[ITK-users] why can the ImageSeriesWriter not stream?

Sat Apr 25 13:46:35 EDT 2015

Dear Brad, dear mailing list members,

While the ImageSeriesReader is capable of streaming it seems the 
ImageSeriesWriter (although suggested: 
http://www.kitware.com/media/html/IOStreamingInITK.html) cannot (my simple try 
does not work: 
https://github.com/romangrothausmann/ITK-CLIs/commit/f21c624057b3010d864d527988d1c67a151c1e94). 

Is that just not implemented yet or intentionally avoided?
I was able to create a streaming version by using 
Modules/Filtering/ImageCompose/test/itkJoinSeriesImageFilterStreamingTest.cxx as 
an example: 
https://github.com/romangrothausmann/ITK-CLIs/commit/e588c6635c60e4bcb5b946cf0cb985727197df9c
Is that the way to go?

Is there a reason why the MetaImageIO 
(http://www.itk.org/Doxygen47/html/classitk_1_1MetaImageIO.html) although it 
supports streaming does not inherit StreamingImageIOBase as other streamable 
ImageIO like MRC?

Thanks for any hints.
Roman

On 20/04/15 20:09, Bradley Lowekamp wrote:
> Roman,
>
> On Apr 20, 2015, at 4:30 AM, Grothausmann, Roman Dr.
> <grothausmann.roman at mh-hannover.de> wrote:
>
>> Many thanks for Your answers and for also fixing the progress reporting.
>> Just tested and it works like a charm. It's a really great contribution
>> especially for those having to work with very big images. I'll give it a
>> try to use Your itkImageSinc to implement a "chunk writer" taking
>> StreamingStatisticsImage as an example and
>> ImageRegionSplitterMultidimensional to create the chunks.
>
> If you are implementing a writer derived from StreamingSinc, you should
> implement StreamedGenerateData, not ThreadedStreamedGenerate data as you
> don't want threading.
>
>>
>> If I set the NumberOfStreamDivisions to the number of slices in the 3D
>> Stack Input, is it guaranteed that each slice will be processed on its own
>> for the default ImageRegionSplitterSlowDimension? Or would I have to use an
>> approach as in itkJoinSeriesImageFilterStreamingTest.cxx employing
>> itkExtractImageFilter for each slice?
>
> The StreamedGenerateData method would get invoked for each slice with that
> slice being the specified region. However, the specified region provided to
> StreamedGenerateData may be smaller than the buffered region of the image. It
> may be best and most general to use the ExtractImageFilter to make sure the
> buffer is as expected.
>
>
>>
>> In the docs of ImageSeriesWriter it says: "Usually, the output image type
>> will have fewer dimensions than the input image type." Is there a way to
>> use the ImageSeriesWriter to save a series of hypercubes as
>> ImageRegionSplitterMultidimensional would yield internally?
>
> I don't think it has this feature.
>
>>
>> Thanks for any help or hints. Roman
>>
>> On 17/04/15 20:13, Bradley Lowekamp wrote:
>>> Hello,
>>>
>>> Glad to hear it worked for you.
>>>
>>> I have just fixed the progress reporting [1].
>>>
>>> The StreamingImageFilter overloads the UpdateData method [2], by passing
>>> the standard ImageToImage/ImageSource methods such and GenerateData,
>>> ThreadedGenerateData etc. It's actually not really designed to be
>>> derived from, and it used mostly to drive the streaming of a pipeline. It
>>> can be seen as slicing up the output image in to pieces, and requesting
>>> those pieces from the pipeline, the assembling them into the output
>>> image.
>>>
>>> The resulting behavior of the ImageSinc, with the StreamingProcessObject
>>> goes something like this:
>>>
>>>
>>> BeforeStreamedGenerateData()
>>>
>>> For each requested streamed chunk: For each thread process part of
>>> streamed chunk: ThreadedStreamedGenerateData()
>>>
>>> AfterStreamedGenerateData()
