[ome-users] bioformats and ITK

Joe Ping-Lin Hsiao phsiao at cs.unc.edu
Thu May 16 22:30:10 BST 2013 

Mark,

Yes, I was using the command "ITKIOSCIFIOTestDriver itkSCIFIOImageIOTest
inputfile outputfile".

I am on Windows 7. The two jars (loci_tools.jar and
scifio-itk-bridge-1.0.0.jar) are in ITK/lib/jars.

I manually added the path to classpath, and my classpath is now:
CLASSPATH=.;C:\Program Files
(x86)\Java\jre6\lib\ext\QTJava.zip;D:\Joe\dev\ITK\lib\jars

But I still have no luck.

After running the command, I first get a dialog of
"Could not find the main class: loci.scifio.itk.SCIFIOITKBridge. Program
will exit."
Please see attached image.

And there are also error messages in the console:

D:\Joe\dev\ITK\bin\Release>ITKIOSCIFIOTestDriver itkSCIFIOImageIOTest
C:\Users\phsiao\Desktop\itk-scifio-build\Release\
chZT.lsm C:\Users\phsiao\Desktop\itk-scifio-build\Release\abc.tif
reader->GetUseStreaming(): 1
done checking streaming usage
itk::ExceptionObject (0000000000A4EF10)
Location: "unknown"
File: .\itkSCIFIOImageIO.cxx
Line: 172
Description: itk::ERROR: SCIFIOImageIO(0000000002A5C080): SCIFIOImageIO
exited abnormally. java.lang.NoClassDefFoundErr
r: loci/scifio/itk/SCIFIOITKBridge
Caused by: java.lang.ClassNotFoundException: loci.scifio.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)
Exception in thread "main"




On Thu, May 16, 2013 at 4:46 PM, Mark Hiner <hiner at wisc.edu> wrote:

> Hi Joe,
>
>  Hmm.. well that is the correct package specification. What was the exact
> command you used? I'm assuming it was something like
>
> "ITKIOSCIFIOTestDriver itkSCIFIOImageIOTest inputfile outputfile"
>
> ?
>
> Anyway it sounds like the scifio-itk-bridge jar isn't on your classpath. I
> just tested a clean build off ITK.git master (commit
> 2e056e0cee1271d3080a9bfc4f7353c1d9165ef9) and it worked for me... but
> that's on OSX.
>
> What's in your build/lib/jars directory? It should have 2 things:
> loci_tools.jar
> scifio-itk-bridge-1.0.0.jar
>
> It's possible that they aren't being added to the classpath correctly
> though, if on Windows there's another directory level (e.g. is it
> build/Release/lib/jars ?). So if they are in a different directory, let me
> know.
>
> If the jars are there, try manually adding them to your classpath for now
> and let me know how that goes. If they're not then it's a problem with the
> download script.
>
> You can download the jars manually from:
>
> http://cvs.openmicroscopy.org.uk/snapshots/bioformats/4.4.5/loci_tools.jar
>
> http://jenkins.imagej.net/view/SCIFIO/job/SCIFIOITKBridge/lastSuccessfulBuild/artifact/target/scifio-itk-bridge-1.0.0.jar
>
> That's all I can think of at the moment...
>
> - Mark
>
>
> On Thu, May 16, 2013 at 1:02 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:
>
>> Hi Mark,
>>
>> Glad to see SCIFIO is now becoming ITK's remote module. Thanks for your
>> continuous working.
>> I did a clean git clone of the latest ITK, and configure it with
>>
>>    Fetch_SCIFIO
>>    BUILD_TESTING
>>
>> set to ON. Then I run ITKIOSCIFIOTestDriver.exe on an image file, but I
>> got the error message
>>
>> "Could not find the main class: loci.scifio.itk.SCIFIOITKBridge. Program
>> will exit."
>>
>> Do I miss setting some path, or it still requires Bio-Formats?
>>
>> Thanks,
>> Joe
>>
>>
>> On Fri, Apr 26, 2013 at 2:43 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>
>>> Hi again Joe,
>>>
>>>  I noticed a couple things that may help you: in the
>>> itkVectorImageSCIFIOImageIOTest you sent me (and in all the test classes I
>>> mentioned in my last e-mail) the PixelType and Dimension variables must be
>>> set carefully.
