Add praire vole atlas packaging script #336
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| ATLAS_BASE_URL = "https://ndownloader.figshare.com/files/" | ||
| ORIENTATION = "..." | ||
| ROOT_ID = 997 | ||
| ATLAS_PACKAGER = "..." |
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| def create_atlas(working_dir): | ||
| ATLAS_NAME = "..." |
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I've emailed the lab that originally made this atlas to see if they have a preference for the name, but for now it can just be prairie_vole_brain.
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| def create_atlas(working_dir): | ||
| ATLAS_NAME = "..." | ||
| SPECIES = "..." |
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This can be Microtus ochrogaster
| def create_atlas(working_dir): | ||
| ATLAS_NAME = "..." | ||
| SPECIES = "..." | ||
| ATLAS_LINK = "https://elifesciences.org/articles/87029#data" |
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This can be Gustison et al. 2024, https://doi.org/10.7554/eLife.87029
| ATLAS_LINK = "https://elifesciences.org/articles/87029#data" | ||
| CITATION = "..." | ||
| ATLAS_BASE_URL = "https://ndownloader.figshare.com/files/" | ||
| ORIENTATION = "..." |
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This is the orientation of the raw data (before packaging), and should be asr. Details here if you're interested.
| ) | ||
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| with zipfile.ZipFile( | ||
| r"C:\Users\sacha\Downloads\atlas shit\PrV_results_datasets.zip", "r" |
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This should be a relative path, defined by Pathlib so it will work on any system, e.g. atlas_path / "PrV_results_datasets.zip"
| decimate_fraction = 0.2 | ||
| smooth = False # smooth meshes after creation | ||
| start = time.time() | ||
| if PARALLEL: |
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Our parallel mesh extraction is broken, so all of this part can be removed, and just keep the stuff after else:.
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
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Thanks @sacha091, this runs well now on my machine. The atlas looks ok, but the main issue is that there seems to be some meshes missing in the packaged atlas. There are 876 structures in |
adamltyson
changed the title
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FYI needs #419 to be merged and released before this atlas can be used. |
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