[ome-users] bioformats and ITK

Joe Ping-Lin Hsiao phsiao at cs.unc.edu
Fri May 17 20:29:46 BST 2013 

Mark,

Just want to let you know that I repeated the same steps on my macbook with
Mac OSX 10.8.3, and program works fine.

Joe


On Fri, May 17, 2013 at 10:45 AM, Mark Hiner <hinerm at gmail.com> wrote:

> Joe,
>
>  That's odd.. not sure why manually adding them to the classpath didn't
> work. I will test locally on a Windows 7 box and let you know if I can
> reproduce and/or resolve the issue.
>
> Thanks for reporting it, hopefully we can get it working for you soon.
>
> - Mark
>
>
> On Thu, May 16, 2013 at 4:30 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:
>
>> 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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