From haratron at gmail.com  Fri Jan  2 12:59:42 2015
From: haratron at gmail.com (haratron)
Date: Fri, 2 Jan 2015 19:59:42 +0200
Subject: [ITK-users] WarpImageFilter wrong output
Message-ID: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>

Hello and happy new year,

I'm using the WarpImageFilter from here:
http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter

I have original.png that I'm using as the movingImage and I'm creating
another one ("empty" image filled with white color, size 1800x1800) that is
the fixedImage.

The problem is that a blank image filled with black is created instead of
the warped image that is expected.

original.png : http://i.imgur.com/QQyXgzg.png
output.png: http://i.imgur.com/LkYnZ6n.png

My full WarpImageFilter.cxx file (includes changes from the original
example code):
http://pastebin.com/WNDb2TgM

What am I doing wrong?

John
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From blowekamp at mail.nih.gov  Fri Jan  2 13:28:05 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 2 Jan 2015 13:28:05 -0500
Subject: [ITK-users] WarpImageFilter wrong output
In-Reply-To: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>
References: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>
Message-ID: <52482848-2F1D-4DB9-A898-E2D197376F13@mail.nih.gov>

Hello,

In your CreateMovingImage2 method how is the "image" argument connected to the pipeline?

Brad

On Jan 2, 2015, at 12:59 PM, haratron <haratron at gmail.com> wrote:

> Hello and happy new year,
> 
> I'm using the WarpImageFilter from here:
> http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
> 
> I have original.png that I'm using as the movingImage and I'm creating another one ("empty" image filled with white color, size 1800x1800) that is the fixedImage.
> 
> The problem is that a blank image filled with black is created instead of the warped image that is expected.
> 
> original.png : http://i.imgur.com/QQyXgzg.png
> output.png: http://i.imgur.com/LkYnZ6n.png
> 
> My full WarpImageFilter.cxx file (includes changes from the original example code):
> http://pastebin.com/WNDb2TgM
> 
> What am I doing wrong?
> 
> John
> _____________________________________
> 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 haratron at gmail.com  Fri Jan  2 22:57:54 2015
From: haratron at gmail.com (haratron)
Date: Sat, 3 Jan 2015 05:57:54 +0200
Subject: [ITK-users] WarpImageFilter wrong output
In-Reply-To: <52482848-2F1D-4DB9-A898-E2D197376F13@mail.nih.gov>
References: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>
 <52482848-2F1D-4DB9-A898-E2D197376F13@mail.nih.gov>
Message-ID: <CAOJPiNCS_AC7L5Og7U1MBo3xbKnTNF4iEYOreViyQqOg4wxYiQ@mail.gmail.com>

Thanks!

What is the difference between:
1. http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
2.
http://www.itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer3.
http://www.itk.org/Wiki/ITK/Examples/Registration/DeformationFieldTransform

On Fri, Jan 2, 2015 at 8:28 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> In your CreateMovingImage2 method how is the "image" argument connected to
> the pipeline?
>
> Brad
>
> On Jan 2, 2015, at 12:59 PM, haratron <haratron at gmail.com> wrote:
>
> Hello and happy new year,
>
> I'm using the WarpImageFilter from here:
> http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
>
> I have original.png that I'm using as the movingImage and I'm creating
> another one ("empty" image filled with white color, size 1800x1800) that is
> the fixedImage.
>
> The problem is that a blank image filled with black is created instead of
> the warped image that is expected.
>
> original.png : http://i.imgur.com/QQyXgzg.png
> output.png: http://i.imgur.com/LkYnZ6n.png
>
> My full WarpImageFilter.cxx file (includes changes from the original
> example code):
> http://pastebin.com/WNDb2TgM
>
> What am I doing wrong?
>
> John
> _____________________________________
> 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 matimontg at gmail.com  Tue Jan  6 19:16:13 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 6 Jan 2015 21:16:13 -0300
Subject: [ITK-users] CT/MR Registration using ITK
Message-ID: <CAKKNfuKMO32wHWJECCEyH22ikZ+hnsxTGKACX2N5cWDVoLptGQ@mail.gmail.com>

I'm trying to do registration of the 2 attached images (test) to implement
CT/RM Registration, which is the best algorithm to achieve the best results?

[image: Inline image 1][image: Inline image 2]Hi,
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From j.plumat at auckland.ac.nz  Tue Jan  6 21:56:00 2015
From: j.plumat at auckland.ac.nz (Jerome Plumat)
Date: Wed, 07 Jan 2015 15:56:00 +1300
Subject: [ITK-users] CT/MR Registration using ITK
In-Reply-To: <CAKKNfuKMO32wHWJECCEyH22ikZ+hnsxTGKACX2N5cWDVoLptGQ@mail.gmail.com>
References: <CAKKNfuKMO32wHWJECCEyH22ikZ+hnsxTGKACX2N5cWDVoLptGQ@mail.gmail.com>
Message-ID: <54ACA040.1030707@auckland.ac.nz>

Hi Matias,
you should look for multimodal algorithms with metrics such as Mutual 
Information. Have a look to ITK software guide book 2 section 3.5.
Hope it helps.

Jerome Plumat
-------
School of Medical Sciences
University of Auckland

If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? ? Hillel HaZaken

On 07/01/15 13:16, Matias Montroull wrote:
> I'm trying to do registration of the 2 attached images (test) to 
> implement CT/RM Registration, which is the best algorithm to achieve 
> the best results?
> Hi,
>
>
>
>
>
>
> _____________________________________
> 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 joel.schaerer at laposte.net  Wed Jan  7 05:36:53 2015
From: joel.schaerer at laposte.net (=?windows-1252?Q?Jo=EBl_Schaerer?=)
Date: Wed, 07 Jan 2015 11:36:53 +0100
Subject: [ITK-users] Possible missing method in itkImageSource
In-Reply-To: <0023FC88-13F9-4ED2-9767-FB324A2EE0CB@mail.nih.gov>
References: <54413DE5.1050108@laposte.net>
 <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com>
 <0023FC88-13F9-4ED2-9767-FB324A2EE0CB@mail.nih.gov>
Message-ID: <54AD0C45.1090102@laposte.net>

Any plans on fixing this? I've run into this issue again when attempting 
a DisconnectPipeline() on a named output. It crashes because the 
SetOutput() method attempts to create a new output after detaching the 
old one using the faulty MakeOutput(key) method:

0x000000000063a3dc in itk::ProcessObject::SetOutput (this=0x1b2e060, 
name=..., output=<optimized out>) at 
../Modules/Core/Common/src/itkProcessObject.cxx:484
483        DataObjectPointer newOutput = this->MakeOutput(key);
484        this->SetOutput(key, newOutput); // Segfault

Thanks,

Jo?l

On 22/10/2014 15:44, Bradley Lowekamp wrote:
> Hello,
>
> I'm going to take a look at this issue.
>
> Brad
>
> On Oct 17, 2014, at 5:01 PM, Jim Miller <millerjv at gmail.com> wrote:
>
>> At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden.
>>
>> Jim
>>
>>> On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer <joel.schaerer at laposte.net> wrote:
>>>
>>> Hi all,
>>>
>>> I've run into a problem with named outputs, which I believe could be a bug in ITK.
>>>
>>> When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs.
>>> .
>>> These methods are declared and defined first in itkProcessObject:
>>>
>>> .h:
>>>   * ...
>>>   * ProcessObject::MakeOutput. Note that MakeOutput always returns a
>>>   * itkSmartPointer to a DataObject. ImageSource and MeshSource override
>>>   * this method to create the correct type of image and mesh respectively.
>>>   * If a filter has multiple outputs of different types, then that
>>>   * filter must provide an implementation of MakeOutput(). */
>>> virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & );
>>> virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx);
>>>
>>> .cxx
>>> DataObject::Pointer
>>> ProcessObject
>>> ::MakeOutput( const DataObjectIdentifierType & name )
>>> {
>>> itkDebugMacro("MakeOutput(" << name << ")");
>>> if( this->IsIndexedOutputName(name) )
>>>    {
>>>    return this->MakeOutput( this->MakeIndexFromOutputName(name) );
>>>    }
>>> return static_cast<DataObject *>(DataObject::New().GetPointer());
>>> }
>>>
>>> DataObject::Pointer
>>> ProcessObject
>>> ::MakeOutput(DataObjectPointerArraySizeType)
>>> {
>>> return static_cast<DataObject *>(DataObject::New().GetPointer());
>>> }
>>>
>>>
>>> For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type.
>>>
>>> template< typename TOutputImage >
>>> ProcessObject::DataObjectPointer
>>> ImageSource< TOutputImage >
>>> ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType)
>>> {
>>> return TOutputImage::New().GetPointer();
>>> }
>>>
>>> So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash.
>>>
>>> Any reason for this behavior? Is this an oversight?
>>>
>>> Thanks,
>>>
>>> Jo?l
>>> _____________________________________
>>>


From joel.schaerer at laposte.net  Wed Jan  7 06:31:41 2015
From: joel.schaerer at laposte.net (=?windows-1252?Q?Jo=EBl_Schaerer?=)
Date: Wed, 07 Jan 2015 12:31:41 +0100
Subject: [ITK-users] Possible missing method in itkImageSource
In-Reply-To: <54AD0C45.1090102@laposte.net>
References: <54413DE5.1050108@laposte.net>
 <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com>
 <0023FC88-13F9-4ED2-9767-FB324A2EE0CB@mail.nih.gov>
 <54AD0C45.1090102@laposte.net>
Message-ID: <54AD191D.4050605@laposte.net>

I just noticed that the problem is fixed in the latest release. Thanks 
for the fix, and sorry for the noise!

Joel

On 07/01/2015 11:36, Jo?l Schaerer wrote:
> Any plans on fixing this? I've run into this issue again when 
> attempting a DisconnectPipeline() on a named output. It crashes 
> because the SetOutput() method attempts to create a new output after 
> detaching the old one using the faulty MakeOutput(key) method:
>
> 0x000000000063a3dc in itk::ProcessObject::SetOutput (this=0x1b2e060, 
> name=..., output=<optimized out>) at 
> ../Modules/Core/Common/src/itkProcessObject.cxx:484
> 483        DataObjectPointer newOutput = this->MakeOutput(key);
> 484        this->SetOutput(key, newOutput); // Segfault
>
> Thanks,
>
> Jo?l
>
> On 22/10/2014 15:44, Bradley Lowekamp wrote:
>> Hello,
>>
>> I'm going to take a look at this issue.
>>
>> Brad
>>
>> On Oct 17, 2014, at 5:01 PM, Jim Miller <millerjv at gmail.com> wrote:
>>
>>> At first glance it looks like an oversight. I would expect, however, 
>>> that we should be seeing warnings about the named version of 
>>> MakeOutput in ProcessObject being hidden.
>>>
>>> Jim
>>>
>>>> On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer 
>>>> <joel.schaerer at laposte.net> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I've run into a problem with named outputs, which I believe could 
>>>> be a bug in ITK.
>>>>
>>>> When using named outputs, one is supposed to create the output data 
>>>> objects in the constructor using the MakeOutput method (see 
>>>> http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs 
>>>> for an example). The MakeOutput method exists for both indexed and 
>>>> named outputs.
>>>> .
>>>> These methods are declared and defined first in itkProcessObject:
>>>>
>>>> .h:
>>>>   * ...
>>>>   * ProcessObject::MakeOutput. Note that MakeOutput always returns a
>>>>   * itkSmartPointer to a DataObject. ImageSource and MeshSource 
>>>> override
>>>>   * this method to create the correct type of image and mesh 
>>>> respectively.
>>>>   * If a filter has multiple outputs of different types, then that
>>>>   * filter must provide an implementation of MakeOutput(). */
>>>> virtual DataObjectPointer MakeOutput( const 
>>>> DataObjectIdentifierType & );
>>>> virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType 
>>>> idx);
>>>>
>>>> .cxx
>>>> DataObject::Pointer
>>>> ProcessObject
>>>> ::MakeOutput( const DataObjectIdentifierType & name )
>>>> {
>>>> itkDebugMacro("MakeOutput(" << name << ")");
>>>> if( this->IsIndexedOutputName(name) )
>>>>    {
>>>>    return this->MakeOutput( this->MakeIndexFromOutputName(name) );
>>>>    }
>>>> return static_cast<DataObject *>(DataObject::New().GetPointer());
>>>> }
>>>>
>>>> DataObject::Pointer
>>>> ProcessObject
>>>> ::MakeOutput(DataObjectPointerArraySizeType)
>>>> {
>>>> return static_cast<DataObject *>(DataObject::New().GetPointer());
>>>> }
>>>>
>>>>
>>>> For indexed outputs, it is redefined in ImageSource in order to 
>>>> create an image object of the correct type.
>>>>
>>>> template< typename TOutputImage >
>>>> ProcessObject::DataObjectPointer
>>>> ImageSource< TOutputImage >
>>>> ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType)
>>>> {
>>>> return TOutputImage::New().GetPointer();
>>>> }
>>>>
>>>> So far, so good. However, the named output version of MakeOutput is 
>>>> not redefined in ImageSource, contrary to what the comment in 
>>>> itkProcessObject.h says. And so if someone tries to use it in an 
>>>> ImageToImageFilter, it will crash.
>>>>
>>>> Any reason for this behavior? Is this an oversight?
>>>>
>>>> Thanks,
>>>>
>>>> Jo?l
>>>> _____________________________________
>>>>
>


From matt.mccormick at kitware.com  Wed Jan  7 14:47:05 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 14:47:05 -0500
Subject: [ITK-users] Discuss what's new ITK in ITK 4.7.0,
	what is coming in ITK 4.8.0
Message-ID: <CALzTN-S9zHv+Q28DCnh_7CCz015uAtW5oDPHcKQJgjXtJgwwRQ@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.  Following the recent
4.7.0, this is also a great time to discuss what was new in ITK 4.7.0,
and what to work on for ITK 4.8.0.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/u/1/events/cmapnnf3gu3adnsdpfjr93a6hr8?authkey=CMbjm5aD2rO68gE


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/u/1/events/cntel7ikg752bo6lmpen8ade22c?authkey=CM2q5_2Bva6asgE


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Wed Jan  7 14:58:03 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 14:58:03 -0500
Subject: [ITK-users] WarpImageFilter wrong output
In-Reply-To: <CAOJPiNCS_AC7L5Og7U1MBo3xbKnTNF4iEYOreViyQqOg4wxYiQ@mail.gmail.com>
References: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>
 <52482848-2F1D-4DB9-A898-E2D197376F13@mail.nih.gov>
 <CAOJPiNCS_AC7L5Og7U1MBo3xbKnTNF4iEYOreViyQqOg4wxYiQ@mail.gmail.com>
Message-ID: <CALzTN-T1QP6cErJ8P3yBsY-t=LudzWt+7vGZEHM4yW7dp58FCA@mail.gmail.com>

Hi John,

The DisplacementFieldTransform can be used with the
ResampleImageFilter like any other Transform. There was a time when
the DisplacementFieldTransform was not available -- the special
WarpImageFilter class was used in this case.

HTH,
Matt

On Fri, Jan 2, 2015 at 10:57 PM, haratron <haratron at gmail.com> wrote:
> Thanks!
>
> What is the difference between:
> 1. http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
> 2.
> http://www.itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer3.
> http://www.itk.org/Wiki/ITK/Examples/Registration/DeformationFieldTransform
>
> On Fri, Jan 2, 2015 at 8:28 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>>
>> Hello,
>>
>> In your CreateMovingImage2 method how is the "image" argument connected to
>> the pipeline?
>>
>> Brad
>>
>> On Jan 2, 2015, at 12:59 PM, haratron <haratron at gmail.com> wrote:
>>
>> Hello and happy new year,
>>
>> I'm using the WarpImageFilter from here:
>> http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
>>
>> I have original.png that I'm using as the movingImage and I'm creating
>> another one ("empty" image filled with white color, size 1800x1800) that is
>> the fixedImage.
>>
>> The problem is that a blank image filled with black is created instead of
>> the warped image that is expected.
>>
>> original.png : http://i.imgur.com/QQyXgzg.png
>> output.png: http://i.imgur.com/LkYnZ6n.png
>>
>> My full WarpImageFilter.cxx file (includes changes from the original
>> example code):
>> http://pastebin.com/WNDb2TgM
>>
>> What am I doing wrong?
>>
>> John
>> _____________________________________
>> 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 matt.mccormick at kitware.com  Wed Jan  7 15:01:01 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 15:01:01 -0500
Subject: [ITK-users] Mesh to stl or ply
In-Reply-To: <CALD_Ep+_AS6YnURFv+ofKG04QvTgpPz1NUZZNy4=q0y2Qsqf1w@mail.gmail.com>
References: <CALD_Ep+_AS6YnURFv+ofKG04QvTgpPz1NUZZNy4=q0y2Qsqf1w@mail.gmail.com>
Message-ID: <CALzTN-RPD20qYFyac0jfVswyVsUm-GAKvNe4OL35qnM-0=AMdQ@mail.gmail.com>

Hi Fabian,

ITK has support for IO of a number of different mesh formats.  See [1] [2].

HTH,
Matt

[1] http://itk.org/Insight/Doxygen/html/group__ITKIOMesh.html


[2] http://itk.org/ITKExamples/src/IO/Mesh/ReadMesh/Documentation.html

On Wed, Dec 31, 2014 at 5:18 AM, Fabian Torres <fabian.trobles at gmail.com> wrote:
> Hi every one
>
> I have a segmented image (object in white, background in black) and I want
> to obtain a mesh for the segmented object.
> I am using tetgen software to use obtain a Delaunay tetrahedralization to
> obtain the mesh. With this software I obtain a list of nodes, a list of
> tethraedrons and a list of triangle faces.
>
> Is there a way to use the information obtained with tetgen with ITK and/or
> VTK to create a mesh that I can use in MeshLab or  Comsol (.py or .stl)?
>
> Thanks
>
> --
> Fabi?n Torres Robles
> Maestria en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> tel. 58081280, 0445534661338
> e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 haratron at gmail.com  Wed Jan  7 15:10:30 2015
From: haratron at gmail.com (haratron)
Date: Wed, 7 Jan 2015 22:10:30 +0200
Subject: [ITK-users] WarpImageFilter wrong output
In-Reply-To: <CALzTN-T1QP6cErJ8P3yBsY-t=LudzWt+7vGZEHM4yW7dp58FCA@mail.gmail.com>
References: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>
 <52482848-2F1D-4DB9-A898-E2D197376F13@mail.nih.gov>
 <CAOJPiNCS_AC7L5Og7U1MBo3xbKnTNF4iEYOreViyQqOg4wxYiQ@mail.gmail.com>
 <CALzTN-T1QP6cErJ8P3yBsY-t=LudzWt+7vGZEHM4yW7dp58FCA@mail.gmail.com>
Message-ID: <CAOJPiND4bD93bkGFV7qtwFrhkM41Y6SXNOO-FWdPe3aKwCLMWQ@mail.gmail.com>

Hi Matt,

thanks for the response.
What about
http://www.itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer
?
I missed a space in the previous email and it didn't parse the URL
correctly.

On Wed, Jan 7, 2015 at 9:58 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi John,
>
> The DisplacementFieldTransform can be used with the
> ResampleImageFilter like any other Transform. There was a time when
> the DisplacementFieldTransform was not available -- the special
> WarpImageFilter class was used in this case.
>
> HTH,
> Matt
>
> On Fri, Jan 2, 2015 at 10:57 PM, haratron <haratron at gmail.com> wrote:
> > Thanks!
> >
> > What is the difference between:
> > 1. http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
> > 2.
> >
> http://www.itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer3
> .
> >
> http://www.itk.org/Wiki/ITK/Examples/Registration/DeformationFieldTransform
> >
> > On Fri, Jan 2, 2015 at 8:28 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
> >
> > wrote:
> >>
> >> Hello,
> >>
> >> In your CreateMovingImage2 method how is the "image" argument connected
> to
> >> the pipeline?
> >>
> >> Brad
> >>
> >> On Jan 2, 2015, at 12:59 PM, haratron <haratron at gmail.com> wrote:
> >>
> >> Hello and happy new year,
> >>
> >> I'm using the WarpImageFilter from here:
> >> http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
> >>
> >> I have original.png that I'm using as the movingImage and I'm creating
> >> another one ("empty" image filled with white color, size 1800x1800)
> that is
> >> the fixedImage.
> >>
> >> The problem is that a blank image filled with black is created instead
> of
> >> the warped image that is expected.
> >>
> >> original.png : http://i.imgur.com/QQyXgzg.png
> >> output.png: http://i.imgur.com/LkYnZ6n.png
> >>
> >> My full WarpImageFilter.cxx file (includes changes from the original
> >> example code):
> >> http://pastebin.com/WNDb2TgM
> >>
> >> What am I doing wrong?
> >>
> >> John
> >> _____________________________________
> >> 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 Jan  7 15:18:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 15:18:24 -0500
Subject: [ITK-users] WarpImageFilter wrong output
In-Reply-To: <CAOJPiND4bD93bkGFV7qtwFrhkM41Y6SXNOO-FWdPe3aKwCLMWQ@mail.gmail.com>
References: <CAOJPiNDWbj+ndv5kzjdo6Lc8ejDQPDEpOGnFdJppgt=A1byCig@mail.gmail.com>
 <52482848-2F1D-4DB9-A898-E2D197376F13@mail.nih.gov>
 <CAOJPiNCS_AC7L5Og7U1MBo3xbKnTNF4iEYOreViyQqOg4wxYiQ@mail.gmail.com>
 <CALzTN-T1QP6cErJ8P3yBsY-t=LudzWt+7vGZEHM4yW7dp58FCA@mail.gmail.com>
 <CAOJPiND4bD93bkGFV7qtwFrhkM41Y6SXNOO-FWdPe3aKwCLMWQ@mail.gmail.com>
Message-ID: <CALzTN-S1uXqDMnTujfP4-GRdFvEwe+yU-21h6toUNyMHKSToXA@mail.gmail.com>

Hi Haratron,

The referenced example is initializing a rigid transform based on
landmarks while the other examples are creating a non-rigid
displacement field based on landmarks.

HTH,
Matt

On Wed, Jan 7, 2015 at 3:10 PM, haratron <haratron at gmail.com> wrote:
> Hi Matt,
>
> thanks for the response.
> What about
> http://www.itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer
> ?
> I missed a space in the previous email and it didn't parse the URL
> correctly.
>
> On Wed, Jan 7, 2015 at 9:58 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi John,
>>
>> The DisplacementFieldTransform can be used with the
>> ResampleImageFilter like any other Transform. There was a time when
>> the DisplacementFieldTransform was not available -- the special
>> WarpImageFilter class was used in this case.
>>
>> HTH,
>> Matt
>>
>> On Fri, Jan 2, 2015 at 10:57 PM, haratron <haratron at gmail.com> wrote:
>> > Thanks!
>> >
>> > What is the difference between:
>> > 1. http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
>> > 2.
>> >
>> > http://www.itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer3.
>> >
>> > http://www.itk.org/Wiki/ITK/Examples/Registration/DeformationFieldTransform
>> >
>> > On Fri, Jan 2, 2015 at 8:28 PM, Bradley Lowekamp
>> > <blowekamp at mail.nih.gov>
>> > wrote:
>> >>
>> >> Hello,
>> >>
>> >> In your CreateMovingImage2 method how is the "image" argument connected
>> >> to
>> >> the pipeline?
>> >>
>> >> Brad
>> >>
>> >> On Jan 2, 2015, at 12:59 PM, haratron <haratron at gmail.com> wrote:
>> >>
>> >> Hello and happy new year,
>> >>
>> >> I'm using the WarpImageFilter from here:
>> >> http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter
>> >>
>> >> I have original.png that I'm using as the movingImage and I'm creating
>> >> another one ("empty" image filled with white color, size 1800x1800)
>> >> that is
>> >> the fixedImage.
>> >>
>> >> The problem is that a blank image filled with black is created instead
>> >> of
>> >> the warped image that is expected.
>> >>
>> >> original.png : http://i.imgur.com/QQyXgzg.png
>> >> output.png: http://i.imgur.com/LkYnZ6n.png
>> >>
>> >> My full WarpImageFilter.cxx file (includes changes from the original
>> >> example code):
>> >> http://pastebin.com/WNDb2TgM
>> >>
>> >> What am I doing wrong?
>> >>
>> >> John
>> >> _____________________________________
>> >> 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 franciscolopezdelafranca at gmail.com  Fri Jan  9 14:59:49 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Fri, 9 Jan 2015 20:59:49 +0100
Subject: [ITK-users] Undefined references to methods of template classes
Message-ID: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>

Hi.
I' like to create a library containing, for example, one template class
with a number of methods.
I've programmed a simple example and the compilation and generation of the
library goes fine. I use the cmake "add_library" command for generating the
library.

The problem arises at the moment of testing the library. I get an undefined
reference for every method in the template class.

I've downloaded a tool to look in the contents (functions) of dynamic
libraries, and there is no function in the library. If I add another class
(not a template class), then, this tool shows me only the functions in this
latter class.

Has anyone ever come across with this problem?

Thanks a lot in advance.
Regards
/Francisco
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From matt.mccormick at kitware.com  Fri Jan  9 15:02:52 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 9 Jan 2015 15:02:52 -0500
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
Message-ID: <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>

Hi Francisco,

In order for the templates to be available in the library, they must
be explicitly instantiated [1].

HTH,
Matt

[1] http://www.cplusplus.com/articles/1C75fSEw/

On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
<franciscolopezdelafranca at gmail.com> wrote:
> Hi.
> I' like to create a library containing, for example, one template class with
> a number of methods.
> I've programmed a simple example and the compilation and generation of the
> library goes fine. I use the cmake "add_library" command for generating the
> library.
>
> The problem arises at the moment of testing the library. I get an undefined
> reference for every method in the template class.
>
> I've downloaded a tool to look in the contents (functions) of dynamic
> libraries, and there is no function in the library. If I add another class
> (not a template class), then, this tool shows me only the functions in this
> latter class.
>
> Has anyone ever come across with this problem?
>
> Thanks a lot in advance.
> Regards
> /Francisco
>
> _____________________________________
> 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 franciscolopezdelafranca at gmail.com  Sat Jan 10 16:16:09 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Sat, 10 Jan 2015 22:16:09 +0100
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
Message-ID: <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>

Thanks to your previous answer the problem was solved, but another one has
come out. It occurs when linking to create the library. It gives an
undefined reference to itk::ExceptionObject::ExceptionObject... as you can
see below.
What it is strange to me is that before including explicit template
instantiation, I created the library without errors, and now that I include
that, I get this error.
I'll appreciate very much any help.

Linking CXX shared library libTFM_Features.dll
CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
1ERKSsjS2_S2_]+0x35): undefined reference to
`itk::ExceptionObject::ExceptionObj
ect(std::string const&, unsigned int, std::string const&, std::string
const&)'
CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
itk::MemoryAllocationEr
ror'
C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
gw32/bin/ld.exe:
CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
d reloc address 0x40 in section
`.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
collect2.exe: error: ld returned 1 exit status
SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
'SRC/libTFM_Fe
atures.dll' failed
mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
CMakeFiles\Makefile2:77: recipe for target
'SRC/CMakeFiles/TFM_Features.dir/all'
 failed
mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
Makefile:74: recipe for target 'all' failed
mingw32-make: *** [all] Error 2

2015-01-09 21:02 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Francisco,
>
> In order for the templates to be available in the library, they must
> be explicitly instantiated [1].
>
> HTH,
> Matt
>
> [1] http://www.cplusplus.com/articles/1C75fSEw/
>
> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
> <franciscolopezdelafranca at gmail.com> wrote:
> > Hi.
> > I' like to create a library containing, for example, one template class
> with
> > a number of methods.
> > I've programmed a simple example and the compilation and generation of
> the
> > library goes fine. I use the cmake "add_library" command for generating
> the
> > library.
> >
> > The problem arises at the moment of testing the library. I get an
> undefined
> > reference for every method in the template class.
> >
> > I've downloaded a tool to look in the contents (functions) of dynamic
> > libraries, and there is no function in the library. If I add another
> class
> > (not a template class), then, this tool shows me only the functions in
> this
> > latter class.
> >
> > Has anyone ever come across with this problem?
> >
> > Thanks a lot in advance.
> > Regards
> > /Francisco
> >
> > _____________________________________
> > 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  Sat Jan 10 16:38:32 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 10 Jan 2015 16:38:32 -0500
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
Message-ID: <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>

Hi Francisco,

Nice to hear about the progress!

You will need to link your library to the ITK libraries:

  target_link_libraries( mylibrary ${ITK_LIBRARIES} )

HTH,
Matt

On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca <
franciscolopezdelafranca at gmail.com> wrote:

> Thanks to your previous answer the problem was solved, but another one has
> come out. It occurs when linking to create the library. It gives an
> undefined reference to itk::ExceptionObject::ExceptionObject... as you can
> see below.
> What it is strange to me is that before including explicit template
> instantiation, I created the library without errors, and now that I include
> that, I get this error.
> I'll appreciate very much any help.
>
> Linking CXX shared library libTFM_Features.dll
>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> 1ERKSsjS2_S2_]+0x35): undefined reference to
> `itk::ExceptionObject::ExceptionObj
> ect(std::string const&, unsigned int, std::string const&, std::string
> const&)'
>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
> itk::MemoryAllocationEr
> ror'
>
> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
> gw32/bin/ld.exe:
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
> d reloc address 0x40 in section
> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
> collect2.exe: error: ld returned 1 exit status
> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
> 'SRC/libTFM_Fe
> atures.dll' failed
> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
> CMakeFiles\Makefile2:77: recipe for target
> 'SRC/CMakeFiles/TFM_Features.dir/all'
>  failed
> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
> Makefile:74: recipe for target 'all' failed
> mingw32-make: *** [all] Error 2
>
>
> 2015-01-09 21:02 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> Hi Francisco,
>>
>> In order for the templates to be available in the library, they must
>> be explicitly instantiated [1].
>>
>> HTH,
>> Matt
>>
>> [1] http://www.cplusplus.com/articles/1C75fSEw/
>>
>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
>> <franciscolopezdelafranca at gmail.com> wrote:
>> > Hi.
>> > I' like to create a library containing, for example, one template class
>> with
>> > a number of methods.
>> > I've programmed a simple example and the compilation and generation of
>> the
>> > library goes fine. I use the cmake "add_library" command for generating
>> the
>> > library.
>> >
>> > The problem arises at the moment of testing the library. I get an
>> undefined
>> > reference for every method in the template class.
>> >
>> > I've downloaded a tool to look in the contents (functions) of dynamic
>> > libraries, and there is no function in the library. If I add another
>> class
>> > (not a template class), then, this tool shows me only the functions in
>> this
>> > latter class.
>> >
>> > Has anyone ever come across with this problem?
>> >
>> > Thanks a lot in advance.
>> > Regards
>> > /Francisco
>> >
>> > _____________________________________
>> > 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 rekha.pyage at gmail.com  Mon Jan 12 02:42:22 2015
From: rekha.pyage at gmail.com (reks)
Date: Mon, 12 Jan 2015 00:42:22 -0700 (MST)
Subject: [ITK-users] itk Canny segmentation level set on 3d data
Message-ID: <1421048542766-35103.post@n7.nabble.com>

Hi all,

I am trying to make use of itkCannySegmentationLevelSet 2d example on 3d
data. Here I am giving the output of thresholdsegmentationlevelset as one of
the input to the filter and input image as the feature input. I am giving
The parameters to this filter as given in 2d example( canny threshold=7.0,
CannyVariance= 0.1 ,AdvectionScaling=10.0,IsoSurfaceValue=
127.5,NumberOfIterations= 15) but I am not getting the expected output. I am
getting thresholdsegmentationlevelset output as it is as the cannylevelset
output. do I have to change the parameters to this filter ? I dont know
where I am going wrong. please do help me..

any help will be appreciated.
thanks in advance.

reks






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

From mathias.richter at informatik.uni-luebeck.de  Mon Jan 12 04:36:29 2015
From: mathias.richter at informatik.uni-luebeck.de (mathew)
Date: Mon, 12 Jan 2015 02:36:29 -0700 (MST)
Subject: [ITK-users] extending label object's line iterator / cpp question
Message-ID: <1421055389237-7586769.post@n2.nabble.com>

Dear ITK users,

Currently, I am working with the LabelObject class and its iterators (i.e.
the line iterator).
I have noticed that I can only advance the iterator by one. Unfortunately I
want to step to any element in one step.

I thought of deriving a subclass (ExtIterLabelObject) of the LabelObject,
which lacks on loosing access on the private stuff of the LabelObject. 

The only way I see is defining a new ExtIterLabelObject class, which
inherits from the LightObject and replaces the given LabelObject
implementation. 

Since this is very ugly, I want to ask if there is a better way to extend
the functionality of the LineIterator, so that I can increase the iterator
by an arbitrary (valid) step.

Thanks for your help.