>>>
>>>  For example, with the code in the state you sent me, PixelType is an
>>> unsigned short (which is 16 bits) and the dimension is 3.
>>>
>>>  These settings would be incorrect for the 2chZT.lsm sample data, as it
>>> has an 8 bit unsigned pixel type (so PixelType should be defined as
>>> unsigned char). Also if you're using the SCIFIOImageIO you can typically
>>> set dimensions to 5.
>>>
>>>  I don't know the specifications of your .oif dataset, but the PixelType
>>> and dimensions may need to be adjusted for it.
>>>
>>>   Sorry if you already knew this and were updating these values!
>>>
>>>   Anyway, I've been working on improving the stability of the
>>> SCIFIOImageIO plugin. Using the itkSCIFIOImageIOTest I mentioned
>>> previously, I confirmed that I was able to read and write the 2chsZT.lsm
>>> file and the .oif test images I have access to.
>>>
>>>   These changes aren't in an ITK patch set yet because they include
>>> changes to both the c++ and java code, which will may require some
>>> restructuring of SCIFIOImageIO.
>>>
>>> However, if you're eager to test these changes, you could build off my
>>> development branches:
>>> 1. Clone my ITK repo. <https://github.com/hinerm/ITK> The default
>>> branch is what you want here.
>>> 2. Build ITK as normal (with tests enabled)
>>> 3. Clone my Bio-Formats repo <https://github.com/hinerm/bioformats>.
>>> 4. Check out the itk-bridge-fixes branch in Bio-Formats
>>> 5. From the top level of Bio-Formats, run "ant tools"
>>> 6. Copy the loci_tools.jar from ${bio-formats}/artifacts to
>>> ${ITK_build}/lib/jars/
>>>    (this will overwrite the loci_tools.jar that was downloaded
>>> automatically when ITK built)
>>>
>>>  At this point you can link in the ImageToVTKFilter you were using or
>>> run the SCIFIO ImageIO test programs included in ITK.
>>>
>>>  Whether you build these manually or not, I'll try to get a new official
>>> patch set released soon.
>>>
>>>  Let me know if you run into any problems.
>>>
>>> Thanks,
>>> Mark
>>>
>>>
>>>
>>> On Thu, Apr 25, 2013 at 4:12 PM, Mark Hiner <hinerm at gmail.com> wrote:
>>>
>>>> Hi Joe,
>>>>
>>>>
>>>> Here are my steps to compile the program, in case I missed something:
>>>>> 1. Copy the git commend from the 'Patch set 3' review page, and paste
>>>>> it under the master ITK source, which downloaded a bunch of files and
>>>>> switched me to the branch 'SCIFIOImageIO'.
>>>>> 2. Compile the new ITK source in CMake, with Module_ITKVtkGlue,
>>>>> ITK_USE_REVIEW, and BUILD_SHARED_LIBS checked.
>>>>> 3. Link the program with the ITK with SCIFIOImageIO.
>>>>>
>>>>
>>>> This looks good. Note that a Patch set 4 is now out, and I'm working on
>>>> Patch 5. I'm hoping to include any necessary fixes for your issues in patch
>>>> 5.
>>>>
>>>> So, to clarify here - you're end goal is to convert your .oif dataset
>>>> to .ome.tiff? Is that right? Are you specifically wanting to extract a
>>>> subset of the image or anything? If you're just trying to do a simple
>>>> conversion it may be better to use the tests that are part of the ITK
>>>> SCIFIOImageIO module. You can take a look at them at:
>>>> $ITK/Modules/IO/SCIFIO/test
>>>>
>>>> To build them, just turn the BUILD_TESTING flag on when configuring
>>>> cmake. The ITKIOSCIFIOTestDriver is built to $build/bin
>>>>
>>>> I've been using the itkSCIFIOImageIOTest to test image conversion, for
>>>> example.
>>>>
>>>> The hanging happens after the line printing "post-update".
