vtkITKArchetypeImageSeriesScalarReader:: GetRasToIjkMatrix Same DicomFiles but Different result

Development
1

My C++ Code
#################
vtkSmartPointer volumeReader = vtkSmartPointer::New();
volumeReader->SetArchetype(sortedFiles->GetValue(0).c_str());
for (int i = 0; i < sortedFiles->GetNumberOfValues(); i++) {
volumeReader->AddFileName(sortedFiles->GetValue(i).c_str());
}

volumeReader->SetSingleFile(0);
volumeReader->SetOutputScalarTypeToNative();
volumeReader->SetDesiredCoordinateOrientationToNative();
volumeReader->SetUseNativeOriginOn();
volumeReader->Update();
PrintMatrix4X4(volumeReader->GetRasToIjkMatrix(), "VolumeReader RasIjk");

######### Output ##################
Begin VolumeReader RasIjk#
-1.600000, -0.000000, 0.000000, 240.320000
-0.000000, -1.600000, -0.000000, 256.000000
0.000000, -0.000000, 0.800000, -34.800000
-0.000000, 0.000000, -0.000000, 1.000000
#End VolumeReader RasIjk
########################################

3DSlicer Edit File : Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py
#############

image
image1209×842 60.7 KB

What is happening ?

2 

void PrintMatrix4X4(const vtkMatrix4x4 *matrix4X4, const char *flagName);

int main(int argc, char **argv) {
    vtkLogger::Init(argc, argv);
    // Put every log message in "everything.log":
    vtkLogger::LogToFile("everything.log", vtkLogger::APPEND, vtkLogger::VERBOSITY_MAX);
    // needed to ensure appropriate OpenGL context is created for VTK rendering.
    QSurfaceFormat::setDefaultFormat(QVTKRenderWidget::defaultFormat());
    // QT Stuff
    QApplication app(argc, argv);

    vtkNew<vtkDICOMDirectory> dicomdir;
    dicomdir->SetDirectoryName("/home/dhz/v4486");
    dicomdir->RequirePixelDataOff();
    dicomdir->Update();

    int n = dicomdir->GetNumberOfSeries();
    if (n == 0) {
        std::cerr << "No DICOM images in directory!" << std::endl;
        return EXIT_FAILURE;
    }

    int firstStudy = 0;
    // Get information related to the patient study
    vtkDICOMItem patient = dicomdir->GetPatientRecordForStudy(firstStudy);
    vtkDICOMItem study = dicomdir->GetStudyRecord(firstStudy);


    // Iterate through all the series in this study.
    int j1 = dicomdir->GetFirstSeriesForStudy(firstStudy);
    //  int j2 = dicomdir->GetLastSeriesForStudy(i);
    // get some of the series attributes as a vtkDICOMItem
    vtkDICOMItem series = dicomdir->GetSeriesRecord(j1);
    // get all the files in the series
    vtkStringArray *sortedFiles = dicomdir->GetFileNamesForSeries(j1);


    vtkSmartPointer<vtkITKArchetypeImageSeriesScalarReader> volumeReader = vtkSmartPointer<vtkITKArchetypeImageSeriesScalarReader>::New();
    volumeReader->SetArchetype(sortedFiles->GetValue(0).c_str());
    for (int i = 0; i < sortedFiles->GetNumberOfValues(); i++) {
        volumeReader->AddFileName(sortedFiles->GetValue(i).c_str());
    }



    volumeReader->SetSingleFile(0);
    volumeReader->SetOutputScalarTypeToNative();
    volumeReader->SetDesiredCoordinateOrientationToNative();
    volumeReader->SetUseNativeOriginOn();
    volumeReader->Update();
    PrintMatrix4X4(volumeReader->GetRasToIjkMatrix(), "VolumeReader RasIjk");

    auto imageChangeInformation = vtkSmartPointer<vtkImageChangeInformation>::New();
    imageChangeInformation->SetInputConnection(volumeReader->GetOutputPort());
    imageChangeInformation->SetOutputSpacing(1, 1, 1);
    imageChangeInformation->SetOutputOrigin(0, 0, 0);
    imageChangeInformation->Update();


    auto imageData = imageChangeInformation->GetOutputDataObject(0);
    if (!imageData->IsA("vtkImageData")) {
        vtkLogF(INFO, "ImageData is vtkImageData");
        return EXIT_FAILURE;
    }
    auto pImg = (vtkImageData *) imageData;


    int imageDims[3];
    double origin[3] = {0.0};
    double spacing[3] = {1.0};
    int extentInfo[6] = {0};
    pImg->GetDimensions(imageDims);
    pImg->GetOrigin(origin);
    pImg->GetSpacing(spacing);
////        vtkMatrix3x3 *imageDirection = chgData->GetDirectionMatrix();
//
    pImg->GetExtent(extentInfo);

    vtkLogF(INFO, "Dimensions: %d,%d,%d", imageDims[0], imageDims[1], imageDims[2]);
    vtkLogF(INFO, "    Origin: %f,%f,%f", origin[0], origin[1], origin[2]);
    vtkLogF(INFO, "   Spacing: %f,%f, %f", spacing[0], spacing[1], spacing[2]);
    vtkLogF(INFO, "    Extent: %d,%d,%d,%d,%d,%d", extentInfo[0], extentInfo[1], extentInfo[2],
            extentInfo[3], extentInfo[4], extentInfo[5]);
    return QApplication::exec();
}


void PrintMatrix4X4(const vtkMatrix4x4 *matrix4X4, const char *flagName = nullptr) {
    vtkLogF(INFO, "Begin %s#", flagName);
    auto data = matrix4X4->GetData();
    for (int i = 0; i < 4; ++i) {
        vtkLogF(INFO, "%15.6f,%15.6f,%15.6f,%15.6f", data[4 * i], data[4 * i + 1], data[4 * i + 2],
                data[4 * i + 3]);
    }

    vtkLogF(INFO, "#End %s", flagName);
}
3

I’m not sure anyone has time to read through and comment your C++ code. Do you have a specific issue that would narrow down your concern?

If you think there’s a bug in the library could you provide a reproducible example using public data?