jp2 slicing
- Dominant language
- Python
- Stars
- 226
- Forks
- 56
- PR merge metrics
- No merged PRs in 30d
Description
**Describe the issue**: Hi, I am trying to use dask_image.imread.imread() to speed up the sub-volume extraction on my dataset of .jp2 format, but it throws an error when I extract multiple slices.
**Psudocode Example**:
```python
import dask_image.imread
def read_subvol_stack(path, file_type):
img_array_dask = dask_image.imread.imread(f"{path}/*.{file_type}")
print(img_array_dask)
img_array = img_array_dask[0:900, :, :].compute()
return img_array
```
The print() function gives:
```
dask.array<_map_read_frame, shape=(3770, 1898, 1898), dtype=uint16, chunksize=(1, 1898, 1898), chunktype=numpy.ndarray>
```
When the compute() is running, an error occurs:
```
ValueError: could not broadcast input array from shape (1,1898,1898) into shape (1,1,1898)
```
I have checked, when compute() function activated, the imread() will read an image in shape of (1,1,1898, 1898), so the chunk size of (1, 1898, 1898) can’t be broadcast.
The code works well for .tif or .png images.
**Anything else we need to know?**:
I replicate the error if it helps: https://github.com/YangForever/DaskImageSlicing/tree/main
**Environment**:
- Dask version: 2023.11.0
- Python version: 3.9
- Operating System: Ubuntu 20.04
- Install method (conda, pip, source): conda
Contributor guide
Assessment
This issue has not been assessed yet.