>>>>>
>>>>
>>>> Looking at the script that suggests it read your dataset successfully
>>>> but failed to write.
>>>>
>>>> Using the ImageIOTest mentioned above I tried converting the 2chsZT.lsm
>>>> to an .ome.tiff. It got through half the planes and then crashed (which
>>>> sounds like an improvement over your report, so I'm taking that as a small
>>>> victory).
>>>>
>>>> There are some oddities in the ITK <-> Bio-Formats axis conversion.. it
>>>> looks like only 1 of the 2 channels was detected for some reason. So I'll
>>>> fix that in the next patch set.
>>>>
>>>> I got similar results with an .oif file locally.
>>>>
>>>> So I apologize, as I don't feel I've helped you much yet. I just wanted
>>>> you to know that I'm still looking at these issues. Once I'm to the point
>>>> that I can convert that 2chsZT.lsm and local .oif files I'll try to
>>>> finalize another patch and see if that fixes things for you.
>>>>
>>>> Thanks,
>>>> Mark
>>>>
>>>>
>>>> On Wed, Apr 24, 2013 at 2:26 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:
>>>>
>>>>> Hi Mark,
>>>>>
>>>>>     Thanks for the explanation. I have tried switching to
>>>>> SCIFIOImageIO in the cpp code, but unfortunately the program still hangs
>>>>> during writing files out (with a .oif input). I have attached the source
>>>>> code. What I did was just replacing itk::BioFormatsImageIO with
>>>>> itk::SCIFIOImageIO and a change of the included header file.
>>>>>
>>>>> Here are my steps to compile the program, in case I missed something:
>>>>> 1. Copy the git commend from the 'Patch set 3' review page, and paste
>>>>> it under the master ITK source, which downloaded a bunch of files and
>>>>> switched me to the branch 'SCIFIOImageIO'.
>>>>> 2. Compile the new ITK source in CMake, with Module_ITKVtkGlue,
>>>>> ITK_USE_REVIEW, and BUILD_SHARED_LIBS checked.
>>>>> 3. Link the program with the ITK with SCIFIOImageIO.
>>>>>
>>>>> The hanging happens after the line printing "post-update".
>>>>> By the way, I am using VS 2008 sp1 on Windows 7 64-bit.
>>>>>
>>>>> I also tested the latest bf-itk-pipe code. The hanging happens after
>>>>> the line printing "pre-update" in this case.
>>>>> Note that I had to link bf-itk-pipe against the SCIFIOImageIO ITK
>>>>> otherwise there'd be a link error if linked against the master ITK.
>>>>>
>>>>> Thanks,
>>>>> Joe
>>>>>
>>>>>
>>>>> On Tue, Apr 23, 2013 at 4:11 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>>>>
>>>>>> Hi Joe,
>>>>>>
>>>>>>  First of all, in case you are using the bf-itk-pipes plugin, you
>>>>>> should know that we currently have a patch under review<http://review.source.kitware.com/9450>by the ITK developers. This patch adds a true Bio-Formats (SCIFIO) ITK
>>>>>> ImageIO, which will be available by default in ITK.
>>>>>>
>>>>>>  This means that the old bf-itk-pipes plugin won't be supported, as
>>>>>> all development efforts are going towards the SCIFIOImageIO.
>>>>>>
>>>>>>  As this code is still under review, there are issues that I'm
>>>>>> currently working on resolving.
>>>>>>
>>>>>>  So first I'd ask that you check out the latest patch code using the
>>>>>> links on that review site and rework the splitting code to use
>>>>>> SCIFIOImageIO<http://review.source.kitware.com/#/c/9450/3/Modules/IO/SCIFIO/include/itkSCIFIOImageIO.h>instead of the BioFormatsImageIO. You can also look at the test
>>>>>> directory<http://review.source.kitware.com/#/c/9450/3/Modules/IO/SCIFIO/test/itkSCIFIOImageIOTest.cxx>for more sample code.
>>>>>>
>>>>>>  If you have any trouble updating your code, please let me know and
>>>>>> I'll be happy to help.
