Hi Klaus.
The values in my code are right to the point where i write them into
the RGBABuffer. When i read the output some values of RGBABuffer, they
are very strange (some special characters).
I think
RGBABuffer[bufferIndex*4+0] = (unsigned char)red;
RGBABuffer[bufferIndex*4+1] = (unsigned char)green;
RGBABuffer[bufferIndex*4+2] = (unsigned char)blue;
RGBABuffer[bufferIndex*4+3] = (unsigned char)alpha;
is an illegal line. On weekend I'll have also a look on your informations.
Thanks and best regards
Frank
> Thu, 23 Sep 2010 15:15:48 +0200 - Fritzsche Klaus
> <[email protected]>:
> AW: [mitk-users] MITK Plugin different color for timeNr
> Hi Frank,
>
> your code looks fine principally. I think your cast from [0 ..
> 1]-floating point values to uchar makes your image black. Try
> multiplying with 255.0f.
>
> At the moment there is no function like SetVoxelColor. We normaly
> use the mitk::ImageToItk filter (in cases where the pixeltype and
> dimension are known) or the AccessByItk/AccessFixedDimensionByItk
> Macros to manipulate images in ITK-Style (usually by using
> iterators) and convert them back to MITK by calling
>
> mitkImage->InitializeByItk(itkImage.GetPointer());
> mitkImage->SetVolume(itkImage.GetBufferedPointer());
>
> Did you have a look at the mitkTensorImage class? It already gets
> displayed in RGB and an alpha-channel display will be added and
> supported soon. Internally this class uses the
> ItkTensorToRgbImageFilter which is also part of the diffusion
> imaging module in MITK and shows you how to generate RGB-images (the
> itk::RGBPixelType can simply be replaced by the itk::RGBAPixelType
> and will be rendered correctly in MITK).
>
> Hope this helps, please don't hesitate to ask further questions. I
> am sure we will manage to get your code running. I am sorry for
> having missed your posts on the list!
>
> Best regards,
> Klaus
>
> ---
> Dr. rer. nat. Klaus H. Fritzsche
> Deutsches Krebsforschungszentrum (DKFZ) in der Helmholtz-Gemeinschaft
> Abteilung Medizinische und Biologische Informatik
> Im Neuenheimer Feld 280, D-69120 Heidelberg
> Tel: 49-(0)6221-42-3545, Fax: 49-(0)6221-42-2354
> E-Mail: [email protected], Web: www.dkfz.de
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche
> und/oder nur für den/die Empfänger bestimmte Informationen
> enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein,
> kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht
> ist untersagt.
>
>
> -----Ursprüngliche Nachricht-----
> Von: Frank Blaschke [mailto:[email protected]]
> Gesendet: Dienstag, 14. September 2010 17:35
> An: [email protected]
> Betreff: Re: [mitk-users] MITK Plugin different color for timeNr
>
> Hi again.
>
> I've an image with 3 time channels (0,1 and 2). So my vectors are
> saved. Now I want to create a new image node with color informations.
> So i try to save for every voxel a color in RGBA in my mitk-Image.
>
> normalized x -> red
> normalized y -> green
> normalized z -> blue
> 1 -> alpha (first, later length of vector)
>
> Has mitk function to set a voxel a specific color like
>
> mitkImage->SetVoxelColor(x,y,z,r,g,b,a) ?
>
> I tried it like my code down here. But in the new ImageNode are no
> color informations and the values are not set or very high (displayed
> is everything in black).
>
> thanks for help
>
> Frank
>
> MITK_INFO << "Performing image processing.";
>
> //ToDo
> //Erstelle Farbwerte aus den normalen der Zeiten für X Y Z
> //Erstelle neues MITK Bild und schreibe werte hinein
> //Erstelle neue MITK DataNode für DataManager der ExtApp
>
> //Image dimensions
> unsigned int *dimensionImage = image->GetDimensions();
>
> unsigned int dimensions[3];
> dimensions[0] = dimensionImage[0];
> dimensions[1] = dimensionImage[1];
> dimensions[2] = dimensionImage[2];
>
> //Number of voxels in image
> int voxel = dimensions[0] * dimensions[1] * dimensions[2];
>
> //number of all RGBA color values
> unsigned char* RGBABuffer = new unsigned char[4*voxel];
>
> double red,green,blue,tmp = 0;
> int bufferIndex = 0;
> double alpha = 1;
> //Voxel-coordinates to get color value from image.
