// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RequiredZThickness::execute()
{
  setErrorCondition(0);
  dataCheck();
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer dataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerSelection());
  if (getErrorCondition() < 0) { return; }

  ImageGeom::Pointer image = dataContainer->getGeometryAs<ImageGeom>();

  size_t dims[3] = { 0, 0, 0 };
  image->getDimensions(dims);


  if (dims[2] < getNumZVoxels())
  {
    QString str;
    QTextStream ss(&str);
    ss << "Number of Z Voxels does not meet required value during execution of the filter. \n";
    ss << "  Required Z Voxels: " << m_NumZVoxels << "\n";
    ss << "  Current Z Voxels: " << dims[2];

    setErrorCondition(-7788);
    notifyErrorMessage(getHumanLabel(), str, getErrorCondition());
    bool needMoreData = true;
    emit decisionMade(needMoreData);
  }

  notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RequiredZThickness::dataCheck()
{
  setErrorCondition(0);
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer dataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerSelection());
  if (getErrorCondition() < 0) { return; }

  ImageGeom::Pointer image = dataContainer->getGeometryAs<ImageGeom>();
  if( NULL == image.get() )
  {
    setErrorCondition(-7789);
    notifyErrorMessage(getHumanLabel(), "Missing Image Geometry in the selected DataContainer", getErrorCondition());
    return;
  }

  size_t dims[3] = { 0, 0, 0 };
  image->getDimensions(dims);


  if (dims[2] < getNumZVoxels() && m_PreflightCheck)
  {
    setErrorCondition(-7787);
    QString str;
    QTextStream ss(&str);
    ss << "Number of Z Voxels does not meet required value during preflight of the filter. \n";
    ss << "  Required Z Voxels: " << m_NumZVoxels << "\n";
    ss << "  Current Z Voxels: " << dims[2];

    notifyErrorMessage(getHumanLabel(), str, getErrorCondition());
  } 
  else if (dims[2] < getNumZVoxels() && !m_PreflightCheck)
  {
    QString str;
    QTextStream ss(&str);
    ss << "Number of Z Voxels does not meet required value during preflight but will be checked during pipeline execution.\n";
    ss << "  Required Z Voxels: " << m_NumZVoxels << "\n";
    ss << "  Current Z Voxels: " << dims[2];

    notifyWarningMessage(getHumanLabel(), str, getErrorCondition());
  }

}
Ejemplo n.º 3
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CropImageGeometry::dataCheck()
{
  if(getErrorCondition() < 0) { return; }
  setErrorCondition(0);

  // Validate the incoming DataContainer, Geometry, and AttributeMatrix ; bail if any do not exist since we plan on using them later on in the dataCheck
  // Error messages are handled by the getPrereq functions
  DataContainer::Pointer srcCellDataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
  ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
  AttributeMatrix::Pointer srcCellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellAttributeMatrixPath(), -301);
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer destCellDataContainer = srcCellDataContainer;
  AttributeMatrix::Pointer destCellAttrMat;

  if (m_SaveAsNewDataContainer == true)
  {
    float ox = 0.0f, oy = 0.0f, oz = 0.0f, rx = 0.0f, ry = 0.0f, rz = 0.0f;
    size_t dx = 0, dy = 0, dz = 0;
    image->getOrigin(ox, oy, oz);
    image->getResolution(rx, ry, rz);
    image->getDimensions(dx, dy, dz);

    destCellDataContainer = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getNewDataContainerName());
    if(NULL == destCellDataContainer.get() || getErrorCondition() < 0)
    {
      return;
    }
    IGeometry::Pointer imageCopy = image->deepCopy();
    destCellDataContainer->setGeometry(imageCopy);

    destCellAttrMat = srcCellAttrMat->deepCopy();
    destCellDataContainer->addAttributeMatrix(destCellAttrMat->getName(), destCellAttrMat);
  }
  else
  {
    destCellAttrMat = srcCellAttrMat;
  }

  if(NULL == destCellDataContainer.get() || NULL == destCellAttrMat.get() || getErrorCondition() < 0)
  {
    return;
  }

