From fisidoro at ethz.ch  Sun Oct  2 04:50:24 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Sun, 2 Oct 2016 08:50:24 +0000
Subject: [ITK-users] itk Python Wrapping: supported metrics and optimizers
Message-ID: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>

Hallo,

I am using itk v 9.0 with Python wrapping.

Which metrics and optimizers are supported in the wrapped version? I see that the metrics of itkv3 are not.

Thank you,
Fabio.

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From michkapopoff at gmail.com  Sun Oct  2 16:32:58 2016
From: michkapopoff at gmail.com (Michka Popoff)
Date: Sun, 2 Oct 2016 22:32:58 +0200
Subject: [ITK-users] itk Python Wrapping: supported metrics and
	optimizers
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>
Message-ID: <73989CE5-3400-4AE3-A943-F0DD7D1E87E2@gmail.com>

Hi

I think you are talking about itk V4 ?
If you want to use wrappings, it is really recommended to used one of the latests versions
of ITK. There were many improvements lately, and support for newer compilers was added.

The following metrics and optimizers are available:
https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Metricsv4/wrapping <https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Metricsv4/wrapping>
https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Numerics/Optimizersv4/wrapping <https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Numerics/Optimizersv4/wrapping>

If you need a specific metric or optimizer which is missing, feel free to ask,
we will try to add it.

Michka

> On 2 Oct 2016, at 10:50, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
> 
> Hallo,
>  
> I am using itk v 9.0 with Python wrapping.
>  
> Which metrics and optimizers are supported in the wrapped version? I see that the metrics of itkv3 are not.
>  
> Thank you,
> Fabio.
>  
> _____________________________________
> 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>
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From matt.mccormick at kitware.com  Sun Oct  2 21:14:29 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 2 Oct 2016 21:14:29 -0400
Subject: [ITK-users] itk Python Wrapping: supported metrics and
	optimizers
In-Reply-To: <73989CE5-3400-4AE3-A943-F0DD7D1E87E2@gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>
 <73989CE5-3400-4AE3-A943-F0DD7D1E87E2@gmail.com>
Message-ID: <CALzTN-QKi4_ROSe9DvVikgFihF9q3KmLQK9TXtuJES6MznZh_g@mail.gmail.com>

In addition, the ITKv3 wrapped metrics can be found here:

  https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Common/wrapping

As Michka mentioned, if there is a missing class, it can be added.

Thanks,
Matt

On Sun, Oct 2, 2016 at 4:32 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Hi
>
> I think you are talking about itk V4 ?
> If you want to use wrappings, it is really recommended to used one of the
> latests versions
> of ITK. There were many improvements lately, and support for newer compilers
> was added.
>
> The following metrics and optimizers are available:
> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Metricsv4/wrapping
> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Numerics/Optimizersv4/wrapping
>
> If you need a specific metric or optimizer which is missing, feel free to
> ask,
> we will try to add it.
>
> Michka
>
> On 2 Oct 2016, at 10:50, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
> Hallo,
>
> I am using itk v 9.0 with Python wrapping.
>
> Which metrics and optimizers are supported in the wrapped version? I see
> that the metrics of itkv3 are not.
>
> Thank you,
> Fabio.
>
> _____________________________________
> 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
>
>
>
> _____________________________________
> 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
>

From adariush at ast.cam.ac.uk  Mon Oct  3 10:01:49 2016
From: adariush at ast.cam.ac.uk (adariush)
Date: Mon, 03 Oct 2016 15:01:49 +0100
Subject: [ITK-users] read/write images in ITK
Message-ID: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>

Hello,

I am using ITK 10.0 on a MacBook Pro running on OS X El Capitan.

I have problem with reading/writing images. For example to read/write 
PNG image formats, I expect to do something like this:

=========================================================
#include "itkImage.h"
#include "itkImageFileReader.h"

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName('image name');
reader->Update();
=========================================================
However, the above code returns an error since it seems that 
"itkImage.h" does nothing at all!

Instead every time I want to read/write a PNG image, I should modify the 
above code as follow:


=========================================================
#include "itkImageFileReader.h"
#include "itkPNGImageIOFactory.h"                        // new line

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
itk::PNGImageIOFactory::RegisterOneFactory();             // new line
reader->SetFileName('image name');
reader->Update();
=========================================================


In short, I expect by including "itkImage.h", ITK automatically identify 
input/output image format. However, I have to do it manually. The 
problem is when I want to read for example a '.mha' file format.

Does anyone know what might be the problem and how could I 'SOLVE' it?

Thanks, Ali

From tevain at telecom-paristech.fr  Mon Oct  3 10:47:44 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 3 Oct 2016 16:47:44 +0200 (CEST)
Subject: [ITK-users] [ITK]  read/write images in ITK
In-Reply-To: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
References: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
Message-ID: <529249601.78344932.1475506064097.JavaMail.zimbra@enst.fr>

Hi,

Including the itkImage header as nothing to do with the ImageReader correctly calling the needed ImageIO.
Could you provide the error that arise when you try to read your image ?

Tim

----- Mail original -----
De: "adariush" <adariush at ast.cam.ac.uk>
?: insight-users at itk.org
Envoy?: Lundi 3 Octobre 2016 16:01:49
Objet: [ITK] [ITK-users] read/write images in ITK

Hello,

I am using ITK 10.0 on a MacBook Pro running on OS X El Capitan.

I have problem with reading/writing images. For example to read/write 
PNG image formats, I expect to do something like this:

=========================================================
#include "itkImage.h"
#include "itkImageFileReader.h"

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName('image name');
reader->Update();
=========================================================
However, the above code returns an error since it seems that 
"itkImage.h" does nothing at all!

Instead every time I want to read/write a PNG image, I should modify the 
above code as follow:


=========================================================
#include "itkImageFileReader.h"
#include "itkPNGImageIOFactory.h"                        // new line

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
itk::PNGImageIOFactory::RegisterOneFactory();             // new line
reader->SetFileName('image name');
reader->Update();
=========================================================


In short, I expect by including "itkImage.h", ITK automatically identify 
input/output image format. However, I have to do it manually. The 
problem is when I want to read for example a '.mha' file format.

Does anyone know what might be the problem and how could I 'SOLVE' it?

Thanks, Ali
_____________________________________
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
_______________________________________________
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From francois.budin at kitware.com  Mon Oct  3 10:49:32 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 3 Oct 2016 10:49:32 -0400
Subject: [ITK-users] read/write images in ITK
In-Reply-To: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
References: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
Message-ID: <CAHwLD2VdU_JvkFH7a4M2m9O7kr3QnYMjei9+9KFQ=PkkKaMx7A@mail.gmail.com>

Hello,

If you use the ITK IO factory, your first piece of code should work. The
automatic detection of the image format does not rely on the inclusion of
"itkImage.h", but relies on itkImageFileReader.h.
Do you use CMake to configure your project? If so, if you have the
following lines in your CMakeLists files, everything should be done
automatically:
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

After configuring your project, your build directory should contain a
folder named ITKIOFactoryRegistration.
If you do not use CMake to configure your project, I strongly suggest you
to do so. It will simplify a lot of things.
You can also manually register the ITK IOs that you want to support before
use reading your file. You can find some information in the last part of
the documentation provided on this page:
https://itk.org/Wiki/ITK/FAQ

Hope this helps,

Francois


On Mon, Oct 3, 2016 at 10:01 AM, adariush <adariush at ast.cam.ac.uk> wrote:

> Hello,
>
> I am using ITK 10.0 on a MacBook Pro running on OS X El Capitan.
>
> I have problem with reading/writing images. For example to read/write PNG
> image formats, I expect to do something like this:
>
> =========================================================
> #include "itkImage.h"
> #include "itkImageFileReader.h"
>
> typedef unsigned char  InputPixelType;
> typedef itk::Image< InputPixelType , 2 > InputImageType;
> typedef itk::ImageFileReader<InputImageType> ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName('image name');
> reader->Update();
> =========================================================
> However, the above code returns an error since it seems that "itkImage.h"
> does nothing at all!
>
> Instead every time I want to read/write a PNG image, I should modify the
> above code as follow:
>
>
> =========================================================
> #include "itkImageFileReader.h"
> #include "itkPNGImageIOFactory.h"                        // new line
>
> typedef unsigned char  InputPixelType;
> typedef itk::Image< InputPixelType , 2 > InputImageType;
> typedef itk::ImageFileReader<InputImageType> ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> itk::PNGImageIOFactory::RegisterOneFactory();             // new line
> reader->SetFileName('image name');
> reader->Update();
> =========================================================
>
>
> In short, I expect by including "itkImage.h", ITK automatically identify
> input/output image format. However, I have to do it manually. The problem
> is when I want to read for example a '.mha' file format.
>
> Does anyone know what might be the problem and how could I 'SOLVE' it?
>
> Thanks, Ali
> _____________________________________
> 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
>
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From swetha.bsharma at gmail.com  Tue Oct  4 06:37:51 2016
From: swetha.bsharma at gmail.com (swetha)
Date: Tue, 4 Oct 2016 03:37:51 -0700 (MST)
Subject: [ITK-users] C# wrapper ITk -unresolved external symbol issues
Message-ID: <1475577471463-7589328.post@n2.nabble.com>

Hi, 

  I have developed an application using itk and I am trying to integrate it
with c#.I have written a wrapper ,in the wrapper application I have included
all ITK .libs in the linker input tab.I am still getting unresolved external
errors. These are the errors which I am getting: 


Error	4	error LNK2019: unresolved external symbol __imp__UuidCreate at 4
referenced in function "protected: static bool __cdecl
gdcm::UIDGenerator::GenerateUUID(unsigned char *)"
(?GenerateUUID at UIDGenerator@gdcm@@KA_NPAE at Z)
\ObliquePlaneWrapper\itkgdcmMSFF-4.9.lib(gdcmUIDGenerator.obj)
ObliquePlaneWrapper 


Error	2	error LNK2019: unresolved external symbol _gethostname at 8 referenced
in function "public: static bool __cdecl gdcm::System::GetHostName(char *
const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
\ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
ObliquePlaneWrapper 

Error	1	error LNK2019: unresolved external symbol _WSACleanup at 0 referenced
in function "public: static bool __cdecl gdcm::System::GetHostName(char *
const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
\ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
ObliquePlaneWrapper 

Error	3	error LNK2019: unresolved external symbol _WSAStartup at 8 referenced
in function "public: static bool __cdecl gdcm::System::GetHostName(char *
const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
\ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
ObliquePlaneWrapper 


How do i fix these errors? 
-swetha 



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From dzenanz at gmail.com  Tue Oct  4 10:15:27 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 4 Oct 2016 10:15:27 -0400
Subject: [ITK-users] C# wrapper ITk -unresolved external symbol issues
In-Reply-To: <1475577471463-7589328.post@n2.nabble.com>
References: <1475577471463-7589328.post@n2.nabble.com>
Message-ID: <CAPf2UMTvv6DAhyWTemt=AnsWe1NhPCjR+BR4OGe4BDLiaRAk5Q@mail.gmail.com>

Hi Swetha,

are you using CMake to configure you wrapper "application", or are you
manually listing all the libraries? Manual enumeration is very error-prone
(some parts of GDCM seem to be missing). If so, try configuring one example
application using CMake to see which libraries get linked to it. Here is a
part of list on my computer which contains "gdcm", copy pasted from Visual
Studio project properties->linker->input->additional dependencies:
C:\Dev\ITK-2015\lib\Debug\itkgdcmDICT-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmMSFF-4.11.lib
C:\Dev\ITK-2015\lib\Debug\ITKIOGDCM-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmIOD-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmDSED-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmCommon-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmjpeg8-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmjpeg12-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmjpeg16-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmopenjpeg-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmcharls-4.11.lib

Are you trying to link a C# library into a C++ application or the other way
around?

Regards,
D?enan

On Tue, Oct 4, 2016 at 6:37 AM, swetha <swetha.bsharma at gmail.com> wrote:

> Hi,
>
>   I have developed an application using itk and I am trying to integrate it
> with c#.I have written a wrapper ,in the wrapper application I have
> included
> all ITK .libs in the linker input tab.I am still getting unresolved
> external
> errors. These are the errors which I am getting:
>
>
> Error   4       error LNK2019: unresolved external symbol
> __imp__UuidCreate at 4
> referenced in function "protected: static bool __cdecl
> gdcm::UIDGenerator::GenerateUUID(unsigned char *)"
> (?GenerateUUID at UIDGenerator@gdcm@@KA_NPAE at Z)
> \ObliquePlaneWrapper\itkgdcmMSFF-4.9.lib(gdcmUIDGenerator.obj)
> ObliquePlaneWrapper
>
>
> Error   2       error LNK2019: unresolved external symbol _gethostname at 8
> referenced
> in function "public: static bool __cdecl gdcm::System::GetHostName(char *
> const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
> \ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
> ObliquePlaneWrapper
>
> Error   1       error LNK2019: unresolved external symbol _WSACleanup at 0
> referenced
> in function "public: static bool __cdecl gdcm::System::GetHostName(char *
> const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
> \ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
> ObliquePlaneWrapper
>
> Error   3       error LNK2019: unresolved external symbol _WSAStartup at 8
> referenced
> in function "public: static bool __cdecl gdcm::System::GetHostName(char *
> const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
> \ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
> ObliquePlaneWrapper
>
>
> How do i fix these errors?
> -swetha
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/C-wrapper-ITk-unresolved-external-symbol-issues-
> tp7589328.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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From swetha.bsharma at gmail.com  Wed Oct  5 01:57:39 2016
From: swetha.bsharma at gmail.com (swetha)
Date: Tue, 4 Oct 2016 22:57:39 -0700 (MST)
Subject: [ITK-users] C# wrapper ITk -unresolved external symbol issues
In-Reply-To: <CAPf2UMTvv6DAhyWTemt=AnsWe1NhPCjR+BR4OGe4BDLiaRAk5Q@mail.gmail.com>
References: <1475577471463-7589328.post@n2.nabble.com>
 <CAPf2UMTvv6DAhyWTemt=AnsWe1NhPCjR+BR4OGe4BDLiaRAk5Q@mail.gmail.com>
Message-ID: <1475647059485-7589330.post@n2.nabble.com>

Hi Dzenan,

  I used CMAKe and it worked,I had manually added all the .lib files.
Thankyou so much Dzenan.
-swetha



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From ivan.granata.na at gmail.com  Wed Oct  5 01:50:13 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 4 Oct 2016 22:50:13 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
Message-ID: <1475646613139-37633.post@n7.nabble.com>

i tried this example and after 161 iteration


itk::simple::Transform
 TranslationTransform (0000000019D26F10)
   RTTI typeinfo:   class itk::TranslationTransform<double,3>
   Reference Count: 3
   Modified Time: 3008
   Debug: Off
   Object Name: 
   Observers: 
     none
   Offset: [-6.65479, -19.5028, -85.532]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Step too
small after 162 iterations. Current step (0.0078125) is less than minimum
step (0.01).
 Iteration: 163
 Metric value: 3451114,037376


run this error:    



Exception thrown in SimpleITK Transform_writeTransform:
c:\d\vs9-pkg\simpleitk-build\itk-prefix\include\itk-4.7\itkTransformFileWriter.hxx:202:
itk::ERROR: TransformFileWriterTemplate(0000000019D2DBA0): Can't Create IO
object for file
C:\Users\Ivan\workspace\ImageRegistrationMethod1\registrata.nii



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From blowekamp at mail.nih.gov  Wed Oct  5 08:53:51 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 5 Oct 2016 12:53:51 +0000
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <1475646613139-37633.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
Message-ID: <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>

What is the command line you used?

Does the output path C:\Users\Ivan\workspace\ImageRegistrationMethod1? already exists?

Brad

> On Oct 5, 2016, at 1:50 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> i tried this example and after 161 iteration
> 
> 
> itk::simple::Transform
> TranslationTransform (0000000019D26F10)
>   RTTI typeinfo:   class itk::TranslationTransform<double,3>
>   Reference Count: 3
>   Modified Time: 3008
>   Debug: Off
>   Object Name: 
>   Observers: 
>     none
>   Offset: [-6.65479, -19.5028, -85.532]
> 
> Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Step too
> small after 162 iterations. Current step (0.0078125) is less than minimum
> step (0.01).
> Iteration: 163
> Metric value: 3451114,037376
> 
> 
> run this error:    
> 
> 
> 
> Exception thrown in SimpleITK Transform_writeTransform:
> c:\d\vs9-pkg\simpleitk-build\itk-prefix\include\itk-4.7\itkTransformFileWriter.hxx:202:
> itk::ERROR: TransformFileWriterTemplate(0000000019D2DBA0): Can't Create IO
> object for file
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\registrata.nii
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37633.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
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> 
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> 
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From ivan.granata.na at gmail.com  Wed Oct  5 07:51:30 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 04:51:30 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
Message-ID: <1475668290769-37635.post@n7.nabble.com>

i must coreg these 
CT with T1

the path already exist, yes


i use eclipse ide with these arguments
C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\Headt1mpragesagp2iso08s007a1001.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\registrata.nii


i tried this
http://review.source.kitware.com/#/c/21596/1/Examples/Java/ImageRegistrationMethod1.java
, but several errors appear
if i change parameters...change error

for example
i take a  minStep > 0.01; and error is on numberOfIterazions
i take a numberOfIterations > 20 or <200 and the error return on minStep
  same things on relaxationFactor = 0.5; or =0.8

i tried also this script but it is the same


import org.itk.simple.*;


class IterationUpdate  extends Command {

	  private ImageRegistrationMethod m_Method;

	  public IterationUpdate(ImageRegistrationMethod m) {
	    super();
	    m_Method=m;
	  }

	  public void execute() {
	    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
	    System.out.format("%3d = %10.5f : [%f, %f]\n",
	                      m_Method.getOptimizerIteration(),
	                      m_Method.getMetricValue(),
	                      pos.get(0), pos.get(1));
	  }
	}

class ImageRegistrationMethod1 {

  public static void main(String argv[]) {

  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethod1");
      System.exit(-1);
    }

  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );

  reader.setFileName(argv[0]);
  Image fixed = reader.execute();

  reader.setFileName(argv[1]);
  Image moving = reader.execute();

  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
  
  
  

  
 
   int numberOfBins = 64;
  
  R.setMetricAsMattesMutualInformation(numberOfBins);
  
  double LearningRate = 8.0;
  long numberOfIterations = 100;
  double convergenceMinimumValue = 1e-6;
  long convergenceWindowSize = 10;
  double lineSearchLowerLimit = 0;
  
  R.setOptimizerAsGradientDescentLineSearch( LearningRate,
          numberOfIterations,
          convergenceMinimumValue,
          convergenceWindowSize,
          lineSearchLowerLimit
          );
  
  

  R.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkLinear );

  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);

  org.itk.simple.Transform outTx = R.execute( fixed, moving );

  System.out.println("-------");
  System.out.println(outTx.toString());
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());

  outTx.writeTransform(argv[2]);

  }

}






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From blowekamp at mail.nih.gov  Wed Oct  5 09:24:17 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 5 Oct 2016 13:24:17 +0000
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <1475668290769-37635.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
Message-ID: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>

I would look at the test parameter used for this example:

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Java/CMakeLists.txt#L24

The third parameter is a transform and not an image format. Supported extensions include ?txt?, ?hdf5? and I believe ?mat?.

Please try to reproduce the test before moving on.

Brad


From ivan.granata.na at gmail.com  Wed Oct  5 08:12:56 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:12:56 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475669576013-37637.post@n7.nabble.com>

and the output?
i would read System.out.format( "Usage: %s <fixedImageFilter>
<movingImageFile> <outputTransformFile>\n", "ImageRegistrationMethod1");



C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\Headt1mpragesagp2iso08s007a1001.nii 

..........  third arguments?



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From ivan.granata.na at gmail.com  Wed Oct  5 08:22:42 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:22:42 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475670162009-37638.post@n7.nabble.com>

ok i use these

C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\Headt1mpragesagp2iso08s007a1001.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\reg.txt

but if i open txt file i've 

#Insight Transform File V1.0
#Transform 0
Transform: TranslationTransform_double_3_3
Parameters: 2.4513961563310462 -15.82828376173809 -69.1961914372912
FixedParameters: 



what about this? i would an image coreg



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From ivan.granata.na at gmail.com  Wed Oct  5 08:23:57 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:23:57 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475670237866-37639.post@n7.nabble.com>

i receive this

  0 = 665122,88518 : [0,134024, -1,321073]
  1 = 669400,27636 : [0,251056, -2,660742]
  2 = 674931,78583 : [0,349982, -4,100354]
  3 = 681844,66614 : [0,474374, -5,702413]
  4 = 689465,45986 : [0,626028, -7,323900]
  5 = 698185,32936 : [0,843615, -9,192783]
  6 = 707489,19565 : [1,050153, -10,999621]
  7 = 717268,70721 : [1,204555, -12,460959]
  8 = 743987,25838 : [1,327348, -13,160174]
  9 = 757137,55193 : [1,453234, -13,474015]
 10 = 771437,65405 : [1,623318, -13,741873]
 11 = 786922,16242 : [1,816794, -14,097160]
 12 = 803545,10774 : [2,077654, -14,547859]
 13 = 840861,28970 : [2,338309, -14,986500]
 14 = 858852,80038 : [2,454045, -15,316711]
 15 = 877420,96469 : [2,459722, -15,519754]
 16 = 893981,36101 : [2,456281, -15,687996]
 17 = 902994,83757 : [2,451396, -15,828284]
-------
itk::simple::Transform
 TranslationTransform (0000000019B04710)
   RTTI typeinfo:   class itk::TranslationTransform<double,3>
   Reference Count: 3
   Modified Time: 2576
   Debug: Off
   Object Name: 
   Observers: 
     none
   Offset: [2.4514, -15.8283, -69.1962]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Gradient
magnitude tolerance met after 18 iterations. Gradient magnitude (0) is less
than gradient magnitude tolerance (0.0001).
 Iteration: 19
 Metric value:
179769313486231570000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000,000000




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From ivan.granata.na at gmail.com  Wed Oct  5 08:34:29 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:34:29 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475670869976-37640.post@n7.nabble.com>

with my example where i use


  R.setMetricAsMattesMutualInformation(numberOfBins);
  
  double LearningRate = 8.0;
  double minStep = 0.001;
  long numberOfIterations = 100;
  double relaxationFactor = 0.5;
  double gradientMagnitudeTolerance = 1e-006;
  
  R.setOptimizerAsRegularStepGradientDescent



 i receive a txt file and this video output

  0 =   -0,15630 : [0,746321, -7,955376]
  1 =   -0,17854 : [1,437118, -15,910358]
  2 =   -0,19452 : [1,031387, -23,317717]
  3 =   -0,20341 : [3,410042, -21,038059]
  4 =   -0,19856 : [1,526970, -21,439759]
  5 =   -0,20108 : [0,143113, -22,783732]
  6 =   -0,20340 : [1,089391, -22,619125]
  7 =   -0,20366 : [1,647981, -21,912288]
  8 =   -0,20073 : [1,184824, -22,085392]
  9 =   -0,20140 : [0,993548, -22,508374]
 10 =   -0,20281 : [1,192105, -22,356475]
 11 =   -0,20253 : [1,117475, -22,167086]
 12 =   -0,20169 : [1,075827, -22,241268]
 13 =   -0,20225 : [1,126952, -22,206076]
 14 =   -0,20222 : [1,122912, -22,147089]
 15 =   -0,20209 : [1,108291, -22,166964]
 16 =   -0,20222 : [1,118988, -22,159212]
 17 =   -0,20224 : [1,125776, -22,145295]
 18 =   -0,20224 : [1,118157, -22,146866]
 19 =   -0,20226 : [1,119790, -22,149387]
-------
itk::simple::Transform
 TranslationTransform (0000000019CD54D0)
   RTTI typeinfo:   class itk::TranslationTransform<double,3>
   Reference Count: 3
   Modified Time: 2659
   Debug: Off
   Object Name: 
   Observers: 
     none
   Offset: [1.11979, -22.1494, 4.96231]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Gradient
magnitude tolerance met after 20 iterations. Gradient magnitude (9.89e-007)
is less than gradient magnitude tolerance (1e-006).
 Iteration: 21
 Metric value: -0,202264




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From ibr_ex at yahoo.com  Wed Oct  5 13:52:48 2016
From: ibr_ex at yahoo.com (Ibraheem)
Date: Wed, 5 Oct 2016 10:52:48 -0700 (MST)
Subject: [ITK-users] [ITK]  Linker errors on example
In-Reply-To: <CALzTN-TVB=bdBzbXogtXypwkbmBouxxYGZ1ZQLEketfOztJ72w@mail.gmail.com>
References: <CAPEEyN5p03uQ7TeEAkZi1dihT-=U5KsMufwXZ7s-kdS8JiHS4A@mail.gmail.com>
 <CADZJ4hOYhZT5TwUaVy+r=DYEk1+QAEg_QTPwHyiZLdnrHJrYWw@mail.gmail.com>
 <CAPEEyN4KGmayTk0arRegTakUrAJ0QCFuu+QAMXgY66=n+CJ4DA@mail.gmail.com>
 <CALzTN-TVB=bdBzbXogtXypwkbmBouxxYGZ1ZQLEketfOztJ72w@mail.gmail.com>
Message-ID: <1475689968144-37641.post@n7.nabble.com>

I just downloaded the example. It works but I think the visualization part is
missing. I think it is already implemented because of the figures. Is it
possible to add the QuickView part or itkImageFileWriter to visualize the
result? I tried to do so but it didn't works. 
Best regards!



