[vtkusers] vtkImageData, vtkImageReslice, setting/changing voxel size of image data

[Rohan.Venkatraman at csiro.au]

Hi All,

 

I was comiling the medical3.cxx class from vtk Examples. It generates a
3D image of the head.  I am trying to change the voxel size of the
image, but it only seems to be changing the size of the render window.
The Image Data remains unaffected. I have compiled it using vtk 4.2.6
and vtk 5.0 without any change in results.

I have attached the code below. I have highlighted the section where I
have inserted code to change the spacing ( i.e. voxel size) of the
image. I have also tried using the SetSpacing() method of vtkImageData
on another example, but again all it seems to be doing is the changing
the size of  the render window and not the image data. How do I get it
to actually act upon the image data itself and not just on the render
window??

Any help will be appreciated.

 

Thanks

 

Regards

Rohan

 

/*======================================================================
===

 

  Program:   Visualization Toolkit

  Module:    $RCSfile: Medical3.cxx,v $

  Language:  C++

  Date:      $Date: 2002/12/02 20:39:46 $

  Version:   $Revision: 1.4 $

 

  Copyright (c) 1993-2002 Ken Martin, Will Schroeder, Bill Lorensen 

  All rights reserved.

  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

 

     This software is distributed WITHOUT ANY WARRANTY; without even 

     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR


     PURPOSE.  See the above copyright notice for more information.

 

========================================================================
=*/

 

// 

// This example reads a volume dataset, extracts two isosurfaces that

// represent the skin and bone, creates three orthogonal planes 

// (saggital, axial, coronal), and displays them.

//

#include "vtkRenderer.h"

#include "vtkRenderWindow.h"

#include "vtkRenderWindowInteractor.h"

#include "vtkVolume16Reader.h"

#include "vtkPolyDataMapper.h"

#include "vtkActor.h"

#include "vtkOutlineFilter.h"

#include "vtkCamera.h"

#include "vtkStripper.h"

#include "vtkLookupTable.h"

#include "vtkImageDataGeometryFilter.h"

#include "vtkProperty.h"

#include "vtkPolyDataNormals.h"

#include "vtkContourFilter.h"

#include "vtkImageData.h"

#include "vtkImageMapToColors.h"

#include "vtkImageActor.h"

#include "vtkImageReslice.h"

 

int main (int argc, char **argv)

{

  if (argc < 2)

    {

      cout << "Usage: " << argv[0] << " DATADIR/headsq/quarter" << endl;

    return 1;

    }

 

  // Create the renderer, the render window, and the interactor. The

  // renderer draws into the render window, the interactor enables

  // mouse- and keyboard-based interaction with the data within the

  // render window.

  //

  vtkRenderer *aRenderer = vtkRenderer::New();

  vtkRenderWindow *renWin = vtkRenderWindow::New();

    renWin->AddRenderer(aRenderer);

  vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();

    iren->SetRenderWindow(renWin);

 

  // The following reader is used to read a series of 2D slices (images)

  // that compose the volume. The slice dimensions are set, and the

  // pixel spacing. The data Endianness must also be specified. The

  // reader usese the FilePrefix in combination with the slice number to

  // construct filenames using the format FilePrefix.%d. (In this case

  // the FilePrefix is the root name of the file: quarter.)

  vtkVolume16Reader *v16 = vtkVolume16Reader::New();

    v16->SetDataDimensions(64,64);

    v16->SetDataByteOrderToLittleEndian();

    v16->SetFilePrefix (argv[1]);

    v16->SetImageRange(1, 93);

    v16->SetDataSpacing (3.2, 3.2, 1.5);

 

  // An isosurface, or contour value of 500 is known to correspond to

  // the skin of the patient. Once generated, a vtkPolyDataNormals

  // filter is is used to create normals for smooth surface shading

  // during rendering.  The triangle stripper is used to create triangle

  // strips from the isosurface; these render much faster on may

  // systems.

