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Update use of brainio to brainglobe-utils #288

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May 15, 2024
Merged

Update use of brainio to brainglobe-utils #288

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8 changes: 3 additions & 5 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,9 @@
import treelib
import urllib3
from allensdk.core.structure_tree import StructureTree
from brainio import brainio
from brainglobe_utils.IO.image.load import load_any

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brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py#L11 

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from rich.progress import track

# import sys
# sys.path.append("./")
from brainglobe_atlasapi.atlas_generation.mesh_utils import (
Region,
create_region_mesh,
Expand Down Expand Up @@ -99,8 +97,8 @@
# ---------------- #
# GET TEMPLATE #
# ---------------- #
annotation = brainio.load_any(annotations_image) # shape (394, 466, 378)
anatomy = brainio.load_any(anatomy_image) # shape (394, 466, 378)
annotation = load_any(annotations_image) # shape (394, 466, 378)
anatomy = load_any(anatomy_image) # shape (394, 466, 378)

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brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py#L100-L101 

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# Remove weird artefact
annotation = annotation[:200, :, :]
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2 changes: 0 additions & 2 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py
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Expand Up @@ -14,8 +14,6 @@
from rich.progress import track
from scipy.ndimage import zoom

# import sys
# sys.path.append("./")
from brainglobe_atlasapi import utils
from brainglobe_atlasapi.atlas_generation.mesh_utils import (
Region,
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1 change: 0 additions & 1 deletion brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@
import SimpleITK as sitk
from rich.progress import track

# from allensdk.core.reference_space_cache import ReferenceSpaceCache
from brainglobe_atlasapi import utils
from brainglobe_atlasapi.atlas_generation.mesh_utils import (
Region,
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