From f9799310fb344be88a3b7b415f0ab97d7f8d4515 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 19 Aug 2024 15:39:36 -0400
Subject: [PATCH 1/4] feat(schema): Move coordsystem.json rules out of
 rules.sidecars

---
 src/schema/rules/json/eeg.yaml      |  91 ++++++++++++++++++
 src/schema/rules/json/ieeg.yaml     |  50 ++++++++++
 src/schema/rules/json/meg.yaml      | 141 ++++++++++++++++++++++++++++
 src/schema/rules/json/nirs.yaml     |  93 ++++++++++++++++++
 src/schema/rules/sidecars/eeg.yaml  |  85 -----------------
 src/schema/rules/sidecars/ieeg.yaml |  44 ---------
 src/schema/rules/sidecars/meg.yaml  | 136 ---------------------------
 src/schema/rules/sidecars/nirs.yaml |  93 ------------------
 8 files changed, 375 insertions(+), 358 deletions(-)
 create mode 100644 src/schema/rules/json/eeg.yaml
 create mode 100644 src/schema/rules/json/ieeg.yaml
 create mode 100644 src/schema/rules/json/meg.yaml
 create mode 100644 src/schema/rules/json/nirs.yaml

diff --git a/src/schema/rules/json/eeg.yaml b/src/schema/rules/json/eeg.yaml
new file mode 100644
index 0000000000..f42956671f
--- /dev/null
+++ b/src/schema/rules/json/eeg.yaml
@@ -0,0 +1,91 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+---
+# General fields
+EEGCoordsystemGeneral:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+  fields:
+    IntendedFor:
+      level: optional
+      description_addendum: |
+        This identifies the MRI or CT scan associated with the electrodes,
+        landmarks, and fiducials.
+
+# Fields relating to the EEG electrode positions
+EEGCoordsystemPositions:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+  fields:
+    EEGCoordinateSystem: required
+    EEGCoordinateUnits: required
+    EEGCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if `EEGCoordinateSystem` is `"Other"`
+
+EEGCoordsystemOther:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - '"EEGCoordinateSystem" in json'
+    - json.EEGCoordinateSystem == "Other"
+  fields:
+    EEGCoordinateSystemDescription: required
+
+# Fields relating to the position of fiducials measured during an EEG session/run
+EEGCoordsystemFiducials:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+  fields:
+    FiducialsDescription: optional
+    FiducialsCoordinates: recommended
+    FiducialsCoordinateSystem: recommended
+    FiducialsCoordinateUnits: recommended
+    FiducialsCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if `FiducialsCoordinateSystem` is `"Other"`
+
+EEGCoordsystemOtherFiducialCoordinateSystem:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - json.FiducialsCoordinateSystem == "Other"
+  fields:
+    FiducialsCoordinateSystemDescription: required
+
+# Fields relating to the position of anatomical landmark measured during an EEG session/run
+EEGCoordsystemLandmark:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+  fields:
+    AnatomicalLandmarkCoordinates: recommended
+    AnatomicalLandmarkCoordinateSystem:
+      level: recommended
+      description_addendum: Preferably the same as the `EEGCoordinateSystem`.
+    AnatomicalLandmarkCoordinateUnits: recommended
+
+EEGCoordsystemLandmarkDescriptionRec:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - json.AnatomicalLandmarkCoordinateSystem != "Other"
+  fields:
+    AnatomicalLandmarkCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if `AnatomicalLandmarkCoordinateSystem` is `"Other"`
+
+EEGCoordsystemLandmarkDescriptionReq:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - json.AnatomicalLandmarkCoordinateSystem == "Other"
+  fields:
+    AnatomicalLandmarkCoordinateSystemDescription: required
diff --git a/src/schema/rules/json/ieeg.yaml b/src/schema/rules/json/ieeg.yaml
new file mode 100644
index 0000000000..4271cfe952
--- /dev/null
+++ b/src/schema/rules/json/ieeg.yaml
@@ -0,0 +1,50 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+---
+# General fields
+iEEGCoordsystemGeneral:
+  selectors:
+    - datatype == "ieeg"
+    - suffix == "coordsystem"
+  fields:
+    IntendedFor__ds_relative:
+      level: optional
+      description_addendum: |
+        If only a surface reconstruction is available, this should point to
+        the surface reconstruction file.
+        Note that this file should have the same coordinate system
+        specified in `iEEGCoordinateSystem`.
+        For example, **T1**: `'bids::sub-<label>/ses-<label>/anat/sub-01_T1w.nii.gz'`
+        **Surface**: `'bids::derivatives/surfaces/sub-<label>/ses-<label>/anat/
+        sub-01_hemi-R_desc-T1w_pial.surf.gii'`
+        **Operative photo**: `'bids::sub-<label>/ses-<label>/ieeg/
+        sub-0001_ses-01_acq-photo1_photo.jpg'`
+        **Talairach**: `'bids::derivatives/surfaces/sub-Talairach/ses-01/anat/
+        sub-Talairach_hemi-R_pial.surf.gii'`
+
+# Fields relating to the iEEG electrode positions
