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java.lang.Object TurboReg_
public class TurboReg_
This class is the only one that is accessed directly by imageJ;
it launches a modeless dialog and dies. Note that it implements
PlugIn
rather than PlugInFilter
.
Constructor Summary  

TurboReg_()

Method Summary  

double[][] 
getSourcePoints()
Accessor method for the (double[][])sourcePoints variable. 
double[][] 
getTargetPoints()
Accessor method for the (double[][])targetPoints variable. 
ij.ImagePlus 
getTransformedImage()
Accessor method for the (ImagePlus)transformedImage
variable. 
void 
run(java.lang.String commandLine)
This method is the only one called by ImageJ. 
Methods inherited from class java.lang.Object 

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

public TurboReg_()
Method Detail 

public void run(java.lang.String commandLine)
command  parameter  index  comment 

−help  00  prints out the syntax  
−align  00  do refine the landmarks  
−file −window 
01  reference type  
sourceFilename sourceWindowTitle  02  string with optional quotes  
sourceCropLeft  03  integer  
sourceCropTop  04  integer  
sourceCropRight  05  integer  
sourceCropBottom  06  integer  
−file −window  07  reference type  
targetFilename targetWindowTitle  08  string with optional quotes  
targetCropLeft  09  integer  
targetCropTop  10  integer  
targetCropRight  11  integer  
targetCropBottom  12  integer  
−translation −rigidBody −scaledRotation −affine −bilinear 
13  transformation (TRSAB)  
sourcePoints[0][0]  14  floatingpoint (TRSAB)  
sourcePoints[0][1]  15  floatingpoint (TRSAB)  
targetPoints[0][0]  16  floatingpoint (TRSAB)  
targetPoints[0][1]  17  floatingpoint (TRSAB)  
sourcePoints[1][0]  18  floatingpoint (RSAB)  
sourcePoints[1][1]  19  floatingpoint (RSAB)  
targetPoints[1][0]  20  floatingpoint (RSAB)  
targetPoints[1][1]  21  floatingpoint (RSAB)  
sourcePoints[2][0]  22  floatingpoint (RAB)  
sourcePoints[2][1]  23  floatingpoint (RAB)  
targetPoints[2][0]  24  floatingpoint (RAB)  
targetPoints[2][1]  25  floatingpoint (RAB)  
sourcePoints[3][0]  26  floatingpoint (B)  
sourcePoints[3][1]  27  floatingpoint (B)  
targetPoints[3][0]  28  floatingpoint (B)  
targetPoints[3][1]  29  floatingpoint (B)  
−hideOutput −showOutput  18 (T) 22 (S) 26 (RA) 30 (B)  
−transform  00  do not refine the landmarks  
−file −window  01  reference type  
sourceFilename sourceWindowTitle  02  string with optional quotes  
outputWidth  03  integer  
outputHeight  04  integer  
−translation −rigidBody −scaledRotation −affine −bilinear  05  transformation (TRSAB)  
sourcePoints[0][0]  06  floatingpoint (TRSAB)  
sourcePoints[0][1]  07  floatingpoint (TRSAB)  
targetPoints[0][0]  08  floatingpoint (TRSAB)  
targetPoints[0][1]  09  floatingpoint (TRSAB)  
sourcePoints[1][0]  10  floatingpoint (RSAB)  
sourcePoints[1][1]  11  floatingpoint (RSAB)  
targetPoints[1][0]  12  floatingpoint (RSAB)  
targetPoints[1][1]  13  floatingpoint (RSAB)  
sourcePoints[2][0]  14  floatingpoint (RAB)  
sourcePoints[2][1]  15  floatingpoint (RAB)  
targetPoints[2][0]  16  floatingpoint (RAB)  
targetPoints[2][1]  17  floatingpoint (RAB)  
sourcePoints[3][0]  18  floatingpoint (B)  
sourcePoints[3][1]  19  floatingpoint (B)  
targetPoints[3][0]  20  floatingpoint (B)  
targetPoints[3][1]  21  floatingpoint (B)  
−hideOutput −showOutput  10 (T) 14 (S) 18 (RA) 22 (B) 
−align −file path/source.tif 40 80 639 479
−file path/target.tif 0 0 639 479
−translation 320 240 331.7 210 −showOutput
"my path/my file"
. Escape characters (e.g., a
backslash) are not interpreted.
run
in interface ij.plugin.PlugIn
commandLine
 String
optional list of parameters.public double[][] getSourcePoints()
(double[][])sourcePoints
variable.
This variable is valid only after a call to run
with the
option align
has been issued. What is returned is a
twodimensional array of type double[][]
that contains
coordinates from the image sourceFilename
. These coordinates
are given relative to the original image, before that the cropping
described by the sourceCropLeft
, sourceCropTop
,
sourceCropRight
, and sourceCropBottom
has been
applied. These coordinates match those available from
targetPoints
. The total number of coordinates, equal to
sourcePoints[*].length
, is given by the constant
turboRegPointHandler.NUM_POINTS
which corresponds to four
coordinates in the present version. The second index gives the horizontal
component for [0]
and the vertical component for
[1]
. The number of useful coordinates depends on the
specific transformation for which the alignment has been performed:
translation (1), scaled rotation (2), rotation (3), affine transformation
(3), and bilinear transformation (4).
run(java.lang.String)
,
getTargetPoints()
public double[][] getTargetPoints()
(double[][])targetPoints
variable.
This variable is valid only after a call to run
with the
option align
has been issued. What is returned is a
twodimensional array of type double[][]
that contains
coordinates from the image targetFilename
. These coordinates
are given relative to the original image, before that the cropping
described by the targetCropLeft
, targetCropTop
,
targetCropRight
, and targetCropBottom
has been
applied. These coordinates match those available from
sourcePoints
. The total number of coordinates, equal to
targetPoints[*].length
, is given by the constant
turboRegPointHandler.NUM_POINTS
which corresponds to four
coordinates in the present version. The second index gives the horizontal
component for [0]
and the vertical component for
[1]
. The number of useful coordinates depends on the
specific transformation for which the alignment has been performed:
translation (1), scaled rotation (2), rotation (3), affine transformation
(3), and bilinear transformation (4).
run(java.lang.String)
,
getSourcePoints()
public ij.ImagePlus getTransformedImage()
(ImagePlus)transformedImage
variable. This variable is valid only after a call to run
with the option transform
has been issued. What is returned
is an ImagePlus
object of the size described by the
outputWidth
and outputHeight
parameters of
the call to the run
method of TurboReg_
.
run(java.lang.String)


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