>>>>>>
>>>>>>  As to your actual issue of the .oif image hanging, I actually just
>>>>>> fixed a bug in the last week regarding hanging when plane size is
>>>>>> miscalculated by the plugin, so with any luck that was your issue. :)
>>>>>>
>>>>>>  If the latest SCIFIOImageIO still gives you problems with your .oif
>>>>>> dataset though let me know and I'll investigate.
>>>>>>
>>>>>>  As for the 2chZT data, that sounds unrelated to the hanging so I'll
>>>>>> take a look at it locally when I get a chance.
>>>>>>
>>>>>>  Thanks for using our software and reporting these issues!
>>>>>>
>>>>>> - Mark
>>>>>>
>>>>>>
>>>>>> On Tue, Apr 23, 2013 at 2:40 PM, Joe Ping-Lin Hsiao <
>>>>>> phsiao at cs.unc.edu> wrote:
>>>>>>
>>>>>>> Mark,
>>>>>>>      I tested your code with the .lsm download from
>>>>>>> http://www.loci.wisc.edu/files/software/data/2chZT.zip. The program
>>>>>>> just crashed with the error message
>>>>>>>
>>>>>>> "This application has requested the Runtime to terminate it in an
>>>>>>> unusual way.
>>>>>>> Please contact the application's support team for more information."
>>>>>>>
>>>>>>> If I tested with my own 5D .oif image collection, the execution
>>>>>>> hangs at 'extractor->Update()' and it does not even use any CPU. Any idea
>>>>>>> how to fix it?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Joe
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Oct 19, 2012 at 12:41 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>>>>>>
>>>>>>>> Hi Kishore,
>>>>>>>>
>>>>>>>>  I updated your test<https://gist.github.com/3900888/81064cf96fb06b4575a64e81481fda0936cd9056>to use an ExtractImageFilter in the IO pipeline. When a Reader's output is
>>>>>>>> piped to this Filter, the reader->Update() call only reads the extracted
>>>>>>>> region.
>>>>>>>>
>>>>>>>>  When I tested on the
>>>>>>>> ConfocalMemCitrine516LeftEar18hpfAug17_2012_Fish1.lsm test image you
>>>>>>>> uploaded, it correctly splits out the stacks for each time point. And when
>>>>>>>> I tested on a 9GB image it processed each time point without reading the
>>>>>>>> entire file.
>>>>>>>>
>>>>>>>>  So I'm hoping this solves your issue. If not, just let me know how
>>>>>>>> it's failing for you and I'll try again!
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Mark
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Oct 17, 2012 at 2:34 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>>>>>>>
>>>>>>>>> One thought is that, as the itkBioFormatsImageIO is a
>>>>>>>>> StreamingImageIOBase<http://www.itk.org/Doxygen320/html/classitk_1_1StreamingImageIOBase.html>,
>>>>>>>>> you could just set the desired region (as you were) and use *its*Read and Write methods instead of wrapping it in a Reader or a Writer.
>>>>>>>>>
>>>>>>>>> I'll try to put a code example up using this approach. It would be
>>>>>>>>> a good test case for the bf-itk-pipe plug-in anyway.
>>>>>>>>>
>>>>>>>>> - Mark
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Oct 17, 2012 at 1:56 PM, Mark Hiner <hinerm at gmail.com>wrote:
>>>>>>>>>
>>>>>>>>>> Hi Kishore,
>>>>>>>>>>
>>>>>>>>>>  Just wanted to let you know that I'm still looking at your issue
>>>>>>>>>> today. I updated the gist<https://gist.github.com/3900888/7aab8fddb38af87ea98cd49dd921524ace6430c8>to reflect the topics discussed in this e-mail, using the region setting
>>>>>>>>>> method calls instead of pipelining, and added some (hopefully) helpful
>>>>>>>>>> print statements to see what's going on with the regions.
>>>>>>>>>>
>>>>>>>>>>  From what I can tell there are two separate issues preventing
>>>>>>>>>> your code from writing the desired regions.