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From francois.budin at kitware.com  Wed Oct  5 15:24:43 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 5 Oct 2016 15:24:43 -0400
Subject: [ITK-users] [ITK] Linker errors on example
In-Reply-To: <1475689968144-37641.post@n7.nabble.com>
References: <CAPEEyN5p03uQ7TeEAkZi1dihT-=U5KsMufwXZ7s-kdS8JiHS4A@mail.gmail.com>
 <CADZJ4hOYhZT5TwUaVy+r=DYEk1+QAEg_QTPwHyiZLdnrHJrYWw@mail.gmail.com>
 <CAPEEyN4KGmayTk0arRegTakUrAJ0QCFuu+QAMXgY66=n+CJ4DA@mail.gmail.com>
 <CALzTN-TVB=bdBzbXogtXypwkbmBouxxYGZ1ZQLEketfOztJ72w@mail.gmail.com>
 <1475689968144-37641.post@n7.nabble.com>
Message-ID: <CAHwLD2V+FxvuRjvJW_mr+-sn6nc54vVndjrf3-Y=kP0DEZ9ybA@mail.gmail.com>

Hello Ibraheem,

ITK does not provide visualization as part of the toolkit. If you want to
look at the output of this example, I would advise you to either use an
existing tool, such as ITKSnap [1] or 3DSlicer[ 2], or if you want to
create your own visualization tool, you can use VTK [3] with ITK.
Hope this helps,

Francois
[1] http://www.itksnap.org/pmwiki/pmwiki.php
[2] https://www.slicer.org/
[3] https://itk.org/Wiki/ITK/Examples/IO/ImageToVTKImageFilter

On Wed, Oct 5, 2016 at 1:52 PM, Ibraheem via Insight-users <
insight-users at itk.org> wrote:

> I just downloaded the example. It works but I think the visualization part
> is
> missing. I think it is already implemented because of the figures. Is it
> possible to add the QuickView part or itkImageFileWriter to visualize the
> result? I tried to do so but it didn't works.
> Best regards!
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-ITK-Linker-errors-on-example-tp33858p37641.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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From ibr_ex at yahoo.com  Thu Oct  6 02:23:31 2016
From: ibr_ex at yahoo.com (Ibraheem)
Date: Wed, 5 Oct 2016 23:23:31 -0700 (MST)
Subject: [ITK-users] [ITK] Linker errors on example
In-Reply-To: <CAHwLD2V+FxvuRjvJW_mr+-sn6nc54vVndjrf3-Y=kP0DEZ9ybA@mail.gmail.com>
References: <CAPEEyN5p03uQ7TeEAkZi1dihT-=U5KsMufwXZ7s-kdS8JiHS4A@mail.gmail.com>
 <CADZJ4hOYhZT5TwUaVy+r=DYEk1+QAEg_QTPwHyiZLdnrHJrYWw@mail.gmail.com>
 <CAPEEyN4KGmayTk0arRegTakUrAJ0QCFuu+QAMXgY66=n+CJ4DA@mail.gmail.com>
 <CALzTN-TVB=bdBzbXogtXypwkbmBouxxYGZ1ZQLEketfOztJ72w@mail.gmail.com>
 <1475689968144-37641.post@n7.nabble.com>
 <CAHwLD2V+FxvuRjvJW_mr+-sn6nc54vVndjrf3-Y=kP0DEZ9ybA@mail.gmail.com>
Message-ID: <1475735011331-37643.post@n7.nabble.com>

Hi Francois,
thanks for your quick response :-) . I've already seen some ITK examples
with the visualization part so it would be nice if the author of this
example provided the complete code (from the figures, it is clear he already
did the visualization part). 
Have a nice day!
Ibraheem



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From ivan.granata.na at gmail.com  Thu Oct  6 02:27:14 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 23:27:14 -0700 (MST)
Subject: [ITK-users] SITK Java Multicomponent PatchBasedDenoisingImageFilter
 not run for 4D images or multicomponent.. a similar filter for 4D images?
Message-ID: <1475735234617-37644.post@n7.nabble.com>

i tried PatchBasedDenoisingImageFilter simple itk  Java version for 4d images
but it work just with 3d images

can anyone know some similar filter for 4d images?

something for multicomponent filter?

thx



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Sent from the ITK - Users mailing list archive at Nabble.com.

From ivan.granata.na at gmail.com  Thu Oct  6 08:32:21 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 05:32:21 -0700 (MST)
Subject: [ITK-users] SimpleITK JAVA ImageSeriesReader and
 PatchBasedDenoisingImageFilter and 4d images
Message-ID: <1475757141426-37645.post@n7.nabble.com>

hi 

can anyone help me how to write ImageSeriesReader in Java with simple itk

i wolud read a dicom series in a path and after apply a
PatchBasedDenoisingImageFilter

if possible i would work also with 4d image (multicomponent filter)


thx


this is my code

import org.itk.simple.*;

import java.util.Vector; 
class PatchBasedDenoisingImageFilter {
public static void main(String argv[]) {
		
	if ( argv.length < 5 ) {
System.out.println("Immetti prima:  <input_img> <patch_radius> <smoothness>
<patch_number> <noise_sigma> <output_img>");
return;
}

org.itk.simple.ImageSeriesReader reader = new
org.itk.simple.ImageSeriesReader();

VectorString inputdicom = new VectorString();
inputdicom.toString(argv[0]);
reader.setFileNames(inputdicom);


//reader.setVectorString (argv[0]);
//reader.setFileNames(inputdicom);


Image img = reader.execute();

System.out.println(img.getDimension());

org.itk.simple.PatchBasedDenoisingImageFilter filter = new
org.itk.simple.PatchBasedDenoisingImageFilter();

filter.getAlwaysTreatComponentsAsEuclidean ();
boolean setKBE = false;
filter.setKernelBandwidthEstimation ( setKBE );
//filter.getKernelBandwidthUpdateFrequency ();
//filter.getKernelBandwidthFractionPixelsForEstimation ();
//filter.getKernelBandwidthMultiplicationFactor ();
//filter.getKernelBandwidthSigma ();
filter.setNoiseModel(org.itk.simple.PatchBasedDenoisingImageFilter.NoiseModelType.GAUSSIAN);
filter.getNumberOfIterations (); //cablato
filter.getSampleVariance ();
filter.setPatchRadius ( Long.valueOf ( argv[1] ).longValue() );
filter.setNoiseModelFidelityWeight ( Double.valueOf ( argv[2]
).doubleValue() );

if ( argv.length < 5 ) filter.getNumberOfSamplePatches ();
else filter.setNumberOfSamplePatches ( Long.valueOf ( argv[3] ).longValue()
);

if ( argv.length < 6 ) 
	filter.getNoiseSigma ();
else filter.setNoiseSigma (Double.valueOf ( argv[4] ).doubleValue() );

Image blurredImg  = filter.execute(img);

CastImageFilter caster = new CastImageFilter();
caster.setOutputPixelType( img.getPixelIDValue() );
Image castImg = caster.execute( blurredImg );
ImageFileWriter writer = new ImageFileWriter();

writer.setFileName(argv[5]);
writer.execute( castImg ); 
}


}
}












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From blowekamp at mail.nih.gov  Thu Oct  6 10:01:24 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 6 Oct 2016 14:01:24 +0000
Subject: [ITK-users] SimpleITK JAVA ImageSeriesReader and
 PatchBasedDenoisingImageFilter and 4d images
In-Reply-To: <1475757141426-37645.post@n7.nabble.com>
References: <1475757141426-37645.post@n7.nabble.com>
Message-ID: <6858503C-9EEE-44DF-8DEC-636AF4ACA3FA@mail.nih.gov>

I would look at the python examples and usage for reference:

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/DicomSeriesReader.py
https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/DicomSeriesReader2.py

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/CMakeLists.txt#L73-L89

HTH,
Brad

> On Oct 6, 2016, at 8:32 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> hi 
> 
> can anyone help me how to write ImageSeriesReader in Java with simple itk
> 
> i wolud read a dicom series in a path and after apply a
> PatchBasedDenoisingImageFilter
> 
> if possible i would work also with 4d image (multicomponent filter)
> 
> 
> thx
> 
> 
> this is my code
> 
> import org.itk.simple.*;
> 
> import java.util.Vector; 
> class PatchBasedDenoisingImageFilter {
> public static void main(String argv[]) {
> 		
> 	if ( argv.length < 5 ) {
> System.out.println("Immetti prima:  <input_img> <patch_radius> <smoothness>
> <patch_number> <noise_sigma> <output_img>");
> return;
> }
> 
> org.itk.simple.ImageSeriesReader reader = new
> org.itk.simple.ImageSeriesReader();
> 
> VectorString inputdicom = new VectorString();
> inputdicom.toString(argv[0]);
> reader.setFileNames(inputdicom);
> 
> 
> //reader.setVectorString (argv[0]);
> //reader.setFileNames(inputdicom);
> 
> 
> Image img = reader.execute();
> 
> System.out.println(img.getDimension());
> 
> org.itk.simple.PatchBasedDenoisingImageFilter filter = new
> org.itk.simple.PatchBasedDenoisingImageFilter();
> 
> filter.getAlwaysTreatComponentsAsEuclidean ();
> boolean setKBE = false;
> filter.setKernelBandwidthEstimation ( setKBE );
> //filter.getKernelBandwidthUpdateFrequency ();
> //filter.getKernelBandwidthFractionPixelsForEstimation ();
> //filter.getKernelBandwidthMultiplicationFactor ();
> //filter.getKernelBandwidthSigma ();
> filter.setNoiseModel(org.itk.simple.PatchBasedDenoisingImageFilter.NoiseModelType.GAUSSIAN);
> filter.getNumberOfIterations (); //cablato
> filter.getSampleVariance ();
> filter.setPatchRadius ( Long.valueOf ( argv[1] ).longValue() );
> filter.setNoiseModelFidelityWeight ( Double.valueOf ( argv[2]
> ).doubleValue() );
> 
> if ( argv.length < 5 ) filter.getNumberOfSamplePatches ();
> else filter.setNumberOfSamplePatches ( Long.valueOf ( argv[3] ).longValue()
> );
> 
> if ( argv.length < 6 ) 
> 	filter.getNoiseSigma ();
> else filter.setNoiseSigma (Double.valueOf ( argv[4] ).doubleValue() );
> 
> Image blurredImg  = filter.execute(img);
> 
> CastImageFilter caster = new CastImageFilter();
> caster.setOutputPixelType( img.getPixelIDValue() );
> Image castImg = caster.execute( blurredImg );
> ImageFileWriter writer = new ImageFileWriter();
> 
> writer.setFileName(argv[5]);
> writer.execute( castImg ); 
> }
> 
> 
> }
> }
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-JAVA-ImageSeriesReader-and-PatchBasedDenoisingImageFilter-and-4d-images-tp37645.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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


From dzenanz at gmail.com  Thu Oct  6 10:25:58 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 10:25:58 -0400
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <1475670162009-37638.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670162009-37638.post@n7.nabble.com>
Message-ID: <CAPf2UMSF+oT9u=k7KZ+-Jp2Vqb1GHucg132Y5qYLEYANkGhe9Q@mail.gmail.com>

Hi Ivan,

the reg.txt file is a saved transform, and you should be able to use it to
resample <https://itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html>
your input image to the space of your target image.

Regards,
D?enan

On Wed, Oct 5, 2016 at 8:22 AM, ivan <ivan.granata.na at gmail.com> wrote:

> ok i use these
>
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\
> Headt1mpragesagp2iso08s007a1001.nii
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\reg.txt
>
> but if i open txt file i've
>
> #Insight Transform File V1.0
> #Transform 0
> Transform: TranslationTransform_double_3_3
> Parameters: 2.4513961563310462 -15.82828376173809 -69.1961914372912
> FixedParameters:
>
>
>
> what about this? i would an image coreg
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37638.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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From dzenanz at gmail.com  Thu Oct  6 10:28:22 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 10:28:22 -0400
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <1475670869976-37640.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
Message-ID: <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>

Hi Ivan,

the optimizers in ITK minimize the metric, and since mutual information
needs to be "bigger" it is prefixed by a minus so that optimizers try to
increase its absolute value.

Regards,
D?enan

On Wed, Oct 5, 2016 at 8:34 AM, ivan <ivan.granata.na at gmail.com> wrote:

> with my example where i use
>
>
>   R.setMetricAsMattesMutualInformation(numberOfBins);
>
>   double LearningRate = 8.0;
>   double minStep = 0.001;
>   long numberOfIterations = 100;
>   double relaxationFactor = 0.5;
>   double gradientMagnitudeTolerance = 1e-006;
>
>   R.setOptimizerAsRegularStepGradientDescent
>
>
>
>  i receive a txt file and this video output
>
>   0 =   -0,15630 : [0,746321, -7,955376]
>   1 =   -0,17854 : [1,437118, -15,910358]
>   2 =   -0,19452 : [1,031387, -23,317717]
>   3 =   -0,20341 : [3,410042, -21,038059]
>   4 =   -0,19856 : [1,526970, -21,439759]
>   5 =   -0,20108 : [0,143113, -22,783732]
>   6 =   -0,20340 : [1,089391, -22,619125]
>   7 =   -0,20366 : [1,647981, -21,912288]
>   8 =   -0,20073 : [1,184824, -22,085392]
>   9 =   -0,20140 : [0,993548, -22,508374]
>  10 =   -0,20281 : [1,192105, -22,356475]
>  11 =   -0,20253 : [1,117475, -22,167086]
>  12 =   -0,20169 : [1,075827, -22,241268]
>  13 =   -0,20225 : [1,126952, -22,206076]
>  14 =   -0,20222 : [1,122912, -22,147089]
>  15 =   -0,20209 : [1,108291, -22,166964]
>  16 =   -0,20222 : [1,118988, -22,159212]
>  17 =   -0,20224 : [1,125776, -22,145295]
>  18 =   -0,20224 : [1,118157, -22,146866]
>  19 =   -0,20226 : [1,119790, -22,149387]
> -------
> itk::simple::Transform
>  TranslationTransform (0000000019CD54D0)
>    RTTI typeinfo:   class itk::TranslationTransform<double,3>
>    Reference Count: 3
>    Modified Time: 2659
>    Debug: Off
>    Object Name:
>    Observers:
>      none
>    Offset: [1.11979, -22.1494, 4.96231]
>
> Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Gradient
> magnitude tolerance met after 20 iterations. Gradient magnitude (9.89e-007)
> is less than gradient magnitude tolerance (1e-006).
>  Iteration: 21
>  Metric value: -0,202264
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37640.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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From ivan.granata.na at gmail.com  Thu Oct  6 09:32:51 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 06:32:51 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
References: <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
Message-ID: <1475760771636-37649.post@n7.nabble.com>

and so < TInputImage, TOutputImage, TInterpolatorPrecisionType,
TTransformPrecisionType >


what about TInterpolatorPrecisionType, TTransformPrecisionType ???



--
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From dzenanz at gmail.com  Thu Oct  6 11:53:29 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 11:53:29 -0400
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <1475760771636-37649.post@n7.nabble.com>
References: <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
Message-ID: <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>

Hi Ivan,

the defaults for those two are double. What is unclear about that?

Regards,
D?enan

On Thu, Oct 6, 2016 at 9:32 AM, ivan <ivan.granata.na at gmail.com> wrote:

> and so < TInputImage, TOutputImage, TInterpolatorPrecisionType,
> TTransformPrecisionType >
>
>
> what about TInterpolatorPrecisionType, TTransformPrecisionType ???
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37649.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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From ivan.granata.na at gmail.com  Thu Oct  6 12:41:01 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 09:41:01 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
References: <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
Message-ID: <1475772061671-37651.post@n7.nabble.com>

if i use my original image here < TInputImage, TOutputImage

where i can use my reg.txt (ImageRegistration function output)

so ok TInterpolatorPrecisionType, TTransformPrecisionType these are other
parameters....and reg.txt file output?



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From dzenanz at gmail.com  Thu Oct  6 14:16:54 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 14:16:54 -0400
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <1475772061671-37651.post@n7.nabble.com>
References: <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
Message-ID: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>

Have you read section "2.9.4 Resample Image Filter" from
itk.org/ItkSoftwareGuide? The reg.txt file contains the transformation
which you want to apply to an image.

Regards

On Thu, Oct 6, 2016 at 12:41 PM, ivan <ivan.granata.na at gmail.com> wrote:

> if i use my original image here < TInputImage, TOutputImage
>
> where i can use my reg.txt (ImageRegistration function output)
>
> so ok TInterpolatorPrecisionType, TTransformPrecisionType these are other
> parameters....and reg.txt file output?
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37651.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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From ivan.granata.na at gmail.com  Thu Oct  6 13:36:06 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 10:36:06 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
References: <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
 <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
Message-ID: <1475775366240-37653.post@n7.nabble.com>

yes  i read but in Java i ve some problems 



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From francois.budin at kitware.com  Thu Oct  6 17:43:55 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 6 Oct 2016 17:43:55 -0400
Subject: [ITK-users] [ANN] ITK 4.10.0 has been released!
Message-ID: <CAHwLD2X5XbGycZmtnfoZYibxPeiuZgHxF+X1W2UGN=KApn35hQ@mail.gmail.com>

On behalf of the Insight Toolkit Community, we are happy to announce the
release of ITK 4.10.1!

Release files can be downloaded from:

 http://itk.org/ITK/resources/software.html

This is a patch release that fixes critical issues, regressions,
documentation, and compiler support. Of the numerous issues addressed in
this release, most notable is a fix to the ITK Python wrapping lazy
loading. This improves load times for many Python scripts by an order of
magnitude! Other important fixes include Python builds with GCC 6.2, which
defaults to C++14, TBB 4.4/VTK 7 compatibility, and CUDA / C++11
compatibility.

The next feature release, 4.11.0, is scheduled for mid-December.

Enjoy ITK!


Changes from v4.10.0 to v4.10.1:

Bradley Lowekamp (9):

     COMP: Address VS9 ambiguous std::abs call in Haung calculator

     COMP: Fix undefined NumericTraits::Zero and One errors with mingw64

     BUG: Address itkHDF5ImageIO test failures for mingw64

     ENH: Enable CMP0063 New behavior

     COMP: Enable hidden visibility property with vxl static libraries

    COMP: Enable hidden visibility property with HDF5 static libraries

     BUG: Match Add2 function to AddImageFilter documentation

     COMP: Bypass XCode 7.3,8 internal compilation error

     ENH: Separate TransformFactory class into separate module

D?enan Zuki? (2):

     COMP: enables TBB 4.4 back-end for VTK7's SMP

     BUG: fixing buffer growing endlessly, as reported by Timothee Evain

Francois Budin (3):

     BUG: lazyAttributes dictionary keys could be over-ridden

     BUG: Missing associated test data

     ENH: Bump CMakeLists.txt version to 4.10.1.

Gert Wollny (1):

     BUG: Relax vnl_complex floating point comparisons for i386

Hans Johnson (1):

     COMP: Add long long usage for HDF5

Hastings Greer (4):

     BUG: ITK-3448 Wrap itkQuadEdgeCellTraitsInfo more specifically

     BUG: remove lsqr because of license issues ITK 1160

     BUG: make itkTriangleHelper instantiable to ease wrapping

     BUG: initialize X to zero in lsmr Solve

Matthew McCormick (13):

     BUG: Fix H5File memory leak in HDF5ImageIO.

     BUG: Limit WRAP_ITK_MODULES when building externally

     COMP: Fix wrapping with a space in the Python include path

     BUG: ResampleImageFilter honor isInside output of the transform method

     COMP: Avoid recursive include of itkMath.h

     COMP: Use add_python_test PythonLazyLoadingImage

     BUG: Index,Size,Offset constructors present in Python with C++11

     COMP: Address missing override it itkFactoryTestLib.cxx

     BUG: Address memory leak, remove NumPy build dep in BridgeNumPy

     COMP: Do not set ITK_LIBRARY_BUILD_TYPE in ITKTransformFactory

     BUG: Check when ITK_WRAP_VECTOR_COMPONENTS doesn't include
ITK_WRAP_IMAGE_DIMS

     BUG: RichardsonLucyDeconvolutionImageFilter with non-null input Image
Origin

     BUG: Fix inconsistent Twister start with Initialize(seed) and
SetSeed(seed)

Pierre Barbier de Reuille (1):

     COMP: Fix function naming error when using FFTWD

Simon Rit (1):

     COMP: remove C++11 compiler warning for CUDA compilations

Vladimir S. FONOV (1):

     COMP: Build against GCC 5.3.1

Ziv Yaniv (1):
     BUG: Metric sampling percentage accepted values outside (0.0, 1.0].
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From ivan.granata.na at gmail.com  Sun Oct  9 02:43:30 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Sat, 8 Oct 2016 23:43:30 -0700 (MST)
Subject: [ITK-users] SimpleITK JAVA ImageRegistrationMethod --> after
 ResampleImageFilter, how?
Message-ID: <1475995410853-37655.post@n7.nabble.com>

i tried to write a registration with simple ITK java code with
ImageRegistrationMethod

in input i've fixedimage movingimage 
in output i've a trasform.txt file


transform.txt contains these informations:



but as final output i want an image coreg not just a parameters in txt

so i read ResampleImageFilter for this goal  (i think is good) but in java i
don't understand how i can integrate in my code

Plese someone can help me?




this is my code



import org.itk.simple.*;


class IterationUpdate  extends Command {

  private ImageRegistrationMethod m_Method;

  public IterationUpdate(ImageRegistrationMethod m) {
    super();
    m_Method=m;
  }

  public void execute() {
    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
    System.out.format("%3d = %10.5f : [%f, %f]\n",
                      m_Method.getOptimizerIteration(),
                      m_Method.getMetricValue(),
                      pos.get(0), pos.get(1));
  }
}

class ImageRegistrationMethodNaplab {

  public static void main(String argv[]) {

  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }

  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );

  reader.setFileName(argv[0]);
  Image fixed = reader.execute();

  reader.setFileName(argv[1]);
  Image moving = reader.execute();

  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
  R.setMetricAsMattesMutualInformation();
  double maxStep = 4.0;
  double minStep = 0.001;
  int numberOfIterations = 200;
  double relaxationFactor = 0.5;
  R.setOptimizerAsRegularStepGradientDescent( maxStep,
                                              minStep,
                                              numberOfIterations,
                                              relaxationFactor );
  R.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkLinear );

  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);

  org.itk.simple.Transform outTx = R.execute( fixed, moving );

  System.out.println("-------");
  System.out.println(outTx.toString());
  //System.out.format(" Fixed Initial Transform: %d\n",
R.getFixedInitialTransform());
  //System.out.format(" Moving Initial Transform: %d\n",
R.getMovingInitialTransform());
  //System.out.format(" Initial Transform: %d\n", R.getInitialTransform());
  System.out.format(" Optimizer Position: %d\n", R.getOptimizerPosition());
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());
  System.out.format(" Interpolator: %f\n", R.getInterpolator());
  //System.out.format(" Translation X", R.getTranslationAlongX());
 // System.out.format(" Translation Y", R.getTranslationAlongY());
  outTx.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
 
  //org.itk.simple.Transform.writeTransform(argv[4]);
  //org.itk.simple.ResampleImageFilter image = new
org.itk.simple.ResampleImageFilter();
  //image.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
 // image.getOutputPixelType(); 
 // image.getSize ();

  //ImageFileWriter writer = new ImageFileWriter();

 // writer.setFileName(argv[5]);
  



  }  

  
 
  
  
  
  
}
  



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From ivan.granata.na at gmail.com  Wed Oct 12 02:02:35 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 11 Oct 2016 23:02:35 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
References: <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
 <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
Message-ID: <1476252155238-37656.post@n7.nabble.com>


I have solved. I have applied the txt to "moving" image



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From ivan.granata.na at gmail.com  Wed Oct 12 02:41:39 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 11 Oct 2016 23:41:39 -0700 (MST)
Subject: [ITK-users]  Image Fusion SimpleITK for Java with wavelet?
Message-ID: <1476254499226-37657.post@n7.nabble.com>

Can anyone help me to find something for apply fusion image in SimpleITK JAVA
version? in particular fusion with wavelet image fusion

something in "org.itk.simple" for image fusion and wavelet image fusion?


Best Regards


Ivan



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From cr at neuro.ma.uni-heidelberg.de  Wed Oct 12 11:57:05 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Wed, 12 Oct 2016 17:57:05 +0200
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
Message-ID: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>

Hi,

I think it would be helpful if the documentation of the filter would 
mention that there are two outputs, one with the surviving labels and 
the second with the removed labels (the input image is the union of 
these images). What is the workflow to achieve this?

Christina


From matt.mccormick at kitware.com  Wed Oct 12 12:03:41 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 12 Oct 2016 12:03:41 -0400
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
In-Reply-To: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
Message-ID: <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>

Hello Christina,

Good idea.

To update the documentation, the class Doxygen documentation can be editted:

  https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46

and after a patch is submitted:

  https://itk.org/Wiki/ITK/Git/Develop

it will show up on the Doxygen web pages.

Please let us know if you have any questions.

Thanks,
Matt

On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
<cr at neuro.ma.uni-heidelberg.de> wrote:
> Hi,
>
> I think it would be helpful if the documentation of the filter would mention
> that there are two outputs, one with the surviving labels and the second
> with the removed labels (the input image is the union of these images). What
> is the workflow to achieve this?
>
> Christina
>
> _____________________________________
> 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

From CAOwens at mdanderson.org  Thu Oct 13 10:48:32 2016
From: CAOwens at mdanderson.org (Owens,Constance A)
Date: Thu, 13 Oct 2016 14:48:32 +0000
Subject: [ITK-users] Lesion Sizing Toolkit Build not successful
Message-ID: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>

I was hoping to speak with someone who may be able to help me with installing and building Lesion Sizing Toolkit. Originally I tried to build LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I'm using Visual Studio 9 2008 64x), 6 projects fail with the following errors:

Error      1              fatal error C1083: Cannot open include file: 'itkLesionSegmentationImageFilter8.h': No such file or directory                c:\itk2\src\modules\remote\lesionsizingtoolkit\examples\itkLesionSegmentationCommandLineProgressReporter.h                22
Error      2              fatal error C1083: Cannot open include file: 'itkImageFileReader.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx   1
Error      3              fatal error C1083: Cannot open include file: 'itkVector.h': No such file or directory                c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\vtkContourVisualizationModule.h                22
Error      4              fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\LesionSurfaceExtraction.cxx     21
Error      5              fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx                21
Error      6              fatal error C1083: Cannot open include file: 'itkVector.h': No such file or directory                c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\vtkContourVisualizationModule.h                22
Error      7              fatal error C1083: Cannot open include file: 'itkCommand.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\ViewImageAndSegmentationSurface.cxx                18
Error      8              error C2039: 'MetaEvent' : is not a member of '`global namespace''                c:\itk2\src\modules\core\spatialobjects\include\itkMetaEvent.h             35
Error      9              error C2499: 'itk::MetaEvent' : a class cannot be its own base class                c:\itk2\src\modules\core\spatialobjects\include\itkMetaEvent.h             35
Error      10           error C2146: syntax error : missing ';' before identifier 'MetaObjectType'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          55
Error      11           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          55
Error      12           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          55
Error      13           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          64
Error      14           error C2143: syntax error : missing ',' before '*'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          64
Error      15           error C2143: syntax error : missing ';' before '*'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType' : 'virtual' not permitted on data declarations             c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      17           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      18           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      20           error C2143: syntax error : missing ';' before '*'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType' : 'virtual' not permitted on data declarations             c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      22           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      23           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      25           error C2143: syntax error : missing ';' before '*'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   100
Error      26           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   100
Error      27           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   102
Error      29           error C2061: syntax error : identifier 'MetaScene'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   104
Error      30           error C2065: 'MetaObject' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   112
Error      31           error C2059: syntax error : '>'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   112
Error      32           error C2143: syntax error : missing ';' before '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   116
Error      33           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   117
Error      34           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   117
Error      35           error C2143: syntax error : missing ';' before '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   121
Error      36           error C2143: syntax error : missing ';' before '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   124
Error      37           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   125
Error      38           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   125
Error      39           error C2143: syntax error : missing ';' before '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   127
Error      40           error C2065: 'transform' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   128
Error      41           error C2143: syntax error : missing ',' before ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   128
Error      42           error C2065: 'MetaObject' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   130
Error      43           error C2065: 'obj' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   130
Error      44           error C2143: syntax error : missing ',' before ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   130
Error      45           error C2143: syntax error : missing ';' before '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   141
Error      46           fatal error C1004: unexpected end-of-file found                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   141

Additionally, I am using CMake v3.6.1.

