Package sc.fiji.snt.gui.cmds

Class FigCreatorCmd

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

sc.fiji.snt.gui.cmds.CommonDynamicCmd

sc.fiji.snt.gui.cmds.FigCreatorCmd

All Implemented Interfaces:

Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.module.Module, org.scijava.module.MutableModule, org.scijava.plugin.SciJavaPlugin

public class FigCreatorCmd
extends CommonDynamicCmd

SciJava Command for creating publication-ready figures of neuronal reconstructions in 2D and 3D formats with customizable styles and layouts.

Field Summary

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	Description
FigCreatorCmd()

Method Summary

Modifier and Type	Method	Description
static Object	render(Collection<Tree> trees, String renderOptions)	Convenience method to quickly display a collection of Trees
void	run()

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

cancel, cancel, error, getPromptWithCloseHandler, getPromptWithCloseHandler, init, isCanceled, msg, notifyExternalDataLoaded, notifyLoadingEnd, notifyLoadingStart, resetUI, resetUI, resetUI, status

Methods inherited from class org.scijava.command.DynamicCommand

context, getCancelReason, getContext, getInfo, getInput, getOutput, 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.Module

getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, isResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

Methods inherited from interface org.scijava.module.MutableModule

addInput, addInput, addOutput, addOutput, removeInput, removeOutput

Constructor Details

FigCreatorCmd

public FigCreatorCmd()

Method Details

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd

render

public static Object render(Collection<Tree> trees,
 String renderOptions)

Convenience method to quickly display a collection of Trees

Parameters:

trees - the collection of trees to be rendered

renderOptions - A string of flags (comma or space separated) specifying rendering options: Example: "montage,2d-raster,xy,zero-origin,upright-geodesic,show"

Multi-panel flag:
montage: whether a multi-panel montage (1 cell/pane) should be obtained in MultiViewer2D/MultiViewer3D as opposed to a single-scene
Viewer-type flag (only one allowed):
2d-raster: trees are rendered as 2D skeletonized images
2d-vector: trees are rendered in a static (non-interactive) Viewer2D
3d: trees are rendered in interactive Viewer3D canvas(es)
View flag (only one allowed):
xz: whether trees should be displayed in a XZ view (default is XY)
zy: whether trees should be displayed in a ZY view (default is XY)
Translation flag:
zero-origin: whether trees should be translated so that their roots/somas are displayed at a common origin (0,0,0)
Rotation flags (only one allowed):
upright-geodesic: whether each tree should be rotated to vertically align its graph geodesic
upright-tips: whether each tree should be rotated to vertically align its [root, tips centroid] vector
"r#": With # specifying a positive integer (e.g., r90): each tree is rotated by the specified angle (in degrees)
Other flags:
in-place: whether any transformation should be applied in-place (i.e., without duplicating the input collection)
show: whether the viewer should be immediately displayed

Returns:

a reference to the viewer. Either an ImagePlus, Viewer2D, Viewer3D, MultiViewer2D or MultiViewer3D

See Also:

• Tree.transform(Collection, String, boolean)