>>>>>>>>>>
>>>>>>>>>>  First of all, the IORegion needs to be set on the Writer, for
>>>>>>>>>> example:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     writer->SetImageIO(io);
>>>>>>>>>>     writer->SetInput(reader->GetOutput());
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     writer->SetIORegion(region);
>>>>>>>>>>     writer->Write();
>>>>>>>>>>
>>>>>>>>>>  In the original code you sent to me, that wasn't happening and
>>>>>>>>>> it was defaulting to the first 3D region and thus the first time point. I
>>>>>>>>>> mentioned this, without providing a code example, in a past e-mail - so
>>>>>>>>>> apologies if you've already updated your code!
>>>>>>>>>>
>>>>>>>>>>  Note that according to the itkImageFileWriter API<http://www.itk.org/Doxygen/html/classitk_1_1ImageFileWriter.html#ab2cba65f716aa75ec962171ee0b46fe3>Write() is a special form of Update() that respects the IORegion. However,
>>>>>>>>>> in practice, for me it still just writes the largest possible region
>>>>>>>>>> instead of what was specified. So that could suggest a bug in the
>>>>>>>>>> bf-itk-pipes plug-in.
>>>>>>>>>>
>>>>>>>>>>  The second issue is that even after manually specifying the IO
>>>>>>>>>> regions, the Reader output still has the largest possible dimensions (T=2)
>>>>>>>>>> so the current gist test ends up creating 2 full copies of the image. I
>>>>>>>>>> think this was always happening at the Reader, but then it was truncated to
>>>>>>>>>> the first time point you saw by the Writer. Anyway, this implies that the
>>>>>>>>>> full image is still being read, despite the region specifications.
>>>>>>>>>>
>>>>>>>>>>  I think this is a side effect of setting using the
>>>>>>>>>> LargestPossibleRegion in the Update() method, as mentioned in the itkProcessObject
>>>>>>>>>> specification<http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#a4041fb21e9105500eee311e265691bd5>
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>>  Right now I'm going through the examples from this ITK Users
>>>>>>>>>> thread<http://itk-insight-users.2283740.n2.nabble.com/Memory-limits-of-ITKImage-object-td5670422.html>about streaming for a better pipelining solution. I'm also testing to see
>>>>>>>>>> what can be done at the ImageIO level, as when Read and Write are hit in
>>>>>>>>>> the itkBioFormatsImageIO, GetIORegion() is already returning the largest
>>>>>>>>>> possible region, instead of the specified region.
>>>>>>>>>>
>>>>>>>>>>  I'll keep you updated.
>>>>>>>>>>
>>>>>>>>>> - Mark
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Tue, Oct 16, 2012 at 1:37 PM, Kishore Mosaliganti <
>>>>>>>>>> kishoreraom at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>>  Dear Mark,
>>>>>>>>>>>
>>>>>>>>>>> Thanks for the clarification. My original problem remains
>>>>>>>>>>> unresolved. For example, in the LSM gist on lines 104-107:
>>>>>>>>>>>
>>>>>>>>>>>     ReaderType::Pointer reader = ReaderType::New();
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>     reader->SetFileName(argv[1]);
>>>>>>>>>>>     reader->SetImageIO(io);
>>>>>>>>>>>
>>>>>>>>>>>     reader->Update();
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Here, calling reader->Update() loads the entire image into
>>>>>>>>>>> memory. If you have a very large LSM file (several gigabytes large), then
>>>>>>>>>>> this code will fail since such an image cannot get into the memory.
>>>>>>>>>>>
>>>>>>>>>>> Hence, I am trying to send the read region directly into the
>>>>>>>>>>> reader using
>>>>>>>>>>>
>>>>>>>>>>> io->SetRegion(region);
>>>>>>>>>>>
>>>>>>>>>>> and then
>>>>>>>>>>>
>>>>>>>>>>> reader->SetImageIO(io);
>>>>>>>>>>> reader->Update();
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> But this step is not giving me two different timepoints. It is
>>>>>>>>>>> writing out the same timepoint.