I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the ITK Bar Camp document provided by this link:
http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/LungNoduleSegmentationWithLSTK.html

However, cmake showed an error requesting a version of VTK 6.0.0 or newer. I will try this version in the meantime, but was hoping to get some help on building LSTK.


Thanks,
Constance Owens
Graduate Research Assistant

The University of Texas Graduate School of Biomedical Sciences at Houston
Medical Physics
CAOwens at mdanderson.org<https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
tel 713-745-3679 | cel 281-770-5210

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
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From dzenanz at gmail.com  Thu Oct 13 11:20:07 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Oct 2016 11:20:07 -0400
Subject: [ITK-users] Lesion Sizing Toolkit Build not successful
In-Reply-To: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
Message-ID: <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>

Hi Constance,

the lesion sizing toolkit builds with master version of ITK with examples
and tests turned off. I will now try building with those on to see if some
problems appear. I used VS2013 x64.

Regards,
D?enan

On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <CAOwens at mdanderson.org>
wrote:

> I was hoping to speak with someone who may be able to help me with
> installing and building Lesion Sizing Toolkit. Originally I tried to build
> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>
>
>
> Error      1              fatal error C1083: Cannot open include file: '
> itkLesionSegmentationImageFilter8.h': No such file or
> directory                c:\itk2\src\modules\remote\
> lesionsizingtoolkit\examples\itkLesionSegmentationCommandLi
> neProgressReporter.h                22
>
> Error      2              fatal error C1083: Cannot open include file:
> 'itkImageFileReader.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
> 1
>
> Error      3              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      4              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> LesionSurfaceExtraction.cxx     21
>
> Error      5              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> IsoSurfaceVolumeEstimation.cxx                21
>
> Error      6              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      7              fatal error C1083: Cannot open include file:
> 'itkCommand.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> ViewImageAndSegmentationSurface.cxx                18
>
> Error      8              error C2039: 'MetaEvent' : is not a member of
> '`global namespace''                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
> be its own base class                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      10           error C2146: syntax error : missing ';' before
> identifier 'MetaObjectType'                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaConverterBase.h          55
>
> Error      11           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      12           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      13           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      14           error C2143: syntax error : missing ',' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      15           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      17           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      18           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      20           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      22           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      23           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      25           error C2143: syntax error : missing ';' before
> '*'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      26           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      27           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 102
>
> Error      29           error C2061: syntax error : identifier
> 'MetaScene'                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   104
>
> Error      30           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      31           error C2059: syntax error : '>'
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      32           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 116
>
> Error      33           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      34           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      35           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 121
>
> Error      36           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 124
>
> Error      37           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      38           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      39           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 127
>
> Error      40           error C2065: 'transform' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      41           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      42           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      43           error C2065: 'obj' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      44           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      45           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
> Error      46           fatal error C1004: unexpected end-of-file
> found                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
>
>
> Additionally, I am using CMake v3.6.1.
>
>
>
> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
> ITK Bar Camp document provided by this link:
>
> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/
> LungNoduleSegmentationWithLSTK.html
>
>
>
> However, cmake showed an error requesting a version of VTK 6.0.0 or newer.
> I will try this version in the meantime, but was hoping to get some help on
> building LSTK.
>
>
>
>
>
> Thanks,
>
> Constance Owens
>
> Graduate Research Assistant
>
> *The University of Texas Graduate School of Biomedical Sciences at Houston*
> Medical Physics
>
> CAOwens at mdanderson.org
> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
> tel 713-745-3679 | cel 281-770-5210
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
> further review, disclosure, use, dissemination, distribution, or copying of
> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
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From dzenanz at gmail.com  Thu Oct 13 11:29:27 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Oct 2016 11:29:27 -0400
Subject: [ITK-users] Lesion Sizing Toolkit Build not successful
In-Reply-To: <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>
Message-ID: <CAPf2UMTDVVLJLYuqfyuuvOXe5m6gDF_8_K5ZHiE21bCV9UaCLA@mail.gmail.com>

Hi Constance,

building it outside of ITK I also get similar errors, e.g.:
5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx(21):
fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such
file or directory

I will investigate later, and in the meantime you can try building it as
part of ITK (turn Module_LesionSizingToolkit ON).

Regards,
D?enan

On Thu, Oct 13, 2016 at 11:20 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Constance,
>
> the lesion sizing toolkit builds with master version of ITK with examples
> and tests turned off. I will now try building with those on to see if some
> problems appear. I used VS2013 x64.
>
> Regards,
> D?enan
>
> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
>> I was hoping to speak with someone who may be able to help me with
>> installing and building Lesion Sizing Toolkit. Originally I tried to build
>> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
>> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>>
>>
>>
>> Error      1              fatal error C1083: Cannot open include file:
>> 'itkLesionSegmentationImageFilter8.h': No such file or
>> directory                c:\itk2\src\modules\remote\les
>> ionsizingtoolkit\examples\itkLesionSegmentationCommandLinePr
>> ogressReporter.h                22
>>
>> Error      2              fatal error C1083: Cannot open include file:
>> 'itkImageFileReader.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
>> 1
>>
>> Error      3              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      4              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\LesionSurfaceExtraction.cxx     21
>>
>> Error      5              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\IsoSurfaceVolumeEstimation.cxx                21
>>
>> Error      6              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      7              fatal error C1083: Cannot open include file:
>> 'itkCommand.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\ViewImageAndSegmentationSurface.cxx                18
>>
>> Error      8              error C2039: 'MetaEvent' : is not a member of
>> '`global namespace''                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
>> be its own base class                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      10           error C2146: syntax error : missing ';' before
>> identifier 'MetaObjectType'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          55
>>
>> Error      11           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      12           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      13           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 64
>>
>> Error      14           error C2143: syntax error : missing ',' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          64
>>
>> Error      15           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          67
>>
>> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      17           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      18           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      20           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          77
>>
>> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      22           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      23           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      25           error C2143: syntax error : missing ';' before
>> '*'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   100
>>
>> Error      26           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 100
>>
>> Error      27           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 102
>>
>> Error      29           error C2061: syntax error : identifier
>> 'MetaScene'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   104
>>
>> Error      30           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   112
>>
>> Error      31           error C2059: syntax error : '>'
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 112
>>
>> Error      32           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   116
>>
>> Error      33           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      34           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      35           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   121
>>
>> Error      36           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   124
>>
>> Error      37           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      38           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      39           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   127
>>
>> Error      40           error C2065: 'transform' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      41           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      42           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      43           error C2065: 'obj' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      44           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      45           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>> Error      46           fatal error C1004: unexpected end-of-file
>> found                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>>
>>
>> Additionally, I am using CMake v3.6.1.
>>
>>
>>
>> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
>> ITK Bar Camp document provided by this link:
>>
>> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/
>> ITK/LungNoduleSegmentationWithLSTK.html
>>
>>
>>
>> However, cmake showed an error requesting a version of VTK 6.0.0 or
>> newer. I will try this version in the meantime, but was hoping to get some
>> help on building LSTK.
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance Owens
>>
>> Graduate Research Assistant
>>
>> *The University of Texas Graduate School of Biomedical Sciences at
>> Houston*
>> Medical Physics
>>
>> CAOwens at mdanderson.org
>> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
>> tel 713-745-3679 | cel 281-770-5210
>>
>>
>>
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From dzenanz at gmail.com  Thu Oct 13 18:31:18 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Oct 2016 18:31:18 -0400
Subject: [ITK-users] FW:  Lesion Sizing Toolkit Build not successful
In-Reply-To: <603A32F9BAA25B4FBF30F3ADF057B0872C75D09F@DCPWPEXMBX01.mdanderson.edu>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
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 <603A32F9BAA25B4FBF30F3ADF057B0872C75CFD3@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMSfX7ne3047BmWNNR+bjyU92Ye17XuYqfu2kxQT12h7Lw@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75CFEB@DCPWPEXMBX01.mdanderson.edu>
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 <603A32F9BAA25B4FBF30F3ADF057B0872C75D045@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRVhVOi9D1awQHZpbRNmjip0HfuW_M1UcsRJYB=B0UzwA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D09F@DCPWPEXMBX01.mdanderson.edu>
Message-ID: <CAPf2UMTTrteznwnx5VZ5fFL1tMcL3JDnE7oGZaHej-OffmpN_w@mail.gmail.com>

Hi Constance,

I am using a recent VTK master.

I am right now looking into lesion sizing toolkit. I have push a commit to
my fork:
https://github.com/dzenanz/LesionSizingToolkit

This solves compile errors for me. I still have link errors (when building
outside of ITK build tree, your first approach).

It is end of workday in US Eastern so I will probably have to postpone this
for tomorrow. But maybe someone else on the list will suggest a fix
meanwhile :)

Regards,
D?enan

On Thu, Oct 13, 2016 at 6:20 PM, Owens,Constance A <CAOwens at mdanderson.org>
wrote:

> Hi D?enan,
>
> My advisor wanted me to ask you what VTK version did you use exactly? He
> tried with VS2015 and still gets the same error. Below was his response to
> me:
>
>
>
> Using the VS2015 doesn?t help. Same errors.
>
>
>
> I believe it?s the problem of combination of ITK and VTK. Try to check
> with Dzenan what the VTK version he used and the cmake options for VTK. It
> seems that when VTK was included, all ITK header files could not be
> located. No ITK directories were included (as shown).
>
>
>
>
>
>
>
> Thanks,
>
> Constance
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 1:45 PM
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Subject:* Re: FW: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> I am using 3.6.2.
>
>
>
> On Thu, Oct 13, 2016 at 2:22 PM, Owens,Constance A <CAOwens at mdanderson.org>
> wrote:
>
> Hi D?enan,
>
> What version of Cmake are you using? So I can rule it out as being a
> possible cause for the issues.
>
>
>
> Thanks,
>
> Constance
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 1:17 PM
>
>
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Hi Constance,
>
>
>
> those are the steps. What could be going on is that LesionSizingToolkit
> does not support such an old VisualStudio. You could try a newer VS, such
> as 2013 or 2015.
>
>
>
> Also, I will try to figure out the problem in standalone build later.
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 1:10 PM, Owens,Constance A <CAOwens at mdanderson.org>
> wrote:
>
> Hi D?enan,
>
> These are the steps that I followed:
>
>
>
> ?  Download ITK
>
> -        Use Git Clone and place in folder C:\ITK-v4.11\src
>
> o   https://itk.org/Wiki/ITK/Git/Download
>
> -        Open Cmake
>
> o   Set source to folder C:\ITK-v4.11\src\ITK
>
> o   Set build to folder C:\ITK-v4.11\bin-x64
>
> o   Click ?configure?
>
> ?         Set settings to ?Visual Studio 9 2008 Win64?
>
> -        Once configuration is complete:
>
> o   These configuration parameters were suggested by ITK
>
> o   Enable
>
> ?         Module_LesionSizingToolkit
>
> ?         LSTK_USE_VTK (Maybe I should not have done this?)
>
> o   Disable
>
> ?         Build_Shared_Libs
>
> ?         Build_Examples
>
> ?         Build_Testing
>
> o   Click ?Configure?, again
>
> -        Generate
>
> -        Double click on file ?ITK.sln?
>
> o   This can be found in folder: C:\ITK-v4.11\bin-x64
>
> -        Right click on ?ALL_BUILD?
>
> o   Select ?Build?
>
> And I still got all the errors that I mentioned in the first e-mail. My
> apologies if I am not understanding the steps you suggested. I am very new
> to Cmake and Visual Studio, having experience only with MATLAB prior to
> this.
>
>
>
> I would like to be able to see the segmentation results when using LSTK.
> The goal would be to run LSTK with their data first, and then to use it on
> our data.
>
>
>
> Thanks,
> Constance
>
>
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 11:57 AM
>
>
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Hi Constance,
>
>
>
> the "master version" is master branch in the official git repository:
>
> git://itk.org/ITK.git
>
> To see how to get it you can take a look here:
>
> itk.org/Wiki/ITK/Git/Develop
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 12:48 PM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
> Hi D?enan,
>
> What exactly is meant by ?master version? of ITK? Am I correct to assume
> that it is the most current release available at the link provided below?
>
> https://itk.org/ITK/resources/software.html
>
>
>
> Thanks,
> Constance
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 10:44 AM
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>
>
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Yes, that's what was successful for me. You can also try turning
> Build_Examples and Build_Testing on later. I mainly keep them off to reduce
> build time - as you might guess, I rebuild ITK a lot :)
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 11:38 AM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
> Hi D?enan,
>
>
>
> Just to confirm, when I configure in Cmake, I should turn OFF
> Build_Examples and Build_Testing, but turn ON Module_LesionSizingToolkit?
>
>
>
> Thanks,
>
> Constance
>
>
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 10:29 AM
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Hi Constance,
>
>
>
> building it outside of ITK I also get similar errors, e.g.:
>
> 5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\
> IsoSurfaceVolumeEstimation.cxx(21): fatal error C1083: Cannot open
> include file: 'vtkPolyDataWriter.h': No such file or directory
>
>
>
> I will investigate later, and in the meantime you can try building it as
> part of ITK (turn Module_LesionSizingToolkit ON).
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 11:20 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
> Hi Constance,
>
>
>
> the lesion sizing toolkit builds with master version of ITK with examples
> and tests turned off. I will now try building with those on to see if some
> problems appear. I used VS2013 x64.
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
> I was hoping to speak with someone who may be able to help me with
> installing and building Lesion Sizing Toolkit. Originally I tried to build
> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>
>
>
> Error      1              fatal error C1083: Cannot open include file: '
> itkLesionSegmentationImageFilter8.h': No such file or
> directory                c:\itk2\src\modules\remote\
> lesionsizingtoolkit\examples\itkLesionSegmentationCommandLi
> neProgressReporter.h                22
>
> Error      2              fatal error C1083: Cannot open include file:
> 'itkImageFileReader.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
> 1
>
> Error      3              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      4              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> LesionSurfaceExtraction.cxx     21
>
> Error      5              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> IsoSurfaceVolumeEstimation.cxx                21
>
> Error      6              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      7              fatal error C1083: Cannot open include file:
> 'itkCommand.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> ViewImageAndSegmentationSurface.cxx                18
>
> Error      8              error C2039: 'MetaEvent' : is not a member of
> '`global namespace''                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
> be its own base class                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      10           error C2146: syntax error : missing ';' before
> identifier 'MetaObjectType'                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaConverterBase.h          55
>
> Error      11           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      12           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      13           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      14           error C2143: syntax error : missing ',' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      15           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      17           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      18           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      20           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      22           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      23           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      25           error C2143: syntax error : missing ';' before
> '*'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      26           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      27           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 102
>
> Error      29           error C2061: syntax error : identifier
> 'MetaScene'                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   104
>
> Error      30           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      31           error C2059: syntax error : '>'
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      32           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 116
>
> Error      33           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      34           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      35           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 121
>
> Error      36           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 124
>
> Error      37           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      38           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      39           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 127
>
> Error      40           error C2065: 'transform' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      41           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      42           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      43           error C2065: 'obj' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      44           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      45           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
> Error      46           fatal error C1004: unexpected end-of-file
> found                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
>
>
> Additionally, I am using CMake v3.6.1.
>
>
>
> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
> ITK Bar Camp document provided by this link:
>
> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/
> LungNoduleSegmentationWithLSTK.html
>
>
>
> However, cmake showed an error requesting a version of VTK 6.0.0 or newer.
> I will try this version in the meantime, but was hoping to get some help on
> building LSTK.
>
>
>
>
>
> Thanks,
>
> Constance Owens
>
> Graduate Research Assistant
>
> *The University of Texas Graduate School of Biomedical Sciences at Houston*
> Medical Physics
>
> CAOwens at mdanderson.org
> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
> tel 713-745-3679 | cel 281-770-5210
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
> further review, disclosure, use, dissemination, distribution, or copying of
> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
>
>
> _____________________________________
> 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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>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
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> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
> further review, disclosure, use, dissemination, distribution, or copying of
> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
> further review, disclosure, use, dissemination, distribution, or copying of
> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
> further review, disclosure, use, dissemination, distribution, or copying of
> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
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> further review, disclosure, use, dissemination, distribution, or copying of
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From bakkari.abdelkhalek at hotmail.fr  Thu Oct 13 19:05:50 2016
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Thu, 13 Oct 2016 23:05:50 +0000
Subject: [ITK-users] Region Growing after seed points
Message-ID: <AM2PR09MB0562AD6C4A1B930FB8CF8D5583DC0@AM2PR09MB0562.eurprd09.prod.outlook.com>

Dear insight-users,


After applying the vtkSeedWidget in order to get Seed Points, I am trying to use the Seed Points to apply the region growing algorithm.

My question is : How to get the index of the seed points as seed[0], seed[1] and seed[2] ?





 void PlaceSeed(double x, double y, double z, vtkRenderWindowInteractor * interactor, vtkRenderer * renderer);
   vtkHandleWidget * GetSeed(int index);
   void RemoveSeeds();


   // Set seed
  ImageType::IndexType seed;
  seed[0] = x ;
  seed[1] = y ;
  seed[2] = z ;


Thank you in advance.

Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From francois.budin at kitware.com  Fri Oct 14 07:09:15 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Fri, 14 Oct 2016 07:09:15 -0400
Subject: [ITK-users] Region Growing after seed points
In-Reply-To: <AM2PR09MB0562AD6C4A1B930FB8CF8D5583DC0@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB0562AD6C4A1B930FB8CF8D5583DC0@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <CAHwLD2VzHt5o4tTiRW5ea8fna7_MCkqjb_syhnu+j_B7E9rUgg@mail.gmail.com>

Dear Abdelkhalek,

You may want to contact the VTK user mailing list for your question as it
concerns VTK. You can register on this webpage:
http://www.vtk.org/mailing-lists/ .You will get better answers there.

Best,
Francois

On Thu, Oct 13, 2016 at 7:05 PM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Dear insight-users,
>
>
> After applying the vtkSeedWidget in order to get Seed Points, I am trying
> to use the Seed Points to apply the region growing algorithm.
>
> My question is : How to get the index of the seed points as seed[0],
> seed[1] and seed[2] ?
>
>
>
>
>
>  void PlaceSeed(double x, double y, double z, vtkRenderWindowInteractor *
> interactor, vtkRenderer * renderer);
>    vtkHandleWidget * GetSeed(int index);
>    void RemoveSeeds();
>
>
>    // Set seed
>   ImageType::IndexType seed;
>   seed[0] = x ;
>   seed[1] = y ;
>   seed[2] = z ;
>
> Thank you in advance.
>
> Best regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
> _____________________________________
> 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
>
>
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From cr at neuro.ma.uni-heidelberg.de  Fri Oct 14 08:52:35 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 14 Oct 2016 14:52:35 +0200
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
In-Reply-To: <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
Message-ID: <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>

Hi Matt,

I've forked on github, extended the documentation and created a pull 
request. Or is gerrit the only way to get a patch merged?

Christina


On 12.10.2016 18:03, Matt McCormick wrote:
> Hello Christina,
>
> Good idea.
>
> To update the documentation, the class Doxygen documentation can be editted:
>
>    https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>
> and after a patch is submitted:
>
>    https://itk.org/Wiki/ITK/Git/Develop
>
> it will show up on the Doxygen web pages.
>
> Please let us know if you have any questions.
>
> Thanks,
> Matt
>
> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>> Hi,
>>
>> I think it would be helpful if the documentation of the filter would mention
>> that there are two outputs, one with the surviving labels and the second
>> with the removed labels (the input image is the union of these images). What
>> is the workflow to achieve this?
>>
>> Christina
>>
>> _____________________________________
>> 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



From dzenanz at gmail.com  Fri Oct 14 09:00:48 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Oct 2016 09:00:48 -0400
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
In-Reply-To: <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
Message-ID: <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>

Hi Christina,

gerrit is the only way to merge patches. Can you submit it as a patch to
gerrit?

Thanks,
D?enan

On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> Hi Matt,
>
> I've forked on github, extended the documentation and created a pull
> request. Or is gerrit the only way to get a patch merged?
>
> Christina
>
>
>
> On 12.10.2016 18:03, Matt McCormick wrote:
>
>> Hello Christina,
>>
>> Good idea.
>>
>> To update the documentation, the class Doxygen documentation can be
>> editted:
>>
>>    https://github.com/InsightSoftwareConsortium/ITK/blob/
>> master/Modules/Filtering/LabelMap/include/itkAttributeSelect
>> ionLabelMapFilter.h#L27-L46
>>
>> and after a patch is submitted:
>>
>>    https://itk.org/Wiki/ITK/Git/Develop
>>
>> it will show up on the Doxygen web pages.
>>
>> Please let us know if you have any questions.
>>
>> Thanks,
>> Matt
>>
>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>>> Hi,
>>>
>>> I think it would be helpful if the documentation of the filter would
>>> mention
>>> that there are two outputs, one with the surviving labels and the second
>>> with the removed labels (the input image is the union of these images).
>>> What
>>> is the workflow to achieve this?
>>>
>>> Christina
>>>
>>> _____________________________________
>>> 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
>>>
>>
>
> _____________________________________
> 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
>
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From dzenanz at gmail.com  Fri Oct 14 09:21:18 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Oct 2016 09:21:18 -0400
Subject: [ITK-users] FW:  Lesion Sizing Toolkit Build not successful
In-Reply-To: <CAPf2UMTTrteznwnx5VZ5fFL1tMcL3JDnE7oGZaHej-OffmpN_w@mail.gmail.com>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>
 <CAPf2UMTDVVLJLYuqfyuuvOXe5m6gDF_8_K5ZHiE21bCV9UaCLA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75CFD3@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMSfX7ne3047BmWNNR+bjyU92Ye17XuYqfu2kxQT12h7Lw@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75CFEB@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMTnfo=e0kHDZCiQOHOEDPamqgtHaHQvm_hMEdtMOy-+NQ@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D003@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMSx=swhrf4+PLLLkZAJA=hBT0rJ29+nrxF75V9y7f-MKA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D045@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRVhVOi9D1awQHZpbRNmjip0HfuW_M1UcsRJYB=B0UzwA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D09F@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMTTrteznwnx5VZ5fFL1tMcL3JDnE7oGZaHej-OffmpN_w@mail.gmail.com>
Message-ID: <CAPf2UMQKXv2xa_8-B2FvMjq=xzO3mCxemCDZP2RJhebcjKbJ4A@mail.gmail.com>

Hi Christina,

I pushed a new commit to my fork
<https://github.com/dzenanz/LesionSizingToolkit> which resolves all build
and link errors on my VS2013 setup. Can you give it a try?

Regards,
D?enan

On Thu, Oct 13, 2016 at 6:31 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Constance,
>
> I am using a recent VTK master.
>
> I am right now looking into lesion sizing toolkit. I have push a commit to
> my fork:
> https://github.com/dzenanz/LesionSizingToolkit
>
> This solves compile errors for me. I still have link errors (when building
> outside of ITK build tree, your first approach).
>
> It is end of workday in US Eastern so I will probably have to postpone
> this for tomorrow. But maybe someone else on the list will suggest a fix
> meanwhile :)
>
> Regards,
> D?enan
>
> On Thu, Oct 13, 2016 at 6:20 PM, Owens,Constance A <CAOwens at mdanderson.org
> > wrote:
>
>> Hi D?enan,
>>
>> My advisor wanted me to ask you what VTK version did you use exactly? He
>> tried with VS2015 and still gets the same error. Below was his response to
>> me:
>>
>>
>>
>> Using the VS2015 doesn?t help. Same errors.
>>
>>
>>
>> I believe it?s the problem of combination of ITK and VTK. Try to check
>> with Dzenan what the VTK version he used and the cmake options for VTK. It
>> seems that when VTK was included, all ITK header files could not be
>> located. No ITK directories were included (as shown).
>>
>>
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 1:45 PM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: FW: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> I am using 3.6.2.
>>
>>
>>
>> On Thu, Oct 13, 2016 at 2:22 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>> What version of Cmake are you using? So I can rule it out as being a
>> possible cause for the issues.
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 1:17 PM
>>
>>
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> those are the steps. What could be going on is that LesionSizingToolkit
>> does not support such an old VisualStudio. You could try a newer VS, such
>> as 2013 or 2015.
>>
>>
>>
>> Also, I will try to figure out the problem in standalone build later.
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 1:10 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>> These are the steps that I followed:
>>
>>
>>
>> ?  Download ITK
>>
>> -        Use Git Clone and place in folder C:\ITK-v4.11\src
>>
>> o   https://itk.org/Wiki/ITK/Git/Download
>>
>> -        Open Cmake
>>
>> o   Set source to folder C:\ITK-v4.11\src\ITK
>>
>> o   Set build to folder C:\ITK-v4.11\bin-x64
>>
>> o   Click ?configure?
>>
>> ?         Set settings to ?Visual Studio 9 2008 Win64?
>>
>> -        Once configuration is complete:
>>
>> o   These configuration parameters were suggested by ITK
>>
>> o   Enable
>>
>> ?         Module_LesionSizingToolkit
>>
>> ?         LSTK_USE_VTK (Maybe I should not have done this?)
>>
>> o   Disable
>>
>> ?         Build_Shared_Libs
>>
>> ?         Build_Examples
>>
>> ?         Build_Testing
>>
>> o   Click ?Configure?, again
>>
>> -        Generate
>>
>> -        Double click on file ?ITK.sln?
>>
>> o   This can be found in folder: C:\ITK-v4.11\bin-x64
>>
>> -        Right click on ?ALL_BUILD?
>>
>> o   Select ?Build?
>>
>> And I still got all the errors that I mentioned in the first e-mail. My
>> apologies if I am not understanding the steps you suggested. I am very new
>> to Cmake and Visual Studio, having experience only with MATLAB prior to
>> this.
>>
>>
>>
>> I would like to be able to see the segmentation results when using LSTK.
>> The goal would be to run LSTK with their data first, and then to use it on
>> our data.
>>
>>
>>
>> Thanks,
>> Constance
>>
>>
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 11:57 AM
>>
>>
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> the "master version" is master branch in the official git repository:
>>
>> git://itk.org/ITK.git
>>
>> To see how to get it you can take a look here:
>>
>> itk.org/Wiki/ITK/Git/Develop
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 12:48 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>> What exactly is meant by ?master version? of ITK? Am I correct to assume
>> that it is the most current release available at the link provided below?
>>
>> https://itk.org/ITK/resources/software.html
>>
>>
>>
>> Thanks,
>> Constance
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 10:44 AM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>>
>>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Yes, that's what was successful for me. You can also try turning
>> Build_Examples and Build_Testing on later. I mainly keep them off to reduce
>> build time - as you might guess, I rebuild ITK a lot :)
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 11:38 AM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>>
>>
>> Just to confirm, when I configure in Cmake, I should turn OFF
>> Build_Examples and Build_Testing, but turn ON Module_LesionSizingToolkit?
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 10:29 AM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Cc:* insight-users at itk.org
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> building it outside of ITK I also get similar errors, e.g.:
>>
>> 5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx(21):
>> fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such
>> file or directory
>>
>>
>>
>> I will investigate later, and in the meantime you can try building it as
>> part of ITK (turn Module_LesionSizingToolkit ON).
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 11:20 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>> Hi Constance,
>>
>>
>>
>> the lesion sizing toolkit builds with master version of ITK with examples
>> and tests turned off. I will now try building with those on to see if some
>> problems appear. I used VS2013 x64.
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> I was hoping to speak with someone who may be able to help me with
>> installing and building Lesion Sizing Toolkit. Originally I tried to build
>> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
>> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>>
>>
>>
>> Error      1              fatal error C1083: Cannot open include file:
>> 'itkLesionSegmentationImageFilter8.h': No such file or
>> directory                c:\itk2\src\modules\remote\les
>> ionsizingtoolkit\examples\itkLesionSegmentationCommandLinePr
>> ogressReporter.h                22
>>
>> Error      2              fatal error C1083: Cannot open include file:
>> 'itkImageFileReader.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
>> 1
>>
>> Error      3              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      4              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\LesionSurfaceExtraction.cxx     21
>>
>> Error      5              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\IsoSurfaceVolumeEstimation.cxx                21
>>
>> Error      6              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      7              fatal error C1083: Cannot open include file:
>> 'itkCommand.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\ViewImageAndSegmentationSurface.cxx                18
>>
>> Error      8              error C2039: 'MetaEvent' : is not a member of
>> '`global namespace''                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
>> be its own base class                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      10           error C2146: syntax error : missing ';' before
>> identifier 'MetaObjectType'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          55
>>
>> Error      11           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      12           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      13           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 64
>>
>> Error      14           error C2143: syntax error : missing ',' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          64
>>
>> Error      15           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          67
>>
>> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      17           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      18           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      20           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          77
>>
>> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      22           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      23           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      25           error C2143: syntax error : missing ';' before
>> '*'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   100
>>
>> Error      26           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 100
>>
>> Error      27           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 102
>>
>> Error      29           error C2061: syntax error : identifier
>> 'MetaScene'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   104
>>
>> Error      30           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   112
>>
>> Error      31           error C2059: syntax error : '>'
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 112
>>
>> Error      32           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   116
>>
>> Error      33           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      34           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      35           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   121
>>
>> Error      36           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   124
>>
>> Error      37           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      38           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      39           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   127
>>
>> Error      40           error C2065: 'transform' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      41           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      42           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      43           error C2065: 'obj' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      44           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      45           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>> Error      46           fatal error C1004: unexpected end-of-file
>> found                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>>
>>
>> Additionally, I am using CMake v3.6.1.
>>
>>
>>
>> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
>> ITK Bar Camp document provided by this link:
>>
>> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/
>> ITK/LungNoduleSegmentationWithLSTK.html
>>
>>
>>
>> However, cmake showed an error requesting a version of VTK 6.0.0 or
>> newer. I will try this version in the meantime, but was hoping to get some
>> help on building LSTK.
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance Owens
>>
>> Graduate Research Assistant
>>
>> *The University of Texas Graduate School of Biomedical Sciences at
>> Houston*
>> Medical Physics
>>
>> CAOwens at mdanderson.org
>> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
>> tel 713-745-3679 | cel 281-770-5210
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> _____________________________________
>> 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
>>
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>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>
>
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From cr at neuro.ma.uni-heidelberg.de  Fri Oct 14 09:21:33 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 14 Oct 2016 15:21:33 +0200
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
In-Reply-To: <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
 <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
Message-ID: <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>

When visiting review.source.kitware.com -> sign in -> provide github 
credentials  I find myself on a page telling me "forbidden". But without 
a gerrit user I'm stuck...Any hints? I've double checked the credentials 
by signing in into github.

