dask-image
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Published
20 hours ago •
dask
dask
`find_objects` throws `AttributeError`
Describe the issue:
I am trying to use dask_image.ndmeasure.find_objects for bounding box detection. I have a label-image (dtype int32) with values [0, 149] of shape = (249, 1000, 1250).
This is my dataset: labeling.zarr.zip
This is the error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[62], line 1
----> 1 bbox_df = dask_image.ndmeasure.find_objects(tmp).compute()
File .../run-stardist/lib/python3.11/site-packages/dask/base.py:375, in DaskMethodsMixin.compute(self, **kwargs)
351 def compute(self, **kwargs):
352 """Compute this dask collection
353
354 This turns a lazy Dask collection into its in-memory equivalent.
(...)
373 dask.compute
374 """
--> 375 (result,) = compute(self, traverse=False, **kwargs)
376 return result
File .../run-stardist/lib/python3.11/site-packages/dask/base.py:661, in compute(traverse, optimize_graph, scheduler, get, *args, **kwargs)
658 postcomputes.append(x.__dask_postcompute__())
660 with shorten_traceback():
--> 661 results = schedule(dsk, keys, **kwargs)
663 return repack([f(r, *a) for r, (f, a) in zip(results, postcomputes)])
File .../run-stardist/lib/python3.11/site-packages/dask_image/ndmeasure/_utils/_find_objects.py:60, in _merge_bounding_boxes(x, ndim)
55 for i in range(ndim):
56 # Array dimensions are labelled by a number followed by an underscroe
57 # i.e. column labels are: 0_x, 1_x, 2_x, ... 0_y, 1_y, 2_y, ...
58 # (x and y represent the pair of chunks label slices are merged from)
59 slices = [x[ii] for ii in x.index if str(ii).startswith(str(i))]
---> 60 combined_slices = _combine_slices(slices)
61 data[i] = combined_slices
62 result = pd.Series(data=data, index=[i for i in range(ndim)], name=x.name)
File .../run-stardist/lib/python3.11/site-packages/dask_image/ndmeasure/_utils/_find_objects.py:42, in _combine_slices(slices)
40 return slices[0]
41 else:
---> 42 start = min([sl.start for sl in slices])
43 stop = max([sl.stop for sl in slices])
44 return slice(start, stop)
File .../run-stardist/lib/python3.11/site-packages/dask_image/ndmeasure/_utils/_find_objects.py:42, in <listcomp>(.0)
40 return slices[0]
41 else:
---> 42 start = min([sl.start for sl in slices])
43 stop = max([sl.stop for sl in slices])
44 return slice(start, stop)
AttributeError: 'str' object has no attribute 'start'
Minimal Complete Verifiable Example:
import dask.array as da
import dask_image
labeling = da.from_zarr('labeling.zarr')
bbox_df = dask_image.ndmeasure.find_objects(labeling).compute()
Anything else we need to know?:
Environment:
- Dask version: 2024.2.1
- Dask-core version: 2024.2.1
- Dask-image version: 2023.8.1
- Python version: 3.11.8
- Operating System: Operating System: Rocky Linux 8.6 (Green Obsidian); Kernel: Linux 4.18.0-372.26.1.el8_6.x86_64; Architecture: x86-64
- Install method (conda, pip, source): mamba
Full Env:
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traitlets 5.14.1 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.20240106 pyhd8ed1ab_0 conda-forge
typing-extensions 4.10.0 hd8ed1ab_0 conda-forge
typing_extensions 4.10.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
ucx 1.15.0 h75e419f_3 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wandb 0.16.3 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.10 pyhd8ed1ab_0 conda-forge
wrapt 1.14.1 py311hd4cff14_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xyzservices 2023.10.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 py311h459d7ec_0 conda-forge
zarr 2.17.0 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h59595ed_1 conda-forge
zfp 1.0.1 h59595ed_0 conda-forge
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
