The documentation for BF-ITK needs to be updated to include the new ITK plugin implementations:

online documentation should cover bf-itk-pipes create readme's for bf-itk-jace and -jni

The following wiki pages also still need to be updated:

• http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/MacTutorial
• http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/WinTutorial
• http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/LinTutorial
• http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/UsrTutorial

Migrated from OME #8203.

There's no reason this has to be ITK specific. We should create a general C++ SCIFIO API that pipes to a JVM, which can then be consumed by the ITK imageIO.

Reported on ome-users by Michael Meuli:

I've converted my .lif file with

./bfconvert /path/to/wt-dead-A.lif output_series_%s.ome.tiff

and it produces the expected files (20 multi-channel-z-stacks), which I can open with Fiji. 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. Whereas multi-channel-z-series.ome.tif works.

I guess the problem is the dimension order which seems not to be XYZCT as with multi-channel-z-series.ome.tif, but something like XYCZT.

It seems that the image spacing information is not saved when using SCIFIO to save these formats.
I have written a small reader and writer that use SCIFIO, for test purposes:
https://github.com/fbudin69500/scifio-spacing-test

When using the default PNG and TIFF writers, the spacing information is saved in the image.
Is this a known issue? I looked in the bioformat library and I had the impression that the spacing was not handled [1] [2].

[1] https://github.com/openmicroscopy/bioformats/blob/v5.0.0/docs/sphinx/formats/png-metadata.txt
[2] https://github.com/openmicroscopy/bioformats/blob/v5.0.0/docs/sphinx/formats/tiff-metadata.txt

Additionally, the spacing information does not seem to be passed from scifio-imageio to bioformat:
https://github.com/scifio/scifio-itk-bridge/blob/master/src/main/java/io/scif/itk/SCIFIOITKBridge.java#L538-L550

@thewtex @ctrueden
Do you think I am doing anything wrong or that this issue would be easy to address?

We have entered development cycle for ITKv5. @hjmjohnson is leading the charge, but he needs write permissions for this repo to make his life easier while transitioning the remote modules. Can write permission be granted, or ownership of this repository transferred to InsightSoftwareConsortium organization?

Reported by Michael Meuli:

Problem encoutered while reading image file : single-channel.ome.tif

itk::ExceptionObject (0x81520e0)
Location: "unknown"
File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO
/src/itkSCIFIOImageIO.cxx
Line: 180
Description: itk::ERROR: SCIFIOImageIO(0x8150fb0): SCIFIOImageIO
exited abnormally. Exception in thread "main"
java.lang.IllegalStateException: ImageReader.getSeries: Current file
should not be null; call setId(String) first
at loci.formats.FormatTools.assertId(FormatTools.java:724)
at loci.formats.ImageReader.getReader(ImageReader.java:200)
at loci.formats.ImageReader.getSeries(ImageReader.java:441)
at loci.formats.ReaderWrapper.getSeries(ReaderWrapper.java:343)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:116)
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)

There could be an issue where the reader can be constructed with a null id, and then its getSeries method checked. Should probably at least check if the current file is null before checking the series...

This CircleCI configuration is running a 1.0 configuration, which will be discontinued on August 31, 2018

Needed over 3 gigs of memory to convert one plane of a 1.3 GB ome.tiff dataset.

On the page : http://www.openmicroscopy.org/site/support/bio-formats5/users/itk/
Fetch_SCIFIO = ON

This should be :
Module_SCIFIO = ON

EDIT:

ITKIOSCIFIOTestDriver should be SCIFIOTestDriver on the same page

The current SCIFIOImageIO, as an ImageIOBase, can not properly supported mixed-size multi-series datasets. The itk::VectorImage is intended only for equally sized multi-series datasets.

The video framework should provide a more complete solution for multi-series datasets, which will require the construction of a SCIFIO video IO.

Cross-platform builds without timeouts, continuous deployment of Python packages.

