<div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Something just occurred to me. Why not make your code like this:</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">define CastFilter cF;</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">define SmoothFilter s0</font></div><div class="gmail_default" style="font-size:small"><span style="font-family:monospace,monospace">s0->SetInput(cF->GetOutput());</span><font face="monospace, monospace"><br></font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">SmoothFilter::Pointer previous=s0;</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">for (int i=1 to Dim)</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">{</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> define SmoothFilter sI</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> sI->SetInput(previous->GetOutput());</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> previous=sI;<br></font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">}</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">output=sI->GetOutput();</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">output->Update(); //or writer->Update</font></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">My attempt at it is attached. This code seems to have other bugs besides the for loop (this crashes for me with "access violation"). Also, your big for loops seems to be implementing an already existing filter: <a href="https://itk.org/Doxygen/html/classitk_1_1SmoothingRecursiveGaussianImageFilter.html">SmoothingRecursiveGaussianImageFilter</a>.</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">HTH,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Dženan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 16, 2016 at 9:49 AM, Dženan Zukić <span dir="ltr"><<a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Hi Roman,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">I tried some modifications of your second <a href="https://github.com/romangrothausmann/ITK-CLIs/blob/d9b5c3f1a786b595255a9153da9ceafd88d2a189/resample.cxx" target="_blank">attempt</a>, but couldn't get it to compile. But your code reminded me very much of <a href="https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit" target="_blank">BRAINSFit</a>, so you might take inspiration from that.</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">I am sorry I could not be of more help.</div><span class="HOEnZb"><font color="#888888"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Dženan</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 16, 2016 at 7:42 AM, Grothausmann, Roman Dr. <span dir="ltr"><<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>On 12/09/16 17:41, Dženan Zukić wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
can you turn<br>
smoother->SetInput(savedPointe<wbr>rs[i]->GetOutput());<br>
into<br>
if (i==0)<br>
<br>
smoother->SetInput(static_cast<wbr><CastFilterType::Pointer>(save<wbr>dPointers[i])->GetOutput());<br>
else<br>
<br>
smoother->SetInput(static_cast<wbr><GaussianFilterType::Pointer>(<wbr>savedPointers[i])->GetOutput()<wbr>);<br>
or something similar and see whether that works?<br>
</blockquote>
<br></span>
Did so,<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/2cd1fbe4406eccbd6552e88e8be0a0ab1aad4ba6" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/commit/2cd1fbe<wbr>4406eccbd6552e88e8be0a0ab1aad4<wbr>ba6</a><br>
but still getting compile errors like:<br>
resample.cxx:73:5: error: no matching function for call to ?std::vector<itk::SmartPointer<wbr><itk::ProcessObject> >::push_back(itk::CastImageFil<wbr>ter<itk::Image<float, 1u>, itk::Image<float, 1u> >::Pointer&)?<br>
savedPointers.push_back(caste<wbr>r);<br>
<br>
and<br>
<br>
resample.cxx:80:25: error: invalid user-defined conversion from ?itk::SmartPointer<itk::Proces<wbr>sObject>? to ?itk::SmartPointer<itk::CastIm<wbr>ageFilter<itk::Image<float, 1u>, itk::Image<float, 1u> > >::ObjectType* {aka itk::CastImageFilter<itk::Imag<wbr>e<float, 1u>, itk::Image<float, 1u> >*}? [-fpermissive]<br>
