# Synthetic teaching example, validated against main commit 0c8c4e3.
# Paths do not identify real files. This chooses a corner-origin physical frame.
# This is NOT an instance of the stricter cets-rigid/0.2 converter profile.
name: synthetic_cets_example
regions:
  - id: region_1
    tilt_series:
      - id: tilt_series_1
        path: example/tilts.mrcs
        images:
          - id: tilt_0
            section: 0
            width: 64
            height: 64
            nominal_tilt_angle: 0.0
            accumulated_dose: 0.0
    tomograms:
      - id: tomo_1
        tilt_series_id: tilt_series_1
        path: example/tomo.mrc
        width: 64
        height: 64
        depth: 32
        coordinate_systems:
          - name: voxel_xyz
            axes:
              - {name: x, axis_type: array, axis_unit: voxel}
              - {name: y, axis_type: array, axis_unit: voxel}
              - {name: z, axis_type: array, axis_unit: voxel}
          - name: physical_xyz
            axes:
              - {name: x, axis_type: space, axis_unit: angstrom}
              - {name: y, axis_type: space, axis_unit: angstrom}
              - {name: z, axis_type: space, axis_unit: angstrom}
        coordinate_transformations:
          - transformation_type: scale
            input: voxel_xyz
            output: physical_xyz
            scale: [4.0, 4.0, 4.0]
    annotations:
      - id: picks_1
        name: Example particle picks; no biological identification asserted
        annotation_type: point_set_3D
        source_tomogram_id: tomo_1
        coordinate_systems:
          - name: physical_xyz
            axes:
              - {name: x, axis_type: space, axis_unit: angstrom}
              - {name: y, axis_type: space, axis_unit: angstrom}
              - {name: z, axis_type: space, axis_unit: angstrom}
        origin3D:
          - [40.0, 80.0, 24.0]
averages:
  - name: example_particle_extraction
    particle_maps:
      - path: example/particle_0.mrc
        source_region_id: region_1
        source_annotation_id: picks_1
        coord_index: 0
        width: 16
        height: 16
        depth: 16