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java.lang.ObjectTurboReg_
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 | floating-point (TRSAB) | |
| sourcePoints[0][1] | 15 | floating-point (TRSAB) | |
| targetPoints[0][0] | 16 | floating-point (TRSAB) | |
| targetPoints[0][1] | 17 | floating-point (TRSAB) | |
| sourcePoints[1][0] | 18 | floating-point (RSAB) | |
| sourcePoints[1][1] | 19 | floating-point (RSAB) | |
| targetPoints[1][0] | 20 | floating-point (RSAB) | |
| targetPoints[1][1] | 21 | floating-point (RSAB) | |
| sourcePoints[2][0] | 22 | floating-point (RAB) | |
| sourcePoints[2][1] | 23 | floating-point (RAB) | |
| targetPoints[2][0] | 24 | floating-point (RAB) | |
| targetPoints[2][1] | 25 | floating-point (RAB) | |
| sourcePoints[3][0] | 26 | floating-point (B) | |
| sourcePoints[3][1] | 27 | floating-point (B) | |
| targetPoints[3][0] | 28 | floating-point (B) | |
| targetPoints[3][1] | 29 | floating-point (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 | floating-point (TRSAB) | |
| sourcePoints[0][1] | 07 | floating-point (TRSAB) | |
| targetPoints[0][0] | 08 | floating-point (TRSAB) | |
| targetPoints[0][1] | 09 | floating-point (TRSAB) | |
| sourcePoints[1][0] | 10 | floating-point (RSAB) | |
| sourcePoints[1][1] | 11 | floating-point (RSAB) | |
| targetPoints[1][0] | 12 | floating-point (RSAB) | |
| targetPoints[1][1] | 13 | floating-point (RSAB) | |
| sourcePoints[2][0] | 14 | floating-point (RAB) | |
| sourcePoints[2][1] | 15 | floating-point (RAB) | |
| targetPoints[2][0] | 16 | floating-point (RAB) | |
| targetPoints[2][1] | 17 | floating-point (RAB) | |
| sourcePoints[3][0] | 18 | floating-point (B) | |
| sourcePoints[3][1] | 19 | floating-point (B) | |
| targetPoints[3][0] | 20 | floating-point (B) | |
| targetPoints[3][1] | 21 | floating-point (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.PlugIncommandLine - 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
two-dimensional 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
two-dimensional 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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