Constructor Detail

• DetectionUtils

  public DetectionUtils()

Method Detail

• preview

  public static final void preview(Model model,
                                   Settings settings,
                                   SpotDetectorFactoryBase<?> detectorFactory,
                                   Map<String,Object> detectorSettings,
                                   int frame,
                                   Logger logger,
                                   Consumer<Boolean> buttonEnabler)

  Preview a detection results.

  This method returns immediately and execute the detection in a separate thread. It executes the detection in one frame only and writes the results in the specified model object.

  Parameters:

  model - the model to write detection results in.

  settings - the settings to use for the image input and the ROI input.

  detectorFactory - the detector factory to use for detection.

  detectorSettings - the settings for the detection, specific to the detector factory/

  frame - the frame (0-based) to execute the detection in.

  logger - a logger to write results and error messages to.

  buttonEnabler - a consumer that will receive false at the beginning of the preview, and true at its end. Can be used to disable GUI elements.

• is2D

  public static final boolean is2D(ImgPlus<?> img)

  Returns true if the specified image is 2D. It can have multiple channels and multiple time-points; this method only looks at whether several Z-slices can be found.

  Parameters:

  img - the image.

  Returns:

  true if the image is 2D, regardless of time and channel.

• is2D

  public static final boolean is2D(ij.ImagePlus imp)

• createLoGKernel

  public static final Img<FloatType> createLoGKernel(double radius,
                                                     int nDims,
                                                     double[] calibration)

  Creates a laplacian of gaussian (LoG) kernel tuned for blobs with a radius specified using calibrated units. The specified calibration is used to determine the dimensionality of the kernel and to map it on a pixel grid.

  Parameters:

  radius - the blob radius (in image unit).

  nDims - the dimensionality of the desired kernel. Must be 1, 2 or 3.

  calibration - the pixel sizes, specified as double[] array.

  Returns:

  a new image containing the LoG kernel.

• copyToFloatImg

  public static final <T extends RealType<T>> Img<FloatType> copyToFloatImg(RandomAccessible<T> img,
                                                                            Interval interval,
                                                                            ImgFactory<FloatType> factory)

  Copy an interval of the specified source image on a float image.

  Parameters:

  img - the source image.

  interval - the interval in the source image to copy.

  factory - a factory used to build the float image.

  Returns:

  a new float Img. Careful: even if the specified interval does not start at (0, 0), the new image will have its first pixel at coordinates (0, 0).

• squeeze

  public static final Interval squeeze(Interval interval)

  Returns a new Interval, built by squeezing out singleton dimensions from the specified interval.

  Parameters:

  interval - the interval to squeeze.

  Returns:

  a new interval.

• applyMedianFilter

  public static final <R extends RealType<R> & NativeType<R>> Img<R> applyMedianFilter(RandomAccessibleInterval<R> image)

  Apply a simple 3x3 median filter to the target image.

• findLocalMaxima

  public static final List<Spot> findLocalMaxima(RandomAccessibleInterval<FloatType> source,
                                                 double threshold,
                                                 double[] calibration,
                                                 double radius,
                                                 boolean doSubPixelLocalization,
                                                 int numThreads)

• prepareFrameImg

  public static final <T extends Type<T>> RandomAccessibleInterval<T> prepareFrameImg(ImgPlus<T> img,
                                                                                      int channel,
                                                                                      int frame)

  Return a view of the specified input image, at the specified channel (0-based) and the specified frame (0-based too).

  Type Parameters:

  T - the type of the input image.

  Parameters:

  img - the input image.

  channel - the channel to extract.

  frame - the frame to extract.

  Returns:

  a view of the input image.