Fix tabulation in a .tsv + convert to use yaw, pitch, roll

Co-authored-by: Ben Dichter <[email protected]>

src/modality-specific-files/microelectrode-electrophysiology.md

@@ -195,11 +195,11 @@ at the location:
 Example of `_probes.tsv`:
 
 ```Text
-probe_id	hemisphere	x	y	z	type		material	location
-p023		left		-11.87	-1.30	-3.37	utah-array	iridium-oxide	V1
-p023		left		-11.64	0.51	-4.20	utah-array	iridium-oxide	V2
-p021		left		-12.11	-3.12	-2.54	utah-array	iridium-oxide	V4
-p021		left		-9.94	-1.19	-2.86	utah-array	iridium-oxide	V3
+probe_id	hemisphere	x	y	z	type	material	location
+p023	left	-11.87	-1.30	-3.37	utah-array	iridium-oxide	V1
+p023	left	-11.64	0.51	-4.20	utah-array	iridium-oxide	V2
+p021	left	-12.11	-3.12	-2.54	utah-array	iridium-oxide	V4
+p021	left	-9.94	-1.19	-2.86	utah-array	iridium-oxide	V3
 ```
 
 

src/schema/objects/columns.yaml

@@ -45,11 +45,11 @@ age:
     "Description": "Subject age in postnatal years",
     "Units": "year",
   }
-alpha_rotation:
-  name: alpha_rotation
-  display_name: Alpha rotation
+roll:
+  name: roll
+  display_name: Roll rotation
   description: |
-    Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.
+    Clockwise rotation when looking down at the probe.
   unit: degree
 associated_brain_region:
   name: associated_brain_region
@@ -72,11 +72,10 @@ associated_brain_region_quality_type:
     The method used to identify the associated brain region (estimated|proof)
     depending on anatomical pictures proofing the location or indirect estimation of the location.
   type: string
-beta_rotation:
-  name: beta_rotation
-  display_name: Beta rotation
-  description: |
-    Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.
+pitch:
+  name: pitch
+  display_name: Pitch rotation
+  description: Rotation in the direction of the electrode face, in degrees.
   unit: degree
   type: number
 cardiac:
@@ -299,11 +298,10 @@ gain:
     to the signal stored in the data file.
     If no gain factor is provided it is assumed to be 1.
   type: number
-gamma_rotation:
-  name: gamma_rotation
-  display_name: Gamma rotation
-  description: |
-    Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.
+yaw:
+  name: yaw
+  display_name: Yaw rotation
+  description: Rotation clockwise when looking down.
   unit: degree
 # TODO: Clarify if the optionality of the column be defined here or as an addendum in the rules.
 ground:

src/schema/rules/tabular_data/microephys.yaml

@@ -23,9 +23,9 @@ microephysProbes:
     height__probes: optional
     depth__probes: optional
     dimension_unit: optional
-    alpha_rotation: recommended
-    beta_rotation: recommended
-    gamma_rotation: recommended
+    yaw: recommended
+    pitch: recommended
+    roll: recommended
     coordinate_reference_point: recommended
     hemisphere__probes: recommended
     associated_brain_region: recommended