Re: vtkusers Digest, Vol 156, Issue 13

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Re: vtkusers Digest, Vol 156, Issue 13

cartik sharma-3

Dear VTK Users/Developers,

I'm trying to build VTK 5.10.1 on Mac OS X El Capitan and am getting a compilation error..

[ 66%] Building CXX object Rendering/CMakeFiles/vtkRendering.dir/vtkCocoaRenderWindowInteractor.mm.o

clang: error: garbage collection is no longer supported

make[2]: *** [Rendering/CMakeFiles/vtkRendering.dir/vtkCocoaRenderWindowInteractor.mm.o] Error 1

make[1]: *** [Rendering/CMakeFiles/vtkRendering.dir/all] Error 2

make: *** [all] Error 2

Please let me know the fix so I can build VTK.

Best regards,

Cartik


On Tue, Apr 11, 2017 at 11:00 AM, <[hidden email]> wrote:
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Today's Topics:

   1. Visualising vorticity from NC file structured grid (henlau)
   2. Displaying 2D image with vtkPolyData (Eric Petersen)
   3. Re: Displaying 2D image with vtkPolyData (Bill Lorensen)
   4. VTK *.app Abort trap:6 (henlau)
   5. Re: VTK *.app Abort trap:6 (Bill Lorensen)
   6. Re: VTK *.app Abort trap:6 (henlau)
   7. Re: VTK *.app Abort trap:6 (henlau)
   8. Re: How to rotate around a arbitrary world coordinate?
      (Rakesh  Patil)
   9. Re: error LNK1112: module machine type 'X86' conflicts with
      target machine type 'x64' (Madan Kumar Y)
  10. Re: Visualize .mha MRI volume (Megha Kalia)
  11. Using system fonts on Windows (fontconfig equivalent?)
      (Elvis Stansvik)
  12. Re: Rendering Very Large Images (Ang)
  13. Re: error LNK1112: module machine type 'X86' conflicts with
      target machine type 'x64' (Cory Quammen)


----------------------------------------------------------------------

Message: 1
Date: Mon, 10 Apr 2017 09:09:41 -0700 (MST)
From: henlau <[hidden email]>
To: [hidden email]
Subject: [vtkusers] Visualising vorticity from NC file structured grid
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Hi all,

I am new to VTK. I have a NC file and reading it with "vtknetCDFCFReader".
In my NC file, there are 2 variable arrays and their corresponding
dimension:

"ua" - (height, lon, lat) - Description: Eastward_wind - Unit: m s-1
"va" - (height, lon, lat) - Description: Northward_wind - Unit: m s-1

I safeDownCast the output of the reader and got a vtkStructuredGrid, with
only cell data. The thing is I want to render the vorticity of the data. I
saw people working with vtkHedgeHog, and the following is what I am doing:

   //reader
   vtkNetCDFCFReader *reader = vtkNetCDFCFReader::New();
   reader->SetFileName(fileName);
   reader->SetOutputTypeToStructured();
   reader->UpdateMetaData();
   reader->Update();

   reader->SetVariableArrayStatus("ua", 1);
   reader->SetVariableArrayStatus("va", 1);

  reader->SphericalCoordinatesOff();

  //SafeDownCast reader output to structuredGrid
   vtkStructuredGrid *weatherGrid =
vtkStructuredGrid::SafeDownCast(reader->GetOutput());


  //Cell data to point data
    vtkCellDataToPointData *c2p = vtkCellDataToPointData::New();
    c2p->SetInputData(weatherGrid);
    c2p->PassCellDataOn();
    c2p->Update();

  //Convert it back to a structured grid
    vtkStructuredGrid* reformedWeatherGrid = c2p->GetStructuredGridOutput();


  //In the following code, I start doing the hedgehog
  //Here I am creating vector data for the "reformedWeatherGrid"
  //1430*1557*151 is the dimension of my first structured grid
    vtkFloatArray* vector = vtkFloatArray::New();
    vector->SetNumberOfComponents(3);
    vector->SetNumberOfTuples(1430*1557*151);
    for(int i = 0; i < 151; i++){

      double v[2];
      v[0] =
reformedWeatherGrid->GetPointData()->GetArray("ua")->GetComponent(i,0);
      v[1] =
reformedWeatherGrid->GetPointData()->GetArray("va")->GetComponent(i,0);
      vector->InsertTuple(i,v);
    }