> mitk::Index3D position;
> // typedef double PixelType;
> // static const unsigned int Dimension = 3;
> // typedef itk::Image <PixelType,Dimension> ImageType;
> // ImageType::IndexType index;//Voxel-coordinates to save
> new color values in new image. (Needet for projection on axis.)
>
> //or other order for X Y Z <--> Z Y X ?
> for(int i=0; i<dimensions[2];i++)
> {
> position[2]=i;
> for(int j=0; j<dimensions[1];j++)
> {
> position[1]=j;
> for(int k=0; k<dimensions[0];k++)
> {
> position[0]=k;
> //In image are also negative values, so we
> need absolute numbers.
>
> red = image->GetPixelValueByIndex(position,0);
> red = abs(red);
> green = image->GetPixelValueByIndex(position,1) ;
> green = abs(green);
> blue = image->GetPixelValueByIndex(position,2) ;
> blue = abs(blue);
>
> //Normalize colors.
> tmp = sqrt(pow(red,2) + pow(green,2) + pow(blue,2));
> red /= tmp;
> green /= tmp;
> blue /= tmp;
>
> //fill RGBABuffer
> //bufferIndex=0
> //Voxel 1 -> RGBABuffer ( t*4+0 t*4+1 t*4+2
> t*4+2 t*4+3 ;)
> //bufferIndex++
> //voxel 2 -> RGBABuffer ( t*4+0 t*4+1 t*4+2
> t*4+2 t*4+3 ;)
> // RGBABuffer[bufferIndex*4+0] =
> *reinterpret_cast<char**>(&red);//red
> RGBABuffer[bufferIndex*4+0] = (unsigned char)red;
> RGBABuffer[bufferIndex*4+1] = (unsigned char)green;
> RGBABuffer[bufferIndex*4+2] = (unsigned char)blue;
> RGBABuffer[bufferIndex*4+3] = (unsigned char)alpha;
> bufferIndex++;
>
> }
> }
> }
>
> //Create the new Image
> mitk::Image::Pointer coloredMitkImage = mitk::Image::New();
> //missing geometry informations, so that it will have the
> same size like original image
> typedef itk::RGBAPixel <unsigned char> RGBAPixel;
> mitk::PixelType pixelType( typeid(RGBAPixel), 1,
> itk::ImageIOBase::RGBA );
> coloredMitkImage->Initialize(pixelType, 3, dimensions);
> coloredMitkImage->SetImportChannel(RGBABuffer, 0,
> mitk::Image::ManageMemory);
>
> //Create new DataNode
> mitk::DataNode::Pointer nodeMitkImage = mitk::DataNode::New();
> nodeMitkImage->SetData(coloredMitkImage);
> nodeMitkImage->SetName(node->GetName() + "_ColoredMitkImage");
> //nodeMitkImage->SetProperty ( "TransferFunction",
> mitk::TransferFunctionProperty::New(tfX.GetPointer()));
> this->GetDefaultDataStorage()->Add(nodeMitkImage);//Will
> add as child.(doesn't work)
> //ToDo unmark shown-property for parent image
>
>
>
>
>
>
>
>> Fri, 10 Sep 2010 13:10:59 +0200 - Frank Blaschke
>> <[email protected]>:
>> [mitk-users] MITK Plugin different color for timeNr
>
>> Hi,
>>
>> I have a diffusion image in *.nii format. It include value from -1
>> until 1. X-values are in time 0, Y-values in time 1 and Z-values in
>> time 2.
>> I wanna turn X-values red, Y green and Z in blue. But when I use the
>> code here, all values in X,Y and Z time will be colored.