Christina

On 14.10.2016 15:00, D?enan Zuki? wrote:
> Hi Christina,
>
> gerrit is the only way to merge patches. Can you submit it as a patch 
> to gerrit?
>
> Thanks,
> D?enan
>
> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith 
> <cr at neuro.ma.uni-heidelberg.de <mailto:cr at neuro.ma.uni-heidelberg.de>> 
> wrote:
>
>     Hi Matt,
>
>     I've forked on github, extended the documentation and created a
>     pull request. Or is gerrit the only way to get a patch merged?
>
>     Christina
>
>
>
>     On 12.10.2016 18:03, Matt McCormick wrote:
>
>         Hello Christina,
>
>         Good idea.
>
>         To update the documentation, the class Doxygen documentation
>         can be editted:
>
>         https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>         <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46>
>
>         and after a patch is submitted:
>
>         https://itk.org/Wiki/ITK/Git/Develop
>         <https://itk.org/Wiki/ITK/Git/Develop>
>
>         it will show up on the Doxygen web pages.
>
>         Please let us know if you have any questions.
>
>         Thanks,
>         Matt
>
>         On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>         <cr at neuro.ma.uni-heidelberg.de
>         <mailto:cr at neuro.ma.uni-heidelberg.de>> wrote:
>
>             Hi,
>
>             I think it would be helpful if the documentation of the
>             filter would mention
>             that there are two outputs, one with the surviving labels
>             and the second
>             with the removed labels (the input image is the union of
>             these images). What
>             is the workflow to achieve this?
>
>             Christina
>
>             _____________________________________
>             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>
>
>
>
>     _____________________________________
>     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>
>
>

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From dzenanz at gmail.com  Fri Oct 14 09:23:38 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Oct 2016 09:23:38 -0400
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
In-Reply-To: <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
 <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
 <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>
Message-ID: <CAPf2UMST7UHoxc8s1U6irZwt2A2dFrDa7i4S=XPBP1GBdKjeog@mail.gmail.com>

Matt, what was the problem with this?

On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> When visiting review.source.kitware.com -> sign in -> provide github
> credentials  I find myself on a page telling me "forbidden". But without a
> gerrit user I'm stuck...Any hints? I've double checked the credentials by
> signing in into github.
>
> Christina
>
>
> On 14.10.2016 15:00, D?enan Zuki? wrote:
>
> Hi Christina,
>
> gerrit is the only way to merge patches. Can you submit it as a patch to
> gerrit?
>
> Thanks,
> D?enan
>
> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith <
> cr at neuro.ma.uni-heidelberg.de> wrote:
>
>> Hi Matt,
>>
>> I've forked on github, extended the documentation and created a pull
>> request. Or is gerrit the only way to get a patch merged?
>>
>> Christina
>>
>>
>>
>> On 12.10.2016 18:03, Matt McCormick wrote:
>>
>>> Hello Christina,
>>>
>>> Good idea.
>>>
>>> To update the documentation, the class Doxygen documentation can be
>>> editted:
>>>
>>>    https://github.com/InsightSoftwareConsortium/ITK/blob/maste
>>> r/Modules/Filtering/LabelMap/include/itkAttributeSelectionL
>>> abelMapFilter.h#L27-L46
>>>
>>> and after a patch is submitted:
>>>
>>>    https://itk.org/Wiki/ITK/Git/Develop
>>>
>>> it will show up on the Doxygen web pages.
>>>
>>> Please let us know if you have any questions.
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I think it would be helpful if the documentation of the filter would
>>>> mention
>>>> that there are two outputs, one with the surviving labels and the second
>>>> with the removed labels (the input image is the union of these images).
>>>> What
>>>> is the workflow to achieve this?
>>>>
>>>> Christina
>>>>
>>>> _____________________________________
>>>> 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
>>>>
>>>
>>
>> _____________________________________
>> 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
>>
>
>
>
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From matt.mccormick at kitware.com  Fri Oct 14 10:46:00 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 14 Oct 2016 10:46:00 -0400
Subject: [ITK-users] Documentation: itk::AttributeSelectionLabelMapFilter
In-Reply-To: <CAPf2UMST7UHoxc8s1U6irZwt2A2dFrDa7i4S=XPBP1GBdKjeog@mail.gmail.com>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
 <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
 <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>
 <CAPf2UMST7UHoxc8s1U6irZwt2A2dFrDa7i4S=XPBP1GBdKjeog@mail.gmail.com>
Message-ID: <CALzTN-QP+kQ3fHm0dUZEhQDAG-NtdQa1L+8zj=3RJZ+bsi+TTQ@mail.gmail.com>

Hi,

This is a problem with old accounts that were not used for a few years
after the GitHub authentication transition. I will contact the
sys-admins to get it resolved.

Thanks,
Matt

On Fri, Oct 14, 2016 at 9:23 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Matt, what was the problem with this?
>
> On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>> When visiting review.source.kitware.com -> sign in -> provide github
>> credentials  I find myself on a page telling me "forbidden". But without a
>> gerrit user I'm stuck...Any hints? I've double checked the credentials by
>> signing in into github.
>>
>> Christina
>>
>>
>> On 14.10.2016 15:00, D?enan Zuki? wrote:
>>
>> Hi Christina,
>>
>> gerrit is the only way to merge patches. Can you submit it as a patch to
>> gerrit?
>>
>> Thanks,
>> D?enan
>>
>> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> Hi Matt,
>>>
>>> I've forked on github, extended the documentation and created a pull
>>> request. Or is gerrit the only way to get a patch merged?
>>>
>>> Christina
>>>
>>>
>>>
>>> On 12.10.2016 18:03, Matt McCormick wrote:
>>>>
>>>> Hello Christina,
>>>>
>>>> Good idea.
>>>>
>>>> To update the documentation, the class Doxygen documentation can be
>>>> editted:
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>>>>
>>>> and after a patch is submitted:
>>>>
>>>>    https://itk.org/Wiki/ITK/Git/Develop
>>>>
>>>> it will show up on the Doxygen web pages.
>>>>
>>>> Please let us know if you have any questions.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I think it would be helpful if the documentation of the filter would
>>>>> mention
>>>>> that there are two outputs, one with the surviving labels and the
>>>>> second
>>>>> with the removed labels (the input image is the union of these images).
>>>>> What
>>>>> is the workflow to achieve this?
>>>>>
>>>>> Christina
>>>>>
>>>>> _____________________________________
>>>>> 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
>>>
>>>
>>>
>>> _____________________________________
>>> 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
>>
>>
>>
>

From tamanupadhaya at gmail.com  Mon Oct 17 08:35:23 2016
From: tamanupadhaya at gmail.com (Tmn)
Date: Mon, 17 Oct 2016 05:35:23 -0700 (MST)
Subject: [ITK-users] ITK GLCM Matrix
Message-ID: <1476707723670-7589370.post@n2.nabble.com>

I am using itk library to extract Haralick texture feature using
itk::Statistics::ScalarImageToTextureFeaturesFilter<>; But I am unable to
find the function to print GLCM matrix.

Can someone please provide me a small example on how to print the GLCM
matrix?

Thank you for your time!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-GLCM-Matrix-tp7589370.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From tevain at telecom-paristech.fr  Mon Oct 17 08:50:36 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 17 Oct 2016 14:50:36 +0200 (CEST)
Subject: [ITK-users] [ITK]  ITK GLCM Matrix
In-Reply-To: <1476707723670-7589370.post@n2.nabble.com>
References: <1476707723670-7589370.post@n2.nabble.com>
Message-ID: <1774750007.10144382.1476708636069.JavaMail.zimbra@enst.fr>

Hi,

If you want to access directly to the matrix, I would suggest to use the Statistics::ScalarImageToCooccurrenceMatrixFilter, which output what you want as a histogram.

HTH,

Tim

----- Mail original -----
De: "Tmn" <tamanupadhaya at gmail.com>
?: insight-users at itk.org
Envoy?: Lundi 17 Octobre 2016 14:35:23
Objet: [ITK] [ITK-users] ITK GLCM Matrix

I am using itk library to extract Haralick texture feature using
itk::Statistics::ScalarImageToTextureFeaturesFilter<>; But I am unable to
find the function to print GLCM matrix.

Can someone please provide me a small example on how to print the GLCM
matrix?

Thank you for your time!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-GLCM-Matrix-tp7589370.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
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
_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

From swetha.bsharma at gmail.com  Wed Oct 19 05:49:55 2016
From: swetha.bsharma at gmail.com (swetha)
Date: Wed, 19 Oct 2016 02:49:55 -0700 (MST)
Subject: [ITK-users] Cmake clrsupport c# wrapper for itk
Message-ID: <1476870595135-7589372.post@n2.nabble.com>

Hi,

   I am trying to create a wrapper in c# for c++ code in itk. Because I am
using ITK i am forced to use cmake to add the relevant header files which i
would need.

This is the script which i have added

SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "/clr") 
 STRING(REPLACE "/EHsc" "/EHa" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
 STRING(REPLACE "/RTC1" "" CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /clr") 

The problem I've found, is that while CMake sets the "Common Language
RunTime Support" option in the C/C++ section of the configuration properties
if "/clr" is in the CXX_FLAGS, it does not set the "Common Language RunTime
Support" in the general configuration properties, and that causes problems
with linking/.NET references.

How do i solve this?
-swetha



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Cmake-clrsupport-c-wrapper-for-itk-tp7589372.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From zeinsalah at gmail.com  Wed Oct 19 06:55:10 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Wed, 19 Oct 2016 12:55:10 +0200
Subject: [ITK-users] Loading multiframe dicom with itk
Message-ID: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>

Hi,

to organizational reasons, I must use an old release of itk (3.14).

I am trying to load multiframe dicom images with itk reader. I noticed
 a strange behavior in the itk::ImageFileReader.
when I load a multiframe dicom image with the reader, the output of the reader
has a correct z-spacing. But the x- and y- spacings are always 1.0. I
also could reproduce this using itk 3.20.1.

I also noticed that at lease the orientation is wrong.

a short search led me to this:

http://www.na-mic.org/Bug/view.php?id=725

is this aknow issue in itk? has it been fiyed in later versions?

Thanks,
Zein

From dzenanz at gmail.com  Wed Oct 19 09:29:59 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 19 Oct 2016 09:29:59 -0400
Subject: [ITK-users] [ITK]  Cmake clrsupport c# wrapper for itk
In-Reply-To: <1476870595135-7589372.post@n2.nabble.com>
References: <1476870595135-7589372.post@n2.nabble.com>
Message-ID: <CAPf2UMRP7wfZywKnYGSY5Gk9txz3TafwXuEmvn86FdbHWAAFUg@mail.gmail.com>

Hi Swetha,

this sounds more like a question for CMake mailing list. Can you try
searching if it was already answered or posting it there?

Regards,
D?enan

On Wed, Oct 19, 2016 at 5:49 AM, swetha <swetha.bsharma at gmail.com> wrote:

> Hi,
>
>    I am trying to create a wrapper in c# for c++ code in itk. Because I am
> using ITK i am forced to use cmake to add the relevant header files which i
> would need.
>
> This is the script which i have added
>
> SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "/clr")
>  STRING(REPLACE "/EHsc" "/EHa" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
>  STRING(REPLACE "/RTC1" "" CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
>  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /clr")
>
> The problem I've found, is that while CMake sets the "Common Language
> RunTime Support" option in the C/C++ section of the configuration
> properties
> if "/clr" is in the CXX_FLAGS, it does not set the "Common Language RunTime
> Support" in the general configuration properties, and that causes problems
> with linking/.NET references.
>
> How do i solve this?
> -swetha
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/Cmake-clrsupport-c-wrapper-for-itk-tp7589372.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> 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
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From matt.mccormick at kitware.com  Wed Oct 19 09:40:32 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Oct 2016 09:40:32 -0400
Subject: [ITK-users] [ITK] Loading multiframe dicom with itk
In-Reply-To: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>
References: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>
Message-ID: <CALzTN-SsLtOdZV6Yz+=i-jDU0_3wxaE8BK0Q7RT6XxycAGLaDQ@mail.gmail.com>

Hi Zein,

There has been fixes for this issue in later versions of ITK via both
ITK's handling of the spacing and the DICOM library used to parse the
files. It is worthwhile to try with a recent version of ITK to see if
the issue has been addressed.

HTH,
Matt

On Wed, Oct 19, 2016 at 6:55 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hi,
>
> to organizational reasons, I must use an old release of itk (3.14).
>
> I am trying to load multiframe dicom images with itk reader. I noticed
>  a strange behavior in the itk::ImageFileReader.
> when I load a multiframe dicom image with the reader, the output of the reader
> has a correct z-spacing. But the x- and y- spacings are always 1.0. I
> also could reproduce this using itk 3.20.1.
>
> I also noticed that at lease the orientation is wrong.
>
> a short search led me to this:
>
> http://www.na-mic.org/Bug/view.php?id=725
>
> is this aknow issue in itk? has it been fiyed in later versions?
>
> Thanks,
> Zein
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From matt.mccormick at kitware.com  Wed Oct 19 09:45:33 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Oct 2016 09:45:33 -0400
Subject: [ITK-users] [ITK] Cmake clrsupport c# wrapper for itk
In-Reply-To: <CAPf2UMRP7wfZywKnYGSY5Gk9txz3TafwXuEmvn86FdbHWAAFUg@mail.gmail.com>
References: <1476870595135-7589372.post@n2.nabble.com>
 <CAPf2UMRP7wfZywKnYGSY5Gk9txz3TafwXuEmvn86FdbHWAAFUg@mail.gmail.com>
Message-ID: <CALzTN-SG4c8FsSk4TAmj4vd6zGXsOjWDEk55e8Gmx9a37q+Utg@mail.gmail.com>

Hi Swetha,

There is improved C# support in the "csharp" branch of this repository:

  https://github.com/micst/CMake

they are working on upstreaming the improvements. You may want to try
it out and prove feedback on the CMake mailing lists.

HTH,
Matt

On Wed, Oct 19, 2016 at 9:29 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Swetha,
>
> this sounds more like a question for CMake mailing list. Can you try
> searching if it was already answered or posting it there?
>
> Regards,
> D?enan
>
> On Wed, Oct 19, 2016 at 5:49 AM, swetha <swetha.bsharma at gmail.com> wrote:
>>
>> Hi,
>>
>>    I am trying to create a wrapper in c# for c++ code in itk. Because I am
>> using ITK i am forced to use cmake to add the relevant header files which
>> i
>> would need.
>>
>> This is the script which i have added
>>
>> SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "/clr")
>>  STRING(REPLACE "/EHsc" "/EHa" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
>>  STRING(REPLACE "/RTC1" "" CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
>>  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /clr")
>>
>> The problem I've found, is that while CMake sets the "Common Language
>> RunTime Support" option in the C/C++ section of the configuration
>> properties
>> if "/clr" is in the CXX_FLAGS, it does not set the "Common Language
>> RunTime
>> Support" in the general configuration properties, and that causes problems
>> with linking/.NET references.
>>
>> How do i solve this?
>> -swetha
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/Cmake-clrsupport-c-wrapper-for-itk-tp7589372.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> 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
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>
>
>
> _____________________________________
> 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
>

From cr at neuro.ma.uni-heidelberg.de  Wed Oct 19 10:35:11 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Wed, 19 Oct 2016 16:35:11 +0200
Subject: [ITK-users] Fwd: Re: Documentation:
 itk::AttributeSelectionLabelMapFilter
In-Reply-To: <224c14a0-de28-6c4c-fc8f-6f160b4c7d4d@neuro.ma.uni-heidelberg.de>
References: <224c14a0-de28-6c4c-fc8f-6f160b4c7d4d@neuro.ma.uni-heidelberg.de>
Message-ID: <5817e91f-8551-66fd-45d9-f160a9e70ff9@neuro.ma.uni-heidelberg.de>

And now the copy for the ML

Christina



-------- Forwarded Message --------
Subject: 	Re: [ITK-users] Documentation: 
itk::AttributeSelectionLabelMapFilter
Date: 	Wed, 19 Oct 2016 16:33:44 +0200
From: 	Chr. Rossmanith <cr at neuro.ma.uni-heidelberg.de>
To: 	Matt McCormick <matt.mccormick at kitware.com>



Hi Matt,

login is working now for reviews.source.kitware.com, but authentication
on the command line fails, maybe because I'm behind a firewall. Now I'm
sending the patch to the mailing list as recommended on
https://itk.org/Wiki/ITK/Git/Account#Gerrit

Christina

On 14.10.2016 18:55, Matt McCormick wrote:
> Hi Christina,
>
> Could you please try logging into to review.source.kitware.com again?
>
> Thanks,
> Matt
>
> On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>> When visiting review.source.kitware.com -> sign in -> provide github
>> credentials  I find myself on a page telling me "forbidden". But without a
>> gerrit user I'm stuck...Any hints? I've double checked the credentials by
>> signing in into github.
>>
>> Christina
>>
>>
>> On 14.10.2016 15:00, D?enan Zuki? wrote:
>>
>> Hi Christina,
>>
>> gerrit is the only way to merge patches. Can you submit it as a patch to
>> gerrit?
>>
>> Thanks,
>> D?enan
>>
>> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>> Hi Matt,
>>>
>>> I've forked on github, extended the documentation and created a pull
>>> request. Or is gerrit the only way to get a patch merged?
>>>
>>> Christina
>>>
>>>
>>>
>>> On 12.10.2016 18:03, Matt McCormick wrote:
>>>> Hello Christina,
>>>>
>>>> Good idea.
>>>>
>>>> To update the documentation, the class Doxygen documentation can be
>>>> editted:
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>>>>
>>>> and after a patch is submitted:
>>>>
>>>>     https://itk.org/Wiki/ITK/Git/Develop
>>>>
>>>> it will show up on the Doxygen web pages.
>>>>
>>>> Please let us know if you have any questions.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>> Hi,
>>>>>
>>>>> I think it would be helpful if the documentation of the filter would
>>>>> mention
>>>>> that there are two outputs, one with the surviving labels and the second
>>>>> with the removed labels (the input image is the union of these images).
>>>>> What
>>>>> is the workflow to achieve this?
>>>>>
>>>>> Christina
>>>>>
>>>>> _____________________________________
>>>>> 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
>>>
>>>
>>> _____________________________________
>>> 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
>>
>>
>>
>> _____________________________________
>> 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
>>


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From matt.mccormick at kitware.com  Wed Oct 19 10:47:17 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Oct 2016 10:47:17 -0400
Subject: [ITK-users] Fwd: Re: Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <5817e91f-8551-66fd-45d9-f160a9e70ff9@neuro.ma.uni-heidelberg.de>
References: <224c14a0-de28-6c4c-fc8f-6f160b4c7d4d@neuro.ma.uni-heidelberg.de>
 <5817e91f-8551-66fd-45d9-f160a9e70ff9@neuro.ma.uni-heidelberg.de>
Message-ID: <CALzTN-S1DoeAkGo6pgMzu_jthh2jyMZTgqRFOoaWrUg87XGsKw@mail.gmail.com>

Thanks for your persistence and the contribution, Christina!

The patch has been uploaded here:

  http://review.source.kitware.com/#/c/21646/

On Wed, Oct 19, 2016 at 10:35 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> And now the copy for the ML
>
> Christina
>
>
> -------- Forwarded Message --------
> Subject: Re: [ITK-users] Documentation: itk::
> AttributeSelectionLabelMapFilter
> Date: Wed, 19 Oct 2016 16:33:44 +0200
> From: Chr. Rossmanith <cr at neuro.ma.uni-heidelberg.de>
> <cr at neuro.ma.uni-heidelberg.de>
> To: Matt McCormick <matt.mccormick at kitware.com>
> <matt.mccormick at kitware.com>
>
>
> Hi Matt,
>
> login is working now for reviews.source.kitware.com, but authentication
> on the command line fails, maybe because I'm behind a firewall. Now I'm
> sending the patch to the mailing list as recommended on https://itk.org/Wiki/ITK/Git/Account#Gerrit
>
> Christina
>
> On 14.10.2016 18:55, Matt McCormick wrote:
> > Hi Christina,
> >
> > Could you please try logging into to review.source.kitware.com again?
> >
> > Thanks,
> > Matt
> >
> > On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith
> > <cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >> When visiting review.source.kitware.com -> sign in -> provide github
> >> credentials  I find myself on a page telling me "forbidden". But without a
> >> gerrit user I'm stuck...Any hints? I've double checked the credentials by
> >> signing in into github.
> >>
> >> Christina
> >>
> >>
> >> On 14.10.2016 15:00, D?enan Zuki? wrote:
> >>
> >> Hi Christina,
> >>
> >> gerrit is the only way to merge patches. Can you submit it as a patch to
> >> gerrit?
> >>
> >> Thanks,
> >> D?enan
> >>
> >> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith
> >> <cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>> Hi Matt,
> >>>
> >>> I've forked on github, extended the documentation and created a pull
> >>> request. Or is gerrit the only way to get a patch merged?
> >>>
> >>> Christina
> >>>
> >>>
> >>>
> >>> On 12.10.2016 18:03, Matt McCormick wrote:
> >>>> Hello Christina,
> >>>>
> >>>> Good idea.
> >>>>
> >>>> To update the documentation, the class Doxygen documentation can be
> >>>> editted:
> >>>>
> >>>>
> >>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
> >>>>
> >>>> and after a patch is submitted:
> >>>>
> >>>>     https://itk.org/Wiki/ITK/Git/Develop
> >>>>
> >>>> it will show up on the Doxygen web pages.
> >>>>
> >>>> Please let us know if you have any questions.
> >>>>
> >>>> Thanks,
> >>>> Matt
> >>>>
> >>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
> >>>> <cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> I think it would be helpful if the documentation of the filter would
> >>>>> mention
> >>>>> that there are two outputs, one with the surviving labels and the second
> >>>>> with the removed labels (the input image is the union of these images).
> >>>>> What
> >>>>> is the workflow to achieve this?
> >>>>>
> >>>>> Christina
> >>>>>
> >>>>> _____________________________________
> >>>>> 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
> >>>
> >>>
> >>> _____________________________________
> >>> 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
> >>
> >>
> >>
> >> _____________________________________
> >> 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
> >>
>
>
>
>
> _____________________________________
> 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
>
>
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From CAOwens at mdanderson.org  Wed Oct 19 11:07:40 2016
From: CAOwens at mdanderson.org (Owens,Constance A)
Date: Wed, 19 Oct 2016 15:07:40 +0000
Subject: [ITK-users] Lesion Sizing Toolkit (Visualization errors)
Message-ID: <603A32F9BAA25B4FBF30F3ADF057B0872C75E5B9@DCPWPEXMBX01.mdanderson.edu>

Hi,

I am using ITKv4.11.0, VTKv7.0.0 with CMAKE 3.6.1.

I am trying to use LSTK (Lesion Sizing Toolkit).

I am using Windows. After typing in Command Prompt (as per this link's instructions https://public.kitware.com/LesionSizingKit/index.php/Users/Run_LesionSegmentation )


LesionSegmentation.exe -InputDICOMDir ./54478 -OutputImage ./outputTumorImage.mha -Seeds 3 23.35 115.93 -73.8 -MaximumRadius 20 -OutputROI ./outputROI.mhd -OutputMesh ./output.stl -Visualize 1 -Screenshot ./screenShotTumor


LesionSegmentation.exe is inside the directory: C:\ITKv4.11.0\bin-x64\bin\Debug
I placed the series of DICOM images inside the directory: C:\ITKv4.11.0\bin-x64\bin\Debug\54478


Inside the vtkOutputWindow I get several errors saying 'no override found for 'vtkRenderer'... etc (I put a printscreen below)

[cid:image002.png at 01D229F0.9BCB7DA0]

And another screen pops up to tell me that there is an APPCRASH:

Problem signature:
  Problem Event Name:                        APPCRASH
  Application Name:                             LesionSegmentation.exe
  Application Version:                           0.0.0.0
  Application Timestamp:                     58068b71
  Fault Module Name:                          LesionSegmentation.exe
  Fault Module Version:                        0.0.0.0
  Fault Module Timestamp:                  58068b71
  Exception Code:                                  c0000005
  Exception Offset:                                00000000008f2118
  OS Version:                                          6.1.7601.2.1.0.256.4
  Locale ID:                                             1033
  Additional Information 1:                  45a3
  Additional Information 2:                  45a37769920ca79c15f1c3d86dd9b3c1
  Additional Information 3:                  aa5b
  Additional Information 4:                  aa5b3031c12edfd5a504d3d326ceefa3



I was hoping someone could point me in the right direction in order to resolve this issue. Additionally, I noticed that there is a Visualization.sln file inside (C:\ITKv4.11.0\bin-x64\Modules\Remote\LesionSizingToolkit\Utilities\Visualization) and was wondering if this could be part of the issue, as I have not built it yet.