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/extending-label-object-s-line-iterator-cpp-question-tp7586769.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Mon Jan 12 08:36:19 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 12 Jan 2015 08:36:19 -0500
Subject: [ITK-users] itk Canny segmentation level set on 3d data
In-Reply-To: <1421048542766-35103.post@n7.nabble.com>
References: <1421048542766-35103.post@n7.nabble.com>
Message-ID: <CALzTN-QAv7sW1u1=hEtO_Qfi7p4VsS7SfyuYeAScbgvZVz1uyw@mail.gmail.com>

Hi reks,

The parameters will likely need tweaking.  To understand how the
change the parameters, look at the documentation for the filters and
the parameters and the intermediate images that are generated. The
documentation can be found in The Software Guide [1], the example code
that is used to generate the Software Guide [2], and the Doxygen for
classes [3].

As suggested in the Software Guide, you may want to pre-process your
input image also to remove noise.

HTH,
Matt

[1] http://itk.org/ITK/resources/software.html

[2] http://www.itk.org/Doxygen/html/Examples_2Segmentation_2CannySegmentationLevelSetImageFilter_8cxx-example.html

[3] http://www.itk.org/Doxygen/html/classitk_1_1CannySegmentationLevelSetImageFilter.html

On Mon, Jan 12, 2015 at 2:42 AM, reks <rekha.pyage at gmail.com> wrote:
> Hi all,
>
> I am trying to make use of itkCannySegmentationLevelSet 2d example on 3d
> data. Here I am giving the output of thresholdsegmentationlevelset as one of
> the input to the filter and input image as the feature input. I am giving
> The parameters to this filter as given in 2d example( canny threshold=7.0,
> CannyVariance= 0.1 ,AdvectionScaling=10.0,IsoSurfaceValue=
> 127.5,NumberOfIterations= 15) but I am not getting the expected output. I am
> getting thresholdsegmentationlevelset output as it is as the cannylevelset
> output. do I have to change the parameters to this filter ? I dont know
> where I am going wrong. please do help me..
>
> any help will be appreciated.
> thanks in advance.
>
> reks
>
>
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/itk-Canny-segmentation-level-set-on-3d-data-tp35103.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 matt.mccormick at kitware.com  Mon Jan 12 08:44:14 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 12 Jan 2015 08:44:14 -0500
Subject: [ITK-users] extending label object's line iterator / cpp
	question
In-Reply-To: <1421055389237-7586769.post@n2.nabble.com>
References: <1421055389237-7586769.post@n2.nabble.com>
Message-ID: <CALzTN-Tmu5hK5Cf=07+0-abE6JR9SCw84atzjn6s9KJ78CxiJw@mail.gmail.com>

Hi Mathew,

If some required members are private that need to be protected for
your extension, we can do that.  Please submit a patch with the
changes required [1].

Thanks,
Matt

[1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html

On Mon, Jan 12, 2015 at 4:36 AM, mathew
<mathias.richter at informatik.uni-luebeck.de> wrote:
> Dear ITK users,
>
> Currently, I am working with the LabelObject class and its iterators (i.e.
> the line iterator).
> I have noticed that I can only advance the iterator by one. Unfortunately I
> want to step to any element in one step.
>
> I thought of deriving a subclass (ExtIterLabelObject) of the LabelObject,
> which lacks on loosing access on the private stuff of the LabelObject.
>
> The only way I see is defining a new ExtIterLabelObject class, which
> inherits from the LightObject and replaces the given LabelObject
> implementation.
>
> Since this is very ugly, I want to ask if there is a better way to extend
> the functionality of the LineIterator, so that I can increase the iterator
> by an arbitrary (valid) step.
>
> Thanks for your help.
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/extending-label-object-s-line-iterator-cpp-question-tp7586769.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

From yiyu.chou at gmail.com  Mon Jan 12 13:55:38 2015
From: yiyu.chou at gmail.com (Yi-Yu Chou)
Date: Mon, 12 Jan 2015 13:55:38 -0500
Subject: [ITK-users] 2 parameters registration
Message-ID: <CADxeGzcVAzLfSvixA+HugpZb06EC32o1dSNmyv_Ti+joNq2++w@mail.gmail.com>

Dear ITK experts,

I would like to implement a 2 parameters (one pitch rotation + one global
scaling) 3D image registration with ITK.

It is highly appreciated if you could shed some light on this matter.
Thanks in advance !!

Yi-Yu
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From matt.mccormick at kitware.com  Mon Jan 12 17:46:57 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 12 Jan 2015 17:46:57 -0500
Subject: [ITK-users] 2 parameters registration
In-Reply-To: <CADxeGzcVAzLfSvixA+HugpZb06EC32o1dSNmyv_Ti+joNq2++w@mail.gmail.com>
References: <CADxeGzcVAzLfSvixA+HugpZb06EC32o1dSNmyv_Ti+joNq2++w@mail.gmail.com>
Message-ID: <CALzTN-TYO6tcQv+2UC1ct=TYQApwUWG6yWeMpWQ-opPpS+QoyA@mail.gmail.com>

Hi Yi-Yu,

You may want to use a transform like the Similarity3DTransform [1] and
set the Weights on the Optimizer appropriately [2] to hold parameters
that should be fixed constant.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1Similarity3DTransform.html

[2] http://www.itk.org/Doxygen/html/classitk_1_1ObjectToObjectOptimizerBaseTemplate.html

On Mon, Jan 12, 2015 at 1:55 PM, Yi-Yu Chou <yiyu.chou at gmail.com> wrote:
> Dear ITK experts,
>
> I would like to implement a 2 parameters (one pitch rotation + one global
> scaling) 3D image registration with ITK.
>
> It is highly appreciated if you could shed some light on this matter.
> Thanks in advance !!
>
> Yi-Yu
>
>
>
> _____________________________________
> 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  Wed Jan 14 10:50:20 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 14 Jan 2015 10:50:20 -0500
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-R+uTMDeyTjZiSf0hb5rruo8gOuybEFVK2nWyzPOSc=Ag@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/ctg03o79vsd0irnhpugquuatfoc


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/events/cidukboj4bn3k2ndetr1rqdk3a0


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From emily-hammond at uiowa.edu  Wed Jan 14 11:55:22 2015
From: emily-hammond at uiowa.edu (Hammond, Emily M)
Date: Wed, 14 Jan 2015 16:55:22 +0000
Subject: [ITK-users] concept checking error - RegistrationMethodv4
Message-ID: <2609C492EC89AB4CAAD3647B8D1A43CC2F173BD7@ITSNT437.iowa.uiowa.edu>

Hello,

I am working with very large images and would like to use a short pixel type for my fixed and moving images within the ImageRegistrationMethodv4; however, my code does not build until a float pixel type is used. Here is a snippet of my code (looks pretty standard):

const unsigned int Dimension = 3;
typedef short PixelType;

typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;

typedef itk::MattesMutualInformationImageToImageMetricv4< FixedImageType, MovingImageType > MetricType;
typedef itk::ImageRegistrationMethodv4< FixedImageType, MovingImageType, TransformType > RegistrationType;

RegistrationType::Pointer registration = RegistrationType::New();
MetricType::Pointer metric = MetricType::New();

At this point in the code, the following error is thrown (not seen if using float pixel type):
error C2440: 'initializing' : cannot convert from 'itk::Concept::Detail::UniqueType_bool<__formal>' to 'itk::Concept::Detail::UniqueType_bool<__formal>'

Can anyone give me some insight into this problem? From previous experience I know that short pixel types work with the metrics and registration method from the previous version. Does version 4 not have these capabilities?

Thanks!
Emily Hammond
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From blowekamp at mail.nih.gov  Wed Jan 14 12:57:10 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 14 Jan 2015 12:57:10 -0500
Subject: [ITK-users] concept checking error - RegistrationMethodv4
In-Reply-To: <2609C492EC89AB4CAAD3647B8D1A43CC2F173BD7@ITSNT437.iowa.uiowa.edu>
References: <2609C492EC89AB4CAAD3647B8D1A43CC2F173BD7@ITSNT437.iowa.uiowa.edu>
Message-ID: <804E5EFC-A383-471A-ABD2-6A51E3016E81@mail.nih.gov>

Hello,

The current ITKv4 registration frame work is limited to real type (float/double). I believe it could be changed with some work, I think much of the reasoning for this requirement has to do with the way the multi-scale and gradient magnitude are implemented.

If you image is large, perhaps you should reduce the resolution before performing registration?

Brad

On Jan 14, 2015, at 11:55 AM, Hammond, Emily M <emily-hammond at uiowa.edu> wrote:

> Hello,
> 
> I am working with very large images and would like to use a short pixel type for my fixed and moving images within the ImageRegistrationMethodv4; however, my code does not build until a float pixel type is used. Here is a snippet of my code (looks pretty standard):
> 
> const unsigned int Dimension = 3;
> typedef short PixelType;
> 
> typedef itk::Image< PixelType, Dimension > FixedImageType;
> typedef itk::Image< PixelType, Dimension > MovingImageType;
> 
> typedef itk::MattesMutualInformationImageToImageMetricv4< FixedImageType, MovingImageType > MetricType;
> typedef itk::ImageRegistrationMethodv4< FixedImageType, MovingImageType, TransformType > RegistrationType;
> 
> RegistrationType::Pointer registration = RegistrationType::New();
> MetricType::Pointer metric = MetricType::New();
> 
> At this point in the code, the following error is thrown (not seen if using float pixel type):
> error C2440: 'initializing' : cannot convert from 'itk::Concept::Detail::UniqueType_bool<__formal>' to 'itk::Concept::Detail::UniqueType_bool<__formal>'
> 
> Can anyone give me some insight into this problem? From previous experience I know that short pixel types work with the metrics and registration method from the previous version. Does version 4 not have these capabilities?
> 
> Thanks!
> Emily Hammond
> _____________________________________
> 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 franciscolopezdelafranca at gmail.com  Wed Jan 14 17:05:19 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Wed, 14 Jan 2015 23:05:19 +0100
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
Message-ID: <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>

Hi again.
I fixed all the errors and got my library, now ready to be tested.
It contains an encapsulation, on the one hand, of the class
itkBinaryImageToShapeLabelMapFilter in order to get image shape descriptors
of a 3D binary image, and on the other hand, the same for the class
itkScalarImageToTextureFeaturesFilter to get image texture features of a 3D
scalar image.

I pass as input image to both classes a binary 3D Nifti image (150x150x150)
containing a cylinder where the inside voxels are 255 and the outside
voxels are 0.

As for the shape issue, it's very strange to me that the call to
GetNumberOfLabelObjects on a itk::LabelMap object returns a value of 0. The
main code is as follows:

binaryImageToShapeLabelMapFilter->SetInput(_input);
binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
binaryImageToShapeLabelMapFilter->Update();

LabelMapType::Pointer labelMap =
binaryImageToShapeLabelMapFilter->GetOutput();

int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();


And, as for the texture features, the result of the filter does not seem to
be very logic:

Energy = 1
Entropy = 0
Correlation = 1
Local Homogeneity = 0
Inertia = 0
Cluster Shade = 0
Cluster Prominence = 0

I've also tested this with a scalar 3D Nifti image and the results are the
same.

And the question is: What kind of image do I have to pass to the filters so
that the code would return a more logic expected answer?

Thank you very much in advance.
My best regars.
/Francisco

2015-01-10 22:38 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Francisco,
>
> Nice to hear about the progress!
>
> You will need to link your library to the ITK libraries:
>
>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
>
> HTH,
> Matt
>
> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca <
> franciscolopezdelafranca at gmail.com> wrote:
>
>> Thanks to your previous answer the problem was solved, but another one
>> has come out. It occurs when linking to create the library. It gives an
>> undefined reference to itk::ExceptionObject::ExceptionObject... as you can
>> see below.
>> What it is strange to me is that before including explicit template
>> instantiation, I created the library without errors, and now that I include
>> that, I get this error.
>> I'll appreciate very much any help.
>>
>> Linking CXX shared library libTFM_Features.dll
>>
>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>>
>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>> 1ERKSsjS2_S2_]+0x35): undefined reference to
>> `itk::ExceptionObject::ExceptionObj
>> ect(std::string const&, unsigned int, std::string const&, std::string
>> const&)'
>>
>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>>
>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
>> itk::MemoryAllocationEr
>> ror'
>>
>> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
>> gw32/bin/ld.exe:
>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
>> d reloc address 0x40 in section
>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
>> collect2.exe: error: ld returned 1 exit status
>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
>> 'SRC/libTFM_Fe
>> atures.dll' failed
>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
>> CMakeFiles\Makefile2:77: recipe for target
>> 'SRC/CMakeFiles/TFM_Features.dir/all'
>>  failed
>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
>> Makefile:74: recipe for target 'all' failed
>> mingw32-make: *** [all] Error 2
>>
>>
>> 2015-01-09 21:02 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>>> Hi Francisco,
>>>
>>> In order for the templates to be available in the library, they must
>>> be explicitly instantiated [1].
>>>
>>> HTH,
>>> Matt
>>>
>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
>>>
>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
>>> <franciscolopezdelafranca at gmail.com> wrote:
>>> > Hi.
>>> > I' like to create a library containing, for example, one template
>>> class with
>>> > a number of methods.
>>> > I've programmed a simple example and the compilation and generation of
>>> the
>>> > library goes fine. I use the cmake "add_library" command for
>>> generating the
>>> > library.
>>> >
>>> > The problem arises at the moment of testing the library. I get an
>>> undefined
>>> > reference for every method in the template class.
>>> >
>>> > I've downloaded a tool to look in the contents (functions) of dynamic
>>> > libraries, and there is no function in the library. If I add another
>>> class
>>> > (not a template class), then, this tool shows me only the functions in
>>> this
>>> > latter class.
>>> >
>>> > Has anyone ever come across with this problem?
>>> >
>>> > Thanks a lot in advance.
>>> > Regards
>>> > /Francisco
>>> >
>>> > _____________________________________
>>> > 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 nhadar at surgicaltheater.net  Wed Jan 14 17:40:48 2015
From: nhadar at surgicaltheater.net (Nissim Hadar)
Date: Wed, 14 Jan 2015 15:40:48 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
Message-ID: <1421275248945-35113.post@n7.nabble.com>

Hello,

I am trying to use the /HessianToObjectnessMeasureImageFilter/ to segment
brain tissue.  As this code is part of a larger system, I am providing the
image as an array of /shorts/.  Other segmentation methods, such as Otsu,
flag the segmentation, so the result is a binary image (e.g. 255 and 0).  I
do not understand the results I am getting with the Hessian method.

My code is as follows:

*void HessianSegmentation(
	// Input data
	short			*inputVoxels,	const int		dim,
	const double    xSpacing,		const double	ySpacing,	const double	zSpacing,

	// Output data
	short			*outputVoxels
) {
	try
	{
		const   unsigned int Dimension = 3;

		typedef double                              InternalPixelType;
		typedef Image<InternalPixelType, Dimension> InternalImageType;
		
		typedef short                               VoxelPixelType;
		typedef Image<VoxelPixelType, Dimension>    VoxelImageType;

		// Image Importer - converts linear array of pixels in short format to an
Image
		//
		typedef ImportImageFilter<VoxelPixelType, Dimension> ImportFilterType;
		ImportFilterType::Pointer importFilter = ImportFilterType::New();

		ImportFilterType::IndexType start;
		start.Fill(0);
	
		ImportFilterType::SizeType size;
		size[0] = size[1] = size[2] = dim;
	
		ImportFilterType::RegionType region;
		region.SetIndex(start);
		region.SetSize (size );
		importFilter->SetRegion(region);

		const SpacePrecisionType origin[Dimension] = {0, 0, 0};
		importFilter->SetOrigin(origin);

		const SpacePrecisionType spacing[Dimension] = {xSpacing, ySpacing,
zSpacing};
		importFilter->SetSpacing(spacing);

		importFilter->SetImportPointer(inputVoxels, dim * dim * dim, false);

		// Caster from short to float (input is shorts, detection needs floats)
		typedef CastImageFilter<VoxelImageType, InternalImageType>
CastFilterTypeVoxelToInternal;		
		CastFilterTypeVoxelToInternal::Pointer casterVoxelToInternal =
CastFilterTypeVoxelToInternal::New();

		casterVoxelToInternal->	SetInput(importFilter->GetOutput());

		// Set up Hessian filter
		//
		typedef SymmetricSecondRankTensor<double, Dimension> HessianPixelType;
		typedef Image<HessianPixelType, Dimension>           HessianImageType;
		typedef HessianToObjectnessMeasureImageFilter<HessianImageType,
InternalImageType> ObjectnessFilterType;
		ObjectnessFilterType::Pointer objectnessFilter =
ObjectnessFilterType::New();
		
		objectnessFilter->SetBrightObject(true);
		objectnessFilter->SetScaleObjectnessMeasure(false);
		objectnessFilter->SetAlpha(0.5);
		objectnessFilter->SetBeta (0.5);
		objectnessFilter->SetGamma(5.0);

		typedef MultiScaleHessianBasedMeasureImageFilter<InternalImageType,
HessianImageType, InternalImageType> MultiScaleEnhancementFilterType;
		MultiScaleEnhancementFilterType::Pointer multiScaleEnhancementFilter =
MultiScaleEnhancementFilterType::New();
		multiScaleEnhancementFilter->SetHessianToMeasureFilter(objectnessFilter);
		multiScaleEnhancementFilter->SetSigmaStepMethodToLogarithmic();

		multiScaleEnhancementFilter->SetSigmaMinimum(0.2);
		multiScaleEnhancementFilter->SetSigmaMaximum(2.0);
		multiScaleEnhancementFilter->SetNumberOfSigmaSteps(10);

		multiScaleEnhancementFilter->SetInput(casterVoxelToInternal->GetOutput());

		// Setup rescaler
		//
		typedef RescaleIntensityImageFilter<InternalImageType, InternalImageType>
RescaleFilterType;
		RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
		rescaleFilter->SetOutputMinimum(0);
		rescaleFilter->SetOutputMaximum(2000);

		rescaleFilter->	SetInput(multiScaleEnhancementFilter->GetOutput());

		// Cast back from  float to short
		typedef CastImageFilter<InternalImageType, VoxelImageType>
CastFilterTypeInternalToVoxel;		
		CastFilterTypeInternalToVoxel::Pointer casterInternalToVoxel =
CastFilterTypeInternalToVoxel::New();

		casterInternalToVoxel->SetInput(rescaleFilter->GetOutput());
		
		// Run pipeline
		//
		casterInternalToVoxel->Update();

		// Extract results
		//
		VoxelImageType *outputImage = casterInternalToVoxel->GetOutput();
		InternalImageType::RegionType outputRegion =
outputImage->GetBufferedRegion();

		typedef itk::ImageRegionConstIterator<VoxelImageType> IteratorType;
		IteratorType it(outputImage, outputRegion);

		VoxelPixelType *ptr = outputVoxels;

		it.GoToBegin();
		while(!it.IsAtEnd())
		{
			*ptr = it.Get();
			++it;
			++ptr;
		}
	}
	catch (const std::exception& ex)
	{
		std::string s = ex.what();
		bool error = true;			// put breakpoint here to debug
	}
}*

The input data is a block of voxels from CT/MRI images.

Thank you very much
Cheers



--
View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Wed Jan 14 20:25:46 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 14 Jan 2015 20:25:46 -0500
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421275248945-35113.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
Message-ID: <CALzTN-RHhZdkD-UF8JMgQ5Gqtv2YsQY8BHVdwv-h5fFn2A-tGA@mail.gmail.com>

Hi Nissim,

It is unclear from your message what you do not understand about the results.

More information on the filters can be found in Doxygen [1] and The
ITK Software Guide [2].

HTH,
Matt

[1]  http://www.itk.org/Doxygen/html/classitk_1_1HessianToObjectnessMeasureImageFilter.html

[2]  http://itk.org/ItkSoftwareGuide.pdf

On Wed, Jan 14, 2015 at 5:40 PM, Nissim Hadar
<nhadar at surgicaltheater.net> wrote:
> Hello,
>
> I am trying to use the /HessianToObjectnessMeasureImageFilter/ to segment
> brain tissue.  As this code is part of a larger system, I am providing the
> image as an array of /shorts/.  Other segmentation methods, such as Otsu,
> flag the segmentation, so the result is a binary image (e.g. 255 and 0).  I
> do not understand the results I am getting with the Hessian method.
>
> My code is as follows:
>
> *void HessianSegmentation(
>         // Input data
>         short                   *inputVoxels,   const int               dim,
>         const double    xSpacing,               const double    ySpacing,       const double    zSpacing,
>
>         // Output data
>         short                   *outputVoxels
> ) {
>         try
>         {
>                 const   unsigned int Dimension = 3;
>
>                 typedef double                              InternalPixelType;
>                 typedef Image<InternalPixelType, Dimension> InternalImageType;
>
>                 typedef short                               VoxelPixelType;
>                 typedef Image<VoxelPixelType, Dimension>    VoxelImageType;
>
>                 // Image Importer - converts linear array of pixels in short format to an
> Image
>                 //
>                 typedef ImportImageFilter<VoxelPixelType, Dimension> ImportFilterType;
>                 ImportFilterType::Pointer importFilter = ImportFilterType::New();
>
>                 ImportFilterType::IndexType start;
>                 start.Fill(0);
>
>                 ImportFilterType::SizeType size;
>                 size[0] = size[1] = size[2] = dim;
>
>                 ImportFilterType::RegionType region;
>                 region.SetIndex(start);
>                 region.SetSize (size );
>                 importFilter->SetRegion(region);
>
>                 const SpacePrecisionType origin[Dimension] = {0, 0, 0};
>                 importFilter->SetOrigin(origin);
>
>                 const SpacePrecisionType spacing[Dimension] = {xSpacing, ySpacing,
> zSpacing};
>                 importFilter->SetSpacing(spacing);
>
>                 importFilter->SetImportPointer(inputVoxels, dim * dim * dim, false);
>
>                 // Caster from short to float (input is shorts, detection needs floats)
>                 typedef CastImageFilter<VoxelImageType, InternalImageType>
> CastFilterTypeVoxelToInternal;
>                 CastFilterTypeVoxelToInternal::Pointer casterVoxelToInternal =
> CastFilterTypeVoxelToInternal::New();
>
>                 casterVoxelToInternal-> SetInput(importFilter->GetOutput());
>
>                 // Set up Hessian filter
>                 //
>                 typedef SymmetricSecondRankTensor<double, Dimension> HessianPixelType;
>                 typedef Image<HessianPixelType, Dimension>           HessianImageType;
>                 typedef HessianToObjectnessMeasureImageFilter<HessianImageType,
> InternalImageType> ObjectnessFilterType;
>                 ObjectnessFilterType::Pointer objectnessFilter =
> ObjectnessFilterType::New();
>
>                 objectnessFilter->SetBrightObject(true);
>                 objectnessFilter->SetScaleObjectnessMeasure(false);
>                 objectnessFilter->SetAlpha(0.5);
>                 objectnessFilter->SetBeta (0.5);
>                 objectnessFilter->SetGamma(5.0);
>
>                 typedef MultiScaleHessianBasedMeasureImageFilter<InternalImageType,
> HessianImageType, InternalImageType> MultiScaleEnhancementFilterType;
>                 MultiScaleEnhancementFilterType::Pointer multiScaleEnhancementFilter =
> MultiScaleEnhancementFilterType::New();
>                 multiScaleEnhancementFilter->SetHessianToMeasureFilter(objectnessFilter);
>                 multiScaleEnhancementFilter->SetSigmaStepMethodToLogarithmic();
>
>                 multiScaleEnhancementFilter->SetSigmaMinimum(0.2);
>                 multiScaleEnhancementFilter->SetSigmaMaximum(2.0);
>                 multiScaleEnhancementFilter->SetNumberOfSigmaSteps(10);
>
>                 multiScaleEnhancementFilter->SetInput(casterVoxelToInternal->GetOutput());
>
>                 // Setup rescaler
>                 //
>                 typedef RescaleIntensityImageFilter<InternalImageType, InternalImageType>
> RescaleFilterType;
>                 RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
>                 rescaleFilter->SetOutputMinimum(0);
>                 rescaleFilter->SetOutputMaximum(2000);
>
>                 rescaleFilter-> SetInput(multiScaleEnhancementFilter->GetOutput());
>
>                 // Cast back from  float to short
>                 typedef CastImageFilter<InternalImageType, VoxelImageType>
> CastFilterTypeInternalToVoxel;
>                 CastFilterTypeInternalToVoxel::Pointer casterInternalToVoxel =
> CastFilterTypeInternalToVoxel::New();
>
>                 casterInternalToVoxel->SetInput(rescaleFilter->GetOutput());
>
>                 // Run pipeline
>                 //
>                 casterInternalToVoxel->Update();
>
>                 // Extract results
>                 //
>                 VoxelImageType *outputImage = casterInternalToVoxel->GetOutput();
>                 InternalImageType::RegionType outputRegion =
> outputImage->GetBufferedRegion();
>
>                 typedef itk::ImageRegionConstIterator<VoxelImageType> IteratorType;
>                 IteratorType it(outputImage, outputRegion);
>
>                 VoxelPixelType *ptr = outputVoxels;
>
>                 it.GoToBegin();
>                 while(!it.IsAtEnd())
>                 {
>                         *ptr = it.Get();
>                         ++it;
>                         ++ptr;
>                 }
>         }
>         catch (const std::exception& ex)
>         {
>                 std::string s = ex.what();
>                 bool error = true;                      // put breakpoint here to debug
>         }
> }*
>
> The input data is a block of voxels from CT/MRI images.
>
> Thank you very much
> Cheers
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113.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 matt.mccormick at kitware.com  Wed Jan 14 20:30:21 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 14 Jan 2015 20:30:21 -0500
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
Message-ID: <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>

Hi Francisco,

Great to hear about the progress!

The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
which should have an integer pixel type, like unsigned char or
unsigned short.  It is important to set the BackgroundValue and
ForegroundValue [1] to get this filter to work correctly.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html

On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
<franciscolopezdelafranca at gmail.com> wrote:
> Hi again.
> I fixed all the errors and got my library, now ready to be tested.
> It contains an encapsulation, on the one hand, of the class
> itkBinaryImageToShapeLabelMapFilter in order to get image shape descriptors
> of a 3D binary image, and on the other hand, the same for the class
> itkScalarImageToTextureFeaturesFilter to get image texture features of a 3D
> scalar image.
>
> I pass as input image to both classes a binary 3D Nifti image (150x150x150)
> containing a cylinder where the inside voxels are 255 and the outside voxels
> are 0.
>
> As for the shape issue, it's very strange to me that the call to
> GetNumberOfLabelObjects on a itk::LabelMap object returns a value of 0. The
> main code is as follows:
>
> binaryImageToShapeLabelMapFilter->SetInput(_input);
> binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
> binaryImageToShapeLabelMapFilter->Update();
>
> LabelMapType::Pointer labelMap =
> binaryImageToShapeLabelMapFilter->GetOutput();
>
> int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
>
>
> And, as for the texture features, the result of the filter does not seem to
> be very logic:
>
> Energy = 1
> Entropy = 0
> Correlation = 1
> Local Homogeneity = 0
> Inertia = 0
> Cluster Shade = 0
> Cluster Prominence = 0
>
> I've also tested this with a scalar 3D Nifti image and the results are the
> same.
>
> And the question is: What kind of image do I have to pass to the filters so
> that the code would return a more logic expected answer?
>
> Thank you very much in advance.
> My best regars.
> /Francisco
>
> 2015-01-10 22:38 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hi Francisco,
>>
>> Nice to hear about the progress!
>>
>> You will need to link your library to the ITK libraries:
>>
>>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
>>
>> HTH,
>> Matt
>>
>> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
>> <franciscolopezdelafranca at gmail.com> wrote:
>>>
>>> Thanks to your previous answer the problem was solved, but another one
>>> has come out. It occurs when linking to create the library. It gives an
>>> undefined reference to itk::ExceptionObject::ExceptionObject... as you can
>>> see below.
>>> What it is strange to me is that before including explicit template
>>> instantiation, I created the library without errors, and now that I include
>>> that, I get this error.
>>> I'll appreciate very much any help.
>>>
>>> Linking CXX shared library libTFM_Features.dll
>>>
>>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>>>
>>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>>> 1ERKSsjS2_S2_]+0x35): undefined reference to
>>> `itk::ExceptionObject::ExceptionObj
>>> ect(std::string const&, unsigned int, std::string const&, std::string
>>> const&)'
>>>
>>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>>>
>>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
>>> itk::MemoryAllocationEr
>>> ror'
>>>
>>> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
>>> gw32/bin/ld.exe:
>>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
>>> d reloc address 0x40 in section
>>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
>>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
>>> collect2.exe: error: ld returned 1 exit status
>>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
>>> 'SRC/libTFM_Fe
>>> atures.dll' failed
>>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
>>> CMakeFiles\Makefile2:77: recipe for target
>>> 'SRC/CMakeFiles/TFM_Features.dir/all'
>>>  failed
>>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
>>> Makefile:74: recipe for target 'all' failed
>>> mingw32-make: *** [all] Error 2
>>>
>>>
>>> 2015-01-09 21:02 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>>>
>>>> Hi Francisco,
>>>>
>>>> In order for the templates to be available in the library, they must
>>>> be explicitly instantiated [1].
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
>>>>
>>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
>>>> <franciscolopezdelafranca at gmail.com> wrote:
>>>> > Hi.
>>>> > I' like to create a library containing, for example, one template
>>>> > class with
>>>> > a number of methods.
>>>> > I've programmed a simple example and the compilation and generation of
>>>> > the
>>>> > library goes fine. I use the cmake "add_library" command for
>>>> > generating the
>>>> > library.
>>>> >
>>>> > The problem arises at the moment of testing the library. I get an
>>>> > undefined
>>>> > reference for every method in the template class.
>>>> >
>>>> > I've downloaded a tool to look in the contents (functions) of dynamic
>>>> > libraries, and there is no function in the library. If I add another
>>>> > class
>>>> > (not a template class), then, this tool shows me only the functions in
>>>> > this
>>>> > latter class.
>>>> >
>>>> > Has anyone ever come across with this problem?
>>>> >
>>>> > Thanks a lot in advance.
>>>> > Regards
>>>> > /Francisco
>>>> >
>>>> > _____________________________________
>>>> > 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 franciscolopezdelafranca at gmail.com  Thu Jan 15 01:32:43 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Thu, 15 Jan 2015 07:32:43 +0100
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
 <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
Message-ID: <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>

Hi Matt,
Thanks a lot for your answers. I'll try this afternoon what you suggest
regarding the shape filter, but what do you think about my results as for
the texture filter?
Regards.
/Francisco

2015-01-15 2:30 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Francisco,
>
> Great to hear about the progress!
>
> The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
> which should have an integer pixel type, like unsigned char or
> unsigned short.  It is important to set the BackgroundValue and
> ForegroundValue [1] to get this filter to work correctly.
>
> HTH,
> Matt
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
>
> On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
> <franciscolopezdelafranca at gmail.com> wrote:
> > Hi again.
> > I fixed all the errors and got my library, now ready to be tested.
> > It contains an encapsulation, on the one hand, of the class
> > itkBinaryImageToShapeLabelMapFilter in order to get image shape
> descriptors
> > of a 3D binary image, and on the other hand, the same for the class
> > itkScalarImageToTextureFeaturesFilter to get image texture features of a
> 3D
> > scalar image.
> >
> > I pass as input image to both classes a binary 3D Nifti image
> (150x150x150)
> > containing a cylinder where the inside voxels are 255 and the outside
> voxels
> > are 0.
> >
> > As for the shape issue, it's very strange to me that the call to
> > GetNumberOfLabelObjects on a itk::LabelMap object returns a value of 0.
> The
> > main code is as follows:
> >
> > binaryImageToShapeLabelMapFilter->SetInput(_input);
> > binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
> > binaryImageToShapeLabelMapFilter->Update();
> >
> > LabelMapType::Pointer labelMap =
> > binaryImageToShapeLabelMapFilter->GetOutput();
> >
> > int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
> >
> >
> > And, as for the texture features, the result of the filter does not seem
> to
> > be very logic:
> >
> > Energy = 1
> > Entropy = 0
> > Correlation = 1
> > Local Homogeneity = 0
> > Inertia = 0
> > Cluster Shade = 0
> > Cluster Prominence = 0
> >
> > I've also tested this with a scalar 3D Nifti image and the results are
> the
> > same.
> >
> > And the question is: What kind of image do I have to pass to the filters
> so
> > that the code would return a more logic expected answer?
> >
> > Thank you very much in advance.
> > My best regars.
> > /Francisco
> >
> > 2015-01-10 22:38 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> >>
> >> Hi Francisco,
> >>
> >> Nice to hear about the progress!
> >>
> >> You will need to link your library to the ITK libraries:
> >>
> >>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
> >>
> >> HTH,
> >> Matt
> >>
> >> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
> >> <franciscolopezdelafranca at gmail.com> wrote:
> >>>
> >>> Thanks to your previous answer the problem was solved, but another one
> >>> has come out. It occurs when linking to create the library. It gives an
> >>> undefined reference to itk::ExceptionObject::ExceptionObject... as you
> can
> >>> see below.
> >>> What it is strange to me is that before including explicit template
> >>> instantiation, I created the library without errors, and now that I
> include
> >>> that, I get this error.
> >>> I'll appreciate very much any help.
> >>>
> >>> Linking CXX shared library libTFM_Features.dll
> >>>
> >>>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
> >>>
> >>>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> >>> 1ERKSsjS2_S2_]+0x35): undefined reference to
> >>> `itk::ExceptionObject::ExceptionObj
> >>> ect(std::string const&, unsigned int, std::string const&, std::string
> >>> const&)'
> >>>
> >>>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
> >>>
> >>>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> >>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
> >>> itk::MemoryAllocationEr
> >>> ror'
> >>>
> >>>
> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
> >>> gw32/bin/ld.exe:
> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
> >>> d reloc address 0x40 in section
> >>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
> >>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
> >>> collect2.exe: error: ld returned 1 exit status
> >>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
> >>> 'SRC/libTFM_Fe
> >>> atures.dll' failed
> >>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
> >>> CMakeFiles\Makefile2:77: recipe for target
> >>> 'SRC/CMakeFiles/TFM_Features.dir/all'
> >>>  failed
> >>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
> >>> Makefile:74: recipe for target 'all' failed
> >>> mingw32-make: *** [all] Error 2
> >>>
> >>>
> >>> 2015-01-09 21:02 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com
> >:
> >>>>
> >>>> Hi Francisco,
> >>>>
> >>>> In order for the templates to be available in the library, they must
> >>>> be explicitly instantiated [1].
> >>>>
> >>>> HTH,
> >>>> Matt
> >>>>
> >>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
> >>>>
> >>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
> >>>> <franciscolopezdelafranca at gmail.com> wrote:
> >>>> > Hi.
> >>>> > I' like to create a library containing, for example, one template
> >>>> > class with
> >>>> > a number of methods.
> >>>> > I've programmed a simple example and the compilation and generation
> of
> >>>> > the
> >>>> > library goes fine. I use the cmake "add_library" command for
> >>>> > generating the
> >>>> > library.
> >>>> >
> >>>> > The problem arises at the moment of testing the library. I get an
> >>>> > undefined
> >>>> > reference for every method in the template class.
> >>>> >
> >>>> > I've downloaded a tool to look in the contents (functions) of
> dynamic
> >>>> > libraries, and there is no function in the library. If I add another
> >>>> > class
> >>>> > (not a template class), then, this tool shows me only the functions
> in
> >>>> > this
> >>>> > latter class.
> >>>> >
> >>>> > Has anyone ever come across with this problem?
> >>>> >
> >>>> > Thanks a lot in advance.
> >>>> > Regards
> >>>> > /Francisco
> >>>> >
> >>>> > _____________________________________
> >>>> > 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 nhadar at surgicaltheater.net  Thu Jan 15 02:28:41 2015
From: nhadar at surgicaltheater.net (Nissim Hadar)
Date: Thu, 15 Jan 2015 00:28:41 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421275248945-35113.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
Message-ID: <1421306921950-35117.post@n7.nabble.com>

The array of shorts I supply is a block of raw DICOM data (with, or without
windowing).  The result is an array of similar size, containing a lot of
zeros, but the non-zero values seem to be quite random.  Does each short
represent a filtered voxel, or do the values have a specific meaning, like
they do in the Segmentation algorithms?  When I view the result as an image
it seems very noisy, even though there /is/ some resemblance to the blood
vessels.
I don't know if my understanding is wrong, my parameters are way off, or
there is a bug in the method....
The images I am using are MRI scans of brain aneurysms and the like.