    //Set new vector into reformedWeatherGrid
    reformedWeatherGrid->GetPointData()->SetVectors(vector);

    //HedgeHog
    vtkHedgeHog* hedgehog = vtkHedgeHog::New();
    hedgehog->SetInputData(reformedWeatherGrid);
    hedgehog->SetScaleFactor(0.1);

    //PolyDataMapper and Actor
    vtkPolyDataMapper* hhMapper = vtkPolyDataMapper::New();
    hhMapper->SetInputConnection(hedgehog->GetOutputPort());
    vtkActor* hhActor = vtkActor::New();
    hhActor->SetMapper(hhMapper);

   //renderer and render window
   .............

The problem is I got the following error:
vtkPointData (0x7fbb1af13d80): Can not set attribute Vectors. Incorrect
number of components.
vtkHedgeHog (0x7fbb1af1def0): No vectors in input data

What should I do in order to solve this problem? Or is there any
alternatives to render the vorticity of my data?

TIA







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------------------------------

Message: 2
Date: Mon, 10 Apr 2017 14:10:30 -0500
From: Eric Petersen <[hidden email]>
To: [hidden email]
Subject: [vtkusers] Displaying 2D image with vtkPolyData
Message-ID:
        <CAGL8Xss33HPnSQm-MqksrD+5-F2CfqLbQtYx-vw=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hello,

I have various cardiac CT scans where I've segmented various areas and
created STL files (using Mimics) of the objects.  I then have Python
scripts where I am able to read, and display, these objects using VTK.  I
don't have any issue with this part.  I also have bi-plane fluoroscopy (2D)
images of the same patients where I would like to display the bi-plane
images with the imported vtkPolyData (from CT scans) to fuse the two
imaging modalities.

I've been looking around for how to display 2D images (either directly from
DICOM or 2D numpy array) with 3D vtkPolyData objects and I'm struggling to
find a good example.

Can anyone suggest some filters and usage to get me started?

Eric
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Message: 3
Date: Mon, 10 Apr 2017 15:41:27 -0400
From: Bill Lorensen <[hidden email]>
To: Eric Petersen <[hidden email]>
Cc: VTK Users <[hidden email]>
Subject: Re: [vtkusers] Displaying 2D image with vtkPolyData
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Take a look at this example
http://www.vtk.org/Wiki/VTK/Examples/Cxx/Medical/MedicalDemo3

On Apr 10, 2017 3:10 PM, "Eric Petersen" <[hidden email]> wrote:

> Hello,
>
> I have various cardiac CT scans where I've segmented various areas and
> created STL files (using Mimics) of the objects.  I then have Python
> scripts where I am able to read, and display, these objects using VTK.  I
> don't have any issue with this part.  I also have bi-plane fluoroscopy (2D)
> images of the same patients where I would like to display the bi-plane
> images with the imported vtkPolyData (from CT scans) to fuse the two
> imaging modalities.
>
> I've been looking around for how to display 2D images (either directly
> from DICOM or 2D numpy array) with 3D vtkPolyData objects and I'm
> struggling to find a good example.
>
> Can anyone suggest some filters and usage to get me started?
>
> Eric
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
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Message: 4
Date: Mon, 10 Apr 2017 17:07:11 -0700 (MST)
From: henlau <[hidden email]>
To: [hidden email]
Subject: [vtkusers] VTK *.app Abort trap:6
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Hi all,

I was trying to visualize my actor on mac but seems like it is not working.
I got the following error when the program was adding the actor to the
renderer:
Abort trap: 6

Does anyone know what that means? How am I able to solve it?
My code is just simply visualizing the vtkHedgeHog.

