[ome-users] bioformats and ITK

Mark Hiner hiner at wisc.edu
Wed Oct 17 20:34:20 BST 2012 

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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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