Thanks



--
View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113p35117.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Thu Jan 15 10:07:58 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 15 Jan 2015 10:07:58 -0500
Subject: [ITK-users] SimpleITK | read a 3D image from a non DICOM file
	and write it as a series of DICOM slices
In-Reply-To: <FC4D270F-46B6-4935-8919-C38AFCF408C8@mail.nih.gov>
References: <CAKKNfuLN-pq7D097_CAq5vwe6yJBuSh=yeiOAgUbYNJu28Go-A@mail.gmail.com>
 <FC4D270F-46B6-4935-8919-C38AFCF408C8@mail.nih.gov>
Message-ID: <9B24E4DF-447C-42CA-A8EC-609DABA2B630@mail.nih.gov>

Hello,

I have just added an ImageSeriesWriter to SimpleITK:

http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageSeriesWriter.html

The hooks for getting the meta-data dictionary in the dicom series aren't quite there yet. But its a step closer. It's actually rather confusing how the tags are handled in the example you linked too, and I'm not sure what exactly needs to be done to create a "valid" dicom series.

Brad

On Dec 31, 2014, at 10:46 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:

> Hello,
> 
> Sorry for the slow reply. Earlier you linked to this nice example for reference:
> http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html
> 
> With SimpleITK I have done the following when I needed to write a series in Python:
> 
> for i in range(img.GetSize()[2]):
>     sitk.WriteImage(img[:,:,i],"test_{0:04}.tif".format(i))
> 
> 
> However it is not quite this simple for a DICOM series. The metadata tags need to be correct too. SimpleITK is not designed to be a full fledge interface to DICOM files. Other tools may be better for that. But this seems like a reasonable thing to do but it's not currently readily available in the SimpleITK interface. Perhaps after some discussion on the best way to do it it and be added.
> 
> 
> There are 3 main components to this example:
> 
> 1) MetaDataDictionary
> 
> In SimpleITK the MetaDataDictionary interface is only part of the Image class. Currently it provides a read only interface, with the GetMetaDataKeys(), and GetMetaData(key) methods[1]. This get method only returns the type of data in the dictionary converted to a string.
> 
> The required method would be Image::SetMetaData(key,value). The issue would be what types of value need to be supported. For this example only std::string is needed, perhaps others should be overloaded?
> 
> 2) NumericSeriesFileNameGenerator
> 
> This class only produces a "list" of file names. I think that many of the languages may have a more convenient way to do this. For example in Python:
> 
> [ "test_{0:04}.png".format(i) for i in range(img.GetSize()[2]) ]
> 
> So I don't think this is so important.
> 
> 3) SeriesWriter
> 
> What we just used above is different then the SeriesWriter, as special metadata is passed from the ImageSeriesWriter to the ImageIO [2]. Here is the JIRA issue for this task [3].
> 
> 
> So after these get done something like the following would do what you ask:
> 
> import SimpleITK as sitk
> 
> img = stik.ReadImage(argv[1])
> img.SetMetaData("008|0060", "MR") // Modality
> img.SetMetaData("008|0008", "DERIVED\\SECONDARY") // Image Type
> img.SetMetaData("008|0064", "DV") // Conversion Type
> sitk.WriteImage(img, [ "test_{0:04}.dcm".format(i) for i in range(img.GetSize()[2]) ])
> 
> Does that look like what you are looking for?
> 
> Brad
> 
> [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html#a3d6cb12a211352ee38da5405b9c75928
> [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx#L327-L368
> [3] https://issues.itk.org/jira/browse/SIMPLEITK-122
> 
> On Dec 29, 2014, at 2:48 PM, Matias Montroull <matimontg at gmail.com> wrote:
> 
>> Hi,
>> 
>> Is there an example for SimpleITK to read a 3D image from a non Dicom file such as mhd and then write it as a series of DICOM Slices?
>> 
>> I can do this with C++ but I haven't been able to figure out how to do it using simpleITK.
>> 
>> Thanks,
>> 
>> Matias.
>> _____________________________________
>> 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  Thu Jan 15 10:41:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 15 Jan 2015 10:41:24 -0500
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
 <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
 <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>
Message-ID: <CALzTN-QM5QK22uHV0PQT=jYEuPqPGCsxUucv1AjzjFAJNP5gvg@mail.gmail.com>

Hi Francisco,

There is definitely something wrong with the textures features.  It is
not possible to know what is going on without more details, though.

Matt

On Thu, Jan 15, 2015 at 1:32 AM, Francisco Lopez de la Franca
<franciscolopezdelafranca at gmail.com> wrote:
> Hi Matt,
> Thanks a lot for your answers. I'll try this afternoon what you suggest
> regarding the shape filter, but what do you think about my results as for
> the texture filter?
> Regards.
> /Francisco
>
> 2015-01-15 2:30 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hi Francisco,
>>
>> Great to hear about the progress!
>>
>> The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
>> which should have an integer pixel type, like unsigned char or
>> unsigned short.  It is important to set the BackgroundValue and
>> ForegroundValue [1] to get this filter to work correctly.
>>
>> HTH,
>> Matt
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
>>
>> On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
>> <franciscolopezdelafranca at gmail.com> wrote:
>> > Hi again.
>> > I fixed all the errors and got my library, now ready to be tested.
>> > It contains an encapsulation, on the one hand, of the class
>> > itkBinaryImageToShapeLabelMapFilter in order to get image shape
>> > descriptors
>> > of a 3D binary image, and on the other hand, the same for the class
>> > itkScalarImageToTextureFeaturesFilter to get image texture features of a
>> > 3D
>> > scalar image.
>> >
>> > I pass as input image to both classes a binary 3D Nifti image
>> > (150x150x150)
>> > containing a cylinder where the inside voxels are 255 and the outside
>> > voxels
>> > are 0.
>> >
>> > As for the shape issue, it's very strange to me that the call to
>> > GetNumberOfLabelObjects on a itk::LabelMap object returns a value of 0.
>> > The
>> > main code is as follows:
>> >
>> > binaryImageToShapeLabelMapFilter->SetInput(_input);
>> > binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
>> > binaryImageToShapeLabelMapFilter->Update();
>> >
>> > LabelMapType::Pointer labelMap =
>> > binaryImageToShapeLabelMapFilter->GetOutput();
>> >
>> > int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
>> >
>> >
>> > And, as for the texture features, the result of the filter does not seem
>> > to
>> > be very logic:
>> >
>> > Energy = 1
>> > Entropy = 0
>> > Correlation = 1
>> > Local Homogeneity = 0
>> > Inertia = 0
>> > Cluster Shade = 0
>> > Cluster Prominence = 0
>> >
>> > I've also tested this with a scalar 3D Nifti image and the results are
>> > the
>> > same.
>> >
>> > And the question is: What kind of image do I have to pass to the filters
>> > so
>> > that the code would return a more logic expected answer?
>> >
>> > Thank you very much in advance.
>> > My best regars.
>> > /Francisco
>> >
>> > 2015-01-10 22:38 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>> >>
>> >> Hi Francisco,
>> >>
>> >> Nice to hear about the progress!
>> >>
>> >> You will need to link your library to the ITK libraries:
>> >>
>> >>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
>> >>
>> >> HTH,
>> >> Matt
>> >>
>> >> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
>> >> <franciscolopezdelafranca at gmail.com> wrote:
>> >>>
>> >>> Thanks to your previous answer the problem was solved, but another one
>> >>> has come out. It occurs when linking to create the library. It gives
>> >>> an
>> >>> undefined reference to itk::ExceptionObject::ExceptionObject... as you
>> >>> can
>> >>> see below.
>> >>> What it is strange to me is that before including explicit template
>> >>> instantiation, I created the library without errors, and now that I
>> >>> include
>> >>> that, I get this error.
>> >>> I'll appreciate very much any help.
>> >>>
>> >>> Linking CXX shared library libTFM_Features.dll
>> >>>
>> >>>
>> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>> >>>
>> >>>
>> >>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>> >>> 1ERKSsjS2_S2_]+0x35): undefined reference to
>> >>> `itk::ExceptionObject::ExceptionObj
>> >>> ect(std::string const&, unsigned int, std::string const&, std::string
>> >>> const&)'
>> >>>
>> >>>
>> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>> >>>
>> >>>
>> >>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>> >>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
>> >>> itk::MemoryAllocationEr
>> >>> ror'
>> >>>
>> >>>
>> >>> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
>> >>> gw32/bin/ld.exe:
>> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
>> >>> d reloc address 0x40 in section
>> >>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
>> >>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
>> >>> collect2.exe: error: ld returned 1 exit status
>> >>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
>> >>> 'SRC/libTFM_Fe
>> >>> atures.dll' failed
>> >>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
>> >>> CMakeFiles\Makefile2:77: recipe for target
>> >>> 'SRC/CMakeFiles/TFM_Features.dir/all'
>> >>>  failed
>> >>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
>> >>> Makefile:74: recipe for target 'all' failed
>> >>> mingw32-make: *** [all] Error 2
>> >>>
>> >>>
>> >>> 2015-01-09 21:02 GMT+01:00 Matt McCormick
>> >>> <matt.mccormick at kitware.com>:
>> >>>>
>> >>>> Hi Francisco,
>> >>>>
>> >>>> In order for the templates to be available in the library, they must
>> >>>> be explicitly instantiated [1].
>> >>>>
>> >>>> HTH,
>> >>>> Matt
>> >>>>
>> >>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
>> >>>>
>> >>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
>> >>>> <franciscolopezdelafranca at gmail.com> wrote:
>> >>>> > Hi.
>> >>>> > I' like to create a library containing, for example, one template
>> >>>> > class with
>> >>>> > a number of methods.
>> >>>> > I've programmed a simple example and the compilation and generation
>> >>>> > of
>> >>>> > the
>> >>>> > library goes fine. I use the cmake "add_library" command for
>> >>>> > generating the
>> >>>> > library.
>> >>>> >
>> >>>> > The problem arises at the moment of testing the library. I get an
>> >>>> > undefined
>> >>>> > reference for every method in the template class.
>> >>>> >
>> >>>> > I've downloaded a tool to look in the contents (functions) of
>> >>>> > dynamic
>> >>>> > libraries, and there is no function in the library. If I add
>> >>>> > another
>> >>>> > class
>> >>>> > (not a template class), then, this tool shows me only the functions
>> >>>> > in
>> >>>> > this
>> >>>> > latter class.
>> >>>> >
>> >>>> > Has anyone ever come across with this problem?
>> >>>> >
>> >>>> > Thanks a lot in advance.
>> >>>> > Regards
>> >>>> > /Francisco
>> >>>> >
>> >>>> > _____________________________________
>> >>>> > 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 Jan 15 10:44:41 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 15 Jan 2015 10:44:41 -0500
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421306921950-35117.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421306921950-35117.post@n7.nabble.com>
Message-ID: <CALzTN-RGBBvxVQF7tzCkG_Ns+1skuNX7d9aa9QqSm8aj7=K9fA@mail.gmail.com>

Hi Nissim,

I would suggest reading in the DICOM data with an ITK reader as an ITK
Image and writing out the output in an ITK supported file format, at
least until the source of the problem is determined.  There are many
errors that can occurs when passing around blocks of bytes.

HTH,
Matt

On Thu, Jan 15, 2015 at 2:28 AM, Nissim Hadar
<nhadar at surgicaltheater.net> wrote:
> The array of shorts I supply is a block of raw DICOM data (with, or without
> windowing).  The result is an array of similar size, containing a lot of
> zeros, but the non-zero values seem to be quite random.  Does each short
> represent a filtered voxel, or do the values have a specific meaning, like
> they do in the Segmentation algorithms?  When I view the result as an image
> it seems very noisy, even though there /is/ some resemblance to the blood
> vessels.
> I don't know if my understanding is wrong, my parameters are way off, or
> there is a bug in the method....
> The images I am using are MRI scans of brain aneurysms and the like.
>
> Thanks
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113p35117.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 franciscolopezdelafranca at gmail.com  Thu Jan 15 12:26:30 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Thu, 15 Jan 2015 18:26:30 +0100
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CALzTN-QM5QK22uHV0PQT=jYEuPqPGCsxUucv1AjzjFAJNP5gvg@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
 <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
 <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>
 <CALzTN-QM5QK22uHV0PQT=jYEuPqPGCsxUucv1AjzjFAJNP5gvg@mail.gmail.com>
Message-ID: <CAJqi3EJQmKszSvabMXsLVtRS_ruc4u8J8OUM-RZLWtYVS6guWw@mail.gmail.com>

Hi Matt again.
You were fully right about setting the background/foreground values for the
filter. I

2015-01-15 16:41 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Francisco,
>
> There is definitely something wrong with the textures features.  It is
> not possible to know what is going on without more details, though.
>
> Matt
>
> On Thu, Jan 15, 2015 at 1:32 AM, Francisco Lopez de la Franca
> <franciscolopezdelafranca at gmail.com> wrote:
> > Hi Matt,
> > Thanks a lot for your answers. I'll try this afternoon what you suggest
> > regarding the shape filter, but what do you think about my results as for
> > the texture filter?
> > Regards.
> > /Francisco
> >
> > 2015-01-15 2:30 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> >>
> >> Hi Francisco,
> >>
> >> Great to hear about the progress!
> >>
> >> The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
> >> which should have an integer pixel type, like unsigned char or
> >> unsigned short.  It is important to set the BackgroundValue and
> >> ForegroundValue [1] to get this filter to work correctly.
> >>
> >> HTH,
> >> Matt
> >>
> >> [1]
> >>
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
> >>
> >> On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
> >> <franciscolopezdelafranca at gmail.com> wrote:
> >> > Hi again.
> >> > I fixed all the errors and got my library, now ready to be tested.
> >> > It contains an encapsulation, on the one hand, of the class
> >> > itkBinaryImageToShapeLabelMapFilter in order to get image shape
> >> > descriptors
> >> > of a 3D binary image, and on the other hand, the same for the class
> >> > itkScalarImageToTextureFeaturesFilter to get image texture features
> of a
> >> > 3D
> >> > scalar image.
> >> >
> >> > I pass as input image to both classes a binary 3D Nifti image
> >> > (150x150x150)
> >> > containing a cylinder where the inside voxels are 255 and the outside
> >> > voxels
> >> > are 0.
> >> >
> >> > As for the shape issue, it's very strange to me that the call to
> >> > GetNumberOfLabelObjects on a itk::LabelMap object returns a value of
> 0.
> >> > The
> >> > main code is as follows:
> >> >
> >> > binaryImageToShapeLabelMapFilter->SetInput(_input);
> >> > binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
> >> > binaryImageToShapeLabelMapFilter->Update();
> >> >
> >> > LabelMapType::Pointer labelMap =
> >> > binaryImageToShapeLabelMapFilter->GetOutput();
> >> >
> >> > int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
> >> >
> >> >
> >> > And, as for the texture features, the result of the filter does not
> seem
> >> > to
> >> > be very logic:
> >> >
> >> > Energy = 1
> >> > Entropy = 0
> >> > Correlation = 1
> >> > Local Homogeneity = 0
> >> > Inertia = 0
> >> > Cluster Shade = 0
> >> > Cluster Prominence = 0
> >> >
> >> > I've also tested this with a scalar 3D Nifti image and the results are
> >> > the
> >> > same.
> >> >
> >> > And the question is: What kind of image do I have to pass to the
> filters
> >> > so
> >> > that the code would return a more logic expected answer?
> >> >
> >> > Thank you very much in advance.
> >> > My best regars.
> >> > /Francisco
> >> >
> >> > 2015-01-10 22:38 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com
> >:
> >> >>
> >> >> Hi Francisco,
> >> >>
> >> >> Nice to hear about the progress!
> >> >>
> >> >> You will need to link your library to the ITK libraries:
> >> >>
> >> >>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
> >> >>
> >> >> HTH,
> >> >> Matt
> >> >>
> >> >> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
> >> >> <franciscolopezdelafranca at gmail.com> wrote:
> >> >>>
> >> >>> Thanks to your previous answer the problem was solved, but another
> one
> >> >>> has come out. It occurs when linking to create the library. It gives
> >> >>> an
> >> >>> undefined reference to itk::ExceptionObject::ExceptionObject... as
> you
> >> >>> can
> >> >>> see below.
> >> >>> What it is strange to me is that before including explicit template
> >> >>> instantiation, I created the library without errors, and now that I
> >> >>> include
> >> >>> that, I get this error.
> >> >>> I'll appreciate very much any help.
> >> >>>
> >> >>> Linking CXX shared library libTFM_Features.dll
> >> >>>
> >> >>>
> >> >>>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
> >> >>>
> >> >>>
> >> >>>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> >> >>> 1ERKSsjS2_S2_]+0x35): undefined reference to
> >> >>> `itk::ExceptionObject::ExceptionObj
> >> >>> ect(std::string const&, unsigned int, std::string const&,
> std::string
> >> >>> const&)'
> >> >>>
> >> >>>
> >> >>>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
> >> >>>
> >> >>>
> >> >>>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> >> >>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
> >> >>> itk::MemoryAllocationEr
> >> >>> ror'
> >> >>>
> >> >>>
> >> >>>
> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
> >> >>> gw32/bin/ld.exe:
> >> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
> >> >>> d reloc address 0x40 in section
> >> >>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
> >> >>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
> >> >>> collect2.exe: error: ld returned 1 exit status
> >> >>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
> >> >>> 'SRC/libTFM_Fe
> >> >>> atures.dll' failed
> >> >>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
> >> >>> CMakeFiles\Makefile2:77: recipe for target
> >> >>> 'SRC/CMakeFiles/TFM_Features.dir/all'
> >> >>>  failed
> >> >>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
> >> >>> Makefile:74: recipe for target 'all' failed
> >> >>> mingw32-make: *** [all] Error 2
> >> >>>
> >> >>>
> >> >>> 2015-01-09 21:02 GMT+01:00 Matt McCormick
> >> >>> <matt.mccormick at kitware.com>:
> >> >>>>
> >> >>>> Hi Francisco,
> >> >>>>
> >> >>>> In order for the templates to be available in the library, they
> must
> >> >>>> be explicitly instantiated [1].
> >> >>>>
> >> >>>> HTH,
> >> >>>> Matt
> >> >>>>
> >> >>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
> >> >>>>
> >> >>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
> >> >>>> <franciscolopezdelafranca at gmail.com> wrote:
> >> >>>> > Hi.
> >> >>>> > I' like to create a library containing, for example, one template
> >> >>>> > class with
> >> >>>> > a number of methods.
> >> >>>> > I've programmed a simple example and the compilation and
> generation
> >> >>>> > of
> >> >>>> > the
> >> >>>> > library goes fine. I use the cmake "add_library" command for
> >> >>>> > generating the
> >> >>>> > library.
> >> >>>> >
> >> >>>> > The problem arises at the moment of testing the library. I get an
> >> >>>> > undefined
> >> >>>> > reference for every method in the template class.
> >> >>>> >
> >> >>>> > I've downloaded a tool to look in the contents (functions) of
> >> >>>> > dynamic
> >> >>>> > libraries, and there is no function in the library. If I add
> >> >>>> > another
> >> >>>> > class
> >> >>>> > (not a template class), then, this tool shows me only the
> functions
> >> >>>> > in
> >> >>>> > this
> >> >>>> > latter class.
> >> >>>> >
> >> >>>> > Has anyone ever come across with this problem?
> >> >>>> >
> >> >>>> > Thanks a lot in advance.
> >> >>>> > Regards
> >> >>>> > /Francisco
> >> >>>> >
> >> >>>> > _____________________________________
> >> >>>> > 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 franciscolopezdelafranca at gmail.com  Thu Jan 15 12:34:22 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Thu, 15 Jan 2015 18:34:22 +0100
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CAJqi3EJQmKszSvabMXsLVtRS_ruc4u8J8OUM-RZLWtYVS6guWw@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
 <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
 <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>
 <CALzTN-QM5QK22uHV0PQT=jYEuPqPGCsxUucv1AjzjFAJNP5gvg@mail.gmail.com>
 <CAJqi3EJQmKszSvabMXsLVtRS_ruc4u8J8OUM-RZLWtYVS6guWw@mail.gmail.com>
Message-ID: <CAJqi3ELd6ogd4R3sAhRneRRoUnBfE=j3kbp6mTM-Lzn3VfexuA@mail.gmail.com>

Sorry, I might press the wrong key.
Hi Matt again.
You were fully right about setting the background/foreground values for the
filter. I wasn't using them because I followed the examples and there was
no reference to them. Now my shape related functions are working.

As for the textures, I attach my code so that anyone can see if i am doing
something wrong:

typedef itk::Statistics::ScalarImageToTextureFeaturesFilter<TInputImage>
TextureFilterType;
typedef typename TextureFilterType::Pointer TextureFilterPtr;
typedef typename TextureFilterType::FeatureValueVector
FeatureValueVectorType;

TextureFilterPtr textureFilter = TextureFilterType::New();
textureFilter->SetInput(_input);
textureFilter->Update();

FeatureValueVectorType* output = textureFilter->GetFeatureMeans();

cout << "Energy = " << (*output)[0]) << endl;
cout << "Entropy " << (*output)[1]);
cout << "LocalHomogeneity = " << (*output)[3]) << endl;
cout << "Inertia = " << (*output)[4]) << endl;
cout << "ClusterShade " << (*output)[5]) << endl;
cout << "ClusterProminence = " << (*output)[6]) << endl;

Sincereously, I thank you a lot your help.
Regards.
/Francisco



2015-01-15 18:26 GMT+01:00 Francisco Lopez de la Franca <
franciscolopezdelafranca at gmail.com>:

> Hi Matt again.
> You were fully right about setting the background/foreground values for
> the filter. I
>
> 2015-01-15 16:41 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> Hi Francisco,
>>
>> There is definitely something wrong with the textures features.  It is
>> not possible to know what is going on without more details, though.
>>
>> Matt
>>
>> On Thu, Jan 15, 2015 at 1:32 AM, Francisco Lopez de la Franca
>> <franciscolopezdelafranca at gmail.com> wrote:
>> > Hi Matt,
>> > Thanks a lot for your answers. I'll try this afternoon what you suggest
>> > regarding the shape filter, but what do you think about my results as
>> for
>> > the texture filter?
>> > Regards.
>> > /Francisco
>> >
>> > 2015-01-15 2:30 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>> >>
>> >> Hi Francisco,
>> >>
>> >> Great to hear about the progress!
>> >>
>> >> The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
>> >> which should have an integer pixel type, like unsigned char or
>> >> unsigned short.  It is important to set the BackgroundValue and
>> >> ForegroundValue [1] to get this filter to work correctly.
>> >>
>> >> HTH,
>> >> Matt
>> >>
>> >> [1]
>> >>
>> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
>> >>
>> >> On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
>> >> <franciscolopezdelafranca at gmail.com> wrote:
>> >> > Hi again.
>> >> > I fixed all the errors and got my library, now ready to be tested.
>> >> > It contains an encapsulation, on the one hand, of the class
>> >> > itkBinaryImageToShapeLabelMapFilter in order to get image shape
>> >> > descriptors
>> >> > of a 3D binary image, and on the other hand, the same for the class
>> >> > itkScalarImageToTextureFeaturesFilter to get image texture features
>> of a
>> >> > 3D
>> >> > scalar image.
>> >> >
>> >> > I pass as input image to both classes a binary 3D Nifti image
>> >> > (150x150x150)
>> >> > containing a cylinder where the inside voxels are 255 and the outside
>> >> > voxels
>> >> > are 0.
>> >> >
>> >> > As for the shape issue, it's very strange to me that the call to
>> >> > GetNumberOfLabelObjects on a itk::LabelMap object returns a value of
>> 0.
>> >> > The
>> >> > main code is as follows:
>> >> >
>> >> > binaryImageToShapeLabelMapFilter->SetInput(_input);
>> >> > binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
>> >> > binaryImageToShapeLabelMapFilter->Update();
>> >> >
>> >> > LabelMapType::Pointer labelMap =
>> >> > binaryImageToShapeLabelMapFilter->GetOutput();
>> >> >
>> >> > int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
>> >> >
>> >> >
>> >> > And, as for the texture features, the result of the filter does not
>> seem
>> >> > to
>> >> > be very logic:
>> >> >
>> >> > Energy = 1
>> >> > Entropy = 0
>> >> > Correlation = 1
>> >> > Local Homogeneity = 0
>> >> > Inertia = 0
>> >> > Cluster Shade = 0
>> >> > Cluster Prominence = 0
>> >> >
>> >> > I've also tested this with a scalar 3D Nifti image and the results
>> are
>> >> > the
>> >> > same.
>> >> >
>> >> > And the question is: What kind of image do I have to pass to the
>> filters
>> >> > so
>> >> > that the code would return a more logic expected answer?
>> >> >
>> >> > Thank you very much in advance.
>> >> > My best regars.
>> >> > /Francisco
>> >> >
>> >> > 2015-01-10 22:38 GMT+01:00 Matt McCormick <
>> matt.mccormick at kitware.com>:
>> >> >>
>> >> >> Hi Francisco,
>> >> >>
>> >> >> Nice to hear about the progress!
>> >> >>
>> >> >> You will need to link your library to the ITK libraries:
>> >> >>
>> >> >>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
>> >> >>
>> >> >> HTH,
>> >> >> Matt
>> >> >>
>> >> >> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
>> >> >> <franciscolopezdelafranca at gmail.com> wrote:
>> >> >>>
>> >> >>> Thanks to your previous answer the problem was solved, but another
>> one
>> >> >>> has come out. It occurs when linking to create the library. It
>> gives
>> >> >>> an
>> >> >>> undefined reference to itk::ExceptionObject::ExceptionObject... as
>> you
>> >> >>> can
>> >> >>> see below.
>> >> >>> What it is strange to me is that before including explicit template
>> >> >>> instantiation, I created the library without errors, and now that I
>> >> >>> include
>> >> >>> that, I get this error.
>> >> >>> I'll appreciate very much any help.
>> >> >>>
>> >> >>> Linking CXX shared library libTFM_Features.dll
>> >> >>>
>> >> >>>
>> >> >>>
>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>> >> >>>
>> >> >>>
>> >> >>>
>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>> >> >>> 1ERKSsjS2_S2_]+0x35): undefined reference to
>> >> >>> `itk::ExceptionObject::ExceptionObj
>> >> >>> ect(std::string const&, unsigned int, std::string const&,
>> std::string
>> >> >>> const&)'
>> >> >>>
>> >> >>>
>> >> >>>
>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>> >> >>>
>> >> >>>
>> >> >>>
>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>> >> >>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
>> >> >>> itk::MemoryAllocationEr
>> >> >>> ror'
>> >> >>>
>> >> >>>
>> >> >>>
>> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
>> >> >>> gw32/bin/ld.exe:
>> >> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
>> >> >>> d reloc address 0x40 in section
>> >> >>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
>> >> >>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
>> >> >>> collect2.exe: error: ld returned 1 exit status
>> >> >>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
>> >> >>> 'SRC/libTFM_Fe
>> >> >>> atures.dll' failed
>> >> >>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
>> >> >>> CMakeFiles\Makefile2:77: recipe for target
>> >> >>> 'SRC/CMakeFiles/TFM_Features.dir/all'
>> >> >>>  failed
>> >> >>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
>> >> >>> Makefile:74: recipe for target 'all' failed
>> >> >>> mingw32-make: *** [all] Error 2
>> >> >>>
>> >> >>>
>> >> >>> 2015-01-09 21:02 GMT+01:00 Matt McCormick
>> >> >>> <matt.mccormick at kitware.com>:
>> >> >>>>
>> >> >>>> Hi Francisco,
>> >> >>>>
>> >> >>>> In order for the templates to be available in the library, they
>> must
>> >> >>>> be explicitly instantiated [1].
>> >> >>>>
>> >> >>>> HTH,
>> >> >>>> Matt
>> >> >>>>
>> >> >>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
>> >> >>>>
>> >> >>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
>> >> >>>> <franciscolopezdelafranca at gmail.com> wrote:
>> >> >>>> > Hi.
>> >> >>>> > I' like to create a library containing, for example, one
>> template
>> >> >>>> > class with
>> >> >>>> > a number of methods.
>> >> >>>> > I've programmed a simple example and the compilation and
>> generation
>> >> >>>> > of
>> >> >>>> > the
>> >> >>>> > library goes fine. I use the cmake "add_library" command for
>> >> >>>> > generating the
>> >> >>>> > library.
>> >> >>>> >
>> >> >>>> > The problem arises at the moment of testing the library. I get
>> an
>> >> >>>> > undefined
>> >> >>>> > reference for every method in the template class.
>> >> >>>> >
>> >> >>>> > I've downloaded a tool to look in the contents (functions) of
>> >> >>>> > dynamic
>> >> >>>> > libraries, and there is no function in the library. If I add
>> >> >>>> > another
>> >> >>>> > class
>> >> >>>> > (not a template class), then, this tool shows me only the
>> functions
>> >> >>>> > in
>> >> >>>> > this
>> >> >>>> > latter class.
>> >> >>>> >
>> >> >>>> > Has anyone ever come across with this problem?
>> >> >>>> >
>> >> >>>> > Thanks a lot in advance.
>> >> >>>> > Regards
>> >> >>>> > /Francisco
>> >> >>>> >
>> >> >>>> > _____________________________________
>> >> >>>> > 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  Thu Jan 15 13:01:49 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 15 Jan 2015 13:01:49 -0500
Subject: [ITK-users] SimpleITK | read a 3D image from a non DICOM file
 and write it as a series of DICOM slices
In-Reply-To: <9B24E4DF-447C-42CA-A8EC-609DABA2B630@mail.nih.gov>
References: <CAKKNfuLN-pq7D097_CAq5vwe6yJBuSh=yeiOAgUbYNJu28Go-A@mail.gmail.com>
 <FC4D270F-46B6-4935-8919-C38AFCF408C8@mail.nih.gov>
 <9B24E4DF-447C-42CA-A8EC-609DABA2B630@mail.nih.gov>
Message-ID: <CALzTN-RqQzv8UiCxL6hEfCXjGOQ9gy5xk9q6qPxCNXcJwQPcig@mail.gmail.com>

Hi,

Generating a valid DICOM series can be a pretty complex task.