On the website, there was no mention to build this for the lesion segmentation to work. I followed directions given by video here: https://www.youtube.com/watch?v=dFtipGL6SEs


Thanks,
Constance Owens
Graduate Research Assistant

The University of Texas Graduate School of Biomedical Sciences at Houston
Medical Physics
CAOwens at mdanderson.org<https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
tel 713-745-3679 | cel 281-770-5210

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
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From ivan.granata.na at gmail.com  Thu Oct 20 04:20:08 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 20 Oct 2016 01:20:08 -0700 (MST)
Subject: [ITK-users] SimpleITK for Java Image Fusion and Co-registration?
In-Reply-To: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
References: <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
 <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
Message-ID: <1476951608524-37682.post@n7.nabble.com>

i solved for TranslationTransofrm in Java

but now i would to try a deformable transform (Java)


with simple itk i've found these class but i don't now how to convert in
java

BSplineTransform	2D or 3D, deformable transformation represented by a sparse
regular grid of control points.
DisplacementFieldTransform	2D or 3D, deformable transformation represented
as a dense regular grid of vectors.

anyone can help me?

thx



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From ivan.granata.na at gmail.com  Thu Oct 20 04:23:12 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 20 Oct 2016 01:23:12 -0700 (MST)
Subject: [ITK-users] Deformable Transformation for Coregistration Simple ITK
 JAVA code
Message-ID: <1476951792366-37683.post@n7.nabble.com>

i solved for TranslationTransofrm in Java with this
http://review.source.kitware.com/#/c/21596/1/Examples/Java/ImageRegistrationMethod1.java
and some change in source code to obtain final image

but now i would to try a deformable transform (Java)


with simple itk i've found these class but i don't now how to convert in
java

BSplineTransform	2D or 3D, deformable transformation represented by a sparse
regular grid of control points.
DisplacementFieldTransform	2D or 3D, deformable transformation represented
as a dense regular grid of vectors.

anyone can help me?

thx



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Deformable-Transformation-for-Coregistration-Simple-ITK-JAVA-code-tp37683.html
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From blowekamp at mail.nih.gov  Thu Oct 20 08:56:12 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 20 Oct 2016 12:56:12 +0000
Subject: [ITK-users] Deformable Transformation for Coregistration Simple
 ITK JAVA code
In-Reply-To: <1476951792366-37683.post@n7.nabble.com>
References: <1476951792366-37683.post@n7.nabble.com>
Message-ID: <8DC4E43E-8021-4807-8463-5AE5C2BCDB2F@mail.nih.gov>

Ivan,

Have you found the python examples:

https://github.com/SimpleITK/SimpleITK/blob/522e60bb293a2581b8a56912658aff824b7e6c1c/Examples/Python/ImageRegistrationMethodBSpline1.py

https://github.com/SimpleITK/SimpleITK/blob/522e60bb293a2581b8a56912658aff824b7e6c1c/Examples/Python/ImageRegistrationMethodDisplacement1.py

Hopefully you have figured out the SimpleITK Java interface a little more so that you can translate this python code into the Java.

Also keep in mind that these deformable registration is are generally for finer grain registration after gross transform initialization and affine registration has been done. The latter displacement example show how this is done with a composite transform. You will need to consult the ITK Software Guide [1] for more information about ITK registration framework. As well as being familiar with the theory [2].

HTH,
Brad


[1] https://itk.org/ITK/help/documentation.html 
[2] http://journal.frontiersin.org/article/10.3389/fninf.2014.00044/full



> On Oct 20, 2016, at 4:23 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> i solved for TranslationTransofrm in Java with this
> http://review.source.kitware.com/#/c/21596/1/Examples/Java/ImageRegistrationMethod1.java
> and some change in source code to obtain final image
> 
> but now i would to try a deformable transform (Java)
> 
> 
> with simple itk i've found these class but i don't now how to convert in
> java
> 
> BSplineTransform	2D or 3D, deformable transformation represented by a sparse
> regular grid of control points.
> DisplacementFieldTransform	2D or 3D, deformable transformation represented
> as a dense regular grid of vectors.
> 
> anyone can help me?
> 
> thx
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Deformable-Transformation-for-Coregistration-Simple-ITK-JAVA-code-tp37683.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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


From ivan.granata.na at gmail.com  Thu Oct 20 07:51:55 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 20 Oct 2016 04:51:55 -0700 (MST)
Subject: [ITK-users] Deformable Transformation for Coregistration Simple
 ITK JAVA code
In-Reply-To: <8DC4E43E-8021-4807-8463-5AE5C2BCDB2F@mail.nih.gov>
References: <1476951792366-37683.post@n7.nabble.com>
 <8DC4E43E-8021-4807-8463-5AE5C2BCDB2F@mail.nih.gov>
Message-ID: <1476964315973-37685.post@n7.nabble.com>

i try with this code

Affine and After BSpline

but after 190 iterations return error code

-------
itk::simple::Transform
 AffineTransform (000000001966EA60)
   RTTI typeinfo:   class itk::AffineTransform<double,3>
   Reference Count: 3
   Modified Time: 3451
   Debug: Off
   Object Name: 
   Observers: 
     none
   Matrix: 
     -0.0283494 0.437495 -0.558782 
     -0.215329 2.14011 2.01216 
     0.661568 -8.35499 1.81576 
   Offset: [0.0377555, -0.0313043, -0.251059]
   Center: [0, 0, 0]
   Translation: [0.0377555, -0.0313043, -0.251059]
   Inverse: 
     -435.991 -81.6103 -43.7342 
     -36.2773 -6.70277 -3.73619 
     -8.07294 -1.10745 -0.706396 
   Singular: 0

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Maximum
number of iterations (200) exceeded.
 Iteration: 200
 Metric value: -0,176593
Exception in thread "main" java.lang.RuntimeException: Exception thrown in
SimpleITK new_BSplineTransform:
..\..\..\..\..\SimpleITK\Code\Common\src\sitkBSplineTransform.cxx:188:
sitk::ERROR: Transform is not of type BSplineTransform!
	at org.itk.simple.SimpleITKJNI.new_BSplineTransform__SWIG_3(Native Method)
	at org.itk.simple.BSplineTransform.<init>(BSplineTransform.java:75)
	at ImageRegistrationMethodNaplab.main(IterationUpdate.java:68)


this is my code



import org.itk.simple.*;
class IterationUpdate  extends Command {
  private ImageRegistrationMethod m_Method;
  public IterationUpdate(ImageRegistrationMethod m) {
    super();
    m_Method=m;
  }
  
  public void execute() {
    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
    System.out.format("%3d = %10.5f : [%f, %f]\n",
                      m_Method.getOptimizerIteration(),
                      m_Method.getMetricValue(),
                      pos.get(0), pos.get(1));
  }
}

class ImageRegistrationMethodNaplab {
  public static void main(String argv[]) {
  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }
  
  

  int   ImageDimension = 3;
  char   PixelType;

  
  
  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
  reader.setFileName(argv[0]);
  Image fixed  = reader.execute();
  reader.setFileName(argv[1]);
  Image moving = reader.execute();
  
  
  
  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
  R.setMetricAsMattesMutualInformation();
  double maxStep = 4.0;
  double minStep = 0.01;
  int numberOfIterations = 200;
  double relaxationFactor = 0.5;
  R.setOptimizerAsRegularStepGradientDescent( maxStep,
                                              minStep,
                                              numberOfIterations,
                                              relaxationFactor );
  R.setInitialTransform( new org.itk.simple.AffineTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkBSpline );
  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);
  
  
  org.itk.simple.Transform outTx = R.execute( fixed, moving );
  System.out.println("-------");
  System.out.println(outTx.toString());
  
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());

  outTx.writeTransform(argv[2]);
  
  org.itk.simple.BSplineTransform R2 = new 
org.itk.simple.BSplineTransform(outTx);
    
  
  
  
  fixed.getSpacing();
  fixed.getOrigin();
  //fixed.getLargestPossibleRegion();
  fixed.getDirection();
   

 int SplineOrder = 3;
  long SpaceDimension = ImageDimension;
 double CoordinateRepType;
  
  
 
 //org.itk.simple.Transform R = new 
org.itk.simple.BSplineTransform(SpaceDimension,SplineOrder);
 
 

 
  
  //org.itk.simple.BSplineTransformInitializerFilter R = new 
org.itk.simple.BSplineTransformInitializerFilter();
  //R.getTransformDomainMeshSize();
  //R.getOrder();
  
 
  //org.itk.simple.Transform outTx = R.execute(moving);
  
  //org.itk.simple.BSplineTransform R2 = new 
org.itk.simple.BSplineTransform(outTx);
  //R2.getDomainOrigin();
  
 
  
  
  
 // IterationUpdate cmd = new IterationUpdate(R);
 // R.addCommand( EventEnum.sitkIterationEvent, cmd);
  

  
  
  

  //getDimension Return the dimension of the Transform ( 2D or 3D )
 // R.setInitialTransform( new
org.itk.simple.BSplineTransform(SplineOrder,SpaceDimension ) );
 //R.getDomainDirection();
 
  //fixed.getDimension()
  
    
  
  System.out.println("-------");
  System.out.println(outTx.toString());
  //System.out.format(" Fixed Initial Transform: %d\n",
R.getFixedInitialTransform());
  //System.out.format(" Moving Initial Transform: %d\n",
R.getMovingInitialTransform());
  //System.out.format(" Initial Transform: %d\n", R.getInitialTransform());
  //System.out.format(" Optimizer Position: %d\n",
R.getOptimizerPosition());
               //System.out.format("Optimizer stop condition: %s\n",
R2.getOptimizerStopConditionDescription());
              //System.out.format(" Iteration: %d\n",
R2.getOptimizerIteration());
                        //System.out.format(" Metric value: %f\n",
R2.getMetricValue());
  //System.out.format(" Interpolator: %f\n", R.getInterpolator());
  //System.out.format(" Translation X", R.getTranslationAlongX());
 // System.out.format(" Translation Y", R.getTranslationAlongY());
  R2.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
   //org.itk.simple.Transform.writeTransform(argv[4]);
  //org.itk.simple.ResampleImageFilter image = new
org.itk.simple.ResampleImageFilter();
  //image.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
 // image.getOutputPixelType(); 
 // image.getSize ();
  //ImageFileWriter writer = new ImageFileWriter();
 // writer.setFileName(argv[5]);
    org.itk.simple.Transform transform = new org.itk.simple.Transform();
  reader.setFileName(argv[2]);
  // Write result image
  ImageFileWriter writer2 = new org.itk.simple.ImageFileWriter();
  writer2.setFileName(argv[3]);
  
  
  
  org.itk.simple.ResampleImageFilter transf = new 
org.itk.simple.ResampleImageFilter();
    transf.setReferenceImage(fixed);
  transf.setTransform(outTx);
  transf.setOutputPixelType(PixelIDValueEnum.sitkUInt32);
  //InterpolatorEnum interp = 
		  transf.getInterpolator();
  //transf.setInterpolator(interp);
//  VectorDouble orig = 
		  transf.getOutputOrigin();
  //VectorDouble spac = 
		  transf.getOutputSpacing();
 // VectorDouble dir = 
		  transf.getOutputDirection();
  //Double pix = 
		  transf.getDefaultPixelValue();
  //transf.setInterpolator(dir);
  //VectorUInt32 pts = new VectorUInt32();
  transf.getSize();
  transf.execute(moving);
   Image blurredImg = transf.execute(moving);
    //Image castImg = caster.execute(blurredImg);
    ImageFileWriter writer3 = new ImageFileWriter();
    writer3.setFileName(argv[3]);
     writer3.execute(blurredImg);
     //writer.execute(transform.getResultImage()); 
     // transform.setParameters(reader.execute());
      //Image transform = reader.execute();
  //Transform.setParameters();
    // Perform warp
//  transform.logToConsoleOn();
 // transform.execute();
    }  
}




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From matt.mccormick at kitware.com  Thu Oct 20 10:23:19 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 20 Oct 2016 10:23:19 -0400
Subject: [ITK-users] [vtkusers] Testing ITK/VTK/PV contributions with
	(kitware) Gitlab-CI
In-Reply-To: <CAPf2UMQOckvhyn0fd_XmYPgfh=kU+uj60JONT5gFH-0qnxx6eg@mail.gmail.com>
References: <b559f993-9283-7f14-b7ad-66eb85c5d52a@mh-hannover.de>
 <20160908131417.GB13993@megas.kitware.com>
 <CAPf2UMRfLtz1Cd_kYy0uX3V3nA96F2BqGuNGn=zY6_wg_5mkEw@mail.gmail.com>
 <ddc193b4-0cc5-7cb5-4cd6-47c2409435ba@mh-hannover.de>
 <CAPf2UMQOckvhyn0fd_XmYPgfh=kU+uj60JONT5gFH-0qnxx6eg@mail.gmail.com>
Message-ID: <CALzTN-RbcRnPc0k9ppbLxza2dj7EgPFwQ2oGC0SdPo_dafVKNQ@mail.gmail.com>

Hi,

Yes, the Insight and Midas journals testing infrastructure is no
longer functional.

Matt

On Mon, Sep 12, 2016 at 9:10 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Roman,
>
> I don't think that Insight and Midas journals' testing infrastructure is
> functional any more. Perhaps Matt can provide more info?
>
> Regards,
> D?enan
>
> On Mon, Sep 12, 2016 at 5:49 AM, Grothausmann, Roman Dr.
> <grothausmann.roman at mh-hannover.de> wrote:
>>
>> Many thanks Ben and D?enan for Your replies and pointing me to CircleCI. I
>> see that testing contributions employing PV,VTK and ITK all together is
>> rather challenging.
>>
>> I wonder though why my pure VTK (PV) based contribution did not get tested
>> when submitted to the VTK-Journal, e.g.
>> http://www.midasjournal.org/browse/publication/949
>>
>> Is the testing the VTK/Midas Journals used to do not available any more?
>>
>> Regards,
>> Roman
>>
>> On 08/09/16 16:26, D?enan Zuki? wrote:
>>>
>>> Hi Roman,
>>>
>>> some of ITK's remote modules are using CircleCI for testing. Two recent
>>> examples
>>> are RLEImage <https://github.com/KitwareMedical/ITKRLEImage> and
>>> MorphologicalContourInterpolation
>>> <https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation>.
>>> Of
>>> course, you should be familiar, or familiarize yourself with CircleCI
>>> <https://circleci.com/docs/configuration/>.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Thu, Sep 8, 2016 at 9:14 AM, Ben Boeckel <ben.boeckel at kitware.com
>>> <mailto:ben.boeckel at kitware.com>> wrote:
>>>
>>>     On Thu, Sep 08, 2016 at 12:36:40 +0200, Grothausmann, Roman Dr.
>>> wrote:
>>>     > Just getting to know Gitlab-CI, I am wondering whether it is
>>> possible to test
>>>     > contributions to ITK/VTK/PV with Gitlab-CI from gitlab.com
>>> <http://gitlab.com> or
>>>     > gitlab.kitware.com <http://gitlab.kitware.com>. As far as I
>>> understand, this
>>>     basically needs runners, in
>>>     > this case specific to ITK/VTK/PV. Since kitware has done CI even
>>> before the use
>>>     > of gitlab, I wonder if the former testing environments are
>>> available for use
>>>     > with Gitlab-CI and if so how to use them.
>>>
>>>     We're (VTK and ParaView) using buildbot to manage our testing. The
>>>     number of settings we test across machines is hard to specify in YAML
>>>     files (machines also have different settings based on what you're
>>>     testing, e.g., load up a different compiler or Qt4 or Qt5 and the
>>> paths
>>>     they live in, etc.). We're working on improving the hardware
>>> situation
>>>     buildbot is currently in; things should be getting better over the
>>> next
>>>     few months on that front.
>>>
>>>     > For example, none of my contributions to the ITK/VTK/Midas Journals
>>> got into the
>>>     > testing phase even though marked for testing during submission. So
>>> a possibility
>>>     > to use Gitlab-CI to test the compilation and to run the project
>>> test would be
>>>     > really great, especially for continued development and testing on
>>> other OSs.
>>>     > Specifically, for e.g. testing my FacetAnalyser contribution
>>>     > (http://www.midasjournal.org/browse/publication/951
>>>     <http://www.midasjournal.org/browse/publication/951>
>>>     > https://gitlab.com/romangrothausmann/FacetAnalyser
>>>     <https://gitlab.com/romangrothausmann/FacetAnalyser>) I would need a
>>> runner
>>>     > environment with PV, VTK and ITK ideally for Linux, MacOS and
>>> Windows.
>>>
>>>     ITK is using Gerrit and Jenkins, not Gitlab.
>>>
>>>     --Ben
>>>     _______________________________________________
>>>     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>
>>>
>>>     Please keep messages on-topic and check the VTK FAQ at:
>>>     http://www.vtk.org/Wiki/VTK_FAQ <http://www.vtk.org/Wiki/VTK_FAQ>
>>>
>>>     Search the list archives at: http://markmail.org/search/?q=vtkusers
>>>     <http://markmail.org/search/?q=vtkusers>
>>>
>>>     Follow this link to subscribe/unsubscribe:
>>>     http://public.kitware.com/mailman/listinfo/vtkusers
>>>     <http://public.kitware.com/mailman/listinfo/vtkusers>
>>>
>>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-2900
>
>

From zeinsalah at gmail.com  Fri Oct 21 08:30:04 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Fri, 21 Oct 2016 14:30:04 +0200
Subject: [ITK-users] [ITK] Loading multiframe dicom with itk
In-Reply-To: <CALzTN-SsLtOdZV6Yz+=i-jDU0_3wxaE8BK0Q7RT6XxycAGLaDQ@mail.gmail.com>
References: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>
 <CALzTN-SsLtOdZV6Yz+=i-jDU0_3wxaE8BK0Q7RT6XxycAGLaDQ@mail.gmail.com>
Message-ID: <CADiSopPqqVe1kpF3FqUZdWgjfwQJKfg1U_MN_qN1edUNFuUb-g@mail.gmail.com>

Hi Matt,

thanks for the response!

I tested with itk 4.10 and have the following remarks/questions:

1. First, the behavior is different from itk 3.14 and 3.20, but I
think the reader still has bugs.

2. for some data sets, I got a negative z spacing, what does this mean?

3. I have a multiframe-dicom in which the image patient positions
(0020,0032) are stored
individually for each frame under the PerFrame Functional Group
Sequence. Are these positions
taken into account when reconstructing the 3D volume from the block of
data is read?
I am asking because the positions of the slices are going in the
negative z-direction,
which means that the slices are stored in the oopsite order, i.e., the
farthest slice in z
is stored first. Does the reader respect this?

thanks,
Zein



2016-10-19 15:40 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
> Hi Zein,
>
> There has been fixes for this issue in later versions of ITK via both
> ITK's handling of the spacing and the DICOM library used to parse the
> files. It is worthwhile to try with a recent version of ITK to see if
> the issue has been addressed.
>
> HTH,
> Matt
>
> On Wed, Oct 19, 2016 at 6:55 AM, Zein Salah <zeinsalah at gmail.com> wrote:
>> Hi,
>>
>> to organizational reasons, I must use an old release of itk (3.14).
>>
>> I am trying to load multiframe dicom images with itk reader. I noticed
>>  a strange behavior in the itk::ImageFileReader.
>> when I load a multiframe dicom image with the reader, the output of the reader
>> has a correct z-spacing. But the x- and y- spacings are always 1.0. I
>> also could reproduce this using itk 3.20.1.
>>
>> I also noticed that at lease the orientation is wrong.
>>
>> a short search led me to this:
>>
>> http://www.na-mic.org/Bug/view.php?id=725
>>
>> is this aknow issue in itk? has it been fiyed in later versions?
>>
>> Thanks,
>> Zein
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community

From bnagaev at gmail.com  Sun Oct 23 17:09:29 2016
From: bnagaev at gmail.com (Nagaev Boris)
Date: Mon, 24 Oct 2016 00:09:29 +0300
Subject: [ITK-users] mingw,
	gcc5: "too many sections" and "undefined reference to vtable" errors
Message-ID: <CAFC_Vt6KrHP4uOjRZUpb05dgz3mzKdb0iDFGc5DTZ0yGUp6KoA@mail.gmail.com>

Hello,

I need help building ITK 4.8.0. I cross-compile on gcc 5.3.0 from
Linux to Windows using MinGW-w64. Everything was Ok on gcc 4.9.4.

I get the same errors as in this tread:
https://cmake.org/pipermail/insight-users/2015-September/052511.html
My log: https://git.io/vPNmf

I added -Wa,-mbig-obj flags and the same error:
https://cmake.org/pipermail/insight-users/2015-September/052512.html
My log: https://git.io/vPNqh
I added the flags by adding the following to cmake command:
-DCMAKE_C_FLAGS='-Wa,-mbig-obj'
-DCMAKE_CXX_FLAGS='-Wa,-mbig-obj'

If I add these flags and compile with gcc 4.9.0, it works.

-- 
Best regards,
Boris Nagaev

From bnagaev at gmail.com  Sun Oct 23 18:57:34 2016
From: bnagaev at gmail.com (Nagaev Boris)
Date: Mon, 24 Oct 2016 01:57:34 +0300
Subject: [ITK-users] mingw,
 gcc5: "too many sections" and "undefined reference to vtable" errors
In-Reply-To: <CAFC_Vt6KrHP4uOjRZUpb05dgz3mzKdb0iDFGc5DTZ0yGUp6KoA@mail.gmail.com>
References: <CAFC_Vt6KrHP4uOjRZUpb05dgz3mzKdb0iDFGc5DTZ0yGUp6KoA@mail.gmail.com>
Message-ID: <CAFC_Vt6xxjBU26KLomL+p11c4RHr7LQeiUfSMk5fPS4K71kr4A@mail.gmail.com>

On Mon, Oct 24, 2016 at 12:09 AM, Nagaev Boris <bnagaev at gmail.com> wrote:
> Hello,
>
> I need help building ITK 4.8.0. I cross-compile on gcc 5.3.0 from
> Linux to Windows using MinGW-w64. Everything was Ok on gcc 4.9.4.
>
> I get the same errors as in this tread:
> https://cmake.org/pipermail/insight-users/2015-September/052511.html
> My log: https://git.io/vPNmf
>
> I added -Wa,-mbig-obj flags and the same error:
> https://cmake.org/pipermail/insight-users/2015-September/052512.html
> My log: https://git.io/vPNqh
> I added the flags by adding the following to cmake command:
> -DCMAKE_C_FLAGS='-Wa,-mbig-obj'
> -DCMAKE_CXX_FLAGS='-Wa,-mbig-obj'
>
> If I add these flags and compile with gcc 4.9.0, it works.

Latest ITK (4.10.1) builds successfully with gcc 6 after disabling
try-run (https://gist.github.com/starius/b7b1ee84faa76de1f52efe3f1959dc1d).


-- 
Best regards,
Boris Nagaev

From mustafa at inode.at  Mon Oct 24 06:02:00 2016
From: mustafa at inode.at (Mustafa Arikan)
Date: Mon, 24 Oct 2016 12:02:00 +0200
Subject: [ITK-users] Reading a DICOM file in SimpleITK and ITK (spacing
	error)
Message-ID: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>

Dear all,

reading a DICOM file (.dcm) in SimpleITK leads to following problem:

> RuntimeError: Exception thrown in SimpleITK ReadImage: 
> c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageBase.hxx:192:
> itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not allowed: 
> Spacing is [0, 0, 1]

The code looks like this:

> import SimpleITK
>
> inputFileName = 
> "D:\\workspace\\exports\\51871876-25-ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZVWGHRLQ+TNXWEN\\bscan.dcm"
> reader = SimpleITK.ImageSeriesReader()
> image= SimpleITK.ReadImage(inputFileName)
> reader.SetFileName ( inputFileName )
> imageIn = reader.Execute()

And I am getting the same error within ITK.

But opening the .dcm file with some DICOM-Viewer works.


thanks in advance,
Mustafa

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From zeinsalah at gmail.com  Mon Oct 24 08:50:39 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 24 Oct 2016 14:50:39 +0200
Subject: [ITK-users] meaning of negative spacing
Message-ID: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>

Hi,

I have a question regarding reading dicom files with itk,
particularly, multiframe dicom file (all slices in one single file).