+iEEGCoordsystemPositions:
+  selectors:
+    - datatype == "ieeg"
+    - suffix == "coordsystem"
+  fields:
+    iEEGCoordinateSystem: required
+    iEEGCoordinateUnits: required
+    iEEGCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if `iEEGCoordinateSystem` is `"Other"`
+    iEEGCoordinateProcessingDescription: recommended
+    iEEGCoordinateProcessingReference: recommended
+
+iEEGCoordsystemOther:
+  selectors:
+    - datatype == "ieeg"
+    - suffix == "coordsystem"
+    - '"iEEGCoordinateSystem" in json'
+    - json.iEEGCoordinateSystem == "Other"
+  fields:
+    iEEGCoordinateSystemDescription: required
diff --git a/src/schema/rules/json/meg.yaml b/src/schema/rules/json/meg.yaml
new file mode 100644
index 0000000000..4c18d99eaa
--- /dev/null
+++ b/src/schema/rules/json/meg.yaml
@@ -0,0 +1,141 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+---
+# MEG and EEG sensors
+MEGCoordsystemWithEEG:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+  fields:
+    MEGCoordinateSystem: required
+    MEGCoordinateUnits: required
+    MEGCoordinateSystemDescription:
+      level: optional
+      level_addendum: required if `MEGCoordinateSystem` is `Other`
+    EEGCoordinateSystem:
+      level: optional
+      description_addendum: |
+        See [Recording EEG simultaneously with MEG]
+        (/modality-specific-files/magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
+        Preferably the same as the `MEGCoordinateSystem`.
+    EEGCoordinateUnits: optional
+    EEGCoordinateSystemDescription:
+      level: optional
+      level_addendum: required if `EEGCoordinateSystem` is `Other`
+      description_addendum: |
+        See [Recording EEG simultaneously with MEG]
+        (/modality-specific-files/magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
+
+MEGCoordsystemWithEEGMEGCoordinateSystem:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - '"MEGCoordinateSystem" in json'
+    - json.MEGCoordinateSystem == "Other"
+  fields:
+    MEGCoordinateSystemDescription: required
+
+# NOTE: Not sure if this requires simult. EEG
+MEGCoordsystemWithEEGEEGCoordinateSystem:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - '"EEGCoordinateSystem" in json'
+    - json.EEGCoordinateSystem == "Other"
+  fields:
+    EEGCoordinateSystemDescription: required
+
+# Head localization coils
+MEGCoordsystemHeadLocalizationCoils:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+  fields:
+    HeadCoilCoordinates: optional
+    HeadCoilCoordinateSystem: optional
+    HeadCoilCoordinateUnits: optional
+    HeadCoilCoordinateSystemDescription:
+      level: optional
+      level_addendum: required if `HeadCoilCoordinateSystem` is `Other`
+
+MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - '"HeadCoilCoordinateSystem" in json'
+    - json.HeadCoilCoordinateSystem == "Other"
+  fields:
+    HeadCoilCoordinateSystemDescription: required
+
+# Digitized head points
+MEGCoordsystemDigitizedHeadPoints:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+  fields:
+    DigitizedHeadPoints__coordsystem: optional
+    DigitizedHeadPointsCoordinateSystem: optional
+    DigitizedHeadPointsCoordinateUnits: optional
+    DigitizedHeadPointsCoordinateSystemDescription:
+      level: optional
+      level_addendum: required if `DigitizedHeadPointsCoordinateSystem` is `Other`
+
+MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - '"DigitizedHeadPointsCoordinateSystem" in json'
+    - json.DigitizedHeadPointsCoordinateSystem == "Other"
+  fields:
+    DigitizedHeadPointsCoordinateSystemDescription: required
+
+# Anatomical MRI
+MEGCoordsystemAnatomicalMRI:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - intersects(dataset.datatypes, ["anat"])
+  fields:
+    IntendedFor:
+      level: optional
+      description_addendum: |
+        This is used to identify the structural MRI(s),
+        possibly of different types if a list is specified,
+        to be used with the MEG recording.
+
+# Anatomical landmarks
+MEGCoordsystemAnatomicalLandmarks:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+  fields:
+    AnatomicalLandmarkCoordinates: optional
+    AnatomicalLandmarkCoordinateSystem:
+      level: optional
+      description_addendum: |
+        Preferably the same as the `MEGCoordinateSystem`.
+    AnatomicalLandmarkCoordinateUnits: optional
+    AnatomicalLandmarkCoordinateSystemDescription:
+      level: optional
+      level_addendum: required if `AnatomicalLandmarkCoordinateSystem` is `Other`
+
+MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - '"AnatomicalLandmarkCoordinateSystem" in json'
+    - json.AnatomicalLandmarkCoordinateSystem == "Other"
+  fields:
+    AnatomicalLandmarkCoordinateSystemDescription: required
+
+# Fiducials information
+MEGCoordsystemFiducialsInformation:
