de.embl.cmci.registration

Class MultiStackReg_

java.lang.Object

de.embl.cmci.registration.MultiStackReg_

public class MultiStackReg_
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	AFFINE
static int	RIGID_BODY
static int	SCALED_ROTATION
static int	TRANSLATION

Constructor Summary

Constructors

Constructor and Description
MultiStackReg_()

Method Summary

Methods

Modifier and Type	Method and Description
void	core(java.lang.String srcFile, java.lang.String tgtFile) srcFile: full path to a text file, (1) If "Align" or "As Reference" is selected and save transformation is checked, transformation will be logged.
ImagePlus[]	createAdmissibleImageList()
int	processDirectives(ImagePlus imp, boolean loadBool) ....................................................................
void	run(java.lang.String arg) ImagePlus
void	setLoadFile(java.lang.String loadFile)
void	setLoadPath(java.lang.String loadPath)
void	setSaveFile(java.lang.String saveFile)
void	setSavePath(java.lang.String savePath)
void	setSaveTransform(boolean saveTransform)
void	setSrcAction(java.lang.String srcAction)
void	setSrcImg(ImagePlus srcImg)
void	setTgtAction(java.lang.String tgtAction)
void	setTgtImg(ImagePlus tgtImg)
void	setTransformation(int transformation) Use field values for setting the translformation type.
void	setTwoStackAlign(boolean twoStackAlign)
void	setViewManual(boolean viewManual)

Methods inherited from class java.lang.Object

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

Field Detail

TRANSLATION

public static final int TRANSLATION

See Also:

Constant Field Values

RIGID_BODY

public static final int RIGID_BODY

See Also:

Constant Field Values

SCALED_ROTATION

public static final int SCALED_ROTATION

See Also:

Constant Field Values

AFFINE

public static final int AFFINE

See Also:

Constant Field Values

Constructor Detail

MultiStackReg_

public MultiStackReg_()

Method Detail

run

public void run(java.lang.String arg)

ImagePlus

core

public void core(java.lang.String srcFile,
        java.lang.String tgtFile)

srcFile: full path to a text file, (1) If "Align" or "As Reference" is selected and save transformation is checked, transformation will be logged. (2) If "As Reference" is selected and srcFile=="", then a dummy text file is created. (3) If "Load Transformation file" is selected, this file will be the reference. If srfFile =="", then a dialog pops up. tgtFile: full path to a textfile, (1) If "Align to first stack" is selected, then srcFile or dummy file is referred for transformation. (2) If "Load Transformation File" is selected, then tgtFile will be the reference for transformation. If tgtFile=="", then diaplog pops up.

processDirectives

public int processDirectives(ImagePlus imp,
                    boolean loadBool)

.................................................................... ....................................................................

createAdmissibleImageList

public ImagePlus[] createAdmissibleImageList()

setSrcImg

public void setSrcImg(ImagePlus srcImg)

setSrcAction

public void setSrcAction(java.lang.String srcAction)

setTgtImg

public void setTgtImg(ImagePlus tgtImg)

setTgtAction

public void setTgtAction(java.lang.String tgtAction)

setTransformation

public void setTransformation(int transformation)

Use field values for setting the translformation type.

setSaveTransform

public void setSaveTransform(boolean saveTransform)

setViewManual

public void setViewManual(boolean viewManual)

setLoadFile

public void setLoadFile(java.lang.String loadFile)

Parameters:

loadFile - the loadFile to set

setLoadPath

public void setLoadPath(java.lang.String loadPath)

Parameters:

loadPath - the loadPath to set

setTwoStackAlign

public void setTwoStackAlign(boolean twoStackAlign)

Parameters:

twoStackAlign - the twoStackAlign to set

setSaveFile

public void setSaveFile(java.lang.String saveFile)

Parameters:

saveFile - the saveFile to set

setSavePath

public void setSavePath(java.lang.String savePath)

Parameters:

savePath - the savePath to set