>>>
>>> So the input image is getting sliced up twice the first for streaming and
>>> the second for multi-threading.
>>>
>>> The StreamingImageFitler could be rewritten onto this framework to
>>> perhaps provide a generalized base class.
>>>
>>> For the StreamingStatisticsImage filter, the statistics are accumulated
>>> for each thread multiple times ( for each streamed chunk ), then the
>>> totals from the threads are reduced to the results.
>>>
>>> These classes certainly need more documentation before further
>>> integration into ITK.
>>>
>>> Brad
>>>
>>> [1]
>>> https://github.com/blowekamp/itkStreamingSinc/commit/d8415cf137d69a0e81b6dd46145d8cb7df2825c3
>>>
>>>
>>
>>>
[2] 
https://github.com/InsightSoftwareConsortium/ITK/blob/8f7c404aff99f5ae3dfedce6e480701f0304864c/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L118-Lundefined
>>>
>>> On Apr 17, 2015, at 12:12 PM, Grothausmann, Roman Dr.
>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>
>>>> Dear Brad, dear Richard,
>>>>
>>>>
>>>> Many thanks for Your replies. So, if I understand You correctly, the
>>>> problem is that the current framework (with StreamingImageFilter) will
>>>> run AfterThreadedGenerateData for each chunk and not just when the
>>>> whole image has been processed. So one would need to combine
>>>> StatisticsImageFilter and StreamingImageFilter into one filter, i.e.
>>>> basically that the part of AfterThreadedGenerateData is executed by
>>>> StreamingImageFilter. If I understand the code of itkStreamingSinc
>>>> correctly, this is what it does? itkStreamingSinc provides a base class
>>>> to combine multi-threaded filters with a StreamingImageFilter to make
>>>> them streamable. This comes with the trade-off that the resulting
>>>> filter will not provide an output, which is no problem if it is not
>>>> needed. So, e.g. itkStreamingStatisticsImageFilter cannot be connected
>>>> to itkPipelineMonitorImageFilter as it would need an output of
>>>> itkStreamingStatisticsImageFilter?
>>>>
>>>> Many thanks Brad for implementing itkStreamingStatisticsImageFilter. I
>>>> just tested it and it works perfectly
>>>> (https://github.com/romangrothausmann/ITK-CLIs/commit/38bcad35bf004feaf2189bdaaffcf398fbca1f60).
>>>>
>>>>
>>
>>>>
Though, I do not understand the changes You made in: 
https://github.com/blowekamp/itkStreamingSinc/commit/b4ae9b61dc08388fbf1b3bfd9e5cf570dd40a0c6
>>>> Is the accumulation that still resides in AfterStreamedGenerateData
>>>> not used at all?
>>>> (https://github.com/blowekamp/itkStreamingSinc/commit/dae948bea0966a2c3924351bf9c15bfcef318ac6#diff-ad64d497b8f9aadd5da97c5e1c793dc9R210)
>>>>
>>>>
>>
>>>>
Just as a side note: The progress reported by itkStreamingStatisticsImageFilter 
jumps to 100% for each chunk.
>>>>
>>>> All in all Your itkStreamingSinc and the implemented streaming-filters
>>>> are really a great contribution to ITK and I fully recommend
>>>> incorporating it into ITK.
>>>>
>>>> Many thanks again Roman
>>>>
>>>>
>>>> On 17/04/15 15:47, Bradley Lowekamp wrote:
>>>>> Hi,
>>>>>
>>>>> I was able to easy update a the StatisticsImageFilter to use my
>>>>> streaming base class for reduction algorithms [1]. It runs basically
>>>>> the same expect that you can set the number of stream divisions[2],
>>>>> there is the potential for setting the way the input image is split
>>>>> via the RegionSplitter in a base class [3].
>>>>>
>>>>> You should be able to just clone the repository into you
>>>>> ITK/Modules/External directory, then enable it in the CMake
>>>>> configuration to use.
>>>>>
>>>>> Please let me know if it works for you.
>>>>>
>>>>> This should help :) Brad > [1]
>>>>> https://github.com/blowekamp/itkStreamingSinc/blob/master/include/itkStreamingStatisticsImageFilter.h
