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
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
|
package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Calibration;
import ij.macro.Interpreter;
import ij.io.FileInfo;
import ij.plugin.frame.Recorder;
import java.awt.image.ColorModel;
/** Implements the "Stack to HyperStack", "RGB to HyperStack"
and "HyperStack to Stack" commands. */
public class HyperStackConverter implements PlugIn {
public static final int CZT=0, CTZ=1, ZCT=2, ZTC=3, TCZ=4, TZC=5;
static final int C=0, Z=1, T=2;
static final String[] orders = {"xyczt(default)", "xyctz", "xyzct", "xyztc", "xytcz", "xytzc"};
static int ordering = CZT;
static boolean splitRGB = true;
public void run(String arg) {
if (arg.equals("new"))
{newHyperStack(); return;}
ImagePlus imp = IJ.getImage();
if (arg.equals("stacktohs"))
convertStackToHS(imp);
else if (arg.equals("hstostack"))
convertHSToStack(imp);
}
/** Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and
't' frames using the default ordering ("xyczt") and display mode ("Composite"). */
public static ImagePlus toHyperStack(ImagePlus imp, int c, int z, int t) {
return toHyperStack(imp, c, z, t, null, null);
}
/** Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and
't' frames using the default ordering ("xyczt") and the specified display
mode ("composite", "color" or "grayscale"). */
public static ImagePlus toHyperStack(ImagePlus imp, int c, int z, int t, String mode) {
return toHyperStack(imp, c, z, t, null, mode);
}
/** Converts the specified stack into a hyperstack with 'c' channels,
* 'z' slices and 't' frames. The default "xyczt" order is used if
* 'order' is null. The default "composite" display mode is used
* if 'mode' is null.
* @param imp the stack to be converted
* @param c channels
* @param z slices
* @param t frames
* @param order hyperstack order ("default", "xyctz", "xyzct", "xyztc", "xytcz" or "xytzc")
* @param mode display mode ("composite", "color" or "grayscale")
* @return the resulting hyperstack
*/
public static ImagePlus toHyperStack(ImagePlus imp, int c, int z, int t, String order, String mode) {
int n = imp.getStackSize();
if (n==1 || imp.getBitDepth()==24)
throw new IllegalArgumentException("Non-RGB stack required");
if (c*z*t!=n)
throw new IllegalArgumentException("C*Z*T not equal stack size");
imp.setDimensions(c, z, t);
if (order==null || order.equals("default") || order.equals("xyczt"))
order = orders[0];
int intOrder = CZT;
for (int i=0; i<orders.length; i++) {
if (order.equals(orders[i])) {
intOrder = i;
break;
}
}
if (intOrder!=CZT && imp.getStack().isVirtual())
throw new IllegalArgumentException("Virtual stacks must by in XYCZT order");
(new HyperStackConverter()).shuffle(imp, intOrder);
ImagePlus imp2 = imp;
int intMode = IJ.COMPOSITE;
if (mode!=null) {
if (mode.equalsIgnoreCase("color"))
intMode = IJ.COLOR;
else if (mode.equalsIgnoreCase("grayscale"))
intMode = IJ.GRAYSCALE;
}
if (c>1) {
LUT[] luts = imp.getLuts();
if (luts!=null && luts.length<c)
luts = null;
imp2 = new CompositeImage(imp, intMode);
if (luts!=null)
((CompositeImage)imp2).setLuts(luts);
}
imp2.setOpenAsHyperStack(true);
imp2.setOverlay(imp.getOverlay());
return imp2;
}
/** Displays the specified stack in a HyperStack window. Based on the
Stack_to_Image5D class in Joachim Walter's Image5D plugin. */
void convertStackToHS(ImagePlus imp) {
int nChannels = imp.getNChannels();
int nSlices = imp.getNSlices();
int nFrames = imp.getNFrames();
int stackSize = imp.getImageStackSize();
if (stackSize==1) {
IJ.error("Stack to HyperStack", "Stack required");
return;
}
boolean rgb = imp.getBitDepth()==24;
String[] modes = {"Composite", "Color", "Grayscale"};
GenericDialog gd = new GenericDialog("Convert to HyperStack");
gd.addChoice("Order:", orders, orders[ordering]);
gd.addNumericField("Channels (c):", nChannels, 0);
gd.addNumericField("Slices (z):", nSlices, 0);
gd.addNumericField("Frames (t):", nFrames, 0);
gd.addChoice("Display Mode:", modes, modes[1]);
if (rgb) {
gd.setInsets(15, 0, 0);
gd.addCheckbox("Convert RGB to 3 Channel Hyperstack", splitRGB);
}
gd.showDialog();
if (gd.wasCanceled()) return;
ordering = gd.getNextChoiceIndex();