+  selectors:
+    - datatype == "meg"
+    - suffix == "coordsystem"
+  fields:
+    FiducialsDescription: optional
diff --git a/src/schema/rules/json/nirs.yaml b/src/schema/rules/json/nirs.yaml
new file mode 100644
index 0000000000..c44492d8a4
--- /dev/null
+++ b/src/schema/rules/json/nirs.yaml
@@ -0,0 +1,93 @@
+---
+CoordinateSystem:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+  fields:
+    NIRSCoordinateSystem: required
+    NIRSCoordinateUnits: required
+    NIRSCoordinateProcessingDescription: recommended
+
+Fiducials:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+  fields:
+    FiducialsDescription: optional
+    FiducialsCoordinates: recommended
+    FiducialsCoordinateUnits: recommended
+    FiducialsCoordinateSystem: recommended
+
+AnatomicalLandmark:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+  fields:
+    AnatomicalLandmarkCoordinates: recommended
+    AnatomicalLandmarkCoordinateSystem: recommended
+    AnatomicalLandmarkCoordinateUnits: recommended
+
+CoordsystemGeneral:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+  fields:
+    IntendedFor:
+      level: optional
+      description_addendum: |
+        This identifies the MRI or CT scan associated with the optodes,
+        landmarks, and fiducials.
+
+CoordinateSystemDescriptionRec:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+    - json.NIRSCoordinateSystem != "other"
+  fields:
+    NIRSCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if NIRSCoordinateSystem is "other"
+
+CoordinateSystemDescriptionReq:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+    - json.NIRSCoordinateSystem == "other"
+  fields:
+    NIRSCoordinateSystemDescription: required
+
+AnatomicalLandmarkCoordinateSystemDescriptionRec:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+    - json.AnatomicalLandmarkCoordinateSystem != "other"
+  fields:
+    AnatomicalLandmarkCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if NIRSCoordinateSystem is "other"
+
+AnatomicalLandmarkCoordinateSystemDescriptionReq:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+    - json.AnatomicalLandmarkCoordinateSystem == "other"
+  fields:
+    AnatomicalLandmarkCoordinateSystemDescription: required
+
+FiducialsCoordinateSystemDescriptionRec:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+    - json.FiducialsCoordinateSystem != "other"
+  fields:
+    FiducialsCoordinateSystemDescription:
+      level: recommended
+      level_addendum: required if FiducialsCoordinateSystem is "other"
+
+FiducialsCoordinateSystemDescriptionReq:
+  selectors:
+    - datatype == "nirs"
+    - suffix == "coordsystem"
+    - json.FiducialsCoordinateSystem == "other"
+  fields:
+    FiducialsCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 7a7252d69b..a30195758b 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -89,88 +89,3 @@ EEGOptional:
   fields:
     ElectricalStimulation: optional
     ElectricalStimulationParameters: optional
-
-# General fields
-EEGCoordsystemGeneral:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-  fields:
-    IntendedFor:
-      level: optional
-      description_addendum: |
-        This identifies the MRI or CT scan associated with the electrodes,
-        landmarks, and fiducials.
-
-# Fields relating to the EEG electrode positions
-EEGCoordsystemPositions:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-  fields:
-    EEGCoordinateSystem: required
-    EEGCoordinateUnits: required
-    EEGCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if `EEGCoordinateSystem` is `"Other"`
-
-EEGCoordsystemOther:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-    - '"EEGCoordinateSystem" in sidecar'
-    - sidecar.EEGCoordinateSystem == "Other"
-  fields:
-    EEGCoordinateSystemDescription: required
-
-# Fields relating to the position of fiducials measured during an EEG session/run
-EEGCoordsystemFiducials:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-  fields:
-    FiducialsDescription: optional
-    FiducialsCoordinates: recommended
-    FiducialsCoordinateSystem: recommended
-    FiducialsCoordinateUnits: recommended
-    FiducialsCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if `FiducialsCoordinateSystem` is `"Other"`
-
-EEGCoordsystemOtherFiducialCoordinateSystem:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-    - sidecar.FiducialsCoordinateSystem == "Other"
-  fields:
-    FiducialsCoordinateSystemDescription: required
-
-# Fields relating to the position of anatomical landmark measured during an EEG session/run
-EEGCoordsystemLandmark:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-  fields:
-    AnatomicalLandmarkCoordinates: recommended
-    AnatomicalLandmarkCoordinateSystem:
-      level: recommended
-      description_addendum: Preferably the same as the `EEGCoordinateSystem`.