smoother->SetInput(static_cast<wbr><typename CastFilterType::Pointer>(saved<wbr>Pointers[i])->GetOutput());<br>
<br>
<br>
<br>
I also tried Your suggestion on the .GetPointer() variant:<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/4a96d962430461c0b26de9363a1ccf623b9c9840" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/commit/4a96d96<wbr>2430461c0b26de9363a1ccf623b9c9<wbr>840</a><br>
which compiles but segfaults when executed.<br>
<br>
<br>
<br>
A third variant stores the Output SPs in a separate list:<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/d9b5c3f1a786b595255a9153da9ceafd88d2a189" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/commit/d9b5c3f<wbr>1a786b595255a9153da9ceafd88d2a<wbr>189</a><br>
but compilation stops with:<span><br>
resample.cxx:77:5: error: request for member ?GetPointer? in ?caster.itk::SmartPointer<TObj<wbr>ectType>::operator-><itk::Cast<wbr>ImageFilter<itk::Image<float, 1u>, itk::Image<float, 1u> > >()->itk::CastImageFilter<itk:<wbr>:Image<float, 1u>, itk::Image<float, 1u> >::<anonymous>.itk::UnaryFunct<wbr>orImageFilter<itk::Image<float<wbr>, 1u>, itk::Image<float, 1u>, itk::Functor::Cast<float, float> >::<anonymous>.itk::InPlaceIma<wbr>geFilter<itk::Image<float, 1u>, itk::Image<float, 1u> >::<anonymous>.itk::ImageToIma<wbr>geFilter<itk::Image<float, 1u>, itk::Image<float, 1u> >::<anonymous>.itk::ImageSourc<wbr>e<TOutputImage>::GetOutput<itk<wbr>::Image<float, 1u> >()?, which is of pointer type ?itk::ImageSource<itk::Image<f<wbr>loat, 1u> >::OutputImageType* {aka itk::Image<float, 1u>*}? (maybe you meant to use ?->? ?)<br>
savedOutPointers.push_back(ca<wbr>ster->GetOutput().GetPointer()<wbr>);<br>
^<br>
<br></span>
Any other ideas how to get this working?<br>
<br>
Many thanks for looking into this.<br>
Roman<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>
On Mon, Sep 12, 2016 at 5:41 AM, Grothausmann, Roman Dr.<br></span>
<<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-hannove<wbr>r.de</a> <mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>>><div><div><br>
wrote:<br>
<br>
On 09/09/16 16:21, Dženan Zukić wrote:<br>
<br>
Hi Roman,<br>
<br>
you should not save the pointer the SmartPointer encapsulates, but<br>
rather the<br>
SmartPointer itself. The saving line of code should not be<br>
savedPointers.push_back(caster<wbr>.GetPointer());<br>
but rather<br>
savedPointers.push_back(caster<wbr>);<br>
and later usage should not be<br>
smoother->SetInput(dynamic_cas<wbr>t<ISType*>(savedPointers[i].Ge<wbr>tPointer())->GetOutput());<br>
but rather<br>
smoother->SetInput(savedPointe<wbr>rs[i]->GetOutput());<br>
<br>
<br>
Many thanks Dženan for Your reply. I tried as You suggested:<br>
<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/b00551faf951192f50e4090d683300524b4c95ba" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/commit/b00551f<wbr>af951192f50e4090d683300524b4c9<wbr>5ba</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/b00551faf951192f50e4090d683300524b4c95ba" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/b00551<wbr>faf951192f50e4090d683300524b4c<wbr>95ba</a>><br>
<br>
but am getting:<br>
<br>
resample.cxx:79:49: error: no matching function for call to<br>
?itk::ProcessObject::GetOutput<wbr>()?<br>
smoother->SetInput(savedPointe<wbr>rs[i]->GetOutput());<br>
^<br>
resample.cxx:79:49: note: candidates are:<br>
In file included from resample.cxx:5:<br>
/opt/itk-4.9.1/include/ITK-4.9<wbr>/itkProcessObject.h:612:16: note:<br>
itk::DataObject* itk::ProcessObject::GetOutput(<wbr>const DataObjectIdentifierType&)<br>
DataObject * GetOutput(const DataObjectIdentifierType & key);<br>
^<br>
<br>
I also tried:<br>
std::vector<itk::ProcessObject<wbr>> savedPointers;<br>
std::vector<itk::ISType> savedPointers;<br>
std::vector< itk::SmartPointer<itk::Process<wbr>Object> > savedPointers;<br>
but always got compile errors.<br>
I am confused when to use the smart-pointer as is and when with .GetPointer().<br>
<br>
According to<br>
<br>
<a href="https://cmake.org/pipermail/insight-users/2007-May/022374.html" rel="noreferrer" target="_blank">https://cmake.org/pipermail/in<wbr>sight-users/2007-May/022374.ht<wbr>ml</a><br>