nChannels = (int) gd.getNextNumber();
nSlices = (int) gd.getNextNumber();
nFrames = (int) gd.getNextNumber();
int mode = gd.getNextChoiceIndex();
if (rgb)
splitRGB = gd.getNextBoolean();
if (rgb && splitRGB==true) {
new CompositeConverter().run(mode==0?"composite":"color");
return;
}
if (rgb && nChannels>1) {
IJ.error("HyperStack Converter", "RGB stacks are limited to one channel");
return;
}
if (nChannels*nSlices*nFrames!=stackSize) {
IJ.error("HyperStack Converter", "channels x slices x frames <> stack size");
return;
}
imp.setDimensions(nChannels, nSlices, nFrames);
if (ordering!=CZT && imp.getStack().isVirtual())
IJ.error("HyperStack Converter", "Virtual stacks must by in XYCZT order.");
else {
shuffle(imp, ordering);
ImagePlus imp2 = imp;
if (nChannels>1 && imp.getBitDepth()!=24) {
LUT[] luts = imp.getLuts();
if (luts!=null && luts.length<nChannels) luts = null;
imp2 = new CompositeImage(imp, mode+1);
if (luts!=null)
((CompositeImage)imp2).setLuts(luts);
} else if (imp.getClass().getName().indexOf("Image5D")!=-1) {
imp2 = imp.createImagePlus();
imp2.setStack(imp.getTitle(), imp.getImageStack());
imp2.setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
imp2.getProcessor().resetMinAndMax();
}
imp2.setOpenAsHyperStack(true);
if (imp.getWindow()!=null || imp!=imp2)
new StackWindow(imp2);
if (imp!=imp2) {
imp2.setOverlay(imp.getOverlay());
imp.hide();
WindowManager.setCurrentWindow(imp2.getWindow());
}
}
if (Recorder.record && Recorder.scriptMode()) {
String order = orders[ordering];
if (order.equals(orders[0])) { // default order
Recorder.recordCall("imp2 = HyperStackConverter.toHyperStack(imp, "+nChannels+", "+
nSlices+", "+nFrames+", \""+modes[mode]+"\");");
} else {
Recorder.recordCall("imp2 = HyperStackConverter.toHyperStack(imp, "+nChannels+", "+
nSlices+", "+nFrames+", \""+order+"\", \""+modes[mode]+"\");");
}
}
}
/** Changes the dimension order of a 4D or 5D stack from
the specified order (CTZ, ZCT, ZTC, TCZ or TZC) to
the XYCZT order used by ImageJ. */
public void shuffle(ImagePlus imp, int order) {
int nChannels = imp.getNChannels();
int nSlices = imp.getNSlices();
int nFrames = imp.getNFrames();
int first=C, middle=Z, last=T;
int nFirst=nChannels, nMiddle=nSlices, nLast=nFrames;
switch (order) {
case CTZ: first=C; middle=T; last=Z;
nFirst=nChannels; nMiddle=nFrames; nLast=nSlices;
break;
case ZCT: first=Z; middle=C; last=T;
nFirst=nSlices; nMiddle=nChannels; nLast=nFrames;
break;
case ZTC: first=Z; middle=T; last=C;
nFirst=nSlices; nMiddle=nFrames; nLast=nChannels;
break;
case TCZ: first=T; middle=C; last=Z;
nFirst=nFrames; nMiddle=nChannels; nLast=nSlices;
break;
case TZC: first=T; middle=Z; last=C;
nFirst=nFrames; nMiddle=nSlices; nLast=nChannels;
break;
}
if (order!=CZT) {
ImageStack stack = imp.getImageStack();
Object[] images1 = stack.getImageArray();
Object[] images2 = new Object[images1.length];
System.arraycopy(images1, 0, images2, 0, images1.length);
String[] labels1 = stack.getSliceLabels();
String[] labels2 = new String[labels1.length];
System.arraycopy(labels1, 0, labels2, 0, labels1.length);
int[] index = new int[3];
for (index[2]=0; index[2]<nFrames; ++index[2]) {
for (index[1]=0; index[1]<nSlices; ++index[1]) {
for (index[0]=0; index[0]<nChannels; ++index[0]) {
int dstIndex = index[0] + index[1]*nChannels + index[2]*nChannels*nSlices;
int srcIndex = index[first] + index[middle]*nFirst + index[last]*nFirst*nMiddle;
images1[dstIndex] = images2[srcIndex];
labels1[dstIndex] = labels2[srcIndex];
}
}
}
}
}
void convertHSToStack(ImagePlus imp) {
if (!(imp.isHyperStack()||imp.isComposite()))
return;
ImagePlus imp2 = imp;
if (imp.isComposite()) {
ImageStack stack = imp.getStack();
imp2 = imp.createImagePlus();
imp2.setStack(imp.getTitle(), stack);
int[] dim = imp.getDimensions();
imp2.setDimensions(dim[2], dim[3], dim[4]);
ImageProcessor ip2 = imp2.getProcessor();
ip2.setColorModel(ip2.getDefaultColorModel());
}
imp2.setOpenAsHyperStack(false);
if (imp.getWindow()!=null || imp!=imp2)
new StackWindow(imp2);
if (imp!=imp2) {
imp2.setOverlay(imp.getOverlay());
imp.hide();
}
}
void newHyperStack() {
IJ.runMacroFile("ij.jar:HyperStackMaker", "");
}
}
|
