probabilistic_segmentation: - $ref: rules.files.atlas.anat.nonparametric - suffixes: - - probseg - entities: - $ref: rules.files.atlas.anat.nonparametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - label: optional - description: optional - -func_probabilistic_segmentation: - $ref: rules.files.atlas.func.func - suffixes: - - probseg - entities: - $ref: rules.files.atlas.func.func.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - label: optional - description: optional - -dwi_probabilistic_segmentation: - $ref: rules.files.atlas.dwi.dwi - suffixes: - - probseg - entities: - $ref: rules.files.atlas.dwi.dwi.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - label: optional - description: optional - -anat_parametic_discrete_surface: - $ref: rules.files.atlas.anat.parametric - suffixes: - - dseg - extensions: - - .label.gii - - .dlabel.nii - - .json - - .tsv - entities: - $ref: rules.files.atlas.anat.parametric.entities - hemisphere: optional - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional - -anat_nonparametic_discrete_surface: - $ref: rules.files.atlas.anat.nonparametric - suffixes: - - dseg - extensions: - - .label.gii - - .dlabel.nii - - .json - - .tsv - entities: - $ref: rules.files.atlas.anat.nonparametric.entities - hemisphere: optional - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional diff --git a/src/schema/rules/files/atlas/dwi.yaml b/src/schema/rules/files/atlas/dwi.yaml deleted file mode 100644 index 55f51e1ac7..0000000000 --- a/src/schema/rules/files/atlas/dwi.yaml +++ /dev/null @@ -1,38 +0,0 @@ ---- -dwi: - suffixes: - - dwi - extensions: - - .nii.gz - - .nii - - .json - - .bvec - - .bval - datatypes: - - dwi - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional - part: optional - chunk: optional - -sbref: - suffixes: - - sbref - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - dwi - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional - part: optional - chunk: optional diff --git a/src/schema/rules/files/atlas/fmap.yaml b/src/schema/rules/files/atlas/fmap.yaml deleted file mode 100644 index 33162acc69..0000000000 --- a/src/schema/rules/files/atlas/fmap.yaml +++ /dev/null @@ -1,144 +0,0 @@ ---- -fieldmaps: - suffixes: - - phasediff - - phase1 - - phase2 - - magnitude1 - - magnitude2 - - magnitude - - fieldmap - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - run: optional - chunk: optional - -pepolar: - suffixes: - - epi - - m0scan - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - ceagent: optional - direction: required - run: optional - part: optional - chunk: optional - -TB1DAM: - suffixes: - - TB1DAM - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - flip: required - inversion: optional - part: optional - chunk: optional - -TB1EPI: - suffixes: - - TB1EPI - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: required - flip: required - inversion: optional - part: optional - chunk: optional - -RFFieldMaps: - suffixes: - - TB1AFI - - TB1TFL - - TB1RFM - - RB1COR - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: optional - flip: optional - inversion: optional - part: optional - chunk: optional - -TB1SRGE: - suffixes: - - TB1SRGE - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - echo: optional - flip: required - inversion: required - part: optional - chunk: optional - -parametric: - suffixes: - - TB1map - - RB1map - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - fmap - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - chunk: optional diff --git a/src/schema/rules/files/atlas/func.yaml b/src/schema/rules/files/atlas/func.yaml deleted file mode 100644 index 586a0eb342..0000000000 --- a/src/schema/rules/files/atlas/func.yaml +++ /dev/null @@ -1,43 +0,0 @@ ---- -func: - suffixes: - - bold - - cbv - - sbref - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - func - entities: - $ref: meta.templates.atlas_base_entities - task: required - acquisition: optional - ceagent: optional - reconstruction: optional - direction: optional - run: optional - echo: optional - part: optional - chunk: optional - -phase: - suffixes: - - phase # deprecated - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - func - entities: - $ref: meta.templates.atlas_base_entities - task: required - acquisition: optional - ceagent: optional - reconstruction: optional - direction: optional - run: optional - echo: optional - chunk: optional diff --git a/src/schema/rules/files/atlas/micr.yaml b/src/schema/rules/files/atlas/micr.yaml deleted file mode 100644 index 9ffd68e465..0000000000 --- a/src/schema/rules/files/atlas/micr.yaml +++ /dev/null @@ -1,36 +0,0 @@ ---- -microscopy: - suffixes: - - TEM - - SEM - - uCT - - BF - - DF - - PC - - DIC - - FLUO - - CONF - - PLI - - CARS - - 2PE - - MPE - - SR - - NLO - - OCT - - SPIM - extensions: - - .ome.tif - - .ome.btf - - .ome.zarr/ - - .png - - .tif - - .json - datatypes: - - micr - entities: - $ref: meta.templates.atlas_base_entities - sample: required - acquisition: optional - stain: optional - run: optional - chunk: optional diff --git a/src/schema/rules/files/atlas/perf.yaml b/src/schema/rules/files/atlas/perf.yaml deleted file mode 100644 index aec5ae7b80..0000000000 --- a/src/schema/rules/files/atlas/perf.yaml +++ /dev/null @@ -1,46 +0,0 @@ ---- -asl: - suffixes: - - asl - - m0scan - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - perf - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional - -aslcontext: - suffixes: - - aslcontext - extensions: - - .tsv - datatypes: - - perf - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional - -asllabeling: - suffixes: - - asllabeling - extensions: - - .jpg - - .png - - .tif - datatypes: - - perf - entities: - $ref: meta.templates.atlas_base_entities - acquisition: optional - reconstruction: optional - run: optional diff --git a/src/schema/rules/files/atlas/pet.yaml b/src/schema/rules/files/atlas/pet.yaml deleted file mode 100644 index 277d28bf8a..0000000000 --- a/src/schema/rules/files/atlas/pet.yaml +++ /dev/null @@ -1,32 +0,0 @@ ---- -pet: - suffixes: - - pet - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - pet - entities: - $ref: meta.templates.atlas_base_entities - task: optional - tracer: optional - reconstruction: optional - run: optional - -blood: - suffixes: - - blood - extensions: - - .tsv - - .json - datatypes: - - pet - entities: - $ref: meta.templates.atlas_base_entities - task: optional - tracer: optional - reconstruction: optional - run: optional - recording: required diff --git a/src/schema/rules/files/deriv/imaging.yaml b/src/schema/rules/files/deriv/imaging.yaml index 4353c67b48..0d7d051a0c 100644 --- a/src/schema/rules/files/deriv/imaging.yaml +++ b/src/schema/rules/files/deriv/imaging.yaml @@ -1,311 +1,551 @@ +# 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: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.parametric + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.anat.parametric