Re: Memory issues with bfconvert
Posted: Thu Feb 09, 2017 4:23 pm
Here is what I get when I try to use this version.
- Code: Select all
Command is time /hpcf/apps/bioformats/test/bioformats/tools/bfconvert /scratch_space/jmichael/LightMicroscopy/data/filename.czi filename.tiff
*** A new stable version is available. ***
*** Install the new version using: ***
*** 'upgradechecker -install' ***
/scratch_space/jmichael/LightMicroscopy/data/filename.czi
ZeissCZIReader initializing /scratch_space/jmichael/LightMicroscopy/data/filename.czi
Exception in thread "main" loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2947)
at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2919)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:565)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:367)
at loci.formats.tools.ImageConverter.main(ImageConverter.java:874)
2.11user 0.15system 0:01.86elapsed 121%CPU (0avgtext+0avgdata 817568maxresident)k
0inputs+760outputs (0major+23551minor)pagefaults 0swaps