PathProfiler (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.module.AbstractModule
- - org.scijava.module.DefaultMutableModule
  - - org.scijava.command.DynamicCommand
    - - sc.fiji.snt.gui.cmds.CommonDynamicCmd
      - sc.fiji.snt.analysis.PathProfiler

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, Module, MutableModule, SciJavaPlugin
```
public class PathProfiler
extends CommonDynamicCmd
```
Command to retrieve Profile plots (plots of voxel intensities values along a Path) from reconstructions.

Author:

Tiago Ferreira, Cameron Arshadi

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`CENTERLINE`
`static String`	`CIRCLE`
`static String`	`DISK`
`static String`	`SPHERE`
`static String`	`X_VALUES` Flag for retrieving distances from `getValues(Path)`
`static String`	`Y_VALUES` Flag for retrieving intensities from `getValues(Path)`

Fields inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd
EMPTY_LABEL, HEADER_HTML, snt, sntService, statusService, ui, uiService

Fields inherited from class org.scijava.command.DynamicCommand
moduleService, pluginService

Constructor Summary

Constructors
Constructor and Description
`PathProfiler()`
`PathProfiler(Path path, Dataset dataset)`
`PathProfiler(Path path, ij.ImagePlus imp)` Instantiates a new Profiler from a single path
`PathProfiler(Tree tree, Dataset dataset)`
`PathProfiler(Tree tree, ij.ImagePlus imp)` Instantiates a new Profiler

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`assignValues()` Calls `assignValues(Path)` on the Paths of the profiled Tree
`void`	`assignValues(int channel)`
`void`	`assignValues(Path p)` Retrieves pixel intensities at each node of the Path storing them as Path `values`
`<T extends RealType<T>> void`	`assignValues(Path p, int channel)`
`Plot`	`getPlot()` Gets the plot profile as an IJ1 `Plot`.
`Plot`	`getPlot(int channel)`
`Plot`	`getPlot(Path path)`
`Map<String,List<Double>>`	`getValues(Path p)` 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").
`Map<String,List<Double>>`	`getValues(Path p, int channel)`
`net.imagej.plot.XYPlot`	`getXYPlot()` Gets the plot profile as an `PlotService` plot.
`net.imagej.plot.XYPlot`	`getXYPlot(int channel)`
`static void`	`main(String[] args)`
`void`	`run()`
`void`	`setFrame(int frame)`
`void`	`setMetric(ProfileProcessor.Metric metric)`
`void`	`setNodeIndicesAsDistances(boolean nodeIndices)` Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based).
`void`	`setRadius(int radius)`
`void`	`setShape(ProfileProcessor.Shape shape)`

Methods inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd
cancel, cancel, error, init, msg, notifyExternalDataLoaded, notifyLoadingEnd, notifyLoadingStart, resetUI, resetUI, status

Methods inherited from class org.scijava.command.DynamicCommand
context, getCancelReason, getContext, getInfo, getInput, getOutput, isCanceled, saveInputs, setContext, setInput, setOutput, uncancel

Methods inherited from class org.scijava.module.AbstractModule
getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, unresolveInput, unresolveOutput

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.module.MutableModule
addInput, addInput, addOutput, addOutput, removeInput, removeOutput

Methods inherited from interface org.scijava.module.Module
getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, isResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

- Field Detail
  - CIRCLE
```
public static final String CIRCLE
```
    See Also:
    
    Constant Field Values
  - DISK
```
public static final String DISK
```
    See Also:
    
    Constant Field Values
  - SPHERE
```
public static final String SPHERE
```
    See Also:
    
    Constant Field Values
  - CENTERLINE
```
public static final String CENTERLINE
```
    See Also:
    
    Constant Field Values
  - X_VALUES
```
public static final String X_VALUES
```
    Flag for retrieving distances from getValues(Path)
    
    See Also:
    
    Constant Field Values
  - Y_VALUES
```
public static final String Y_VALUES
```
    Flag for retrieving intensities from getValues(Path)
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - PathProfiler
```
public PathProfiler()
```
  - PathProfiler
```
public PathProfiler(Tree tree,
                    ij.ImagePlus imp)
```
    Instantiates a new Profiler
    
    Parameters:
    
    tree - the Tree to be profiled
    
    imp - the image from which pixel intensities will be retrieved. If paths in the Tree are assigned different frames, it is assumed by default that the active frame of the image defines the time-point to be profiled. Note that no effort is made to ensure that the image is suitable for profiling.
  - PathProfiler
```
public PathProfiler(Tree tree,
                    Dataset dataset)
```
  - PathProfiler
```
public PathProfiler(Path path,
                    ij.ImagePlus imp)
```
    Instantiates a new Profiler from a single path
    