entities: - $ref: rules.files.raw.anat.parametric.entities - space: optional - resolution: optional - density: optional - description: optional + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.anat.parametric.entities + +anat_parametric_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_parametric_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_parametric_volumetric.entities anat_nonparametric_volumetric: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.nonparametric - entities: - $ref: rules.files.raw.anat.nonparametric.entities - space: optional - resolution: optional - density: optional - description: optional - -dwi_volumetric: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.dwi.dwi - entities: - $ref: rules.files.raw.dwi.dwi.entities - space: optional - resolution: optional - density: optional - description: optional - -dwi_scannerderivatives: - $ref: rules.files.raw.dwi.ScannerDerivatives - entities: - $ref: rules.files.raw.dwi.ScannerDerivatives.entities - space: optional - resolution: optional - density: optional - description: optional + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.anat.nonparametric + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.anat.nonparametric.entities + +anat_nonparametric_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_nonparametric_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_nonparametric_volumetric.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_defacemask_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_defacemask_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_defacemask_volumetric.entities + +anat_multiecho_volumetric: + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.anat.multiecho + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.anat.multiecho.entities + +anat_multiecho_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_multiecho_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_multiecho_volumetric.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_multiflip_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_multiflip_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_multiflip_volumetric.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_multiinversion_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_multiinversion_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_multiinversion_volumetric.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_mp2rage_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_mp2rage_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_mp2rage_volumetric.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_vfamt_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_vfamt_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_vfamt_volumetric.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 + +anat_mtr_volumetric_atlas: + $ref: rules.files.deriv.imaging.anat_mtr_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_mtr_volumetric.entities + +dwi_dwi_volumetric: + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.dwi.dwi + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.dwi.dwi.entities + +dwi_dwi_volumetric_atlas: + $ref: rules.files.deriv.imaging.dwi_dwi_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.dwi_dwi_volumetric.entities + +dwi_sbref_volumetric: + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.dwi.sbref + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.dwi.sbref.entities + +dwi_sbref_volumetric_atlas: + $ref: rules.files.deriv.imaging.dwi_sbref_volumetric + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.deriv.imaging.dwi_sbref_volumetric.entities + +dwi_scannerderivatives_volumetric: + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.dwi.ScannerDerivatives + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.dwi.ScannerDerivatives.entities + +dwi_scannerderivatives_volumetric_atlas: + $ref: rules.files.deriv.imaging.dwi_scannerderivatives_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.dwi_scannerderivatives_volumetric.entities func_volumetric: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.func.func - entities: - $ref: rules.files.raw.func.func.entities - space: optional - resolution: optional - density: optional - description: optional - -anat_parametric_mask: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.parametric - suffixes: - - mask - entities: - $ref: rules.files.raw.anat.parametric.entities - space: optional - resolution: optional - label: optional - description: optional - -anat_nonparametric_mask: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.nonparametric - suffixes: - - mask - entities: - $ref: rules.files.raw.anat.nonparametric.entities - space: optional - resolution: optional - label: optional - description: optional + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.func.func + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.func.func.entities + +func_volumetric_atlas: + $ref: rules.files.deriv.imaging.func_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.func_volumetric.entities + +func_phase_volumetric: + $ref: + - meta.templates.deriv.volumetric + - rules.files.raw.func.phase + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.raw.func.phase.entities + +# NB: Not permitting deprecated phase suffix for atlases + +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_fieldmaps_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_fieldmaps_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_fieldmaps_volumetric.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_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_pepolar_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_pepolar_volumetric.entities + +fmap_pepolar_m0scan_volumetric: + $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_pepolar_m0scan_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_pepolar_m0scan_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_pepolar_m0scan_volumetric.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_TB1DAM_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_TB1DAM_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_TB1DAM_volumetric.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_TB1EPI_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_TB1EPI_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_TB1EPI_volumetric.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_RFFieldMaps_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_RFFieldMaps_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_RFFieldMaps_volumetric.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_TB1SRGE_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_TB1SRGE_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_TB1SRGE_volumetric.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 + +fmap_parametric_volumetric_atlas: + $ref: rules.files.deriv.imaging.fmap_parametric_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.fmap_parametric_volumetric.