  vtkContourFilter *skinExtractor = vtkContourFilter::New();

    skinExtractor->SetInput( v16->GetOutput());

    skinExtractor->SetValue(0, 500);

  vtkPolyDataNormals *skinNormals = vtkPolyDataNormals::New();

    skinNormals->SetInput(skinExtractor->GetOutput());

    skinNormals->SetFeatureAngle(60.0);

  vtkStripper *skinStripper = vtkStripper::New();

    skinStripper->SetInput(skinNormals->GetOutput());

  vtkPolyDataMapper *skinMapper = vtkPolyDataMapper::New();

    skinMapper->SetInput(skinStripper->GetOutput());

    skinMapper->ScalarVisibilityOff();

  vtkActor *skin = vtkActor::New();

    skin->SetMapper(skinMapper);

    skin->GetProperty()->SetDiffuseColor(1, .49, .25);

    skin->GetProperty()->SetSpecular(.3);

    skin->GetProperty()->SetSpecularPower(20);

 

  // An isosurface, or contour value of 1150 is known to correspond to

  // the skin of the patient. Once generated, a vtkPolyDataNormals

  // filter is is used to create normals for smooth surface shading

  // during rendering.  The triangle stripper is used to create triangle

  // strips from the isosurface; these render much faster on may

  // systems.

  vtkContourFilter *boneExtractor = vtkContourFilter::New();

    boneExtractor->SetInput((vtkDataSet *) v16->GetOutput());

    boneExtractor->SetValue(0, 1150);

  vtkPolyDataNormals *boneNormals = vtkPolyDataNormals::New();

    boneNormals->SetInput(boneExtractor->GetOutput());

    boneNormals->SetFeatureAngle(60.0);

  vtkStripper *boneStripper = vtkStripper::New();

    boneStripper->SetInput(boneNormals->GetOutput());

  vtkPolyDataMapper *boneMapper = vtkPolyDataMapper::New();

    boneMapper->SetInput(boneStripper->GetOutput());

    boneMapper->ScalarVisibilityOff();

  vtkActor *bone = vtkActor::New();

    bone->SetMapper(boneMapper);

    bone->GetProperty()->SetDiffuseColor(1, 1, .9412);

 

  // An outline provides context around the data.

  //

  vtkOutlineFilter *outlineData = vtkOutlineFilter::New();

    outlineData->SetInput((vtkDataSet *) v16->GetOutput());

  vtkPolyDataMapper *mapOutline = vtkPolyDataMapper::New();

    mapOutline->SetInput(outlineData->GetOutput());

  vtkActor *outline = vtkActor::New();

    outline->SetMapper(mapOutline);

    outline->GetProperty()->SetColor(0,0,0);

 

  // Now we are creating three orthogonal planes passing through the

  // volume. Each plane uses a different texture map and therefore has

  // diferent coloration.

 

  // Start by creatin a black/white lookup table.

  vtkLookupTable *bwLut = vtkLookupTable::New();

    bwLut->SetTableRange (0, 2000);

    bwLut->SetSaturationRange (0, 0);

    bwLut->SetHueRange (0, 0);

    bwLut->SetValueRange (0, 1);

    bwLut->Build();

 

  // Now create a lookup table that consists of the full hue circle

  // (from HSV).

  vtkLookupTable *hueLut = vtkLookupTable::New();

    hueLut->SetTableRange (0, 2000);

    hueLut->SetHueRange (0, 1);

    hueLut->SetSaturationRange (1, 1);

    hueLut->SetValueRange (1, 1);

    hueLut->Build();

 

  // Finally, create a lookup table with a single hue but having a range

  // in the saturation of the hue.

  vtkLookupTable *satLut = vtkLookupTable::New();

    satLut->SetTableRange (0, 2000);

    satLut->SetHueRange (.6, .6);

    satLut->SetSaturationRange (0, 1);

    satLut->SetValueRange (1, 1);

    satLut->Build();

 

// Code inserted by me

 vtkImageReslice *sagittalReslice = vtkImageReslice::New();

 

 sagittalReslice->SetInput(v16->GetOutput());

 float sag_spacing[] = {2.0, 2.0, 5.0};

 int sag_extents[] = {0, 63, 0, 63, 0, 93};

 

 sagittalReslice->SetOutputExtent(sag_extents);

 sagittalReslice->SetOutputSpacing(sag_spacing);

 sagittalReslice->Update();

 

  // Create the first of the three planes. The filter
vtkImageMapToColors

  // maps the data through the corresponding lookup table created above.
The

  // vtkImageActor is a type of vtkProp and conveniently displays an
image on

  // a single quadrilateral plane. It does this using texture mapping
and as

  // a result is quite fast. (Note: the input image has to be unsigned
char

  // values, which the vtkImageMapToColors produces.) Note also that by

  // specifying the DisplayExtent, the pipeline requests data of this
extent

  // and the vtkImageMapToColors only processes a slice of data.

