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

Fri Sep 9 10:21:05 EDT 2016

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());

Can you try this?

Regards,
Dženan

On Fri, Sep 9, 2016 at 8:29 AM, Grothausmann, Roman Dr. <
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
> 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) 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/romangroth
> ausmann/ITK-CLIs/commit/0968dd25af2abc37ffb0c0503cc4c2972b3b
> 2098#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> 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
>>>
>>>
>>>
>>> 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
>>>
>>>
>>>
>>> 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
>>>>
>>>>
>>>>
>>>
>>>> [2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImag
> eFilter.html
>
>>
>>>> On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr.
>>>>> <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/4fdf5778
>>>>> 022598dcf83fb38e6002df72bd67bef3/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_2AppendTwo3DVolume
> s_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/ebfc0ae
>>>>> a37d28cbbf2bb22c3f56be52453cebde9
>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>>> 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 _____________________________________ Powered by
>>>>> www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects 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
>>>
>>
>>
> --
> 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
>
> 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:
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