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 + +perf_asl_volumetric_atlas: + $ref: rules.files.deriv.imaging.perf_asl_volumetric + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.perf_asl_volumetric.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 + +pet_pet_volumetric_atlas: + $ref: rules.files.deriv.imaging.pet_pet_volumetric + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.deriv.imaging.pet_pet_volumetric.entities + +# Masks +anat_mask: + $ref: + - meta.templates.deriv.mask + - rules.files.raw.anat.nonparametric + entities: + # The nonparametric entities are a superset of parametric entities, + # so no need to duplicate. + $ref: + - meta.templates.deriv.mask.entities + - rules.files.raw.anat.nonparametric.entities + +anat_mask_atlas: + $ref: rules.files.deriv.imaging.anat_mask + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_mask.entities dwi_mask: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.dwi.dwi - suffixes: - - mask - extensions: - - .nii.gz - - .nii - - .json - entities: - $ref: rules.files.raw.dwi.dwi.entities - space: optional - resolution: optional - label: optional - description: optional + $ref: + - meta.templates.deriv.mask + - rules.files.raw.dwi.dwi + entities: + $ref: + - meta.templates.deriv.mask.entities + - rules.files.raw.dwi.dwi.entities + +dwi_mask_atlas: + $ref: rules.files.deriv.imaging.dwi_mask + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.dwi_mask.entities func_mask: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.func.func - suffixes: - - mask - entities: - $ref: rules.files.raw.func.func.entities - space: optional - resolution: optional - label: optional - description: optional - -anat_parametric_discrete_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.parametric - suffixes: - - dseg - entities: - $ref: rules.files.raw.anat.parametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - - .tsv - -anat_nonparametric_discrete_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.nonparametric - suffixes: - - dseg - entities: - $ref: rules.files.raw.anat.nonparametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - - .tsv + $ref: + - meta.templates.deriv.mask + - rules.files.raw.func.func + entities: + $ref: + - meta.templates.deriv.mask.entities + - rules.files.raw.func.func.entities + +func_mask_atlas: + $ref: rules.files.deriv.imaging.func_mask + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.deriv.imaging.func_mask.entities + +# Discrete and probabilistic segmentations +anat_discrete_segmentation: + $ref: + - meta.templates.deriv.dseg + - rules.files.raw.anat.nonparametric + entities: + # ibid + $ref: + - meta.templates.deriv.dseg.entities + - rules.files.raw.anat.nonparametric.entities + +anat_discrete_segmentation_atlas: + $ref: rules.files.deriv.imaging.anat_discrete_segmentation + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_discrete_segmentation.entities func_discrete_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.func.func - suffixes: - - dseg - entities: - $ref: rules.files.raw.func.func.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - - .tsv + $ref: + - meta.templates.deriv.dseg + - rules.files.raw.func.func + entities: + $ref: + - meta.templates.deriv.dseg.entities + - rules.files.raw.func.func.entities + +func_discrete_segmentation_atlas: + $ref: rules.files.deriv.imaging.func_discrete_segmentation + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.func_discrete_segmentation.entities dwi_discrete_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.dwi.dwi - suffixes: - - dseg - entities: - $ref: rules.files.raw.dwi.dwi.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - - .tsv - -anat_parametric_probabilistic_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.parametric - suffixes: - - probseg - entities: - $ref: rules.files.raw.anat.parametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - label: optional - description: optional - -anat_nonparametric_probabilistic_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.nonparametric - suffixes: - - probseg - entities: - $ref: rules.files.raw.anat.nonparametric.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - label: optional - description: optional + $ref: + - meta.templates.deriv.dseg + - rules.files.raw.dwi.dwi + entities: + $ref: + - meta.templates.deriv.dseg.entities + - rules.files.raw.dwi.dwi.entities + +dwi_discrete_segmentation_atlas: + $ref: rules.files.deriv.imaging.dwi_discrete_segmentation + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.dwi_discrete_segmentation.entities + +anat_probabilistic_segmentation: + $ref: + - meta.templates.deriv.probseg + - rules.files.raw.anat.nonparametric + entities: + # ibid + $ref: + - meta.templates.deriv.probseg.entities + - rules.files.raw.anat.nonparametric.entities + +anat_probabilistic_segmentation_atlas: + $ref: rules.files.deriv.imaging.anat_probabilistic_segmentation + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.anat_probabilistic_segmentation.entities func_probabilistic_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.func.func - suffixes: - - probseg - entities: - $ref: rules.files.raw.func.func.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - label: optional - description: optional + $ref: + - meta.templates.deriv.probseg + - rules.files.raw.func.func + entities: + $ref: + - meta.templates.deriv.probseg.entities + - rules.files.raw.func.func.entities + +func_probabilistic_segmentation_atlas: + $ref: rules.files.deriv.imaging.func_probabilistic_segmentation + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.func_probabilistic_segmentation.entities dwi_probabilistic_segmentation: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.dwi.dwi - suffixes: - - probseg - entities: - $ref: rules.files.raw.dwi.dwi.entities - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - label: optional - description: optional - extensions: - - .nii.gz - - .nii - - .json - -anat_parametric_discrete_surface: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.parametric - suffixes: - - dseg - extensions: - - .label.gii - - .dlabel.nii - - .json - - .tsv - entities: - $ref: rules.files.raw.anat.parametric.entities - hemisphere: optional - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional - -anat_nonparametric_discrete_surface: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.nonparametric - suffixes: - - dseg - extensions: - - .label.gii - - .dlabel.nii - - .json - - .tsv - entities: - $ref: rules.files.raw.anat.nonparametric.entities - hemisphere: optional - cohort: optional - space: optional - atlas: optional - segmentation: optional - scale: optional - resolution: optional - density: optional - description: optional + $ref: + - meta.templates.deriv.probseg + - rules.files.raw.dwi.dwi + entities: + $ref: + - meta.templates.deriv.probseg.entities + - rules.files.raw.dwi.dwi.entities + +dwi_probabilistic_segmentation_atlas: + $ref: rules.files.deriv.imaging.dwi_probabilistic_segmentation + entities: + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.imaging.dwi_probabilistic_segmentation.entities + +anat_discrete_surface: + $ref: + - meta.templates.deriv.dseg_surface + - rules.files.raw.anat.nonparametric + entities: + # ibid + $ref: + - meta.templates.deriv.dseg_surface.entities + - rules.files.raw.anat.nonparametric.entities + +anat_discrete_surface_atlas: + $ref: rules.files.deriv.imaging.anat_discrete_surface + entities: + $ref: + - meta.templates.deriv.volumetric.entities + - rules.files.deriv.imaging.anat_discrete_surface.entities diff --git a/src/schema/rules/files/deriv/preprocessed_data.yaml b/src/schema/rules/files/deriv/preprocessed_data.yaml index c023cbd406..029e5a3a2d 100644 --- a/src/schema/rules/files/deriv/preprocessed_data.yaml +++ b/src/schema/rules/files/deriv/preprocessed_data.yaml @@ -1,369 +1,182 @@ +# This document implements the common derivatives specification, +# generally adding space and description entities to most raw data. +# +# Imaging files are generally omitted, due to redundancy with imaging.yaml --- -anat_nonparametric_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.nonparametric - entities: - $ref: rules.files.raw.anat.nonparametric.entities - space: optional - description: optional - -anat_parametric_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.parametric - entities: - $ref: rules.files.raw.anat.parametric.entities - space: optional - description: optional - -anat_defacemask_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.defacemask - entities: - $ref: rules.files.raw.anat.defacemask.entities - space: optional - description: optional - -anat_multiecho_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.multiecho - entities: - $ref: rules.files.raw.anat.multiecho.entities - space: optional - description: optional - -anat_multiflip_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.multiflip - entities: - $ref: rules.files.raw.anat.multiflip.entities - space: optional - description: optional - -anat_multiinversion_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.multiinversion - entities: - $ref: rules.files.raw.anat.multiinversion.entities - space: optional - description: optional - -anat_mp2rage_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.mp2rage - entities: - $ref: rules.files.raw.anat.mp2rage.entities - space: optional - description: optional - -anat_vfamt_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.vfamt - entities: - $ref: rules.files.raw.anat.vfamt.entities - space: optional - description: optional - -anat_mtr_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.anat.mtr - entities: - $ref: rules.files.raw.anat.mtr.entities - space: optional - description: optional - beh_noncontinuous_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.beh.noncontinuous + $ref: + - meta.templates.deriv.base + - rules.files.raw.beh.noncontinuous entities: - $ref: rules.files.raw.beh.noncontinuous.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.beh.noncontinuous.entities channels_channels_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.channels + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.channels entities: - $ref: rules.files.raw.channels.channels.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.channels.entities channels_channels__meg_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.channels__meg + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.channels__meg entities: - $ref: rules.files.raw.channels.channels__meg.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.channels__meg.entities channels_channels__motion_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.channels__motion + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.channels__motion entities: - $ref: rules.files.raw.channels.channels__motion.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.channels__motion.entities channels_coordsystem_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.coordsystem + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.coordsystem entities: - $ref: rules.files.raw.channels.coordsystem.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.coordsystem.entities channels_coordsystem__eeg_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.coordsystem__eeg + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.coordsystem__eeg entities: - $ref: rules.files.raw.channels.coordsystem__eeg.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.coordsystem__eeg.entities channels_electrodes_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.electrodes + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.electrodes entities: - $ref: rules.files.raw.channels.electrodes.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.electrodes.entities channels_electrodes__meg_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.electrodes__meg - entities: - $ref: rules.files.raw.channels.electrodes__meg.entities - description: optional - -channels_electrodes_optodes_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.channels.optodes - entities: - $ref: rules.files.raw.channels.optodes.entities - description: optional - -dwi_dwi_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.dwi.dwi + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.electrodes__meg entities: - $ref: rules.files.raw.dwi.dwi.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.electrodes__meg.entities -dwi_sbref_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.dwi.sbref +channels_optodes_common: + $ref: + - meta.templates.deriv.base + - rules.files.raw.channels.optodes entities: - $ref: rules.files.raw.dwi.sbref.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.channels.optodes.entities eeg_eeg_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.eeg.eeg + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.eeg.eeg entities: - $ref: rules.files.raw.eeg.eeg.entities - space: optional - description: optional - -fmap_fieldmaps_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.fieldmaps - entities: - $ref: rules.files.raw.fmap.fieldmaps.entities - space: optional - description: optional - -fmap_pepolar_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.pepolar - entities: - $ref: rules.files.raw.fmap.pepolar.entities - space: optional - description: optional - -fmap_pepolar_m0scan: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.pepolar_m0scan - entities: - $ref: rules.files.raw.fmap.pepolar.entities - space: optional - description: optional - -fmap_TB1DAM_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.TB1DAM - entities: - $ref: rules.files.raw.fmap.TB1DAM.entities - space: optional - description: optional - -fmap_TB1EPI_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.TB1EPI - entities: - $ref: rules.files.raw.fmap.TB1EPI.entities - space: optional - description: optional - -fmap_RFFieldMaps_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.RFFieldMaps - entities: - $ref: rules.files.raw.fmap.RFFieldMaps.entities - space: optional - description: optional - -fmap_TB1SRGE_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.TB1SRGE - entities: - $ref: rules.files.raw.fmap.TB1SRGE.entities - space: optional - description: optional - -fmap_parametric_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.fmap.parametric - entities: - $ref: rules.files.raw.fmap.parametric.entities - space: optional - description: optional - -func_func_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.func.func - entities: - $ref: rules.files.raw.func.func.entities - space: optional - description: optional - -func_phase_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.func.phase - entities: - $ref: rules.files.raw.func.phase.