  if (getXMax() < getXMin())
  {
    QString ss = QObject::tr("X Max (%1) less than X Min (%2)").arg(getXMax()).arg(getXMin());
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }
  if (getYMax() < getYMin())
  {
    QString ss = QObject::tr("Y Max (%1) less than Y Min (%2)").arg(getYMax()).arg(getYMin());
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }
  if (getZMax() < getZMin())
  {
    QString ss = QObject::tr("Z Max (%1) less than Z Min (%2)").arg(getZMax()).arg(getZMin());
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }
  if (getXMin() < 0)
  {
    QString ss = QObject::tr("X Min (%1) less than 0").arg(getXMin());
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }
  if (getYMin() < 0)
  {
    QString ss = QObject::tr("Y Min (%1) less than 0").arg(getYMin());
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }
  if (getZMin() < 0)
  {
    QString ss = QObject::tr("Z Min (%1) less than 0").arg(getZMin());
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }

  if (getXMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints()) - 1))
  {
    QString ss = QObject::tr("The X Max (%1) is greater than the Image Geometry X extent (%2)").arg(getXMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints()) - 1);
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }

  if (getYMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints()) - 1))
  {
    QString ss = QObject::tr("The Y Max (%1) is greater than the Image Geometry Y extent (%2)").arg(getYMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints()) - 1);
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }

  if (getZMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getZPoints()) - 1))
  {
    QString ss = QObject::tr("The Z Max (%1) is greater than the Image Geometry Z extent (%2)").arg(getZMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getZPoints()) - 1);
    notifyErrorMessage(getHumanLabel(), ss, -5550);
    setErrorCondition(-5550);
  }

  QVector<size_t> tDims(3, 0);
  if (getXMax() - getXMin() < 0) { setXMax(getXMin() + 1); }
  if (getYMax() - getYMin() < 0) { setYMax(getYMin() + 1); }
  if (getZMax() - getZMin() < 0) { setZMax(getZMin() + 1); }
  tDims[0] = (getXMax() - getXMin()) + 1;
  tDims[1] = (getYMax() - getYMin()) + 1;
  tDims[2] = (getZMax() - getZMin()) + 1;

  destCellDataContainer->getGeometryAs<ImageGeom>()->setDimensions(tDims[0], tDims[1], tDims[2]);

  // If any of the sanity checks fail above then we should NOT attempt to go any further.
  if (getErrorCondition() < 0) { return; }

  size_t totalPoints = 1;
  for(int i = 0; i < 3; i++) {
    if(tDims[i] != 0) { totalPoints *= tDims[i]; }
  }
  AttributeMatrix::Pointer newCellAttrMat = AttributeMatrix::New(tDims, destCellAttrMat->getName(), destCellAttrMat->getType());

  QList<QString> voxelArrayNames = destCellAttrMat->getAttributeArrayNames();
  for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
  {
    IDataArray::Pointer p = destCellAttrMat->getAttributeArray(*iter);
    //
    IDataArray::Pointer data = p->createNewArray(totalPoints, p->getComponentDimensions(), p->getName(), false);

    destCellAttrMat->removeAttributeArray(*iter);
    newCellAttrMat->addAttributeArray(*iter, data);
  }
  destCellDataContainer->removeAttributeMatrix(destCellAttrMat->getName());
  destCellDataContainer->addAttributeMatrix(newCellAttrMat->getName(), newCellAttrMat);


  if(m_RenumberFeatures == true)
  {
    QVector<size_t> cDims(1, 1);
    m_FeatureIdsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeatureIdsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
    if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
    {
      m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0);
    } /* Now assign the raw pointer to data from the DataArray<T> object */

    AttributeMatrix::Pointer cellFeatureAttrMat = srcCellDataContainer->getAttributeMatrix(getCellFeatureAttributeMatrixPath().getAttributeMatrixName());
    if(NULL == cellFeatureAttrMat.get()) { return; }
    QVector<bool> activeObjects(cellFeatureAttrMat->getNumTuples(), true);
    cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
  }
}
Ejemplo n.º 4
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadImage::dataCheck()
{
  setErrorCondition(0);