New UID's need to be generated, for example. Some more information can
be found here [1].

HTH,
Matt

[1]  http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM

On Thu, Jan 15, 2015 at 10:07 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Hello,
>
> I have just added an ImageSeriesWriter to SimpleITK:
>
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageSeriesWriter.html
>
> The hooks for getting the meta-data dictionary in the dicom series aren't
> quite there yet. But its a step closer. It's actually rather confusing how
> the tags are handled in the example you linked too, and I'm not sure what
> exactly needs to be done to create a "valid" dicom series.
>
> Brad
>
> On Dec 31, 2014, at 10:46 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
> Hello,
>
> Sorry for the slow reply. Earlier you linked to this nice example for
> reference:
> http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html
>
> With SimpleITK I have done the following when I needed to write a series in
> Python:
>
> for i in range(img.GetSize()[2]):
>     sitk.WriteImage(img[:,:,i],"test_{0:04}.tif".format(i))
>
>
> However it is not quite this simple for a DICOM series. The metadata tags
> need to be correct too. SimpleITK is not designed to be a full fledge
> interface to DICOM files. Other tools may be better for that. But this seems
> like a reasonable thing to do but it's not currently readily available in
> the SimpleITK interface. Perhaps after some discussion on the best way to do
> it it and be added.
>
>
> There are 3 main components to this example:
>
> 1) MetaDataDictionary
>
> In SimpleITK the MetaDataDictionary interface is only part of the Image
> class. Currently it provides a read only interface, with the
> GetMetaDataKeys(), and GetMetaData(key) methods[1]. This get method only
> returns the type of data in the dictionary converted to a string.
>
> The required method would be Image::SetMetaData(key,value). The issue would
> be what types of value need to be supported. For this example only
> std::string is needed, perhaps others should be overloaded?
>
> 2) NumericSeriesFileNameGenerator
>
> This class only produces a "list" of file names. I think that many of the
> languages may have a more convenient way to do this. For example in Python:
>
> [ "test_{0:04}.png".format(i) for i in range(img.GetSize()[2]) ]
>
> So I don't think this is so important.
>
> 3) SeriesWriter
>
> What we just used above is different then the SeriesWriter, as special
> metadata is passed from the ImageSeriesWriter to the ImageIO [2]. Here is
> the JIRA issue for this task [3].
>
>
> So after these get done something like the following would do what you ask:
>
> import SimpleITK as sitk
>
> img = stik.ReadImage(argv[1])
> img.SetMetaData("008|0060", "MR") // Modality
> img.SetMetaData("008|0008", "DERIVED\\SECONDARY") // Image Type
> img.SetMetaData("008|0064", "DV") // Conversion Type
> sitk.WriteImage(img, [ "test_{0:04}.dcm".format(i) for i in
> range(img.GetSize()[2]) ])
>
> Does that look like what you are looking for?
>
> Brad
>
> [1]
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html#a3d6cb12a211352ee38da5405b9c75928
> [2]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx#L327-L368
> [3] https://issues.itk.org/jira/browse/SIMPLEITK-122
>
> On Dec 29, 2014, at 2:48 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> Hi,
>
> Is there an example for SimpleITK to read a 3D image from a non Dicom file
> such as mhd and then write it as a series of DICOM Slices?
>
> I can do this with C++ but I haven't been able to figure out how to do it
> using simpleITK.
>
> Thanks,
>
> Matias.
> _____________________________________
> 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
>

From matt.mccormick at kitware.com  Thu Jan 15 14:08:02 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 15 Jan 2015 14:08:02 -0500
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CAJqi3ELd6ogd4R3sAhRneRRoUnBfE=j3kbp6mTM-Lzn3VfexuA@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
 <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
 <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>
 <CALzTN-QM5QK22uHV0PQT=jYEuPqPGCsxUucv1AjzjFAJNP5gvg@mail.gmail.com>
 <CAJqi3EJQmKszSvabMXsLVtRS_ruc4u8J8OUM-RZLWtYVS6guWw@mail.gmail.com>
 <CAJqi3ELd6ogd4R3sAhRneRRoUnBfE=j3kbp6mTM-Lzn3VfexuA@mail.gmail.com>
Message-ID: <CALzTN-R_Eqk-Kz0xoiYAg5KYm8JNfLQJY17aeSFwVXTP-iyVDA@mail.gmail.com>

Hi Francisco,

Good to hear the BinaryImageToShapeLabelMapFilter is working.

This is probably not the source of your issues, but this line

  FeatureValueVectorType* output = textureFilter->GetFeatureMeans();

should be

  FeatureValueVectorType::Pointer output = textureFilter->GetFeatureMeans();

since itk::SmartPointer's [1] are different from raw pointers.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1SmartPointer.html


On Thu, Jan 15, 2015 at 12:34 PM, Francisco Lopez de la Franca
<franciscolopezdelafranca at gmail.com> wrote:
> Sorry, I might press the wrong key.
> Hi Matt again.
> You were fully right about setting the background/foreground values for the
> filter. I wasn't using them because I followed the examples and there was no
> reference to them. Now my shape related functions are working.
>
> As for the textures, I attach my code so that anyone can see if i am doing
> something wrong:
>
> typedef itk::Statistics::ScalarImageToTextureFeaturesFilter<TInputImage>
> TextureFilterType;
> typedef typename TextureFilterType::Pointer TextureFilterPtr;
> typedef typename TextureFilterType::FeatureValueVector
> FeatureValueVectorType;
>
> TextureFilterPtr textureFilter = TextureFilterType::New();
> textureFilter->SetInput(_input);
> textureFilter->Update();
>
> FeatureValueVectorType* output = textureFilter->GetFeatureMeans();
>
> cout << "Energy = " << (*output)[0]) << endl;
> cout << "Entropy " << (*output)[1]);
> cout << "LocalHomogeneity = " << (*output)[3]) << endl;
> cout << "Inertia = " << (*output)[4]) << endl;
> cout << "ClusterShade " << (*output)[5]) << endl;
> cout << "ClusterProminence = " << (*output)[6]) << endl;
>
> Sincereously, I thank you a lot your help.
> Regards.
> /Francisco
>
>
>
> 2015-01-15 18:26 GMT+01:00 Francisco Lopez de la Franca
> <franciscolopezdelafranca at gmail.com>:
>>
>> Hi Matt again.
>> You were fully right about setting the background/foreground values for
>> the filter. I
>>
>> 2015-01-15 16:41 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>>
>>> Hi Francisco,
>>>
>>> There is definitely something wrong with the textures features.  It is
>>> not possible to know what is going on without more details, though.
>>>
>>> Matt
>>>
>>> On Thu, Jan 15, 2015 at 1:32 AM, Francisco Lopez de la Franca
>>> <franciscolopezdelafranca at gmail.com> wrote:
>>> > Hi Matt,
>>> > Thanks a lot for your answers. I'll try this afternoon what you suggest
>>> > regarding the shape filter, but what do you think about my results as
>>> > for
>>> > the texture filter?
>>> > Regards.
>>> > /Francisco
>>> >
>>> > 2015-01-15 2:30 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>> >>
>>> >> Hi Francisco,
>>> >>
>>> >> Great to hear about the progress!
>>> >>
>>> >> The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
>>> >> which should have an integer pixel type, like unsigned char or
>>> >> unsigned short.  It is important to set the BackgroundValue and
>>> >> ForegroundValue [1] to get this filter to work correctly.
>>> >>
>>> >> HTH,
>>> >> Matt
>>> >>
>>> >> [1]
>>> >>
>>> >> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
>>> >>
>>> >> On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
>>> >> <franciscolopezdelafranca at gmail.com> wrote:
>>> >> > Hi again.
>>> >> > I fixed all the errors and got my library, now ready to be tested.
>>> >> > It contains an encapsulation, on the one hand, of the class
>>> >> > itkBinaryImageToShapeLabelMapFilter in order to get image shape
>>> >> > descriptors
>>> >> > of a 3D binary image, and on the other hand, the same for the class
>>> >> > itkScalarImageToTextureFeaturesFilter to get image texture features
>>> >> > of a
>>> >> > 3D
>>> >> > scalar image.
>>> >> >
>>> >> > I pass as input image to both classes a binary 3D Nifti image
>>> >> > (150x150x150)
>>> >> > containing a cylinder where the inside voxels are 255 and the
>>> >> > outside
>>> >> > voxels
>>> >> > are 0.
>>> >> >
>>> >> > As for the shape issue, it's very strange to me that the call to
>>> >> > GetNumberOfLabelObjects on a itk::LabelMap object returns a value of
>>> >> > 0.
>>> >> > The
>>> >> > main code is as follows:
>>> >> >
>>> >> > binaryImageToShapeLabelMapFilter->SetInput(_input);
>>> >> > binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
>>> >> > binaryImageToShapeLabelMapFilter->Update();
>>> >> >
>>> >> > LabelMapType::Pointer labelMap =
>>> >> > binaryImageToShapeLabelMapFilter->GetOutput();
>>> >> >
>>> >> > int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
>>> >> >
>>> >> >
>>> >> > And, as for the texture features, the result of the filter does not
>>> >> > seem
>>> >> > to
>>> >> > be very logic:
>>> >> >
>>> >> > Energy = 1
>>> >> > Entropy = 0
>>> >> > Correlation = 1
>>> >> > Local Homogeneity = 0
>>> >> > Inertia = 0
>>> >> > Cluster Shade = 0
>>> >> > Cluster Prominence = 0
>>> >> >
>>> >> > I've also tested this with a scalar 3D Nifti image and the results
>>> >> > are
>>> >> > the
>>> >> > same.
>>> >> >
>>> >> > And the question is: What kind of image do I have to pass to the
>>> >> > filters
>>> >> > so
>>> >> > that the code would return a more logic expected answer?
>>> >> >
>>> >> > Thank you very much in advance.
>>> >> > My best regars.
>>> >> > /Francisco
>>> >> >
>>> >> > 2015-01-10 22:38 GMT+01:00 Matt McCormick
>>> >> > <matt.mccormick at kitware.com>:
>>> >> >>
>>> >> >> Hi Francisco,
>>> >> >>
>>> >> >> Nice to hear about the progress!
>>> >> >>
>>> >> >> You will need to link your library to the ITK libraries:
>>> >> >>
>>> >> >>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
>>> >> >>
>>> >> >> HTH,
>>> >> >> Matt
>>> >> >>
>>> >> >> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
>>> >> >> <franciscolopezdelafranca at gmail.com> wrote:
>>> >> >>>
>>> >> >>> Thanks to your previous answer the problem was solved, but another
>>> >> >>> one
>>> >> >>> has come out. It occurs when linking to create the library. It
>>> >> >>> gives
>>> >> >>> an
>>> >> >>> undefined reference to itk::ExceptionObject::ExceptionObject... as
>>> >> >>> you
>>> >> >>> can
>>> >> >>> see below.
>>> >> >>> What it is strange to me is that before including explicit
>>> >> >>> template
>>> >> >>> instantiation, I created the library without errors, and now that
>>> >> >>> I
>>> >> >>> include
>>> >> >>> that, I get this error.
>>> >> >>> I'll appreciate very much any help.
>>> >> >>>
>>> >> >>> Linking CXX shared library libTFM_Features.dll
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>>> >> >>> 1ERKSsjS2_S2_]+0x35): undefined reference to
>>> >> >>> `itk::ExceptionObject::ExceptionObj
>>> >> >>> ect(std::string const&, unsigned int, std::string const&,
>>> >> >>> std::string
>>> >> >>> const&)'
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
>>> >> >>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
>>> >> >>> itk::MemoryAllocationEr
>>> >> >>> ror'
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
>>> >> >>> gw32/bin/ld.exe:
>>> >> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
>>> >> >>> d reloc address 0x40 in section
>>> >> >>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
>>> >> >>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
>>> >> >>> collect2.exe: error: ld returned 1 exit status
>>> >> >>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for target
>>> >> >>> 'SRC/libTFM_Fe
>>> >> >>> atures.dll' failed
>>> >> >>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
>>> >> >>> CMakeFiles\Makefile2:77: recipe for target
>>> >> >>> 'SRC/CMakeFiles/TFM_Features.dir/all'
>>> >> >>>  failed
>>> >> >>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all] Error 2
>>> >> >>> Makefile:74: recipe for target 'all' failed
>>> >> >>> mingw32-make: *** [all] Error 2
>>> >> >>>
>>> >> >>>
>>> >> >>> 2015-01-09 21:02 GMT+01:00 Matt McCormick
>>> >> >>> <matt.mccormick at kitware.com>:
>>> >> >>>>
>>> >> >>>> Hi Francisco,
>>> >> >>>>
>>> >> >>>> In order for the templates to be available in the library, they
>>> >> >>>> must
>>> >> >>>> be explicitly instantiated [1].
>>> >> >>>>
>>> >> >>>> HTH,
>>> >> >>>> Matt
>>> >> >>>>
>>> >> >>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
>>> >> >>>>
>>> >> >>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
>>> >> >>>> <franciscolopezdelafranca at gmail.com> wrote:
>>> >> >>>> > Hi.
>>> >> >>>> > I' like to create a library containing, for example, one
>>> >> >>>> > template
>>> >> >>>> > class with
>>> >> >>>> > a number of methods.
>>> >> >>>> > I've programmed a simple example and the compilation and
>>> >> >>>> > generation
>>> >> >>>> > of
>>> >> >>>> > the
>>> >> >>>> > library goes fine. I use the cmake "add_library" command for
>>> >> >>>> > generating the
>>> >> >>>> > library.
>>> >> >>>> >
>>> >> >>>> > The problem arises at the moment of testing the library. I get
>>> >> >>>> > an
>>> >> >>>> > undefined
>>> >> >>>> > reference for every method in the template class.
>>> >> >>>> >
>>> >> >>>> > I've downloaded a tool to look in the contents (functions) of
>>> >> >>>> > dynamic
>>> >> >>>> > libraries, and there is no function in the library. If I add
>>> >> >>>> > another
>>> >> >>>> > class
>>> >> >>>> > (not a template class), then, this tool shows me only the
>>> >> >>>> > functions
>>> >> >>>> > in
>>> >> >>>> > this
>>> >> >>>> > latter class.
>>> >> >>>> >
>>> >> >>>> > Has anyone ever come across with this problem?
>>> >> >>>> >
>>> >> >>>> > Thanks a lot in advance.
>>> >> >>>> > Regards
>>> >> >>>> > /Francisco
>>> >> >>>> >
>>> >> >>>> > _____________________________________
>>> >> >>>> > 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 jmerkow at gmail.com  Thu Jan 15 17:09:20 2015
From: jmerkow at gmail.com (jmerkow)
Date: Thu, 15 Jan 2015 15:09:20 -0700 (MST)
Subject: [ITK-users] Setting constants in ternary functor filters
Message-ID: <1421359760646-35125.post@n7.nabble.com>

Hello,

I am writing a ternary functor filter and I want to allow constants to be
set for inputs 2 and 3 (1 and 2 in SetNthInput).
I believe I followed the example in BinaryFunctor but when I set them I get
NULL pointers for the inputs:
"At least one input is missing. Input1 is 0xb212190,  Input2 is 0,  Input3
is 0"

My filter looks something like this (I trimmed it down to just the relevant
parts):

...
class MyTernaryFunctorImageFilter:
		public itk::TernaryFunctorImageFilter< TInputImage1, TInputImage2,
TInputImage3, TOutputImage,
		MyTernaryFunctor<
		typename TInputImage1::PixelType,
		typename TInputImage2::PixelType,
		typename TInputImage3::PixelType,
		typename TOutputImage::PixelType >   >
{
...
//Common Typedefs are here
...

typedef TInputImage2                           Input2ImageType;
typedef typename Input2ImageType::ConstPointer Input2ImagePointer;
typedef typename Input2ImageType::RegionType   Input2ImageRegionType;
typedef typename Input2ImageType::PixelType    Input2ImagePixelType;
typedef itk::SimpleDataObjectDecorator<Input2ImagePixelType>
DecoratedInput2ImagePixelType;

typedef TInputImage3                           Input3ImageType;
typedef typename Input3ImageType::ConstPointer Input3ImagePointer;
typedef typename Input3ImageType::RegionType   Input3ImageRegionType;
typedef typename Input3ImageType::PixelType    Input3ImagePixelType;
typedef itk::SimpleDataObjectDecorator<Input3ImagePixelType>
DecoratedInput3ImagePixelType;

virtual void SetConstant2(const Input2ImagePixelType &input);
virtual void SetConstant2(const DecoratedInput2ImagePixelType *input);	
/** Set the Third operand as a constant */
virtual void SetConstant3(const Input3ImagePixelType &input);
virtual void SetConstant3(const DecoratedInput3ImagePixelType *input);
};

template<...>
void
MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
TOutputImage>
::SetConstant2(const Input2ImagePixelType &input)
{
	 itkDebugMacro("setting SetConstant2 to " << input);
	 typename DecoratedInput2ImagePixelType::Pointer newInput =
DecoratedInput2ImagePixelType::New();
	 newInput->Set(input);
	 this->SetConstant2(newInput);
}

template<...>
void
MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
TOutputImage>
::SetConstant2(const DecoratedInput2ImagePixelType *input)
{
	this->SetNthInput( 1,const_cast<DecoratedInput2ImagePixelType*>(input));
}
template<...>
void
MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
TOutputImage>
::SetConstant3(const Input3ImagePixelType &input)
{
	 itkDebugMacro("setting SetConstant3 to " << input);
	 typename DecoratedInput3ImagePixelType::Pointer newInput =
DecoratedInput3ImagePixelType::New();
	 newInput->Set(input);
	 this->SetConstant3(newInput);
}

template<...>
void
MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
TOutputImage>
::SetConstant3(const DecoratedInput3ImagePixelType *input)
{
	this->SetNthInput( 2,const_cast<DecoratedInput3ImagePixelType*>(input));
}

I pass this function an image for input1, then floats for other two inputs.

Am I missing an ingredient here?

-Jameson



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From jmerkow at gmail.com  Thu Jan 15 17:15:51 2015
From: jmerkow at gmail.com (jmerkow)
Date: Thu, 15 Jan 2015 15:15:51 -0700 (MST)
Subject: [ITK-users] Create java VM failure SimpleITK, Python, Windows
In-Reply-To: <1419773770742-35075.post@n7.nabble.com>
References: <1379456385734-32371.post@n7.nabble.com>
 <CALzTN-SKpQ1yUK-KBtH4cikY5qKU6tKMfyUKbHYArX8-kX8Lfg@mail.gmail.com>
 <1379463383239-32376.post@n7.nabble.com>
 <1403721309106-34160.post@n7.nabble.com>
 <1419771563210-35074.post@n7.nabble.com>
 <1419773770742-35075.post@n7.nabble.com>
Message-ID: <1421360151382-35126.post@n7.nabble.com>

Change them in the standard way.
Google search turned up these two tutorials:
https://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/sysdm_advancd_environmnt_addchange_variable.mspx?mfr=true
http://www.nextofwindows.com/how-to-addedit-environment-variables-in-windows-7/
which seems to cover it.



--
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From franciscolopezdelafranca at gmail.com  Fri Jan 16 02:02:24 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Fri, 16 Jan 2015 08:02:24 +0100
Subject: [ITK-users] Undefined references to methods of template classes
In-Reply-To: <CALzTN-R_Eqk-Kz0xoiYAg5KYm8JNfLQJY17aeSFwVXTP-iyVDA@mail.gmail.com>
References: <CAJqi3EKyCJeCnTZdO0NPZCf+Yi-xCX2bAf3GwwEmvRRx8g22Dg@mail.gmail.com>
 <CALzTN-SfMzUuCWDAXKqf6fzWp2wkNKCNaMCEvAGb=-RU=Z8iXA@mail.gmail.com>
 <CAJqi3E+5fNUq+XKFrTRJsTU3uraZHqDFy_kXSoO1HbJovctC-g@mail.gmail.com>
 <CALzTN-SZ-GsO+1O-OB2V50Fzf=0ufqGQj0-a-F2=oGedTUWhXA@mail.gmail.com>
 <CAJqi3EK642tsnO3VFZwLNWK0ejOEQ6skNaeYfspK1AaHDQaaFA@mail.gmail.com>
 <CALzTN-RA3+9DsB7Vj3ZON4+Kr6qxipCzZ9nuQMXM--MX_ZCeAA@mail.gmail.com>
 <CAJqi3E+zN8zf2BNVw4pqoBN0KzyvGkky7df2MkQJtNiYm2c3og@mail.gmail.com>
 <CALzTN-QM5QK22uHV0PQT=jYEuPqPGCsxUucv1AjzjFAJNP5gvg@mail.gmail.com>
 <CAJqi3EJQmKszSvabMXsLVtRS_ruc4u8J8OUM-RZLWtYVS6guWw@mail.gmail.com>
 <CAJqi3ELd6ogd4R3sAhRneRRoUnBfE=j3kbp6mTM-Lzn3VfexuA@mail.gmail.com>
 <CALzTN-R_Eqk-Kz0xoiYAg5KYm8JNfLQJY17aeSFwVXTP-iyVDA@mail.gmail.com>
Message-ID: <CAJqi3EL=OmgCr5k4ti0TrRnSy6yYMxid2aZUHwMU7bCGCfV3-Q@mail.gmail.com>

Hi Matt.
I've already solved the texture features problem.
The solution is similar to that of the shape features. You must set a value
or values to the filter in order to be able to calculate the features. I've
used the SetPixelValueMinMax
<http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToTextureFeaturesFilter.html#a373867fa4b665bc5e4b56fea305ed774>()
method and everything OK.
Thank you very much for your support.
/Francisco

2015-01-15 20:08 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Francisco,
>
> Good to hear the BinaryImageToShapeLabelMapFilter is working.
>
> This is probably not the source of your issues, but this line
>
>   FeatureValueVectorType* output = textureFilter->GetFeatureMeans();
>
> should be
>
>   FeatureValueVectorType::Pointer output =
> textureFilter->GetFeatureMeans();
>
> since itk::SmartPointer's [1] are different from raw pointers.
>
> HTH,
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1SmartPointer.html
>
>
> On Thu, Jan 15, 2015 at 12:34 PM, Francisco Lopez de la Franca
> <franciscolopezdelafranca at gmail.com> wrote:
> > Sorry, I might press the wrong key.
> > Hi Matt again.
> > You were fully right about setting the background/foreground values for
> the
> > filter. I wasn't using them because I followed the examples and there
> was no
> > reference to them. Now my shape related functions are working.
> >
> > As for the textures, I attach my code so that anyone can see if i am
> doing
> > something wrong:
> >
> > typedef itk::Statistics::ScalarImageToTextureFeaturesFilter<TInputImage>
> > TextureFilterType;
> > typedef typename TextureFilterType::Pointer TextureFilterPtr;
> > typedef typename TextureFilterType::FeatureValueVector
> > FeatureValueVectorType;
> >
> > TextureFilterPtr textureFilter = TextureFilterType::New();
> > textureFilter->SetInput(_input);
> > textureFilter->Update();
> >
> > FeatureValueVectorType* output = textureFilter->GetFeatureMeans();
> >
> > cout << "Energy = " << (*output)[0]) << endl;
> > cout << "Entropy " << (*output)[1]);
> > cout << "LocalHomogeneity = " << (*output)[3]) << endl;
> > cout << "Inertia = " << (*output)[4]) << endl;
> > cout << "ClusterShade " << (*output)[5]) << endl;
> > cout << "ClusterProminence = " << (*output)[6]) << endl;
> >
> > Sincereously, I thank you a lot your help.
> > Regards.
> > /Francisco
> >
> >
> >
> > 2015-01-15 18:26 GMT+01:00 Francisco Lopez de la Franca
> > <franciscolopezdelafranca at gmail.com>:
> >>
> >> Hi Matt again.
> >> You were fully right about setting the background/foreground values for
> >> the filter. I
> >>
> >> 2015-01-15 16:41 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> >>>
> >>> Hi Francisco,
> >>>
> >>> There is definitely something wrong with the textures features.  It is
> >>> not possible to know what is going on without more details, though.
> >>>
> >>> Matt
> >>>
> >>> On Thu, Jan 15, 2015 at 1:32 AM, Francisco Lopez de la Franca
> >>> <franciscolopezdelafranca at gmail.com> wrote:
> >>> > Hi Matt,
> >>> > Thanks a lot for your answers. I'll try this afternoon what you
> suggest
> >>> > regarding the shape filter, but what do you think about my results as
> >>> > for
> >>> > the texture filter?
> >>> > Regards.
> >>> > /Francisco
> >>> >
> >>> > 2015-01-15 2:30 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com
> >:
> >>> >>
> >>> >> Hi Francisco,
> >>> >>
> >>> >> Great to hear about the progress!
> >>> >>
> >>> >> The itk::BinaryImageToShapeLabelMapFilter  requires a binary input,
> >>> >> which should have an integer pixel type, like unsigned char or
> >>> >> unsigned short.  It is important to set the BackgroundValue and
> >>> >> ForegroundValue [1] to get this filter to work correctly.
> >>> >>
> >>> >> HTH,
> >>> >> Matt
> >>> >>
> >>> >> [1]
> >>> >>
> >>> >>
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
> >>> >>
> >>> >> On Wed, Jan 14, 2015 at 5:05 PM, Francisco Lopez de la Franca
> >>> >> <franciscolopezdelafranca at gmail.com> wrote:
> >>> >> > Hi again.
> >>> >> > I fixed all the errors and got my library, now ready to be tested.
> >>> >> > It contains an encapsulation, on the one hand, of the class
> >>> >> > itkBinaryImageToShapeLabelMapFilter in order to get image shape
> >>> >> > descriptors
> >>> >> > of a 3D binary image, and on the other hand, the same for the
> class
> >>> >> > itkScalarImageToTextureFeaturesFilter to get image texture
> features
> >>> >> > of a
> >>> >> > 3D
> >>> >> > scalar image.
> >>> >> >
> >>> >> > I pass as input image to both classes a binary 3D Nifti image
> >>> >> > (150x150x150)
> >>> >> > containing a cylinder where the inside voxels are 255 and the
> >>> >> > outside
> >>> >> > voxels
> >>> >> > are 0.
> >>> >> >
> >>> >> > As for the shape issue, it's very strange to me that the call to
> >>> >> > GetNumberOfLabelObjects on a itk::LabelMap object returns a value
> of
> >>> >> > 0.
> >>> >> > The
> >>> >> > main code is as follows:
> >>> >> >
> >>> >> > binaryImageToShapeLabelMapFilter->SetInput(_input);
> >>> >> > binaryImageToShapeLabelMapFilter->ComputePerimeterOn();
> >>> >> > binaryImageToShapeLabelMapFilter->Update();
> >>> >> >
> >>> >> > LabelMapType::Pointer labelMap =
> >>> >> > binaryImageToShapeLabelMapFilter->GetOutput();
> >>> >> >
> >>> >> > int nrOfLabelObjects = labelMap->GetNumberOfLabelObjects();
> >>> >> >
> >>> >> >
> >>> >> > And, as for the texture features, the result of the filter does
> not
> >>> >> > seem
> >>> >> > to
> >>> >> > be very logic:
> >>> >> >
> >>> >> > Energy = 1
> >>> >> > Entropy = 0
> >>> >> > Correlation = 1
> >>> >> > Local Homogeneity = 0
> >>> >> > Inertia = 0
> >>> >> > Cluster Shade = 0
> >>> >> > Cluster Prominence = 0
> >>> >> >
> >>> >> > I've also tested this with a scalar 3D Nifti image and the results
> >>> >> > are
> >>> >> > the
> >>> >> > same.
> >>> >> >
> >>> >> > And the question is: What kind of image do I have to pass to the
> >>> >> > filters
> >>> >> > so
> >>> >> > that the code would return a more logic expected answer?
> >>> >> >
> >>> >> > Thank you very much in advance.
> >>> >> > My best regars.
> >>> >> > /Francisco
> >>> >> >
> >>> >> > 2015-01-10 22:38 GMT+01:00 Matt McCormick
> >>> >> > <matt.mccormick at kitware.com>:
> >>> >> >>
> >>> >> >> Hi Francisco,
> >>> >> >>
> >>> >> >> Nice to hear about the progress!
> >>> >> >>
> >>> >> >> You will need to link your library to the ITK libraries:
> >>> >> >>
> >>> >> >>   target_link_libraries( mylibrary ${ITK_LIBRARIES} )
> >>> >> >>
> >>> >> >> HTH,
> >>> >> >> Matt
> >>> >> >>
> >>> >> >> On Sat, Jan 10, 2015 at 4:16 PM, Francisco Lopez de la Franca
> >>> >> >> <franciscolopezdelafranca at gmail.com> wrote:
> >>> >> >>>
> >>> >> >>> Thanks to your previous answer the problem was solved, but
> another
> >>> >> >>> one
> >>> >> >>> has come out. It occurs when linking to create the library. It
> >>> >> >>> gives
> >>> >> >>> an
> >>> >> >>> undefined reference to itk::ExceptionObject::ExceptionObject...
> as
> >>> >> >>> you
> >>> >> >>> can
> >>> >> >>> see below.
> >>> >> >>> What it is strange to me is that before including explicit
> >>> >> >>> template
> >>> >> >>> instantiation, I created the library without errors, and now
> that
> >>> >> >>> I
> >>> >> >>> include
> >>> >> >>> that, I get this error.
> >>> >> >>> I'll appreciate very much any help.
> >>> >> >>>
> >>> >> >>> Linking CXX shared library libTFM_Features.dll
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> >>> >> >>> 1ERKSsjS2_S2_]+0x35): undefined reference to
> >>> >> >>> `itk::ExceptionObject::ExceptionObj
> >>> >> >>> ect(std::string const&, unsigned int, std::string const&,
> >>> >> >>> std::string
> >>> >> >>> const&)'
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj):TFM_Features.cpp:(.t
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> ext$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC
> >>> >> >>> 1ERKSsjS2_S2_]+0x40): undefined reference to `vtable for
> >>> >> >>> itk::MemoryAllocationEr
> >>> >> >>> ror'
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> >>> >> >>>
> C:/CV/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-min
> >>> >> >>> gw32/bin/ld.exe:
> >>> >> >>> CMakeFiles\TFM_Features.dir/objects.a(TFM_Features.cpp.obj): ba
> >>> >> >>> d reloc address 0x40 in section
> >>> >> >>> `.text$_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_
> >>> >> >>> S2_[_ZN3itk21MemoryAllocationErrorC1ERKSsjS2_S2_]'
> >>> >> >>> collect2.exe: error: ld returned 1 exit status
> >>> >> >>> SRC\CMakeFiles\TFM_Features.dir\build.make:219: recipe for
> target
> >>> >> >>> 'SRC/libTFM_Fe
> >>> >> >>> atures.dll' failed
> >>> >> >>> mingw32-make[2]: *** [SRC/libTFM_Features.dll] Error 1
> >>> >> >>> CMakeFiles\Makefile2:77: recipe for target
> >>> >> >>> 'SRC/CMakeFiles/TFM_Features.dir/all'
> >>> >> >>>  failed
> >>> >> >>> mingw32-make[1]: *** [SRC/CMakeFiles/TFM_Features.dir/all]
> Error 2
> >>> >> >>> Makefile:74: recipe for target 'all' failed
> >>> >> >>> mingw32-make: *** [all] Error 2
> >>> >> >>>
> >>> >> >>>
> >>> >> >>> 2015-01-09 21:02 GMT+01:00 Matt McCormick
> >>> >> >>> <matt.mccormick at kitware.com>:
> >>> >> >>>>
> >>> >> >>>> Hi Francisco,
> >>> >> >>>>
> >>> >> >>>> In order for the templates to be available in the library, they
> >>> >> >>>> must
> >>> >> >>>> be explicitly instantiated [1].
> >>> >> >>>>
> >>> >> >>>> HTH,
> >>> >> >>>> Matt
> >>> >> >>>>
> >>> >> >>>> [1] http://www.cplusplus.com/articles/1C75fSEw/
> >>> >> >>>>
> >>> >> >>>> On Fri, Jan 9, 2015 at 2:59 PM, Francisco Lopez de la Franca
> >>> >> >>>> <franciscolopezdelafranca at gmail.com> wrote:
> >>> >> >>>> > Hi.
> >>> >> >>>> > I' like to create a library containing, for example, one
> >>> >> >>>> > template
> >>> >> >>>> > class with
> >>> >> >>>> > a number of methods.
> >>> >> >>>> > I've programmed a simple example and the compilation and
> >>> >> >>>> > generation
> >>> >> >>>> > of
> >>> >> >>>> > the
> >>> >> >>>> > library goes fine. I use the cmake "add_library" command for
> >>> >> >>>> > generating the
> >>> >> >>>> > library.
> >>> >> >>>> >
> >>> >> >>>> > The problem arises at the moment of testing the library. I
> get
> >>> >> >>>> > an
> >>> >> >>>> > undefined
> >>> >> >>>> > reference for every method in the template class.
> >>> >> >>>> >
> >>> >> >>>> > I've downloaded a tool to look in the contents (functions) of
> >>> >> >>>> > dynamic
> >>> >> >>>> > libraries, and there is no function in the library. If I add
> >>> >> >>>> > another
> >>> >> >>>> > class
> >>> >> >>>> > (not a template class), then, this tool shows me only the
> >>> >> >>>> > functions
> >>> >> >>>> > in
> >>> >> >>>> > this
> >>> >> >>>> > latter class.
> >>> >> >>>> >
> >>> >> >>>> > Has anyone ever come across with this problem?
> >>> >> >>>> >
> >>> >> >>>> > Thanks a lot in advance.
> >>> >> >>>> > Regards
> >>> >> >>>> > /Francisco
> >>> >> >>>> >
> >>> >> >>>> > _____________________________________
> >>> >> >>>> > 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 david.m.welch at gmail.com  Fri Jan 16 11:31:59 2015
From: david.m.welch at gmail.com (dmwelch)
Date: Fri, 16 Jan 2015 09:31:59 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421275248945-35113.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
Message-ID: <1421425919413-35128.post@n7.nabble.com>

This is off topic, but have you looked at using VMTK? It's a ITK-based Python
package designed for vessel segmentation, so you don't have to re-invent the
wheel, ICYI.  I used it to create a semi-automated cerebral aneurysm
segmentation app several years back.  ;-)

Cheers, 
Dave W.