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.eeg.eeg.entities ieeg_ieeg_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.ieeg.ieeg + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.ieeg.ieeg entities: - $ref: rules.files.raw.ieeg.ieeg.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.ieeg.ieeg.entities meg_meg_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.meg.meg + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.meg.meg entities: - $ref: rules.files.raw.meg.meg.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.meg.meg.entities meg_calibration_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.meg.calibration + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.meg.calibration entities: - $ref: rules.files.raw.meg.calibration.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.meg.calibration.entities meg_crosstalk_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.meg.crosstalk + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.meg.crosstalk entities: - $ref: rules.files.raw.meg.crosstalk.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.meg.crosstalk.entities meg_headshape_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.meg.headshape + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.meg.headshape entities: - $ref: rules.files.raw.meg.headshape.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.meg.headshape.entities meg_markers_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.meg.markers + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.meg.markers entities: - $ref: rules.files.raw.meg.markers.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.meg.markers.entities micr_microscopy_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.micr.microscopy - entities: - $ref: rules.files.raw.micr.microscopy.entities - space: optional - description: optional - -perf_asl_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.perf.asl + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.micr.microscopy entities: - $ref: rules.files.raw.perf.asl.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.micr.microscopy.entities -pet_pet_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.pet.pet +micr_microscopy_atlas: + $ref: rules.files.deriv.preprocessed_data.micr_microscopy_common entities: - $ref: rules.files.raw.pet.pet.entities - space: optional - description: optional + $ref: + - meta.templates.atlas.base.entities + - rules.files.deriv.preprocessed_data.micr_microscopy_common.entities pet_blood_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.pet.blood + $ref: + - meta.templates.deriv.spatial + - rules.files.raw.pet.blood entities: - $ref: rules.files.raw.pet.blood.entities - space: optional - description: optional + $ref: + - meta.templates.deriv.spatial.entities + - rules.files.raw.pet.blood.entities task_events_common: - selectors: - - dataset.dataset_description.DatasetType == 'derivative' - $ref: rules.files.raw.task.events + $ref: + - meta.templates.deriv.base + - rules.files.raw.task.events entities: - $ref: rules.files.raw.task.events.entities - description: optional + $ref: + - meta.templates.deriv.base.entities + - rules.files.raw.task.events.entities diff --git a/src/schema/rules/files/raw/anat.yaml b/src/schema/rules/files/raw/anat.yaml index bc19e331ae..2533f3fe29 100644 --- a/src/schema/rules/files/raw/anat.yaml +++ b/src/schema/rules/files/raw/anat.yaml @@ -20,15 +20,10 @@ nonparametric: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional echo: optional part: optional - chunk: optional parametric: suffixes: @@ -55,13 +50,8 @@ parametric: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - chunk: optional defacemask: suffixes: @@ -73,14 +63,9 @@ defacemask: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional modality: optional - chunk: optional multiecho: suffixes: @@ -93,15 +78,10 @@ multiecho: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional echo: required part: optional - chunk: optional multiflip: suffixes: @@ -113,16 +93,11 @@ multiflip: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional echo: optional flip: required part: optional - chunk: optional multiinversion: suffixes: @@ -134,15 +109,10 @@ multiinversion: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional inversion: required part: optional - chunk: optional mp2rage: suffixes: @@ -154,17 +124,12 @@ mp2rage: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional echo: optional flip: optional inversion: required part: optional - chunk: optional vfamt: suffixes: @@ -177,17 +142,12 @@ vfamt: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional echo: optional flip: required mtransfer: required part: optional - chunk: optional mtr: suffixes: @@ -199,12 +159,7 @@ mtr: datatypes: - anat entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.mri.entities task: optional - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional mtransfer: required part: optional - chunk: optional diff --git a/src/schema/rules/files/raw/beh.yaml b/src/schema/rules/files/raw/beh.yaml index 8757a3206f..df6f9dac06 100644 --- a/src/schema/rules/files/raw/beh.yaml +++ b/src/schema/rules/files/raw/beh.yaml @@ -1,6 +1,7 @@ --- # Non-continuous data noncontinuous: + $ref: meta.templates.raw.task suffixes: - beh extensions: @@ -8,8 +9,3 @@ noncontinuous: - .json datatypes: - beh - entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional diff --git a/src/schema/rules/files/raw/channels.yaml b/src/schema/rules/files/raw/channels.yaml index 76996a7468..4f2c9e774b 100644 --- a/src/schema/rules/files/raw/channels.yaml +++ b/src/schema/rules/files/raw/channels.yaml @@ -1,5 +1,6 @@ --- channels: + $ref: meta.templates.raw.task suffixes: - channels extensions: @@ -9,11 +10,6 @@ channels: - eeg - ieeg - nirs - entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional # MEG has an additional entity available channels__meg: @@ -42,7 +38,7 @@ coordsystem: - meg - nirs entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities task: optional acquisition: optional @@ -66,10 +62,8 @@ electrodes: - eeg - ieeg entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.recording.entities task: optional - acquisition: optional - run: optional space: optional # MEG has an additional entity available @@ -90,5 +84,5 @@ optodes: datatypes: - nirs entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities acquisition: optional diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml index f11e7642fd..cc211150a0 100644 --- a/src/schema/rules/files/raw/dwi.yaml +++ b/src/schema/rules/files/raw/dwi.yaml @@ -11,13 +11,10 @@ dwi: datatypes: - dwi entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional - part: optional - chunk: optional + $ref: meta.templates.raw.epi.entities + # Historically BIDS has not permitted ceagent for DWI + # This could be relaxed without backwards incompatibility + ceagent: null sbref: suffixes: @@ -29,13 +26,8 @@ sbref: datatypes: - dwi entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional - part: optional - chunk: optional + $ref: meta.templates.raw.epi.entities + ceagent: null # Common scanner-generated derivatives need raw names ScannerDerivatives: @@ -53,10 +45,7 @@ ScannerDerivatives: datatypes: - dwi entities: - subject: required - session: optional - acquisition: optional - reconstruction: optional - direction: optional - run: optional - chunk: optional + $ref: meta.templates.raw.epi.entities + # part is also not defined for derivative maps + ceagent: null + part: null diff --git a/src/schema/rules/files/raw/eeg.yaml b/src/schema/rules/files/raw/eeg.yaml index 6ce05c8703..0fa2e21feb 100644 --- a/src/schema/rules/files/raw/eeg.yaml +++ b/src/schema/rules/files/raw/eeg.yaml @@ -1,5 +1,6 @@ --- eeg: + $ref: meta.templates.raw.task suffixes: - eeg extensions: @@ -13,8 +14,3 @@ eeg: - .bdf datatypes: - eeg - entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional diff --git a/src/schema/rules/files/raw/fmap.yaml b/src/schema/rules/files/raw/fmap.yaml index be1f7df34e..7d04c547a4 100644 --- a/src/schema/rules/files/raw/fmap.yaml +++ b/src/schema/rules/files/raw/fmap.yaml @@ -15,12 +15,11 @@ fieldmaps: datatypes: - fmap entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - run: optional + $ref: meta.templates.raw.recording.entities chunk: optional pepolar: + $ref: meta.templates.raw.epi suffixes: - epi extensions: @@ -31,17 +30,9 @@ pepolar: - .bvec datatypes: - fmap - entities: - subject: required - session: optional - acquisition: optional - ceagent: optional - direction: required - run: optional - part: optional - chunk: optional pepolar_m0scan: + $ref: meta.templates.raw.epi suffixes: - m0scan extensions: @@ -50,14 +41,6 @@ pepolar_m0scan: - .json datatypes: - fmap - entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - ceagent: optional - direction: required - run: optional - part: optional - chunk: optional TB1DAM: suffixes: @@ -69,15 +52,10 @@ TB1DAM: datatypes: - fmap entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional + $ref: meta.templates.raw.mri.entities flip: required inversion: optional part: optional - chunk: optional TB1EPI: suffixes: @@ -89,16 +67,11 @@ TB1EPI: datatypes: - fmap entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional + $ref: meta.templates.raw.mri.entities echo: required flip: required inversion: optional part: optional - chunk: optional RFFieldMaps: suffixes: @@ -113,16 +86,11 @@ RFFieldMaps: datatypes: - fmap entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional + $ref: meta.templates.raw.mri.entities echo: optional flip: optional inversion: optional part: optional - chunk: optional TB1SRGE: suffixes: @@ -134,18 +102,14 @@ TB1SRGE: datatypes: - fmap entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional + $ref: meta.templates.raw.mri.entities echo: optional flip: required inversion: required part: optional - chunk: optional parametric: + $ref: meta.templates.raw.mri suffixes: - TB1map - RB1map @@ -155,10 +119,3 @@ parametric: - .json datatypes: - fmap - entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - ceagent: optional - reconstruction: optional - run: optional - chunk: optional diff --git a/src/schema/rules/files/raw/func.yaml b/src/schema/rules/files/raw/func.yaml index f54a8f3e02..4072d04437 100644 --- a/src/schema/rules/files/raw/func.yaml +++ b/src/schema/rules/files/raw/func.yaml @@ -11,16 +11,10 @@ func: datatypes: - func entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - ceagent: optional - reconstruction: optional - direction: optional - run: optional + $ref: + - meta.templates.raw.epi.entities + - meta.templates.raw.task.entities echo: optional - part: optional - chunk: optional norf: $ref: rules.files.raw.func.func @@ -31,21 +25,9 @@ norf: modality: optional phase: + $ref: rules.files.raw.func.func suffixes: - phase # deprecated - extensions: - - .nii.gz - - .nii - - .json - datatypes: - - func entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - ceagent: optional - reconstruction: optional - direction: optional - run: optional - echo: optional - chunk: optional + $ref: rules.files.raw.func.func.entities + part: null diff --git a/src/schema/rules/files/raw/ieeg.yaml b/src/schema/rules/files/raw/ieeg.yaml index c74f363699..9197aa9676 100644 --- a/src/schema/rules/files/raw/ieeg.yaml +++ b/src/schema/rules/files/raw/ieeg.yaml @@ -1,5 +1,6 @@ --- ieeg: + $ref: meta.templates.raw.task suffixes: - ieeg extensions: @@ -14,8 +15,3 @@ ieeg: - .nwb datatypes: - ieeg - entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional diff --git a/src/schema/rules/files/raw/meg.yaml b/src/schema/rules/files/raw/meg.yaml index 438022accf..48de894cdd 100644 --- a/src/schema/rules/files/raw/meg.yaml +++ b/src/schema/rules/files/raw/meg.yaml @@ -19,10 +19,7 @@ meg: datatypes: - meg entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional + $ref: meta.templates.raw.task.entities processing: optional split: optional @@ -34,7 +31,7 @@ calibration: datatypes: - meg entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities acquisition: level: required enum: @@ -48,7 +45,7 @@ crosstalk: datatypes: - meg entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities acquisition: level: required enum: @@ -63,7 +60,7 @@ headshape: datatypes: - meg entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities acquisition: optional markers: @@ -75,7 +72,7 @@ markers: datatypes: - meg entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities task: optional acquisition: optional space: optional diff --git a/src/schema/rules/files/raw/micr.yaml b/src/schema/rules/files/raw/micr.yaml index 5539d3d43d..ba88843472 100644 --- a/src/schema/rules/files/raw/micr.yaml +++ b/src/schema/rules/files/raw/micr.yaml @@ -29,9 +29,7 @@ microscopy: datatypes: - micr entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.recording.entities