-    AnatomicalLandmarkCoordinateUnits: recommended
-
-EEGCoordsystemLandmarkDescriptionRec:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-    - sidecar.AnatomicalLandmarkCoordinateSystem != "Other"
-  fields:
-    AnatomicalLandmarkCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if `AnatomicalLandmarkCoordinateSystem` is `"Other"`
-
-EEGCoordsystemLandmarkDescriptionReq:
-  selectors:
-    - datatype == "eeg"
-    - suffix == "coordsystem"
-    - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
-  fields:
-    AnatomicalLandmarkCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
index 066e17a8bf..457c409a3b 100644
--- a/src/schema/rules/sidecars/ieeg.yaml
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -94,47 +94,3 @@ iEEGOptional:
   fields:
     ElectricalStimulation: optional
     ElectricalStimulationParameters: optional
-
-# General fields
-iEEGCoordsystemGeneral:
-  selectors:
-    - datatype == "ieeg"
-    - suffix == "coordsystem"
-  fields:
-    IntendedFor__ds_relative:
-      level: optional
-      description_addendum: |
-        If only a surface reconstruction is available, this should point to
-        the surface reconstruction file.
-        Note that this file should have the same coordinate system
-        specified in `iEEGCoordinateSystem`.
-        For example, **T1**: `'bids::sub-<label>/ses-<label>/anat/sub-01_T1w.nii.gz'`
-        **Surface**: `'bids::derivatives/surfaces/sub-<label>/ses-<label>/anat/
-        sub-01_hemi-R_desc-T1w_pial.surf.gii'`
-        **Operative photo**: `'bids::sub-<label>/ses-<label>/ieeg/
-        sub-0001_ses-01_acq-photo1_photo.jpg'`
-        **Talairach**: `'bids::derivatives/surfaces/sub-Talairach/ses-01/anat/
-        sub-Talairach_hemi-R_pial.surf.gii'`
-
-# Fields relating to the iEEG electrode positions
-iEEGCoordsystemPositions:
-  selectors:
-    - datatype == "ieeg"
-    - suffix == "coordsystem"
-  fields:
-    iEEGCoordinateSystem: required
-    iEEGCoordinateUnits: required
-    iEEGCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if `iEEGCoordinateSystem` is `"Other"`
-    iEEGCoordinateProcessingDescription: recommended
-    iEEGCoordinateProcessingReference: recommended
-
-iEEGCoordsystemOther:
-  selectors:
-    - datatype == "ieeg"
-    - suffix == "coordsystem"
-    - '"iEEGCoordinateSystem" in sidecar'
-    - sidecar.iEEGCoordinateSystem == "Other"
-  fields:
-    iEEGCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index 2390766900..b921db19de 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -131,139 +131,3 @@ MEGwithEEG:
     CapManufacturer: optional
     CapManufacturersModelName: optional
     EEGReference: optional
-
-# MEG and EEG sensors
-MEGCoordsystemWithEEG:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-  fields:
-    MEGCoordinateSystem: required
-    MEGCoordinateUnits: required
-    MEGCoordinateSystemDescription:
-      level: optional
-      level_addendum: required if `MEGCoordinateSystem` is `Other`
-    EEGCoordinateSystem:
-      level: optional
-      description_addendum: |
-        See [Recording EEG simultaneously with MEG]
-        (/modality-specific-files/magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
-        Preferably the same as the `MEGCoordinateSystem`.
-    EEGCoordinateUnits: optional
-    EEGCoordinateSystemDescription:
-      level: optional
-      level_addendum: required if `EEGCoordinateSystem` is `Other`
-      description_addendum: |
-        See [Recording EEG simultaneously with MEG]
-        (/modality-specific-files/magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
-
-# NOTE: The JSON isn't really a sidecar, so "sidecar.MEGCoordinateSystem" is misleading.
-MEGCoordsystemWithEEGMEGCoordinateSystem:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-    - '"MEGCoordinateSystem" in sidecar'
-    - sidecar.MEGCoordinateSystem == "Other"
-  fields:
-    MEGCoordinateSystemDescription: required
-
-# NOTE: Not sure if this requires simult. EEG
-MEGCoordsystemWithEEGEEGCoordinateSystem:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-    - '"EEGCoordinateSystem" in sidecar'
-    - sidecar.EEGCoordinateSystem == "Other"
-  fields:
-    EEGCoordinateSystemDescription: required
-
-# Head localization coils
-MEGCoordsystemHeadLocalizationCoils:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-  fields:
-    HeadCoilCoordinates: optional
-    HeadCoilCoordinateSystem: optional
-    HeadCoilCoordinateUnits: optional
-    HeadCoilCoordinateSystemDescription:
-      level: optional
-      level_addendum: required if `HeadCoilCoordinateSystem` is `Other`
-
-MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-    - '"HeadCoilCoordinateSystem" in sidecar'
-    - sidecar.HeadCoilCoordinateSystem == "Other"