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From matt.mccormick at kitware.com  Fri Jan 16 11:54:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 16 Jan 2015 11:54:24 -0500
Subject: [ITK-users] Setting constants in ternary functor filters
In-Reply-To: <1421359760646-35125.post@n7.nabble.com>
References: <1421359760646-35125.post@n7.nabble.com>
Message-ID: <CALzTN-QzXr81ZceTABJ=9PtKCU-E5dgqBLG2geqid5h_PSrUwA@mail.gmail.com>

Hi Jameson,

The TernaryFunctorImageFilter was designed to work on three input
images.  For this case, it would be better to inherit from
UnaryFunctorImageFilter, then set the constants on the functor.  See,
for example, the itk::ExpNegativeImageFilter [1], which also has a
constant input.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1ExpNegativeImageFilter.html

On Thu, Jan 15, 2015 at 5:09 PM, jmerkow <jmerkow at gmail.com> wrote:
> Hello,
>
> I am writing a ternary functor filter and I want to allow constants to be
> set for inputs 2 and 3 (1 and 2 in SetNthInput).
> I believe I followed the example in BinaryFunctor but when I set them I get
> NULL pointers for the inputs:
> "At least one input is missing. Input1 is 0xb212190,  Input2 is 0,  Input3
> is 0"
>
> My filter looks something like this (I trimmed it down to just the relevant
> parts):
>
> ...
> class MyTernaryFunctorImageFilter:
>                 public itk::TernaryFunctorImageFilter< TInputImage1, TInputImage2,
> TInputImage3, TOutputImage,
>                 MyTernaryFunctor<
>                 typename TInputImage1::PixelType,
>                 typename TInputImage2::PixelType,
>                 typename TInputImage3::PixelType,
>                 typename TOutputImage::PixelType >   >
> {
> ...
> //Common Typedefs are here
> ...
>
> typedef TInputImage2                           Input2ImageType;
> typedef typename Input2ImageType::ConstPointer Input2ImagePointer;
> typedef typename Input2ImageType::RegionType   Input2ImageRegionType;
> typedef typename Input2ImageType::PixelType    Input2ImagePixelType;
> typedef itk::SimpleDataObjectDecorator<Input2ImagePixelType>
> DecoratedInput2ImagePixelType;
>
> typedef TInputImage3                           Input3ImageType;
> typedef typename Input3ImageType::ConstPointer Input3ImagePointer;
> typedef typename Input3ImageType::RegionType   Input3ImageRegionType;
> typedef typename Input3ImageType::PixelType    Input3ImagePixelType;
> typedef itk::SimpleDataObjectDecorator<Input3ImagePixelType>
> DecoratedInput3ImagePixelType;
>
> virtual void SetConstant2(const Input2ImagePixelType &input);
> virtual void SetConstant2(const DecoratedInput2ImagePixelType *input);
> /** Set the Third operand as a constant */
> virtual void SetConstant3(const Input3ImagePixelType &input);
> virtual void SetConstant3(const DecoratedInput3ImagePixelType *input);
> };
>
> template<...>
> void
> MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
> TOutputImage>
> ::SetConstant2(const Input2ImagePixelType &input)
> {
>          itkDebugMacro("setting SetConstant2 to " << input);
>          typename DecoratedInput2ImagePixelType::Pointer newInput =
> DecoratedInput2ImagePixelType::New();
>          newInput->Set(input);
>          this->SetConstant2(newInput);
> }
>
> template<...>
> void
> MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
> TOutputImage>
> ::SetConstant2(const DecoratedInput2ImagePixelType *input)
> {
>         this->SetNthInput( 1,const_cast<DecoratedInput2ImagePixelType*>(input));
> }
> template<...>
> void
> MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
> TOutputImage>
> ::SetConstant3(const Input3ImagePixelType &input)
> {
>          itkDebugMacro("setting SetConstant3 to " << input);
>          typename DecoratedInput3ImagePixelType::Pointer newInput =
> DecoratedInput3ImagePixelType::New();
>          newInput->Set(input);
>          this->SetConstant3(newInput);
> }
>
> template<...>
> void
> MyTernaryFunctorImageFilter< TInputImage1, TInputImage2, TInputImage3,
> TOutputImage>
> ::SetConstant3(const DecoratedInput3ImagePixelType *input)
> {
>         this->SetNthInput( 2,const_cast<DecoratedInput3ImagePixelType*>(input));
> }
>
> I pass this function an image for input1, then floats for other two inputs.
>
> Am I missing an ingredient here?
>
> -Jameson
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Setting-constants-in-ternary-functor-filters-tp35125.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 jmerkow at gmail.com  Fri Jan 16 11:56:57 2015
From: jmerkow at gmail.com (jmerkow)
Date: Fri, 16 Jan 2015 09:56:57 -0700 (MST)
Subject: [ITK-users] Setting constants in ternary functor filters
In-Reply-To: <CALzTN-QzXr81ZceTABJ=9PtKCU-E5dgqBLG2geqid5h_PSrUwA@mail.gmail.com>
References: <1421359760646-35125.post@n7.nabble.com>
 <CALzTN-QzXr81ZceTABJ=9PtKCU-E5dgqBLG2geqid5h_PSrUwA@mail.gmail.com>
Message-ID: <1421427417375-35130.post@n7.nabble.com>

I originally debated using a unary functor, though this will generally be
used with constants, there may be some cases where don't want it to be
constant, so I thought it best to write one image filter and have the
ability to set constants or image inputs.
Is there any reason that what Im trying to do won't work?

-Jameson



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From blowekamp at mail.nih.gov  Fri Jan 16 12:06:12 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 16 Jan 2015 12:06:12 -0500
Subject: [ITK-users] Setting constants in ternary functor filters
In-Reply-To: <1421427417375-35130.post@n7.nabble.com>
References: <1421359760646-35125.post@n7.nabble.com>
 <CALzTN-QzXr81ZceTABJ=9PtKCU-E5dgqBLG2geqid5h_PSrUwA@mail.gmail.com>
 <1421427417375-35130.post@n7.nabble.com>
Message-ID: <DFD202CD-2E70-4309-AF98-C73C29C43112@mail.nih.gov>

Hello,

You will need to look at the implementation of the TernaryFunctorImageFilter. You'll see that it expects the inputs to be images. I used image iterators and dynamics casts under this assumption.

On the other hand the implementation BinaryFunctorImageFilter, this handles the case where the inputs are decorators and the other complications that are needed.

Now, this is certainly a nice feature that could be added to the TernaryFunctorImageFilter, but I think there are really to many possible permutations for it to be worth the effort.

Brad

On Jan 16, 2015, at 11:56 AM, jmerkow <jmerkow at gmail.com> wrote:

> I originally debated using a unary functor, though this will generally be
> used with constants, there may be some cases where don't want it to be
> constant, so I thought it best to write one image filter and have the
> ability to set constants or image inputs.
> Is there any reason that what Im trying to do won't work?
> 
> -Jameson
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Setting-constants-in-ternary-functor-filters-tp35125p35130.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 jmerkow at gmail.com  Fri Jan 16 12:20:12 2015
From: jmerkow at gmail.com (jmerkow)
Date: Fri, 16 Jan 2015 10:20:12 -0700 (MST)
Subject: [ITK-users] Setting constants in ternary functor filters
In-Reply-To: <DFD202CD-2E70-4309-AF98-C73C29C43112@mail.nih.gov>
References: <1421359760646-35125.post@n7.nabble.com>
 <CALzTN-QzXr81ZceTABJ=9PtKCU-E5dgqBLG2geqid5h_PSrUwA@mail.gmail.com>
 <1421427417375-35130.post@n7.nabble.com>
 <DFD202CD-2E70-4309-AF98-C73C29C43112@mail.nih.gov>
Message-ID: <1421428812539-35132.post@n7.nabble.com>

Ahhh, I see. You have an if-else block that checked for NULL pointers, and
then call GetConstant on the null pointer.

I guess I misunderstood the decorated data object for pixel types.  I
thought that they were constant images, so that GetPixel returns the
constant at all locations. I re-read [1] more carefully and see my mistake.

Im going to switch to the unary functor, but is there a constant image class
like Im describing? It would be an easy way to set constants for functors
(or anything) without wasting memory by CreateImage -> Fill.

Thanks for your help!
-Jameson



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From nhadar at surgicaltheater.net  Fri Jan 16 12:43:15 2015
From: nhadar at surgicaltheater.net (Nissim Hadar)
Date: Fri, 16 Jan 2015 10:43:15 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <CALzTN-RGBBvxVQF7tzCkG_Ns+1skuNX7d9aa9QqSm8aj7=K9fA@mail.gmail.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421306921950-35117.post@n7.nabble.com>
 <CALzTN-RGBBvxVQF7tzCkG_Ns+1skuNX7d9aa9QqSm8aj7=K9fA@mail.gmail.com>
Message-ID: <1421430195087-35133.post@n7.nabble.com>

Thanks Matt.  I can try reading in the DICOM images, but I am not sure about
the "supported ITK file format".  Can I produce a DICOM output?  I do not
use VTK, so I do not understand how I will be able to view the output, in
any non-DICOM format.



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From nhadar at surgicaltheater.net  Fri Jan 16 12:58:42 2015
From: nhadar at surgicaltheater.net (Nissim Hadar)
Date: Fri, 16 Jan 2015 10:58:42 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421425919413-35128.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421425919413-35128.post@n7.nabble.com>
Message-ID: <1421431122358-35134.post@n7.nabble.com>

Actually - very on topic :)
I have built and started playing with VMTK, but the Python interface put me
off.  Our application has a C# GUI that calls ITK through a SWIG wrapper.
Your application sounds very interesting ... can we talk about it? (So ...
very interested...)



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From matt.mccormick at kitware.com  Fri Jan 16 14:07:46 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 16 Jan 2015 14:07:46 -0500
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421430195087-35133.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421306921950-35117.post@n7.nabble.com>
 <CALzTN-RGBBvxVQF7tzCkG_Ns+1skuNX7d9aa9QqSm8aj7=K9fA@mail.gmail.com>
 <1421430195087-35133.post@n7.nabble.com>
Message-ID: <CALzTN-Sg2vp6tL6sGhOhaMSUxmBU83=WLDW9Nh-fhFFxNOE51Q@mail.gmail.com>

ITK supports a number of file formats [1].  While it is technically
possible to create DICOM, this is very complicated, and one of the
other research formats, i.e. MetaImage, are recommended. There are
programs like 3D Slicer, based on ITK, that can be used to visualize
the output [2]. It is also possible to output PNG, JPG, TIFF,
representations, too. Write the resulting image to file in one of
these formats with ITK classes should be useful for debugging
purposes.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/group__Group-IO.html

[2] http://slicer.org/

On Fri, Jan 16, 2015 at 12:43 PM, Nissim Hadar
<nhadar at surgicaltheater.net> wrote:
> Thanks Matt.  I can try reading in the DICOM images, but I am not sure about
> the "supported ITK file format".  Can I produce a DICOM output?  I do not
> use VTK, so I do not understand how I will be able to view the output, in
> any non-DICOM format.
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113p35133.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 matt.mccormick at kitware.com  Fri Jan 16 14:09:18 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 16 Jan 2015 14:09:18 -0500
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421431122358-35134.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421425919413-35128.post@n7.nabble.com>
 <1421431122358-35134.post@n7.nabble.com>
Message-ID: <CALzTN-Q4CVVfA-=vP15kmPmQNFRvF_EtyRdQRDZ+eEqjCtKykA@mail.gmail.com>

Hi,

I would also recommend TubeTK [1] -- its forte is vessel segmentation,
and it works well with ITK.

Thanks,
Matt

[1] http://tubetk.org/

On Fri, Jan 16, 2015 at 12:58 PM, Nissim Hadar
<nhadar at surgicaltheater.net> wrote:
> Actually - very on topic :)
> I have built and started playing with VMTK, but the Python interface put me
> off.  Our application has a C# GUI that calls ITK through a SWIG wrapper.
> Your application sounds very interesting ... can we talk about it? (So ...
> very interested...)
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113p35134.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 nhadar at surgicaltheater.net  Fri Jan 16 17:00:04 2015
From: nhadar at surgicaltheater.net (Nissim Hadar)
Date: Fri, 16 Jan 2015 15:00:04 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <CALzTN-Q4CVVfA-=vP15kmPmQNFRvF_EtyRdQRDZ+eEqjCtKykA@mail.gmail.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421425919413-35128.post@n7.nabble.com>
 <1421431122358-35134.post@n7.nabble.com>
 <CALzTN-Q4CVVfA-=vP15kmPmQNFRvF_EtyRdQRDZ+eEqjCtKykA@mail.gmail.com>
Message-ID: <1421445604453-35137.post@n7.nabble.com>

I am also trying TubeTK.  Trying to compile that is :)



--
View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113p35137.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From emmasaunders123 at gmail.com  Mon Jan 19 11:47:58 2015
From: emmasaunders123 at gmail.com (Emma Saunders)
Date: Mon, 19 Jan 2015 16:47:58 +0000
Subject: [ITK-users] Upsample images or Deformation field - accuracy?
Message-ID: <CABQY8kS_TPSK5yYHfY2FRan0Erxs6eh7vBj7VfUmewHn_pcCCg@mail.gmail.com>

Hi,

Just wondering peoples experiences, would it be more or less accurate to
upsample to images and register them, than register two images and upsample
the deformation field?

Thanks

Emma
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From matt.mccormick at kitware.com  Mon Jan 19 13:59:08 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 19 Jan 2015 13:59:08 -0500
Subject: [ITK-users] Upsample images or Deformation field - accuracy?
In-Reply-To: <CABQY8kS_TPSK5yYHfY2FRan0Erxs6eh7vBj7VfUmewHn_pcCCg@mail.gmail.com>
References: <CABQY8kS_TPSK5yYHfY2FRan0Erxs6eh7vBj7VfUmewHn_pcCCg@mail.gmail.com>
Message-ID: <CALzTN-S_SeXHSJeU6SPigaSNwxF=YJb_jeE4rhtVgk_Q=oRS9Q@mail.gmail.com>

Hi Emma,

In practice, for many cases it probably does not make much of a difference.

However, if it does make a difference, upsampling the images first
with an accurate interpolator, like windowed-sinc interpolation,
should be best.

HTH,
Matt

On Mon, Jan 19, 2015 at 11:47 AM, Emma Saunders
<emmasaunders123 at gmail.com> wrote:
> Hi,
>
> Just wondering peoples experiences, would it be more or less accurate to
> upsample to images and register them, than register two images and upsample
> the deformation field?
>
> Thanks
>
> Emma
>
> _____________________________________
> 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 Erik.Olsson at neuro.gu.se  Tue Jan 20 15:04:10 2015
From: Erik.Olsson at neuro.gu.se (Erik Olsson)
Date: Tue, 20 Jan 2015 20:04:10 +0000
Subject: [ITK-users] Command line use of N4 in MacOS terminal
In-Reply-To: <CF231B882947A3469230E981C592EB80011081CE21@exchccr1.neuro.gu.se>
References: <CF231B882947A3469230E981C592EB80011081CE21@exchccr1.neuro.gu.se>
Message-ID: <CF231B882947A3469230E981C592EB80011081CE70@exchccr1.neuro.gu.se>



Hi,

I have recently started to use N4 as a command line installation and the bias field correction works great in general.

I am trying to figure out how to configure the flags for best performance on our T2 MRI images and when trying the rescale intensities I get the error message "segmentation fault 11" for both options ( -r 1   as well as -r 0). I also have a problem with the convergence flag -c, all works fine when I leave this flag out but when trying for example -c 50x50x50x50,0.0001 it stops after 1 iteration (Current level = 1
  Iteration 1 (of 50).   Current convergence value = 0.000816419 (threshold = 0.001). It does not seem like my specification of the threshold is read but the default value is used. Do you have an example of a typical setting for the -c flag other than the default values?

best regards
Erik

Erik Olsson
PhD

Institute of Psychiatry and Neurochemistry
Department of Neuroscience & physiology
The Sahlgrenska academy
Gothenburg University
Sweden
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From ntustison at gmail.com  Tue Jan 20 17:05:19 2015
From: ntustison at gmail.com (Nicholas Tustison)
Date: Tue, 20 Jan 2015 14:05:19 -0800
Subject: [ITK-users] Command line use of N4 in MacOS terminal
In-Reply-To: <CF231B882947A3469230E981C592EB80011081CE70@exchccr1.neuro.gu.se>
References: <CF231B882947A3469230E981C592EB80011081CE21@exchccr1.neuro.gu.se>
 <CF231B882947A3469230E981C592EB80011081CE70@exchccr1.neuro.gu.se>
Message-ID: <B5A129E4-E711-4B69-873F-79F545AC7B8C@gmail.com>

Hi Erik,

It sounds like this is an ANTs-specific issue.  If you have any further 
questions, I would recommend asking at that forum.

https://github.com/stnava/ANTs/issues <https://github.com/stnava/ANTs/issues>

The command line interface that you reference is ANTs-specific and
should have brackets around it e.g.,

-c [50x50x50x50,0.0001]

I don?t know about the rescale problem.  Does it happen on any image 
or just that specific T2?

Anyway, meet me over on the ANTs forum if you have further questions/
issues.

Nick


> On Jan 20, 2015, at 12:04 PM, Erik Olsson <Erik.Olsson at neuro.gu.se> wrote:
> 
> 
> 
> Hi,
> 
> I have recently started to use N4 as a command line installation and the bias field correction works great in general. 
> 
> I am trying to figure out how to configure the flags for best performance on our T2 MRI images and when trying the rescale intensities I get the error message "segmentation fault 11" for both options ( -r 1   as well as -r 0). I also have a problem with the convergence flag -c, all works fine when I leave this flag out but when trying for example -c 50x50x50x50,0.0001 it stops after 1 iteration (Current level = 1
>   Iteration 1 (of 50).   Current convergence value = 0.000816419 (threshold = 0.001). It does not seem like my specification of the threshold is read but the default value is used. Do you have an example of a typical setting for the -c flag other than the default values?
> 
> best regards
> Erik
> 
> Erik Olsson
> PhD 
> 
> Institute of Psychiatry and Neurochemistry 
> Department of Neuroscience & physiology
> The Sahlgrenska academy
> Gothenburg University
> Sweden
> _____________________________________
> 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  Wed Jan 21 09:09:14 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 21 Jan 2015 09:09:14 -0500
Subject: [ITK-users] FastMarching UpwindGradient Filters difference
Message-ID: <02EFACE9-9946-4546-9403-1A2709CB7B41@mail.nih.gov>

Hello,

I am trying to figure out the difference between the FastMarchingUpwindGradientImageFilterBase[1] and the FastMarchingUpwindGradientImageFilter[2].

The first thing to notice is that the "Base" class is NOT a parent of the other. Secondly, the non-Base implements a stopping criteria of reaching  a number of target nodes. This is now incorporated as an optional stopping criteria [3], in the framework. Then both of the filters add the upwind gradient image as an output, with what appears to be duplicated code. 

I don't see a real difference here. I think one should be deprecated.

Brad

[1] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingUpwindGradientImageFilterBase.html
[2] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingUpwindGradientImageFilter.html
[3] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingReachedTargetNodesStoppingCriterion.html

From arnaudgelas at gmail.com  Wed Jan 21 09:33:48 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 21 Jan 2015 15:33:48 +0100
Subject: [ITK-users] FastMarching UpwindGradient Filters difference
In-Reply-To: <02EFACE9-9946-4546-9403-1A2709CB7B41@mail.nih.gov>
References: <02EFACE9-9946-4546-9403-1A2709CB7B41@mail.nih.gov>
Message-ID: <3C7C228B-B1B1-4DF5-8CFF-06F82A542FD6@gmail.com>

Hi Brad,

FastMarchingUpwindGradientImageFilter is from ITKv3 while the other one is from ITKv4. Note that in terms of features, FastMarchingUpwiindGradientImageFilter would be a subset of the ?Base" one?

Arnaud



> On 21 Jan 2015, at 15:09, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 
> Hello,
> 
> I am trying to figure out the difference between the FastMarchingUpwindGradientImageFilterBase[1] and the FastMarchingUpwindGradientImageFilter[2].
> 
> The first thing to notice is that the "Base" class is NOT a parent of the other. Secondly, the non-Base implements a stopping criteria of reaching  a number of target nodes. This is now incorporated as an optional stopping criteria [3], in the framework. Then both of the filters add the upwind gradient image as an output, with what appears to be duplicated code. 
> 
> I don't see a real difference here. I think one should be deprecated.
> 
> Brad
> 
> [1] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingUpwindGradientImageFilterBase.html
> [2] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingUpwindGradientImageFilter.html
> [3] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingReachedTargetNodesStoppingCriterion.html


From ra.corredor at gmail.com  Wed Jan 21 12:50:06 2015
From: ra.corredor at gmail.com (Ricardo A Corredor)
Date: Wed, 21 Jan 2015 10:50:06 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <CALzTN-Sg2vp6tL6sGhOhaMSUxmBU83=WLDW9Nh-fhFFxNOE51Q@mail.gmail.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421306921950-35117.post@n7.nabble.com>
 <CALzTN-RGBBvxVQF7tzCkG_Ns+1skuNX7d9aa9QqSm8aj7=K9fA@mail.gmail.com>
 <1421430195087-35133.post@n7.nabble.com>
 <CALzTN-Sg2vp6tL6sGhOhaMSUxmBU83=WLDW9Nh-fhFFxNOE51Q@mail.gmail.com>
Message-ID: <1421862606723-35144.post@n7.nabble.com>

Hi,

For medical image visualization using a non-DICOM format I often use the
MHD/RAW (MetaImage) format. You only need to use a ImageFileWriter, set as
input the image you want to save and put a filename with .mhd as extension,
e.g. "./theImage.mhd". It is possible to visualize these files in multiple
programs: ParaView, MeVisLab, 3D Slicer, itkSNAP,  ... Usually I suggest
those tools on that order. Check also that the way you're constructing the
image is the same as stored in the array (row-major order or column-major
order) and that you're constructing an image with the correct data type,
correct size.

Hope that works!

Best,

RaC



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From mpinkert at wisc.edu  Wed Jan 21 14:44:53 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Wed, 21 Jan 2015 12:44:53 -0700 (MST)
Subject: [ITK-users] [ITK-Users] Multiple Inputs of different types
Message-ID: <1421869493940-7586810.post@n2.nabble.com>

Hi all,

I'm trying to develop a Vector Connected Component Filter/pipeline that
checks the direction of the eigenvector as well as whether or not the pixels
are touching.  I am doing this by modifying the three following filters that
build off of each other. 

itkSymmetricEigenAnalysisImageFilter.h so that it returns the largest
eigenvector rather than the eigenvalues

itkBinaryImageToLabelMapFilter.h to check that the eigenvectors for each
pixel are aligned after checking that they are touching

itkBinaryShapeKeepNObjectsImageFilter.h to simply pass the hessian into the
LabelMapFilter.

The problem is that I need to include a image that contains the hessian for
each pixel along with the normal input image, so that the KeepNObjects
filter can send it down to the LabelMapFilter and then to the
EigenAnalysisFilter.  However, none of the methods I have tried to get the
hessian image into the filters work, and I do not understand how to allow
for this second input.

So far I have tried modifying the template as follows

class BinaryVectorConnectedShapeKeepNObjectsImageFilter:
  public ImageToImageFilter< TInputImage, THessianImage, TInputImage >

Combined with using the SetInputX functions as seen in other filters as
follows

  void SetInput1(const TInputImage *image1)
  {
	  this->SetNthInput(0, const_cast <TInputImage * >( image1));
  }

This produces an error of "Too many template arguments".  

I have tried to make the hessian image a member variable and to use the
normal Get/Set macros, but that also produces errors of being unable to
convert between types when the function is used in main.

I have also tried to simply define a new function to set the Hessian, like
such

  void SetHessian(HessianImageType::Pointer hessianImage)
  {
     m_HessianImage = hessianImage;
  }

And alternate versions with different input arguments, which include "const
HessianImage *hessianImage".  These also run into errors where it won't
covert between types when I use the function in main.

I have looked around at different filters that have multiple inputs, and all
of them seem to be based on Functors/the BinaryFunctorImageFilter, but I am
very unsure of how I would go about modifying the filters, and have very
little experience with Functors.  Also, the arguments for the other filters
based on Functors all seem to include an operator as a fourth argument, and
I do not want to perform any operations on the Hessian until the
SymmetricAnalysis filter.

Does anyone know how I could set this second input simply, or could point me
to an example that does similar?

Best regards,
Michael Pinkert






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From matt.mccormick at kitware.com  Wed Jan 21 15:11:02 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Jan 2015 15:11:02 -0500
Subject: [ITK-users] [ITK-Users] Multiple Inputs of different types
In-Reply-To: <1421869493940-7586810.post@n2.nabble.com>
References: <1421869493940-7586810.post@n2.nabble.com>
Message-ID: <CALzTN-TaMS3jsMwLuhfLTJSsU4Kpp9GnDJ3=Yq=SBjPPgHx8dg@mail.gmail.com>

Hi Michael,

The ImageToImageFilter will still need to be templated over
TInputImage and TOutputImage.

For example filters that have multiple inputs to study, see, e.g.,

ConvolutionImageFilterBase [1]  (has a KernalImage input)
MaskedFFTNormalizedCorrelationImageFilter [2] (has MaskImage input)
HistogramThresholdImageFilter [3] (has MaskImage input)

HTH,
Matt

[1] http://itk.org/Doxygen/html/classitk_1_1ConvolutionImageFilterBase.html

[2]  http://itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html#a238b7f7d871a81849e66a12e0564825a

[3] http://itk.org/Doxygen/html/classitk_1_1HistogramThresholdImageFilter.html#a19a692e8043422ba6721815f94f04944

On Wed, Jan 21, 2015 at 2:44 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:
> Hi all,
>
> I'm trying to develop a Vector Connected Component Filter/pipeline that
> checks the direction of the eigenvector as well as whether or not the pixels
> are touching.  I am doing this by modifying the three following filters that
> build off of each other.
>
> itkSymmetricEigenAnalysisImageFilter.h so that it returns the largest
> eigenvector rather than the eigenvalues
>
> itkBinaryImageToLabelMapFilter.h to check that the eigenvectors for each
> pixel are aligned after checking that they are touching
>
> itkBinaryShapeKeepNObjectsImageFilter.h to simply pass the hessian into the
> LabelMapFilter.
>
> The problem is that I need to include a image that contains the hessian for
> each pixel along with the normal input image, so that the KeepNObjects
> filter can send it down to the LabelMapFilter and then to the
> EigenAnalysisFilter.  However, none of the methods I have tried to get the
> hessian image into the filters work, and I do not understand how to allow
> for this second input.
>
> So far I have tried modifying the template as follows
>
> class BinaryVectorConnectedShapeKeepNObjectsImageFilter:
>   public ImageToImageFilter< TInputImage, THessianImage, TInputImage >
>
> Combined with using the SetInputX functions as seen in other filters as
> follows
>
>   void SetInput1(const TInputImage *image1)
>   {
>           this->SetNthInput(0, const_cast <TInputImage * >( image1));
>   }
>
> This produces an error of "Too many template arguments".
>
> I have tried to make the hessian image a member variable and to use the
> normal Get/Set macros, but that also produces errors of being unable to
> convert between types when the function is used in main.
>
> I have also tried to simply define a new function to set the Hessian, like
> such
>
>   void SetHessian(HessianImageType::Pointer hessianImage)
>   {
>      m_HessianImage = hessianImage;
>   }
>
> And alternate versions with different input arguments, which include "const
> HessianImage *hessianImage".  These also run into errors where it won't
> covert between types when I use the function in main.
>
> I have looked around at different filters that have multiple inputs, and all
> of them seem to be based on Functors/the BinaryFunctorImageFilter, but I am
> very unsure of how I would go about modifying the filters, and have very
> little experience with Functors.  Also, the arguments for the other filters
> based on Functors all seem to include an operator as a fourth argument, and
> I do not want to perform any operations on the Hessian until the
> SymmetricAnalysis filter.
>
> Does anyone know how I could set this second input simply, or could point me
> to an example that does similar?
>
> Best regards,
> Michael Pinkert
>
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Users-Multiple-Inputs-of-different-types-tp7586810.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

From ted.florez at gmail.com  Wed Jan 21 15:26:28 2015
From: ted.florez at gmail.com (=?UTF-8?Q?Edward_Fl=C3=B3rez_Pacheco?=)
Date: Wed, 21 Jan 2015 14:26:28 -0600
Subject: [ITK-users] Files not found
Message-ID: <CAFxdfT1VFe_0dsKY+dsXxabr5oHs5p91tvkzyxwKV4H10i9W-A@mail.gmail.com>

Hi everyone

I am a new ITK user.
Currently, I am using a set of algorithms that use ITK.
I installed the *InsightToolkit - version 4.6.1* but I had these troubles:

CMakeFiles/DicomSeriesReadImageWrite2.dir/DicomSeriesReadImageWrite2.cxx.o
Linking CXX executable DicomSeriesReadImageWrite2
/usr/bin/ld: cannot find -lITKAlgorithms
/usr/bin/ld: cannot find -lITKIO
collect2: ld returned 1 exit status
make[2]: ** [DicomSeriesReadImageWrite2] Erro 1
make[1]: ** [CMakeFiles/DicomSeriesReadImageWrite2.dir/all] Erro 2
make: ** [all] Erro 2

If anyone has some idea about these issues and can give me some help I'll
be very thankful.
Thank you in advance.

Best regards.

-- 
*Edward Fl?rez*
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From matt.mccormick at kitware.com  Wed Jan 21 15:40:44 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Jan 2015 15:40:44 -0500
Subject: [ITK-users] [ITK] Files not found
In-Reply-To: <CAFxdfT1VFe_0dsKY+dsXxabr5oHs5p91tvkzyxwKV4H10i9W-A@mail.gmail.com>
References: <CAFxdfT1VFe_0dsKY+dsXxabr5oHs5p91tvkzyxwKV4H10i9W-A@mail.gmail.com>
Message-ID: <CALzTN-S-XpuJUJSXeOKxDibJU50=1mNVoPjQOasURjD0FuJ73A@mail.gmail.com>

Hi Edward,

It looks like you are trying to use a project that had a CMake
configuration for ITKv3.  To update the configuration for ITKv4,
change

target_link_libraries(myexecutable
  ITKAlgorithms
  ITKIO
  )

with

target_link_libraries(myexecutable
  ${ITK_LIBRARIES}
  )

HTH,
Matt

On Wed, Jan 21, 2015 at 3:26 PM, Edward Fl?rez Pacheco
<ted.florez at gmail.com> wrote:
> Hi everyone
>
> I am a new ITK user.
> Currently, I am using a set of algorithms that use ITK.
> I installed the InsightToolkit - version 4.6.1 but I had these troubles:
>
> CMakeFiles/DicomSeriesReadImageWrite2.dir/DicomSeriesReadImageWrite2.cxx.o
> Linking CXX executable DicomSeriesReadImageWrite2
> /usr/bin/ld: cannot find -lITKAlgorithms
> /usr/bin/ld: cannot find -lITKIO
> collect2: ld returned 1 exit status
> make[2]: ** [DicomSeriesReadImageWrite2] Erro 1
> make[1]: ** [CMakeFiles/DicomSeriesReadImageWrite2.dir/all] Erro 2
> make: ** [all] Erro 2
>
> If anyone has some idea about these issues and can give me some help I'll be
> very thankful.
> Thank you in advance.
>
> Best regards.
>
> --
> Edward Fl?rez
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From ted.florez at gmail.com  Wed Jan 21 16:21:28 2015
From: ted.florez at gmail.com (=?UTF-8?Q?Edward_Fl=C3=B3rez_Pacheco?=)
Date: Wed, 21 Jan 2015 15:21:28 -0600
Subject: [ITK-users] [ITK] Files not found
In-Reply-To: <CALzTN-S-XpuJUJSXeOKxDibJU50=1mNVoPjQOasURjD0FuJ73A@mail.gmail.com>
References: <CAFxdfT1VFe_0dsKY+dsXxabr5oHs5p91tvkzyxwKV4H10i9W-A@mail.gmail.com>
 <CALzTN-S-XpuJUJSXeOKxDibJU50=1mNVoPjQOasURjD0FuJ73A@mail.gmail.com>
Message-ID: <CAFxdfT0KfnPniSNCmUjMG88MPhZoR2uCmc16fwZQjNh8Y42GKQ@mail.gmail.com>

Dear Matt
Thank you so much!
I made the change you suggested and now it is working fine.