I have read an image with itk 4.10 and write it into an mhd-raw image.
I noticed that the z-spacin is negative.
What does negative spacing mean?

thanks,
Zein

From ivan.granata.na at gmail.com  Mon Oct 24 08:53:53 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Mon, 24 Oct 2016 05:53:53 -0700 (MST)
Subject: [ITK-users] Coregistration Transform Phyton to Java please help me
Message-ID: <1477313633399-37692.post@n7.nabble.com>

i've this

https://itk.org/SimpleITKDoxygen/html/Python_2ImageRegistrationMethodDisplacement1_8py-example.html


and in java i try to translate in this:
 but i've some errors
can anyone help me please?






import org.itk.simple.*;
class IterationUpdate  extends Command {
  private ImageRegistrationMethod m_Method;
  public IterationUpdate(ImageRegistrationMethod m) {
    super();
    m_Method=m;
  }
  
  public void execute() {
    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
    System.out.format("%3d = %10.5f : [%f, %f]\n",
                      m_Method.getOptimizerIteration(),
                      m_Method.getMetricValue(),
                      pos.get(0), pos.get(1));
  }
}

class ImageRegistrationMethodNaplab {
  public static void main(String argv[]) {
  if ( argv.length < 4 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }
  
  

  int   ImageDimension = 3;
  char   PixelType;

  
  
  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
  reader.setFileName(argv[0]);
  Image fixed  = reader.execute();
  reader.setFileName(argv[1]);
  Image moving = reader.execute();
  

  
  
  
  org.itk.simple.Transform initialTx = new org.itk.simple.Transform();
  
  //initialTx.CenteredTransformInitializerFilter( new
org.itk.simple.AffineTransform( fixed.getDimension() ) );
  
    
 initialTx.execute( fixed, moving, AffineTransform( fixed.getDimension() ));
  
  
  
  //org.itk.simple.Transform transf1 = new org.itk.simple.Transform();
  //org.itk.simple.AffineTransform afftransf = new
org.itk.simple.AffineTransform();
  //CenteredTransformInitializerFilter initialTx =
transf1.execute(fixed,moving, Transform.Affine(fixed.getDimension()));
  //org.itk.simple.AffineTransform Aff = new 
org.itk.simple.AffineTransform();
  
 // org.itk.simple.ImageRegistrationMethod initialTx = new 
org.itk.simple.ImageRegistrationMethod();
  
 // CenteredTransformInitializerFilter transform1 = new
CenteredTransformInitializerFilter();
 // initialTx.execute(fixed, moving, transform1( fixed.getDimension()));
  
  
  //initialTx.CenteredTransformInitializerFilter( new
org.itk.simple.AffineTransform( fixed.getDimension() ) );

 // Transform initialTx = new Transform();
  //ord.add(initialTx);
  
  //org.itk.simple.Transform transform =  new Transform();
  
 // initialTx.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );

  
 // initialTx.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );
  
  
  
  
  // initialTx.setTransform( new org.itk.simple.AffineTransform(
fixed.getDimension() ) );
  
//
 
  //org.itk.simple.Transform initialTx =
CenteredTransformInitializerFilter.execute(fixed, moving, Aff);
 
  //fixed, moving, Transform(fixed.getDimension(),TransformEnum.sitkAffine)
  
  
  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
 
//VectorUInt32 b = [(3,2,1)];
  //VectorUInt32 b = new VectorUInt32 {(3,2,1)};
  long a1= 321;
  VectorUInt32 x1 = new VectorUInt32(a1);
  R.setShrinkFactorsPerLevel(x1);
  //Vector<Double> (3,2,1);
  
  
  long b1 = 211;
  VectorDouble y1 = new VectorDouble(b1);
 
  R.setSmoothingSigmasPerLevel(y1);
  
  //SET Metric
  R.setMetricAsMattesMutualInformation(20);
  //R.setMetricAsJointHistogramMutualInformation(20);
  R.setMetricUseFixedImageGradientFilter(false);
  
  double learningRate = 1.0 ;
  double minStep = 0.01;
  int numberOfIterations = 100;
  
  R.setOptimizerAsRegularStepGradientDescent( learningRate,
                                              minStep,
                                              numberOfIterations);
  //R.setOptimizerAsGradientDescent(learningRate=1.0,  // 
numberOfIterations=100, //  estimateLearningRate = R.EachIteration)
  
  
  
//SET Optimizer
  R.setOptimizerScalesFromPhysicalShift();
  
  
  R.setInitialTransform(initialTx,true);
  
//SET Interpolator
  R.setInterpolator(InterpolatorEnum.sitkLinear);
  
  
  org.itk.simple.Transform outTx = R.execute( fixed, moving );
  System.out.println("-------");
  System.out.println(outTx.toString());
  
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());
  
  
  
 org.itk.simple.Image displacementField = new 
org.itk.simple.Image(fixed.getSize(), PixelIDValueEnum.sitkVectorFloat64);
  
  //displacementField.Image();
  
  org.itk.simple.DisplacementFieldTransform displacementTx =  new
org.itk.simple.DisplacementFieldTransform(displacementField);
  
  double varianceForUpdateField = 0.0 ;
  double varianceForTotalField = 1.5;
  
  displacementTx.setSmoothingGaussianOnUpdate(varianceForUpdateField,
varianceForTotalField);
  
  
  R.setMovingInitialTransform(outTx);
  R.setInitialTransform(displacementTx,true);
  
 
    
  R.setMetricAsANTSNeighborhoodCorrelation(4);
  R.setMetricUseFixedImageGradientFilter(false);
  R.setMetricUseFixedImageGradientFilter(false);
  
  
  //VectorUInt32 b = [(3,2,1)];
  //VectorUInt32 b = new VectorUInt32 {(3,2,1)};
  long a2= 321;
  VectorUInt32 x2 = new VectorUInt32(a2);
  R.setShrinkFactorsPerLevel(x2);
  //Vector<Double> (3,2,1);
  
  
  long b2 = 211;
  VectorDouble y2 = new VectorDouble(b2);
 
  R.setSmoothingSigmasPerLevel(y2);

  
  R.setOptimizerScalesFromPhysicalShift();
  
  double learningRate2 = 1.0 ;
  double minStep2 = 0.01;
  int numberOfIterations2 = 300;
  
  R.setOptimizerAsRegularStepGradientDescent( learningRate2,
                                              minStep2,
                                              numberOfIterations2);
  
  
  
  
  
  //outTx.AddTransform( R.Execute(fixed, moving) )
  
  outTx.addTransform ( R.execute( fixed, moving ));
  System.out.println("-------");
  System.out.println(outTx.toString());
  
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());
  
  
  
  outTx.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
  
  
  
  org.itk.simple.Transform transform = new org.itk.simple.Transform();
  reader.setFileName(argv[2]);
  // Write result image
  ImageFileWriter writer2 = new org.itk.simple.ImageFileWriter();
  writer2.setFileName(argv[3]);
  
  
  
  org.itk.simple.ResampleImageFilter transf = new 
org.itk.simple.ResampleImageFilter();
    transf.setReferenceImage(fixed);
  transf.setTransform(outTx);
  transf.setOutputPixelType(PixelIDValueEnum.sitkUInt32);
  //InterpolatorEnum interp = 
		  transf.getInterpolator();
  //transf.setInterpolator(interp);
//  VectorDouble orig = 
		  transf.getOutputOrigin();
  //VectorDouble spac = 
		  transf.getOutputSpacing();
 // VectorDouble dir = 
		  transf.getOutputDirection();
  //Double pix = 
		  transf.getDefaultPixelValue();
  //transf.setInterpolator(dir);
  //VectorUInt32 pts = new VectorUInt32();
  transf.getSize();
  transf.execute(moving);
   Image blurredImg = transf.execute(moving);
    //Image castImg = caster.execute(blurredImg);
    ImageFileWriter writer3 = new ImageFileWriter();
    writer3.setFileName(argv[3]);
     writer3.execute(blurredImg);
     //writer.execute(transform.getResultImage()); 
     // transform.setParameters(reader.execute());
      //Image transform = reader.execute();
  //Transform.setParameters();
    // Perform warp
//  transform.logToConsoleOn();
 // transform.execute();
  }

private static Transform AffineTransform(long dimension) {
	// TODO Auto-generated method stub
	return null;
}
  }




--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Coregistration-Transform-Phyton-to-Java-please-help-me-tp37692.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From dzenanz at gmail.com  Mon Oct 24 10:55:14 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 10:55:14 -0400
Subject: [ITK-users] [ITK] meaning of negative spacing
In-Reply-To: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
References: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
Message-ID: <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>

Hi Zein,

I suppose you could invert the 3rd row (Z component) of the TransformMatrix
and have the spacing positive. It should have the same effect and is more
logical.

Regards,
D?enan

On Mon, Oct 24, 2016 at 8:50 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi,
>
> I have a question regarding reading dicom files with itk,
> particularly, multiframe dicom file (all slices in one single file).
>
> I have read an image with itk 4.10 and write it into an mhd-raw image.
> I noticed that the z-spacin is negative.
> What does negative spacing mean?
>
> thanks,
> Zein
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From dzenanz at gmail.com  Mon Oct 24 11:01:02 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 11:01:02 -0400
Subject: [ITK-users] Reading a DICOM file in SimpleITK and ITK (spacing
	error)
In-Reply-To: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
References: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
Message-ID: <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>

Hi Mustafa,

since the offending .dcm is in folder "exports", I assume some tool's DICOM
export is broken. Spacing should never be 0. If spacing is not known, it
should be set to 1. ITK has a right to complain about this. Can you
re-export this file, and perhaps fiddle with export settings a bit?

Regards,
D?enan

On Mon, Oct 24, 2016 at 6:02 AM, Mustafa Arikan <mustafa at inode.at> wrote:

> Dear all,
>
> reading a DICOM file (.dcm) in SimpleITK leads to following problem:
>
> RuntimeError: Exception thrown in SimpleITK ReadImage:
> c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\
> include\itkImageBase.hxx:192:
> itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not allowed:
> Spacing is [0, 0, 1]
>
> The code looks like this:
>
> import SimpleITK
>
> inputFileName = "D:\\workspace\\exports\\51871876-25-
> ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZ
> VWGHRLQ+TNXWEN\\bscan.dcm"
> reader = SimpleITK.ImageSeriesReader()
> image= SimpleITK.ReadImage(inputFileName)
> reader.SetFileName ( inputFileName )
> imageIn = reader.Execute()
>
> And I am getting the same error within ITK.
>
> But opening the .dcm file with some DICOM-Viewer works.
>
>
> thanks in advance,
> Mustafa
>
> _____________________________________
> 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
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>
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From zeinsalah at gmail.com  Mon Oct 24 11:12:49 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 24 Oct 2016 17:12:49 +0200
Subject: [ITK-users] [ITK] meaning of negative spacing
In-Reply-To: <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>
References: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
 <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>
Message-ID: <CADiSopOgno7=XAm-ZDqgjfaMV5YDk=RWH6WJzfC2rD7eZq7-Lw@mail.gmail.com>

Hi D?enan,

thanks for the response.

but I still wonder what does this mean. The reason for the question is:

The input image is a multiframe dicom, in which the image position
patient (0020, 0032)
is stored in the header for every frame. and these values are having
decreasing values
in the z-coordinate. So I am asking myself

1. if the itkimagereader considers this when it reconstructs the 3D volume?

2. if this is the reason for negative z-spacing? if this is the case,
I can this to
interpret the meaning of the z-spacing.




2016-10-24 16:55 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
> Hi Zein,
>
> I suppose you could invert the 3rd row (Z component) of the TransformMatrix
> and have the spacing positive. It should have the same effect and is more
> logical.
>
> Regards,
> D?enan
>
> On Mon, Oct 24, 2016 at 8:50 AM, Zein Salah <zeinsalah at gmail.com> wrote:
>>
>> Hi,
>>
>> I have a question regarding reading dicom files with itk,
>> particularly, multiframe dicom file (all slices in one single file).
>>
>> I have read an image with itk 4.10 and write it into an mhd-raw image.
>> I noticed that the z-spacin is negative.
>> What does negative spacing mean?
>>
>> thanks,
>> Zein
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>
>

From dzenanz at gmail.com  Mon Oct 24 11:16:35 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 11:16:35 -0400
Subject: [ITK-users] [ITK] meaning of negative spacing
In-Reply-To: <CADiSopOgno7=XAm-ZDqgjfaMV5YDk=RWH6WJzfC2rD7eZq7-Lw@mail.gmail.com>
References: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
 <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>
 <CADiSopOgno7=XAm-ZDqgjfaMV5YDk=RWH6WJzfC2rD7eZq7-Lw@mail.gmail.com>
Message-ID: <CAPf2UMTtxYznJ9zuyEH0wyPmQiQzNg7HgU69KsO1hgKT+nXfFQ@mail.gmail.com>

Hi Zein,

image position patient is the authoritative tag to reconstruct slice
spacing and the vector of Z position/orientation. But I am surprised that
result is negative spacing instead of negative direction cosine
(orientation vector). Can you provide the offending DICOM file?

Regards,
D?enan

On Mon, Oct 24, 2016 at 11:12 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi D?enan,
>
> thanks for the response.
>
> but I still wonder what does this mean. The reason for the question is:
>
> The input image is a multiframe dicom, in which the image position
> patient (0020, 0032)
> is stored in the header for every frame. and these values are having
> decreasing values
> in the z-coordinate. So I am asking myself
>
> 1. if the itkimagereader considers this when it reconstructs the 3D volume?
>
> 2. if this is the reason for negative z-spacing? if this is the case,
> I can this to
> interpret the meaning of the z-spacing.
>
>
>
>
> 2016-10-24 16:55 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
> > Hi Zein,
> >
> > I suppose you could invert the 3rd row (Z component) of the
> TransformMatrix
> > and have the spacing positive. It should have the same effect and is more
> > logical.
> >
> > Regards,
> > D?enan
> >
> > On Mon, Oct 24, 2016 at 8:50 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> I have a question regarding reading dicom files with itk,
> >> particularly, multiframe dicom file (all slices in one single file).
> >>
> >> I have read an image with itk 4.10 and write it into an mhd-raw image.
> >> I noticed that the z-spacin is negative.
> >> What does negative spacing mean?
> >>
> >> thanks,
> >> Zein
> >> _______________________________________________
> >> Community mailing list
> >> Community at itk.org
> >> http://public.kitware.com/mailman/listinfo/community
> >
> >
>
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From sg.ele.eng at gmail.com  Mon Oct 24 12:49:06 2016
From: sg.ele.eng at gmail.com (Sara Gh)
Date: Mon, 24 Oct 2016 12:49:06 -0400
Subject: [ITK-users] SimpleITK - Subpixel shift detection in MRI
Message-ID: <CACjcMuaszDddNws2X01qcK9WxMKH2sncsAcLWSvxyzo35KJMAA@mail.gmail.com>

Hello,

I have three orthogonal intrasubject MRI volumes. Is there any way in
SimpleITK to check if the volumes have subpixel (subvoxel) shifts or not?

Thanks,
Sara Gh
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From zivrafael.yaniv at nih.gov  Mon Oct 24 16:29:12 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Mon, 24 Oct 2016 20:29:12 +0000
Subject: [ITK-users] SimpleITK - Subpixel shift detection in MRI
In-Reply-To: <CACjcMuaszDddNws2X01qcK9WxMKH2sncsAcLWSvxyzo35KJMAA@mail.gmail.com>
References: <CACjcMuaszDddNws2X01qcK9WxMKH2sncsAcLWSvxyzo35KJMAA@mail.gmail.com>
Message-ID: <D433E71A.D26C%yanivz@mail.nih.gov>

Hello Sara,

As you did not give the specifics of the problem you want to address the  suggested approaches are rather generic. Assuming here that the anatomical structure of interest in the scans did not deform (not MRs of the heart in different phases of the cardiac cycle):

1. Prospective approach -

If you can accurately identify three or more corresponding points in each of the datasets you can use the LandmarkBasedTransformInitializer (https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1LandmarkBasedTransformInitializerFilter.html) to estimate the transformation. Ideally these points can be localized with sub-voxel accuracy - possibly derived from markers which occupy a large number of voxels so that undersegmentation/oversegmentation has minimal impact on the point localization.

2. Retrospective approach -

Run a rigid registration between the images and see if the results have a visibly better alignment. After registration you can use a linked cursor to see if corresponding points appear closer to their expected locations.

An example of using a linked cursor with SimpleITK Python notebooks can be found here:
https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/master/67_Registration_Semiautomatic_Homework.ipynb

Another option is to resample the moving image and view the images using ITK-SNAP's linked cursor.

    Ziv


From: Sara Gh <sg.ele.eng at gmail.com<mailto:sg.ele.eng at gmail.com>>
Date: Monday, October 24, 2016 at 12:49 PM
To: "insight-users at itk.org<mailto:insight-users at itk.org>" <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: [ITK-users] SimpleITK - Subpixel shift detection in MRI

Hello,

I have three orthogonal intrasubject MRI volumes. Is there any way in SimpleITK to check if the volumes have subpixel (subvoxel) shifts or not?

Thanks,
Sara Gh

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From ndel314 at gmail.com  Mon Oct 24 17:43:26 2016
From: ndel314 at gmail.com (Nico Del Piano)
Date: Mon, 24 Oct 2016 18:43:26 -0300
Subject: [ITK-users] Unknown issue (realloc() invalid pointer)
Message-ID: <CAAq9_B4aF=nLCt_k6McGQ1bzQVQwaEXQ-u7mPLBj5uZQnpMadQ@mail.gmail.com>

Hello,

I have a project which uses ITK + VTK + Qt: it worked well till I
messed up something with some of the libraries/frameworks already
mentioned. I remember installing a new version of either ITK or VTK,
and then the program, after being compiled, returns the following
error when executed:

$ ./app
*** Error in `./app': realloc(): invalid pointer: 0x00007f5065aa3840 ***
Aborted (core dumped)

As I said, it worked well and stopped working after compiling a new
version of ITK or VTK. I don't know what to do, since I haven't
changed the program's code.

Sorry about this *horrible* description of my problem, but if someone
have run into this and could help me, or have an idea of how to fix
it, I'd really appreciate that :).

Thanks,

Nico.

From ivan.granata.na at gmail.com  Tue Oct 25 03:42:24 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 25 Oct 2016 00:42:24 -0700 (MST)
Subject: [ITK-users]  VectorUInt32 and VectorDouble in Java...How?
Message-ID: <1477381344050-37700.post@n7.nabble.com>

hi 

how can i specify  VectorUInt32 and VectorDouble in Java...

i ve this in python
R.SetShrinkFactorsPerLevel([3,2,1])
R.SetSmoothingSigmasPerLevel([2,1,1])

SetShrinkFactorsPerLevel would  VectorUInt32 
and
SetSmoothingSigmasPerLevel would  VectorDouble 


thanks





--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-VectorUInt32-and-VectorDouble-in-Java-How-tp37700.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Tue Oct 25 08:57:26 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 25 Oct 2016 12:57:26 +0000
Subject: [ITK-users] VectorUInt32 and VectorDouble in Java...How?
In-Reply-To: <1477381344050-37700.post@n7.nabble.com>
References: <1477381344050-37700.post@n7.nabble.com>
Message-ID: <CD7E50E4-6BCF-4C04-8B01-4C5E193C471B@mail.nih.gov>

Hello,

That is a very good question I can help with!

These vector classes are wrappers for the C++ std::vector<T> template classes. SWIG generates these data structures, and provides a JAVA like interface for the object. Unlike Python, JAVA is a strongly type language and requires explicit types and constructors. Here is the snippet that I think you need:

VectorUInt32 shrinkFactors = new VectorUIn32(3)
shrinkFactors.set(3)
shrinkFactors.set(2)
shrinkFactors.set(1)

VectorDouble smoothingSigmas = new VectorDouble(3)
smoothingSigmas.set(2)
smoothingSigmas.set(1)
smoothingSigmas.set(1)

HTH,
Brad



> On Oct 25, 2016, at 3:42 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> hi 
> 
> how can i specify  VectorUInt32 and VectorDouble in Java...
> 
> i ve this in python
> R.SetShrinkFactorsPerLevel([3,2,1])
> R.SetSmoothingSigmasPerLevel([2,1,1])
> 
> SetShrinkFactorsPerLevel would  VectorUInt32 
> and
> SetSmoothingSigmasPerLevel would  VectorDouble 
> 
> 
> thanks
> 
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-VectorUInt32-and-VectorDouble-in-Java-How-tp37700.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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


From dzenanz at gmail.com  Tue Oct 25 09:52:12 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 25 Oct 2016 09:52:12 -0400
Subject: [ITK-users] Unknown issue (realloc() invalid pointer)
In-Reply-To: <CAAq9_B4aF=nLCt_k6McGQ1bzQVQwaEXQ-u7mPLBj5uZQnpMadQ@mail.gmail.com>
References: <CAAq9_B4aF=nLCt_k6McGQ1bzQVQwaEXQ-u7mPLBj5uZQnpMadQ@mail.gmail.com>
Message-ID: <CAPf2UMRBWL-8j4rkFw7WFK-0-BK5Vcd3FYt0VH2AVRyq6SuOkw@mail.gmail.com>

Hi Nico,

try doing a clean build of all the libraries and your program. If that does
not solve the problem, compile it in debug mode and you should get more
useful information about where does the crash occur.

Regards,
D?enan

On Mon, Oct 24, 2016 at 5:43 PM, Nico Del Piano <ndel314 at gmail.com> wrote:

> Hello,
>
> I have a project which uses ITK + VTK + Qt: it worked well till I
> messed up something with some of the libraries/frameworks already
> mentioned. I remember installing a new version of either ITK or VTK,
> and then the program, after being compiled, returns the following
> error when executed:
>
> $ ./app
> *** Error in `./app': realloc(): invalid pointer: 0x00007f5065aa3840 ***
> Aborted (core dumped)
>
> As I said, it worked well and stopped working after compiling a new
> version of ITK or VTK. I don't know what to do, since I haven't
> changed the program's code.
>
> Sorry about this *horrible* description of my problem, but if someone
> have run into this and could help me, or have an idea of how to fix
> it, I'd really appreciate that :).
>
> Thanks,
>
> Nico.
> _____________________________________
> 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
>
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From ivan.granata.na at gmail.com  Tue Oct 25 12:18:06 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 25 Oct 2016 09:18:06 -0700 (MST)
Subject: [ITK-users] VectorUInt32 and VectorDouble in Java...How?
In-Reply-To: <CD7E50E4-6BCF-4C04-8B01-4C5E193C471B@mail.nih.gov>
References: <1477381344050-37700.post@n7.nabble.com>
 <CD7E50E4-6BCF-4C04-8B01-4C5E193C471B@mail.nih.gov>
Message-ID: <1477412286443-37703.post@n7.nabble.com>

i tried whit this

what do u think about? is it the same?

  VectorUInt32 pts1 = new VectorUInt32(3);
 // org.itk.simple.VectorUInt32 pts1;
  pts1.clear();
  pts1.push_back(3);
  pts1.push_back(2);
  pts1.push_back(1);
  
  
  System.out.println(pts1);
  R.setShrinkFactorsPerLevel(pts1);



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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-VectorUInt32-and-VectorDouble-in-Java-How-tp37700p37703.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From Brian.Chapman at utah.edu  Tue Oct 25 17:15:48 2016
From: Brian.Chapman at utah.edu (Brian E Chapman)
Date: Tue, 25 Oct 2016 21:15:48 +0000
Subject: [ITK-users] Using Python SimpleITK to Read/Write to BytesIO
 instance rather than file
Message-ID: <7812F318-6175-47DA-986B-54969007D094@umail.utah.edu>

Hi,

We are looking at using SimpleITK in conjunction with Girder to read images from girder manipulate the images with a Python script and then write the contents back up to Girder. We would prefer to do this using Byte streams rather than saving to a local file, reading/writing to the local file and then uploading the file to Girder, but we have not been able to find a way within SimpleITK (within Python) to read and write from/to streams rather than files.

Any guidance would be appreciated.

Brian


From zivrafael.yaniv at nih.gov  Wed Oct 26 10:22:43 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 26 Oct 2016 14:22:43 +0000
Subject: [ITK-users] Using Python SimpleITK to Read/Write to BytesIO
 instance rather than file
Message-ID: <D43633E7.D293%yanivz@mail.nih.gov>

Hi Brian,

Currently ITK/SimpleITK do not have components for reading an image
directly from a stream. We usually download, save to disk, and read from
disk using the appropriate IO. We used this approach with our Jupyter
notebooks where the read function either finds the data in a cache or
fetches it from MIDAS into the cache and then reads it
(https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/mast
er/downloaddata.py).

The challenge with streaming is that we currently don't have a protocol
for interpreting the streamed data (meta-data-dictionary + intensity/color
values). A possible solution is to use a client-server architecture with
the OpenIGTLink protocol (http://openigtlink.org). You can transfer
meta-data (patient name etc.) and complete images. See the specification
on their website.

Out of curiosity, what is the motivation for the streaming only approach
(girder -> SimpleITK -> girder)?

   hope this helps
     Ziv





On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:

>Hi,
>
>We are looking at using SimpleITK in conjunction with Girder to read
>images from girder manipulate the images with a Python script and then
>write the contents back up to Girder. We would prefer to do this using
>Byte streams rather than saving to a local file, reading/writing to the
>local file and then uploading the file to Girder, but we have not been
>able to find a way within SimpleITK (within Python) to read and write
>from/to streams rather than files.
>
>Any guidance would be appreciated.
>
>Brian
>
>_____________________________________
>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


From Brian.Chapman at utah.edu  Wed Oct 26 11:26:48 2016
From: Brian.Chapman at utah.edu (Brian E Chapman)
Date: Wed, 26 Oct 2016 15:26:48 +0000
Subject: [ITK-users] Using Python SimpleITK to Read/Write to BytesIO
 instance rather than file
In-Reply-To: <D43633E7.D293%yanivz@mail.nih.gov>
References: <D43633E7.D293%yanivz@mail.nih.gov>
Message-ID: <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>

Ziv,

Thanks for your reply and the pointer to opneigtlink. Our main motivation is speed: just trying to save the write-to-disk/read-from-disk costs. Using PyDICOM we can read directly from Girder via streams and I believe we also can with nibabel. But ultimately our processing will be done with ITK and I was hoping to have SimpleITK so I was hoping to avoid all the challenges of reading in one format, passing to simpleitk and trying to keep track of all the meta data appropriately in the process.

Brian

------
Brian E. Chapman, Ph.D.
Associate Professor
Department of Radiology and Imaging Sciences
University of Utah

> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> 
> Hi Brian,
> 
> Currently ITK/SimpleITK do not have components for reading an image
> directly from a stream. We usually download, save to disk, and read from
> disk using the appropriate IO. We used this approach with our Jupyter
> notebooks where the read function either finds the data in a cache or
> fetches it from MIDAS into the cache and then reads it
> (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/mast
> er/downloaddata.py).
> 
> The challenge with streaming is that we currently don't have a protocol
> for interpreting the streamed data (meta-data-dictionary + intensity/color
> values). A possible solution is to use a client-server architecture with
> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
> meta-data (patient name etc.) and complete images. See the specification
> on their website.
> 
> Out of curiosity, what is the motivation for the streaming only approach
> (girder -> SimpleITK -> girder)?
> 
>   hope this helps
>     Ziv
> 
> 
> 
> 
> 
> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
> 
>> Hi,
>> 
>> We are looking at using SimpleITK in conjunction with Girder to read
>> images from girder manipulate the images with a Python script and then
>> write the contents back up to Girder. We would prefer to do this using
>> Byte streams rather than saving to a local file, reading/writing to the
>> local file and then uploading the file to Girder, but we have not been
>> able to find a way within SimpleITK (within Python) to read and write
>> from/to streams rather than files.
>> 
>> Any guidance would be appreciated.
>> 
>> Brian
>> 
>> _____________________________________
>> 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
> 


From blowekamp at mail.nih.gov  Wed Oct 26 11:37:26 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 26 Oct 2016 15:37:26 +0000
Subject: [ITK-users] [ITK] Using Python SimpleITK to Read/Write to
 BytesIO instance rather than file
In-Reply-To: <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>
References: <D43633E7.D293%yanivz@mail.nih.gov>
 <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>
Message-ID: <3E57C5F3-1776-4601-9CB5-FBBD0B12335C@mail.nih.gov>

Hi,

Have you done a performance comparison? These other libraries may just download and cache the files, before doing file IO.

I recall there was a URL/HTTP based ITK ImageIO, but that just downloaded the files and then use the actual file ImageIO. It was wrapped in a nice package to enable seamless passing of ?http? URLS as filename strings to ITK.

