[ome-users] convert .lif file with bfconvert

[Michael Meuli]

Hi Mark

I can import the bfconvert output into Fiji with no problem.
(If I do "./bfconvert /path/to/wt-dead-A.lif /path/to/output.ome.tiff" or
"./bfconvert /path/to/wt-dead-A.lif /path/to/output_series_%s.ome.tiff"
I can open the file(s) with Fiji.)
If I open the .lif file with Fiji and export one series to ome.tiff I
can read the output with ./SCIFIOTestDriver itkSCIFIOImageIOTest ...
whereas I'm not able to read the output of bfconvert.

Thanks a lot and best regards
Michael



On 30 May 2014 16:18, Mark Hiner <hinerm at gmail.com> wrote:
> Hi Michael,
>
>> "./SCIFIOTestDriver itkSCIFIOImageIOTest/path/to/output_series_0.ome.tiff
>> /path/to/scifio-test.ome.tiff"
>
> Just a reminder, since you're writing ome.tiff you should have a "-w" flag
> at the end of this command. It sounds like you were using -w, just wanted to
> clarify for anyone else reading this thread.
>
>> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>
>  There are two problems here. First, it seems that in SCIFIOImageIO the use
> of Bio-Formats is overly aggressive in pulling in all the series, thus the
> OutOfMemoryError. If you physically isolate a single series (e.g. delete or
> move to another directory series 1-19) the application will run, but we get
> another exception (at least on my end):
>
> ./SCIFIOTestDriver itkSCIFIOImageIOTest output_series_0.ome.tiff
> scifio-test.ome.tiff -w
>
> reader->GetUseStreaming(): 1
> done checking streaming usage
> ITK test driver caught an ITK exception:
>
> itk::ExceptionObject (0x7ff8838b6ae8)
> Location: "unknown"
> File:
> /Users/mhiner/loci/ITK/build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
> Line: 180
> Description: itk::ERROR: SCIFIOImageIO(0x7ff8838b4f00): SCIFIOImageIO exited
> abnormally. Creating new reader for output_series_0.ome.tiff
>
> log4j:WARN No appenders could be found for logger
> (loci.common.services.ServiceFactory).
> log4j:WARN Please initialize the log4j system properly.
> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> more info.
> Exception in thread "main" loci.formats.FormatException: Unmatched UUID:
> urn:uuid:b72fe97b-02c9-4029-a876-ca2bae46cbac
>     at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:456)
>
>     at loci.formats.FormatReader.setId(FormatReader.java:1244)
>     at loci.formats.ImageReader.setId(ImageReader.java:727)
>     at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
>     at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
>     at
> loci.scifio.itk.SCIFIOITKBridge.createReader(SCIFIOITKBridge.java:617)
>     at
> loci.scifio.itk.SCIFIOITKBridge.readImageInfo(SCIFIOITKBridge.java:268)
>     at
> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:133)
>
>     at
> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)
>     at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)
>     at
> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:163)
>     at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:688)
>
> I also get this exception when importing with Bio-Formats into Fiji.
>
> As a side note, there are flags for itkSCIFIOImageIOTest that, in theory,
> should help the out of memory side:
>
> "-s <n1, n2>" should limit the series read.
> "-v <n>" should divide the data into divisions, which might mitigate the
> risk of OutOfMemoryErrors.
>
> But neither of these will help the UUID exception. Also, I still got
> OutOfMemoryErrors with these, so it was still trying to initialize using all
> the series. So I created a new issue in the SCIFIO-ImageIO tracker.
>
> Anyway, try importing the bfconvert output into Fiji with Bio-Formats and
> let me know if you don't get the UUID exception. If you do, then I think the
> bfconvert output is just invalid..
>
> Regards,
> Mark
>
>
> On Thu, May 29, 2014 at 12:17 PM, Michael Meuli <michael.meuli at gmail.com>
> wrote:
>>
>> Hi Mark,
>>
>> Thanks for the quick response. I can see I was using
>> itkSCIFIOImageIOTest the wrong way and it doesn't make sense to use it
>> like this.
>> If I use the -w flag I get an error in all cases but at the moment I
>> don't care as my aim now is to read ome.tiff files with itk.
>> I've written a small program (mainly by copy paste from examples /
>> https://github.com/michaelmeuli/bactelize) which so far reads the
>> multi-channel-z-series.ome.tif file, does a maximum intensity
>> projection of one channel and writes a 2D image and it seems to work
>> with the multi-channel-z-series.ome.tif but not with the files
>> converted with bfconvert.
>>
>> Expressed with itkSCIFIOImageIOTest:
>> "./SCIFIOTestDriver itkSCIFIOImageIOTest
>> /path/to/multi-channel-z-series.ome.tif /path/to/scifio-test.ome.tiff"
>> doesn't give an error and seems to produce a tiff file of the first
