Field Detail

• ds

  protected static final int[] ds

• downsampleChoiceXY

  public static String[] downsampleChoiceXY

• downsampleChoiceZ

  public static String[] downsampleChoiceZ

• localizationChoice

  public static String[] localizationChoice

• brightnessChoice

  public static String[] brightnessChoice

• limitDetectionChoice

  public static String[] limitDetectionChoice

• defaultDownsampleXYIndex

  public static int defaultDownsampleXYIndex

• defaultDownsampleZIndex

  public static int defaultDownsampleZIndex

• defaultLocalization

  public static int defaultLocalization

• defaultBrightness

  public static int[] defaultBrightness

• defaultImageSigmaX

  public static double defaultImageSigmaX

• defaultImageSigmaY

  public static double defaultImageSigmaY

• defaultImageSigmaZ

  public static double defaultImageSigmaZ

• defaultViewChoice

  public static int defaultViewChoice

• defaultAdditionalSigmaX

  public static double defaultAdditionalSigmaX

• defaultAdditionalSigmaY

  public static double defaultAdditionalSigmaY

• defaultAdditionalSigmaZ

  public static double defaultAdditionalSigmaZ

• defaultMinIntensity

  public static double defaultMinIntensity

• defaultMaxIntensity

  public static double defaultMaxIntensity

• defaultMaxDetections

  public static int defaultMaxDetections

• defaultMaxDetectionsTypeIndex

  public static int defaultMaxDetectionsTypeIndex

• limitDetections

  protected boolean limitDetections

• imageSigmaX

  protected double imageSigmaX

• imageSigmaY

  protected double imageSigmaY

• imageSigmaZ

  protected double imageSigmaZ

• additionalSigmaX

  protected double additionalSigmaX

• additionalSigmaY

  protected double additionalSigmaY

• additionalSigmaZ

  protected double additionalSigmaZ

• minIntensity

  protected double minIntensity

• maxIntensity

  protected double maxIntensity

• maxDetections

  protected int maxDetections

• maxDetectionsTypeIndex

  protected int maxDetectionsTypeIndex

• localization

  protected int localization

• downsampleXY

  protected int downsampleXY

• downsampleZ

  protected int downsampleZ

Constructor Detail

• DifferenceOf

  public DifferenceOf(SpimData2 spimData,
                      List<ViewId> viewIdsToProcess)

Method Detail

• addAddtionalParameters

  protected abstract void addAddtionalParameters(GenericDialog gd)

• queryAdditionalParameters

  protected abstract boolean queryAdditionalParameters(GenericDialog gd)

• queryParameters

  public boolean queryParameters(boolean downsample,
                                 boolean defineAnisotropy,
                                 boolean additionalSmoothing,
                                 boolean setMinMax,
                                 boolean limitDetections)

  Description copied from class: InterestPointDetection
  Query the necessary parameters for the interestpoint detection

  Specified by:

  queryParameters in class InterestPointDetection

  Parameters:

  downsample - - whether to downsample the images before performing the blob detection

  defineAnisotropy - - whether to use/query for anisotropy in resolution of the data

  additionalSmoothing - - smooth in certain dimensions before computing the segmentation

  setMinMax - - whether to define minimal and maximal intensity relative to whom everything is normalized to [0...1]

  Returns:

• preSmooth

  protected <T extends RealType<T>> void preSmooth(RandomAccessibleInterval<T> img)

• limitList

  public static List<InterestPoint> limitList(int maxDetections,
                                              int maxDetectionsTypeIndex,
                                              List<InterestPoint> list)

• getViewSelection

  protected ViewId getViewSelection(String dialogHeader,
                                    String text,
                                    Channel channel)

  Figure out which view to use for the interactive preview

  Parameters:

  dialogHeader -

  text -

  channel -

  Returns:

• init

  protected abstract void init(int numChannels)

  This is only necessary to make static objects so that the ImageJ dialog remembers choices for the right channel

  Parameters:

  numChannels - - the TOTAL number of channels (not only the ones to process)

• setDefaultValues

  protected abstract boolean setDefaultValues(Channel channel,
                                              int brightness)

• setAdvancedValues

  protected abstract boolean setAdvancedValues(Channel channel)

• setInteractiveValues

  protected abstract boolean setInteractiveValues(Channel channel)

• correctForDownsampling

  protected void correctForDownsampling(List<InterestPoint> ips,
                                        AffineTransform3D t)

• downsampleFactor

  public int downsampleFactor(int downsampleXY,
                              int downsampleZ,
                              VoxelDimensions v)

• openAndDownsample

  protected RandomAccessibleInterval<FloatType> openAndDownsample(SpimData2 spimData,
                                                                  ViewDescription vd,
                                                                  AffineTransform3D t)