  //check file name exists
  if(getInputFileName().isEmpty())
  {
    setErrorCondition(-1);
    notifyErrorMessage(getHumanLabel(), "The input file name must be set before executing this filter.", getErrorCondition());
    return;
  }

  //read image metadata
  itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(getInputFileName().toLocal8Bit().constData(), itk::ImageIOFactory::ReadMode);
  if(NULL == imageIO)
  {
    setErrorCondition(-2);
    QString message = QObject::tr("Unable to read image '%1'").arg(getInputFileName());
    notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
    return;
  }
  imageIO->SetFileName(getInputFileName().toLocal8Bit().data());
  imageIO->ReadImageInformation();

  //get size of image
  const size_t numDimensions = imageIO->GetNumberOfDimensions();
  int xdim = imageIO->GetDimensions(0);
  int ydim = imageIO->GetDimensions(1);
  int zdim = 1;
  if(3 != numDimensions)
  {
    if(2 == numDimensions)
    {
      //allow 2 dimensional images (as 3d image with size 1 in the z direction)
    }
    else
    {
      QString message = QObject::tr("3 dimensional image required (slected image dimensions: %1)").arg(numDimensions);
      setErrorCondition(-3);
      notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
      return;
    }
  }
  else
  {
    zdim = imageIO->GetDimensions(2);
  }

  //determine if container/attribute matrix already exist. if so check size compatibility
  DataArrayPath createdPath;
  DataContainer::Pointer m;
  AttributeMatrix::Pointer cellAttrMat;
  createdPath.update(getDataContainerName(), getCellAttributeMatrixName(), getImageDataArrayName() );

  m = getDataContainerArray()->getDataContainer(getDataContainerName());
  bool createAttributeMatrix = false;

  if(NULL == m.get()) //datacontainer doesn't exist->create
  {
    m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
    ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
    m->setGeometry(image);
    m->getGeometryAs<ImageGeom>()->setDimensions(xdim, ydim, zdim);
    double zRes = 1;
    double zOrigin = 0;
    if(3 == numDimensions)
    {
      zRes = imageIO->GetSpacing(2);
      zOrigin = imageIO->GetOrigin(2);
    }
    m->getGeometryAs<ImageGeom>()->setResolution(imageIO->GetSpacing(0), imageIO->GetSpacing(0), zRes);
    m->getGeometryAs<ImageGeom>()->setOrigin(imageIO->GetOrigin(0), imageIO->GetOrigin(1), zOrigin);
    createAttributeMatrix = true;
    if(getErrorCondition() < 0) { return; }
  }
  else   //datacontainer exists, check if attribute matrix exists
  {
    bool dcExists = m->doesAttributeMatrixExist(getCellAttributeMatrixName());
    ImageGeom::Pointer image = m->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
    if(getErrorCondition() < 0) { return; }

    size_t iDims[3] = { 0, 0, 0 };
    float iRes[3] = { 0.0f, 0.0f, 0.0f };
    float iOrigin[4] = { 0.0f, 0.0f, 0.0f };
    image->getDimensions(iDims);
    image->getResolution(iRes);
    image->getOrigin(iOrigin);

    if(dcExists &&  NULL != image.get())//attribute matrix exists, check compatibility
    {
      //get matrix
      cellAttrMat = m->getPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), false);
      if(getErrorCondition() < 0) { return; }

