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feat(zettasets): Fall back to zettasets images #26

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feat(zettasets): Fall back to zettasets images #26

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29 changes: 21 additions & 8 deletions deepem/data/dataset/multi_zettaset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import re

from cloudvolume import CloudVolume, Bbox
from cloudvolume.exceptions import InfoUnavailableError

from zettasets.dataset import Dataset as Zettaset
from zettasets.sample import Sample
Expand Down Expand Up @@ -199,14 +200,26 @@ def convert_array(arr: ArrayLike) -> np.ndarray:
else (0, 0, 0)
)
image_bbox = Bbox(bbox.minpt - xyz_padding, bbox.maxpt + xyz_padding)

# Image
vol = CloudVolume( # pylint: disable=unsubscriptable-object
sample.src_image_path,
mip=resolution,
fill_missing=True,
bounded=False,
)[image_bbox.to_slices()]

# Image: try src_image_path first for backward compatibility,
# fall back to sample's own image volume
try:
if sample.src_image_path is None:
raise ValueError("No src_image_path available")
vol = CloudVolume( # pylint: disable=unsubscriptable-object
sample.src_image_path,
mip=resolution,
fill_missing=True,
bounded=False,
)[image_bbox.to_slices()]
except (InfoUnavailableError, ValueError) as e:
print(f"\tWarning: src_image_path failed ({e}), falling back to sample image volume")
vol = CloudVolume( # pylint: disable=unsubscriptable-object
sample.volumes["image"].cloudpath,
mip=resolution,
fill_missing=True,
bounded=False,
)[image_bbox.to_slices()]
dset["input"] = convert_array(vol) / 255.0
print(f"\tinput: {dset['input'].shape}")

Expand Down
27 changes: 20 additions & 7 deletions deepem/data/dataset/zettaset.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

from cloudvolume import CloudVolume, Bbox
from cloudvolume.exceptions import InfoUnavailableError
import numpy as np
from numpy.typing import ArrayLike
import re
Expand Down Expand Up @@ -90,13 +91,25 @@ def convert_array(arr: ArrayLike) -> np.ndarray:
)
image_bbox = Bbox(bbox.minpt - xyz_padding, bbox.maxpt + xyz_padding)

# Image
vol = CloudVolume( # pylint: disable=unsubscriptable-object
sample.src_image_path,
mip=resolution,
fill_missing=True,
bounded=False,
)[image_bbox.to_slices()]
# Image: try src_image_path first for backward compatibility,
# fall back to sample's own image volume
try:
if sample.src_image_path is None:
raise ValueError("No src_image_path available")
vol = CloudVolume( # pylint: disable=unsubscriptable-object
sample.src_image_path,
mip=resolution,
fill_missing=True,
bounded=False,
)[image_bbox.to_slices()]
except (InfoUnavailableError, ValueError) as e:
print(f"\tWarning: src_image_path failed ({e}), falling back to sample image volume")
vol = CloudVolume( # pylint: disable=unsubscriptable-object
sample.volumes["image"].cloudpath,
mip=resolution,
fill_missing=True,
bounded=False,
)[image_bbox.to_slices()]
dset["input"] = convert_array(vol)
dset["input"] = (dset["input"] / 255.).astype('float32')
print(f"input: {dset['input'].shape}")
Expand Down