-  fields:
-    HeadCoilCoordinateSystemDescription: required
-
-# Digitized head points
-MEGCoordsystemDigitizedHeadPoints:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-  fields:
-    DigitizedHeadPoints__coordsystem: optional
-    DigitizedHeadPointsCoordinateSystem: optional
-    DigitizedHeadPointsCoordinateUnits: optional
-    DigitizedHeadPointsCoordinateSystemDescription:
-      level: optional
-      level_addendum: required if `DigitizedHeadPointsCoordinateSystem` is `Other`
-
-MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-    - '"DigitizedHeadPointsCoordinateSystem" in sidecar'
-    - sidecar.DigitizedHeadPointsCoordinateSystem == "Other"
-  fields:
-    DigitizedHeadPointsCoordinateSystemDescription: required
-
-# Anatomical MRI
-MEGCoordsystemAnatomicalMRI:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-    - intersects(dataset.datatypes, ["anat"])
-  fields:
-    IntendedFor:
-      level: optional
-      description_addendum: |
-        This is used to identify the structural MRI(s),
-        possibly of different types if a list is specified,
-        to be used with the MEG recording.
-
-# Anatomical landmarks
-MEGCoordsystemAnatomicalLandmarks:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-  fields:
-    AnatomicalLandmarkCoordinates: optional
-    AnatomicalLandmarkCoordinateSystem:
-      level: optional
-      description_addendum: |
-        Preferably the same as the `MEGCoordinateSystem`.
-    AnatomicalLandmarkCoordinateUnits: optional
-    AnatomicalLandmarkCoordinateSystemDescription:
-      level: optional
-      level_addendum: required if `AnatomicalLandmarkCoordinateSystem` is `Other`
-
-MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-    - '"AnatomicalLandmarkCoordinateSystem" in sidecar'
-    - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
-  fields:
-    AnatomicalLandmarkCoordinateSystemDescription: required
-
-# Fiducials information
-MEGCoordsystemFiducialsInformation:
-  selectors:
-    - datatype == "meg"
-    - suffix == "coordsystem"
-  fields:
-    FiducialsDescription: optional
diff --git a/src/schema/rules/sidecars/nirs.yaml b/src/schema/rules/sidecars/nirs.yaml
index de84a85536..43b32545d5 100644
--- a/src/schema/rules/sidecars/nirs.yaml
+++ b/src/schema/rules/sidecars/nirs.yaml
@@ -1,97 +1,4 @@
 ---
-CoordinateSystem:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-  fields:
-    NIRSCoordinateSystem: required
-    NIRSCoordinateUnits: required
-    NIRSCoordinateProcessingDescription: recommended
-
-Fiducials:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-  fields:
-    FiducialsDescription: optional
-    FiducialsCoordinates: recommended
-    FiducialsCoordinateUnits: recommended
-    FiducialsCoordinateSystem: recommended
-
-AnatomicalLandmark:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-  fields:
-    AnatomicalLandmarkCoordinates: recommended
-    AnatomicalLandmarkCoordinateSystem: recommended
-    AnatomicalLandmarkCoordinateUnits: recommended
-
-CoordsystemGeneral:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-  fields:
-    IntendedFor:
-      level: optional
-      description_addendum: |
-        This identifies the MRI or CT scan associated with the optodes,
-        landmarks, and fiducials.
-
-CoordinateSystemDescriptionRec:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-    - json.NIRSCoordinateSystem != "other"
-  fields:
-    NIRSCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if NIRSCoordinateSystem is "other"
-
-CoordinateSystemDescriptionReq:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-    - json.NIRSCoordinateSystem == "other"
-  fields:
-    NIRSCoordinateSystemDescription: required
-
-AnatomicalLandmarkCoordinateSystemDescriptionRec:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-    - json.AnatomicalLandmarkCoordinateSystem != "other"
-  fields:
-    AnatomicalLandmarkCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if NIRSCoordinateSystem is "other"
-
-AnatomicalLandmarkCoordinateSystemDescriptionReq:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-    - json.AnatomicalLandmarkCoordinateSystem == "other"
-  fields:
-    AnatomicalLandmarkCoordinateSystemDescription: required
-
-FiducialsCoordinateSystemDescriptionRec:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-    - json.FiducialsCoordinateSystem != "other"
-  fields:
-    FiducialsCoordinateSystemDescription:
-      level: recommended
-      level_addendum: required if FiducialsCoordinateSystem is "other"
-
-FiducialsCoordinateSystemDescriptionReq:
-  selectors:
-    - datatype == "nirs"
-    - suffix == "coordsystem"
-    - json.FiducialsCoordinateSystem == "other"
-  fields:
-    FiducialsCoordinateSystemDescription: required
-
 NirsHardware:
   selectors:
     - datatype == "nirs"

