[SCIFIO] [ome-users] converting lif files to ome-tiff

[Michael Meuli]

Hi Mark

I've converted my files with Bio-Formats 5.0.5 and with the master ITK
branch I was also able to fully convert my images as multi-series
image, using the command:
SCIFIOTestDriver ko-A.ome.tiff out.ome.tif -w -a -d 5

Hower I think there is still a related problem. If I modify the
RunTest() function in itkSCIFIOImageIOTest.cxx just a little bit to
get hold of the image for processing it, I get the following error
which appears, like the previous one, depending on the file, after a
certain number of series were processed with the following error:

terminate called after throwing an instance of
'itk::InvalidRequestedRegionError'
  what():  /home/michael/bioimage/itk/itk-master/InsightToolkit/Modules/Core/Common/src/itkDataObject.cxx:393:
Requested region is (at least partially) outside the largest possible region.
Aborted (core dumped)

In case of dead-A.ome.tiff after processing the first two series.

Please fnd attached the runnable code.
The files can still be found here:
https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea

Googling for the poblem I found the following about the Update() fuction:
http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#a4041fb21e9105500eee311e265691bd5
I don't really understand it but I've tried
UpdateLargestPossibleRegion() instead of Update() but the complier
didn't eat it.

Many thanks and best regards
Michael


On 10 September 2014 22:11, Mark Hiner <hiner at wisc.edu> wrote:
> Hi Michael,
>
> I opened a pull request to get the latest SCIFIO-ITK imageIO incorporated
> into the master ITK branch.
>
> This fixes the metadata bug suspected by Roger (the dimensions of the first
> series were always being used, which would crash on encountering a dataset
> with smaller dimensions). It also upgrades the ImageIO to use Bio-Formats
> 5.0.4, and has some other minor fixes and improvements.
>
> With these updates I was able to fully convert your image as a multi-series
> image, using the command:
> SCIFIOTestDriver ko-A.ome.tiff out.ome.tif -w -a -d 5
>
> Thanks for the report, it was very helpful. Please let us know if you run
> into any more problems.
>
> Regards,
> Mark
>
> On Wed, Aug 20, 2014 at 12:05 PM, Mark Hiner <hinerm at gmail.com> wrote:
>>
>> Hi all,
>>
>> >While I'm not entirely sure of the separation of responsibilities between
>> > ITK, SCIFIO and Bio-Formats for this
>> >particular task
>>
>> The readme for the SCIFIO-ITK ImageIO
>> (https://github.com/scifio/scifio-imageio) was out of date. It should now
>> correctly instruct users to e-mail scifio at scif.io (copied) for ITK imageIO
>> troubleshooting.
>>
>> > I found this only occurs when you enable "-w" to use SCIFIO for output.
>>
>> Note that without the -w flag, the default ITK TIFF writer will be used,
>> which I thought was limited to 3 dimensions (or at least it was at one
>> time). If you want to write an .ome.tiff it has to be written with
>> Bio-Formats, anyway.
>>
>> > Looks like it's trying to read z plane 60 when there are only 60 planes
>>
>> I'm assuming the # of planes to read isn't being updated for each series..
>> I'll look into it when I get a chance.
>>
>> Thanks for the report,
>> Mark
>>
>>
>> On Wed, Aug 20, 2014 at 9:53 AM, Roger Leigh <rleigh at dundee.ac.uk> wrote:
>>>
>>> On 19/08/14 19:52, Michael Meuli wrote:
>>>
>>> Dear Michael,
>>>
>>>
>>>> I have some problems converting my .lif files to ome-tiff.
>>>> I have converted my .lif files originating from a "CLSM Leica SP 8"
>>>> with bfconvert of Bio-Formats 5.0.3.
>>>> Trying to make it reproducible I took the file "ko-A.ome.tiff" which
>>>> can be found here:
>>>> "https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea"
>>>>    in the ome-tiff-files folder.
>>>
>>>
>>> Thanks.  I've been able to reproduce the validation problems.  I have
>>> opened a ticket for this and CC'd you on it; please see
>>> https://trac.openmicroscopy.org.uk/ome/ticket/12532
>>>
>>> Note however that the above validation error is harmless; it does not
>>> affect bioformats' correct reading of the OME-TIFF and I was able to
>>> read all planes of every series without trouble, and also convert the
>>> file to a new OME-TIFF which strips out the MetadataOnly elements.  I
>>> don't think this is in any way related to your other problem, below.
>>>
>>>
>>>> Below you can find the output of bfconvert, xmlvalid and
>>>> SCIFIOTestDriver itkSCIFIOImageIOTest with the -a flag.
>>>> The output of tiffcomment you can find as attachment.
>>>> itkSCIFIOImageIOTest in this example crashes trying to read the third
>>>> series.
>>>
>>>
>>> I built ITK with itkscifio to test this.  I found this only occurs when
>>> you enable "-w" to use SCIFIO for output.
>>>
>>> While I'm not entirely sure of the separation of responsibilities
>>> between ITK, SCIFIO and Bio-Formats for this particular task, I don't
>>> think the problem is in Bio-Formats, but in SCIFIO setting the wrong
>>> plane index when reading the image data, as shown by your stacktrace.
>>> Looks like it's trying to read z plane 60 when there are only 60 planes
>>> (0-59), assuming it's series 2; the others all have too different z
>>> sizes.  I would suggest reporting this to the SCIFIO developers at
>>> https://github.com/scifio/scifio
>>>
>>>
>>> Regards,
>>> Roger Leigh
>>>
>>> --
>>> Dr Roger Leigh -- Open Microscopy Environment
>>> Wellcome Trust Centre for Gene Regulation and Expression,
>>> College of Life Sciences, University of Dundee, Dow Street,
>>> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
>
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cmake_minimum_required(VERSION 2.8)
 
project(bactelize)
 
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

if(NOT SCIFIO_LOADED)
  message(FATAL_ERROR "SCIFIO module is required but not available.")
endif() 

add_executable(bactelize MACOSX_BUNDLE main.cxx)
 
if( "${ITK_VERSION_MAJOR}" LESS 4 )
  target_link_libraries(bactelize ITKReview ${ITK_LIBRARIES})
else( "${ITK_VERSION_MAJOR}" LESS 4 )
  target_link_libraries(bactelize ${ITK_LIBRARIES})
endif( "${ITK_VERSION_MAJOR}" LESS 4 )
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