  vtkImageMapToColors *saggitalColors = vtkImageMapToColors::New();

    saggitalColors->SetInput(sagittalReslice->GetOutput());

    saggitalColors->SetLookupTable(bwLut);

  vtkImageActor *saggital = vtkImageActor::New();

    saggital->SetInput(saggitalColors->GetOutput());

    saggital->SetDisplayExtent(32,32, 0,63, 0,92);

 

 

 

  // Create the second (axial) plane of the three planes. We use the

  // same approach as before except that the extent differs.

  vtkImageMapToColors *axialColors = vtkImageMapToColors::New();

    axialColors->SetInput(v16->GetOutput());

    axialColors->SetLookupTable(hueLut);

  vtkImageActor *axial = vtkImageActor::New();

    axial->SetInput(axialColors->GetOutput());

    axial->SetDisplayExtent(0,63, 0,63, 46,46);

 

  // Create the third (coronal) plane of the three planes. We use 

  // the same approach as before except that the extent differs.

  vtkImageMapToColors *coronalColors = vtkImageMapToColors::New();

    coronalColors->SetInput(v16->GetOutput());

    coronalColors->SetLookupTable(satLut);

  vtkImageActor *coronal = vtkImageActor::New();

    coronal->SetInput(coronalColors->GetOutput());

    coronal->SetDisplayExtent(0,63, 32,32, 0,92);

 

  // It is convenient to create an initial view of the data. The

  // FocalPoint and Position form a vector direction. Later on

  // (ResetCamera() method) this vector is used to position the camera

  // to look at the data in this direction.

  vtkCamera *aCamera = vtkCamera::New();

    aCamera->SetViewUp (0, 0, -1);

    aCamera->SetPosition (0, 1, 0);

    aCamera->SetFocalPoint (0, 0, 0);

    aCamera->ComputeViewPlaneNormal();

 

  // Actors are added to the renderer. 

//  aRenderer->AddActor(outline);

  aRenderer->AddActor(saggital);

  aRenderer->AddActor(axial);

  aRenderer->AddActor(coronal);

//  aRenderer->AddActor(axial);

//  aRenderer->AddActor(coronal);

//  aRenderer->AddActor(skin);

//  aRenderer->AddActor(bone);

 

  // Turn off bone for this example.

  bone->VisibilityOff();

 

  // Set skin to semi-transparent.

  skin->GetProperty()->SetOpacity(0.5);

 

  // An initial camera view is created.  The Dolly() method moves 

  // the camera towards the FocalPoint, thereby enlarging the image.

  aRenderer->SetActiveCamera(aCamera);

  aRenderer->ResetCamera ();

  aCamera->Dolly(1.5);

 

  // Set a background color for the renderer and set the size of the

  // render window (expressed in pixels).

  aRenderer->SetBackground(1,1,1);

  renWin->SetSize(640, 480);

 

  // Note that when camera movement occurs (as it does in the Dolly()

  // method), the clipping planes often need adjusting. Clipping planes

  // consist of two planes: near and far along the view direction. The 

  // near plane clips out objects in front of the plane; the far plane

  // clips out objects behind the plane. This way only what is drawn

  // between the planes is actually rendered.

  aRenderer->ResetCameraClippingRange ();

 

  // interact with data

  iren->Initialize();

  iren->Start(); 

 

  // It is important to delete all objects created previously to prevent

  // memory leaks. In this case, since the program is on its way to

  // exiting, it is not so important. But in applications it is

  // essential.

  v16->Delete();

  skinExtractor->Delete();

  skinNormals->Delete();

  skinStripper->Delete();

  skinMapper->Delete();

  skin->Delete();

  boneExtractor->Delete();

  boneNormals->Delete();

  boneStripper->Delete();

  boneMapper->Delete();

  bone->Delete();

  outlineData->Delete();

  mapOutline->Delete();

  outline->Delete();

  bwLut->Delete();

  hueLut->Delete();

  satLut->Delete();

  saggitalColors->Delete();

  saggital->Delete();

  axialColors->Delete();

  axial->Delete();

  coronalColors->Delete();

  coronal->Delete();

  aCamera->Delete();

  aRenderer->Delete();

  renWin->Delete();

  iren->Delete();

 

  return 0;

}

 

 

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