Field Detail

• DEFAULT_MAX_RADIUS

  public static int DEFAULT_MAX_RADIUS

  The default max radius constraining the fit.

• RADII

  public static final int RADII

  Flag specifying that the computed path should only inherit fitted radii attributes

  See Also:

  Constant Field Values

• MIDPOINTS

  public static final int MIDPOINTS

  Flag specifying that the computed path should only inherit midpoint refinement of node coordinates

  See Also:

  Constant Field Values

• RADII_AND_MIDPOINTS

  public static final int RADII_AND_MIDPOINTS

  Flag specifying that the computed path should inherit both midpoint refinement of node coordinates and radii

  See Also:

  Constant Field Values

Constructor Detail

• PathFitter

  public PathFitter(ij.ImagePlus imp,
                    Path path)

  Instantiates a new PathFitter.

  Parameters:

  imp - the Image containing the signal to which the fit will be performed

  path - the Path to be fitted

• PathFitter

  public PathFitter(SNT plugin,
                    Path path)

  Instantiates a new PathFitter.

  Parameters:

  plugin - the SNT instance specifying input image. The computation will be performed on the image currently loaded by the plugin.

  path - the Path to be fitted

Method Detail

• setShowAnnotatedView

  public void setShowAnnotatedView(boolean showAnnotatedView)

  Sets whether an interactive image of the result should be displayed.

  Parameters:

  showAnnotatedView - If true, an interactive stack (cross-section view) of the fit is displayed. Note that this is probably only useful if SNT's UI is visible and functional.

• setProgressCallback

  public void setProgressCallback(int fitterIndex,
                                  sc.fiji.snt.MultiTaskProgress progress)

• call

  public Path call()
            throws IllegalArgumentException

  Takes the signal from the image specified in the constructor to fit cross-section circles around the nodes of input path. Computation of fit is confined to the neighborhood specified by setMaxRadius(int). Note that connectivity of path may need to be rebuild upon fit.

  Specified by:

  call in interface Callable<Path>

  Returns:

  the reference to the computed result. This Path is automatically set as the fitted version of input Path.

  Throws:

  IllegalArgumentException - If path already has been fitted, and its fitted version not nullified

  See Also:

  setScope(int)

• getPath

  public Path getPath()

• getSucceeded

  public boolean getSucceeded()

  Checks whether the fit succeeded.

  Returns:

  true if fit was successful, false otherwise

• getMaxRadius

  public int getMaxRadius()

  Gets the current max radius

  Returns:

  the maximum radius currently being considered, or DEFAULT_MAX_RADIUS if setMaxRadius(int) has not been called

• setMaxRadius

  public void setMaxRadius(int maxRadius)

  Sets the max radius (side search) for constraining the fit.

  Parameters:

  maxRadius - the new maximum radius

• setScope

  public void setScope(int scope)

  Sets the fitting scope.

  Parameters:

  scope - Either RADII, MIDPOINTS, or RADII_AND_MIDPOINTS

• setReplaceNodes

  public void setReplaceNodes(boolean replaceNodes)

  Sets whether fitting should occur "in place".

  Parameters:

  replaceNodes - If true, the nodes of the input Path will be replaced by those of the fitted result. If false, the fitted result is kept as a separated Path linked to the input as per Path.getFitted(). Note that in the latter case, some topological operations (e.g., forking) performed on the fitted result may not percolate to the unfitted Path.

• setImp

  public void setImp(ij.ImagePlus imp)

  Sets the target image

  Parameters:

  imp - the Image containing the signal to which the fit will be performed