>>>>>>>>>>>
>>>>>>>>>>> Kishore
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Oct 16, 2012 at 2:13 PM, Mark Hiner <hiner at wisc.edu>wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hello again,
>>>>>>>>>>>>
>>>>>>>>>>>>  I created a gist for your LSM test and updated it with my most
>>>>>>>>>>>> recent code:
>>>>>>>>>>>> https://gist.github.com/3900888
>>>>>>>>>>>>
>>>>>>>>>>>>  That example is currently working for me, in that it writes
>>>>>>>>>>>> out 2 images of 72 planes - one for T=0 and one for T=1. Since everything
>>>>>>>>>>>> in ITK seems to be pipeline-oriented, I am not sure there is a solution to
>>>>>>>>>>>> splitting out channels just using Setters like we were both trying.
>>>>>>>>>>>>
>>>>>>>>>>>>  Instead, I followed this ROI Filter example<http://www.vtk.org/Wiki/ITK/Examples/ImageProcessing/RegionOfInterestImageFilter>and used the logic from my last e-mail.
>>>>>>>>>>>>
>>>>>>>>>>>>  I do need to correct one thing I said in my last e-mail: SizeT
>>>>>>>>>>>> should always be 1, as it is a relative offset to the Index value.
>>>>>>>>>>>>
>>>>>>>>>>>>  When I ran that test, both images went to grayscale.. I'm
>>>>>>>>>>>> going to see if that's an error in the bf-itk-pipes logic, or just
>>>>>>>>>>>> something that needs to be set up differently in using the ITK API.
>>>>>>>>>>>>
>>>>>>>>>>>>  Let me know if you run into any more problems with this code,
>>>>>>>>>>>> or if you just want to discuss any part of it.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks again for using our software :)
>>>>>>>>>>>> - Mark
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Oct 16, 2012 at 11:00 AM, Mark Hiner <hiner at wisc.edu>wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Kishore,
>>>>>>>>>>>>>
>>>>>>>>>>>>>  I am sorry I wasn't able to get to your issue yesterday.
>>>>>>>>>>>>> Looking at it today, I think there are a couple of things going on here.
>>>>>>>>>>>>>
>>>>>>>>>>>>>  First of all: in your test class
>>>>>>>>>>>>> - I consolidated a BioFormatsImageIO and the ImageIOBase.
>>>>>>>>>>>>> - In the region updating loop, the wrong region (dim-3 instead
>>>>>>>>>>>>> of dim-2) was being set, and only the index is set. I suspect both the
>>>>>>>>>>>>> index and size need to be set.
>>>>>>>>>>>>>
>>>>>>>>>>>>>  I attached an updated version of your test, where in the
>>>>>>>>>>>>> first iteration it sets IndexT = 0, sizeT = 1. The second iteration sets
>>>>>>>>>>>>> IndexT = 1, sizeT = 2.  I believe those regions will split the time points
>>>>>>>>>>>>> as you wanted.
>>>>>>>>>>>>>
>>>>>>>>>>>>> But there is a second issue: although the Reader IORegion is
>>>>>>>>>>>>> correct (I think) the Writer is not. It is defaulting to the ITK base 3D
>>>>>>>>>>>>> region. When I tried setting the Writer's region to our desired region, it
>>>>>>>>>>>>> throws an exception because the 5D region can't be contained by what it
>>>>>>>>>>>>> thinks is the largest possible (3D) region. I am refreshing myself on the
>>>>>>>>>>>>> ITK API and once we figure out how to set that region, I think it will
>>>>>>>>>>>>> write the images correctly (or we can move on to the next problem).