sample: required - acquisition: optional stain: optional - run: optional chunk: optional diff --git a/src/schema/rules/files/raw/motion.yaml b/src/schema/rules/files/raw/motion.yaml index c71e09f6df..818a979792 100644 --- a/src/schema/rules/files/raw/motion.yaml +++ b/src/schema/rules/files/raw/motion.yaml @@ -8,8 +8,5 @@ motion: datatypes: - motion entities: - $ref: meta.templates.raw_base_entities - task: required + $ref: meta.templates.raw.task.entities tracksys: required - acquisition: optional - run: optional diff --git a/src/schema/rules/files/raw/mrs.yaml b/src/schema/rules/files/raw/mrs.yaml index fe95f08f3a..9f8d941ef1 100644 --- a/src/schema/rules/files/raw/mrs.yaml +++ b/src/schema/rules/files/raw/mrs.yaml @@ -12,12 +12,9 @@ mrs: datatypes: - mrs entities: - subject: required - session: optional + $ref: meta.templates.raw.recording.entities task: optional - acquisition: optional reconstruction: optional - run: optional echo: optional inversion: optional nucleus: optional diff --git a/src/schema/rules/files/raw/nirs.yaml b/src/schema/rules/files/raw/nirs.yaml index 41f3062784..aafce13fa9 100644 --- a/src/schema/rules/files/raw/nirs.yaml +++ b/src/schema/rules/files/raw/nirs.yaml @@ -1,5 +1,6 @@ --- nirs: + $ref: meta.templates.raw.task suffixes: - nirs extensions: @@ -7,8 +8,3 @@ nirs: - .json datatypes: - nirs - entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional diff --git a/src/schema/rules/files/raw/perf.yaml b/src/schema/rules/files/raw/perf.yaml index 1668c8eeba..330bdc087a 100644 --- a/src/schema/rules/files/raw/perf.yaml +++ b/src/schema/rules/files/raw/perf.yaml @@ -10,13 +10,10 @@ asl: datatypes: - perf entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional + $ref: meta.templates.raw.epi.entities echo: optional - part: optional + ceagent: null + chunk: null aslcontext: suffixes: @@ -26,11 +23,10 @@ aslcontext: datatypes: - perf entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - reconstruction: optional - direction: optional - run: optional + $ref: meta.templates.raw.epi.entities + ceagent: null + part: null + chunk: null asllabeling: suffixes: @@ -42,10 +38,8 @@ asllabeling: datatypes: - perf entities: - $ref: meta.templates.raw_base_entities - acquisition: optional + $ref: meta.templates.raw.recording.entities reconstruction: optional - run: optional norf: $ref: rules.files.raw.perf.asl diff --git a/src/schema/rules/files/raw/pet.yaml b/src/schema/rules/files/raw/pet.yaml index fac07a5c7c..50d393761c 100644 --- a/src/schema/rules/files/raw/pet.yaml +++ b/src/schema/rules/files/raw/pet.yaml @@ -9,7 +9,7 @@ pet: datatypes: - pet entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities task: optional tracer: optional reconstruction: optional @@ -24,7 +24,7 @@ blood: datatypes: - pet entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities task: optional tracer: optional reconstruction: optional diff --git a/src/schema/rules/files/raw/photo.yaml b/src/schema/rules/files/raw/photo.yaml index 49914099ed..65706b02d8 100644 --- a/src/schema/rules/files/raw/photo.yaml +++ b/src/schema/rules/files/raw/photo.yaml @@ -12,7 +12,7 @@ photo: - meg - nirs entities: - $ref: meta.templates.raw_base_entities + $ref: meta.templates.raw.base.entities acquisition: optional photo__micr: diff --git a/src/schema/rules/files/raw/task.yaml b/src/schema/rules/files/raw/task.yaml index df398cce2c..b9956d0fcc 100644 --- a/src/schema/rules/files/raw/task.yaml +++ b/src/schema/rules/files/raw/task.yaml @@ -1,5 +1,6 @@ --- events: + $ref: meta.templates.raw.task suffixes: - events extensions: @@ -11,11 +12,6 @@ events: - ieeg - meg - nirs - entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional timeseries: suffixes: @@ -30,10 +26,7 @@ timeseries: - ieeg - nirs entities: - $ref: meta.templates.raw_base_entities - task: required - acquisition: optional - run: optional + $ref: meta.templates.raw.task.entities recording: optional timeseries__mri_no_task: @@ -47,9 +40,7 @@ timeseries__mri_no_task: - dwi - perf entities: - $ref: meta.templates.raw_base_entities - acquisition: optional - run: optional + $ref: meta.templates.raw.recording.entities reconstruction: optional direction: optional recording: optional @@ -80,12 +71,11 @@ events__pet: datatypes: - pet entities: - # Most events allow acquisition, PET doesn't - $ref: meta.templates.raw_base_entities - task: required + $ref: meta.templates.raw.task.entities tracer: optional reconstruction: optional - run: optional + # Most events allow acquisition, PET doesn't + acquisition: null events__mrs: $ref: rules.files.raw.task.events @@ -102,12 +92,11 @@ timeseries__anat: datatypes: - anat entities: - $ref: rules.files.raw.task.timeseries.entities - ceagent: optional - reconstruction: optional + $ref: + - rules.files.raw.task.timeseries.entities + - meta.templates.raw.mri.entities echo: optional part: optional - chunk: optional modality: optional timeseries__func: @@ -141,10 +130,8 @@ timeseries__pet: datatypes: - pet entities: - # Most timeseries allow acquisition, PET doesn't - $ref: meta.templates.raw_base_entities - task: required + $ref: rules.files.raw.task.timeseries.entities tracer: optional reconstruction: optional - run: optional - recording: optional + # Most timeseries allow acquisition, PET doesn't + acquisition: null diff --git a/tools/schemacode/docs/quickstart.md b/tools/schemacode/docs/quickstart.md new file mode 100644 index 0000000000..c4912c3a07 --- /dev/null +++ b/tools/schemacode/docs/quickstart.md @@ -0,0 +1,191 @@ +--- +jupytext: + formats: md:myst + text_representation: + extension: .md + format_name: myst + format_version: 0.13 + jupytext_version: 1.17.2 +kernelspec: + name: python3 + display_name: Python 3 (ipykernel) + language: python +--- + ++++ {"editable": true, "slideshow": {"slide_type": "slide"}} + +# BIDS Schema Tools Quick Start + +The `bidsschematools` package is a Python package that is bundled with the [BIDS specification](https://github.com/bids-standard/bids-specification/) in order to render the components of the specification document from the BIDS schema. + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +import bidsschematools as bst +import bidsschematools.schema +``` + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: skip +tags: [hide-cell] +--- +# Hidden cell to import useful tools +import os +from pathlib import Path +from pprint import pprint +``` + ++++ {"editable": true, "slideshow": {"slide_type": "slide"}} + +## Schema loading + +Schemas are loaded with the `load_schema()` function. The default schema is the one that is bundled as part of the package: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +schema = bst.schema.load_schema() +``` + ++++ {"editable": true, "slideshow": {"slide_type": "subslide"}} + +In the BIDS repository, the schema source is a subdirectory of YAML documents that need to be compiled before they can be used. Passing such a