[ITK] [ITK-users] get outputs from a std::vector list of smart-pointers of image-filters

Dženan Zukić dzenanz at gmail.com
Mon Sep 12 11:41:27 EDT 2016


Hi Roman,

can you turn
smoother->SetInput(savedPointers[i]->GetOutput());
into
if (i==0)

smoother->SetInput(static_cast<CastFilterType::Pointer>(savedPointers[i])->GetOutput());
else

smoother->SetInput(static_cast<GaussianFilterType::Pointer>(savedPointers[i])->GetOutput());
or something similar and see whether that works?

Regards,
Dženan

On Mon, Sep 12, 2016 at 5:41 AM, Grothausmann, Roman Dr. <
grothausmann.roman at mh-hannover.de> wrote:

> On 09/09/16 16:21, Dženan Zukić wrote:
>
>> Hi Roman,
>>
>> you should not save the pointer the SmartPointer encapsulates, but rather
>> the
>> SmartPointer itself. The saving line of code should not be
>> savedPointers.push_back(caster.GetPointer());
>> but rather
>> savedPointers.push_back(caster);
>> and later usage should not be
>> smoother->SetInput(dynamic_cast<ISType*>(savedPointers[i].
>> GetPointer())->GetOutput());
>> but rather
>> smoother->SetInput(savedPointers[i]->GetOutput());
>>
>
> Many thanks Dženan for Your reply. I tried as You suggested:
>
> https://github.com/romangrothausmann/ITK-CLIs/commit/b00551f
> af951192f50e4090d683300524b4c95ba
>
> but am getting:
>
> resample.cxx:79:49: error: no matching function for call to
> ?itk::ProcessObject::GetOutput()?
>   smoother->SetInput(savedPointers[i]->GetOutput());
>                                                  ^
> resample.cxx:79:49: note: candidates are:
> In file included from resample.cxx:5:
> /opt/itk-4.9.1/include/ITK-4.9/itkProcessObject.h:612:16: note:
> itk::DataObject* itk::ProcessObject::GetOutput(const
> DataObjectIdentifierType&)
>    DataObject * GetOutput(const DataObjectIdentifierType & key);
>                 ^
>
> I also tried:
> std::vector<itk::ProcessObject> savedPointers;
> std::vector<itk::ISType> savedPointers;
> std::vector< itk::SmartPointer<itk::ProcessObject> > savedPointers;
> but always got compile errors.
> I am confused when to use the smart-pointer as is and when with
> .GetPointer().
>
> According to
>
> https://cmake.org/pipermail/insight-users/2007-May/022374.html
>
> I also tried storing the output-pointers (without pipe-line disconnection)
> in a separate list
>
> https://github.com/romangrothausmann/ITK-CLIs/commit/d9b5c3f
> 1a786b595255a9153da9ceafd88d2a189
>
> which does not compile either:
>
> resample.cxx:77:5: error: request for member ?GetPointer? in
> ?caster.itk::SmartPointer<TObjectType>::operator-><itk::CastImageFilter<itk::Image<float,
> 1u>, itk::Image<float, 1u> > >()->itk::CastImageFilter<itk::Image<float,
> 1u>, itk::Image<float, 1u> >::<anonymous>.itk::UnaryFunct
> orImageFilter<itk::Image<float, 1u>, itk::Image<float, 1u>,
> itk::Functor::Cast<float, float> >::<anonymous>.itk::InPlaceImageFilter<itk::Image<float,
> 1u>, itk::Image<float, 1u> >::<anonymous>.itk::ImageToImageFilter<itk::Image<float,
> 1u>, itk::Image<float, 1u> >::<anonymous>.itk::ImageSourc
> e<TOutputImage>::GetOutput<itk::Image<float, 1u> >()?, which is of
> pointer type ?itk::ImageSource<itk::Image<float, 1u> >::OutputImageType*
> {aka itk::Image<float, 1u>*}? (maybe you meant to use ?->? ?)
>      savedOutPointers.push_back(caster->GetOutput().GetPointer());
>      ^
>
> I'm wondering if construct as needed is not possible at all because I
> can't find anything like that in the ITK-sources or examples. For the code
> snippets I can find in the MLs it is not clear whether they got tested and
> were accepted by a compiler.
>
> Any further ideas?
>
> Best
> Roman
>
>
> On Fri, Sep 9, 2016 at 8:29 AM, Grothausmann, Roman Dr.
>> <grothausmann.roman at mh-hannover.de <mailto:grothausmann.roman at mh-
>> hannover.de>>
>> wrote:
>>
>>     On 22/07/16 14:49, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>>
>>         Hi,
>>
>>         Who is holding the pointer to the newly created ImageFileReader
>> outside of
>>         the loop? For that type of operation I’ll frequently just stash
>> smart
>>         pointers into a std::vector or list.
>>
>>
>>     I tried to change the resample example
>>     (https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleV
>> olumesToBeIsotropic_8cxx-example.html
>>     <https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleV
>> olumesToBeIsotropic_8cxx-example.html>
>>     that uses itkRecursiveGaussianImageFilter for each dimension) such
>> that it works
>>     for any dimensional image.
>>     Doing as Brad suggested and storing each smart-pointer of
>>     itkRecursiveGaussianImageFilter in a std::vector I get a program
>>     (https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25
>> af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx
>>     <https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25
>> af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx>)
>>     that compiles but segfaults when used. I guess the way I'm trying to
>>     dereference a pointer from the list is not correct