<<a href="https://cmake.org/pipermail/insight-users/2007-May/022374.html" rel="noreferrer" target="_blank">https://cmake.org/pipermail/i<wbr>nsight-users/2007-May/022374.h<wbr>tml</a>><br>
<br>
I also tried storing the output-pointers (without pipe-line disconnection)<br>
in a separate list<br>
<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/d9b5c3f1a786b595255a9153da9ceafd88d2a189" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/commit/d9b5c3f<wbr>1a786b595255a9153da9ceafd88d2a<wbr>189</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/d9b5c3f1a786b595255a9153da9ceafd88d2a189" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/d9b5c3<wbr>f1a786b595255a9153da9ceafd88d2<wbr>a189</a>><br>
<br>
which does not compile either:<br>
<br>
resample.cxx:77:5: error: request for member ?GetPointer? in<br>
?caster.itk::SmartPointer<TObj<wbr>ectType>::operator-><itk::Cast<wbr>ImageFilter<itk::Image<float,<br>
1u>, itk::Image<float, 1u> > >()->itk::CastImageFilter<itk:<wbr>:Image<float,<br>
1u>, itk::Image<float, 1u><br>
>::<anonymous>.itk::UnaryFunct<wbr>orImageFilter<itk::Image<float<wbr>, 1u>,<br>
itk::Image<float, 1u>, itk::Functor::Cast<float, float><br>
>::<anonymous>.itk::InPlaceIma<wbr>geFilter<itk::Image<float, 1u>,<br>
itk::Image<float, 1u><br>
>::<anonymous>.itk::ImageToIma<wbr>geFilter<itk::Image<float, 1u>,<br>
itk::Image<float, 1u><br>
>::<anonymous>.itk::ImageSourc<wbr>e<TOutputImage>::GetOutput<itk<wbr>::Image<float,<br>
1u> >()?, which is of pointer type ?itk::ImageSource<itk::Image<f<wbr>loat, 1u><br>
>::OutputImageType* {aka itk::Image<float, 1u>*}? (maybe you meant to use<br>
?->? ?)<br>
savedOutPointers.push_back(ca<wbr>ster->GetOutput().GetPointer()<wbr>);<br>
^<br>
<br>
I'm wondering if construct as needed is not possible at all because I can't<br>
find anything like that in the ITK-sources or examples. For the code<br>
snippets I can find in the MLs it is not clear whether they got tested and<br>
were accepted by a compiler.<br>
<br>
Any further ideas?<br>
<br>
Best<br>
Roman<br>
<br>
<br>
On Fri, Sep 9, 2016 at 8:29 AM, Grothausmann, Roman Dr.<br>
<<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-hannove<wbr>r.de</a><br>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>><br></div></div>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a><div><div><br>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>>>><br>
wrote:<br>
<br>
On 22/07/16 14:49, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:<br>
<br>
Hi,<br>
<br>
Who is holding the pointer to the newly created ImageFileReader<br>
outside of<br>
the loop? For that type of operation I’ll frequently just stash<br>
smart<br>
pointers into a std::vector or list.<br>
<br>
<br>
I tried to change the resample example<br>
<br>
(<a href="https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>Examples_2Filtering_2ResampleV<wbr>olumesToBeIsotropic_8cxx-examp<wbr>le.html</a><br>
<<a href="https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>Examples_2Filtering_2ResampleV<wbr>olumesToBeIsotropic_8cxx-examp<wbr>le.html</a>><br>
<br>
<<a href="https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>Examples_2Filtering_2ResampleV<wbr>olumesToBeIsotropic_8cxx-examp<wbr>le.html</a><br>
<<a href="https://itk.org/Doxygen/html/Examples_2Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>Examples_2Filtering_2ResampleV<wbr>olumesToBeIsotropic_8cxx-examp<wbr>le.html</a>>><br>
that uses itkRecursiveGaussianImageFilte<wbr>r for each dimension) such<br>
that it works<br>
for any dimensional image.<br>
Doing as Brad suggested and storing each smart-pointer of<br>
itkRecursiveGaussianImageFilte<wbr>r in a std::vector I get a program<br>
<br>
(<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/0968dd25<wbr>af2abc37ffb0c0503cc4c2972b3b20<wbr>98/resample.cxx</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/0968dd25<wbr>af2abc37ffb0c0503cc4c2972b3b20<wbr>98/resample.cxx</a>><br>
