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

Grothausmann, Roman Dr. grothausmann.roman at mh-hannover.de
Mon Sep 12 05:41:09 EDT 2016


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/b00551faf951192f50e4090d683300524b4c95ba

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/d9b5c3f1a786b595255a9153da9ceafd88d2a189

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::UnaryFunctorImageFilter<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::ImageSource<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_2ResampleVolumesToBeIsotropic_8cxx-example.html
>     <https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleVolumesToBeIsotropic_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/0968dd25af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx
>     <https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25af2abc37ffb0c0503cc4c2972b3b2098/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/0968dd25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c220250cfdbb36R80
>     <https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c220250cfdbb36R80>)
>     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/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50
>             <https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/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/itkTileImageFilter.hxx#L125-L136
>                 <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136>
>
>
>
>
>     [2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html
>     <https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.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/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx
>                     <https://github.com/romangrothausmann/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/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9
>                     <https://github.com/romangrothausmann/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
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>
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>                     http://www.kitware.com/products/protraining.php
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>
>                     Please keep messages on-topic and check the ITK FAQ at:
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>
>
>
>             -- 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>
>
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>

-- 
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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