>>     (https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd
>> 25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c2
>> 20250cfdbb36R80
>>     <https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd
>> 25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c2
>> 20250cfdbb36R80>)
>>     but I could not find an example except the one referenced in the code
>> line.
>>     So how to correctly dereference a pointer from the list of
>> smart-pointers to
>>     get its output?
>>
>>     Thank for any help or hints
>>     Roman
>>
>>             On Jul 22, 2016, at 6:00 AM, Grothausmann, Roman Dr.
>>             <grothausmann.roman at mh-hannover.de
>>             <mailto:grothausmann.roman at mh-hannover.de>> wrote:
>>
>>             Many thanks Brad for Your detailed reply. I understand now
>> the problems
>>             concerning streaming TileImageFilter. However I still wonder
>> why my
>>             non-streaming version also does not work any more after
>> moving the
>>             creation
>>             of reader instances into the for-loop:
>>             https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea3
>> 7d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50
>>             <https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea
>> 37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50>
>>
>>
>>
>>     Is this construct inappropriate for the TileImageFilter?
>>
>>             Why does it work for:
>>             https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_
>> 2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2
>>             <https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering
>> _2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2>
>>
>>
>>
>>     On 21/07/16 15:41, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>>
>>                 Hello,
>>
>>                 The TileImageFilter does not fully stream [1]. The filter
>> also
>>                 has some
>>                 odd behavior, and other older implementation details. If
>> you are
>>                 going to
>>                 work on a streaming pipelines it is best practice to
>> examine the
>>                 filters
>>                 to determine how the Requested regions behave.
>>
>>                 However, there is no reason that the TileImageFilter
>> algorithm
>>                 couldn’t
>>                 support streaming. It is just a matter of code and a
>> bunch of
>>                 testing. A
>>                 contribution for this issue would be welcomed! Also this
>> filter
>>                 is in
>>                 need a refactoring and bring it up to several other best
>>                 practices. There
>>                 are several issue with the current implementation that
>> would
>>                 cause it not
>>                 to work correctly with a streaming pipeline, and cause
>> excessive
>>                 execution.
>>
>>                 You can also use the PipelieMoniotorImageFilter to record
>> and
>>                 print the
>>                 pipeline interaction during Update [2]. This information
>> helps with
>>                 debugging and diagnosing problems, but if the pipeline is
>>                 mis-behaving (
>>                 as the TileImageFilter may ), the information may not be
>> correct.
>>
>>                 I have tried similar streaming with the
>> JoinSeriesImageFilter.
>>                 However I
>>                 ran into many problems with having hundreds of ImageIO
>> being
>>                 utilized at
>>                 the same time. There were problems with having too many
>> files
>>                 open at the
>>                 same time along with ImageIO libraries that couldn’t
>> handle single
>>                 threaded access to multiple files.
>>
>>                 [1]
>>                 https://github.com/InsightSoftwareConsortium/ITK/blob/
>> master/Modules/Filtering/ImageGrid/include/itkTileImageFilte
>> r.hxx#L125-L136
>>                 <https://github.com/InsightSoftwareConsortium/ITK/blob/
>> master/Modules/Filtering/ImageGrid/include/itkTileImageFilte
>> r.hxx#L125-L136>
>>
>>
>>
>>
>>     [2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImag
>> eFilter.html
>>     <https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorIma
>> geFilter.html>
>>
>>
>>                     On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr.
>>                     <grothausmann.roman at mh-hannover.de
>>                     <mailto:grothausmann.roman at mh-hannover.de>> wrote:
>>
>>                     Dear mailing list members,
>>
>>
>>                     Based on the examples for TileImageFilter I've
>> created a
>>                     working CLI
>>                     to append an arbitrary number of inputs
>>                     (https://github.com/romangroth
>> ausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx
>>                     <https://github.com/romangroth
>> ausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx
>> >).
>>
>>
>>
>>
>>     As there is an example that does not apply Update and
>> DisconnectPipeline on
>>     the readers
>>     (https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering
>> _2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2
>>     <https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering
>> _2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2>)
>>
>>
>>
>>                     I changed my code such that a reader instance is
>> created for
>>                     each input
>>                     in a for-loop:
>>                     https://github.com/romangrotha
>> usmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9
>>                     <https://github.com/romangroth
>> ausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9>
>>
>>
>>
>>
>>
>>     However, the update from the writer seems not to propagate to the
>> readers
>>     whether streaming or not. Can the TileImageFilter not stream in such
>> a case
>>     or are further modifications necessary?
>>
>>
>>                     Thanks for any help or hints Roman
>>
>>
>>                     On 18/08/14 17:01, Michka Popoff wrote:
>>
>>                         Hi
>>
>>                         Going the way described in the CreateVolume
>> example is
>>                         the way to
>>                         go.
>>
>>                         Why did you uncomment the DisconnectPipeline()
>> call and
>>                         Update() call
>>                         in the for loop ? They need to stay there, else
>> you will
>>                         always use
>>                         the last image. That’s why you see the same
>> image, the
>>                         single update
>>                         call will be triggered at the end of the script
>> and read
>>                         only one
>>                         image.
>>
>>                         You don’t need to call tileFilter->Update(), you
>> can
>>                         remove this
>>                         line. The writer->Update() will take care of the
>>                         pipeline update. As
>>                         a bonus, you may wrap your writer->Update() call,
>> to
>>                         fetch errors at
>>                         the end of the pipeline:
>>
>>                         try { writer->Update(); } catch(
>> itk::ExceptionObject &
>>                         error ) {
>>                         std::cerr << "Error: " << error << std::endl;
>> return
>>                         EXIT_FAILURE; }
>>
>>                         I made a little Python prototype, the syntax is a
>> little bit
>>                         different than in C++ but it gives you the main
>> idea.
>>
>>                         Michka
>>
>>
>>                     -- 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 <tel:%2B49%20511%20532-2900>
>>                     _____________________________________ Powered by
>>                     www.kitware.com <http://www.kitware.com>
>>
>>                     Visit other Kitware open-source projects at
>>                     http://www.kitware.com/opensource/opensource.html
>>                     <http://www.kitware.com/opensource/opensource.html>
>>
>>                     Kitware offers ITK Training Courses, for more
>> information visit:
>>                     http://www.kitware.com/products/protraining.php
>>                     <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
>>                     <http://www.itk.org/Wiki/ITK_FAQ>
>>
>>                     Follow this link to subscribe/unsubscribe:
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>> man/listinfo/insight-users
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>> lman/listinfo/insight-users>
>>                     _______________________________________________
>> Community
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>>                     http://public.kitware.com/mailman/listinfo/community
>>                     <http://public.kitware.com/mailman/listinfo/community
>> >
>>
>>
>>
>>             -- 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 <tel:%2B49%20511%20532-2900>
>>
>>
>>
>>     --
>>     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 <tel:%2B49%20511%20532-2900>
>>     _____________________________________
>>     Powered by www.kitware.com <http://www.kitware.com>
>>
>>     Visit other Kitware open-source projects at
>>     http://www.kitware.com/opensource/opensource.html
>>     <http://www.kitware.com/opensource/opensource.html>
>>
>>     Kitware offers ITK Training Courses, for more information visit:
>>     http://www.kitware.com/products/protraining.php
>>     <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 <http://www.itk.org/Wiki/ITK_FAQ>
>>
>>     Follow this link to subscribe/unsubscribe:
>>     http://public.kitware.com/mailman/listinfo/insight-users
>>     <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
>
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