<br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/0968dd25<wbr>af2abc37ffb0c0503cc4c2972b3b20<wbr>98/resample.cxx</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/0968dd25af2abc37ffb0c0503cc4c2972b3b2098/resample.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/0968dd25<wbr>af2abc37ffb0c0503cc4c2972b3b20<wbr>98/resample.cxx</a>>>)<br>
that compiles but segfaults when used. I guess the way I'm trying to<br>
dereference a pointer from the list is not correct<br>
<br>
(<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c220250cfdbb36R80" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/0968dd<wbr>25af2abc37ffb0c0503cc4c2972b3b<wbr>2098#diff-cb1b1c6837c6074372c2<wbr>20250cfdbb36R80</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c220250cfdbb36R80" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/0968dd<wbr>25af2abc37ffb0c0503cc4c2972b3b<wbr>2098#diff-cb1b1c6837c6074372c2<wbr>20250cfdbb36R80</a>><br>
<br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c220250cfdbb36R80" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/0968dd<wbr>25af2abc37ffb0c0503cc4c2972b3b<wbr>2098#diff-cb1b1c6837c6074372c2<wbr>20250cfdbb36R80</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/0968dd25af2abc37ffb0c0503cc4c2972b3b2098#diff-cb1b1c6837c6074372c220250cfdbb36R80" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/0968dd<wbr>25af2abc37ffb0c0503cc4c2972b3b<wbr>2098#diff-cb1b1c6837c6074372c2<wbr>20250cfdbb36R80</a>>>)<br>
but I could not find an example except the one referenced in the<br>
code line.<br>
So how to correctly dereference a pointer from the list of<br>
smart-pointers to<br>
get its output?<br>
<br>
Thank for any help or hints<br>
Roman<br>
<br>
On Jul 22, 2016, at 6:00 AM, Grothausmann, Roman Dr.<br>
<<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-hannove<wbr>r.de</a><br>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>><br></div></div>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a><div><div><br>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>>>> wrote:<br>
<br>
Many thanks Brad for Your detailed reply. I understand now<br>
the problems<br>
concerning streaming TileImageFilter. However I still wonder<br>
why my<br>
non-streaming version also does not work any more after<br>
moving the<br>
creation<br>
of reader instances into the for-loop:<br>
<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/blob/ebfc0aea3<wbr>7d28cbbf2bb22c3f56be52453cebde<wbr>9/tile.cxx#L46-L50</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/ebfc0aea<wbr>37d28cbbf2bb22c3f56be52453cebd<wbr>e9/tile.cxx#L46-L50</a>><br>
<br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/ebfc0aea<wbr>37d28cbbf2bb22c3f56be52453cebd<wbr>e9/tile.cxx#L46-L50</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/ebfc0aea<wbr>37d28cbbf2bb22c3f56be52453cebd<wbr>e9/tile.cxx#L46-L50</a>>><br>
<br>
<br>
<br>
Is this construct inappropriate for the TileImageFilter?<br>
<br>
Why does it work for:<br>
<br>
<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/S<wbr>phinxExamples_2src_2Filtering_<wbr>2ImageGrid_2AppendTwo3DVolumes<wbr>_2Code_8cxx-example.html#_a2</a><br>
<<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a>><br>
<br>
<<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a><br>
<<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a>><wbr>><br>
<br>
<br>
<br>
On 21/07/16 15:41, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:<br>
<br>
Hello,<br>
<br>
The TileImageFilter does not fully stream [1]. The<br>
filter also<br>
has some<br>
odd behavior, and other older implementation details. If<br>
you are<br>
going to<br>
work on a streaming pipelines it is best practice to<br>
examine the<br>
filters<br>
to determine how the Requested regions behave.<br>
<br>
However, there is no reason that the TileImageFilter<br>
algorithm<br>
couldn’t<br>
support streaming. It is just a matter of code and a<br>
bunch of<br>
testing. A<br>
contribution for this issue would be welcomed! Also this<br>
filter<br>
is in<br>
need a refactoring and bring it up to several other best<br>
practices. There<br>
are several issue with the current implementation that would<br>
cause it not<br>
to work correctly with a streaming pipeline, and cause<br>