      //check dimension compatibility
      QVector<size_t> tDims = cellAttrMat->getTupleDimensions();
      if(tDims[0] != xdim || iDims[0] != xdim)
      {
        QString message = QObject::tr("The x size of '%1' (%2) does not match the x size of '%3' (%4)").arg(getInputFileName()).arg(xdim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName()).arg(tDims[0]);
        setErrorCondition(-4);
        notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
        return;
      }
      if(tDims[1] != ydim || iDims[1] != ydim)
      {
        QString message = QObject::tr("The y size of '%1' (%2) does not match the x size of '%3' (%4)").arg(getInputFileName()).arg(ydim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName()).arg(tDims[1]);
        setErrorCondition(-5);
        notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
        return;
      }
      if(3 == numDimensions)
      {
        if(tDims[2] != zdim || iDims[2] != zdim)
        {
          QString message = QObject::tr("The z size of '%1' (%2) does not match the x size of '%3' (%4)").arg(getInputFileName()).arg(zdim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName()).arg(tDims[2]);
          setErrorCondition(-6);
          notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
          return;
        }
      }
      else
      {
        if(tDims[2] != 1 || iDims[2] != 1)
        {
          QString message = QObject::tr("The z size of '%1' (%2) does not match the x size of '%3' (1)").arg(getInputFileName()).arg(zdim).arg(getDataContainerName() + "/" + getCellAttributeMatrixName());
          setErrorCondition(-7);
          notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
          return;
        }
      }
    }
    else //attribute matrix doesn't exist, create
    {
      createAttributeMatrix = true;
    }
  }

  //image/attribute matrix dimensions
  QVector<size_t> tDims(3, 0);
  tDims[0] = xdim;
  tDims[1] = ydim;
  tDims[2] = zdim;

  //create attribute matrix if needed
  if(createAttributeMatrix)
  {
    //create attribute matrix
    cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
    if(getErrorCondition() < 0) { return; }
  }

  //check pixel type (scalar, vector, etc) for support
  QVector<size_t> componentDims(1, 0);
  itk::ImageIOBase::IOPixelType pixelType = imageIO->GetPixelType();

  switch(pixelType)
  {

    case itk::ImageIOBase::SCALAR:
      componentDims[0] = 1;
      break;
    case itk::ImageIOBase::RGB:
      componentDims[0] = 3;
      break;
    case itk::ImageIOBase::RGBA:
      componentDims[0] = 4;
      break;
    default:
      setErrorCondition(-80001);
      notifyErrorMessage(getHumanLabel(), "The Pixel Type of the image is not supported with DREAM3D.", getErrorCondition());
  }

  // Check to make sure everything is OK with reading the image
  if(getErrorCondition() < 0)
  {
    std::string pixelTypeName = itk::ImageIOBase::GetPixelTypeAsString(pixelType);
    QString message = QObject::tr("The pixel type of '%1' (%2) is unsupported").arg(getInputFileName()).arg(QString::fromStdString(pixelTypeName));
    notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
    return;
  }

  //Now get how the actual image data is stored.
  IDataArray::Pointer data;
  itk::ImageIOBase::IOComponentType componentType = imageIO->GetComponentType();
  if(itk::ImageIOBase::CHAR == componentType)
  {
    data = Int8ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::UCHAR == componentType)
  {
    data = UInt8ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::SHORT == componentType)
  {
    data = Int16ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::USHORT == componentType)
  {
    data = UInt16ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::INT == componentType)
  {
    data = Int32ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::UINT == componentType)
  {
    data = UInt32ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::LONG == componentType)
  {
    data = Int64ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::ULONG == componentType)
  {
    data = UInt64ArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::FLOAT == componentType)
  {
    data = FloatArrayType::CreateArray(0, "Temp", false);
  }
  else if(itk::ImageIOBase::DOUBLE == componentType)
  {
    data = DoubleArrayType::CreateArray(0, "Temp", false);
  }
  else
  {
    std::string componentTypeName = itk::ImageIOBase::GetComponentTypeAsString(componentType);
    QString message = QObject::tr("The component type type of '%1' (%2) is unsupported").arg(getInputFileName()).arg(QString::fromStdString(componentTypeName));
    setErrorCondition(-9);
    notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
    return;
  }

  if(getErrorCondition() < 0) { return; }

  m_ImageDataPtr = TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, createdPath, componentDims, data);
  if( NULL != m_ImageDataPtr.lock().get() )
  {
    m_ImageData = m_ImageDataPtr.lock()->getVoidPointer(0);
  }
}