From 2096fcae816023a044e193b409471e4d0d0f2984 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 19 Aug 2024 15:41:00 -0400
Subject: [PATCH 2/4] feat: Add make_json_table macro

---
 tools/mkdocs_macros_bids/macros.py            | 25 +++++++++++
 tools/mkdocs_macros_bids/main.py              |  1 +
 .../bidsschematools/render/__init__.py        |  2 +
 .../bidsschematools/render/tables.py          | 43 ++++++++++++++++++-
 4 files changed, 69 insertions(+), 2 deletions(-)

diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index e43e8449d3..18d295a195 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -233,6 +233,31 @@ def make_metadata_table(field_info, src_path=None):
     return table
 
 
+def make_json_table(table_name, src_path=None):
+    """Generate a markdown table of metadata field information.
+
+    Parameters
+    ----------
+    table_name : str or list of str
+        Qualified name(s) in schema.rules.sidecars
+    src_path : str or None
+        The file where this macro is called, which may be explicitly provided
+        by the "page.file.src_path" variable.
+
+    Returns
+    -------
+    table : str
+        A Markdown-format table containing the corresponding table for
+        the requested fields.
+    """
+    if src_path is None:
+        src_path = _get_source_path()
+
+    schema_obj = schema.load_schema()
+    table = render.make_json_table(schema_obj, table_name, src_path=src_path)
+    return table
+
+
 def make_sidecar_table(table_name, src_path=None):
     """Generate a markdown table of metadata field information.
 
diff --git a/tools/mkdocs_macros_bids/main.py b/tools/mkdocs_macros_bids/main.py
index 13bb5caf44..f927ae2699 100644
--- a/tools/mkdocs_macros_bids/main.py
+++ b/tools/mkdocs_macros_bids/main.py
@@ -39,6 +39,7 @@ def define_env(env):
     env.macro(macros.make_glossary, "MACROS___make_glossary")
     env.macro(macros.make_suffix_table, "MACROS___make_suffix_table")
     env.macro(macros.make_metadata_table, "MACROS___make_metadata_table")
+    env.macro(macros.make_json_table, "MACROS___make_json_table")
     env.macro(macros.make_sidecar_table, "MACROS___make_sidecar_table")
     env.macro(macros.make_subobject_table, "MACROS___make_subobject_table")
     env.macro(macros.make_columns_table, "MACROS___make_columns_table")
diff --git a/tools/schemacode/bidsschematools/render/__init__.py b/tools/schemacode/bidsschematools/render/__init__.py
index a251a1f3cd..7042126476 100644
--- a/tools/schemacode/bidsschematools/render/__init__.py
+++ b/tools/schemacode/bidsschematools/render/__init__.py
@@ -3,6 +3,7 @@
 from bidsschematools.render.tables import (
     make_columns_table,
     make_entity_table,
+    make_json_table,
     make_metadata_table,
     make_sidecar_table,
     make_subobject_table,
@@ -20,6 +21,7 @@
 __all__ = [
     "make_entity_table",
     "make_suffix_table",
+    "make_json_table",
     "make_sidecar_table",
     "make_metadata_table",
     "make_subobject_table",
diff --git a/tools/schemacode/bidsschematools/render/tables.py b/tools/schemacode/bidsschematools/render/tables.py
index 31b6e13fd0..8eb6b386a4 100644
--- a/tools/schemacode/bidsschematools/render/tables.py
+++ b/tools/schemacode/bidsschematools/render/tables.py
@@ -173,7 +173,7 @@ def _make_table_from_rule(
     elements: dict[str, str | dict[str, str]] = {}
     for table in table_name:
         if table_type == "metadata":
-            table_schema = schema.rules.sidecars[table]
+            table_schema = schema.rules[table]
             new_elements = table_schema.fields
         elif table_type == "columns":
             table_schema = schema.rules.tabular_data[table]
@@ -407,7 +407,7 @@ def preproc_suffix(row):
     return table_str
 