>> z-plane, but
>> "./SCIFIOTestDriver itkSCIFIOImageIOTest
>> /path/to/output_series_0.ome.tiff /path/to/scifio-test.ome.tiff" gives
>> an error:
>>
>> reader->GetUseStreaming(): 1
>> done checking streaming usage
>> ITK test driver caught an ITK exception:
>>
>> itk::ExceptionObject (0x2f87680)
>> Location: "unknown"
>> File:
>> /home/michael/Colocalization/ITK-Release-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
>> Line: 180
>> Description: itk::ERROR: SCIFIOImageIO(0x2f78970): SCIFIOImageIO
>> exited abnormally. Creating new reader for
>>
>> /home/michael/bioimage/ome/data/wt-dead-A-ome-tiff/output_series_0.ome.tiff
>> log4j:WARN No appenders could be found for logger
>> (loci.common.services.ServiceFactory).
>> log4j:WARN Please initialize the log4j system properly.
>> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
>> for more info.
>> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>> at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39)
>> at java.nio.ByteBuffer.allocate(ByteBuffer.java:312)
>> at
>> loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:132)
>> at
>> loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
>> at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
>> at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
>> at
>> loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
>> at loci.formats.tiff.TiffParser.getIFDOffsets(TiffParser.java:308)
>> at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:226)
>> at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:426)
>> at loci.formats.FormatReader.setId(FormatReader.java:1244)
>> at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:704)
>> at loci.formats.FormatReader.setId(FormatReader.java:1244)
>> at loci.formats.ImageReader.setId(ImageReader.java:727)
>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
>> at loci.scifio.itk.SCIFIOITKBridge.createReader(SCIFIOITKBridge.java:622)
>> at loci.scifio.itk.SCIFIOITKBridge.readImageInfo(SCIFIOITKBridge.java:266)
>> at
>> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:131)
>> at
>> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)
>> at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)
>> at
>> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:161)
>> at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:693)
>>
>> Best regards
>> Michael Meuli
>>
>>
>>
>> On 29 May 2014 17:41, Mark Hiner <hiner at wisc.edu> wrote:
>> > Hi Michael,
>> >
>> >
>> >> The problem is that ./SCIFIOTestDriver itkSCIFIOImageIOTest
>> >> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
>> >> (and my little program) throws an exception.
>> > ...
>> >
>> >> How do I use bfconvert the correct way for my case?
>> >
>> > You used bfconvert correctly to convert your dataset. Just so it's
>> > clear, if
>> > your goal was to produce an OME-TIFF:
>> >
>> >> /SCIFIOTestDriver itkSCIFIOImageIOTest
>> >> /path/to/output_series_0.ome.tiff
>> >> /path/to/scifiotest.ome.tiff
>> >
>> > would be unnecessary, as you already have the OME-TIFF output from
>> > bfconvert. The itkSCIFIOImageIOTest is an analogous tool to bfconvert
>> > written in the Bio-Formats C++ framework. (although comparing the
>> > outputs of
>> > the itkSCIFIOImageIOTest conversion would be a good way to check for
>> > errors
>> > in the conversion process)
>> >
>> > That said, I believe your conversion failed because the output was
>> > picked up
>> > by the ITK TIFF ImageIO, which I believe only supports 3D data. The
>> > itkSCIFIOImageIOTest utility does basically no automation - you have to
>> > tell
>> > it exactly how to run, and because the SCIFIOImageIO is an external
>> > module
>> > it is not prioritized by the ITK format detection framework over
>> > internal
>> > modules (I'm not sure it's part of the automatic detection framework at
>> > all,
>> > actually). So you need to force the use of the SCIFIOImageIO for
>> > writing.
>> >
>> > If you run:
>> >
>> >  /SCIFIOTestDriver itkSCIFIOImageIOTest
>> >
>> > with no arguments from the command line, it will print the usage +
>> > available
>> > flags. The flag you wanted here is "-w"  to write with the SCIFIOImageIO
>> > (which will use Bio-Formats, and thus the OME-TIFF writer).
>> >
>> > So the final syntax is:
>> >
>> > /SCIFIOTestDriver itkSCIFIOImageIOTest /path/to/output_series_0.ome.tiff
>> > /path/to/scifiotest.ome.tiff -w
>> >
>> > which worked for me locally.
>> >
>> > Let me know if you have any other questions or issues!
>> >
>> > Regards,
>> > Mark
>> >
>> > On Thu, May 29, 2014 at 4:40 AM, Michael Meuli <michael.meuli at gmail.com>
>> > wrote:
>> >>
>> >> ./SCIFIOTestDriver itkSCIFIOImageIOTest
>> >> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
>> >
>> >
>> >
>
>