Regards.
Edward

2015-01-21 14:40 GMT-06:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Edward,
>
> It looks like you are trying to use a project that had a CMake
> configuration for ITKv3.  To update the configuration for ITKv4,
> change
>
> target_link_libraries(myexecutable
>   ITKAlgorithms
>   ITKIO
>   )
>
> with
>
> target_link_libraries(myexecutable
>   ${ITK_LIBRARIES}
>   )
>
> HTH,
> Matt
>
> On Wed, Jan 21, 2015 at 3:26 PM, Edward Fl?rez Pacheco
> <ted.florez at gmail.com> wrote:
> > Hi everyone
> >
> > I am a new ITK user.
> > Currently, I am using a set of algorithms that use ITK.
> > I installed the InsightToolkit - version 4.6.1 but I had these troubles:
> >
> >
> CMakeFiles/DicomSeriesReadImageWrite2.dir/DicomSeriesReadImageWrite2.cxx.o
> > Linking CXX executable DicomSeriesReadImageWrite2
> > /usr/bin/ld: cannot find -lITKAlgorithms
> > /usr/bin/ld: cannot find -lITKIO
> > collect2: ld returned 1 exit status
> > make[2]: ** [DicomSeriesReadImageWrite2] Erro 1
> > make[1]: ** [CMakeFiles/DicomSeriesReadImageWrite2.dir/all] Erro 2
> > make: ** [all] Erro 2
> >
> > If anyone has some idea about these issues and can give me some help
> I'll be
> > very thankful.
> > Thank you in advance.
> >
> > Best regards.
> >
> > --
> > Edward Fl?rez
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
>
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From mpinkert at wisc.edu  Wed Jan 21 15:29:15 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Wed, 21 Jan 2015 20:29:15 +0000
Subject: [ITK-users] [ITK-Users] Multiple Inputs of different types
In-Reply-To: <CALzTN-TaMS3jsMwLuhfLTJSsU4Kpp9GnDJ3=Yq=SBjPPgHx8dg@mail.gmail.com>
References: <1421869493940-7586810.post@n2.nabble.com>
 <CALzTN-TaMS3jsMwLuhfLTJSsU4Kpp9GnDJ3=Yq=SBjPPgHx8dg@mail.gmail.com>
Message-ID: <1421872155297.63645@wisc.edu>

Hi Matt,

Following the example of those filters seems to have worked, I'm no longer getting errors related to the multiple inputs.  Thank you very much.

Best regards,
Michael Pinkert

________________________________________
From: Matt McCormick <matt.mccormick at kitware.com>
Sent: Wednesday, January 21, 2015 2:11 PM
To: Michael Pinkert
Cc: insight-users at itk.org
Subject: Re: [ITK-users] [ITK-Users] Multiple Inputs of different types

Hi Michael,

The ImageToImageFilter will still need to be templated over
TInputImage and TOutputImage.

For example filters that have multiple inputs to study, see, e.g.,

ConvolutionImageFilterBase [1]  (has a KernalImage input)
MaskedFFTNormalizedCorrelationImageFilter [2] (has MaskImage input)
HistogramThresholdImageFilter [3] (has MaskImage input)

HTH,
Matt

[1] http://itk.org/Doxygen/html/classitk_1_1ConvolutionImageFilterBase.html

[2]  http://itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html#a238b7f7d871a81849e66a12e0564825a

[3] http://itk.org/Doxygen/html/classitk_1_1HistogramThresholdImageFilter.html#a19a692e8043422ba6721815f94f04944

On Wed, Jan 21, 2015 at 2:44 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:
> Hi all,
>
> I'm trying to develop a Vector Connected Component Filter/pipeline that
> checks the direction of the eigenvector as well as whether or not the pixels
> are touching.  I am doing this by modifying the three following filters that
> build off of each other.
>
> itkSymmetricEigenAnalysisImageFilter.h so that it returns the largest
> eigenvector rather than the eigenvalues
>
> itkBinaryImageToLabelMapFilter.h to check that the eigenvectors for each
> pixel are aligned after checking that they are touching
>
> itkBinaryShapeKeepNObjectsImageFilter.h to simply pass the hessian into the
> LabelMapFilter.
>
> The problem is that I need to include a image that contains the hessian for
> each pixel along with the normal input image, so that the KeepNObjects
> filter can send it down to the LabelMapFilter and then to the
> EigenAnalysisFilter.  However, none of the methods I have tried to get the
> hessian image into the filters work, and I do not understand how to allow
> for this second input.
>
> So far I have tried modifying the template as follows
>
> class BinaryVectorConnectedShapeKeepNObjectsImageFilter:
>   public ImageToImageFilter< TInputImage, THessianImage, TInputImage >
>
> Combined with using the SetInputX functions as seen in other filters as
> follows
>
>   void SetInput1(const TInputImage *image1)
>   {
>           this->SetNthInput(0, const_cast <TInputImage * >( image1));
>   }
>
> This produces an error of "Too many template arguments".
>
> I have tried to make the hessian image a member variable and to use the
> normal Get/Set macros, but that also produces errors of being unable to
> convert between types when the function is used in main.
>
> I have also tried to simply define a new function to set the Hessian, like
> such
>
>   void SetHessian(HessianImageType::Pointer hessianImage)
>   {
>      m_HessianImage = hessianImage;
>   }
>
> And alternate versions with different input arguments, which include "const
> HessianImage *hessianImage".  These also run into errors where it won't
> covert between types when I use the function in main.
>
> I have looked around at different filters that have multiple inputs, and all
> of them seem to be based on Functors/the BinaryFunctorImageFilter, but I am
> very unsure of how I would go about modifying the filters, and have very
> little experience with Functors.  Also, the arguments for the other filters
> based on Functors all seem to include an operator as a fourth argument, and
> I do not want to perform any operations on the Hessian until the
> SymmetricAnalysis filter.
>
> Does anyone know how I could set this second input simply, or could point me
> to an example that does similar?
>
> Best regards,
> Michael Pinkert
>
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Users-Multiple-Inputs-of-different-types-tp7586810.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

From nhadar at surgicaltheater.net  Wed Jan 21 17:04:06 2015
From: nhadar at surgicaltheater.net (Nissim Hadar)
Date: Wed, 21 Jan 2015 15:04:06 -0700 (MST)
Subject: [ITK-users] Vessel Segmentation
In-Reply-To: <1421862606723-35144.post@n7.nabble.com>
References: <1421275248945-35113.post@n7.nabble.com>
 <1421306921950-35117.post@n7.nabble.com>
 <CALzTN-RGBBvxVQF7tzCkG_Ns+1skuNX7d9aa9QqSm8aj7=K9fA@mail.gmail.com>
 <1421430195087-35133.post@n7.nabble.com>
 <CALzTN-Sg2vp6tL6sGhOhaMSUxmBU83=WLDW9Nh-fhFFxNOE51Q@mail.gmail.com>
 <1421862606723-35144.post@n7.nabble.com>
Message-ID: <1421877846342-35151.post@n7.nabble.com>

Thanks!
I now have the vessel segmentation working with my format (a sub-volume of
shorts extracted from the DICOM) - and can see the results in my 3D viewer
(see http://surgicaltheater.net if it interests you) .  The issue I have now
is settup up the parameters.  I have noticed that the algorithm is very
sensitive to gamma; the rest I am not sure of yet.
Cheers



--
View this message in context: http://itk-users.7.n7.nabble.com/Vessel-Segmentation-tp35113p35151.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Wed Jan 21 17:25:12 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Jan 2015 17:25:12 -0500
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-S1RznTTo97hT4QbwrVTDJKeM1_F6MBO=u0wDNwm2zTFw@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/cjudsaidlnb7v4tpiob79q92n8s


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/events/c4jvg33epbvaldg25skbm81fag4


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From grothausmann.roman at mh-hannover.de  Thu Jan 22 05:21:34 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Thu, 22 Jan 2015 11:21:34 +0100
Subject: [ITK-users] compile itk (VTKGlue ON) with vtk from paraview
Message-ID: <54C0CF2E.3060106@mh-hannover.de>

Dear mailing list members,


What configuration is needed to compile itk (4.6.1) with VTKGlue enabled with 
vtk from paraview (4.3.1) in order to compile Paraview plugins making use of ITK 
and VTK?


If I configure ITK to with:
BUILD_SHARED_LIBS                ON
Module_ITKVtkGlue                ON
VTK_DIR                          /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3

cmake complains about a missing VTKTargets.cmake even though 
PARAVIEW_INSTALL_DEVELOPMENT_FILES was set to ON. After a

cp VTK/VTKTargets.cmake /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3/

cmake is happy but I get linker errors at the end of the compilation of ITK when 
the VTKGlue is due:

Linking CXX shared library ../../../../lib/libITKVtkGlue-4.6.so
/usr/bin/ld: cannot find -lvtkSciberQuest
/usr/bin/ld: cannot find -lvtkEyeDomeLighting
/usr/bin/ld: cannot find -lvtkQvis
/usr/bin/ld: cannot find -lvtkPointSpriteRendering
/usr/bin/ld: cannot find -lvtkPVPythonCatalyst
/usr/bin/ld: cannot find -lvtkPointSpriteGraphics
/usr/bin/ld: cannot find -lvtkUtilitiesPythonInitializer


Switching off all PV plugin builds only leaves:

Linking CXX shared library ../../../../lib/libITKVtkGlue-4.6.so
/usr/bin/ld: cannot find -lvtkPVPythonCatalyst
/usr/bin/ld: cannot find -lvtkUtilitiesPythonInitializer

However, the files are there:

find /opt/paraview-4.3.1_git/ -name '*vtkPVPythonCatalyst*so*'
/opt/paraview-4.3.1_git/lib/paraview-4.3/site-packages/vtk/vtkPVPythonCatalystPython.so
/opt/paraview-4.3.1_git/lib/paraview-4.3/libvtkPVPythonCatalyst-pv4.3.so.1
/opt/paraview-4.3.1_git/lib/paraview-4.3/libvtkPVPythonCatalystPython27D-pv4.3.so.1
/opt/paraview-4.3.1_git/lib/paraview-4.3/libvtkPVPythonCatalyst-pv4.3.so
/opt/paraview-4.3.1_git/lib/paraview-4.3/libvtkPVPythonCatalystPython27D-pv4.3.so

find /opt/paraview-4.3.1_git/ -name '*vtkUtilitiesPythonInitializer*so*'
/opt/paraview-4.3.1_git/lib/paraview-4.3/libvtkUtilitiesPythonInitializer-pv4.3.so.1
/opt/paraview-4.3.1_git/lib/paraview-4.3/libvtkUtilitiesPythonInitializer-pv4.3.so


Adding the abs. file locations to the build command does not help nor does 
-L/opt/paraview-4.3.1_git/lib/paraview-4.3/


Using the build dir of VTK in PV-tree instead for ITK does not help either:
VTK_DIR                          /opt/compilation/ParaView-v4.3.1/build/VTK



If I configure ITK to with:
BUILD_SHARED_LIBS                OFF


I get linker errors in the last stage when compiling a PV plugin that makes use 
of VTK and ITK:

/usr/bin/ld: 
/opt/compilation/InsightToolkit-4.6.1/build/lib/libitkvnl_algo-4.6.a(vnl_real_eigensystem.cxx.o): 
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a 
shared object; recompile with -fPIC
/opt/compilation/InsightToolkit-4.6.1/build/lib/libitkvnl_algo-4.6.a: could not 
read symbols: Bad value

After I've added
CMAKE_CXX_FLAGS                  -fPIC

to Paraview and ITK and recompiled both I get:

/usr/bin/ld: 
/opt/compilation/InsightToolkit-4.6.1/build/lib/libitkv3p_netlib-4.6.a(dlamch.c.o): 
relocation R_X86_64_32 against `.bss' can not be used when making a shared 
object; recompile with -fPIC
/opt/compilation/InsightToolkit-4.6.1/build/lib/libitkv3p_netlib-4.6.a: could 
not read symbols: Bad value


What am I missing in my configuration of PV and ITK?

When and where should I specify:
CMAKE_CXX_FLAGS                  -fPIC
BUILD_SHARED_LIBS                ON/OFF

Is this the right VTK_DIR specification for ITK:
/opt/compilation/ParaView-v4.3.1/build/VTK
or
/opt/paraview-4.3.1_git/lib/cmake/paraview-4.3



Many thanks for any help or hints.
Roman


-- 
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. +49 511 532-9574

From rbar9508 at uni.sydney.edu.au  Thu Jan 22 18:02:32 2015
From: rbar9508 at uni.sydney.edu.au (rbar9508 at uni.sydney.edu.au)
Date: Thu, 22 Jan 2015 23:02:32 +0000
Subject: [ITK-users] NucMed DICOM slice thickness
Message-ID: <1421967755984.90298@uni.sydney.edu.au>


ITK seems to be misinterpreting the slice thickness reported in reconstructed nuc med images. The problem is that the slice thickness is being set to 1mm for some reason.


This wasn't a problem for ITK version 3.14, but it seems to have started to occur with versions 4.4.2 and 4.7.0 - probably since GDCM was merged into the ITK project.


The slice thickness tag is 0018,0050.


What's the best workaround if I want to use ITK version 4?


Thanks


Robbie

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From matt.mccormick at kitware.com  Thu Jan 22 19:01:16 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 22 Jan 2015 19:01:16 -0500
Subject: [ITK-users] NucMed DICOM slice thickness
In-Reply-To: <1421967755984.90298@uni.sydney.edu.au>
References: <1421967755984.90298@uni.sydney.edu.au>
Message-ID: <CALzTN-RQnA4bMu-OMj=8ihVuL1Bh66Bf4uUwftrKbkUgdwa4jQ@mail.gmail.com>

Hi Robbie,

This slice thickness, how thick the slab of tissue is that is
irradiated, is different from the spacing between slices -- the slice
thickness tag should not be used for spacing.  However, to override
this, use the ChangeInformationImageFilter with the slice thickness
taken from the MetaDataDictionary.

Hope this helps,
Matt

On Thu, Jan 22, 2015 at 6:02 PM, rbar9508 at uni.sydney.edu.au
<rbar9508 at uni.sydney.edu.au> wrote:
>
> ITK seems to be misinterpreting the slice thickness reported in
> reconstructed nuc med images. The problem is that the slice thickness is
> being set to 1mm for some reason.
>
>
> This wasn't a problem for ITK version 3.14, but it seems to have started to
> occur with versions 4.4.2 and 4.7.0 - probably since GDCM was merged into
> the ITK project.
>
>
> The slice thickness tag is 0018,0050.
>
>
> What's the best workaround if I want to use ITK version 4?
>
>
> Thanks
>
>
> Robbie
>
>
>
> _____________________________________
> 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 rbar9508 at uni.sydney.edu.au  Thu Jan 22 19:19:14 2015
From: rbar9508 at uni.sydney.edu.au (rbar9508 at uni.sydney.edu.au)
Date: Fri, 23 Jan 2015 00:19:14 +0000
Subject: [ITK-users] NucMed DICOM slice thickness
In-Reply-To: <CALzTN-RQnA4bMu-OMj=8ihVuL1Bh66Bf4uUwftrKbkUgdwa4jQ@mail.gmail.com>
References: <1421967755984.90298@uni.sydney.edu.au>,
 <CALzTN-RQnA4bMu-OMj=8ihVuL1Bh66Bf4uUwftrKbkUgdwa4jQ@mail.gmail.com>
Message-ID: <E3FC7660-EBBB-470C-9CF4-868A264BEA23@uni.sydney.edu.au>


Thanks Matt.

Actually, it looks like both slice spacing and slice thickness are set to 2.697mm for this particular spect recon image. It looks like it is in accordance with the nuc med IOD.

Sent from my iPad

> On 23 Jan 2015, at 11:01 am, "Matt McCormick" <matt.mccormick at kitware.com> wrote:
> 
> Hi Robbie,
> 
> This slice thickness, how thick the slab of tissue is that is
> irradiated, is different from the spacing between slices -- the slice
> thickness tag should not be used for spacing.  However, to override
> this, use the ChangeInformationImageFilter with the slice thickness
> taken from the MetaDataDictionary.
> 
> Hope this helps,
> Matt
> 
> On Thu, Jan 22, 2015 at 6:02 PM, rbar9508 at uni.sydney.edu.au
> <rbar9508 at uni.sydney.edu.au> wrote:
>> 
>> ITK seems to be misinterpreting the slice thickness reported in
>> reconstructed nuc med images. The problem is that the slice thickness is
>> being set to 1mm for some reason.
>> 
>> 
>> This wasn't a problem for ITK version 3.14, but it seems to have started to
>> occur with versions 4.4.2 and 4.7.0 - probably since GDCM was merged into
>> the ITK project.
>> 
>> 
>> The slice thickness tag is 0018,0050.
>> 
>> 
>> What's the best workaround if I want to use ITK version 4?
>> 
>> 
>> Thanks
>> 
>> 
>> Robbie
>> 
>> 
>> 
>> _____________________________________
>> 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 grothausmann.roman at mh-hannover.de  Fri Jan 23 04:20:29 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Fri, 23 Jan 2015 10:20:29 +0100
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
	paraview
In-Reply-To: <54C0CF2E.3060106@mh-hannover.de>
References: <54C0CF2E.3060106@mh-hannover.de>
Message-ID: <54C2125D.7090801@mh-hannover.de>


On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
> Adding the abs. file locations to the build command does not help nor does
> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/

I figured that the vtk dynamic libraries of PV have the ending *-pv4.3.so which 
seems to be the reason why the linker does not find them. If I create symbolic 
links to these files without the extension:

cd /opt/compilation/paraview-git_build/lib/
for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done

and adding -L/opt/compilation/paraview-git_build/lib/ to CMAKE_CXX_FLAGS
the compilation of ITK succeeds.

I wonder, is that the way it's meant to be done?


> What am I missing in my configuration of PV and ITK?
>
> When and where should I specify:
> CMAKE_CXX_FLAGS                  -fPIC
> BUILD_SHARED_LIBS                ON/OFF
>
> Is this the right VTK_DIR specification for ITK:
> /opt/compilation/ParaView-v4.3.1/build/VTK
> or
> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>
>
>
> Many thanks for any help or hints.
> Roman
>
>

-- 
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. +49 511 532-9574

From blowekamp at mail.nih.gov  Fri Jan 23 08:31:47 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 23 Jan 2015 08:31:47 -0500
Subject: [ITK-users] FastMarching UpwindGradient Filters difference
In-Reply-To: <3C7C228B-B1B1-4DF5-8CFF-06F82A542FD6@gmail.com>
References: <02EFACE9-9946-4546-9403-1A2709CB7B41@mail.nih.gov>
 <3C7C228B-B1B1-4DF5-8CFF-06F82A542FD6@gmail.com>
Message-ID: <A43C4B70-81F4-4C6C-B549-2E4DF01EDB6F@mail.nih.gov>

Arnaud,

Thanks for the info on this.

I am looked through the code in the FastMarchingImageFilterBase [1], it looks like its using std::vector a surprising number of times, and that it is getting re-allocated very frequently. Some cases look like they should be stack allocated templated array. Do you know why this class is this way? This may be the reason why it's so slow in debug mode, i.e. too much dynamic allocation on a per-pixel basis.

Brad


[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilterBase.hxx


On Jan 21, 2015, at 9:33 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Brad,
> 
> FastMarchingUpwindGradientImageFilter is from ITKv3 while the other one is from ITKv4. Note that in terms of features, FastMarchingUpwiindGradientImageFilter would be a subset of the ?Base" one?
> 
> Arnaud
> 
> 
> 
>> On 21 Jan 2015, at 15:09, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> 
>> Hello,
>> 
>> I am trying to figure out the difference between the FastMarchingUpwindGradientImageFilterBase[1] and the FastMarchingUpwindGradientImageFilter[2].
>> 
>> The first thing to notice is that the "Base" class is NOT a parent of the other. Secondly, the non-Base implements a stopping criteria of reaching  a number of target nodes. This is now incorporated as an optional stopping criteria [3], in the framework. Then both of the filters add the upwind gradient image as an output, with what appears to be duplicated code. 
>> 
>> I don't see a real difference here. I think one should be deprecated.
>> 
>> Brad
>> 
>> [1] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingUpwindGradientImageFilterBase.html
>> [2] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingUpwindGradientImageFilter.html
>> [3] http://www.itk.org/Doxygen/html/classitk_1_1FastMarchingReachedTargetNodesStoppingCriterion.html
> 


From taylor at braun-jones.org  Fri Jan 23 09:43:30 2015
From: taylor at braun-jones.org (Taylor Braun-Jones)
Date: Fri, 23 Jan 2015 09:43:30 -0500
Subject: [ITK-users] Implementation of DBSCAN clustering algorithm in ITK
Message-ID: <CAKfKJYtnHK3odQ017kU3kNGxUHtFRWww8raC+kw5RHy41FJNag@mail.gmail.com>

Hello insight-users,

Does ITK include an implementation of the DBSCAN algorithm[1] or are there
plans to add one? Searching through the code didn't turn anything up, but
maybe I missed it.

Thanks,
Taylor

[1] http://en.wikipedia.org/wiki/DBSCAN
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From flymolo at gmail.com  Fri Jan 23 10:29:37 2015
From: flymolo at gmail.com (Jonathan Grimm)
Date: Fri, 23 Jan 2015 10:29:37 -0500
Subject: [ITK-users] Job opening
Message-ID: <CAOxz2w8HG8TpqoXTCQED0bVJvEUszWvsFH8sWSh8E0ZF-tmH-w@mail.gmail.com>

Our lab is looking for a programmer. We use Fiji and ITK heavily.
Job flyer is linked below.

Also check out the rest of website, we do microscopy and have
collaborations to do Optical Coherence Tomography and MRI.

http://ocularbiomechanics.com/pdfs/ProgrammerJobFlyer.pdf

-- 
Sometimes it's hard to tell the dancer from the dance - Corwin in CoC
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From matt.mccormick at kitware.com  Fri Jan 23 10:44:18 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 23 Jan 2015 10:44:18 -0500
Subject: [ITK-users] Implementation of DBSCAN clustering algorithm in ITK
In-Reply-To: <CAKfKJYtnHK3odQ017kU3kNGxUHtFRWww8raC+kw5RHy41FJNag@mail.gmail.com>
References: <CAKfKJYtnHK3odQ017kU3kNGxUHtFRWww8raC+kw5RHy41FJNag@mail.gmail.com>
Message-ID: <CALzTN-TwekVYcz=MfaBhRExdoTi=ovTBpc7=6MKpzxWDjrV8OQ@mail.gmail.com>

Hi Taylor,

I think this algorithm would be great to have!

Thanks,
Matt

On Fri, Jan 23, 2015 at 9:43 AM, Taylor Braun-Jones
<taylor at braun-jones.org> wrote:
> Hello insight-users,
>
> Does ITK include an implementation of the DBSCAN algorithm[1] or are there
> plans to add one? Searching through the code didn't turn anything up, but
> maybe I missed it.
>
> Thanks,
> Taylor
>
> [1] http://en.wikipedia.org/wiki/DBSCAN
>
> _____________________________________
> 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 taylor at braun-jones.org  Fri Jan 23 12:14:24 2015
From: taylor at braun-jones.org (Taylor Braun-Jones)
Date: Fri, 23 Jan 2015 12:14:24 -0500
Subject: [ITK-users] Implementation of DBSCAN clustering algorithm in ITK
In-Reply-To: <CALzTN-TwekVYcz=MfaBhRExdoTi=ovTBpc7=6MKpzxWDjrV8OQ@mail.gmail.com>
References: <CAKfKJYtnHK3odQ017kU3kNGxUHtFRWww8raC+kw5RHy41FJNag@mail.gmail.com>
 <CALzTN-TwekVYcz=MfaBhRExdoTi=ovTBpc7=6MKpzxWDjrV8OQ@mail.gmail.com>
Message-ID: <CAKfKJYu1T-+Gs6S=-mp5=VLG1O-Zr-8x6w+2NY=52scPikVGEA@mail.gmail.com>

Maybe Nico (from the MITK team) can help :-)

Nico, Would you be interested in converting
mitk::UnstructuredGridClusteringFilter
<https://github.com/MITK/MITK/blob/master/Modules/AlgorithmsExt/mitkUnstructuredGridClusteringFilter.h>
into
a (templated) ITK filter and having it live upstream in ITK?

On Fri, Jan 23, 2015 at 10:44 AM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Taylor,
>
> I think this algorithm would be great to have!
>
> Thanks,
> Matt
>
> On Fri, Jan 23, 2015 at 9:43 AM, Taylor Braun-Jones
> <taylor at braun-jones.org> wrote:
> > Hello insight-users,
> >
> > Does ITK include an implementation of the DBSCAN algorithm[1] or are
> there
> > plans to add one? Searching through the code didn't turn anything up, but
> > maybe I missed it.
> >
> > Thanks,
> > Taylor
> >
> > [1] http://en.wikipedia.org/wiki/DBSCAN
> >
> > _____________________________________
> > 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 Jan 23 12:15:45 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 23 Jan 2015 12:15:45 -0500
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
	paraview
In-Reply-To: <54C2125D.7090801@mh-hannover.de>
References: <54C0CF2E.3060106@mh-hannover.de> <54C2125D.7090801@mh-hannover.de>
Message-ID: <CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>

Hi Roman,

Thanks for looking into the issue and reporting it to the mailing list.

Paraview should be installing VTKTargets.cmake, which tells the build
system where to find the libraries.  Note that there might be two
VTKTargets.cmake files that are generated -- one for the build tree
and one for the install tree.

HTH,
Matt

On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
>
> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>
>> Adding the abs. file locations to the build command does not help nor does
>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>
>
> I figured that the vtk dynamic libraries of PV have the ending *-pv4.3.so
> which seems to be the reason why the linker does not find them. If I create
> symbolic links to these files without the extension:
>
> cd /opt/compilation/paraview-git_build/lib/
> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>
> and adding -L/opt/compilation/paraview-git_build/lib/ to CMAKE_CXX_FLAGS
> the compilation of ITK succeeds.
>
> I wonder, is that the way it's meant to be done?
>
>
>
>> What am I missing in my configuration of PV and ITK?
>>
>> When and where should I specify:
>> CMAKE_CXX_FLAGS                  -fPIC
>> BUILD_SHARED_LIBS                ON/OFF
>>
>> Is this the right VTK_DIR specification for ITK:
>> /opt/compilation/ParaView-v4.3.1/build/VTK
>> or
>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>
>>
>>
>> Many thanks for any help or hints.
>> Roman
>>
>>
>
> --
> 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. +49 511 532-9574
> _____________________________________
> 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 mpinkert at wisc.edu  Fri Jan 23 14:36:21 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Fri, 23 Jan 2015 12:36:21 -0700 (MST)
Subject: [ITK-users] Visual Studio 2010 Express autocomplete IntelliSense
 not working with ITK 4.8.0
Message-ID: <1422041781731-7586829.post@n2.nabble.com>

Hi all,

I recently upgraded my install of ITK from 4.5 to 4.8, but it seems to have
broken IntelliSense in Microsoft Visual Studio 2010.

The editor will not autocomplete functions anymore or give a list of
options, making it much more cumbersome to write code.  Normally it will
give a list of options after :: or -> commands, but now I simply get the
error:

IntelliSense: 'No additional information available' (See Troubleshooting
IntelliSense in C++ Projects' for further help)

I am still given a list of included .h files when I use #include, and I can
also right click on declared types to go to the appropriate header files,
but it does not autocomplete otherwise, so the program is locating the files
correctly.

The faq page of "Troubleshooting IntelliSense in C++ projects" has not been
helpful.

Does anyone have experience with a bug like this?

Best regards,
Michael Pinkert



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Visual-Studio-2010-Express-autocomplete-IntelliSense-not-working-with-ITK-4-8-0-tp7586829.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From dzenanz at gmail.com  Fri Jan 23 16:31:17 2015
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 23 Jan 2015 16:31:17 -0500
Subject: [ITK-users] [ITK] Visual Studio 2010 Express autocomplete
 IntelliSense not working with ITK 4.8.0
In-Reply-To: <1422041781731-7586829.post@n2.nabble.com>
References: <1422041781731-7586829.post@n2.nabble.com>
Message-ID: <CAPf2UMQv1tZezDcSsFuJkAaPoTxVveUwk2zDtiue-nb3er8=sQ@mail.gmail.com>

I do remember occasionally have such issues with template-heavy code,
mostly (earlier) versions of ITK. That was years ago. Newer versions of
Visual Studio handle templated code much better. Newest free VS
<http://www.visualstudio.com/en-us/news/vs2013-community-vs.aspx> works
well with ITK.

On Fri, Jan 23, 2015 at 2:36 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:

> Hi all,
>
> I recently upgraded my install of ITK from 4.5 to 4.8, but it seems to have
> broken IntelliSense in Microsoft Visual Studio 2010.
>
> The editor will not autocomplete functions anymore or give a list of
> options, making it much more cumbersome to write code.  Normally it will
> give a list of options after :: or -> commands, but now I simply get the
> error:
>
> IntelliSense: 'No additional information available' (See Troubleshooting
> IntelliSense in C++ Projects' for further help)
>
> I am still given a list of included .h files when I use #include, and I can
> also right click on declared types to go to the appropriate header files,
> but it does not autocomplete otherwise, so the program is locating the
> files
> correctly.
>
> The faq page of "Troubleshooting IntelliSense in C++ projects" has not been
> helpful.
>
> Does anyone have experience with a bug like this?
>
> Best regards,
> Michael Pinkert
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Visual-Studio-2010-Express-autocomplete-IntelliSense-not-working-with-ITK-4-8-0-tp7586829.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 elena.bresciani87 at gmail.com  Mon Jan 26 03:44:48 2015
From: elena.bresciani87 at gmail.com (gmail)
Date: Mon, 26 Jan 2015 09:44:48 +0100
Subject: [ITK-users] Management of big datasets
Message-ID: <E7419960-4AE6-4E66-AD86-A8B141D672FE@gmail.com>

Hi everybody,

I?m having issues with a project that requires using 3D datasets up to 4-5 GB without subsampling. 
The pipeline is something like this:

ImageFileReader -> IntensityWindowingImageFilterType -> MedianImageFilter -> ScalarImageKmeansImageFilter -> RelabelComponentImageFilter -> RescaleIntensityImageFilter -> ImageSeriesWriter

I was getting std::bad_alloc error but I solved this problem with  -> ReleaseDataFlagOn() for each filter of the pipeline. 

My code runs well till the end and all the images of the output stack are written but after only 170 images (of a total of 1990) are written correctly whilst the others have only black pixels.

Any guess on what could be the problem? Maybe I should use ImageFileWriter instead of ImageSeriesWriter?

Best regards

Elena
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From grothausmann.roman at mh-hannover.de  Mon Jan 26 04:02:20 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 26 Jan 2015 10:02:20 +0100
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
 paraview
In-Reply-To: <CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>
References: <54C0CF2E.3060106@mh-hannover.de>	<54C2125D.7090801@mh-hannover.de>
 <CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>
Message-ID: <54C6029C.4040600@mh-hannover.de>

Hi Matt,


Thank You very much for Your reply.
I can only find one VTKTargets.cmake in /opt/compilation/paraview-git_build/VTK/
It seems though that it is lacking the relevant entries for the libraries that 
troubled me, e.g. vtkPVPythonCatalyst and vtkUtilitiesPythonInitializer.

I'm about to publish the ITK-VTK PV plugin in the Midas Journal, what 
installation instructions should I give there?
Will the testing environment be able to compile this plugin and its tests or 
should I disable automatic testing for this contribution?

