quickfix wrapup for admba, fix admba orientation/resolution

Result of mob-programming!

Co-authored-by: Viktor Plattner <[email protected]>
Co-authored-by: sfmig <[email protected]>

brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py

@@ -302,6 +302,7 @@ def create_atlas(
  cleanup_files=False,
  compress=True,
  scale_meshes=True,
+ resolution_mapping=[2, 1, 0],
  )
  print("Done. Atlas generated at: ", output_filename)
  return output_filename
@@ -319,7 +320,12 @@ def create_atlas(
  atlas_link="https://search.kg.ebrains.eu/instances/8ab25629-bdac-47d0-bc86-6f3aa3885f29",
  atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000023_3Drecon-ADMBA-E11pt5_pub",
  orientation="rsa",
- resolution=(16, 20, 16), # possibly try 20, 16, 16
+ resolution=(
+ 16,
+ 16,
+ 20,
+ ), # this is in ASR, the target orientation.
+ # The resolution in LR is lower than SI and AP!
  citation="Young et al. 2021, https://doi.org/10.7554/eLife.61408",
  root_id=15564,
  atlas_packager="Pradeep Rajasekhar, WEHI, Australia, "

brainglobe_atlasapi/atlas_generation/wrapup.py

@@ -48,6 +48,7 @@ def wrapup_atlas_from_data(
  cleanup_files=False,
  compress=True,
  scale_meshes=False,
+ resolution_mapping=None,
  additional_references={},
  additional_metadata={},
 ):
@@ -102,6 +103,9 @@ def wrapup_atlas_from_data(
  If True the meshes points are scaled by the resolution
  to ensure that they are specified in microns,
  regardless of the atlas resolution.
+ resolution_mapping: list, optional
+ a list of three mapping the target space axes to the source axes
+ only needed for mesh scaling of anisotropic atlases
  additional_references: dict, optional
  (Default value = empty dict).
  Dictionary with secondary reference stacks.
@@ -171,7 +175,20 @@ def wrapup_atlas_from_data(
 
  if scale_meshes:
  # Scale the mesh to the desired resolution, BEFORE transforming:
- mesh.points *= resolution
+ # Note that this transformation happens in original space,
+ # but the resolution is passed in target space (typically ASR)
+ if not resolution_mapping:
+ # isotropic case, so don't need to re-map resolution
+ mesh.points *= resolution
+ else:
+ # resolution needs to be transformed back
+ # to original space in anisotropic case
+ original_resolution = (
+ resolution[resolution_mapping[0]],
+ resolution[resolution_mapping[1]],
+ resolution[resolution_mapping[2]],
+ )
+ mesh.points *= original_resolution
 
  # Reorient points:
  mesh.points = space_convention.map_points_to(