    Parameters:
    
    path - the path to be profiled
    
    imp - the image from which pixel intensities will be retrieved.Note that no effort is made to ensure that the image is suitable for profiling.
  - PathProfiler
```
public PathProfiler(Path path,
                    Dataset dataset)
```
- Method Detail
  - setShape
```
public void setShape(ProfileProcessor.Shape shape)
```
  - setMetric
```
public void setMetric(ProfileProcessor.Metric metric)
```
  - setRadius
```
public void setRadius(int radius)
```
  - setFrame
```
public void setFrame(int frame)
```
  - run
```
public void run()
```
    Specified by:
    
    run in interface Runnable
    
    Specified by:
    
    run in interface MutableModule
    
    Overrides:
    
    run in class CommonDynamicCmd
  - assignValues
```
public void assignValues()
                  throws IllegalArgumentException
```
    Calls assignValues(Path) on the Paths of the profiled Tree
    
    Throws:
    
    IllegalArgumentException
  - assignValues
```
public void assignValues(int channel)
                  throws IllegalArgumentException,
                         ArrayIndexOutOfBoundsException
```
    Throws:
    
    IllegalArgumentException
    
    ArrayIndexOutOfBoundsException
  - assignValues
```
public void assignValues(Path p)
                  throws IllegalArgumentException
```
    Retrieves pixel intensities at each node of the Path storing them as Path values
    
    Parameters:
    
    p - the Path to be profiled
    
    Throws:
    
    IllegalArgumentException - if image does not contain the path's channel
    
    See Also:
    
    Path.setNodeValues(double[])
  - assignValues
```
public <T extends RealType<T>> void assignValues(Path p,
                                                 int channel)
                                          throws ArrayIndexOutOfBoundsException
```
    Throws:
    
    ArrayIndexOutOfBoundsException
  - setNodeIndicesAsDistances
```
public void setNodeIndicesAsDistances(boolean nodeIndices)
```
    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().
    
    Parameters:
    
    nodeIndices - If true, distances will be reported as indices.
  - getValues
```
public Map<String,List<Double>> getValues(Path p)
```
    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").
    
    Parameters:
    
    p - the path to be profiled
    
    Returns:
    
    the profile
  - getValues
```
public Map<String,List<Double>> getValues(Path p,
                                          int channel)
                                   throws IllegalArgumentException
```
    Throws:
    
    IllegalArgumentException
  - getPlot
```
public Plot getPlot()
             throws IllegalArgumentException,
                    ArrayIndexOutOfBoundsException
```
    Gets the plot profile as an IJ1 Plot.
    
    Returns:
    
    the plot
    
    Throws:
    
    IllegalArgumentException
    
    ArrayIndexOutOfBoundsException
  - getPlot
```
public Plot getPlot(int channel)
             throws IllegalArgumentException,
                    ArrayIndexOutOfBoundsException
```
    Throws:
    
    IllegalArgumentException
    
    ArrayIndexOutOfBoundsException
  - getPlot
```
public Plot getPlot(Path path)
```
  - getXYPlot
```
public net.imagej.plot.XYPlot getXYPlot()
```
    Gets the plot profile as an PlotService plot. Requires DynamicCommand.setContext(org.scijava.Context) to be called beforehand.
    
    Returns:
    
    the plot
  - getXYPlot
```
public net.imagej.plot.XYPlot getXYPlot(int channel)
                                 throws IllegalArgumentException
```
    Throws:
    
    IllegalArgumentException
  - main
```
public static void main(String[] args)
```

Class PathProfiler

Field Summary

Fields inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

Fields inherited from class org.scijava.command.DynamicCommand

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

Methods inherited from class org.scijava.command.DynamicCommand

Methods inherited from class org.scijava.module.AbstractModule

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.module.MutableModule

Methods inherited from interface org.scijava.module.Module

Field Detail

CIRCLE

DISK

SPHERE

CENTERLINE

X_VALUES

Y_VALUES

Constructor Detail

PathProfiler

PathProfiler

PathProfiler

PathProfiler

PathProfiler

Method Detail

setShape

setMetric

setRadius

setFrame

run

assignValues

assignValues

assignValues

assignValues

setNodeIndicesAsDistances

getValues

getValues

getPlot

getPlot

getPlot

getXYPlot

getXYPlot

main