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Fix for incorrect data group parsing #18

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merged 4 commits into from
Oct 28, 2024
Merged

Fix for incorrect data group parsing #18

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2666e5c
Convert Path to string to get the group from the zarr file
fercer Oct 28, 2024
afba9a5
Corrected group data parsing from zarr files
fercer Oct 28, 2024
76f9e84
Added step to convert path to string if it was parsed as any Path
fercer Oct 28, 2024
c710f96
Updated conftest.py to reflect the expected data group when parsing f…
fercer Oct 28, 2024
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9 changes: 7 additions & 2 deletions src/napari_activelearning/_tests/conftest.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import pytest
from unittest.mock import MagicMock, patch
from pathlib import Path
from pathlib import Path, PureWindowsPath
import numpy as np
import zarr
import zarrdataset as zds
Expand Down Expand Up @@ -82,7 +82,12 @@ def single_scale_disk_zarr(single_scale_array, tmpdir_factory):
z_group = z_root.create_group(data_group)

z_group.create_dataset(name="0", data=sample_data, overwrite=True)
data_group = str(Path(data_group) / "0")
data_group = Path(data_group) / "0"

if isinstance(data_group, PureWindowsPath):
data_group = data_group.as_posix()

data_group = str(data_group)

return z_root, input_filename, data_group, shape

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17 changes: 8 additions & 9 deletions src/napari_activelearning/_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -496,9 +496,12 @@ def get_source_data(layer: Layer):
range(len(input_filename_parts))))
if extension_idx:
extension_idx = extension_idx[0]
data_group = Path(
*input_filename_parts[extension_idx + 1:]
)
data_group = input_filename_parts[extension_idx + 1:]
if len(data_group):
data_group = Path(*data_group)
else:
data_group = ""

input_path = Path(
*input_filename_parts[:extension_idx + 1]
)
Expand All @@ -509,6 +512,7 @@ def get_source_data(layer: Layer):
if isinstance(input_path, PureWindowsPath):
input_path = input_path.as_posix()

data_group = str(data_group)
input_path = str(input_path)

if input_scheme:
Expand All @@ -520,14 +524,9 @@ def get_source_data(layer: Layer):
input_filename = input_scheme + input_netloc + input_path

if ".zarr" in input_filename:
if data_group:
data_group = Path(data_group)

z_grp = zarr.open(input_filename, mode="r")
while not isinstance(z_grp[data_group], zarr.Array):
data_group = data_group / "0"

data_group = str(data_group)
data_group = str(Path(data_group) / "0")

else:
return layer.data, None
Expand Down
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