org.nanes.slideset.script

Class SlideSetScript

java.lang.Object

org.nanes.slideset.script.SlideSetScript

All Implemented Interfaces:

LogListener

public class SlideSetScript
extends Object
implements LogListener

Use Slide Set in scripts.
Instantiate and access the set of Slide Set services without any GUI elements. Instances of this class provide a DataTypeIDService, XMLService, CSVService, SlideSetLog, and SlideSetPluginLoader, functioning as a complete Slide Set application. In contrast to the ImageJ command, SlideSetScript does not launch a SlideSetLauncher window, and is thus more suitable for programmatic use. To run Slide Set commands without any GUI interactivity, use in conjunction with PluginInputMatcher and PluginOutputMatcher.

Author:

Benjamin Nanes

Field Summary

Fields

Modifier and Type	Field and Description
private CSVService	csvs
private DataTypeIDService	dtids
private HttpHelpLoader	hhl
private net.imagej.ImageJ	ij
private static int	IJCONSOLE
private static int	LOGDEFAULT
private int	logTo
private SlideSetLog	sslg
private SlideSetPluginLoader	sspl
private static int	STDERR
private static int	STDOUT
private XMLService	xmls

Constructor Summary

Constructors

Constructor and Description
SlideSetScript(net.imagej.ImageJ ij)
SlideSetScript(net.imagej.ImageJ ij, boolean showConsole)
SlideSetScript(net.imagej.ImageJ ij, int logTo)
SlideSetScript(net.imagej.ImageJ ij, int logTo, boolean showConsole) Instantiate headless Slide Set services

Method Summary

Modifier and Type	Method and Description
String[]	getColumnText(SlideSet table, int index) Get the contents of a Slide Set table column
String[]	getColumnText(SlideSet table, String colName) Get the contents of a Slide Set table column
DataTypeIDService	getDataTypeIDService() Get the DataTypeIDService for managing and matching data types.
net.imagej.ImageJ	getImaegJ() Get the ImageJ instance bound to this class
SlideSetPluginLoader	getSlideSetPluginLoader() Get the SlideSetPluginLoader for preparing and running Slide Set commands.
XMLService	getXMLService() Get the XMLService for reading and writing Slide Set data files.
SlideSet	loadSlideSet(File file) Load a Slide Set data file
SlideSet	loadSlideSet(String fileName) Load a slide set data file
void	logMessage(String message) Receive a message from the log.
SlideSet	runPlugin(String className, SlideSet table, PluginInputPicker pip, PluginOutputPicker pop) Run a Slide Set command programmatically
void	saveCSV(SlideSet table, File file) Export a Slide Set data table as a CSV file
void	saveCSV(SlideSet table, String fileName) Export a Slide Set data table as a CSV file
void	saveSlideSet(SlideSet table, File file) Save a Slide Set data file
void	saveSlideSet(SlideSet table, String fileName) Save a Slide Set data file

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LOGDEFAULT

private static final int LOGDEFAULT

See Also:

Constant Field Values

IJCONSOLE

private static final int IJCONSOLE

See Also:

Constant Field Values

STDOUT

private static final int STDOUT

See Also:

Constant Field Values

STDERR

private static final int STDERR

See Also:

Constant Field Values

ij

private net.imagej.ImageJ ij

dtids

private DataTypeIDService dtids

xmls

private XMLService xmls

csvs

private CSVService csvs

sslg

private SlideSetLog sslg

hhl

private HttpHelpLoader hhl

sspl

private SlideSetPluginLoader sspl

logTo

private int logTo

Constructor Detail

SlideSetScript

public SlideSetScript(net.imagej.ImageJ ij,
                      int logTo,
                      boolean showConsole)

Instantiate headless Slide Set services

Parameters:

ij - ImageJ instance to attach

logTo - Output options for log messages

• LOGDEFAULT, make a reasonable guess between STDOIT and the ImageJ console
• IJCONSOLE, the ImageJ console (GUI)
• STDOUT
• STDERR

showConsole - If true and logging to the ImageJ console, open the console when starting Slide Set.

SlideSetScript

public SlideSetScript(net.imagej.ImageJ ij)

SlideSetScript

public SlideSetScript(net.imagej.ImageJ ij,
                      int logTo)

SlideSetScript

public SlideSetScript(net.imagej.ImageJ ij,
                      boolean showConsole)

Method Detail

getImaegJ

public net.imagej.ImageJ getImaegJ()

Get the ImageJ instance bound to this class

Returns:

getDataTypeIDService

public DataTypeIDService getDataTypeIDService()

Get the DataTypeIDService for managing and matching data types.

Returns:

getXMLService

public XMLService getXMLService()

Get the XMLService for reading and writing Slide Set data files.

Returns:

getSlideSetPluginLoader

public SlideSetPluginLoader getSlideSetPluginLoader()

Get the SlideSetPluginLoader for preparing and running Slide Set commands.

Returns:

loadSlideSet

public SlideSet loadSlideSet(File file)

Load a Slide Set data file

Parameters:

file -

Returns:

loadSlideSet

public SlideSet loadSlideSet(String fileName)

Load a slide set data file

Parameters:

fileName -

Returns:

saveSlideSet

public void saveSlideSet(SlideSet table,
                         File file)

Save a Slide Set data file

Parameters:

table - Slide Set data table, possibly with children

file -

saveSlideSet

public void saveSlideSet(SlideSet table,
                         String fileName)

Save a Slide Set data file

Parameters:

table - Slide Set data table, possibly with children

fileName -

runPlugin

public SlideSet runPlugin(String className,
                          SlideSet table,
                          PluginInputPicker pip,
                          PluginOutputPicker pop)

Run a Slide Set command programmatically

Parameters:

className - Fully qualified name of the Slide Set command class. Ex: org.nanes.slideset.pi.ROILengths

table - Slide Set table

pip - Instance for selecting command inputs. PluginInputMatcher is recommended for programmatic use.

pop - Instance for managing command results. PluginOutputMatcher is recommended for programmatic use.

Returns:

The results table. Note that this will also be set as a child of the input table.

saveCSV

public void saveCSV(SlideSet table,
                    File file)

Export a Slide Set data table as a CSV file

Parameters:

table -

file -

saveCSV

public void saveCSV(SlideSet table,
                    String fileName)

Export a Slide Set data table as a CSV file

Parameters:

table -

fileName -

getColumnText

public String[] getColumnText(SlideSet table,
                              int index)

Get the contents of a Slide Set table column

Parameters:

table -

index -

Returns:

getColumnText

public String[] getColumnText(SlideSet table,
                              String colName)

Get the contents of a Slide Set table column

Parameters:

table -

colName -

Returns:

logMessage

public void logMessage(String message)

Description copied from interface: LogListener

Receive a message from the log. Implementors should expect this method to be called on the event dispatch thread.

Specified by:

logMessage in interface LogListener