index out of range in vsi2tif and bftools

[mssher07]

Hello. I'm deep in the weeds trying to extract .vsi to .tif. The .vsi images are ~12-15 ROIs acquired on a VS200 olympus that cover the majority of a slide; but each ROI (at full res) is about 15k x 15k pixels. I need to do image registration for multi-round microscopy, so I just want to extract the highest resolution image in each ROI; but, would be fine if all of them are extracted and I can parse through to grab the ones I want.

Got vsi2tif installed along with a java sdk, here's my call in a jupyterlab cell:

path_to_vsi='H:/Folder_20241210/Image.vsi'
path_to_tif='H:/Folder_20241210/Image.tif'

!vsi2tif -i H:/Folder_20241210/Image.vsi -o H:/Folder_20241210/Image.tif -b [my_path]/bftools/bfconvert -v 0

Error:

INFO:root:Performing single conversion...
ERROR:root:Command failed with error: Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 16 out of bounds for length 16
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302)
	at java.base/java.util.Objects.checkIndex(Objects.java:365)
	at java.base/java.util.ArrayList.get(ArrayList.java:428)
	at loci.formats.in.CellSensReader.parseETSFile(CellSensReader.java:1105)
	at loci.formats.in.CellSensReader.initFile(CellSensReader.java:668)
	at loci.formats.FormatReader.setId(FormatReader.java:1397)
	at loci.formats.ImageReader.setId(ImageReader.java:839)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:385)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)

ERROR:root:Failed to convert BigTIFF to tiled, pyramidal TIFF. Skipping image: H:/Folder_20241210/Image.vsi
ERROR:root:Input file not found at: C:\Users\MSS\AppData\Local\Temp\tmptqgu3_ia\temporary.btf
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\python\envs\vsi_to_tif\Scripts\vsi2tif.exe\__main__.py", line 7, in <module>
  File "C:\python\envs\vsi_to_tif\Lib\site-packages\vsi2tif\vsi2tif.py", line 68, in main
    cellsens2tif_single(
  File "C:\python\envs\vsi_to_tif\Lib\site-packages\vsi2tif\src\benchmark.py", line 9, in wrapper
    result = func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
  File "C:\python\envs\vsi_to_tif\Lib\site-packages\vsi2tif\src\process.py", line 52, in cellsens2tif_single
    cellsens2tif(input_path, output_path, bfconvert, compression, tz, plane, quality, max_mem, verbose)
  File "C:\python\envs\vsi_to_tif\Lib\site-packages\vsi2tif\src\convert.py", line 78, in cellsens2tif
    raise e
  File "C:\python\envs\vsi_to_tif\Lib\site-packages\vsi2tif\src\convert.py", line 74, in cellsens2tif
    raw2tif(bigtiff_path, output_path, compression, quality, verbose)
  File "C:\python\envs\vsi_to_tif\Lib\site-packages\vsi2tif\src\convert.py", line 35, in raw2tif
    raise FileNotFoundError(f"Input file not found at: {input_path}")
FileNotFoundError: Input file not found at: C:\Users\MSS\AppData\Local\Temp\tmptqgu3_ia\temporary.btf

I figured I'd try bftools directly, very similar error. With no arguments flags, just the i/o:

CellSensReader initializing H:/Folder_20241210/Image.vsi
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 16 out of bounds for length 16
        at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100)
        at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106)
        at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302)
        at java.base/java.util.Objects.checkIndex(Objects.java:365)
        at java.base/java.util.ArrayList.get(ArrayList.java:428)
        at loci.formats.in.CellSensReader.parseETSFile(CellSensReader.java:1105)
        at loci.formats.in.CellSensReader.initFile(CellSensReader.java:668)
        at loci.formats.FormatReader.setId(FormatReader.java:1397)
        at loci.formats.ImageReader.setId(ImageReader.java:839)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:385)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)

Suggestions?

[andreped]

Hello, @mssher07 :]

This seems to be an issue in bfconvert. Thus, it should be resolved in the bioformats repo. I would open a ticket here instead. Then you can refer to this issue there, such that when it gets resolved, we could potentially add this fix to vsi2tif as well.