1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.Calibration;
import java.awt.*;
/** This plugin implements the Image/Stacks/Tools/Reduce command. */
public class StackReducer implements PlugIn {
ImagePlus imp;
private static int factor = 2;
private boolean hyperstack, reduceSlices;
public void run(String arg) {
imp = WindowManager.getCurrentImage();
if (imp==null)
{IJ.noImage(); return;}
ImageStack stack = imp.getStack();
int size = stack.getSize();
if (size==1 || (imp.getNChannels()==size&&imp.isComposite()))
{IJ.error("Stack or hyperstack required"); return;}
if (!showDialog(stack))
return;
if (hyperstack)
reduceHyperstack(imp, factor, reduceSlices);
else
reduceStack(imp, factor);
}
public boolean showDialog(ImageStack stack) {
hyperstack = imp.isHyperStack();
boolean showCheckbox = false;
if (hyperstack && imp.getNSlices()>1 && imp.getNFrames()>1)
showCheckbox = true;
else if (hyperstack && imp.getNSlices()>1)
reduceSlices = true;
int n = stack.getSize();
GenericDialog gd = new GenericDialog("Reduce Size");
gd.addNumericField("Reduction Factor:", factor, 0);
if (showCheckbox)
gd.addCheckbox("Reduce in Z-Dimension", false);
gd.showDialog();
if (gd.wasCanceled()) return false;
factor = (int) gd.getNextNumber();
if (showCheckbox)
reduceSlices = gd.getNextBoolean();
return true;
}
public void reduceStack(ImagePlus imp, int factor) {
ImageStack stack = imp.getStack();
boolean virtual = stack.isVirtual();
int n = stack.getSize();
ImageStack stack2 = new ImageStack(stack.getWidth(), stack.getHeight());
for (int i=1; i<=n; i+=factor) {
if (virtual) IJ.showProgress(i, n);
stack2.addSlice(stack.getSliceLabel(i), stack.getProcessor(i));
}
imp.setStack(null, stack2);
if (virtual) {
IJ.showProgress(1.0);
imp.setTitle(imp.getTitle());
}
Calibration cal = imp.getCalibration();
if (cal.scaled()) cal.pixelDepth *= factor;
}
public void reduceHyperstack(ImagePlus imp, int factor, boolean reduceSlices) {
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int zfactor = reduceSlices?factor:1;
int tfactor = reduceSlices?1:factor;
ImageStack stack = imp.getStack();
ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight());
boolean virtual = stack.isVirtual();
int slices2 = slices/zfactor + ((slices%zfactor)!=0?1:0);
int frames2 = frames/tfactor + ((frames%tfactor)!=0?1:0);
int n = channels*slices2*frames2;
int count = 1;
for (int t=1; t<=frames; t+=tfactor) {
for (int z=1; z<=slices; z+=zfactor) {
for (int c=1; c<=channels; c++) {
int i = imp.getStackIndex(c, z, t);
IJ.showProgress(i, n);
ImageProcessor ip = stack.getProcessor(imp.getStackIndex(c, z, t));
//IJ.log(count++ +" "+i+" "+c+" "+z+" "+t);
stack2.addSlice(stack.getSliceLabel(i), ip);
}
}
}
imp.setStack(stack2, channels, slices2, frames2);
Calibration cal = imp.getCalibration();
if (cal.scaled()) cal.pixelDepth *= zfactor;
if (virtual) imp.setTitle(imp.getTitle());
IJ.showProgress(1.0);
}
}
|