HTH,
Brad

> On Oct 26, 2016, at 11:26 AM, Brian E Chapman <Brian.Chapman at utah.edu> wrote:
> 
> Ziv,
> 
> Thanks for your reply and the pointer to opneigtlink. Our main motivation is speed: just trying to save the write-to-disk/read-from-disk costs. Using PyDICOM we can read directly from Girder via streams and I believe we also can with nibabel. But ultimately our processing will be done with ITK and I was hoping to have SimpleITK so I was hoping to avoid all the challenges of reading in one format, passing to simpleitk and trying to keep track of all the meta data appropriately in the process.
> 
> Brian
> 
> ------
> Brian E. Chapman, Ph.D.
> Associate Professor
> Department of Radiology and Imaging Sciences
> University of Utah
> 
>> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
>> 
>> Hi Brian,
>> 
>> Currently ITK/SimpleITK do not have components for reading an image
>> directly from a stream. We usually download, save to disk, and read from
>> disk using the appropriate IO. We used this approach with our Jupyter
>> notebooks where the read function either finds the data in a cache or
>> fetches it from MIDAS into the cache and then reads it
>> (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/mast
>> er/downloaddata.py).
>> 
>> The challenge with streaming is that we currently don't have a protocol
>> for interpreting the streamed data (meta-data-dictionary + intensity/color
>> values). A possible solution is to use a client-server architecture with
>> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
>> meta-data (patient name etc.) and complete images. See the specification
>> on their website.
>> 
>> Out of curiosity, what is the motivation for the streaming only approach
>> (girder -> SimpleITK -> girder)?
>> 
>>  hope this helps
>>    Ziv
>> 
>> 
>> 
>> 
>> 
>> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
>> 
>>> Hi,
>>> 
>>> We are looking at using SimpleITK in conjunction with Girder to read
>>> images from girder manipulate the images with a Python script and then
>>> write the contents back up to Girder. We would prefer to do this using
>>> Byte streams rather than saving to a local file, reading/writing to the
>>> local file and then uploading the file to Girder, but we have not been
>>> able to find a way within SimpleITK (within Python) to read and write
>>> from/to streams rather than files.
>>> 
>>> Any guidance would be appreciated.
>>> 
>>> Brian
>>> 
>>> _____________________________________
>>> 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
>> 
> 
> _____________________________________
> 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
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From richard.beare at gmail.com  Wed Oct 26 16:17:14 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Thu, 27 Oct 2016 07:17:14 +1100
Subject: [ITK-users] [ITK] Using Python SimpleITK to Read/Write to
 BytesIO instance rather than file
In-Reply-To: <3E57C5F3-1776-4601-9CB5-FBBD0B12335C@mail.nih.gov>
References: <D43633E7.D293%yanivz@mail.nih.gov>
 <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>
 <3E57C5F3-1776-4601-9CB5-FBBD0B12335C@mail.nih.gov>
Message-ID: <CA+V7QS9-s=_Rd9sEDnRjP7s=Y-WwqH+yGJYDKQVP--Gu-ubVsA@mail.gmail.com>

If you are trying to avoid IO, and the other packages already deal with
streams, an option may be to stream into a numpy array + a python metadata
structure, and convert that to a SimpleITK image. Obviously will be a
little messy and incur a memory overhead, but could avoid disk IO.

On Thu, Oct 27, 2016 at 2:37 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hi,
>
> Have you done a performance comparison? These other libraries may just
> download and cache the files, before doing file IO.
>
> I recall there was a URL/HTTP based ITK ImageIO, but that just downloaded
> the files and then use the actual file ImageIO. It was wrapped in a nice
> package to enable seamless passing of ?http? URLS as filename strings to
> ITK.
>
> HTH,
> Brad
>
> > On Oct 26, 2016, at 11:26 AM, Brian E Chapman <Brian.Chapman at utah.edu>
> wrote:
> >
> > Ziv,
> >
> > Thanks for your reply and the pointer to opneigtlink. Our main
> motivation is speed: just trying to save the write-to-disk/read-from-disk
> costs. Using PyDICOM we can read directly from Girder via streams and I
> believe we also can with nibabel. But ultimately our processing will be
> done with ITK and I was hoping to have SimpleITK so I was hoping to avoid
> all the challenges of reading in one format, passing to simpleitk and
> trying to keep track of all the meta data appropriately in the process.
> >
> > Brian
> >
> > ------
> > Brian E. Chapman, Ph.D.
> > Associate Professor
> > Department of Radiology and Imaging Sciences
> > University of Utah
> >
> >> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
> zivrafael.yaniv at nih.gov> wrote:
> >>
> >> Hi Brian,
> >>
> >> Currently ITK/SimpleITK do not have components for reading an image
> >> directly from a stream. We usually download, save to disk, and read from
> >> disk using the appropriate IO. We used this approach with our Jupyter
> >> notebooks where the read function either finds the data in a cache or
> >> fetches it from MIDAS into the cache and then reads it
> >> (https://github.com/InsightSoftwareConsortium/
> SimpleITK-Notebooks/blob/mast
> >> er/downloaddata.py).
> >>
> >> The challenge with streaming is that we currently don't have a protocol
> >> for interpreting the streamed data (meta-data-dictionary +
> intensity/color
> >> values). A possible solution is to use a client-server architecture with
> >> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
> >> meta-data (patient name etc.) and complete images. See the specification
> >> on their website.
> >>
> >> Out of curiosity, what is the motivation for the streaming only approach
> >> (girder -> SimpleITK -> girder)?
> >>
> >>  hope this helps
> >>    Ziv
> >>
> >>
> >>
> >>
> >>
> >> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
> >>
> >>> Hi,
> >>>
> >>> We are looking at using SimpleITK in conjunction with Girder to read
> >>> images from girder manipulate the images with a Python script and then
> >>> write the contents back up to Girder. We would prefer to do this using
> >>> Byte streams rather than saving to a local file, reading/writing to the
> >>> local file and then uploading the file to Girder, but we have not been
> >>> able to find a way within SimpleITK (within Python) to read and write
> >>> from/to streams rather than files.
> >>>
> >>> Any guidance would be appreciated.
> >>>
> >>> Brian
> >>>
> >>> _____________________________________
> >>> 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
> >>
> >
> > _____________________________________
> > 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
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
>
> _____________________________________
> 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
>
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From mustafa at inode.at  Thu Oct 27 06:48:57 2016
From: mustafa at inode.at (Mustafa Arikan)
Date: Thu, 27 Oct 2016 12:48:57 +0200
Subject: [ITK-users] Reading a DICOM file in SimpleITK and ITK (spacing
 error)
In-Reply-To: <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>
References: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
 <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>
Message-ID: <4de1b61f-e901-39d4-8410-34ec3bd6d226@inode.at>

Hi D?enan,

this is not the problem because the spacing is not 0. And other 
frameworks like ImageJ can
read the .dcm image and save it as a .mhd image.

best regards,
Mustafa

Am 10/24/2016 um 5:01 PM schrieb D?enan Zuki?:
> Hi Mustafa,
>
> since the offending .dcm is in folder "exports", I assume some tool's 
> DICOM export is broken. Spacing should never be 0. If spacing is not 
> known, it should be set to 1. ITK has a right to complain about this. 
> Can you re-export this file, and perhaps fiddle with export settings a 
> bit?
>
> Regards,
> D?enan
>
> On Mon, Oct 24, 2016 at 6:02 AM, Mustafa Arikan <mustafa at inode.at 
> <mailto:mustafa at inode.at>> wrote:
>
>     Dear all,
>
>     reading a DICOM file (.dcm) in SimpleITK leads to following problem:
>
>>     RuntimeError: Exception thrown in SimpleITK ReadImage:
>>     c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageBase.hxx:192:
>>     itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not
>>     allowed: Spacing is [0, 0, 1]
>
>     The code looks like this:
>
>>     import SimpleITK
>>
>>     inputFileName =
>>     "D:\\workspace\\exports\\51871876-25-ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZVWGHRLQ+TNXWEN\\bscan.dcm"
>>     reader = SimpleITK.ImageSeriesReader()
>>     image= SimpleITK.ReadImage(inputFileName)
>>     reader.SetFileName ( inputFileName )
>>     imageIn = reader.Execute()
>
>     And I am getting the same error within ITK.
>
>     But opening the .dcm file with some DICOM-Viewer works.
>
>
>     thanks in advance,
>     Mustafa
>
>
>     _____________________________________
>     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>
>
>

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From blowekamp at mail.nih.gov  Thu Oct 27 09:02:33 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 27 Oct 2016 13:02:33 +0000
Subject: [ITK-users] [ITK] Reading a DICOM file in SimpleITK and ITK
 (spacing error)
In-Reply-To: <4de1b61f-e901-39d4-8410-34ec3bd6d226@inode.at>
References: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
 <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>
 <4de1b61f-e901-39d4-8410-34ec3bd6d226@inode.at>
Message-ID: <E3E0FCD5-D17E-4E39-A705-63E9B251783A@mail.nih.gov>

Hello,

ITK is a physical space aware image processing toolkit. It take into consideration the location, origin and SPACING when doing operations. Since an image with zero spacing has no physical size, ITK refuses to process it. From the physical perspective your image has no extent and does not exist. ITK can not process such data. Other toolkit are not physical space aware and just process pixels.

Please review the history of the file, and see where this error was introduced.

HTH,
Brad

On Oct 27, 2016, at 6:48 AM, Mustafa Arikan <mustafa at inode.at<mailto:mustafa at inode.at>> wrote:

Hi D?enan,

this is not the problem because the spacing is not 0. And other frameworks like ImageJ can
read the .dcm image and save it as a .mhd image.

best regards,
Mustafa

Am 10/24/2016 um 5:01 PM schrieb D?enan Zuki?:
Hi Mustafa,

since the offending .dcm is in folder "exports", I assume some tool's DICOM export is broken. Spacing should never be 0. If spacing is not known, it should be set to 1. ITK has a right to complain about this. Can you re-export this file, and perhaps fiddle with export settings a bit?

Regards,
D?enan

On Mon, Oct 24, 2016 at 6:02 AM, Mustafa Arikan <mustafa at inode.at<mailto:mustafa at inode.at>> wrote:

Dear all,

reading a DICOM file (.dcm) in SimpleITK leads to following problem:

RuntimeError: Exception thrown in SimpleITK ReadImage: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageBase.hxx:192:
itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not allowed: Spacing is [0, 0, 1]
<Mail Attachment.png>

The code looks like this:

import SimpleITK

inputFileName = "D:\\workspace\\exports\\<smb://workspace//exports//>51871876-25-ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZVWGHRLQ+TNXWEN\\bscan.dcm"
reader = SimpleITK.ImageSeriesReader()
image= SimpleITK.ReadImage(inputFileName)
reader.SetFileName ( inputFileName )
imageIn = reader.Execute()

And I am getting the same error within ITK.

But opening the .dcm file with some DICOM-Viewer works.


thanks in advance,
Mustafa

_____________________________________
Powered by www.kitware.com<http://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




_____________________________________
Powered by www.kitware.com<http://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
_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

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From nkwmailinglists at gmail.com  Thu Oct 27 12:57:28 2016
From: nkwmailinglists at gmail.com (Kent Williams)
Date: Thu, 27 Oct 2016 16:57:28 +0000
Subject: [ITK-users] RandomImageSource is terrible no good not very random?
Message-ID: <CAA4Dnn0Zbmd4M=R3uGULL0JNkvdRbApv9taNV8SuHHByngoQfw@mail.gmail.com>

I realize that itk::RandomImageSource is not meant to be a perfect source
of randomness.  But it is pretty bad.  I was trying to generate a noise
video with ITK -- by writing out 2D Images and then combining them using
FFMPEG -- and A) for a given set of dimensions, itk::RandomImageSource
generates exactly the same image. and B) the resulting image is clearly not
that random.

I got better results (without much speed penalty) calling drand48 once per
pixel.

Link to image generated: https://flic.kr/p/Nz1p7w

#include <iostream>
#include <stdio.h>
#include <sys/types.h>
#include <unistd.h>
#include <itkImage.h>
#include <itkImageFileWriter.h>
#include <itkImageRegionIterator.h>
#include <itkRandomImageSource.h>
#include <time.h>
#include <stdlib.h>
typedef itk::Image<unsigned char,2> ImageType;
typedef itk::ImageFileWriter<ImageType> ImageFileWriter;
typedef itk::RandomImageSource<ImageType> RandomImageSource;
typedef itk::ImageRegionIterator<ImageType> Iterator;

// 1080p
//const int XSize(1920);
//const int YSize(1080);
const int XSize(1280);
const int YSize(720);

int main(int argc, char **argv) {


ImageType::SizeType imageSize;
imageSize[0] = XSize;
imageSize[1] = YSize;
// only used for the first GetBufferPointer method
ImageType::Pointer image = ImageType::New();
image->SetRegions(imageSize);
image->Allocate();

ImageFileWriter::Pointer writer = ImageFileWriter::New();
for(unsigned i = 0; i < (60*24); ++i) {
char fname[256];
sprintf(fname,"%04u.tiff", i);
writer->SetFileName(fname);
#if 0
// fill buffer with lrand48 results
unsigned char *cp = image->GetBufferPointer();
unsigned char *end = cp + (XSize * YSize);
for(; cp < end; ++cp)
*cp = lrand48();
writer->SetInput(image);
#else
srand48(getpid() + time(NULL));
RandomImageSource::Pointer rndSource = RandomImageSource::New();
rndSource->SetSize(imageSize);
writer->SetInput(rndSource->GetOutput());
#endif
writer->Update();
std::cout << i << std::endl;
}
}
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From nkwmailinglists at gmail.com  Thu Oct 27 13:00:09 2016
From: nkwmailinglists at gmail.com (Kent Williams)
Date: Thu, 27 Oct 2016 17:00:09 +0000
Subject: [ITK-users] Output to video
Message-ID: <CAA4Dnn322yKfw6te=EGFMbUxY7kaY-XNRBNpNez6HbiOru+xpA@mail.gmail.com>

Is VTK the only way to generate a video file from a series of 2D frames?

I've not been following ITK for a while and don't know how far the library
has progressed with video output.
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From matt.mccormick at kitware.com  Thu Oct 27 13:07:26 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Oct 2016 13:07:26 -0400
Subject: [ITK-users] Output to video
In-Reply-To: <CAA4Dnn322yKfw6te=EGFMbUxY7kaY-XNRBNpNez6HbiOru+xpA@mail.gmail.com>
References: <CAA4Dnn322yKfw6te=EGFMbUxY7kaY-XNRBNpNez6HbiOru+xpA@mail.gmail.com>
Message-ID: <CALzTN-SXASYiazVPDnOWMjhzwfDovE9dkP17uP+d7X-gF203mA@mail.gmail.com>

Hi Kent!

Yes, we have video IO now in ITK:

  https://itk.org/Insight/Doxygen/html/group__ITKVideoIO.html

Cheers,
Matt

On Thu, Oct 27, 2016 at 1:00 PM, Kent Williams
<nkwmailinglists at gmail.com> wrote:
> Is VTK the only way to generate a video file from a series of 2D frames?
>
> I've not been following ITK for a while and don't know how far the library
> has progressed with video output.
>
> _____________________________________
> 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
>

From matt.mccormick at kitware.com  Thu Oct 27 13:08:19 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Oct 2016 13:08:19 -0400
Subject: [ITK-users] RandomImageSource is terrible no good not very
	random?
In-Reply-To: <CAA4Dnn0Zbmd4M=R3uGULL0JNkvdRbApv9taNV8SuHHByngoQfw@mail.gmail.com>
References: <CAA4Dnn0Zbmd4M=R3uGULL0JNkvdRbApv9taNV8SuHHByngoQfw@mail.gmail.com>
Message-ID: <CALzTN-QfYXuopTs=vw_gmJYV5rxRyfpot-_7CkGTqwWXcsc-WA@mail.gmail.com>

Hi Kent,

For A), the seed needs to be changed to get a different output.

HTH,
Matt

On Thu, Oct 27, 2016 at 12:57 PM, Kent Williams
<nkwmailinglists at gmail.com> wrote:
> I realize that itk::RandomImageSource is not meant to be a perfect source of
> randomness.  But it is pretty bad.  I was trying to generate a noise video
> with ITK -- by writing out 2D Images and then combining them using FFMPEG --
> and A) for a given set of dimensions, itk::RandomImageSource generates
> exactly the same image. and B) the resulting image is clearly not that
> random.
>
> I got better results (without much speed penalty) calling drand48 once per
> pixel.
>
> Link to image generated: https://flic.kr/p/Nz1p7w
>
> #include <iostream>
> #include <stdio.h>
> #include <sys/types.h>
> #include <unistd.h>
> #include <itkImage.h>
> #include <itkImageFileWriter.h>
> #include <itkImageRegionIterator.h>
> #include <itkRandomImageSource.h>
> #include <time.h>
> #include <stdlib.h>
> typedef itk::Image<unsigned char,2> ImageType;
> typedef itk::ImageFileWriter<ImageType> ImageFileWriter;
> typedef itk::RandomImageSource<ImageType> RandomImageSource;
> typedef itk::ImageRegionIterator<ImageType> Iterator;
>
> // 1080p
> //const int XSize(1920);
> //const int YSize(1080);
> const int XSize(1280);
> const int YSize(720);
>
> int main(int argc, char **argv) {
>
>
> ImageType::SizeType imageSize;
> imageSize[0] = XSize;
> imageSize[1] = YSize;
> // only used for the first GetBufferPointer method
> ImageType::Pointer image = ImageType::New();
> image->SetRegions(imageSize);
> image->Allocate();
>
> ImageFileWriter::Pointer writer = ImageFileWriter::New();
> for(unsigned i = 0; i < (60*24); ++i) {
> char fname[256];
> sprintf(fname,"%04u.tiff", i);
> writer->SetFileName(fname);
> #if 0
> // fill buffer with lrand48 results
> unsigned char *cp = image->GetBufferPointer();
> unsigned char *end = cp + (XSize * YSize);
> for(; cp < end; ++cp)
> *cp = lrand48();
> writer->SetInput(image);
> #else
> srand48(getpid() + time(NULL));
> RandomImageSource::Pointer rndSource = RandomImageSource::New();
> rndSource->SetSize(imageSize);
> writer->SetInput(rndSource->GetOutput());
> #endif
> writer->Update();
> std::cout << i << std::endl;
> }
> }
>
>
> _____________________________________
> 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
>

From mrguilfoyle at gmail.com  Fri Oct 28 10:11:19 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Fri, 28 Oct 2016 15:11:19 +0100
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
Message-ID: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>

Hi

SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan

This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.

Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).

Not an immediate problem as working with R 3.2.5 is ok.

The error message I get is:

In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
                                             ^
/usr/include/string.h:76:7: note: previous declaration is here
char    *strchr(const char *, int);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
                                             ^
/usr/include/string.h:86:7: note: previous declaration is here
char    *strpbrk(const char *, const char *);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
                                             ^
/usr/include/string.h:87:7: note: previous declaration is here
char    *strrchr(const char *, int);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
                                             ^
/usr/include/string.h:70:7: note: previous declaration is here
void    *memchr(const void *, int, size_t);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
                                             ^
/usr/include/string.h:89:7: note: previous declaration is here
char    *strstr(const char *, const char *);
         ^
5 errors generated.
make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
make: *** [all] Error 2
+ exit 1
ERROR: configuration failed for package ?SimpleITK?
* removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
Error: Command failed (1)

From blowekamp at mail.nih.gov  Fri Oct 28 10:27:50 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 28 Oct 2016 14:27:50 +0000
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
Message-ID: <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>

Hello,

Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?

This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.

I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.

HTH,
Brad

[1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework

> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> 
> Hi
> 
> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
> 
> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
> 
> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
> 
> Not an immediate problem as working with R 3.2.5 is ok.
> 
> The error message I get is:
> 
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
>                                             ^
> /usr/include/string.h:76:7: note: previous declaration is here
> char    *strchr(const char *, int);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
>                                             ^
> /usr/include/string.h:86:7: note: previous declaration is here
> char    *strpbrk(const char *, const char *);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
>                                             ^
> /usr/include/string.h:87:7: note: previous declaration is here
> char    *strrchr(const char *, int);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
>                                             ^
> /usr/include/string.h:70:7: note: previous declaration is here
> void    *memchr(const void *, int, size_t);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
>                                             ^
> /usr/include/string.h:89:7: note: previous declaration is here
> char    *strstr(const char *, const char *);
>         ^
> 5 errors generated.
> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> make[3]: *** [all] Error 2
> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> make: *** [all] Error 2
> + exit 1
> ERROR: configuration failed for package ?SimpleITK?
> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
> Error: Command failed (1)
> _____________________________________
> 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


From mrguilfoyle at gmail.com  Fri Oct 28 11:36:01 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Fri, 28 Oct 2016 16:36:01 +0100
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
Message-ID: <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>

Xcode 8.1 (updated yesterday)
I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.

Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?



> On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> 
> Hello,
> 
> Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> 
> This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> 
> I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.
> 
> HTH,
> Brad
> 
> [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> 
>> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
>> 
>> Hi
>> 
>> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
>> 
>> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
>> 
>> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
>> 
>> Not an immediate problem as working with R 3.2.5 is ok.
>> 
>> The error message I get is:
>> 
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
>>                                            ^
>> /usr/include/string.h:76:7: note: previous declaration is here
>> char    *strchr(const char *, int);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
>>                                            ^
>> /usr/include/string.h:86:7: note: previous declaration is here
>> char    *strpbrk(const char *, const char *);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
>>                                            ^
>> /usr/include/string.h:87:7: note: previous declaration is here
>> char    *strrchr(const char *, int);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
>> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
>>                                            ^
>> /usr/include/string.h:70:7: note: previous declaration is here
>> void    *memchr(const void *, int, size_t);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
>>                                            ^
>> /usr/include/string.h:89:7: note: previous declaration is here
>> char    *strstr(const char *, const char *);
>>        ^
>> 5 errors generated.
>> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
>> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
>> make[3]: *** [all] Error 2
>> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
>> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
>> make: *** [all] Error 2
>> + exit 1
>> ERROR: configuration failed for package ?SimpleITK?
>> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
>> Error: Command failed (1)
>> _____________________________________
>> 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
> 


From richard.beare at gmail.com  Fri Oct 28 17:31:43 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Sat, 29 Oct 2016 08:31:43 +1100
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
Message-ID: <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>

A while back I made an update to swig to do with the way the various R
header files were included in the swig generated code. The errors prompting
that change seemed similar to what you were seeing. Those changes have been
merged into the master swig, but probably haven't made it into a release
yet. You could try giving the superbuild a go with the "system" swig you've
built by hand, or possibly use the "swig from git" option in superbuild.
Note that this last option requires an automake installation too - the brew
version works OK.

On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> Xcode 8.1 (updated yesterday)
> I've checked both R 3.2.5 and R 3.3.1 and they both report
> LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
>
> Looking at the differences in the Rdefines.h header file  (mentioned in
> the error report) between R versions it is documented that this has been
> changed from R 3.3.0 onwards.  Several of the definitions at the top of the
> file are now prepended with Rf_ .  I don't pretend to understand the
> reasons for or implications of this but seems likely to be at least part of
> the problem?
>
>
>
> > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
> >
> > Hello,
> >
> > Do you know what version of Xcode you are using? What OS X SDK is being
> used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> >
> > This seems like it is some type of incompatibility with versions of
> Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> >
> > I am not certain what R compiler flags are passed to the SimpleITK build
> with the ?devtools? method, but some of the above may not match the way the
> old R was compiled.
> >
> > HTH,
> > Brad
> >
> > [1] http://stackoverflow.com/questions/17461196/
> determining-os-x-sdk-and-deployment-target-versions-from-framework
> >
> >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> >>
> >> Hi
> >>
> >> SimpleITK with R wrapping does not build successfully against R 3.3.1
> on OS X 10.11.6 ElCapitan
> >>
> >> This fails both using the devtools method from within R, and when
> trying to build the SuperBuild via Cmake with R wrapping turned on.
> >>
> >> Both methods work fine against the most recent prior R release
> 3.2.4-revised (subsequently relabelled 3.2.5).
> >>
> >> Not an immediate problem as working with R 3.2.5 is ok.
> >>
> >> The error message I get is:
> >>
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error:
> conflicting types for 'strchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s,
> int __c) {return ::strchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:76:7: note: previous declaration is here
> >> char    *strchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error:
> conflicting types for 'strpbrk'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1,
> const char* __s2) {return ::strpbrk(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:86:7: note: previous declaration is here
> >> char    *strpbrk(const char *, const char *);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error:
> conflicting types for 'strrchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s,
> int __c) {return ::strrchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:87:7: note: previous declaration is here
> >> char    *strrchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error:
> conflicting types for 'memchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s,
> int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> >>                                            ^
> >> /usr/include/string.h:70:7: note: previous declaration is here
> >> void    *memchr(const void *, int, size_t);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error:
> conflicting types for 'strstr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1,
> const char* __s2) {return ::strstr(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:89:7: note: previous declaration is here
> >> char    *strstr(const char *, const char *);
> >>        ^
> >> 5 errors generated.
> >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o]
> Error 1
> >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> >> make[3]: *** [all] Error 2
> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build]
> Error 2
> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> >> make: *** [all] Error 2
> >> + exit 1
> >> ERROR: configuration failed for package ?SimpleITK?
> >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/SimpleITK?
> >> Error: Command failed (1)
> >> _____________________________________
> >> 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
> >
>
> _____________________________________
> 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
>
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From mrguilfoyle at gmail.com  Sat Oct 29 04:51:53 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Sat, 29 Oct 2016 09:51:53 +0100
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
Message-ID: <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>

Hi Richard

I've tried using the patched swig you provided several months ago and the latest swig from git option - SimpleITK compiles without error against R 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with either.  The problem previously was not failing to build but string-handling errors generated using certain R-SimpleITK functions.  As mentioned there has been a change in certain header files since 3.3.0 which presumably relates to the problem?  Happy to do any further testing you suggest.


> On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> 
> A while back I made an update to swig to do with the way the various R header files were included in the swig generated code. The errors prompting that change seemed similar to what you were seeing. Those changes have been merged into the master swig, but probably haven't made it into a release yet. You could try giving the superbuild a go with the "system" swig you've built by hand, or possibly use the "swig from git" option in superbuild. Note that this last option requires an automake installation too - the brew version works OK.
> 
> On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> Xcode 8.1 (updated yesterday)
> I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
> 
> Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?
> 
> 
> 
> > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> >
> > Hello,
> >
> > Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> >
> > This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> >
> > I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.
> >
> > HTH,
> > Brad
> >
> > [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> >
> >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> >>
> >> Hi
> >>
> >> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
> >>
> >> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
> >>
> >> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
> >>
> >> Not an immediate problem as working with R 3.2.5 is ok.
> >>
> >> The error message I get is:
> >>
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:76:7: note: previous declaration is here
> >> char    *strchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:86:7: note: previous declaration is here
> >> char    *strpbrk(const char *, const char *);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:87:7: note: previous declaration is here
> >> char    *strrchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> >>                                            ^
> >> /usr/include/string.h:70:7: note: previous declaration is here
> >> void    *memchr(const void *, int, size_t);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:89:7: note: previous declaration is here
> >> char    *strstr(const char *, const char *);
> >>        ^
> >> 5 errors generated.
> >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
> >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> >> make[3]: *** [all] Error 2
> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> >> make: *** [all] Error 2
> >> + exit 1
> >> ERROR: configuration failed for package ?SimpleITK?
> >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
> >> Error: Command failed (1)
> >> _____________________________________
> >> 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
> >
> 
> _____________________________________
> 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
> 


From richard.beare at gmail.com  Sat Oct 29 18:40:52 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Sun, 30 Oct 2016 09:40:52 +1100
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
 <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
Message-ID: <CA+V7QS_pOBXSchSsoom1K0WokKBWeqbHrW2XxdL=pvXk2XOSzw@mail.gmail.com>

I haven't been building on the mac for a while, so I'd better check it out.