excessive<br>
execution.<br>
<br>
You can also use the PipelieMoniotorImageFilter to<br>
record and<br>
print the<br>
pipeline interaction during Update [2]. This information<br>
helps with<br>
debugging and diagnosing problems, but if the pipeline is<br>
mis-behaving (<br>
as the TileImageFilter may ), the information may not be<br>
correct.<br>
<br>
I have tried similar streaming with the<br>
JoinSeriesImageFilter.<br>
However I<br>
ran into many problems with having hundreds of ImageIO being<br>
utilized at<br>
the same time. There were problems with having too many<br>
files<br>
open at the<br>
same time along with ImageIO libraries that couldn’t<br>
handle single<br>
threaded access to multiple files.<br>
<br>
[1]<br>
<br>
<a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136" rel="noreferrer" target="_blank">https://github.com/InsightSoft<wbr>wareConsortium/ITK/blob/master<wbr>/Modules/Filtering/ImageGrid/<wbr>include/itkTileImageFilter.<wbr>hxx#L125-L136</a><br>
<<a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136" rel="noreferrer" target="_blank">https://github.com/InsightSof<wbr>twareConsortium/ITK/blob/maste<wbr>r/Modules/Filtering/ImageGrid/<wbr>include/itkTileImageFilter.<wbr>hxx#L125-L136</a>><br>
<br>
<<a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136" rel="noreferrer" target="_blank">https://github.com/InsightSof<wbr>twareConsortium/ITK/blob/maste<wbr>r/Modules/Filtering/ImageGrid/<wbr>include/itkTileImageFilter.<wbr>hxx#L125-L136</a><br>
<<a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136" rel="noreferrer" target="_blank">https://github.com/InsightSof<wbr>twareConsortium/ITK/blob/maste<wbr>r/Modules/Filtering/ImageGrid/<wbr>include/itkTileImageFilter.<wbr>hxx#L125-L136</a>>><br>
<br>
<br>
<br>
<br>
[2]<br>
<a href="https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/c<wbr>lassitk_1_1PipelineMonitorImag<wbr>eFilter.html</a><br>
<<a href="https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>classitk_1_1PipelineMonitorIma<wbr>geFilter.html</a>><br>
<br>
<<a href="https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>classitk_1_1PipelineMonitorIma<wbr>geFilter.html</a> <<a href="https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>classitk_1_1PipelineMonitorIma<wbr>geFilter.html</a>>><br>
<br>
<br>
On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr.<br>
<<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-hannove<wbr>r.de</a><br>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>><br></div></div>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a><div><div><br>
<mailto:<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-<wbr>hannover.de</a>>>> wrote:<br>
<br>
Dear mailing list members,<br>
<br>
<br>
Based on the examples for TileImageFilter I've created a<br>
working CLI<br>
to append an arbitrary number of inputs<br>
<br>
(<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/4fdf5778<wbr>022598dcf83fb38e6002df72bd67be<wbr>f3/tile.cxx</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/4fdf5778<wbr>022598dcf83fb38e6002df72bd67be<wbr>f3/tile.cxx</a>><br>
<br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/4fdf5778<wbr>022598dcf83fb38e6002df72bd67be<wbr>f3/tile.cxx</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/blob/4fdf5778<wbr>022598dcf83fb38e6002df72bd67be<wbr>f3/tile.cxx</a>>>).<br>
<br>
<br>
<br>
<br>
As there is an example that does not apply Update and<br>
DisconnectPipeline on<br>
the readers<br>
<br>
(<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a><br>
<<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a>><br>
<br>
<<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a><br>
<<a href="https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2" rel="noreferrer" target="_blank">https://itk.org/Doxygen/html/<wbr>SphinxExamples_2src_2Filtering<wbr>_2ImageGrid_2AppendTwo3DVolume<wbr>s_2Code_8cxx-example.html#_a2</a>><wbr>>)<br>
<br>
<br>
<br>
I changed my code such that a reader instance is<br>
created for<br>
each input<br>
in a for-loop:<br>
<br>
