[vtkusers] Having problems importing data to vtk from itk/vnl

[Luis Ibanez]

Hi Arne,


You may want to check your program in several intermediate locations.


1) Inside the method  "importData()" you should check writing
    out the vtkImageData in a .vtk file and then open it using
    ParaView (www.paraview.org). This will verify if the import
    process work well or not.


2) If (1) works fine, then you should try wrting out the vtkImageData
    just after returning from the importData() function. This will
    verify if there is any reference counting issue that may have
    deleted your image when returning from the function.


3) What exactly are you trying to import ?
    Is this an image that you created with ITK ?
    From your email, it seems that you are importing a matrix
    that you created with vnl...

    How did you created that file ?
    Did you created the file in the same machine ?
    (e.g. can you discard endianness problems ?)


Please let us know


   Thanks


      Luis



------------------
Arne Hansen wrote:
> Hello all. I am (still) having problems getting my data correct read 
> into vtk. I have a really strange problem which i absolutely dont 
> understand. I read in the data from binary files...that goes well. Then 
> i put it into a vnl_matrix(goes also well) and extract a certain part of 
> this matrix, import this subpart into a vtkImageData with 3 dimensions 
> using the itkImageImport class.
> When i then try to use this image data, the application crashes because 
> the data has not been put there correctly is my assumption.
> When i call the print() function for the vtkImageData object it tells me 
> that there are the 97*110*129 = 1376430 which there should be. The 
> GetEstimatedMemorySize() and GetActualMemorySize() also returns more or 
> less the correct amount in kb. To check that the values of data is 
> correct I have tried calling GetDataScalarPointer() to get access to the 
> data kept inside this object.
> When i then iterate this data in my unique(...) function(my own, see 
> below), and print the values, it seems that at position 344107 it 
> assumes value -4.2e037, and thereafter -9.1e041and followed by zeros up 
> until index 345072 where the application crashes.
> And it should be able to print out 1376430 elements, since this is the 
> size of the image.
>  
> Furthermore, the application crashes if i try to render the image.
>  
> So I was hoping someone with a bit more experience with me could take a 
> quick look at my code and see if it looks completely wrong. I am really 
> stuck here, and I dont understand why the data is not there, when it 
> should be, and vtk actually tells me that it is there.
>  
> I have copied my program listing below for ease of understanding my 
> problem. I really hope for help since i am pretty stuck here.
> Thank you very much in advance
> - H
>  
> #include<cstdio>
> #include <fstream>
> #include <vtkImageData.h>
> #include "vtkImageImport.h" //Import images for VTK
> #include "vtkActor.h"
> #include "vtkOutlineFilter.h "
> #include "vtkPolyDataMapper.h"
> #include "vtkRenderWindow.h"
> #include "vtkRenderer.h"
> #include "vtkRenderWindowInteractor.h"
> #include "vtkLight.h"
> #include "vtkCamera.h"
> #include "vtkContourFilter.h"
> #include "vtkProperty.h"
> 
> #include<map>
> #include <vnl/vnl_matrix.h>
> 
> typedef float SDMdatatype;
> typedef vnl_matrix<SDMdatatype> mat;
> 
> int D[]={110,129,97};
> unsigned int N=((*D)*(*(D+1))*(*(D+2))); //numel(vol)
> unsigned short m=1;      //Shape count
> unsigned short sm=7;      //Significant modes chosen
> mat meanShape(N*m,1);
> 
> SDMdatatype* readArrayFromFile(char* fn,long size){
>  std::ifstream file;
>  file.open(fn,std::ios::in|std::ios::binary);
