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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
|
package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Calibration;
import java.awt.*;
import java.util.Vector;
/** Implements the Image/HyperStacks/Reduce Dimensionality command. */
public class HyperStackReducer implements PlugIn, DialogListener {
ImagePlus imp;
int channels1, slices1, frames1;
int channels2, slices2, frames2;
double imageSize;
static boolean keep = true;
/** Default constructor */
public HyperStackReducer() {
}
/** Constructs a HyperStackReducer using the specified source image. */
public HyperStackReducer(ImagePlus imp) {
this.imp = imp;
this.channels1 = this.channels2 = imp.getNChannels();
this.slices1 = this.slices2 = imp.getNSlices();
this.frames1 = this.frames2 = imp.getNFrames();
}
public void run(String arg) {
//IJ.log("HyperStackReducer-1");
imp = IJ.getImage();
if (!imp.isHyperStack() && imp.getNChannels()==1) {
IJ.error("Reducer", "HyperStack required");
return;
}
int width = imp.getWidth();
int height = imp.getHeight();
imageSize = width*height*imp.getBytesPerPixel()/(1024.0*1024.0);
channels1 = channels2 = imp.getNChannels();
slices1 = slices2 = imp.getNSlices();
frames1 = frames2 = imp.getNFrames();
int z0 = imp.getSlice();
int t0 = imp.getFrame();
if (!showDialog())
return;
//IJ.log("HyperStackReducer-2: "+keep+" "+channels2+" "+slices2+" "+frames2);
String title2 = keep?WindowManager.getUniqueName(imp.getTitle()):imp.getTitle();
ImagePlus imp2 = null;
if (keep) {
imp2 = IJ.createImage(title2, imp.getBitDepth()+"-bit", width, height, channels2*slices2*frames2);
if (imp2==null) return;
imp2.setDimensions(channels2, slices2, frames2);
imp2.setCalibration(imp.getCalibration());
imp2.setOpenAsHyperStack(true);
} else
imp2 = imp.createHyperStack(title2, channels2, slices2, frames2, imp.getBitDepth());
imp2.setProperty("Info", (String)imp.getProperty("Info"));
imp2.setProperties(imp.getPropertiesAsArray());
reduce(imp2);
if (channels2>1 && channels2==imp.getNChannels() && imp.isComposite()) {
int mode = ((CompositeImage)imp).getMode();
imp2 = new CompositeImage(imp2, mode);
((CompositeImage)imp2).copyLuts(imp);
} else {
imp2.setDisplayRange(imp.getDisplayRangeMin(), imp.getDisplayRangeMax());
if (imp.isComposite() && ((CompositeImage)imp).getMode()==IJ.GRAYSCALE)
IJ.run(imp2, "Grays", "");
}
if (imp.getWindow()==null && !keep) {
imp.setImage(imp2);
return;
}
imp2.show();
if (z0>1 || t0>1)
imp2.setPosition(1, z0, t0);
//IJ.log("HyperStackReducer-4");
if (!keep) {
imp.changes = false;
imp.close();
}
}
public void reduce(ImagePlus imp2) {
this.channels2 = imp2.getNChannels();
this.slices2 = imp2.getNSlices();
this.frames2 = imp2.getNFrames();
int channels = imp2.getNChannels();
int slices = imp2.getNSlices();
int frames = imp2.getNFrames();
int c1 = imp.getChannel();
int z1 = imp.getSlice();
int t1 = imp.getFrame();
int i = 1;
int n = channels*slices*frames;
ImageStack stack = imp.getStack();
ImageStack stack2 = imp2.getStack();
for (int c=1; c<=channels; c++) {
if (channels==1) c = c1;
LUT lut = imp.isComposite()?((CompositeImage)imp).getChannelLut():imp.getProcessor().getLut();