>>
>> Thanks for help
>>
>> Frank
>>
>> <code>
>>
>> MITK_INFO << "Performing diffusion image coloring.";
>>
>> //turn X redr, Y green and Z blue
>> //transfer function from 0 till 1 of [r,g,b] = [0,0,0]
>> until [1,0,0] etc
>> //create new node,, hide the old one
>>
>> //Create new DataNode
>> mitk::DataNode::Pointer dataNode = mitk::DataNode::New();
>> dataNode->SetData(image);
>> dataNode->SetName(node->GetName() + "_DiffusionColor");
>>
>> //TimeSelector to get singe images x,y,z
>> mitk::ImageTimeSelector::Pointer selector =
>> mitk::ImageTimeSelector::New();
>> selector->SetInput(image);
>>
>> //X-image from time 0
>> selector->SetTimeNr(0);//X
>> selector->Update();
>> mitk::Image::Pointer selectedImageX = mitk::Image::New();
>> selectedImageX->Initialize(selector->GetPic());
>> selectedImageX->SetPicVolume(selector->GetPic());
>>
>> //selectedImageX->SetGeometry(selector->GetGeometry());//doesn't work
>> selectedImageX->Update();
>>
>> //Y-image from time 1
>> selector->SetTimeNr(1);//Y
>> selector->Update();
>> mitk::Image::Pointer selectedImageY = mitk::Image::New();
>> selectedImageY->Initialize(selector->GetPic());
>> selectedImageY->SetPicVolume(selector->GetPic());
>>
>> //selectedImageY->SetGeometry(selector->GetGeometry());//doesn't work
>> selectedImageY->Update();
>>
>> //Z-image from time 2
>> selector->SetTimeNr(2);//Z
>> selector->Update();
>> mitk::Image::Pointer selectedImageZ = mitk::Image::New();
>> selectedImageZ->Initialize(selector->GetPic());
>> selectedImageZ->SetPicVolume(selector->GetPic());
>>
>> //selectedImageZ->SetGeometry(selector->GetGeometry());//doesn't work
>> selectedImageZ->Update();
>>
>> // Set the property "volumerendering" to the Boolean
>> value "true"
>> dataNode->SetProperty("volumerendering",
>> mitk::BoolProperty::New(true));
>> //dataNode->SetProperty("color",
>> mitk::BoolProperty::New(true));
>>
>> // Create a transfer function to assign optical
>> properties (color and opacity) to grey-values of the data
>> mitk::TransferFunction::Pointer tfX =
>> mitk::TransferFunction::New();
>> tfX->InitializeByMitkImage(selectedImageX);
>>
>> // Set the color transfer function AddRGBPoint(double
>> x, double r, double g, double b)
>> tfX->GetColorTransferFunction()->AddRGBPoint ( -1.0,
>> 1.0, 0.0, 0.0 );
>> tfX->GetColorTransferFunction()->AddRGBPoint ( 0.0,
>> 0.0, 0.0, 0.0 );
>> // tfX->GetColorTransferFunction()->AddRGBPoint (
>> tfX->GetColorTransferFunction()->GetRange()[0], 0.0, 0.0, 0.0 );
>> tfX->GetColorTransferFunction()->AddRGBPoint ( 1.0,
>> 1.0, 0.0, 0.0 );
>> // tfX->GetColorTransferFunction()->AddRGBPoint (
>> tfX->GetColorTransferFunction()->GetRange()[1], 1.0, 0.0, 0.0 );
>>
>> // Set the piecewise opacity transfer function
>> AddPoint(double x, double y)
>> tfX->GetScalarOpacityFunction()->AddPoint ( -1.0, 1.0 );
>> tfX->GetScalarOpacityFunction()->AddPoint ( 0.0, 0.0 );
>> tfX->GetScalarOpacityFunction()->AddPoint ( 1.0, 1.0);
>> // tfX->GetScalarOpacityFunction()->AddPoint (
>> tfX->GetColorTransferFunction()->GetRange()[1], 1.0);
>>
>> dataNode->SetProperty ( "TransferFunction",
>> mitk::TransferFunctionProperty::New(tfX.GetPointer()));
>>
>> this->GetDefaultDataStorage()->Add(dataNode);//Should
>> add as child, but add as new node next to the others.
>>
>> MITK_INFO << "Done.";
>>
>> </code>
>>
>>
>> --
>>
>> Frank Blaschke
>>
>> Department for Biometry and Medical Informatics
>> web: http://www.med.uni-magdeburg.de/ibmi.html
>> phone: +49 391 67 135 51
>> office: building 2 / room 212
>>
>>
>>
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>>
>
>
>
> --
>
> Frank Blaschke
>
> Department for Biometry and Medical Informatics
> web: http://www.med.uni-magdeburg.de/ibmi.html
> phone: +49 391 67 135 51
> office: building 2 / room 212
>
>
> ------------------------------------------------------------------------------
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>
--
Frank Blaschke
Department for Biometry and Medical Informatics
web: http://www.med.uni-magdeburg.de/ibmi.html
phone: +49 391 67 135 51
office: building 2 / room 212
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