>  if (!file) { printf("file was not opened, issue error msg"); }
>  SDMdatatype* buffer; 
>  buffer = new SDMdatatype[size];
>  file.read(reinterpret_cast<char*>(buffer), sizeof (SDMdatatype) * 
> size);//static_cast <char *> buffer
>  file.close();
>  return buffer;
> }
> 
> vtkImageData* importData(SDMdatatype *data1,int *dims){
>  vtkImageImport *importer = vtkImageImport::New();
>  importer->SetDataScalarTypeToFloat();
>  importer->SetDataOrigin(0,0,0);
>  //importer->SetImportVoidPointer(data1);
>  importer->CopyImportVoidPointer(data1,N);
>  
>  importer->SetWholeExtent(0,dims[0]-1,0,dims[1]-1,0,dims[2]-1);//If not 
> 3D image set 3D extent = 0.
>  importer->SetDataExtentToWholeExtent();
> 
>  importer->Update();
> 
>  vtkImageData *img=importer->GetOutput();
>  img->Update();
>  return img;
> }
> 
> void loadPCAResults(){
>  SDMdatatype* b1=readArrayFromFile(
>   "C:\\thesisIntermediate\\meanshape.dat",
>  N*m);
>  
>  meanShape.copy_in(b1);
>  delete b1;
> }
> void unique(SDMdatatype* data, int size,bool print){
>  typedef std::map<SDMdatatype,long> pixHistType;
>  pixHistType hist;
> 
>  for(int k=0;k<size;k++){
>   //printf("%x\n",data[k]);
>   std::cout<<k<<" : "<<*(data+k)<<std::endl;
>   SDMdatatype val=data[k];
>   //mexPrintf("%4i\n",val);
>   hist[val]++;
>  }
>  if(print){
>   pixHistType::iterator iter;
>   for(iter = hist.begin(); iter != hist.end(); ++iter)
>     std::cout<<"["<<iter->first<<"]:["<<iter->second<<"]"<<std::endl;
>  }
> }
> 
> int main(int argc,char* argv[])
> {
>  loadPCAResults();
> 
>  //structure actors
>  vtkActor *Temporopolar_region_left_actor  = vtkActor::New();
> 
>  //rendering objects
>  vtkRenderer *aRenderer = vtkRenderer::New();
>  vtkRenderWindow *renWin = vtkRenderWindow::New();
>  vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
>  vtkCamera *aCamera = vtkCamera::New();
> 
>  // Get vols from SDM
>  //extract(height,width,top,left)
>  mat t=meanShape.extract(N,1, 0,0);
>  SDMdatatype* b=t.data_block();
>  vtkImageData *Temporopolar_region_left_data = importData(b,D);
> 
>  Temporopolar_region_left_data->Update();
>  Temporopolar_region_left_data->UpdateInformation();
>  Temporopolar_region_left_data->PropagateUpdateExtent();
> 
>  SDMdatatype* a = 
> (SDMdatatype*)Temporopolar_region_left_data->GetScalarPointer();
>  
>  unique(a,N,1);
> 
>  vtkContourFilter *contours = vtkContourFilter::New();
>  contours->SetInput(Temporopolar_region_left_data);
>  contours->SetValue(0,0);
> 
>  vtkPolyDataMapper *mpr = vtkPolyDataMapper::New();
>  mpr->SetInput(contours->GetOutput());
>  
>  Temporopolar_region_left_actor -> SetMapper(mpr);
>  Temporopolar_region_left_actor -> GetProperty() -> SetDiffuseColor(1., 
> 0., 0.);
>  Temporopolar_region_left_actor -> GetProperty() -> SetSpecularPower(50);
>  Temporopolar_region_left_actor -> GetProperty() -> SetSpecular(0.5);
>  Temporopolar_region_left_actor -> GetProperty() -> SetDiffuse( 0.8);
> 
>  // Actors are added to the renderer.
>  aRenderer->AddActor(Temporopolar_region_left_actor);
> 
>  iren->SetRenderWindow(renWin);
>  renWin->AddRenderer(aRenderer);
>  aRenderer->SetActiveCamera(aCamera);
> 
>  // Setting the color and size of the renderwindow,
>  // initializing the camera position
> 
>  // Here we go!
>  iren->Initialize();
>  renWin->Render();
>  iren->Start();
>  //////////////////////////////////////////////////////////////////////////////////
>  //         CLEAN UP         //
>  ////////////////////////////////////////////////////////////////////////////////// 
> 
>  
>  aCamera->Delete();
>  aRenderer->Delete();
>  renWin->Delete();
>  iren->Delete();
> }
> 
> 
> ------------------------------------------------------------------------
> 
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