com.eco.bio7.image

Class ImageMethods

java.lang.Object

org.eclipse.core.commands.common.EventManager

org.eclipse.ui.part.WorkbenchPart

org.eclipse.ui.part.ViewPart

com.eco.bio7.image.ImageMethods

All Implemented Interfaces:

org.eclipse.core.runtime.IAdaptable, org.eclipse.core.runtime.IExecutableExtension, org.eclipse.ui.IPersistable, org.eclipse.ui.IViewPart, org.eclipse.ui.IWorkbenchPart, org.eclipse.ui.IWorkbenchPart2, org.eclipse.ui.IWorkbenchPart3, org.eclipse.ui.part.IWorkbenchPartOrientation

public class ImageMethods
extends org.eclipse.ui.part.ViewPart

This class provides some static methods for the analysis and transfer of images inside the Bio7 application.

Author:

Bio7

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ID

Fields inherited from interface org.eclipse.ui.IWorkbenchPart

PROP_TITLE

Constructor Summary

Constructors

Constructor and Description
ImageMethods()

Method Summary

Modifier and Type	Method and Description
void	createPartControl(org.eclipse.swt.widgets.Composite parent)
static void	deletePoints() Deletes all point values, alpha values, ellipse values and species values in the Points panel and repaints the Points panel.
void	dispose()
static int	getFieldX() Returns the x-size of the Area of Analysis.
static int	getFieldY() Returns the y-size of the Area of Analysis.
static java.awt.image.BufferedImage	getImage()
static ij.ImagePlus	getPanelImage() Returns the current image in the Points panel.
static int	getPointScale() Returns the scale factor for the coordinates of the points from the particle analysis.
static org.eclipse.swt.widgets.Combo	getTransferTypeCombo()
static void	imageFromR(int type, java.lang.String name, int transferDataType) This method creates an ImageJ image from the given named data (matrix or vector) in R.
static void	imageToR(java.lang.String name, boolean matrix, int transferDataType, ij.ImagePlus impPlus) This methods transfers image data from ImageJ to R by means of Rserve.
static boolean	isCentroid() Returns if the centroid method is selected for the points.
static void	setCentroid(boolean centroid) Sets the method for adjusting the points in the Points panel (default = centroid for the particle analysis).
static void	setFieldSize(int x, int y) Sets the field size in the Points panel(Area of Analysis).
void	setFocus()
static void	setPointScale(int pointScale) Sets the scale factor for the coordinates of the points from the particle analysis.
static void	toImageJ() Transfers the current image from the Points panel to the ImageJ panel.
static void	transferImageInPlace(java.lang.String dataName, int type) A method to transfer byte information directly to an image as one container.

Methods inherited from class org.eclipse.ui.part.ViewPart

getViewSite, init, init, saveState, setInitializationData

Methods inherited from class org.eclipse.ui.part.WorkbenchPart

addPartPropertyListener, addPropertyListener, getAdapter, getContentDescription, getOrientation, getPartName, getPartProperties, getPartProperty, getSite, getTitle, getTitleImage, getTitleToolTip, removePartPropertyListener, removePropertyListener, setPartProperty, showBusy

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.eclipse.ui.IWorkbenchPart

addPropertyListener, getSite, getTitle, getTitleImage, getTitleToolTip, removePropertyListener

Methods inherited from interface org.eclipse.core.runtime.IAdaptable

getAdapter

Field Detail

ID

public static final java.lang.String ID

See Also:

Constant Field Values

Constructor Detail

ImageMethods

public ImageMethods()

Method Detail

createPartControl

public void createPartControl(org.eclipse.swt.widgets.Composite parent)

Specified by:

createPartControl in interface org.eclipse.ui.IWorkbenchPart

Specified by:

createPartControl in class org.eclipse.ui.part.WorkbenchPart

deletePoints

public static void deletePoints()

Deletes all point values, alpha values, ellipse values and species values in the Points panel and repaints the Points panel.

setFocus

public void setFocus()

Specified by:

setFocus in interface org.eclipse.ui.IWorkbenchPart

Specified by:

setFocus in class org.eclipse.ui.part.WorkbenchPart

toImageJ

public static void toImageJ()

Transfers the current image from the Points panel to the ImageJ panel.

getPanelImage

public static ij.ImagePlus getPanelImage()

Returns the current image in the Points panel.

Returns:

an ImagePlus object.

getFieldX

public static int getFieldX()

Returns the x-size of the Area of Analysis.

Returns:

the width of the area of analysis.

getFieldY

public static int getFieldY()

Returns the y-size of the Area of Analysis.

Returns:

the height of the area of analysis.

setFieldSize

public static void setFieldSize(int x,
                                int y)

Sets the field size in the Points panel(Area of Analysis).

Parameters:

x - the x-size.

y - the y-size.

getPointScale

public static int getPointScale()

Returns the scale factor for the coordinates of the points from the particle analysis.

Returns:

an integer value of the scale factor.

setPointScale

public static void setPointScale(int pointScale)

Sets the scale factor for the coordinates of the points from the particle analysis.

Parameters:

pointScale - an integer value of the scale factor.

isCentroid

public static boolean isCentroid()

Returns if the centroid method is selected for the points.

Returns:

a boolean value.

setCentroid

public static void setCentroid(boolean centroid)

Sets the method for adjusting the points in the Points panel (default = centroid for the particle analysis).

Parameters:

centroid - a boolean value.

getImage

public static java.awt.image.BufferedImage getImage()

imageToR

public static void imageToR(java.lang.String name,
                            boolean matrix,
                            int transferDataType,
                            ij.ImagePlus impPlus)

This methods transfers image data from ImageJ to R by means of Rserve. Matrix or vector data is created and variables for the width, height and the name of the image will be created.

Parameters:

name - the name for the data.

matrix - a boolean, if true automatically a data matrix will be created (only for double values - in case of an RGB transfer an integer matrix will be created!).

transferDataType - an integer value for the data type which will be transfered. (0=double, 1=integer, 2=byte, 3=RGB as single byte vectors or integer matrix)

impPlus - an optional ImagePlus object as the default image source.

imageFromR

public static void imageFromR(int type,
                              java.lang.String name,
                              int transferDataType)

This method creates an ImageJ image from the given named data (matrix or vector) in R. This method expects the variables imageSizeX, imageSizeY to be present in the R workspace if vector data is transferred.

Parameters:

type - an integer which represents an ImageJ image type.(0=ColourProcessor, 1=ByteProcessor, 2=FloatProcessor, 3=ShortProcessor)

name - a string identifier for the R data.

transferDataType - the data type as transfer type (0=double, 1=integer, 2=byte).

getTransferTypeCombo

public static org.eclipse.swt.widgets.Combo getTransferTypeCombo()

transferImageInPlace

public static void transferImageInPlace(java.lang.String dataName,
                                        int type)

A method to transfer byte information directly to an image as one container. If no image is present a new one will be created. This method expects the variables imageSizeX, imageSizeY to be present in the R workspace.

Parameters:

dataName - the name of the R vector.

type - the type of the image (1 = byte, 2 = float).

dispose

public void dispose()

Specified by:

dispose in interface org.eclipse.ui.IWorkbenchPart

Overrides:

dispose in class org.eclipse.ui.part.WorkbenchPart