Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

File connection opened by read_box is not subsequently closed #69

Open
MattArran opened this issue Mar 1, 2024 · 1 comment · May be fixed by #70
Open

File connection opened by read_box is not subsequently closed #69

MattArran opened this issue Mar 1, 2024 · 1 comment · May be fixed by #70

Comments

@MattArran
Copy link

Hi!

Thanks for the package- it's good to have a GeoTIFF reader that doesn't require struggling with GDAL. Unfortunately, I've been running into a bug in applying geotiff to my use case, in which I need to extract, process, and then remove GeoTIFFs, in Windows. Specifically, GeoTiff.read_box successfully reads data from a GeoTIF file but doesn't close the file connection, so that subsequent attempts to remove the file fail.

Example, using the downloaded GeoTiff https://download.osgeo.org/geotiff/samples/usgs/o41078a7.tif:

>>> from geotiff import GeoTiff
>>> import os
>>> geo_tiff = GeoTiff('o41078a7.tif')
>>> array = geo_tiff.read_box(((-78.85, 41.06), (-78.83, 41.04)))
>>> os.remove('o41078a7.tif')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'o41078a7.tif'

Examining the code, I've identified the problem as the processing of the ZarrTiffStore produced by tif.aszarr in __init__: while store.close() closes the connection, it's reopened by slicing of the Zarr array self._z and, while the Zarr array itself doesn't need closing, the store connection does:

>>> import os
>>> from tifffile import TiffFile
>>> import zarr
>>> tiff = TiffFile('o41078a7.tif')
>>> store = tiff.aszarr()
>>> zarray = zarr.open(store, mode='r')
>>> store.close()
>>> tiff.close()
>>> zarray[:4,:4]
array([[1, 1, 1, 1],
       [1, 1, 1, 1],
       [1, 1, 1, 1],
       [1, 1, 1, 1]], dtype=uint8)
>>> os.remove('o41078a7.tif')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'o41078a7.tif'
>>> store.close()
>>> os.remove('o41078a7.tif')
>>> os.path.isfile('o41078a7.tif')
False

Environment:

Windows 11 Enterprise
requirements.txt
@MattArran
Copy link
Author

I suspect the cleanest approach is to make GeoTiff a derived class of TiffFile, inheriting .close() and the with context managers. But I imagine there's a reason you've not followed that route, so will work on a quick fix with connections closed separately.

@MattArran MattArran linked a pull request Mar 1, 2024 that will close this issue
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Add method to close file connection MattArran/geotiff
1 participant
@MattArran