TIA



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------------------------------

Message: 5
Date: Mon, 10 Apr 2017 20:25:34 -0400
From: Bill Lorensen <[hidden email]>
To: henlau <[hidden email]>
Cc: VTK Users <[hidden email]>
Subject: Re: [vtkusers] VTK *.app Abort trap:6
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Can you provide a small, compilable file that illustrates the problem!? And
the Cmakelists.txt file.

On Apr 10, 2017 8:07 PM, "henlau" <[hidden email]> wrote:

> Hi all,
>
> I was trying to visualize my actor on mac but seems like it is not working.
> I got the following error when the program was adding the actor to the
> renderer:
> Abort trap: 6
>
> Does anyone know what that means? How am I able to solve it?
> My code is just simply visualizing the vtkHedgeHog.
>
> TIA
>
>
>
> --
> View this message in context: http://vtk.1045678.n5.nabble.
> com/VTK-app-Abort-trap-6-tp5742788.html
> Sent from the VTK - 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
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
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Message: 6
Date: Mon, 10 Apr 2017 18:07:57 -0700 (MST)
From: henlau <[hidden email]>
To: [hidden email]
Subject: Re: [vtkusers] VTK *.app Abort trap:6
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Below is my code:

    //Creating vectors and points for hedgehog
    static int dims[3] = {1430, 1557, 151};
    float x[3], v[3];
    int offset, kOffset, jOffset, k, deltaHeight, componentNum;
    vtkStructuredGrid* reformedWeatherGrid = c2p->GetStructuredGridOutput();
    reformedWeatherGrid->SetDimensions(dims[0], dims[1], dims[2]);

    vtkFloatArray* vector = vtkFloatArray::New();
    vector->SetNumberOfComponents(3);
    vector->SetNumberOfTuples(dims[0]*dims[1]*dims[2]);

    vtkPoints* points = vtkPoints::New();
    points->Allocate(dims[0]*dims[1]*dims[2]);

    v[2] = 0.0;
    deltaHeight = dims[0] * dims[1];
    for(int height = 1; height < dims[2]; height++){
      x[2] = height;
      kOffset = height*dims[0]*dims[1];
      for(int lat = 1; lat < dims[1]; lat++){
        jOffset = lat*dims[0];
        for(int lon = 1; lon < dims[0]; lon++){
          x[0] = lon;
          x[1] = lat;
          componentNum = height*lat*lon;
          v[0] =
reformedWeatherGrid->GetPointData()->GetArray("ua")->GetComponent(componentNum,
0);
          v[1] =
reformedWeatherGrid->GetPointData()->GetArray("va")->GetComponent(componentNum,0);
          offset = lon+jOffset+kOffset;
          points->InsertPoint(offset,x);
          vector->InsertTuple(offset,v);
        }
      }
    }

    //Set points and vector to the structuredgrid
    reformedWeatherGrid->SetPoints(points);
    reformedWeatherGrid->GetPointData()->SetVectors(vector);
    reformedWeatherGrid->Print(std::cout);

    //HedgeHog
    vtkHedgeHog* hedgehog = vtkHedgeHog::New();
    hedgehog->SetInputData(reformedWeatherGrid);
    hedgehog->SetScaleFactor(0.05);
    hedgehog->Print(std::cout);

    vtkPolyDataMapper* hhMapper = vtkPolyDataMapper::New();
    hhMapper->SetInputConnection(hedgehog->GetOutputPort());

    vtkActor* hhActor = vtkActor::New();
    hhActor->SetMapper(hhMapper);

    //Renderer, render window
    ......

Just now I tried with a smaller dimension, like 300x300x151 and it works. Is
that because of my computer not able to handle such large amount of data?




