Modifications from data-elements group meeting 27Sep2024

model/DetectorTypes.yml

@@ -2,13 +2,15 @@
 SolidVolume: !record
   fields:
     shape: GeometricShape
-    # TODO could use material_id here
-    material: BulkMaterial
+    # identified referring to `BulkMaterial` list in `ScannerInformation`
+    material_id: uint
 
 # A list of identical SolidVolumes at different locations
 ReplicatedSolidVolume: !record
   fields:
     solidVolume: SolidVolume
+    # list of transforms
+    # constraint: length >= 1
     transforms: RigidTransformation*
     # list of unique ids for every replicated solid volume
     # constraint: size(transforms) == size(ids)

model/MaterialTypes.yml

@@ -15,13 +15,16 @@ BulkMaterial: !record
   fields:
     # unique id that can be used to refer to the material in voxelised maps etc
     id: uint
-    # informative string, not standardised
-    name: string?
+    # informative string, not standardised.
+    # Expected examples: BGO, LSO, LYSO, LaBr, GAGG, plastic
+    name: string
     # density of the material
-    # TODO specify units
+    # Units: g/cc
+    # TODO agree with vendors if this information can be supplied and to what accuracy
     density: float
     # List of atoms and their respective mass fractions
     # sum of massFractions should be 1
-    # This list should be reasonably accurate to be useful for Monte Carlo simulations
+    # TODO agree with vendors if this information can be supplied and to what accuracy
+    # Ideally this list should be reasonably accurate to be useful for Monte Carlo simulations, but can be approximate.
     atoms: AtomAndFraction*
 

model/ScannerInformation.yml

@@ -1,6 +1,4 @@
 
-# Detector ID and location. Units are in mm
-# TODO: this is currently just a sample implementation with "point" detectors.
 # Will be obsolete
 Detector: !record
   fields:
@@ -30,8 +28,11 @@ ScannerInformation: !record
     modelName: string?
 
     # list of geometric information for all detector elements
-    # TODO replace with ScannerGeometry
-    detectors: Detector*
+    scanner_geometry: ScannerGeometry
+
+    # list of materials present in the scanner geometry. The `material_id`s there will refer to the
+    # identifiers in this list below.
+    bulkMaterials: BulkMaterial*
 
     # edge information for TOF bins in mm (given as from first to last edge, so there is one more edge than the number of bins)
     # 0 corresponds to the same arrival time. Negative numbers indicate that the first detector detected first.

model/Shapes.yml

@@ -8,8 +8,8 @@ BoxShape: !record
   fields:
     corners: Coordinate*8
 
-# annulus of certain thickness oriented along the last axis of `orientation`
-# TODO define angles
+# annulus of certain thickness oriented along the [0,0,1] axis
+# in radians. An angle of 0 corresponds to the [1,0,0] axis, Pi/2 corresponds to the [0,1,0] axis.
 AnnulusShape: !record
   fields:
     # inner radius (in mm)
@@ -31,4 +31,3 @@ GeometricShape: !record
   fields:
     # union of different shape types
     shape: [BoxShape, AnnulusShape]
-    # TODO could have rigidTransformation field here. If we do, the `center` and `orientation` fields in `AnnulusShape` should be deleted