`PathProfiler` Class Documentation#

Package: sc.fiji.snt.analysis

Command to retrieve Path profiles (plots of voxel intensities values along a Path)

Methods#

Getters Methods#

getCancelReason()#

getContext()#

getDelegateObject()#

getInfo()#

getInput(String)#

getInputs()#

getOutput(String)#

getOutputs()#

getPlot()#: Gets the plot profile as an ImageJ plot (all channels included).

getValues(Path)#: Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES (“x-values”) and intensities under Y_VALUES (“y-values”).

getXYPlot(int)#: Gets the plot profile as an PlotService plot. It is recommended to call DynamicCommand.setContext(org.scijava.Context) beforehand.

isCanceled()#

isInputResolved(String)#

isOutputResolved(String)#

isResolved(String)#

Setters Methods#

setContext(Context)#

setInput(String, Object)#

setInputs(Map)#

setMetric(ProfileProcessor$Metric)#

setNodeIndicesAsDistances(boolean)#: Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based). Must be called before calling getValues(Path), getPlot() or getXYPlot().

setOutput(String, Object)#

setOutputs(Map)#

setRadius(int)#

Visualization Methods#

preview()#

Other Methods#

addInput(String, Class)#

addOutput(ModuleItem)#

assignValues(Path, int)#: Retrieves pixel intensities at each node of the Path storing them as Path values

cancel(String)#

context()#

findMaxima(Path, int)#: Finds the maxima in the profile of the specified path.

A maxima (peak) will only be considered if protruding more than the profile’s standard deviation from the ridge to a higher maximum

findMinima(Path, int)#: Finds the minima in the profile of the specified path.

A maxima (peak) will only be considered if protruding less than the profile’s standard deviation from the ridge to a lower minimum

initialize()#

static main(String;)

removeInput(ModuleItem)#

removeOutput(ModuleItem)#

resolveInput(String)#

resolveOutput(String)#

run()#

See Also#