>>>>>
>>>>>
>>
>>>>>
[2] 
https://github.com/blowekamp/itkStreamingSinc/blob/master/test/itkStreamingStatisticsImageFilterTest2.cxx#L61
>>>>> [3]
>>>>> https://github.com/blowekamp/itkStreamingSinc/blob/master/include/itkImageSinc.h#L99
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>
>>>>>
On Apr 17, 2015, at 7:14 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
>>>>> wrote:
>>>>>
>>>>>> Hello fellow mailing list member,
>>>>>>
>>>>>> Currently in ITK there are two base classes for streaming images
>>>>>> in ITK. The
>>>> ImageToImageFilter provide the framework of streaming one input region
>>>> to one output region. The other is the StreamingImageFilter which
>>>> provides the framework to stream multiple image regions and merge them
>>>> together into a single output image. This StatisticsImageFilter needs a
>>>> framework which consumes multiple input image regions and reduces the
>>>> data produced. I happen to have implemented such a framework here [1].
>>>> It currently has the LabelStatisticsImageFilter implemented in a
>>>> streaming fashion.
>>>>>>
>>>>>> Let me give it a try and see how quickly I can get the
>>>>>> StatisticsImageFilter
>>>> in this framework. Help writing tests would be appreciated.
>>>>>>
>>>>>> Thanks, Brad
>>>>>>
>>>>>> [1] https://github.com/blowekamp/itkStreamingSinc
>>>>>>
>>>>>> On Apr 17, 2015, at 5:08 AM, Dr. Roman Grothausmann
>>>>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>>>
>>>>>>> Dear mailing list members,
>>>>>>>
>>>>>>>
>>>>>>> I'm wondering why the itkStatisticsImageFilter cannot stream?
>>>>>>> Looking into itkStatisticsImageFilter.hxx it requests the whole
>>>>>>> input in GenerateInputRequestedRegion and
>>>>>>> EnlargeOutputRequestedRegion but in ThreadedGenerateData only
>>>>>>> iterates over the outputRegionForThread. Where in the code is the
>>>>>>> whole input image needed as one single block?
>>>>>>>
>>>>>>> Thanks for any hints Roman
>>>>>>>
>>>>>>> -- Dr. Roman Grothausmann
>>>>>>>
>>>>>>> Tomographie und Digitale Bildverarbeitung Tomography and Digital
>>>>>>> Image Analysis
>>>>>>>
>>>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>>>> Medizinische Hochschule Hannover Carl-Neuberg-Str. 1 D-30625
>>>>>>> Hannover
>>>>>>>
>>>>>>> Tel. +49 511 532-2900 _____________________________________
>>>>>>> Powered by www.kitware.com
>>>>>>>
>>>>>>> Visit other Kitware open-source projects at
>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>
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>>>>>>> http://www.kitware.com/products/protraining.php
>>>>>>>
>>>>>>> Please keep messages on-topic and check the ITK FAQ at:
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>>>>>>>
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>>>>>>
>>>>>> _____________________________________ Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>>> http://www.kitware.com/products/protraining.php
>>>>>>
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>>
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>
>>>> -- Dr. Roman Grothausmann
>>>>
>>>> Tomographie und Digitale Bildverarbeitung Tomography and Digital Image
>>>> Analysis
>>>>
>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>> Medizinische Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover
>>>>
>>>> Tel. +49 511 532-2900
>>>
>>
>> -- Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung Tomography and Digital Image
>> Analysis
>>
>> Institut für Funktionelle und Angewandte Anatomie, OE 4120 Medizinische
>> Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover
>>
>> Tel. +49 511 532-2900
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-2900