Breizorro: Problem in writing outfile

[rramij]

I am trying to make mask with breizorro.

# Make mask using breizorro
recipe.add("cab/breizorro", "test_mask", {
	"restored-image": "initial_image-MFS-image.fits",
	"threshold": 6.5,
	"boxsize": 50,
	"number-islands": True,
	"make-binary": True,
	"fill-holes": True,
	"outfile": "Test_breizorro_mask.fits"
	}, input=OUTPUT, output=OUTPUT, label="test mask")

But it is showing error at the time of writing the output file.

breizorro.breizorro - 2023-08-14 18:46:39,691 INFO - Welcome to breizorro
breizorro.breizorro - 2023-08-14 18:46:39,768 INFO - Version: 0.1.0
breizorro.breizorro - 2023-08-14 18:46:39,768 INFO - Usage: breizorro --help
breizorro.breizorro - 2023-08-14 18:46:39,769 INFO - Reading /stimela_mount/input/initial_image-MFS-image.fits data
breizorro.breizorro - 2023-08-14 18:46:39,871 INFO - Generating mask using threshold 6.5
breizorro.breizorro - 2023-08-14 18:46:39,871 INFO - Generating noise map
breizorro.breizorro - 2023-08-14 18:46:48,264 INFO - Median noise value is 1.8788927263813093e-05
breizorro.breizorro - 2023-08-14 18:46:48,423 INFO - (Re)numbering islands
breizorro.breizorro - 2023-08-14 18:46:48,779 INFO - Number of islands: 372
breizorro.breizorro - 2023-08-14 18:46:48,779 INFO - Converting mask to binary
breizorro.breizorro - 2023-08-14 18:46:48,820 INFO - Filling closed regions
Traceback (most recent call last):
  File "/usr/local/bin/breizorro", line 5, in <module>
    main()
  File "/usr/local/lib/python3.6/dist-packages/breizorro/breizorro.py", line 355, in main
    shutil.copyfile(input_file, out_mask_fits)  # to provide a template
  File "/usr/lib/python3.6/shutil.py", line 122, in copyfile
    copyfileobj(fsrc, fdst)
  File "/usr/lib/python3.6/shutil.py", line 82, in copyfileobj
    fdst.write(buf)
OSError: [Errno 28] No space left on device
Traceback (most recent call last):
  File "/stimela_mount/code/run.py", line 39, in <module>
    subprocess.check_call(shlex.split(_runc))
  File "/usr/lib/python3.6/subprocess.py", line 311, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['breizorro', '--restored-image', '/stimela_mount/input/initial_image-MFS-image.fits', '--threshold', '6.5', '--boxsize', '50', '--number-islands', '--make-binary', '--fill-holes', '--outfile', 'Test_breizorro_mask.fits']' returned non-zero exit status 1.

However, there is no lack of space in the disk.

### THESE ARE YOUR DISK QUOTA USAGES
     Filesystem   space   quota   limit   grace   files   quota   limit   grace
          /home   8104G  10189G  10189G            350k       0       0        
###

Furthermore, if I comment out the "outfile" parameter.

 # Make mask using breizorro
recipe.add("cab/breizorro", "test_mask", {
	"restored-image": "initial_image-MFS-image.fits",
	"threshold": 6.5,
	"boxsize": 50,
	"number-islands": True,
	"make-binary": True,
	"fill-holes": True,
#	"outfile": "Test_breizorro_mask.fits"
	}, input=OUTPUT, output=OUTPUT, label="test mask")

The error changes to

breizorro.breizorro - 2023-08-14 18:54:50,816 INFO - Welcome to breizorro
breizorro.breizorro - 2023-08-14 18:54:50,892 INFO - Version: 0.1.0
breizorro.breizorro - 2023-08-14 18:54:50,892 INFO - Usage: breizorro --help
breizorro.breizorro - 2023-08-14 18:54:50,893 INFO - Reading /stimela_mount/input/initial_image-MFS-image.fits data
breizorro.breizorro - 2023-08-14 18:54:50,994 INFO - Generating mask using threshold 6.5
breizorro.breizorro - 2023-08-14 18:54:50,994 INFO - Generating noise map
breizorro.breizorro - 2023-08-14 18:54:58,019 INFO - Median noise value is 1.8788927263813093e-05
breizorro.breizorro - 2023-08-14 18:54:58,181 INFO - (Re)numbering islands
breizorro.breizorro - 2023-08-14 18:54:58,537 INFO - Number of islands: 372
breizorro.breizorro - 2023-08-14 18:54:58,537 INFO - Converting mask to binary
breizorro.breizorro - 2023-08-14 18:54:58,580 INFO - Filling closed regions
Traceback (most recent call last):
  File "/usr/local/bin/breizorro", line 5, in <module>
    main()
  File "/usr/local/lib/python3.6/dist-packages/breizorro/breizorro.py", line 355, in main
    shutil.copyfile(input_file, out_mask_fits)  # to provide a template
  File "/usr/lib/python3.6/shutil.py", line 121, in copyfile
    with open(dst, 'wb') as fdst:
OSError: [Errno 30] Read-only file system: '/stimela_mount/input/initial_image-MFS-image.mask.fits'
Traceback (most recent call last):
  File "/stimela_mount/code/run.py", line 39, in <module>
    subprocess.check_call(shlex.split(_runc))
  File "/usr/lib/python3.6/subprocess.py", line 311, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['breizorro', '--restored-image', '/stimela_mount/input/initial_image-MFS-image.fits', '--threshold', '6.5', '--boxsize', '50', '--number-islands', '--make-binary', '--fill-holes']' returned non-zero exit status 1.
cd /home/rramij/Work_Dir/A85_700MHz/GWB/GMRT_DI_pipe_run/Useful/selfcal/2run/.stimela_workdir-1692032083524032 && singularity run --workdir /home/rramij/Work_Dir/A85_700MHz/GWB/GMRT_DI_pipe_run/Useful/selfcal/2run/.stimela_workdir-1692032083524032 --containall returns error code 1

Please help me resolve the error.

[o-smirnov]

Is there a reason you're using Stimela classic and not stimela2? https://github.com/caracal-pipeline/stimela

[rramij]

I am shifting to stimela2 and familiarising myself with the syntax and notations. In the meantime, I was trying to add Breizorro cab to my already working stimela1 selfcal pipeline and test out the results.
I guess, I should re-script the pipeline to stimela2 and run to see if I get any errors.

[Athanaseus]

Sorry about this issue @rramij.
It should be fixed (via #779) in the latest release of the stimela-classic or >=v1.7.7.