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------------------------------

Message: 7
Date: Mon, 10 Apr 2017 18:09:03 -0700 (MST)
From: henlau <[hidden email]>
To: [hidden email]
Subject: Re: [vtkusers] VTK *.app Abort trap:6
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

And this is my CMakeList.txt


cmake_minimum_required(VERSION 2.8)

PROJECT(main)

find_package(VTK REQUIRED)
include(${VTK_USE_FILE})

add_executable(main MACOSX_BUNDLE main)

if(VTK_LIBRARIES)
  target_link_libraries(main ${VTK_LIBRARIES})
else()
  target_link_libraries(main vtkHybrid vtkWidgets)
endif()



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------------------------------

Message: 8
Date: Tue, 11 Apr 2017 06:04:14 +0000
From: "Rakesh  Patil" <[hidden email]>
To: Chiranjib Sur <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [vtkusers] How to rotate around a arbitrary world
        coordinate?
Message-ID:
        <[hidden email]>

Content-Type: text/plain; charset="us-ascii"

Hi,


I am sorry, my question was not clear I guess. Most of the interactor styles perform rotation (entire model, not only object) with respect to origin (0, 0, 0). This is happening irrespective of where we pan and zoom. Consider a situation, where the center is away from the viewport. Now when I perform rotation, the default interactor style rotates about (0, 0, 0). In this situation, my requirement is whatever is the center point of the viewport, rotation should happen w.r.t. this center point. How can this be implemented?


Thanks & Regards

Rakesh Patil


TATA ELXSI
Tel (D) +91 80 2297 9621
Cell +91 9890258407

________________________________
From: Chiranjib Sur <[hidden email]>
Sent: Monday, April 10, 2017 12:16:37 PM
To: Rakesh Patil
Cc: [hidden email]
Subject: Re: [vtkusers] How to rotate around a arbitrary world coordinate?

May be this the place to start
http://www.vtk.org/doc/nightly/html/classvtkTransformFilter.html

On Mon, Apr 10, 2017 at 11:33 AM, Rakesh Patil <[hidden email]<mailto:[hidden email]>> wrote:

Hi,


Experts, or experienced people, can you give some information on this?


http://public.kitware.com/pipermail/vtkusers/2017-March/098181.html


How to rotate around a arbitrary world coordinate?


Thanks & Regards

Rakesh Patil

_______________________________________________
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Message: 9
Date: Mon, 10 Apr 2017 23:57:28 -0700 (MST)
From: Madan Kumar Y <[hidden email]>
To: [hidden email]
Subject: Re: [vtkusers] error LNK1112: module machine type 'X86'
        conflicts with target machine type 'x64'
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Hi Cory,
Even i think that's the issue, any suggestions.









Thanks,
Madan



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------------------------------

Message: 10
Date: Tue, 11 Apr 2017 10:09:47 +0200
From: Megha Kalia <[hidden email]>
To: Aashish Chaudhary <[hidden email]>
Cc: [hidden email]
Subject: Re: [vtkusers] Visualize .mha MRI volume
Message-ID:
        <CAKXe2Myisz8ut0T=jNxKMZTZ2Tufq=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hi Ashish ,

Thanks for replying. I see only only one 2D-slice. I can't see rest of the
slices.
I couldn't even find a way to visualize different slices (let's say
according to position)

Thanks :)

On Mon, Apr 10, 2017 at 4:25 PM, Aashish Chaudhary <
[hidden email]> wrote:

> Hi Megha,
>
> You can look at this example to help with your task (
> http://www.vtk.org/gitweb?p=VTK.git;a=blob;f=Examples/VolumeRendering/Cxx/
> GPURenderDemo.cxx). In that example you can use vtkGPUVolumeRayCastMapper instead
> of vtkSmartVolumeMapper to simplify things a bit.
>
> As fas the reader goes, how did you confirm that you only got one slice?
>
> Thanks,
>
>
> On Mon, Apr 10, 2017 at 6:49 AM Megha Kalia <[hidden email]>
> wrote:
>
>> Hi all,
>>
>> I have a .mha file containing MRI volume. I want to do the following:
>> 1- Read .mha volume data.
>> 2- Visualize it in VTK
>> 3- Transfer the data to openGL 3D texture to use it in my own framework.
>>
>> By far I have used vtkMetaImageReader. I get just one slice. I want to
>> see entire volume.
>> Any pointers on this will be really helpful.
>>
>> Thanks a lot   :)
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at http://www.kitware.com/
>> opensource/opensource.html
>>
>> Please keep messages on-topic and check the VTK FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ
>>
>> Search the list archives at: http://markmail.org/search/?q=vtkusers
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/vtkusers
>>
>
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Message: 11
Date: Tue, 11 Apr 2017 10:45:19 +0200
From: Elvis Stansvik <[hidden email]>
To: VTK Users <[hidden email]>, vtkdev <[hidden email]>
Subject: [vtkusers] Using system fonts on Windows (fontconfig
        equivalent?)
Message-ID:
        <CAE-7VJ=[hidden email]>
Content-Type: text/plain; charset=UTF-8