Many thanks for looking into this.
Roman

On 23/01/15 18:15, Matt McCormick wrote:
> Hi Roman,
>
> Thanks for looking into the issue and reporting it to the mailing list.
>
> Paraview should be installing VTKTargets.cmake, which tells the build
> system where to find the libraries.  Note that there might be two
> VTKTargets.cmake files that are generated -- one for the build tree
> and one for the install tree.
>
> HTH,
> Matt
>
> On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>>
>> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>>
>>> Adding the abs. file locations to the build command does not help nor does
>>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>>
>>
>> I figured that the vtk dynamic libraries of PV have the ending *-pv4.3.so
>> which seems to be the reason why the linker does not find them. If I create
>> symbolic links to these files without the extension:
>>
>> cd /opt/compilation/paraview-git_build/lib/
>> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>>
>> and adding -L/opt/compilation/paraview-git_build/lib/ to CMAKE_CXX_FLAGS
>> the compilation of ITK succeeds.
>>
>> I wonder, is that the way it's meant to be done?
>>
>>
>>
>>> What am I missing in my configuration of PV and ITK?
>>>
>>> When and where should I specify:
>>> CMAKE_CXX_FLAGS                  -fPIC
>>> BUILD_SHARED_LIBS                ON/OFF
>>>
>>> Is this the right VTK_DIR specification for ITK:
>>> /opt/compilation/ParaView-v4.3.1/build/VTK
>>> or
>>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>>
>>>
>>>
>>> Many thanks for any help or hints.
>>> Roman
>>>
>>>
>>
>> --
>> 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. +49 511 532-9574
>> _____________________________________
>> 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

-- 
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. +49 511 532-9574

From matt.mccormick at kitware.com  Mon Jan 26 09:39:23 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 26 Jan 2015 09:39:23 -0500
Subject: [ITK-users] Management of big datasets
In-Reply-To: <E7419960-4AE6-4E66-AD86-A8B141D672FE@gmail.com>
References: <E7419960-4AE6-4E66-AD86-A8B141D672FE@gmail.com>
Message-ID: <CALzTN-SXmeYVH3gsMRu+ekEq-SvZzASbYOaxibzwqZmyxDDMTA@mail.gmail.com>

Hi Elena,

Using ImageFileWriter might help debug the problem.  Or, ensuring that
all the data is being processed incrementally along each stage of the
pipeline can help.

Also, it is recommended to conclude each pipeline with

  ->UpdateLargestPossibleRegion();

instead of just

  ->Update();

which helps with some subtle pipeline issues.

Please keep us posted on your progress.

Thanks,
Matt

On Mon, Jan 26, 2015 at 3:44 AM, gmail <elena.bresciani87 at gmail.com> wrote:
> Hi everybody,
>
> I?m having issues with a project that requires using 3D datasets up to 4-5
> GB without subsampling.
> The pipeline is something like this:
>
> ImageFileReader -> IntensityWindowingImageFilterType -> MedianImageFilter ->
> ScalarImageKmeansImageFilter -> RelabelComponentImageFilter ->
> RescaleIntensityImageFilter -> ImageSeriesWriter
>
> I was getting std::bad_alloc error but I solved this problem with  ->
> ReleaseDataFlagOn() for each filter of the pipeline.
>
> My code runs well till the end and all the images of the output stack are
> written but after only 170 images (of a total of 1990) are written correctly
> whilst the others have only black pixels.
>
> Any guess on what could be the problem? Maybe I should use ImageFileWriter
> instead of ImageSeriesWriter?
>
> Best regards
>
> Elena
>
> _____________________________________
> 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  Mon Jan 26 09:43:36 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 26 Jan 2015 09:43:36 -0500
Subject: [ITK-users] Management of big datasets
In-Reply-To: <E7419960-4AE6-4E66-AD86-A8B141D672FE@gmail.com>
References: <E7419960-4AE6-4E66-AD86-A8B141D672FE@gmail.com>
Message-ID: <EBEB5156-3351-4974-AC15-9B8221737BDE@mail.nih.gov>

Hello,

It looks like this should work.

What OS, compiler, architecture are you using? How much memory is on the system you are using?

We need to narrow down where the problem is occurring. Here are some suggestions to track down and to figure out where the problem is:

Your though of switching to a ImageFileWirter is reasonable. My goto format it mha, as I have written the most tests for that IO, and have the highest confidence there.

Does this pipeline work with smaller data? Perhaps just run your data through the BInShrinkFilter in stead of Median?

I have used most of these filters with large data, and expect them to work very well. But I have not used the ScalarImageKmeans so much. Try replacing it with the MultiOtsu.

Also write out some intermediate image to see where the image processing is going awry.

Hope that helps,
Brad

On Jan 26, 2015, at 3:44 AM, gmail <elena.bresciani87 at gmail.com> wrote:

> Hi everybody,
> 
> I?m having issues with a project that requires using 3D datasets up to 4-5 GB without subsampling. 
> The pipeline is something like this:
> 
> ImageFileReader -> IntensityWindowingImageFilterType -> MedianImageFilter -> ScalarImageKmeansImageFilter -> RelabelComponentImageFilter -> RescaleIntensityImageFilter -> ImageSeriesWriter
> 
> I was getting std::bad_alloc error but I solved this problem with  -> ReleaseDataFlagOn() for each filter of the pipeline. 
> 
> My code runs well till the end and all the images of the output stack are written but after only 170 images (of a total of 1990) are written correctly whilst the others have only black pixels.
> 
> Any guess on what could be the problem? Maybe I should use ImageFileWriter instead of ImageSeriesWriter?
> 
> Best regards
> 
> Elena
> _____________________________________
> 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  Mon Jan 26 11:54:53 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 26 Jan 2015 11:54:53 -0500
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
	paraview
In-Reply-To: <54C6029C.4040600@mh-hannover.de>
References: <54C0CF2E.3060106@mh-hannover.de> <54C2125D.7090801@mh-hannover.de>
 <CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>
 <54C6029C.4040600@mh-hannover.de>
Message-ID: <CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>

Hi Roman,

Thanks for the update. Great to hear about the Midas Journal article!

I do not think the Midas Journal will be able to build your plugin.

I would recommend creating build instructions to build against a
ParaView build tree.  I have just verified that ITK builds with the
ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
directory.

I don't see the install tree VTKTargets.cmake file in my ParaView
build, either. In the long term, the ParaView CMake configuration
should be corrected.

HTH,
Matt

On Mon, Jan 26, 2015 at 4:02 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
> Hi Matt,
>
>
> Thank You very much for Your reply.
> I can only find one VTKTargets.cmake in
> /opt/compilation/paraview-git_build/VTK/
> It seems though that it is lacking the relevant entries for the libraries
> that troubled me, e.g. vtkPVPythonCatalyst and
> vtkUtilitiesPythonInitializer.
>
> I'm about to publish the ITK-VTK PV plugin in the Midas Journal, what
> installation instructions should I give there?
> Will the testing environment be able to compile this plugin and its tests or
> should I disable automatic testing for this contribution?
>
> Many thanks for looking into this.
> Roman
>
>
> On 23/01/15 18:15, Matt McCormick wrote:
>>
>> Hi Roman,
>>
>> Thanks for looking into the issue and reporting it to the mailing list.
>>
>> Paraview should be installing VTKTargets.cmake, which tells the build
>> system where to find the libraries.  Note that there might be two
>> VTKTargets.cmake files that are generated -- one for the build tree
>> and one for the install tree.
>>
>> HTH,
>> Matt
>>
>> On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
>> <grothausmann.roman at mh-hannover.de> wrote:
>>>
>>>
>>> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>>>
>>>>
>>>> Adding the abs. file locations to the build command does not help nor
>>>> does
>>>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>>>
>>>
>>>
>>> I figured that the vtk dynamic libraries of PV have the ending *-pv4.3.so
>>> which seems to be the reason why the linker does not find them. If I
>>> create
>>> symbolic links to these files without the extension:
>>>
>>> cd /opt/compilation/paraview-git_build/lib/
>>> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>>>
>>> and adding -L/opt/compilation/paraview-git_build/lib/ to CMAKE_CXX_FLAGS
>>> the compilation of ITK succeeds.
>>>
>>> I wonder, is that the way it's meant to be done?
>>>
>>>
>>>
>>>> What am I missing in my configuration of PV and ITK?
>>>>
>>>> When and where should I specify:
>>>> CMAKE_CXX_FLAGS                  -fPIC
>>>> BUILD_SHARED_LIBS                ON/OFF
>>>>
>>>> Is this the right VTK_DIR specification for ITK:
>>>> /opt/compilation/ParaView-v4.3.1/build/VTK
>>>> or
>>>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>>>
>>>>
>>>>
>>>> Many thanks for any help or hints.
>>>> Roman
>>>>
>>>>
>>>
>>> --
>>> 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. +49 511 532-9574
>>> _____________________________________
>>> 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
>
>
> --
> 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. +49 511 532-9574

From matt.mccormick at kitware.com  Mon Jan 26 12:03:33 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 26 Jan 2015 12:03:33 -0500
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
	paraview
In-Reply-To: <CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>
References: <54C0CF2E.3060106@mh-hannover.de> <54C2125D.7090801@mh-hannover.de>
 <CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>
 <54C6029C.4040600@mh-hannover.de>
 <CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>
Message-ID: <CALzTN-Tqa2ink0bPf8a0aVP-5jyUZsijUuXBNTRD4Qim6bcmBQ@mail.gmail.com>

PS. Another option is to compile / install VTK separately outside of
ParaView.  This may be a better approach.

It is a little tricky to configure ParaView in this way.  See:

  http://www.paraview.org/gitweb?p=ParaView.git;a=blob;f=CMakeLists.txt;h=d80ff535090edc1fa9520d39aa66d269fc1db8b3;hb=HEAD#l516

On Mon, Jan 26, 2015 at 11:54 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Roman,
>
> Thanks for the update. Great to hear about the Midas Journal article!
>
> I do not think the Midas Journal will be able to build your plugin.
>
> I would recommend creating build instructions to build against a
> ParaView build tree.  I have just verified that ITK builds with the
> ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
> directory.
>
> I don't see the install tree VTKTargets.cmake file in my ParaView
> build, either. In the long term, the ParaView CMake configuration
> should be corrected.
>
> HTH,
> Matt
>
> On Mon, Jan 26, 2015 at 4:02 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Hi Matt,
>>
>>
>> Thank You very much for Your reply.
>> I can only find one VTKTargets.cmake in
>> /opt/compilation/paraview-git_build/VTK/
>> It seems though that it is lacking the relevant entries for the libraries
>> that troubled me, e.g. vtkPVPythonCatalyst and
>> vtkUtilitiesPythonInitializer.
>>
>> I'm about to publish the ITK-VTK PV plugin in the Midas Journal, what
>> installation instructions should I give there?
>> Will the testing environment be able to compile this plugin and its tests or
>> should I disable automatic testing for this contribution?
>>
>> Many thanks for looking into this.
>> Roman
>>
>>
>> On 23/01/15 18:15, Matt McCormick wrote:
>>>
>>> Hi Roman,
>>>
>>> Thanks for looking into the issue and reporting it to the mailing list.
>>>
>>> Paraview should be installing VTKTargets.cmake, which tells the build
>>> system where to find the libraries.  Note that there might be two
>>> VTKTargets.cmake files that are generated -- one for the build tree
>>> and one for the install tree.
>>>
>>> HTH,
>>> Matt
>>>
>>> On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>
>>>>
>>>> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>>>>
>>>>>
>>>>> Adding the abs. file locations to the build command does not help nor
>>>>> does
>>>>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>>>>
>>>>
>>>>
>>>> I figured that the vtk dynamic libraries of PV have the ending *-pv4.3.so
>>>> which seems to be the reason why the linker does not find them. If I
>>>> create
>>>> symbolic links to these files without the extension:
>>>>
>>>> cd /opt/compilation/paraview-git_build/lib/
>>>> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>>>>
>>>> and adding -L/opt/compilation/paraview-git_build/lib/ to CMAKE_CXX_FLAGS
>>>> the compilation of ITK succeeds.
>>>>
>>>> I wonder, is that the way it's meant to be done?
>>>>
>>>>
>>>>
>>>>> What am I missing in my configuration of PV and ITK?
>>>>>
>>>>> When and where should I specify:
>>>>> CMAKE_CXX_FLAGS                  -fPIC
>>>>> BUILD_SHARED_LIBS                ON/OFF
>>>>>
>>>>> Is this the right VTK_DIR specification for ITK:
>>>>> /opt/compilation/ParaView-v4.3.1/build/VTK
>>>>> or
>>>>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>>>>
>>>>>
>>>>>
>>>>> Many thanks for any help or hints.
>>>>> Roman
>>>>>
>>>>>
>>>>
>>>> --
>>>> 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. +49 511 532-9574
>>>> _____________________________________
>>>> 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
>>
>>
>> --
>> 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. +49 511 532-9574

From alexandra-judisch at uiowa.edu  Mon Jan 26 12:04:46 2015
From: alexandra-judisch at uiowa.edu (Judisch, Alexandra L)
Date: Mon, 26 Jan 2015 17:04:46 +0000
Subject: [ITK-users] Image Size [0, 0, 0]
Message-ID: <15CDF1AC0152924C817C2D5522E0904F329FA901@ITSNT438.iowa.uiowa.edu>

Hi all!
I am trying to write code to downsample an image using the resample image filter. The problem is that the program keeps failing because it is reading the image size as [0, 0, 0] which is obviously not the case. Has anyone run into this problem before or have any ideas how to fix it?
Thanks,
Alex
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From bill.lorensen at gmail.com  Mon Jan 26 12:27:54 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 26 Jan 2015 12:27:54 -0500
Subject: [ITK-users] Image Size [0, 0, 0]
In-Reply-To: <15CDF1AC0152924C817C2D5522E0904F329FA901@ITSNT438.iowa.uiowa.edu>
References: <15CDF1AC0152924C817C2D5522E0904F329FA901@ITSNT438.iowa.uiowa.edu>
Message-ID: <CADZJ4hPjWwK4uheRNHBVs7Vtfr6oH5OH10pWE5pHE_mFSHdLxQ@mail.gmail.com>

What image format?


On Mon, Jan 26, 2015 at 12:04 PM, Judisch, Alexandra L
<alexandra-judisch at uiowa.edu> wrote:
> Hi all!
> I am trying to write code to downsample an image using the resample image
> filter. The problem is that the program keeps failing because it is reading
> the image size as [0, 0, 0] which is obviously not the case. Has anyone run
> into this problem before or have any ideas how to fix it?
> Thanks,
> Alex
>
> _____________________________________
> 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
>



-- 
Unpaid intern in BillsBasement at noware dot com

From bill.lorensen at gmail.com  Mon Jan 26 12:50:24 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 26 Jan 2015 12:50:24 -0500
Subject: [ITK-users] Image Size [0, 0, 0]
In-Reply-To: <CADZJ4hPjWwK4uheRNHBVs7Vtfr6oH5OH10pWE5pHE_mFSHdLxQ@mail.gmail.com>
References: <15CDF1AC0152924C817C2D5522E0904F329FA901@ITSNT438.iowa.uiowa.edu>
 <CADZJ4hPjWwK4uheRNHBVs7Vtfr6oH5OH10pWE5pHE_mFSHdLxQ@mail.gmail.com>
Message-ID: <CADZJ4hMAFKYQ4KnG4DXhs1UD2tTcnJTdjy=6iu5MpmXex8LkNw@mail.gmail.com>

Can you share code that illustrate the problem?


On Mon, Jan 26, 2015 at 12:27 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> What image format?
>
>
> On Mon, Jan 26, 2015 at 12:04 PM, Judisch, Alexandra L
> <alexandra-judisch at uiowa.edu> wrote:
>> Hi all!
>> I am trying to write code to downsample an image using the resample image
>> filter. The problem is that the program keeps failing because it is reading
>> the image size as [0, 0, 0] which is obviously not the case. Has anyone run
>> into this problem before or have any ideas how to fix it?
>> Thanks,
>> Alex
>>
>> _____________________________________
>> 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
>>
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com

From bill.lorensen at gmail.com  Mon Jan 26 12:57:37 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 26 Jan 2015 12:57:37 -0500
Subject: [ITK-users] Image Size [0, 0, 0]
In-Reply-To: <15CDF1AC0152924C817C2D5522E0904F329FA93E@ITSNT438.iowa.uiowa.edu>
References: <15CDF1AC0152924C817C2D5522E0904F329FA901@ITSNT438.iowa.uiowa.edu>
 <CADZJ4hPjWwK4uheRNHBVs7Vtfr6oH5OH10pWE5pHE_mFSHdLxQ@mail.gmail.com>
 <CADZJ4hMAFKYQ4KnG4DXhs1UD2tTcnJTdjy=6iu5MpmXex8LkNw@mail.gmail.com>
 <15CDF1AC0152924C817C2D5522E0904F329FA93E@ITSNT438.iowa.uiowa.edu>
Message-ID: <CADZJ4hNqaFh6Sz9OtdOL-Ex0J1UhT5xAoecGfZdoOVc1Rga0aA@mail.gmail.com>

Before
input = reader->GetOutput();
apply
reader->Update();


On Mon, Jan 26, 2015 at 12:52 PM, Judisch, Alexandra L
<alexandra-judisch at uiowa.edu> wrote:
> Here it is.
> ________________________________________
> From: Bill Lorensen [bill.lorensen at gmail.com]
> Sent: Monday, January 26, 2015 11:50 AM
> To: Judisch, Alexandra L
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] Image Size [0, 0, 0]
>
> Can you share code that illustrate the problem?
>
>
> On Mon, Jan 26, 2015 at 12:27 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> What image format?
>>
>>
>> On Mon, Jan 26, 2015 at 12:04 PM, Judisch, Alexandra L
>> <alexandra-judisch at uiowa.edu> wrote:
>>> Hi all!
>>> I am trying to write code to downsample an image using the resample image
>>> filter. The problem is that the program keeps failing because it is reading
>>> the image size as [0, 0, 0] which is obviously not the case. Has anyone run
>>> into this problem before or have any ideas how to fix it?
>>> Thanks,
>>> Alex
>>>
>>> _____________________________________
>>> 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
>>>
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com

From bill.lorensen at gmail.com  Mon Jan 26 12:58:51 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 26 Jan 2015 12:58:51 -0500
Subject: [ITK-users] Image Size [0, 0, 0]
In-Reply-To: <CADZJ4hNqaFh6Sz9OtdOL-Ex0J1UhT5xAoecGfZdoOVc1Rga0aA@mail.gmail.com>
References: <15CDF1AC0152924C817C2D5522E0904F329FA901@ITSNT438.iowa.uiowa.edu>
 <CADZJ4hPjWwK4uheRNHBVs7Vtfr6oH5OH10pWE5pHE_mFSHdLxQ@mail.gmail.com>
 <CADZJ4hMAFKYQ4KnG4DXhs1UD2tTcnJTdjy=6iu5MpmXex8LkNw@mail.gmail.com>
 <15CDF1AC0152924C817C2D5522E0904F329FA93E@ITSNT438.iowa.uiowa.edu>
 <CADZJ4hNqaFh6Sz9OtdOL-Ex0J1UhT5xAoecGfZdoOVc1Rga0aA@mail.gmail.com>
Message-ID: <CADZJ4hMFK0QpsDm+0zTk2Ayp79jLGvtV9XBGQ-Tj76nYVfSL-Q@mail.gmail.com>

Or instead of
resample->SetInput( input );
apply
resample->SetInput(reader->GetOutput());


On Mon, Jan 26, 2015 at 12:57 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Before
> input = reader->GetOutput();
> apply
> reader->Update();
>
>
> On Mon, Jan 26, 2015 at 12:52 PM, Judisch, Alexandra L
> <alexandra-judisch at uiowa.edu> wrote:
>> Here it is.
>> ________________________________________
>> From: Bill Lorensen [bill.lorensen at gmail.com]
>> Sent: Monday, January 26, 2015 11:50 AM
>> To: Judisch, Alexandra L
>> Cc: insight-users at itk.org
>> Subject: Re: [ITK-users] Image Size [0, 0, 0]
>>
>> Can you share code that illustrate the problem?
>>
>>
>> On Mon, Jan 26, 2015 at 12:27 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>> What image format?
>>>
>>>
>>> On Mon, Jan 26, 2015 at 12:04 PM, Judisch, Alexandra L
>>> <alexandra-judisch at uiowa.edu> wrote:
>>>> Hi all!
>>>> I am trying to write code to downsample an image using the resample image
>>>> filter. The problem is that the program keeps failing because it is reading
>>>> the image size as [0, 0, 0] which is obviously not the case. Has anyone run
>>>> into this problem before or have any ideas how to fix it?
>>>> Thanks,
>>>> Alex
>>>>
>>>> _____________________________________
>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot com
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com

From mpinkert at wisc.edu  Mon Jan 26 15:30:40 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Mon, 26 Jan 2015 13:30:40 -0700 (MST)
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio 2013/12.0
Message-ID: <1422304240599-7586842.post@n2.nabble.com>

Hi all,

I have been trying to compile ITK on Visual Studio 2013, as I was having
problems with the autocomplete IntelliSense in Visual Studio 2010.  However,
when I try to build ITK I am running into two errors, and do not know what
to do about them.  Does anyone have experience with the following?

Error	1	error C1189: #error :  "No native data type can represent a 16-bit
integer."	C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
75	1	ITKIOLSM

Error	2	error LNK1104: cannot open file
'..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
C:\Build\ITK\Modules\Core\TestKernel\src\LINK	itkTestDriver

Best regards,
Michael Pinkert



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From matt.mccormick at kitware.com  Mon Jan 26 15:36:21 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 26 Jan 2015 15:36:21 -0500
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
	2013/12.0
In-Reply-To: <1422304240599-7586842.post@n2.nabble.com>
References: <1422304240599-7586842.post@n2.nabble.com>
Message-ID: <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>

Hi Michael,

Did you start with a fresh build tree?

Matt

On Mon, Jan 26, 2015 at 3:30 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:
> Hi all,
>
> I have been trying to compile ITK on Visual Studio 2013, as I was having
> problems with the autocomplete IntelliSense in Visual Studio 2010.  However,
> when I try to build ITK I am running into two errors, and do not know what
> to do about them.  Does anyone have experience with the following?
>
> Error   1       error C1189: #error :  "No native data type can represent a 16-bit
> integer."       C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
> 75      1       ITKIOLSM
>
> Error   2       error LNK1104: cannot open file
> '..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
> C:\Build\ITK\Modules\Core\TestKernel\src\LINK   itkTestDriver
>
> Best regards,
> Michael Pinkert
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842.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

From mpinkert at wisc.edu  Mon Jan 26 15:44:00 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Mon, 26 Jan 2015 13:44:00 -0700 (MST)
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
 2013/12.0
In-Reply-To: <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
References: <1422304240599-7586842.post@n2.nabble.com>
 <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
Message-ID: <1422305040386-7586844.post@n2.nabble.com>

Hi Matt,

I am not sure what you mean by fresh build tree.  I cleared my cache in
CMake and deleted the build folder for my old ITK installation, if that is
what you mean.

Best regards,
Michale Pinkert


Matt McCormick-2 wrote
> Hi Michael,
> 
> Did you start with a fresh build tree?
> 
> Matt
> 
> On Mon, Jan 26, 2015 at 3:30 PM, Michael Pinkert &lt;

> mpinkert@

> &gt; wrote:
>> Hi all,
>>
>> I have been trying to compile ITK on Visual Studio 2013, as I was having
>> problems with the autocomplete IntelliSense in Visual Studio 2010. 
>> However,
>> when I try to build ITK I am running into two errors, and do not know
>> what
>> to do about them.  Does anyone have experience with the following?
>>
>> Error   1       error C1189: #error :  "No native data type can represent
>> a 16-bit
>> integer."      
>> C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
>> 75      1       ITKIOLSM
>>
>> Error   2       error LNK1104: cannot open file
>> '..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
>> C:\Build\ITK\Modules\Core\TestKernel\src\LINK   itkTestDriver
>>
>> Best regards,
>> Michael Pinkert
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842.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
> _____________________________________
> 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  Mon Jan 26 15:49:23 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 26 Jan 2015 15:49:23 -0500
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
	2013/12.0
In-Reply-To: <1422305040386-7586844.post@n2.nabble.com>
References: <1422304240599-7586842.post@n2.nabble.com>
 <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
 <1422305040386-7586844.post@n2.nabble.com>
Message-ID: <CALzTN-QFx_ASWBmK7Neg1tdFCFmyrLt41jsF1UEbBd7NVLvNqw@mail.gmail.com>

Hi Michael,

Instead of just clearing the cache, it is necessary to delete the
entry build tree when switching to a new compiler.

HTH,
Matt

On Mon, Jan 26, 2015 at 3:44 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:
> Hi Matt,
>
> I am not sure what you mean by fresh build tree.  I cleared my cache in
> CMake and deleted the build folder for my old ITK installation, if that is
> what you mean.
>
> Best regards,
> Michale Pinkert
>
>
> Matt McCormick-2 wrote
>> Hi Michael,
>>
>> Did you start with a fresh build tree?
>>
>> Matt
>>
>> On Mon, Jan 26, 2015 at 3:30 PM, Michael Pinkert &lt;
>
>> mpinkert@
>
>> &gt; wrote:
>>> Hi all,
>>>
>>> I have been trying to compile ITK on Visual Studio 2013, as I was having
>>> problems with the autocomplete IntelliSense in Visual Studio 2010.
>>> However,
>>> when I try to build ITK I am running into two errors, and do not know
>>> what
>>> to do about them.  Does anyone have experience with the following?
>>>
>>> Error   1       error C1189: #error :  "No native data type can represent
>>> a 16-bit
>>> integer."
>>> C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
>>> 75      1       ITKIOLSM
>>>
>>> Error   2       error LNK1104: cannot open file
>>> '..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
>>> C:\Build\ITK\Modules\Core\TestKernel\src\LINK   itkTestDriver
>>>
>>> Best regards,
>>> Michael Pinkert
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842.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
>> _____________________________________
>> 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
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586844.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

From mpinkert at wisc.edu  Tue Jan 27 10:43:26 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Tue, 27 Jan 2015 08:43:26 -0700 (MST)
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
 2013/12.0
In-Reply-To: <CALzTN-QFx_ASWBmK7Neg1tdFCFmyrLt41jsF1UEbBd7NVLvNqw@mail.gmail.com>
References: <1422304240599-7586842.post@n2.nabble.com>
 <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
 <1422305040386-7586844.post@n2.nabble.com>
 <CALzTN-QFx_ASWBmK7Neg1tdFCFmyrLt41jsF1UEbBd7NVLvNqw@mail.gmail.com>
Message-ID: <1422373406186-7586846.post@n2.nabble.com>

Hi Matt,

I managed to get ITK built by building to a new folder, but I still do not
understand how I am supposed to clear the build tree, as I doubt that is the
correct solution.  I have googled the term, but I have not found anything
that would indicate how I would delete the build tree, if clearing the cache
and deleting the build folder do not count.  

I am still having more errors after trying to build it.  The first is an
error in the compiler:

command-line error: invalid macro definition:
..../ITK/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL.h"

The next is related, in that I am still having trouble with the IntelliSense
autocomplete not functioning in any of my projects, which was my purpose in
updating visual studio.  Do you have any experience with these additional
errors?  I believe the first error may be related to IntelliSense, due to a
quick google turning up that error in relation to it, but nothing I've found
has told me how to solve it.

Best regards,
Michael Pinkert


Matt McCormick-2 wrote
> Hi Michael,
> 
> Instead of just clearing the cache, it is necessary to delete the
> entry build tree when switching to a new compiler.
> 
> HTH,
> Matt
> 
> On Mon, Jan 26, 2015 at 3:44 PM, Michael Pinkert &lt;

> mpinkert@

> &gt; wrote:
>> Hi Matt,
>>
>> I am not sure what you mean by fresh build tree.  I cleared my cache in
>> CMake and deleted the build folder for my old ITK installation, if that
>> is
>> what you mean.
>>
>> Best regards,
>> Michale Pinkert
>>
>>
>> Matt McCormick-2 wrote
>>> Hi Michael,
>>>
>>> Did you start with a fresh build tree?
>>>
>>> Matt
>>>
>>> On Mon, Jan 26, 2015 at 3:30 PM, Michael Pinkert &lt;
>>
>>> mpinkert@
>>
>>> &gt; wrote:
>>>> Hi all,
>>>>
>>>> I have been trying to compile ITK on Visual Studio 2013, as I was
>>>> having
>>>> problems with the autocomplete IntelliSense in Visual Studio 2010.
>>>> However,
>>>> when I try to build ITK I am running into two errors, and do not know
>>>> what
>>>> to do about them.  Does anyone have experience with the following?
>>>>
>>>> Error   1       error C1189: #error :  "No native data type can
>>>> represent
>>>> a 16-bit
>>>> integer."
>>>> C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
>>>> 75      1       ITKIOLSM
>>>>
>>>> Error   2       error LNK1104: cannot open file
>>>> '..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
>>>> C:\Build\ITK\Modules\Core\TestKernel\src\LINK   itkTestDriver
>>>>
>>>> Best regards,
>>>> Michael Pinkert
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842.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
>>> _____________________________________
>>> 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
>>
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586844.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
> _____________________________________
> 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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View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586846.html
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From matt.mccormick at kitware.com  Tue Jan 27 12:45:56 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 27 Jan 2015 12:45:56 -0500
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
	2013/12.0
In-Reply-To: <1422373406186-7586846.post@n2.nabble.com>
References: <1422304240599-7586842.post@n2.nabble.com>
 <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
 <1422305040386-7586844.post@n2.nabble.com>
 <CALzTN-QFx_ASWBmK7Neg1tdFCFmyrLt41jsF1UEbBd7NVLvNqw@mail.gmail.com>
 <1422373406186-7586846.post@n2.nabble.com>
Message-ID: <CALzTN-Scg-+7Y46xpbLu9EWsZ=kn0ony3CgxxKrCSPy-OH4vPg@mail.gmail.com>

Hi Michael,

> I managed to get ITK built by building to a new folder, but I still do not
> understand how I am supposed to clear the build tree, as I doubt that is the
> correct solution.  I have googled the term, but I have not found anything
> that would indicate how I would delete the build tree, if clearing the cache
> and deleting the build folder do not count.

Good to hear it is build . By "clearing the build tree", I meant to
complete delete all the content of the build folder.  Sorry if there
was any confusion.

> I am still having more errors after trying to build it.  The first is an
> error in the compiler:
>
> command-line error: invalid macro definition:
> ..../ITK/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL.h"

This is fixed in ITK's current Git "master" and "release" branches.
Instructions to get the Git version are here [1].

> The next is related, in that I am still having trouble with the IntelliSense
> autocomplete not functioning in any of my projects, which was my purpose in
> updating visual studio.  Do you have any experience with these additional
> errors?  I believe the first error may be related to IntelliSense, due to a
> quick google turning up that error in relation to it, but nothing I've found
> has told me how to solve it.

Sorry, I don't have much experience with IntelliSense.

Be well,
Matt

[1] http://www.itk.org/Wiki/ITK/Git/Download



> Best regards,
> Michael Pinkert
>
>
> Matt McCormick-2 wrote
>> Hi Michael,
>>
>> Instead of just clearing the cache, it is necessary to delete the
>> entry build tree when switching to a new compiler.
>>
>> HTH,
>> Matt
>>
>> On Mon, Jan 26, 2015 at 3:44 PM, Michael Pinkert &lt;
>
>> mpinkert@
>
>> &gt; wrote:
>>> Hi Matt,
>>>
>>> I am not sure what you mean by fresh build tree.  I cleared my cache in
>>> CMake and deleted the build folder for my old ITK installation, if that
>>> is
>>> what you mean.
>>>
>>> Best regards,
>>> Michale Pinkert
>>>
>>>
>>> Matt McCormick-2 wrote
>>>> Hi Michael,
>>>>
>>>> Did you start with a fresh build tree?
>>>>
>>>> Matt
>>>>
>>>> On Mon, Jan 26, 2015 at 3:30 PM, Michael Pinkert &lt;
>>>
>>>> mpinkert@
>>>
>>>> &gt; wrote:
>>>>> Hi all,
>>>>>
>>>>> I have been trying to compile ITK on Visual Studio 2013, as I was
>>>>> having
>>>>> problems with the autocomplete IntelliSense in Visual Studio 2010.
>>>>> However,
>>>>> when I try to build ITK I am running into two errors, and do not know
>>>>> what
>>>>> to do about them.  Does anyone have experience with the following?
>>>>>
>>>>> Error   1       error C1189: #error :  "No native data type can
>>>>> represent
>>>>> a 16-bit
>>>>> integer."
>>>>> C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
>>>>> 75      1       ITKIOLSM
>>>>>
>>>>> Error   2       error LNK1104: cannot open file
>>>>> '..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
>>>>> C:\Build\ITK\Modules\Core\TestKernel\src\LINK   itkTestDriver
>>>>>
>>>>> Best regards,
>>>>> Michael Pinkert
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> View this message in context:
>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842.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
>>>> _____________________________________
>>>> 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
>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586844.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
>> _____________________________________
>> 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
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586846.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

From dzenanz at gmail.com  Tue Jan 27 13:11:11 2015
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 27 Jan 2015 13:11:11 -0500
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
	2013/12.0
In-Reply-To: <1422373406186-7586846.post@n2.nabble.com>
References: <1422304240599-7586842.post@n2.nabble.com>
 <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
 <1422305040386-7586844.post@n2.nabble.com>
 <CALzTN-QFx_ASWBmK7Neg1tdFCFmyrLt41jsF1UEbBd7NVLvNqw@mail.gmail.com>
 <1422373406186-7586846.post@n2.nabble.com>
Message-ID: <CAPf2UMRMXeY88k0mCd=Zbi45MetL2MdAeiLu-1dTF=f9mW8Whw@mail.gmail.com>

Hi Michael,

compile errors in the project can throw off IntelliSense. Once the project
is properly compiling, it takes some time to gather all the information
into a browsing database (*.sdf). Let VS scan all headers and generate this
file. It needs to be done independently for projects using ITK, I think.

