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03e863f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | #!/usr/bin/env python3
"""Download Allen Human Brain Atlas meshes and pre-compute the voxel label grid.
This script MUST be run once before using mindVisualizer. It:
1. Downloads the Allen Human Brain Atlas (500um) via brainglobe
2. Copies OBJ mesh files to data/meshes/
3. Copies structures.json (region name mappings) to data/
4. Pre-computes a 100^3 voxel label grid for fast point-in-region queries
and saves it to data/label_grid_cache.npz
Usage:
pip install brainglobe-atlasapi
python setup_brain_data.py
"""
import shutil
import json
from pathlib import Path
import numpy as np
PROJECT_ROOT = Path(__file__).resolve().parent
DATA_DIR = PROJECT_ROOT / "data"
MESH_DIR = DATA_DIR / "meshes"
ALIGNMENT_FILE = DATA_DIR / "brain_alignment.json"
GRID_CACHE = DATA_DIR / "label_grid_cache.npz"
def main():
# ---- Step 1: Download atlas ----
print("[setup] Downloading Allen Human Brain Atlas (500um)...")
print(" (This is a one-time download, ~269 MB)")
from brainglobe_atlasapi import BrainGlobeAtlas
atlas = BrainGlobeAtlas("allen_human_500um")
atlas_dir = Path.home() / ".brainglobe" / "allen_human_500um_v1.0"
src_meshes = atlas_dir / "meshes"
if not src_meshes.exists():
print(f"[setup] ERROR: Atlas meshes not found at {src_meshes}")
return
# ---- Step 2: Copy meshes to both meshes/ and meshes_obj/ ----
MESH_OBJ_DIR = DATA_DIR / "meshes_obj"
MESH_DIR.mkdir(parents=True, exist_ok=True)
MESH_OBJ_DIR.mkdir(parents=True, exist_ok=True)
obj_files = list(src_meshes.glob("*.obj"))
print(f"[setup] Copying {len(obj_files)} OBJ meshes...")
copied = 0
for obj in obj_files:
for target_dir in (MESH_DIR, MESH_OBJ_DIR):
dst = target_dir / obj.name
if not dst.exists() or dst.stat().st_size != obj.stat().st_size:
shutil.copy2(obj, dst)
copied += 1
print(f"[setup] Copied meshes ({len(obj_files)} files to meshes/ and meshes_obj/)")
# ---- Step 3: Copy structures.json ----
structs_src = atlas_dir / "structures.json"
structs_dst = DATA_DIR / "structures.json"
if structs_src.exists():
shutil.copy2(structs_src, structs_dst)
print(f"[setup] Copied structures.json")
else:
print(f"[setup] WARNING: structures.json not found at {structs_src}")
# ---- Step 4: Build and cache label grid ----
print(f"\n[setup] Building voxel label grid (this takes ~30-60 seconds)...")
import vtk
from src.mesh_overlay import FlowMeshOverlay
ren = vtk.vtkRenderer()
win = vtk.vtkRenderWindow()
win.SetOffScreenRendering(1)
win.AddRenderer(ren)
overlay = FlowMeshOverlay(ren=ren, win=win,
mesh_dir=MESH_DIR,
alignment_file=ALIGNMENT_FILE)
n_regions = len(overlay.get_all_region_keys())
print(f"[setup] Loaded {n_regions} region meshes")
overlay.build_label_grid()
overlay.save_label_grid(GRID_CACHE)
# ---- Summary ----
print(f"\n{'='*50}")
print(f" Setup complete!")
print(f" Meshes: {MESH_DIR}/ ({len(obj_files)} files)")
print(f" Structures: {structs_dst}")
print(f" Label grid: {GRID_CACHE}")
print(f" Regions: {n_regions}")
print(f"{'='*50}")
print(f"\n You can now run:")
print(f" python -m src.main")
print(f" python examples/rdcim_propagation.py")
if __name__ == "__main__":
main()
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