Fixing admba

brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py

@@ -1,16 +1,16 @@
-__version__ = "0"
+__version__ = "1"
 
 import dataclasses
 import json
 import multiprocessing as mp
 import time
-import zipfile
 from os import listdir, path
 from pathlib import Path
 from typing import Tuple
 
 import numpy as np
 import pandas as pd
+import pooch
 from rich.progress import track
 from skimage import io
 
@@ -22,24 +22,27 @@
 from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data
 from brainglobe_atlasapi.structure_tree_util import get_structures_tree
 
-PARALLEL = True
+PARALLEL = False
 
 
 def download_atlas_files(download_dir_path, atlas_file_url, ATLAS_NAME):
  utils.check_internet_connection()
 
- atlas_files_dir = download_dir_path / ATLAS_NAME
  try:
  download_name = ATLAS_NAME + "_atlas.zip"
  except TypeError:
  download_name = ATLAS_NAME / "_atlas.zip"
  destination_path = download_dir_path / download_name
- utils.retrieve_over_http(atlas_file_url, destination_path)
 
- with zipfile.ZipFile(destination_path, "r") as zip_ref:
- zip_ref.extractall(atlas_files_dir)
+ pooch.retrieve(
+ url=atlas_file_url,
+ known_hash=None,
+ path=destination_path,
+ progressbar=True,
+ processor=pooch.Unzip(extract_dir="."),
+ )
 
- return atlas_files_dir
+ return destination_path
 
 
 def parse_structures(structures_file, root_id):
@@ -144,10 +147,11 @@
  total=tree.size(),
  description="Creating meshes",
  ):
+ # root_node = tree.nodes[root_id]
  create_region_mesh(
  (
  meshes_dir_path,
- node,
+ node, # root_node
  tree,
  labels,
  annotated_volume,
@@ -298,14 +302,15 @@
  cleanup_files=False,
  compress=True,
  scale_meshes=True,
+ resolution_mapping=[2, 1, 0],
  )
  print("Done. Atlas generated at: ", output_filename)
  return output_filename
 
 
 if __name__ == "__main__":
  # Generated atlas path:
- bg_root_dir = Path.home() / "brainglobe_workingdir"
+ bg_root_dir = Path.home() / ".brainglobe"
  bg_root_dir.mkdir(exist_ok=True, parents=True)
 
  # set up E11.5 atlas settings and use as template for rest of brains
@@ -314,8 +319,13 @@
  species="Mus musculus",
  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="lsa",
- resolution=(16, 16, 20),
+ orientation="rsa",
+ 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, "
@@ -368,6 +378,7 @@
  # P28 atlas, which has same resolutions as P14
  p28_config = dataclasses.replace(
  p14_config,
+ resolution=(16.752, 16.752, 25),
  atlas_name="admba_3d_p28_mouse",
  atlas_link="https://search.kg.ebrains.eu/instances/3a1153f0-6779-43bd-9f02-f92700a585a4",
  atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000029_3Drecon-ADMBA-P28_pub",

brainglobe_atlasapi/atlas_generation/wrapup.py

@@ -48,6 +48,7 @@
  cleanup_files=False,
  compress=True,
  scale_meshes=False,
+ resolution_mapping=None,
  additional_references={},
  additional_metadata={},
 ):
@@ -102,6 +103,9 @@
  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 @@
 
  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(