In case IntelliSense is broken for a project, try closing VS, deleting its
.sdf file, and then reopening the project's solution file. This should
re-trigger an update of IntelliSense browsing database.

HTH

On Tue, Jan 27, 2015 at 10:43 AM, Michael Pinkert <mpinkert at wisc.edu> wrote:

> Hi Matt,
>
> I managed to get ITK built by building to a new folder, but I still do not
> understand how I am supposed to clear the build tree, as I doubt that is
> the
> correct solution.  I have googled the term, but I have not found anything
> that would indicate how I would delete the build tree, if clearing the
> cache
> and deleting the build folder do not count.
>
> I am still having more errors after trying to build it.  The first is an
> error in the compiler:
>
> command-line error: invalid macro definition:
>
> ..../ITK/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL.h"
>
> The next is related, in that I am still having trouble with the
> IntelliSense
> autocomplete not functioning in any of my projects, which was my purpose in
> updating visual studio.  Do you have any experience with these additional
> errors?  I believe the first error may be related to IntelliSense, due to a
> quick google turning up that error in relation to it, but nothing I've
> found
> has told me how to solve it.
>
> Best regards,
> Michael Pinkert
>
>
> Matt McCormick-2 wrote
> > Hi Michael,
> >
> > Instead of just clearing the cache, it is necessary to delete the
> > entry build tree when switching to a new compiler.
> >
> > HTH,
> > Matt
> >
> > On Mon, Jan 26, 2015 at 3:44 PM, Michael Pinkert &lt;
>
> > mpinkert@
>
> > &gt; wrote:
> >> Hi Matt,
> >>
> >> I am not sure what you mean by fresh build tree.  I cleared my cache in
> >> CMake and deleted the build folder for my old ITK installation, if that
> >> is
> >> what you mean.
> >>
> >> Best regards,
> >> Michale Pinkert
> >>
> >>
> >> Matt McCormick-2 wrote
> >>> Hi Michael,
> >>>
> >>> Did you start with a fresh build tree?
> >>>
> >>> Matt
> >>>
> >>> On Mon, Jan 26, 2015 at 3:30 PM, Michael Pinkert &lt;
> >>
> >>> mpinkert@
> >>
> >>> &gt; wrote:
> >>>> Hi all,
> >>>>
> >>>> I have been trying to compile ITK on Visual Studio 2013, as I was
> >>>> having
> >>>> problems with the autocomplete IntelliSense in Visual Studio 2010.
> >>>> However,
> >>>> when I try to build ITK I am running into two errors, and do not know
> >>>> what
> >>>> to do about them.  Does anyone have experience with the following?
> >>>>
> >>>> Error   1       error C1189: #error :  "No native data type can
> >>>> represent
> >>>> a 16-bit
> >>>> integer."
> >>>> C:\Build\ITK\Modules\ThirdParty\KWSys\src\itksys\FundamentalType.h
> >>>> 75      1       ITKIOLSM
> >>>>
> >>>> Error   2       error LNK1104: cannot open file
> >>>> '..\..\..\..\lib\Debug\ITKIOLSM-4.8.lib'
> >>>> C:\Build\ITK\Modules\Core\TestKernel\src\LINK   itkTestDriver
> >>>>
> >>>> Best regards,
> >>>> Michael Pinkert
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> View this message in context:
> >>>>
> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842.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
> >>> _____________________________________
> >>> 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
> >>
> >>
> >>
> >>
> >>
> >> --
> >> View this message in context:
> >>
> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586844.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
> > _____________________________________
> > 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
>
>
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586846.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 mpinkert at wisc.edu  Tue Jan 27 16:51:03 2015
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Tue, 27 Jan 2015 14:51:03 -0700 (MST)
Subject: [ITK-users] Trouble compiling ITK 4.8.0 on Visual Studio
 2013/12.0
In-Reply-To: <CAPf2UMRMXeY88k0mCd=Zbi45MetL2MdAeiLu-1dTF=f9mW8Whw@mail.gmail.com>
References: <1422304240599-7586842.post@n2.nabble.com>
 <CALzTN-QKk-hMpJKthhwu9ueiJ=1XX3r8oiwefio9njdATg1niQ@mail.gmail.com>
 <1422305040386-7586844.post@n2.nabble.com>
 <CALzTN-QFx_ASWBmK7Neg1tdFCFmyrLt41jsF1UEbBd7NVLvNqw@mail.gmail.com>
 <1422373406186-7586846.post@n2.nabble.com>
 <CAPf2UMRMXeY88k0mCd=Zbi45MetL2MdAeiLu-1dTF=f9mW8Whw@mail.gmail.com>
Message-ID: <1422395463573-7586849.post@n2.nabble.com>

Hi Matt, D?enan,

Thank you both.  Updating ITK again managed to solve both issues, and I will
definitely keep in mind how Visual Studio IntelliSense works in the future
when I am having problems again.

Best regards,
Michael Pinkert



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Trouble-compiling-ITK-4-8-0-on-Visual-Studio-2013-12-0-tp7586842p7586849.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From grothausmann.roman at mh-hannover.de  Wed Jan 28 07:02:10 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Wed, 28 Jan 2015 13:02:10 +0100
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
 paraview
In-Reply-To: <CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>
References: <54C0CF2E.3060106@mh-hannover.de>	<54C2125D.7090801@mh-hannover.de>	<CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>	<54C6029C.4040600@mh-hannover.de>
 <CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>
Message-ID: <54C8CFC2.4000305@mh-hannover.de>

Hi Matt,

On 26/01/15 17:54, Matt McCormick wrote:
 > I do not think the Midas Journal will be able to build your plugin.

OK, so I added a VTK test program. Is there a way to test if the automatic 
testing environment would be able to build and run my VTK test program BEFORE 
submitting the contribution to Midas?
(My last submission never got tested by the system so far, i.e. there is no 
colde review reported:
http://www.vtkjournal.org/browse/publication/949)

 > I would recommend creating build instructions to build against a
 > ParaView build tree.  I have just verified that ITK builds with the
 > ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
 > directory.

Did You use BUILD_SHARED_LIBS ON for both ITK and ParaView? ITK also compiles 
fine without any errors for me if I use BUILD_SHARED_LIBS OFF, however the 
problems then arise when compiling the plugin.
If You like, You can test the compilation of the plugin with the code from the 
git repository:
https://github.com/romangrothausmann/FacetAnalyser

Many thanks for looking into this.
Roman


On 26/01/15 17:54, Matt McCormick wrote:
> Hi Roman,
>
> Thanks for the update. Great to hear about the Midas Journal article!
>
> I do not think the Midas Journal will be able to build your plugin.
>
> I would recommend creating build instructions to build against a
> ParaView build tree.  I have just verified that ITK builds with the
> ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
> directory.
>
> I don't see the install tree VTKTargets.cmake file in my ParaView
> build, either. In the long term, the ParaView CMake configuration
> should be corrected.
>
> HTH,
> Matt
>
> On Mon, Jan 26, 2015 at 4:02 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Hi Matt,
>>
>>
>> Thank You very much for Your reply.
>> I can only find one VTKTargets.cmake in
>> /opt/compilation/paraview-git_build/VTK/
>> It seems though that it is lacking the relevant entries for the libraries
>> that troubled me, e.g. vtkPVPythonCatalyst and
>> vtkUtilitiesPythonInitializer.
>>
>> I'm about to publish the ITK-VTK PV plugin in the Midas Journal, what
>> installation instructions should I give there?
>> Will the testing environment be able to compile this plugin and its tests or
>> should I disable automatic testing for this contribution?
>>
>> Many thanks for looking into this.
>> Roman
>>
>>
>> On 23/01/15 18:15, Matt McCormick wrote:
>>>
>>> Hi Roman,
>>>
>>> Thanks for looking into the issue and reporting it to the mailing list.
>>>
>>> Paraview should be installing VTKTargets.cmake, which tells the build
>>> system where to find the libraries.  Note that there might be two
>>> VTKTargets.cmake files that are generated -- one for the build tree
>>> and one for the install tree.
>>>
>>> HTH,
>>> Matt
>>>
>>> On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>
>>>>
>>>> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>>>>
>>>>>
>>>>> Adding the abs. file locations to the build command does not help nor
>>>>> does
>>>>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>>>>
>>>>
>>>>
>>>> I figured that the vtk dynamic libraries of PV have the ending *-pv4.3.so
>>>> which seems to be the reason why the linker does not find them. If I
>>>> create
>>>> symbolic links to these files without the extension:
>>>>
>>>> cd /opt/compilation/paraview-git_build/lib/
>>>> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>>>>
>>>> and adding -L/opt/compilation/paraview-git_build/lib/ to CMAKE_CXX_FLAGS
>>>> the compilation of ITK succeeds.
>>>>
>>>> I wonder, is that the way it's meant to be done?
>>>>
>>>>
>>>>
>>>>> What am I missing in my configuration of PV and ITK?
>>>>>
>>>>> When and where should I specify:
>>>>> CMAKE_CXX_FLAGS                  -fPIC
>>>>> BUILD_SHARED_LIBS                ON/OFF
>>>>>
>>>>> Is this the right VTK_DIR specification for ITK:
>>>>> /opt/compilation/ParaView-v4.3.1/build/VTK
>>>>> or
>>>>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>>>>
>>>>>
>>>>>
>>>>> Many thanks for any help or hints.
>>>>> Roman
>>>>>
>>>>>
>>>>
>>>> --
>>>> 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. +49 511 532-9574
>>>> _____________________________________
>>>> 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
>>
>>
>> --
>> 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. +49 511 532-9574

-- 
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. +49 511 532-9574

From matimontg at gmail.com  Wed Jan 28 08:45:09 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 28 Jan 2015 10:45:09 -0300
Subject: [ITK-users] ITK Apps | MultiResMIRegistration output slices blank
Message-ID: <CAKKNfu+mTCbv9EZr0J-Ny-On=2wVHPUZDQh42XXTTUagYPLfpQ@mail.gmail.com>

Hi,

I'm working on testing the MultiResMIRegistration example in the ITK-Apps
and it runs ok with my dataset, however, the output mhd file has blank
slices (all black or white depending the Window Level setting)

I get the matrix and overall transform set parameters and the values kinda
make sense but I can't see the resulting slices for some reason.

Both MR and CT 3D files are signed short pixel type.

Thanks for the help.

Matias.
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From emily-hammond at uiowa.edu  Wed Jan 28 10:36:08 2015
From: emily-hammond at uiowa.edu (Hammond, Emily M)
Date: Wed, 28 Jan 2015 15:36:08 +0000
Subject: [ITK-users] STL methods and ITK
Message-ID: <2609C492EC89AB4CAAD3647B8D1A43CC2F1854DB@ITSNT437.iowa.uiowa.edu>

Hello all,

I am trying to wrap some functionality into a class. I am trying to write a function that reads in a transform file, however, I want it to take the list of transform pointers that it reads in and merge/insert them into an already existing list. Here is the relevant code with more details below it:

#include "itkTransform.h"
#include "itkTransformFileReader.h"

public:
typedef itk::TransformFileReaderTemplate< double > TransformReaderType;
typedef TransformReaderType::TransformListType TransformListType;

void ReadTransformFile( const char * transformFilename );

protected:
LandmarkAnalysis()
{
TransformListType * m_TransformList = 0;
TransformListType * m_TransformListTemporary = 0;
}

private:
TransformListType * m_TransformList;
TransformListType * m_TransformListTemporary;
};


.hxx file
void LandmarkAnalysis::ReadTransformFile( const char * transformFilename )
{
TransformReaderType::Pointer reader = TransformReaderType::New();
reader->SetFileName( transformFilename );
reader->Update();

// put output into member variable
m_TransformListTemporary = reader->GetTransformList();
//(*m_TransformList).merge( *m_TransformListTemporary );
// print out to prove that it was completed
TransformListType::const_iterator tempIt = m_TransformListTemporary->begin();
TransformListType::iterator it = m_TransformList->begin(); ***CODE BREAKS AT THIS LINE***

for(; tempIt !=m_TransformListTemporary->end(); tempIt++)
{
std::cout << (*tempIt) << std::endl;
(*m_TransformList).insert(it, (*tempIt));
}

std::cout << transformFilename << " has been read in." << std::endl;
return;
}

Here is my problem: I know that at the base level both m_TransformListTemporary and m_TransformList are lists of transform pointers. However, I cannot use any of the c++ stl list member functions such as merge or insert (I get runtime errors.) Is there some fundamental concept that I do not understand with how ITK interacts with the STL? In addition, through debugging, the line shown above instantiating an iterator for m_TransformList breaks the code, even though the previous line (which, to my understanding, does the same thing, but with a different list) works fine.

Any help would be very much appreciated.

Emily Hammond
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From blowekamp at mail.nih.gov  Wed Jan 28 10:47:50 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 28 Jan 2015 10:47:50 -0500
Subject: [ITK-users] [ITK]  STL methods and ITK
In-Reply-To: <2609C492EC89AB4CAAD3647B8D1A43CC2F1854DB@ITSNT437.iowa.uiowa.edu>
References: <2609C492EC89AB4CAAD3647B8D1A43CC2F1854DB@ITSNT437.iowa.uiowa.edu>
Message-ID: <B1830D76-AF81-4D88-90EC-5A0C657DFAB2@mail.nih.gov>

Hello Emily,

This has recently been fixed in ITK:
https://github.com/InsightSoftwareConsortium/ITK/commit/240b5568b641bb995ba01cbc338ddadffd95d5fa

The return for GetTransformList is now a constant pointer:

const TransformListType * GetTransformList()

Truthfully I am not sure why this method is returning a pointer and not a reference.

So the return should not be modified, which is your issue. The pointer is to an STL list managed by the reader.

The list is of itk::SmartPointers, so doing a copy should be light weight. So you should do something like:

TransformListType m_TransformList;

this->m_TransformList = *(reader->GetTranformList());

Brad

On Jan 28, 2015, at 10:36 AM, Hammond, Emily M <emily-hammond at uiowa.edu> wrote:

> Hello all,
> 
> I am trying to wrap some functionality into a class. I am trying to write a function that reads in a transform file, however, I want it to take the list of transform pointers that it reads in and merge/insert them into an already existing list. Here is the relevant code with more details below it:
> 
> #include "itkTransform.h"
> #include "itkTransformFileReader.h"
> 
> public:
> typedef itk::TransformFileReaderTemplate< double >
> TransformReaderType; 
> typedef TransformReaderType::TransformListType
> TransformListType;
> 
> void ReadTransformFile( const char * transformFilename );
> 
> protected:
> LandmarkAnalysis()
> {
> TransformListType * m_TransformList = 0;
> TransformListType * m_TransformListTemporary = 0;
> }
> 
> private:
> TransformListType * m_TransformList;
> TransformListType * m_TransformListTemporary;
> };
> 
> 
> .hxx file
> void LandmarkAnalysis::ReadTransformFile( const char * transformFilename )
> {
> TransformReaderType::Pointer reader = TransformReaderType::New();
> reader->SetFileName( transformFilename );
> reader->Update();
> 
> // put output into member variable
> m_TransformListTemporary = reader->GetTransformList();
> //(*m_TransformList).merge( *m_TransformListTemporary );
> // print out to prove that it was completed
> TransformListType::const_iterator tempIt = m_TransformListTemporary->begin();
> TransformListType::iterator it = m_TransformList->begin(); ***CODE BREAKS AT THIS LINE***
> 
> for(; tempIt !=m_TransformListTemporary->end(); tempIt++)
> {
> std::cout << (*tempIt) << std::endl;
> (*m_TransformList).insert(it, (*tempIt));
> }
> 
> std::cout << transformFilename << " has been read in." << std::endl;
> return;
> }
> 
> Here is my problem: I know that at the base level both m_TransformListTemporary and m_TransformList are lists of transform pointers. However, I cannot use any of the c++ stl list member functions such as merge or insert (I get runtime errors.) Is there some fundamental concept that I do not understand with how ITK interacts with the STL? In addition, through debugging, the line shown above instantiating an iterator for m_TransformList breaks the code, even though the previous line (which, to my understanding, does the same thing, but with a different list) works fine. 
> 
> Any help would be very much appreciated.
> 
> Emily Hammond
> _____________________________________
> 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  Thu Jan 29 14:04:30 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 29 Jan 2015 14:04:30 -0500
Subject: [ITK-users] [ANNOUNCE] ITK Software Guide hardcopies are available
	on Amazon!
Message-ID: <CALzTN-QcHsKttuS87sWhMubMODeGUycs_7HwYyjw4Zs=wwcHWg@mail.gmail.com>

Hardcopies of The ITK Software Guide are available on Amazon!


Book 1: http://www.amazon.com/ITK-Software-Guide-Book-Introduction/dp/1930934270/

Book 2: http://www.amazon.com/ITK-Software-Guide-Book-Functionality/dp/1930934289/


Thanks to everyone who helped make this happen!


New versions of the book will be available with subsequent releases.
If you would like to contribute to the Guide, see

  http://itk.org/gitweb?p=ITKSoftwareGuide.git;a=blob;f=README.md;h=eadf34576971b36c6f1c64c9f9590d7194fa4463;hb=HEAD

From matt.mccormick at kitware.com  Fri Jan 30 15:00:31 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 30 Jan 2015 15:00:31 -0500
Subject: [ITK-users] [ITK-dev] [ANNOUNCE] ITK Software Guide hardcopies
 are available on Amazon!
In-Reply-To: <CA+7wUsz1Wkd+wVYy8__9yNKV-j1m9GXmC-dYy09DXAkgCKiW8A@mail.gmail.com>
References: <CALzTN-QcHsKttuS87sWhMubMODeGUycs_7HwYyjw4Zs=wwcHWg@mail.gmail.com>
 <CA+7wUsz1Wkd+wVYy8__9yNKV-j1m9GXmC-dYy09DXAkgCKiW8A@mail.gmail.com>
Message-ID: <CALzTN-SG631RJoJDtCrhbTUxPpOe93XCwp71KkrpUErAqrrTTg@mail.gmail.com>

On Fri, Jan 30, 2015 at 3:51 AM, Mathieu Malaterre
<mathieu.malaterre at gmail.com> wrote:
> On Thu, Jan 29, 2015 at 8:04 PM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>> Hardcopies of The ITK Software Guide are available on Amazon!
>>
>>
>> Book 1: http://www.amazon.com/ITK-Software-Guide-Book-Introduction/dp/1930934270/
>>
>> Book 2: http://www.amazon.com/ITK-Software-Guide-Book-Functionality/dp/1930934289/
>>
>>
>> Thanks to everyone who helped make this happen!
>
> If you do so, don't forget to set a charity at smile.amazon.com.
>
> For example some people can pick: Software In The Public Interest Inc
> [*] among the possible charities.
>
> https://en.wikipedia.org/wiki/Software_in_the_Public_Interest

+1!


PS. For community members in Europe, the books are also available on
Amazon's sites for Spain, the United Kingdom, Germany, France, and
Italy. Please see the website for the links:

  http://www.kitware.com/products/books.php

From matimontg at gmail.com  Sat Jan 31 08:17:12 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 31 Jan 2015 10:17:12 -0300
Subject: [ITK-users] uncompress failed
Message-ID: <CAKKNfuKZ3BQQK7whkYza8nRKrecFOxedyj9ULmAH7mUonn+JSA@mail.gmail.com>

Hi,

I'm running the ImageSeriesWriter example:

/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#include "itkGDCMImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"
#include "itkMetaDataObject.h"
#include <vector>
#include "itksys/SystemTools.hxx"
// Software Guide : BeginLatex
//
// This example illustrates how to read a 3D image from a non DICOM file
and write it as a series of DICOM slices.
// with some changed header information. Header
//
// Please note that modifying the content of a DICOM header is a very risky
// operation. The Header contains fundamental information about the patient
// and therefore its consistency must be protected from any data corruption.
// Before attempting to modify the DICOM headers of your files, you must
make
// sure that you have a very good reason for doing so, and that you can
ensure
// that this information change will not result in a lower quality of health
// care to be delivered to the patient.
//
// \index{DICOM!Writing Series}
//
// Software Guide : EndLatex
int main( int argc, char* argv[] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << argv[0];
std::cerr << " InputImage OutputDicomDirectory" << std::endl;
return EXIT_FAILURE;
}
typedef signed short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[1] );
try
{
reader->Update();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
typedef itk::GDCMImageIO ImageIOType;
typedef itk::NumericSeriesFileNames NamesGeneratorType;
ImageIOType::Pointer gdcmIO = ImageIOType::New();
const char * outputDirectory = argv[2];
itksys::SystemTools::MakeDirectory( outputDirectory );
typedef signed short OutputPixelType;
const unsigned int OutputDimension = 2;
typedef itk::Image< OutputPixelType, OutputDimension > Image2DType;
typedef itk::ImageSeriesWriter<
ImageType, Image2DType > SeriesWriterType;
NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
std::string tagkey, value;
tagkey = "0008|0060"; // Modality
value = "MR";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value );
tagkey = "0008|0008"; // Image Type
value = "DERIVED\\SECONDARY";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
tagkey = "0008|0064"; // Conversion Type
value = "DV";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput( reader->GetOutput() );
seriesWriter->SetImageIO( gdcmIO );
ImageType::RegionType region =
reader->GetOutput()->GetLargestPossibleRegion();
ImageType::IndexType start = region.GetIndex();
ImageType::SizeType size = region.GetSize();
std::string format = outputDirectory;
format += "/image%03d.dcm";
namesGenerator->SetSeriesFormat( format.c_str() );
namesGenerator->SetStartIndex( start[2] );
namesGenerator->SetEndIndex( start[2] + size[2] - 1 );
namesGenerator->SetIncrementIndex( 1 );
seriesWriter->SetFileNames( namesGenerator->GetFileNames() );
seriesWriter->UseCompressionOn();
try
{
seriesWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown while writing the series " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}


*And when reading images in .Z format (I believe it is Zraw), it returns an
error indicating: "Uncompress Failed".*

Any hint why this may be happening?

Thank you,

Matias.
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From matt.mccormick at kitware.com  Sat Jan 31 10:53:31 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 31 Jan 2015 10:53:31 -0500
Subject: [ITK-users] uncompress failed
In-Reply-To: <CAKKNfuKZ3BQQK7whkYza8nRKrecFOxedyj9ULmAH7mUonn+JSA@mail.gmail.com>
References: <CAKKNfuKZ3BQQK7whkYza8nRKrecFOxedyj9ULmAH7mUonn+JSA@mail.gmail.com>
Message-ID: <CALzTN-TP6JMUiadBLme8o8kvNtsZ7=mzYur4Lk0e66scNH=uMA@mail.gmail.com>

Hi Matias,

.Z is not a supported file extension as I can tell.  If it is a "raw"
image, the RawImageIO will need to be used explicitly with the correct
metadata added.  See [1].

HTH,
Matt

[1] http://itk.org/Insight/Doxygen/html/classitk_1_1RawImageIO.html

On Sat, Jan 31, 2015 at 8:17 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I'm running the ImageSeriesWriter example:
>
> /*=========================================================================
> *
> * Copyright Insight Software Consortium
> *
> * Licensed under the Apache License, Version 2.0 (the "License");
> * you may not use this file except in compliance with the License.
> * You may obtain a copy of the License at
> *
> * http://www.apache.org/licenses/LICENSE-2.0.txt
> *
> * Unless required by applicable law or agreed to in writing, software
> * distributed under the License is distributed on an "AS IS" BASIS,
> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
> * See the License for the specific language governing permissions and
> * limitations under the License.
> *
> *=========================================================================*/
> #include "itkGDCMImageIO.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageFileReader.h"
> #include "itkImageSeriesWriter.h"
> #include "itkMetaDataObject.h"
> #include <vector>
> #include "itksys/SystemTools.hxx"
> // Software Guide : BeginLatex
> //
> // This example illustrates how to read a 3D image from a non DICOM file and
> write it as a series of DICOM slices.
> // with some changed header information. Header
> //
> // Please note that modifying the content of a DICOM header is a very risky
> // operation. The Header contains fundamental information about the patient
> // and therefore its consistency must be protected from any data corruption.
> // Before attempting to modify the DICOM headers of your files, you must
> make
> // sure that you have a very good reason for doing so, and that you can
> ensure
> // that this information change will not result in a lower quality of health
> // care to be delivered to the patient.
> //
> // \index{DICOM!Writing Series}
> //
> // Software Guide : EndLatex
> int main( int argc, char* argv[] )
> {
> if( argc < 3 )
> {
> std::cerr << "Usage: " << argv[0];
> std::cerr << " InputImage OutputDicomDirectory" << std::endl;
> return EXIT_FAILURE;
> }
> typedef signed short PixelType;
> const unsigned int Dimension = 3;
> typedef itk::Image< PixelType, Dimension > ImageType;
> typedef itk::ImageFileReader< ImageType > ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName( argv[1] );
> try
> {
> reader->Update();
> }
> catch (itk::ExceptionObject &excp)
> {
> std::cerr << "Exception thrown while writing the image" << std::endl;
> std::cerr << excp << std::endl;
> return EXIT_FAILURE;
> }
> typedef itk::GDCMImageIO ImageIOType;
> typedef itk::NumericSeriesFileNames NamesGeneratorType;
> ImageIOType::Pointer gdcmIO = ImageIOType::New();
> const char * outputDirectory = argv[2];
> itksys::SystemTools::MakeDirectory( outputDirectory );
> typedef signed short OutputPixelType;
> const unsigned int OutputDimension = 2;
> typedef itk::Image< OutputPixelType, OutputDimension > Image2DType;
> typedef itk::ImageSeriesWriter<
> ImageType, Image2DType > SeriesWriterType;
> NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
> itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
> std::string tagkey, value;
> tagkey = "0008|0060"; // Modality
> value = "MR";
> itk::EncapsulateMetaData<std::string>(dict, tagkey, value );
> tagkey = "0008|0008"; // Image Type
> value = "DERIVED\\SECONDARY";
> itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
> tagkey = "0008|0064"; // Conversion Type
> value = "DV";
> itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
> SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
> seriesWriter->SetInput( reader->GetOutput() );
> seriesWriter->SetImageIO( gdcmIO );
> ImageType::RegionType region =
> reader->GetOutput()->GetLargestPossibleRegion();
> ImageType::IndexType start = region.GetIndex();
> ImageType::SizeType size = region.GetSize();
> std::string format = outputDirectory;
> format += "/image%03d.dcm";
> namesGenerator->SetSeriesFormat( format.c_str() );
> namesGenerator->SetStartIndex( start[2] );
> namesGenerator->SetEndIndex( start[2] + size[2] - 1 );
> namesGenerator->SetIncrementIndex( 1 );
> seriesWriter->SetFileNames( namesGenerator->GetFileNames() );
> seriesWriter->UseCompressionOn();
> try
> {
> seriesWriter->Update();
> }
> catch( itk::ExceptionObject & excp )
> {
> std::cerr << "Exception thrown while writing the series " << std::endl;
> std::cerr << excp << std::endl;
> return EXIT_FAILURE;
> }
> return EXIT_SUCCESS;
> }
>
>
> And when reading images in .Z format (I believe it is Zraw), it returns an
> error indicating: "Uncompress Failed".
>
> Any hint why this may be happening?
>
> Thank you,
>
> Matias.
>
>
> _____________________________________
> 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  Sat Jan 31 11:25:10 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 31 Jan 2015 11:25:10 -0500
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
	paraview
In-Reply-To: <54C8CFC2.4000305@mh-hannover.de>
References: <54C0CF2E.3060106@mh-hannover.de> <54C2125D.7090801@mh-hannover.de>
 <CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>
 <54C6029C.4040600@mh-hannover.de>
 <CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>
 <54C8CFC2.4000305@mh-hannover.de>
Message-ID: <CALzTN-SEHwLwzO99QcL0JGVn4TZD2c=Tzpy+cB6KCXiEOBR60w@mail.gmail.com>

On Wed, Jan 28, 2015 at 7:02 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
> Hi Matt,
>
> On 26/01/15 17:54, Matt McCormick wrote:
>> I do not think the Midas Journal will be able to build your plugin.
>
> OK, so I added a VTK test program. Is there a way to test if the automatic
> testing environment would be able to build and run my VTK test program
> BEFORE submitting the contribution to Midas?
> (My last submission never got tested by the system so far, i.e. there is no
> colde review reported:
> http://www.vtkjournal.org/browse/publication/949)

Unfortunately, the submission build system is currently opaque and
limited.  We have many thoughts on how to improve the journal
infrastructure but lack the funding to implement it :-(.


>> I would recommend creating build instructions to build against a
>> ParaView build tree.  I have just verified that ITK builds with the
>> ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
>> directory.
>
> Did You use BUILD_SHARED_LIBS ON for both ITK and ParaView? ITK also
> compiles fine without any errors for me if I use BUILD_SHARED_LIBS OFF,
> however the problems then arise when compiling the plugin.
> If You like, You can test the compilation of the plugin with the code from
> the git repository:
> https://github.com/romangrothausmann/FacetAnalyser

Looks like a great project!

I was using BUILD_SHARED_LIBS for both.  What issue were you seeing?

Again, I think the best approach is to build VTK separately, then
build both ParaView and ITK against that version.

HTH,
Matt



>
> On 26/01/15 17:54, Matt McCormick wrote:
>>
>> Hi Roman,
>>
>> Thanks for the update. Great to hear about the Midas Journal article!
>>
>> I do not think the Midas Journal will be able to build your plugin.
>>
>> I would recommend creating build instructions to build against a
>> ParaView build tree.  I have just verified that ITK builds with the
>> ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
>> directory.
>>
>> I don't see the install tree VTKTargets.cmake file in my ParaView
>> build, either. In the long term, the ParaView CMake configuration
>> should be corrected.
>>
>> HTH,
>> Matt
>>
>> On Mon, Jan 26, 2015 at 4:02 AM, Dr. Roman Grothausmann
>> <grothausmann.roman at mh-hannover.de> wrote:
>>>
>>> Hi Matt,
>>>
>>>
>>> Thank You very much for Your reply.
>>> I can only find one VTKTargets.cmake in
>>> /opt/compilation/paraview-git_build/VTK/
>>> It seems though that it is lacking the relevant entries for the libraries
>>> that troubled me, e.g. vtkPVPythonCatalyst and
>>> vtkUtilitiesPythonInitializer.
>>>
>>> I'm about to publish the ITK-VTK PV plugin in the Midas Journal, what
>>> installation instructions should I give there?
>>> Will the testing environment be able to compile this plugin and its tests
>>> or
>>> should I disable automatic testing for this contribution?
>>>
>>> Many thanks for looking into this.
>>> Roman
>>>
>>>
>>> On 23/01/15 18:15, Matt McCormick wrote:
>>>>
>>>>
>>>> Hi Roman,
>>>>
>>>> Thanks for looking into the issue and reporting it to the mailing list.
>>>>
>>>> Paraview should be installing VTKTargets.cmake, which tells the build
>>>> system where to find the libraries.  Note that there might be two
>>>> VTKTargets.cmake files that are generated -- one for the build tree
>>>> and one for the install tree.
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>> On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
>>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Adding the abs. file locations to the build command does not help nor
>>>>>> does
>>>>>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I figured that the vtk dynamic libraries of PV have the ending
>>>>> *-pv4.3.so
>>>>> which seems to be the reason why the linker does not find them. If I
>>>>> create
>>>>> symbolic links to these files without the extension:
>>>>>
>>>>> cd /opt/compilation/paraview-git_build/lib/
>>>>> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>>>>>
>>>>> and adding -L/opt/compilation/paraview-git_build/lib/ to
>>>>> CMAKE_CXX_FLAGS
>>>>> the compilation of ITK succeeds.
>>>>>
>>>>> I wonder, is that the way it's meant to be done?
>>>>>
>>>>>
>>>>>
>>>>>> What am I missing in my configuration of PV and ITK?
>>>>>>
>>>>>> When and where should I specify:
>>>>>> CMAKE_CXX_FLAGS                  -fPIC
>>>>>> BUILD_SHARED_LIBS                ON/OFF
>>>>>>
>>>>>> Is this the right VTK_DIR specification for ITK:
>>>>>> /opt/compilation/ParaView-v4.3.1/build/VTK
>>>>>> or
>>>>>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>>>>>
>>>>>>
>>>>>>
>>>>>> Many thanks for any help or hints.
>>>>>> Roman
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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. +49 511 532-9574
>>>>> _____________________________________
>>>>> 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
>>>
>>>
>>>
>>> --
>>> 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. +49 511 532-9574
>
>
> --
> 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. +49 511 532-9574