>>>>>>>>>>>>>
>>>>>>>>>>>>> In your test I changed the output format to ome.tiff because I
>>>>>>>>>>>>> know that will use the itkBioFormatsImageIO writer code, which I know is
>>>>>>>>>>>>> capable of handling 5D writing.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Also, in testing I found a couple of bugs in the
>>>>>>>>>>>>> ITKPipesBridge code. I started a new branch to fix these and any other
>>>>>>>>>>>>> issues that may be discovered. If you want to use the itkBioFormatsImageIO
>>>>>>>>>>>>> writer code you'll have to use this new branch for now. You can find it
>>>>>>>>>>>>> here:
>>>>>>>>>>>>> https://github.com/hinerm/bioformats/commits/bf-itk-fixes
>>>>>>>>>>>>>
>>>>>>>>>>>>> As always, let me know if this isn't fully addressing your
>>>>>>>>>>>>> issue. Otherwise, I'll let you know as soon as I have the Writer region
>>>>>>>>>>>>> setting properly.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>> - Mark
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Oct 12, 2012 at 11:28 AM, Kishore Mosaliganti <
>>>>>>>>>>>>> kishoreraom at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Mark,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you for the email and invaluable help. The
>>>>>>>>>>>>>> bioformats-itk plugin is wonderful. I am attaching my script here to help
>>>>>>>>>>>>>> you debug. Let me know if you have any questions on my script. I am
>>>>>>>>>>>>>> starting with a 5D (XYZTC) image and trying to write out all the 3D
>>>>>>>>>>>>>> timepoints for the first channel.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Kishore
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Oct 12, 2012 at 12:19 PM, Mark Hiner <
>>>>>>>>>>>>>> hinerm at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Kishore,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>  I helped develop the bf-itk-pipe plugin and am
>>>>>>>>>>>>>>> investigating your issue right now.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>  What you're doing seems reasonable, so I'm trying to
>>>>>>>>>>>>>>> determine if there's a bug in the plugin. My goal is to have some working
>>>>>>>>>>>>>>> example code for you (and a fix if necessary) by the end of the day.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you for using our plugin! I hope we can get it working
>>>>>>>>>>>>>>> for you soon.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> - Mark
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Oct 12, 2012 at 10:54 AM, Kishore Mosaliganti <
>>>>>>>>>>>>>>> kishoreraom at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Dear ITK and OME users,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> To further elaborate, I figured that this has nothing to do
>>>>>>>>>>>>>>>> with the itkStreamingImageFilter.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Instead, the itkImageFileReader seems to be extracting the
>>>>>>>>>>>>>>>> same image region although I update the requested region in the
>>>>>>>>>>>>>>>> BioformatsImageIO class :;
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>     itk::BioFormatsImageIO::Pointer io =
>>>>>>>>>>>>>>>> itk::BioFormatsImageIO::New();
>>>>>>>>>>>>>>>>     io->SetIORegion( region ); // doesn't make a difference
>>>>>>>>>>>>>>>> in terms of image data extracted. Its always from the beginning.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>     ReaderType::Pointer reader = ReaderType::New();
>>>>>>>>>>>>>>>>     reader->SetFileName(argv[1]);
>>>>>>>>>>>>>>>>     reader->SetImageIO(io);
>>>>>>>>>>>>>>>>     reader->Update();
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> So, my general question is whether the BioformatsImageIO
>>>>>>>>>>>>>>>> expects the whole LSM image to be loaded into memory before writing it out?
>>>>>>>>>>>>>>>> I would like to specify small image regions since my LSM is too large to be
>>>>>>>>>>>>>>>> fully loaded into memory. How else can I stream data from large LSM?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Kishore
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Fri, Oct 12, 2012 at 8:53 AM, Kishore Mosaliganti <
>>>>>>>>>>>>>>>> kishoreraom at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi all,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I am trying to use bioformats and itk. I downloaded and
>>>>>>>>>>>>>>>>> compiled bf-itk-pipe using cmake by linking against ITK 3.2:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> https://github.com/openmicroscopy/bioformats/tree/develop/components/native/bf-itk-pipe
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I tested out itkBFImageInfo and
>>>>>>>>>>>>>>>>> ./itkRGBBioFormatsImageIOTest on a few simple LSM images. It works great
>>>>>>>>>>>>>>>>> and writes out all the associated metadata and pixel data for the first
>>>>>>>>>>>>>>>>> timepoint.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> My LSM microscopy image is 5D. It is X-Y-Z-Time-Channel. I
>>>>>>>>>>>>>>>>> am interested in extracting individual timepoints from the LSM file for
>>>>>>>>>>>>>>>>> processing. The filter seems to be using itkStreamingImageFilter. I set the
>>>>>>>>>>>>>>>>> NumberOfStreams to 10 but that still seems to still write out only the
>>>>>>>>>>>>>>>>> first image.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> How do I set the output requestion region for an
>>>>>>>>>>>>>>>>> individual timepoint?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Kishore
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> ome-users mailing list
>>>>>>>>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> ome-users mailing list
>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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