imp.setPositionWithoutUpdate(c, 1, 1);
ImageProcessor ip = imp.getProcessor();
double min = ip.getMin();
double max = ip.getMax();
for (int z=1; z<=slices; z++) {
if (slices==1) z = z1;
for (int t=1; t<=frames; t++) {
if (frames==1) t = t1;
int n1 = imp.getStackIndex(c, z, t);
ip = stack.getProcessor(n1);
String label = stack.getSliceLabel(n1);
int n2 = imp2.getStackIndex(c, z, t);
if (stack2.getPixels(n2)!=null)
stack2.getProcessor(n2).insert(ip, 0, 0);
else
stack2.setPixels(ip.getPixels(), n2);
stack2.setSliceLabel(label, n2);
}
}
if (lut!=null) {
if (imp2.isComposite())
((CompositeImage)imp2).setChannelLut(lut);
else
imp2.getProcessor().setColorModel(lut);
}
imp2.getProcessor().setMinAndMax(min, max);
}
imp.setPosition(c1, z1, t1);
imp2.resetStack();
imp2.setPosition(1, 1, 1);
Overlay overlay = imp.getOverlay();
if (overlay!=null && !imp.getHideOverlay())
imp2.setOverlay(reduce(overlay));
}
//Added by Marcel Boeglin 2013.11.29
/** Returns a copy of 'overlay', limited to the dimensions of the reduced image. */
private Overlay reduce(Overlay overlay) {
int c1 = imp.getChannel();
int z1 = imp.getSlice();
int t1 = imp.getFrame();
Overlay overlay2 = overlay.duplicate();
if (channels2==1 && slices2==slices1 && frames2==frames1)
overlay2.crop(c1, c1, 1, slices1, 1, frames1);
else if (channels2==channels1 && slices2==1 && frames2==frames1)
overlay2.crop(1, channels1, z1, z1, 1, frames1);
else if (channels2==channels1 && slices2==slices1 && frames2==1)
overlay2.crop(1, channels1, 1, slices1, t1, t1);
else if (channels2==channels1 && slices2==1 && frames2==1)
overlay2.crop(1, channels1, z1, z1, t1, t1);
else if (channels2==1 && slices2==slices1 && frames2==1)
overlay2.crop(c1, c1, 1, slices1, t1, t1);
else if (channels2==1 && slices2==1 && frames2==frames1)
overlay2.crop(c1, c1, z1, z1, 1, frames1);
else if (channels2==1 && slices2==1 && frames2==1)
overlay2.crop(c1, c1, z1, z1, t1, t1);
return overlay2;
}
boolean showDialog() {
GenericDialog gd = new GenericDialog("Reduce");
gd.setInsets(10, 20, 5);
gd.addMessage("Create image with:");
gd.setInsets(0, 35, 0);
if (channels1!=1) gd.addCheckbox("Channels ("+channels1+")", true);
gd.setInsets(0, 35, 0);
if (slices1!=1) gd.addCheckbox("Slices ("+slices1+")", true);
gd.setInsets(0, 35, 0);
if (frames1!=1) gd.addCheckbox("Frames ("+frames1+")", true);
gd.setInsets(5, 20, 0);
gd.addMessage(getNewDimensions()+" ");
gd.setInsets(15, 20, 0);
gd.addCheckbox("Keep source", keep);
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled())
return false;
else
return true;
}
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
if (IJ.isMacOSX()) IJ.wait(100);
if (channels1!=1) channels2 = gd.getNextBoolean()?channels1:1;
if (slices1!=1) slices2 = gd.getNextBoolean()?slices1:1;
if (frames1!=1) frames2 = gd.getNextBoolean()?frames1:1;
keep = gd.getNextBoolean();
if (imp!=null && imp.getWindow()!=null)
((Label)gd.getMessage()).setText(getNewDimensions());
return true;
}
String getNewDimensions() {
String s = channels2+"x"+slices2+"x"+frames2;
s += " ("+(int)Math.round(imageSize*channels2*slices2*frames2)+"MB)";
return(s);
}
}
|