 
-def make_sidecar_table(
+def make_json_table(
     schema: Namespace,
     table_name: ty.Union[str, ty.List[str]],
     src_path: ty.Optional[str] = None,
@@ -443,6 +443,45 @@ def make_sidecar_table(
     return table_str
 
 
+def make_sidecar_table(
+    schema: Namespace,
+    table_name: ty.Union[str, ty.List[str]],
+    src_path: ty.Optional[str] = None,
+    tablefmt: str = "github",
+):
+    """Produce metadata table (markdown) based on requested fields.
+
+    Parameters
+    ----------
+    schema : Namespace
+        The BIDS schema.
+    table_name : str or list of str
+        Qualified name(s) in schema.rules.sidecars
+    src_path : str or None
+        The file where this macro is called, which may be explicitly provided
+        by the "page.file.src_path" variable.
+    tablefmt : string, optional
+        The target table format. The default is "github" (GitHub format).
+
+    Returns
+    -------
+    table_str : str
+        The tabulated table as a Markdown string.
+    """
+    table_str = _make_table_from_rule(
+        schema=schema,
+        table_type="metadata",
+        table_name=[
+            f"sidecars.{table}"
+            for table in ([table_name] if isinstance(table_name, str) else table_name)
+        ],
+        src_path=src_path,
+        tablefmt=tablefmt,
+    )
+
+    return table_str
+
+
 def make_metadata_table(schema, field_info, src_path=None, tablefmt="github"):
     """Produce metadata table (markdown) based on requested fields.
 

From 527f6dbf0064dac31fd2f8bff4308d936c5afced Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 19 Aug 2024 15:56:09 -0400
Subject: [PATCH 3/4] feat(spec): Render coordsystem JSON tables

---
 .../electroencephalography.md                        |  8 ++++----
 .../intracranial-electroencephalography.md           |  4 ++--
 .../magnetoencephalography.md                        | 12 ++++++------
 .../near-infrared-spectroscopy.md                    |  8 ++++----
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md
index 8a584bb7a0..782012f3ea 100644
--- a/src/modality-specific-files/electroencephalography.md
+++ b/src/modality-specific-files/electroencephalography.md
@@ -390,7 +390,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("eeg.EEGCoordsystemGeneral") }}
+{{ MACROS___make_json_table("json.eeg.EEGCoordsystemGeneral") }}
 
 Fields relating to the EEG electrode positions:
 
@@ -402,7 +402,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("eeg.EEGCoordsystemPositions") }}
+{{ MACROS___make_json_table("json.eeg.EEGCoordsystemPositions") }}
 
 Fields relating to the position of fiducials measured during an EEG session/run:
 
@@ -414,7 +414,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("eeg.EEGCoordsystemFiducials") }}
+{{ MACROS___make_json_table("json.eeg.EEGCoordsystemFiducials") }}
 
 Fields relating to the position of anatomical landmark measured during an EEG session/run:
 
@@ -426,7 +426,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table(["eeg.EEGCoordsystemLandmark", "eeg.EEGCoordsystemLandmarkDescriptionRec"]) }}
+{{ MACROS___make_json_table(["json.eeg.EEGCoordsystemLandmark", "json.eeg.EEGCoordsystemLandmarkDescriptionRec"]) }}
 
 If the position of anatomical landmarks is measured using the same system or
 device used to measure electrode positions, and if thereby the anatomical
diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md
index 096b96f97d..dc15d9f92d 100644
--- a/src/modality-specific-files/intracranial-electroencephalography.md
+++ b/src/modality-specific-files/intracranial-electroencephalography.md
@@ -389,7 +389,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("ieeg.iEEGCoordsystemGeneral") }}
+{{ MACROS___make_json_table("json.ieeg.iEEGCoordsystemGeneral") }}
 
 Fields relating to the iEEG electrode positions:
 
@@ -401,7 +401,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("ieeg.iEEGCoordsystemPositions") }}
+{{ MACROS___make_json_table("json.ieeg.iEEGCoordsystemPositions") }}
 
 ### Recommended 3D coordinate systems
 
diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
index c3896a908e..babc92be7c 100644
--- a/src/modality-specific-files/magnetoencephalography.md
+++ b/src/modality-specific-files/magnetoencephalography.md
@@ -343,7 +343,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("meg.MEGCoordsystemWithEEG") }}
+{{ MACROS___make_json_table("json.meg.MEGCoordsystemWithEEG") }}
 
 Head localization coils:
 