On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> Hi Richard
>
> I've tried using the patched swig you provided several months ago and the
> latest swig from git option - SimpleITK compiles without error against R
> 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with
> either.  The problem previously was not failing to build but
> string-handling errors generated using certain R-SimpleITK functions.  As
> mentioned there has been a change in certain header files since 3.3.0 which
> presumably relates to the problem?  Happy to do any further testing you
> suggest.
>
>
> > On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> >
> > A while back I made an update to swig to do with the way the various R
> header files were included in the swig generated code. The errors prompting
> that change seemed similar to what you were seeing. Those changes have been
> merged into the master swig, but probably haven't made it into a release
> yet. You could try giving the superbuild a go with the "system" swig you've
> built by hand, or possibly use the "swig from git" option in superbuild.
> Note that this last option requires an automake installation too - the brew
> version works OK.
> >
> > On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > Xcode 8.1 (updated yesterday)
> > I've checked both R 3.2.5 and R 3.3.1 and they both report
> LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
> >
> > Looking at the differences in the Rdefines.h header file  (mentioned in
> the error report) between R versions it is documented that this has been
> changed from R 3.3.0 onwards.  Several of the definitions at the top of the
> file are now prepended with Rf_ .  I don't pretend to understand the
> reasons for or implications of this but seems likely to be at least part of
> the problem?
> >
> >
> >
> > > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
> > >
> > > Hello,
> > >
> > > Do you know what version of Xcode you are using? What OS X SDK is
> being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> > >
> > > This seems like it is some type of incompatibility with versions of
> Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> > >
> > > I am not certain what R compiler flags are passed to the SimpleITK
> build with the ?devtools? method, but some of the above may not match the
> way the old R was compiled.
> > >
> > > HTH,
> > > Brad
> > >
> > > [1] http://stackoverflow.com/questions/17461196/
> determining-os-x-sdk-and-deployment-target-versions-from-framework
> > >
> > >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > >>
> > >> Hi
> > >>
> > >> SimpleITK with R wrapping does not build successfully against R 3.3.1
> on OS X 10.11.6 ElCapitan
> > >>
> > >> This fails both using the devtools method from within R, and when
> trying to build the SuperBuild via Cmake with R wrapping turned on.
> > >>
> > >> Both methods work fine against the most recent prior R release
> 3.2.4-revised (subsequently relabelled 3.2.5).
> > >>
> > >> Not an immediate problem as working with R 3.2.5 is ok.
> > >>
> > >> The error message I get is:
> > >>
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error:
> conflicting types for 'strchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s,
> int __c) {return ::strchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:76:7: note: previous declaration is here
> > >> char    *strchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error:
> conflicting types for 'strpbrk'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char*
> __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:86:7: note: previous declaration is here
> > >> char    *strpbrk(const char *, const char *);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error:
> conflicting types for 'strrchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s,
> int __c) {return ::strrchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:87:7: note: previous declaration is here
> > >> char    *strrchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error:
> conflicting types for 'memchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s,
> int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> > >>                                            ^
> > >> /usr/include/string.h:70:7: note: previous declaration is here
> > >> void    *memchr(const void *, int, size_t);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error:
> conflicting types for 'strstr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1,
> const char* __s2) {return ::strstr(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:89:7: note: previous declaration is here
> > >> char    *strstr(const char *, const char *);
> > >>        ^
> > >> 5 errors generated.
> > >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o]
> Error 1
> > >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> > >> make[3]: *** [all] Error 2
> > >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build]
> Error 2
> > >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> > >> make: *** [all] Error 2
> > >> + exit 1
> > >> ERROR: configuration failed for package ?SimpleITK?
> > >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/SimpleITK?
> > >> Error: Command failed (1)
> > >> _____________________________________
> > >> 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
> > >
> >
> > _____________________________________
> > 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
> >
>
>
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From richard.beare at gmail.com  Sun Oct 30 05:04:47 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Sun, 30 Oct 2016 20:04:47 +1100
Subject: [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
 <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
Message-ID: <CA+V7QS80v=1d8=eV1d_op5yxuSKzM5zmcpdW7N3Vb8gQfcEx5A@mail.gmail.com>

I'm seeing different failures on 3.3.1. Stuff to do with redefining length
in Rdefines.h. These problems seem to relate to sitkRArray.cxx.

It is a bit strange, but the fix for me is to add
#include <iostream>

before
#include <Rdefines.h>

in sitkRArray.cxx

This successfully builds the R package, but I get lots of link warnings
like this:

ld: warning: direct access in itk::LabelMap<itk::ShapeLabelObject<unsigned
long long, 2u> >::Graft(itk::DataObject const*) to global weak symbol
typeinfo name for itk::DataObject const* means the weak symbol cannot be
overridden at runtime. This was likely caused by different translation
units being compiled with different visibility settings.

On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> Hi Richard
>
> I've tried using the patched swig you provided several months ago and the
> latest swig from git option - SimpleITK compiles without error against R
> 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with
> either.  The problem previously was not failing to build but
> string-handling errors generated using certain R-SimpleITK functions.  As
> mentioned there has been a change in certain header files since 3.3.0 which
> presumably relates to the problem?  Happy to do any further testing you
> suggest.
>
>
> > On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> >
> > A while back I made an update to swig to do with the way the various R
> header files were included in the swig generated code. The errors prompting
> that change seemed similar to what you were seeing. Those changes have been
> merged into the master swig, but probably haven't made it into a release
> yet. You could try giving the superbuild a go with the "system" swig you've
> built by hand, or possibly use the "swig from git" option in superbuild.
> Note that this last option requires an automake installation too - the brew
> version works OK.
> >
> > On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > Xcode 8.1 (updated yesterday)
> > I've checked both R 3.2.5 and R 3.3.1 and they both report
> LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
> >
> > Looking at the differences in the Rdefines.h header file  (mentioned in
> the error report) between R versions it is documented that this has been
> changed from R 3.3.0 onwards.  Several of the definitions at the top of the
> file are now prepended with Rf_ .  I don't pretend to understand the
> reasons for or implications of this but seems likely to be at least part of
> the problem?
> >
> >
> >
> > > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
> > >
> > > Hello,
> > >
> > > Do you know what version of Xcode you are using? What OS X SDK is
> being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> > >
> > > This seems like it is some type of incompatibility with versions of
> Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> > >
> > > I am not certain what R compiler flags are passed to the SimpleITK
> build with the ?devtools? method, but some of the above may not match the
> way the old R was compiled.
> > >
> > > HTH,
> > > Brad
> > >
> > > [1] http://stackoverflow.com/questions/17461196/
> determining-os-x-sdk-and-deployment-target-versions-from-framework
> > >
> > >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > >>
> > >> Hi
> > >>
> > >> SimpleITK with R wrapping does not build successfully against R 3.3.1
> on OS X 10.11.6 ElCapitan
> > >>
> > >> This fails both using the devtools method from within R, and when
> trying to build the SuperBuild via Cmake with R wrapping turned on.
> > >>
> > >> Both methods work fine against the most recent prior R release
> 3.2.4-revised (subsequently relabelled 3.2.5).
> > >>
> > >> Not an immediate problem as working with R 3.2.5 is ok.
> > >>
> > >> The error message I get is:
> > >>
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error:
> conflicting types for 'strchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s,
> int __c) {return ::strchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:76:7: note: previous declaration is here
> > >> char    *strchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error:
> conflicting types for 'strpbrk'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char*
> __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:86:7: note: previous declaration is here
> > >> char    *strpbrk(const char *, const char *);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error:
> conflicting types for 'strrchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s,
> int __c) {return ::strrchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:87:7: note: previous declaration is here
> > >> char    *strrchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error:
> conflicting types for 'memchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s,
> int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> > >>                                            ^
> > >> /usr/include/string.h:70:7: note: previous declaration is here
> > >> void    *memchr(const void *, int, size_t);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error:
> conflicting types for 'strstr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1,
> const char* __s2) {return ::strstr(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:89:7: note: previous declaration is here
> > >> char    *strstr(const char *, const char *);
> > >>        ^
> > >> 5 errors generated.
> > >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o]
> Error 1
> > >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> > >> make[3]: *** [all] Error 2
> > >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build]
> Error 2
> > >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> > >> make: *** [all] Error 2
> > >> + exit 1
> > >> ERROR: configuration failed for package ?SimpleITK?
> > >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/SimpleITK?
> > >> Error: Command failed (1)
> > >> _____________________________________
> > >> 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
> > >
> >
> > _____________________________________
> > 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
> >
>
>
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From kolin9105 at gmail.com  Sun Oct 30 14:15:05 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Mon, 31 Oct 2016 01:15:05 +0700
Subject: [ITK-users] my problem
Message-ID: <CAEiw7u5oRqSAFZod69MuwqaBE342ufrwS_KGkACXHcORy5sYhg@mail.gmail.com>

hello everyone I am beginner in ITK.
I got  a problem in my thesis with ITK.
I find different result between using ITK and using imagej.
in itk I am working with BinaryThresholdImageFilter.
O.dcm using ITK
IM-0001-0009.jpeg using Imagej
what I have to do????
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From ivan.granata.na at gmail.com  Mon Oct 31 05:09:34 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Mon, 31 Oct 2016 02:09:34 -0700 (MST)
Subject: [ITK-users]  Simple ITK Wavelet Transform ?? it is possible?
Message-ID: <1477904974504-37723.post@n7.nabble.com>

Is it possibile to apply a wavelet transform to an image in SimpleITK?
Thx



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Simple-ITK-Wavelet-Transform-it-is-possible-tp37723.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Mon Oct 31 08:54:38 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 31 Oct 2016 12:54:38 +0000
Subject: [ITK-users] Simple ITK Wavelet Transform ?? it is possible?
In-Reply-To: <1477904974504-37723.post@n7.nabble.com>
References: <1477904974504-37723.post@n7.nabble.com>
Message-ID: <A2499A6A-F970-4E13-BAF5-9E83E775F9E1@mail.nih.gov>

Hello,

I am unaware of any ITK filters in ITK proper which do wavelet transforms, nor any in any remote modules.

I did find this Insight Journal article: http://www.insight-journal.org/browse/publication/155, but I haven?t used it nor do I know if it has been maintained.

If you are able to find ITK code to do the wavelets in ITK, them with a little effort a JSON description of the filter can be written to extend SimpleITK functionality.

Brad

> On Oct 31, 2016, at 5:09 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> Is it possibile to apply a wavelet transform to an image in SimpleITK?
> Thx
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Simple-ITK-Wavelet-Transform-it-is-possible-tp37723.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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


From dzenanz at gmail.com  Mon Oct 31 10:30:23 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 31 Oct 2016 10:30:23 -0400
Subject: [ITK-users] my problem
In-Reply-To: <CAEiw7u5oRqSAFZod69MuwqaBE342ufrwS_KGkACXHcORy5sYhg@mail.gmail.com>
References: <CAEiw7u5oRqSAFZod69MuwqaBE342ufrwS_KGkACXHcORy5sYhg@mail.gmail.com>
Message-ID: <CAPf2UMQocNiCDckq_0_RyNm9dTf0dO8HA=cfc58MxxDhXMQ5=Q@mail.gmail.com>

Hi Meikolin,

if you gave us the input (and not just outputs), we might be able to
provide some advice.

Regards,
D?enan

On Sun, Oct 30, 2016 at 2:15 PM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> hello everyone I am beginner in ITK.
> I got  a problem in my thesis with ITK.
> I find different result between using ITK and using imagej.
> in itk I am working with BinaryThresholdImageFilter.
> O.dcm using ITK
> IM-0001-0009.jpeg using Imagej
> what I have to do????
>
>
> _____________________________________
> 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
>
>
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From blowekamp at mail.nih.gov  Mon Oct 31 11:40:03 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 31 Oct 2016 15:40:03 +0000
Subject: [ITK-users] [ITK]  SimpleITK build fail with R 3.3.1
In-Reply-To: <CA+V7QS80v=1d8=eV1d_op5yxuSKzM5zmcpdW7N3Vb8gQfcEx5A@mail.gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
 <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
 <CA+V7QS80v=1d8=eV1d_op5yxuSKzM5zmcpdW7N3Vb8gQfcEx5A@mail.gmail.com>
Message-ID: <36C7FF5C-A163-421A-876F-DDE10E0B0240@mail.nih.gov>

Hello,

I am build SimpleITK master with XCode 8.0, R 3.3.1 on OS X 10.11.6 with CMake 3.4.3 by comping with the SimpleITK Superbuild directory.

I get the following error:

Wrapping/R/CMakeFiles/SimpleITK_R.dir/sitkRArray.cxx.o -c /Users/blowekamp/src/SimpleITK/Wrapping/R/sitkRArray.cxx
In file included from /Users/blowekamp/src/SimpleITK/Wrapping/R/sitkRArray.cxx:23:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkImage.h:21:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkCommon.h:21:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkMacro.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/sstream:174:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ostream:138:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ios:216:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:871:34: error: too many arguments provided to function-like macro invocation
    int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
                                 ^
/Library/Frameworks/R.framework/Headers/Rinternals.h:1222:9: note: macro 'length' defined here
#define length(x)               Rf_length(x)


This patch suggested by Richard fixed it for me:
http://review.source.kitware.com/#/c/21678/

This will likely be merged into next at the end of the day.

Brad


On Oct 30, 2016, at 5:04 AM, Richard Beare <richard.beare at gmail.com<mailto:richard.beare at gmail.com>> wrote:

I'm seeing different failures on 3.3.1. Stuff to do with redefining length in Rdefines.h. These problems seem to relate to sitkRArray.cxx.

It is a bit strange, but the fix for me is to add
#include <iostream>

before
#include <Rdefines.h>

in sitkRArray.cxx

This successfully builds the R package, but I get lots of link warnings like this:


ld: warning: direct access in itk::LabelMap<itk::ShapeLabelObject<unsigned long long, 2u> >::Graft(itk::DataObject const*) to global weak symbol typeinfo name for itk::DataObject const* means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.

On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
Hi Richard

I've tried using the patched swig you provided several months ago and the latest swig from git option - SimpleITK compiles without error against R 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with either.  The problem previously was not failing to build but string-handling errors generated using certain R-SimpleITK functions.  As mentioned there has been a change in certain header files since 3.3.0 which presumably relates to the problem?  Happy to do any further testing you suggest.


> On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com<mailto:richard.beare at gmail.com>> wrote:
>
> A while back I made an update to swig to do with the way the various R header files were included in the swig generated code. The errors prompting that change seemed similar to what you were seeing. Those changes have been merged into the master swig, but probably haven't made it into a release yet. You could try giving the superbuild a go with the "system" swig you've built by hand, or possibly use the "swig from git" option in superbuild. Note that this last option requires an automake installation too - the brew version works OK.
>
> On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
> Xcode 8.1 (updated yesterday)
> I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
>
> Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?
>
>
>
> > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
> >
> > Hello,
> >
> > Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> >
> > This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> >
> > I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.
> >
> > HTH,
> > Brad
> >
> > [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> >
> >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
> >>
> >> Hi
> >>
> >> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
> >>
> >> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
> >>
> >> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
> >>
> >> Not an immediate problem as working with R 3.2.5 is ok.
> >>
> >> The error message I get is:
> >>
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:76:7: note: previous declaration is here
> >> char    *strchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:86:7: note: previous declaration is here
> >> char    *strpbrk(const char *, const char *);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:87:7: note: previous declaration is here
> >> char    *strrchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> >>                                            ^
> >> /usr/include/string.h:70:7: note: previous declaration is here
> >> void    *memchr(const void *, int, size_t);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:89:7: note: previous declaration is here
> >> char    *strstr(const char *, const char *);
> >>        ^
> >> 5 errors generated.
> >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
> >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> >> make[3]: *** [all] Error 2
> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> >> make: *** [all] Error 2
> >> + exit 1
> >> ERROR: configuration failed for package ?SimpleITK?
> >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
> >> Error: Command failed (1)
> >> _____________________________________
> >> Powered by www.kitware.com<http://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
> >
>
> _____________________________________
> Powered by www.kitware.com<http://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
>


_____________________________________
Powered by www.kitware.com<http://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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From kolin9105 at gmail.com  Mon Oct 31 13:15:07 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 1 Nov 2016 00:15:07 +0700
Subject: [ITK-users] My problem
Message-ID: <CAEiw7u6dT9m05m5fKOuRnMU=sUsx_xkUzB9vU4+SH+FfNdPrdw@mail.gmail.com>

I have a image with extention dcm.
When I was input the image in binaryimagethreshold.cxx I got the ouput but
when I was input image with extention jpeg with the same image the result
so far different with dcm input.
in my thesis I am just working with extention dcm not jpeg but the result I
Want what I get with  jpeg.
What I Have to do??
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From francois.budin at kitware.com  Mon Oct 31 13:47:51 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 31 Oct 2016 13:47:51 -0400
Subject: [ITK-users] My problem
In-Reply-To: <CAEiw7u6dT9m05m5fKOuRnMU=sUsx_xkUzB9vU4+SH+FfNdPrdw@mail.gmail.com>
References: <CAEiw7u6dT9m05m5fKOuRnMU=sUsx_xkUzB9vU4+SH+FfNdPrdw@mail.gmail.com>
Message-ID: <CAHwLD2W0d6_5Je=UrDOnu3VkbGNFKs3tgG_6K+245XS=gZ+DUA@mail.gmail.com>

Hello,

Have you compared the content of both your images (dcm and jpeg) and made
sure that they were exactly the same? How did you convert one into the
other? Is it possible for you to share the images with us? Maybe the
thresholds that you need to use in both your images are different if your
images are different.
Hope this helps,

Francois

On Mon, Oct 31, 2016 at 1:15 PM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> I have a image with extention dcm.
> When I was input the image in binaryimagethreshold.cxx I got the ouput but
> when I was input image with extention jpeg with the same image the result
> so far different with dcm input.
> in my thesis I am just working with extention dcm not jpeg but the result
> I Want what I get with  jpeg.
> What I Have to do??
>
> _____________________________________
> 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
>
>
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From fisidoro at ethz.ch  Mon Oct 31 14:08:12 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Mon, 31 Oct 2016 18:08:12 +0000
Subject: [ITK-users] cmake build error
Message-ID: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>

Hallo,

I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on Windows 10 with Visual Studio 2015. As "current generator" I tried both "Visual Studio 14 2015" and "Visual Studio 14 2015 Win64" but I immediately get errors with cmake when configuring. Errors are:

The C compiler identification is unknown
CMake Error at CMakeLists.txt:18 (enable_language):
  No CMAKE_C_COMPILER could be found.


Compiling the C compiler identification source file "CMakeCCompilerId.c" failed.
Compiler:
Build flags:
Id flags:

The output was:
1
Microsoft (R) Build Engine version 14.0.25420.1
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 31.10.2016 18:53:27.
Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" on node 1 (default targets).
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
Done Building Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default targets) -- FAILED.

Build FAILED.

"C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default target) (1) ->
(Desktop_PlatformPrepareForBuild target) ->
  C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]

    0 Warning(s)
    1 Error(s)

Time Elapsed 00:00:00.48


Compiling the C compiler identification source file "CMakeCCompilerId.c" failed.
Compiler:
Build flags:
Id flags:

The output was:
1
Microsoft (R) Build Engine version 14.0.25420.1
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 31.10.2016 18:58:27.
Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" on node 1 (default targets).
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
Done Building Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default targets) -- FAILED.

Build FAILED.

"C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default target) (1) ->
(Desktop_PlatformPrepareForBuild target) ->
  C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]

    0 Warning(s)
    1 Error(s)


What can I do to solve the problem?

Thank you
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From matt.mccormick at kitware.com  Mon Oct 31 14:18:42 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 31 Oct 2016 14:18:42 -0400
Subject: [ITK-users] cmake build error
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
Message-ID: <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>

Hi Fabio,

If the command line CMake executable is used, as opposed to the GUI,
the command must be executed from a Visual Studio Command Prompt,
which adjusts the PATH environmental variable to expose the compiler.

HTH,
Matt

On Mon, Oct 31, 2016 at 2:08 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hallo,
>
>
>
> I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on Windows
> 10 with Visual Studio 2015. As ?current generator? I tried both ?Visual
> Studio 14 2015? and ?Visual Studio 14 2015 Win64? but I immediately get
> errors with cmake when configuring. Errors are:
>
>
>
> The C compiler identification is unknown
>
> CMake Error at CMakeLists.txt:18 (enable_language):
>
>   No CMAKE_C_COMPILER could be found.
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:53:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
> Time Elapsed 00:00:00.48
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:58:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
>
>
> What can I do to solve the problem?
>
>
>
> Thank you
>
>
> _____________________________________
> 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
>

From fisidoro at ethz.ch  Mon Oct 31 14:41:56 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Mon, 31 Oct 2016 18:41:56 +0000
Subject: [ITK-users] cmake build error
In-Reply-To: <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
 <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B40943A161805@MBX112.d.ethz.ch>

Thanks, I did it but I got the same kind of error. What else could I try?


-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Sent: Montag, 31. Oktober 2016 19:19
To: D'Isidoro Fabio
Cc: insight-users at itk.org
Subject: Re: [ITK-users] cmake build error

Hi Fabio,

If the command line CMake executable is used, as opposed to the GUI, the command must be executed from a Visual Studio Command Prompt, which adjusts the PATH environmental variable to expose the compiler.

HTH,
Matt

On Mon, Oct 31, 2016 at 2:08 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hallo,
>
>
>
> I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on 
> Windows
> 10 with Visual Studio 2015. As ?current generator? I tried both 
> ?Visual Studio 14 2015? and ?Visual Studio 14 2015 Win64? but I 
> immediately get errors with cmake when configuring. Errors are:
>
>
>
> The C compiler identification is unknown
>
> CMake Error at CMakeLists.txt:18 (enable_language):
>
>   No CMAKE_C_COMPILER could be found.
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:53:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
> Time Elapsed 00:00:00.48
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:58:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
>
>
> What can I do to solve the problem?
>
>
>
> Thank you
>
>
> _____________________________________
> 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
>

From matt.mccormick at kitware.com  Mon Oct 31 14:49:30 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 31 Oct 2016 14:49:30 -0400
Subject: [ITK-users] cmake build error
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40943A161805@MBX112.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
 <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40943A161805@MBX112.d.ethz.ch>
Message-ID: <CALzTN-REaQ8vtx17bH86662_Zptod0VynYgDqaVWx+F2Xw8nxA@mail.gmail.com>

"The Windows SDK version 8.1 was not found. Install the required
version of Windows SDK or change the SDK version in the project
property pages or by right-clicking the solution and selecting
"Retarget solution"."

The installation of Windows SDK along with Visual Studio may have not
been successful -- Visual Studio could be re-installed or Windows SDK
can be installed on its own.

HTH,
Matt

On Mon, Oct 31, 2016 at 2:41 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Thanks, I did it but I got the same kind of error. What else could I try?
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 31. Oktober 2016 19:19
> To: D'Isidoro Fabio
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] cmake build error
>
> Hi Fabio,
>
> If the command line CMake executable is used, as opposed to the GUI, the command must be executed from a Visual Studio Command Prompt, which adjusts the PATH environmental variable to expose the compiler.
>
> HTH,
> Matt
>
> On Mon, Oct 31, 2016 at 2:08 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
>> Hallo,
>>
>>
>>
>> I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on
>> Windows
>> 10 with Visual Studio 2015. As ?current generator? I tried both
>> ?Visual Studio 14 2015? and ?Visual Studio 14 2015 Win64? but I
>> immediately get errors with cmake when configuring. Errors are:
>>
>>
>>
>> The C compiler identification is unknown
>>
>> CMake Error at CMakeLists.txt:18 (enable_language):
>>
>>   No CMAKE_C_COMPILER could be found.
>>
>>
>>
>>
>>
>> Compiling the C compiler identification source file "CMakeCCompilerId.c"
>> failed.
>>
>> Compiler:
>>
>> Build flags:
>>
>> Id flags:
>>
>>
>>
>> The output was:
>>
>> 1
>>
>> Microsoft (R) Build Engine version 14.0.25420.1
>>
>> Copyright (C) Microsoft Corporation. All rights reserved.
>>
>>
>>
>> Build started 31.10.2016 18:53:27.
>>
>> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> on node 1 (default targets).
>>
>> C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>> Done Building Project
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> targets) -- FAILED.
>>
>>
>>
>> Build FAILED.
>>
>>
>>
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> target) (1) ->
>>
>> (Desktop_PlatformPrepareForBuild target) ->
>>
>>   C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>>
>>
>>     0 Warning(s)
>>
>>     1 Error(s)
>>
>>
>>
>> Time Elapsed 00:00:00.48
>>
>>
>>
>>
>>
>> Compiling the C compiler identification source file "CMakeCCompilerId.c"
>> failed.
>>
>> Compiler:
>>
>> Build flags:
>>
>> Id flags:
>>
>>
>>
>> The output was:
>>
>> 1
>>
>> Microsoft (R) Build Engine version 14.0.25420.1
>>
>> Copyright (C) Microsoft Corporation. All rights reserved.
>>
>>
>>
>> Build started 31.10.2016 18:58:27.
>>
>> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> on node 1 (default targets).
>>
>> C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>> Done Building Project
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> targets) -- FAILED.
>>
>>
>>
>> Build FAILED.
>>
>>
>>
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> target) (1) ->
>>
>> (Desktop_PlatformPrepareForBuild target) ->
>>
>>   C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>>
>>
>>     0 Warning(s)
>>
>>     1 Error(s)
>>
>>
>>
>>
>>
>> What can I do to solve the problem?
>>
>>
>>
>> Thank you
>>
>>
>> _____________________________________
>> 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
>>

From dan.muel at gmail.com  Mon Oct 31 16:49:37 2016
From: dan.muel at gmail.com (Dan Mueller)
Date: Tue, 1 Nov 2016 07:19:37 +1030
Subject: [ITK-users] Simple ITK Wavelet Transform ?? it is possible?
In-Reply-To: <1477904974504-37723.post@n7.nabble.com>
References: <1477904974504-37723.post@n7.nabble.com>
Message-ID: <CAPNvZ5ZtFX5jzq+AQM3snJ0o1AR8MLF0rvyswAOax=+JiJ-LYw@mail.gmail.com>

Hi Ivan,

There is also a na?ve (ie. slow) implementation of QMF DWT here:
http://www.insight-journal.org/browse/publication/103

These filters are not wrapped in SimpleITK though...

Good luck, Dan

On 31 Oct 2016 21:05, "ivan" <ivan.granata.na at gmail.com> wrote:

> Is it possibile to apply a wavelet transform to an image in SimpleITK?
> Thx
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-Simple-ITK-Wavelet-Transform-it-is-possible-tp37723.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> 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
>
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