I stumbled over the problem (romangrothausmann/ITK-CLIs@4fa8431) that an MHA created from a DM3 with SCIFIO was not readable by ITK again. It seems that is due to the very long/verbose header possibly containing some info that ITK's metaIO cannot cope with. The test DM3 can be found here:
https://github.com/romangrothausmann/ITK-CLIs/blob/4fa84310e05451aaf94322d0f93f554d21d905a8/tests/data/test.dm3

Update bundled JVM to a newer version that will bring security and performance improvements and work with the latest bioformats library.

@ctrueden any suggestions on what to use?

Object
SHA512=0f278b8a9be5364d001f4fcd93c65d8bbd2fc4ac3bce8101e9fbb19a2999a36ece09002d18bced064a619c7193679586e5f35f437895580a6a22398613fb8efc
not found at:

https://insightsoftwareconsortium.github.io/ITKTestingData/SHA512/0f278b8a9be5364d001f4fcd93c65d8bbd2fc4ac3bce8101e9fbb19a2999a36ece09002d18bced064a619c7193679586e5f35f437895580a6a22398613fb8efc ("HTTP response code said error")
https://data.kitware.com:443/api/v1/file/hashsum/SHA512/0f278b8a9be5364d001f4fcd93c65d8bbd2fc4ac3bce8101e9fbb19a2999a36ece09002d18bced064a619c7193679586e5f35f437895580a6a22398613fb8efc/download ("Timeout was reached")
https://itk.org/files/ExternalData/SHA512/0f278b8a9be5364d001f4fcd93c65d8bbd2fc4ac3bce8101e9fbb19a2999a36ece09002d18bced064a619c7193679586e5f35f437895580a6a22398613fb8efc ("HTTP response code said error")
https://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=0f278b8a9be5364d001f4fcd93c65d8bbd2fc4ac3bce8101e9fbb19a2999a36ece09002d18bced064a619c7193679586e5f35f437895580a6a22398613fb8efc&algorithm=SHA512 (wrong hash SHA512=639526ba1271b833beeb026311a3d40d2b50b8480ce8e938e87ea0dfc9c84e76867be09043f9b15fc5b21d003580c6169f1ba59b2202686b80258d8993ab7a09)

file( DOWNLOAD
    "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${jreTarballMD5}&name=${outputFile}&algorithm=MD5"
    "${outputFile}"
    EXPECTED_HASH MD5=${jreTarballMD5} SHOW_PROGRESS
    )

from Kedar:

I have shared a nrrd file with you on google docs. When I read it with the ITK-SCIFIO
reader it switches the bit ordering LittleEndian/BigEndian whereas if I read it in Fiji or
build ITK without SCIFIO it is read properly. To test this you can use the ITK reader
example and write the image out as a tiff while building with/without SCIFIO.

It seems that when initializating, even if the series for reading is restricted, we still initializate using all the series, which can cause OutOfMemoryErrors anyway. It would be nice if we could try to avoid this.

I got ITK-4.12.2 compiled with Module_SCIFIO = ON and BUILD_TESTING = ON. bin/SCIFIOTestDriver is there but if I try to execute it it fails with:

reader->GetUseStreaming(): 1
done checking streaming usage
ITK test driver caught an ITK exception:

itk::ExceptionObject (0x55fd2ddc0b50)
Location: "unknown" 
File: /opt/compilation/ITK_build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
Line: 180
Description: itk::ERROR: SCIFIOImageIO(0x55fd2ddb2970): SCIFIOImageIO exited abnormally. Exception in thread "main" java.lang.NoClassDefFoundError: io/scif/itk/SCIFIOITKBridge
Caused by: java.lang.ClassNotFoundException: io.scif.itk.SCIFIOITKBridge
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
Could not find the main class: io.scif.itk.SCIFIOITKBridge.  Program will exit.

After installation, there is /opt/itk-4.12.2/lib/jars/scifio-itk-bridge.jar but setting CLASSPATH=/opt/itk-4.12.2/lib/jars/ does not help nor ITK_AUTOLOAD_PATH. How should ITK-programs be told where to look for SCIFIOITKBridge?