@@ -355,7 +355,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("meg.MEGCoordsystemHeadLocalizationCoils") }}
+{{ MACROS___make_json_table("json.meg.MEGCoordsystemHeadLocalizationCoils") }}
 
 Digitized head points:
 
@@ -367,7 +367,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("meg.MEGCoordsystemDigitizedHeadPoints") }}
+{{ MACROS___make_json_table("json.meg.MEGCoordsystemDigitizedHeadPoints") }}
 
 Anatomical MRI:
 
@@ -379,7 +379,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("meg.MEGCoordsystemAnatomicalMRI") }}
+{{ MACROS___make_json_table("json.meg.MEGCoordsystemAnatomicalMRI") }}
 
 Anatomical landmarks:
 
@@ -391,7 +391,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("meg.MEGCoordsystemAnatomicalLandmarks") }}
+{{ MACROS___make_json_table("json.meg.MEGCoordsystemAnatomicalLandmarks") }}
 
 It is also RECOMMENDED that the MRI voxel coordinates of the actual anatomical
 landmarks for co-registration of MEG with structural MRI are stored in the
@@ -419,7 +419,7 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("meg.MEGCoordsystemFiducialsInformation") }}
+{{ MACROS___make_json_table("json.meg.MEGCoordsystemFiducialsInformation") }}
 
 For more information on the definition of anatomical landmarks, please visit:
     [How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/)
diff --git a/src/modality-specific-files/near-infrared-spectroscopy.md b/src/modality-specific-files/near-infrared-spectroscopy.md
index 7382560a43..b423b4c2dd 100644
--- a/src/modality-specific-files/near-infrared-spectroscopy.md
+++ b/src/modality-specific-files/near-infrared-spectroscopy.md
@@ -386,7 +386,7 @@ A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 
-{{ MACROS___make_sidecar_table("nirs.CoordsystemGeneral") }}
+{{ MACROS___make_json_table("json.nirs.CoordsystemGeneral") }}
 
 Fields relating to the NIRS optode positions:
 
@@ -399,7 +399,7 @@ A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 
-{{ MACROS___make_sidecar_table(["nirs.CoordinateSystem", "nirs.CoordinateSystemDescriptionRec"]) }}
+{{ MACROS___make_json_table(["json.nirs.CoordinateSystem", "json.nirs.CoordinateSystemDescriptionRec"]) }}
 
 Fields relating to the position of fiducials measured during an NIRS session/run:
 
@@ -412,7 +412,7 @@ A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 
-{{ MACROS___make_sidecar_table(["nirs.Fiducials", "nirs.FiducialsCoordinateSystemDescriptionRec"]) }}
+{{ MACROS___make_json_table(["json.nirs.Fiducials", "json.nirs.FiducialsCoordinateSystemDescriptionRec"]) }}
 
 Fields relating to the position of anatomical landmarks measured during an NIRS session/run:
 
@@ -425,7 +425,7 @@ A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 
-{{ MACROS___make_sidecar_table(["nirs.AnatomicalLandmark", "nirs.AnatomicalLandmarkCoordinateSystemDescriptionRec"]) }}
+{{ MACROS___make_json_table(["json.nirs.AnatomicalLandmark", "json.nirs.AnatomicalLandmarkCoordinateSystemDescriptionRec"]) }}
 
 ### Example `*_coordsystem.json`
 

From 574f7f659d97ceea7e89adc010c5f4a2faa5590c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 19 Aug 2024 16:17:50 -0400
Subject: [PATCH 4/4] feat(metaschema): Add schema.rules.json

---
 src/metaschema.json | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index f6e5a62d25..7df2856177 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -386,19 +386,25 @@
           "required": ["common", "deriv", "raw"],
           "additionalProperties": false
         },
+        "json": {
+          "type": "object",
+          "additionalProperties": {
+            "$ref": "#/definitions/json"
+          }
+        },
         "sidecars": {
           "type": "object",
           "patternProperties": {
             "^derivatives$": {
               "type": "object",
               "properties": {
-                "common_derivatives": { "$ref": "#/definitions/sidecar" }
+                "common_derivatives": { "$ref": "#/definitions/json" }
               },
               "required": ["common_derivatives"],
               "additionalProperties": false
             },
             "^(?!derivatives$)[a-z_]+$": {
-              "$ref": "#/definitions/sidecar"
+              "$ref": "#/definitions/json"
             },
             "additionalProperties": false
           },
@@ -476,6 +482,7 @@
       "required": [
         "entities",
         "files",
+	"json",
         "sidecars",
         "tabular_data",
         "common_principles",
@@ -586,7 +593,7 @@
         }
       }
     },
-    "sidecar": {
+    "json": {
       "type": "object",
       "patternProperties": {
         "^[a-zA-Z0-9_]+$": {