Hi all,

Cross-posting since I'm not sure if vtkusers@ or vtk-developers@ is
most appropriate for this.

On Linux, I'm using the vtkRendereringFreeTypeFontConfig module, so
that I can use system fonts (e.g. for charts labels et.c). The goal is
to make VTK fonts match those used by Qt, so I'm using
QFontDatabase::system(...) to query for the user's preferred font, and
then use that in my VTK code. This is all working quite well.

I'm now porting the application to Windows. Does VTK have any support
for loading system fonts on Windows? Something similar to the
vtkRendereringFreeTypeFontConfig, but for whatever font backend
Windows uses?

If not, has anyone had luck in building fontconfig for Windows, and
using the vtkRendereringFreeTypeFontConfig module there? (I'm not even
sure if fontconfig has support for hooking into Windows' font backend,
so this may not be a solution at all).

Many thanks in advance,
Elvis


------------------------------

Message: 12
Date: Tue, 11 Apr 2017 02:23:08 -0700 (MST)
From: Ang <[hidden email]>
To: [hidden email]
Subject: Re: [vtkusers] Rendering Very Large Images
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Hi,

The solution link is invalid.

Could someone please give me some advice?

Thanks for help.





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------------------------------

Message: 13
Date: Tue, 11 Apr 2017 07:56:13 -0400
From: Cory Quammen <[hidden email]>
To: Madan Kumar Y <[hidden email]>
Cc: VTK Mailing List <[hidden email]>
Subject: Re: [vtkusers] error LNK1112: module machine type 'X86'
        conflicts with target machine type 'x64'
Message-ID:
        <CAB5Fpx7BAjczd-K4F0cF3MN5N4phjdCG4e210wK=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Either rebuild the 32 bit library as 64 bit, or rebuild the 64 libraries as
32 bit. Those are your only options.

HTH,
Cory

On Apr 11, 2017 2:57 AM, "Madan Kumar Y" <[hidden email]> wrote:

> Hi Cory,
> Even i think that's the issue, any suggestions.
>
>
>
>
>
>
>
>
>
> Thanks,
> Madan
>
>
>
> --
> View this message in context: http://vtk.1045678.n5.nabble.
> com/Re-error-LNK1112-module-machine-type-X86-conflicts-
> with-target-machine-type-x64-tp5742757p5742793.html
> Sent from the VTK - 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
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
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End of vtkusers Digest, Vol 156, Issue 13
*****************************************



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Re: vtkusers Digest, Vol 156, Issue 13

Ben Boeckel
On Tue, Apr 11, 2017 at 12:37:27 -0500, Cartik Sharma wrote:

> I'm trying to build VTK 5.10.1 on Mac OS X El Capitan and am getting a
> compilation error..
>
> [ 66%] Building CXX object
> Rendering/CMakeFiles/vtkRendering.dir/vtkCocoaRenderWindowInteractor.mm.o
>
> clang: error: garbage collection is no longer supported
>
> make[2]: ***
> [Rendering/CMakeFiles/vtkRendering.dir/vtkCocoaRenderWindowInteractor.mm.o]
> Error 1
>
> make[1]: *** [Rendering/CMakeFiles/vtkRendering.dir/all] Error 2
>
> make: *** [all] Error 2
>
> Please let me know the fix so I can build VTK.

It looks like VTK5 is too old to support compilation on newer Apple
platforms. The only fix is likely going to be moving to newer VTK
releases (or getting an older Apple platform).

--Ben
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