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.LIF file doesn't load #596

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arjunrajlab opened this issue Nov 8, 2023 · 6 comments
Closed

.LIF file doesn't load #596

arjunrajlab opened this issue Nov 8, 2023 · 6 comments
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@manthey
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bug Something isn't working
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Alpha-Version

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@arjunrajlab
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This LIF file doesn't seem to parse properly:

https://www.dropbox.com/scl/fi/hfqxqw7qbmyqe5ve81nt4/1031_P_12.lif?rlkey=9jglpahomo6ds8es59hj4j3n8&dl=0

This file has two separate image objects in it, one is an RGB image, and one is 3 color Z stack. Nimbus seems to only recognize the channels. Is it only picking the first object in the LIF file? Or does it pick the largest one?
@arjunrajlab arjunrajlab added the bug Something isn't working label Nov 8, 2023
@arjunrajlab arjunrajlab added this to the Alpha-Version milestone Nov 8, 2023
@manthey
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manthey commented Nov 9, 2023

See girder/large_image#1365

@arjunrajlab
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OK, that worked if I don't transcode to TIFF, but if I do transcode, the following error appears:

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Failed in large image conversion
Traceback (most recent call last):
  File "/venv/lib/python3.11/site-packages/large_image_source_bioformats/__init__.py", line 607, in getTile
    tile = self._bioimage.read(
           ^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/bioformats/formatreader.py", line 840, in read
    index = self.rdr.getIndex(z,c,t)
            ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/javabridge/jutil.py", line 965, in method
    result = call(self.o, name, sig, *args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/javabridge/jutil.py", line 896, in call
    result = fn(*nice_args)
             ^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/javabridge/jutil.py", line 863, in fn
    raise JavaException(x)
javabridge.jutil.JavaException: Invalid Z index: 1/1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/venv/lib/python3.11/site-packages/large_image_tasks/tasks.py", line 136, in convert_image_job
    dest = create_tiff(
           ^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/celery/local.py", line 182, in __call__
    return self._get_current_object()(*a, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/girder_worker/task.py", line 153, in __call__
    results = super().__call__(*_t_args, **_t_kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/celery/app/task.py", line 411, in __call__
    return self.run(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/large_image_tasks/tasks.py", line 67, in create_tiff
    large_image_converter.convert(
  File "/venv/lib/python3.11/site-packages/large_image_converter/__init__.py", line 927, in convert
    _convert_large_image(inputPath, outputPath, tempPath, lidata, **kwargs)
  File "/venv/lib/python3.11/site-packages/large_image_converter/__init__.py", line 563, in _convert_large_image
    _drain_pool(pool, tasks)
  File "/venv/lib/python3.11/site-packages/large_image_converter/__init__.py", line 390, in _drain_pool
    tasks[0][-1].result(0.1)
  File "/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/large_image_converter/__init__.py", line 527, in _convert_large_image_frame
    _drain_pool(pool, tasks)
  File "/venv/lib/python3.11/site-packages/large_image_converter/__init__.py", line 390, in _drain_pool
    tasks[0][-1].result(0.1)
  File "/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/_base.py", line 456, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/large_image_converter/__init__.py", line 479, in _convert_large_image_tile
    data = tile['tile']
           ~~~~^^^^^^^^
  File "/src/large_image/large_image/tilesource/tiledict.py", line 174, in __getitem__
    tileData = self._retileTile()
               ^^^^^^^^^^^^^^^^^^
  File "/src/large_image/large_image/tilesource/tiledict.py", line 127, in _retileTile
    tileData = self.source.getTile(
               ^^^^^^^^^^^^^^^^^^^^
  File "/src/large_image/large_image/cache_util/cache.py", line 98, in wrapper
    v = func(self, *args, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/large_image_source_multi/__init__.py", line 1060, in getTile
    tile = self._addSourceToTile(tile, sourceEntry, corners, scale)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/large_image_source_multi/__init__.py", line 1005, in _addSourceToTile
    sourceTile, _ = ts.getRegion(
                    ^^^^^^^^^^^^^
  File "/src/large_image/large_image/tilesource/base.py", line 2128, in getRegion
    subimage, _ = _imageToNumpy(tile['tile'])
                                ~~~~^^^^^^^^
  File "/src/large_image/large_image/tilesource/tiledict.py", line 166, in __getitem__
    tileData = self.source.getTile(
               ^^^^^^^^^^^^^^^^^^^^
  File "/src/large_image/large_image/cache_util/cache.py", line 98, in wrapper
    v = func(self, *args, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/large_image_source_bioformats/__init__.py", line 621, in getTile
    raise TileSourceError('Failed to get Bioformat region (%s, %r).' % (es, (
large_image.exceptions.TileSourceError: Failed to get Bioformat region (java.lang.IllegalArgumentException: Invalid Z index: 1/1, (0, 1, 0, {'series': [0], 'sizeX': 1600, 'sizeY': 1600}, 1600, 1600, 0, 0, 1600, 1600)).
Failed in large image conversion (Failed to get Bioformat region (java.lang.IllegalArgumentException: Invalid Z index: 1/1, (0, 1, 0, {'series': [0], 'sizeX': 1600, 'sizeY': 1600}, 1600, 1600, 0, 0, 1600, 1600)).)
Processing frame 68/126
Processing frame 69/126

@manthey
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manthey commented Nov 9, 2023

See girder/large_image#1367, and try again.

@arjunrajlab
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arjunrajlab commented Nov 9, 2023 •
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Okay, that worked… but… now I am getting again the very slow performance if I transcode to optimized TIFF. If I just leave the file alone, the performance is fine. I suspect the same front end issue may be at play @bruyeret.

@arjunrajlab
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arjunrajlab commented Nov 10, 2023 •
edited
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@manthey OK, here's another LIF file that we'd like to read:

https://www.dropbox.com/scl/fo/0j7tv3rewd4zew7so4tdr/h?rlkey=aym7dzlfo0n3wwk9ytoxzpxic&dl=0

Also, here's a few more reasonably sized LIF files:
https://www.dropbox.com/sh/cg02548zzkpt281/AABMT4y0PHuYU4t6x0pwaS6Xa?dl=0

https://www.dropbox.com/scl/fi/dr03e7upljov1qe5fq7jx/MixedProjectArjunRaj.lif?rlkey=4572jk63q1c6kuzimfuu7y5cr&dl=0

@arjunrajlab
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LIF files now load, as long as they are not transcoded. Transcoding memory usage issue now put here:

#595

@arjunrajlab arjunrajlab moved this to Done in Alpha Release May 18, 2024
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