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testing and fixing outdated atlas generation scripts #249

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merged 8 commits into from
Mar 1, 2024
Merged

testing and fixing outdated atlas generation scripts #249

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27c035a
first commit, quick fixes of old syntax to try running it on the HPC
viktorpm Feb 27, 2024
0c1584a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 27, 2024
a3e6dcd
humanatlas.py: from brainio import brainio has to be installed manually
viktorpm Feb 27, 2024
a8f4631
fixing azba_zfish issue: replace smoothLaplacian with smooth in mesh_…
viktorpm Feb 28, 2024
58495b6
fixing kim_developmental_ccf_mouse.py issue: pandas syntax and df han…
viktorpm Feb 29, 2024
5d4f4b0
fixing allen_cord.py: updating source URL
viktorpm Feb 29, 2024
a69bf73
adding packages to dependencies
viktorpm Mar 1, 2024
4ab0f5e
removing unnecessary comments
viktorpm Mar 1, 2024
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7 changes: 4 additions & 3 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,11 @@
import numpy as np
import pandas as pd
from rich.progress import track

######## I had to manually install this
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This should be added to the dependencies in pyproject.toml then, I think,

from skimage import io

########
from brainglobe_atlasapi import utils
from brainglobe_atlasapi.atlas_generation.mesh_utils import (
Region,
Expand Down Expand Up @@ -226,9 +229,7 @@ def create_atlas(
if isinstance(working_dir, str):
working_dir = Path(working_dir)
# Generated atlas path:
working_dir = (
working_dir / "brainglobe_workingdir" / atlas_config.atlas_name
)
working_dir = working_dir / "admba_3d_dev_mouse" / atlas_config.atlas_name
working_dir.mkdir(exist_ok=True, parents=True)

download_dir_path = working_dir / "downloads"
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5 changes: 1 addition & 4 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py
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Expand Up @@ -221,10 +221,7 @@ def create_atlas(working_dir):
ORIENTATION = "asr"
RESOLUTION = (20, 10, 10)
ROOT_ID = 250
ATLAS_FILE_URL = (
"https://md-datasets-cache-zipfiles-prod.s3.eu-west-1."
"amazonaws.com/4rrggzv5d5-1.zip"
)
ATLAS_FILE_URL = "https://prod-dcd-datasets-cache-zipfiles.s3.eu-west-1.amazonaws.com/4rrggzv5d5-1.zip"
ATLAS_PACKAGER = "MetaCell LLC, Ltd."

download_dir_path = working_dir / "downloads"
Expand Down
2 changes: 2 additions & 0 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py
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Expand Up @@ -8,6 +8,8 @@
import treelib
import urllib3
from allensdk.core.structure_tree import StructureTree

### I had to install manually
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Again, worth adding to the dependencies. If it is very big or hard-to-install, it can be an optional dependency like allensdk.

from brainio import brainio
from rich.progress import track

Expand Down
6 changes: 4 additions & 2 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py
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Expand Up @@ -133,8 +133,10 @@ def create_atlas(
df = pd.read_csv(structures_file)
clean_up_df_entries(df)

df.loc[len(df)] = ["root", ROOT_ID, "root", ROOT_ID]
df.append(["root", ROOT_ID, "root", ROOT_ID])
new_row = pd.DataFrame(
[["root", ROOT_ID, "root", ROOT_ID]], columns=df.columns
)
df = pd.concat([df, new_row], ignore_index=True)

id_dict = dict(zip(df["ID"], df["Parent ID"]))

Expand Down
4 changes: 2 additions & 2 deletions brainglobe_atlasapi/atlas_generation/mesh_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,10 +158,10 @@ def extract_mesh_from_mask(
mesh = mesh.extractLargestRegion()

# decimate
mesh.decimate(decimate_fraction, method="pro")
mesh.decimate_pro(decimate_fraction)

if smooth:
mesh.smoothLaplacian()
mesh.smooth()

if obj_filepath is not None:
write(mesh, str(obj_filepath))
Expand Down
3 changes: 3 additions & 0 deletions brainglobe_atlasapi/atlas_generation/volume_utils.py
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Expand Up @@ -14,7 +14,10 @@

import os

######## I had to manually install this
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We should depend on brainglobe-utils.imageio instead (see brainglobe/brainglobe-utils#33 for details), which may need to be added to the dependencies.

import imio

########
import numpy as np


Expand Down
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