directory into `load_schema()` will perform the compilation: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +# Build from local repository, or else set `BIDS_SPEC_REPO` environment variable +spec = Path(os.getenv('BIDS_SPEC_REPO', Path(os.getcwd()).parent.parent.parent)) +schema_from_directory = bst.schema.load_schema(spec / 'src' / 'schema') +``` + ++++ {"editable": true, "slideshow": {"slide_type": "subslide"}} + +`load_schema()` can also load a precompiled JSON schema document, such as can be found at . For the purposes of this tutorial, we will use the document compiled into this package: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +schema_path = bst.data.load('schema.json') +schema_from_json = bst.schema.load_schema(schema_path) +``` + ++++ {"editable": true, "slideshow": {"slide_type": "slide"}} + +## Schema organization + +The schema has three top-level subdivisions (`objects`, `rules`, and `meta`) and also contains its own version and the version of the BIDS standard that it encodes: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +print(list(schema.keys())) +print(f'BIDS-Schema version: {schema.schema_version}') +print(f'BIDS version: {schema.bids_version}') +``` + ++++ {"editable": true, "slideshow": {"slide_type": ""}} + +Note that the schema provided by `load_schema()` is a [Namespace](project:bidsschematools.types.namespace.Namespace) object, which is able to access fields with dot notation (`schema.bids_version`) as well as index notation (`schema['bids_version'])`. + ++++ {"editable": true, "slideshow": {"slide_type": "subslide"}} + +We can see the general structure of the schema by listing keys at the second level: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +list(schema.keys(level=2)) +``` + +```{code-cell} ipython3 +schema['meta.associations'] +``` + ++++ {"editable": true, "slideshow": {"slide_type": "fragment"}} + +The `objects` subschema contains definitions of data and metadata used throughout BIDS, while the `rules` subschema contains definitions of constraints that may be validated. `meta` contains definitions that are essential for validation. + ++++ {"editable": true, "slideshow": {"slide_type": "subslide"}} + +To see how these sections interact, consider `rules.files.raw.func.func`, which contains the valid entities, datatypes, extensions and suffixes for functional neuroimaging files: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +pprint(schema.rules.files.raw.func.func.to_dict()) +``` + ++++ {"editable": true, "slideshow": {"slide_type": ""}} + +We can look up the suffix definitions in `objects.suffixes`: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +pprint({ + suffix: schema.objects.suffixes[suffix].to_dict() + for suffix in schema.rules.files.raw.func.func.suffixes +}) +``` + ++++ {"editable": true, "slideshow": {"slide_type": ""}} + +Note that suffixes are duplicated in the `value` field. Because suffixes are valid identifiers, this generally does not cause problems, and `objects.suffixes[suffix]` is a shorthand lookup. + ++++ {"editable": true, "slideshow": {"slide_type": "subslide"}} + +This isn't true in all fields, for example, in extensions: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +schema.objects.extensions.nii_gz +``` + ++++ {"editable": true, "slideshow": {"slide_type": ""}} + +In this case, a lookup table needs to be built on the fly: + +```{code-cell} ipython3 +--- +editable: true +slideshow: + slide_type: '' +--- +ext_lookup = {ext.value: ext for ext in schema.objects.extensions.values()} +pprint({ + ext: ext_lookup[ext].to_dict() + for ext in schema.rules.files.raw.func.func.extensions +}) +``` diff --git a/tools/schemacode/src/bidsschematools/schema.py b/tools/schemacode/src/bidsschematools/schema.py index 07f49c2b31..7883128c03 100644 --- a/tools/schemacode/src/bidsschematools/schema.py +++ b/tools/schemacode/src/bidsschematools/schema.py @@ -5,6 +5,7 @@ import json import os import re +from collections import ChainMap from collections.abc import Iterable, Mapping from copy import deepcopy from functools import cache, lru_cache @@ -90,17 +91,32 @@ def _find(obj, predicate): def _dereference(namespace, base_schema): # In-place, recursively dereference objects - # This allows a referenced object to itself contain a reference - # A dependency graph could be constructed, but would likely be slower - # to build than to duplicate a couple dereferences + # This allows for referencing objects that contain references, + # as well as objects that do not exist until a parent is dereferenced. for struct in _find(namespace, lambda obj: "$ref" in obj): - target = base_schema.get(struct["$ref"]) - if target is None: - raise ValueError(f"Reference {struct['$ref']} not found in schema.") - if isinstance(target, Mapping): + refs = struct["$ref"] + if isinstance(refs, str): + refs = [refs] + targets = [] + for ref in refs: + target = base_schema + for part in ref.split("."): + target = target.get(part) + if target is None: + raise ValueError(f"Reference {ref} not found in schema.") + if "$ref" in target: + _dereference(target, base_schema) + targets.append(target) + + if all(isinstance(target, Mapping) for target in targets): struct.pop("$ref") - _dereference(target, base_schema) - struct.update({**target, **struct}) + + struct.update({**ChainMap(*targets), **struct}) + + # Use `key: null` to delete fields + for key, value in list(struct.items()): + if value is None: + del struct[key] @cache diff --git a/tools/schemacode/src/bidsschematools/tests/test_schema.py b/tools/schemacode/src/bidsschematools/tests/test_schema.py index 439e6cae89..472ef41127 100644 --- a/tools/schemacode/src/bidsschematools/tests/test_schema.py +++ b/tools/schemacode/src/bidsschematools/tests/test_schema.py @@ -407,18 +407,18 @@ def test_valid_schema_with_check_jsonschema(tmp_path, regex_variant): def test_add_legal_field(): """Test that adding a legal field does not raise an error.""" namespace = schema.load_schema() - namespace["rules"]["files"]["deriv"]["preprocessed_data"]["anat_nonparametric_common"][ - "entities" - ]["density"] = "optional" + namespace["rules"]["files"]["deriv"]["imaging"]["anat_nonparametric_volumetric"]["entities"][ + "density" + ] = "optional" schema.validate_schema(namespace) def test_invalid_value(): """Test that an invalid value raises an error.""" namespace = schema.load_schema() - namespace["rules"]["files"]["deriv"]["preprocessed_data"]["anat_nonparametric_common"][ - "entities" - ]["density"] = "invalid" + namespace["rules"]["files"]["deriv"]["imaging"]["anat_nonparametric_volumetric"]["entities"][ + "density" + ] = "invalid" with pytest.raises(ValidationError) as e: schema.validate_schema(namespace) print(e.value) diff --git a/tools/schemacode/uv.lock b/tools/schemacode/uv.lock new file mode 100644 index 0000000000..fb1cb5e431 --- /dev/null +++ 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