Out of memory running nr_stitcher.py on windows 10

[zhusihan-python]

hello sir, im trying to find a tool to stitch microscope tiles into a whole slide image tiff file, when running nr_stitcher on my pc, i got this error:

Reading stitch settings from stitch_settings.txt
flat_000_000.jpg at position [0. 0. 0.], size = [2147483647 2147483647 2147483647]
flat_001_007.jpg at position [2796.    0.    0.], size = [2147483647 2147483647 2147483647]
flat_002_000.jpg at position [5592.    0.    0.], size = [2147483647 2147483647 2147483647]
flat_003_007.jpg at position [8388.    0.    0.], size = [2147483647 2147483647 2147483647]
flat_004_000.jpg at position [11184.     0.     0.], size = [2147483647 2147483647 2147483647]
flat_005_007.jpg at position [13980.     0.     0.], size = [2147483647 2147483647 2147483647]
Calculate displacement field 0 -> 1
blockmatchmemsave("flat_000_000.jpg", "flat_001_007.jpg", "2796", "2147483647", "30", "0", "2147483647", "30", "0", "2147483647", "30", "[-2796, 0, 0]", "stitched_0-1", "[60]", "2", "[1]", "2", "True")
Traceback (most recent call last):
  File "F:\projects\pi2\python_scripts\nr_stitcher.py", line 233, in <module>
    main()
  File "F:\projects\pi2\python_scripts\nr_stitcher.py", line 219, in main
    if calculate_displacement_fields(settings.sample_name, relations, settings.point_spacing, settings.coarse_block_radius, settings.coarse_binning, settings.fine_block_radius, settings.fine_binning, settings.normalize_in_blockmatch, settings.filter_threshold, settings.force_redo):
  File "F:\projects\pi2\python_scripts\base.py", line 578, in calculate_displacement_fields
    calculate_displacement_field(sample_name, scan1, scan2, point_spacing, coarse_block_radius, coarse_binning, fine_block_radius, fine_binning, normalize, filter_threshold)
  File "F:\projects\pi2\python_scripts\base.py", line 335, in calculate_displacement_field
    run_pi2(params, file_prefix)
  File "F:\projects\pi2\python_scripts\base.py", line 106, in run_pi2
    pi.submitjob(pi_script, "normal")
  File "F:\projects\pi2\python_scripts\pi2py2.py", line 591, in <lambda>
    func = lambda *args: self.run_command(cmd_name, args)
  File "F:\projects\pi2\python_scripts\pi2py2.py", line 741, in run_command
    self.run_script(cmd_line)
  File "F:\projects\pi2\python_scripts\pi2py2.py", line 697, in run_script
    self.raise_last_error()
  File "F:\projects\pi2\python_scripts\pi2py2.py", line 687, in raise_last_error
    raise RuntimeError(err)
RuntimeError: Out of memory.

Process finished with exit code 1

my environment windows10, Python 3.9.13, pi2_v4.3-win-no-opencl my config file: stitch_settings.txt

[arttumiettinen]

Hi,

Thanks for reporting the issue.

The problem is that pi2 does not support jpg files at the moment, and nrstitcher script does not seem to correctly report this. I will fix that after summer holidays. Meanwhile, a workaround is to convert the input files e.g. to .tiff.

A list of supported file formats is available at https://pi2-docs.readthedocs.io/en/latest/io.html

[arttumiettinen]

This issue is fixed in the experimental branch (commit 90aaee1ed96f85bdeb52f767d3bb9dd788d87371). Nrstitcher script now gives a meaningful error message if input image file type is not supported. Additionally, jpeg file format support has been added.