<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9" rel="noreferrer" target="_blank">https://github.com/romangrotha<wbr>usmann/ITK-CLIs/commit/ebfc0ae<wbr>a37d28cbbf2bb22c3f56be52453ceb<wbr>de9</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/ebfc0a<wbr>ea37d28cbbf2bb22c3f56be52453ce<wbr>bde9</a>><br>
<br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/ebfc0a<wbr>ea37d28cbbf2bb22c3f56be52453ce<wbr>bde9</a><br>
<<a href="https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9" rel="noreferrer" target="_blank">https://github.com/romangroth<wbr>ausmann/ITK-CLIs/commit/ebfc0a<wbr>ea37d28cbbf2bb22c3f56be52453ce<wbr>bde9</a>>><br>
<br>
<br>
<br>
<br>
<br>
However, the update from the writer seems not to propagate to the<br>
readers<br>
whether streaming or not. Can the TileImageFilter not stream in such<br>
a case<br>
or are further modifications necessary?<br>
<br>
<br>
Thanks for any help or hints Roman<br>
<br>
<br>
On 18/08/14 17:01, Michka Popoff wrote:<br>
<br>
Hi<br>
<br>
Going the way described in the CreateVolume<br>
example is<br>
the way to<br>
go.<br>
<br>
Why did you uncomment the DisconnectPipeline()<br>
call and<br>
Update() call<br>
in the for loop ? They need to stay there, else<br>
you will<br>
always use<br>
the last image. That’s why you see the same<br>
image, the<br>
single update<br>
call will be triggered at the end of the script<br>
and read<br>
only one<br>
image.<br>
<br>
You don’t need to call tileFilter->Update(), you can<br>
remove this<br>
line. The writer->Update() will take care of the<br>
pipeline update. As<br>
a bonus, you may wrap your writer->Update() call, to<br>
fetch errors at<br>
the end of the pipeline:<br>
<br>
try { writer->Update(); } catch(<br>
itk::ExceptionObject &<br>
error ) {<br>
std::cerr << "Error: " << error << std::endl; return<br>
EXIT_FAILURE; }<br>
<br>
I made a little Python prototype, the syntax is<br>
a little bit<br>
different than in C++ but it gives you the main<br>
idea.<br>
<br>
Michka<br>
<br>
<br>
-- Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung Tomography and<br>
Digital Image<br>
Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie,<br>
OE 4120<br>
Medizinische Hochschule Hannover Carl-Neuberg-Str. 1<br>
D-30625<br>
Hannover<br>
<br>
Tel. <a href="tel:%2B49%20511%20532-2900" value="+495115322900" target="_blank">+49 511 532-2900</a> <tel:%2B49%20511%20532-2900><br>
<tel:%2B49%20511%20532-2900><br>
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<br>
-- Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung Tomography and<br>
Digital Image<br>
Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie, OE 4120<br>
Medizinische<br>
Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover<br>
<br>
Tel. <a href="tel:%2B49%20511%20532-2900" value="+495115322900" target="_blank">+49 511 532-2900</a> <tel:%2B49%20511%20532-2900><br>
<tel:%2B49%20511%20532-2900><br>
<br>
<br>
<br>
--<br>
Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung<br>
Tomography and Digital Image Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie, OE 4120<br>
Medizinische Hochschule Hannover<br>
Carl-Neuberg-Str. 1<br>
D-30625 Hannover<br>
<br>
Tel. <a href="tel:%2B49%20511%20532-2900" value="+495115322900" target="_blank">+49 511 532-2900</a> <tel:%2B49%20511%20532-2900><br></span><span>
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--<br>
Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung<br>
Tomography and Digital Image Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie, OE 4120<br>
Medizinische Hochschule Hannover<br>
Carl-Neuberg-Str. 1<br>
D-30625 Hannover<br>
<br></span><span>
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<br>
</span></blockquote><div><div>
<br>
-- <br>
Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung<br>
Tomography and Digital Image Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie, OE 4120<br>
Medizinische Hochschule Hannover<br>
Carl-Neuberg-Str. 1<br>
D-30625 Hannover<br>
<br>
Tel. <a href="tel:%2B49%20511%20532-2900" value="+495115322900" target="_blank">+49 511 532-2900</a><br>
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