public class SilentSlicer extends Object
Modifier and Type | Field and Description |
---|---|
private Vector |
checkboxes |
private double[] |
dx |
private double[] |
dy |
private Vector |
fields |
private boolean |
flip |
private static boolean |
flipS |
private double |
gLength |
private double |
gx1 |
private double |
gx2 |
private double |
gy1 |
private double |
gy2 |
private ij.ImagePlus |
imp |
private double |
inputZSpacing |
private double |
length |
private Color |
lineColor |
private Label |
message |
private int |
n |
private boolean |
nointerpolate |
private boolean |
noRoi |
private boolean |
notFloat |
private int |
outputSlices |
private double |
outputZSpacing |
private boolean |
rgb |
private boolean |
rotate |
private static boolean |
rotateS |
private double[] |
segmentLengths |
private int |
sliceCount |
private static int |
sliceCountS |
private String |
startAt |
private static String |
startAtS |
private static String[] |
starts |
private double[] |
x |
private int |
xbase |
private double[] |
y |
private int |
ybase |
Constructor and Description |
---|
SilentSlicer(ij.ImagePlus imp,
double outputSpacingUm,
int outputSlices,
boolean flipVert,
boolean rotate90deg,
boolean avoidInterp)
Create a slicer with pre-populated settings so that no properties
dialog box is needed.
|
Modifier and Type | Method and Description |
---|---|
(package private) ij.ImageStack |
createOutputStack(ij.ImagePlus imp,
ij.process.ImageProcessor ip) |
(package private) String |
d2s(double n) |
(package private) void |
doIrregularSetup(ij.gui.Roi roi) |
(package private) void |
drawLine(double x1,
double y1,
double x2,
double y2,
ij.ImagePlus imp) |
(package private) int |
getAvailableMemory() |
(package private) float[] |
getIrregularProfile(ij.gui.Roi roi,
ij.process.ImageProcessor ip) |
private float[] |
getLine(ij.process.ImageProcessor ip,
double x1,
double y1,
double x2,
double y2,
float[] data) |
private float[] |
getOrthoLine(ij.process.ImageProcessor ip,
int x1,
int y1,
int x2,
int y2,
float[] data) |
(package private) int |
getOutputStackSize(double inSpacing,
double outSpacing,
int count) |
(package private) String |
getSize(double inSpacing,
double outSpacing,
int count) |
(package private) ij.process.ImageProcessor |
getSlice(ij.ImagePlus imp,
double x1,
double y1,
double x2,
double y2,
String status) |
void |
itemStateChanged(ItemEvent e) |
(package private) void |
makePolygon(int count,
double outSpacing) |
void |
putColumn(ij.process.ImageProcessor ip,
int x,
int y,
float[] data,
int length) |
void |
putRow(ij.process.ImageProcessor ip,
int x,
int y,
float[] data,
int length) |
protected ij.ImagePlus |
reslice(ij.ImagePlus imp) |
protected ij.ImagePlus |
resliceHyperstack(ij.ImagePlus imp) |
(package private) ij.ImagePlus |
resliceRectOrLine(ij.ImagePlus imp) |
protected ij.ImagePlus |
resliceTimeLapseHyperstack(ij.ImagePlus imp) |
(package private) void |
saveLineInfo(ij.gui.Roi roi) |
ij.ImagePlus |
sliceSilently(ij.ImagePlus imp) |
void |
textValueChanged(TextEvent e) |
(package private) void |
updateSize() |
private static final String[] starts
private static String startAtS
private static boolean rotateS
private static boolean flipS
private static int sliceCountS
private String startAt
private boolean rotate
private boolean flip
private int sliceCount
private boolean nointerpolate
private double inputZSpacing
private double outputZSpacing
private int outputSlices
private boolean noRoi
private boolean rgb
private boolean notFloat
private Vector fields
private Vector checkboxes
private Label message
private ij.ImagePlus imp
private double gx1
private double gy1
private double gx2
private double gy2
private double gLength
private Color lineColor
private int n
private double[] x
private double[] y
private int xbase
private int ybase
private double length
private double[] segmentLengths
private double[] dx
private double[] dy
public SilentSlicer(ij.ImagePlus imp, double outputSpacingUm, int outputSlices, boolean flipVert, boolean rotate90deg, boolean avoidInterp)
imp
- - ImagePlus to be sliced (needed mainly for the calibration);
if avoidInterp
is true
this will
be ignored and can be null
.outputSpacingUm
- - For multiple output slices, the spacing in microns.outputSlices
- - Number of output slices.flipVert
- - Flip the result vertically?rotate90deg
- - Rotate the result 90 degress?avoidInterp
- - If true
, ignore calibration and use 1px spacing for everything.public ij.ImagePlus sliceSilently(ij.ImagePlus imp) throws SlideSetException
SlideSetException
protected ij.ImagePlus reslice(ij.ImagePlus imp)
protected ij.ImagePlus resliceHyperstack(ij.ImagePlus imp)
protected ij.ImagePlus resliceTimeLapseHyperstack(ij.ImagePlus imp)
String d2s(double n)
void saveLineInfo(ij.gui.Roi roi)
ij.ImagePlus resliceRectOrLine(ij.ImagePlus imp)
ij.ImageStack createOutputStack(ij.ImagePlus imp, ij.process.ImageProcessor ip)
ij.process.ImageProcessor getSlice(ij.ImagePlus imp, double x1, double y1, double x2, double y2, String status)
public void putRow(ij.process.ImageProcessor ip, int x, int y, float[] data, int length)
public void putColumn(ij.process.ImageProcessor ip, int x, int y, float[] data, int length)
float[] getIrregularProfile(ij.gui.Roi roi, ij.process.ImageProcessor ip)
void doIrregularSetup(ij.gui.Roi roi)
private float[] getLine(ij.process.ImageProcessor ip, double x1, double y1, double x2, double y2, float[] data)
private float[] getOrthoLine(ij.process.ImageProcessor ip, int x1, int y1, int x2, int y2, float[] data)
void drawLine(double x1, double y1, double x2, double y2, ij.ImagePlus imp)
public void textValueChanged(TextEvent e)
public void itemStateChanged(ItemEvent e)
void updateSize()
String getSize(double inSpacing, double outSpacing, int count)
void makePolygon(int count, double outSpacing)
int getOutputStackSize(double inSpacing, double outSpacing, int count)
int getAvailableMemory()
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