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.process.*;
import ij.gui.*;
import ij.io.FileInfo;
import java.awt.Color;
/**
* This plugin implements the Image/Stacks/Tools/Make Substack command.
* What it does is extracts selected images from a stack to make a new substack.
* It takes three types of inputs: a range of images (e.g. 2-14), a range of images
* with an increment (e.g. 2-14-3), or a list of images (e.g. 7,9,25,27,34,132).
* It then copies those images from the active stack to a new stack in the order
* of listing or range.
*
* @author Anthony Padua
* @author Daniel Barboriak, MD
* @author Neuroradiology
* @author Duke University Medical Center
*
* @author Ved P. Sharma, Ph.D.
* @author Anatomy and Structural Biology
* @author Albert Einstein College of Medicine
*
*/
public class SubstackMaker implements PlugIn {
private static boolean delete = false;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
if (imp.isHyperStack() || imp.isComposite()) {
(new SubHyperstackMaker()).run("");
return;
}
String userInput = showDialog();
if (userInput==null)
return;
ImagePlus imp2 = makeSubstack(imp, userInput);
if (imp2!=null)
imp2.show();
}
public ImagePlus makeSubstack(ImagePlus imp, String userInput) {
String stackTitle = "Substack ("+userInput+")";
if (stackTitle.length()>25) {
int idxA = stackTitle.indexOf(",",18);
int idxB = stackTitle.lastIndexOf(",");
if(idxA>=1 && idxB>=1){
String strA = stackTitle.substring(0,idxA);
String strB = stackTitle.substring(idxB+1);
stackTitle = strA + ", ... " + strB;
}
}
ImagePlus imp2 = null;
try {
int idx1 = userInput.indexOf("-");
if (idx1>=1) { // input displayed in range
String rngStart = userInput.substring(0, idx1);
String rngEnd = userInput.substring(idx1+1);
Integer obj = new Integer(rngStart);
int first = obj.intValue();
int inc = 1;
int idx2 = rngEnd.indexOf("-");
if (idx2>=1) {
String rngEndAndInc = rngEnd;
rngEnd = rngEndAndInc.substring(0, idx2);
String rngInc = rngEndAndInc.substring(idx2+1);
obj = new Integer(rngInc);
inc = obj.intValue();
}
obj = new Integer(rngEnd);
int last = obj.intValue();
imp2 = stackRange(imp, first, last, inc, stackTitle);
} else {
int count = 1; // count # of slices to extract
for (int j=0; j<userInput.length(); j++) {
char ch = Character.toLowerCase(userInput.charAt(j));
if (ch==',') {count += 1;}
}
int[] numList = new int[count];
for(int i=0; i<count; i++) {
int idx2 = userInput.indexOf(",");
if(idx2>0) {
String num = userInput.substring(0,idx2);
Integer obj = new Integer(num);
numList[i] = obj.intValue();
userInput = userInput.substring(idx2+1);
}
else{
String num = userInput;
Integer obj = new Integer(num);
numList[i] = obj.intValue();
}
}
imp2 = stackList(imp, count, numList, stackTitle);
}
} catch (Exception e) {
IJ.error("Substack Maker", "Invalid input string: \n \n \""+userInput+"\"");
}
return imp2;
}
String showDialog() {
String options = Macro.getOptions();
if (options!=null && !options.contains("slices=")) {
Macro.setOptions(options.replace("channels=", "slices="));
Macro.setOptions(options.replace("frames=", "slices="));
}
GenericDialog gd = new GenericDialog("Substack Maker");
gd.setInsets(10,45,0);
gd.addMessage("Enter a range (e.g. 2-14), a range with increment\n(e.g. 1-100-2) or a list (e.g. 7,9,25,27)", null, Color.darkGray);
gd.addStringField("Slices:", "", 40);
gd.addCheckbox("Delete slices from original stack", delete);
gd.showDialog();
if (gd.wasCanceled())
return null;
else {
delete = gd.getNextBoolean();
return gd.getNextString();
}
}
// extract specific slices
ImagePlus stackList(ImagePlus imp, int count, int[] numList, String stackTitle) throws Exception {
ImageStack stack = imp.getStack();
ImageStack stack2 = null;
boolean virtualStack = stack.isVirtual();
double min = imp.getDisplayRangeMin();
double max = imp.getDisplayRangeMax();
Roi roi = imp.getRoi();
for (int i=0, j=0; i<count; i++) {
int currSlice = numList[i]-j;
ImageProcessor ip2 = stack.getProcessor(currSlice);
ip2.setRoi(roi);
ip2 = ip2.crop();
if (stack2==null)
stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(stack.getSliceLabel(currSlice), ip2);
if (delete) {
stack.deleteSlice(currSlice);
j++;
}
}
if (delete) {
imp.setStack(stack);
// next three lines for updating the scroll bar
ImageWindow win = imp.getWindow();
StackWindow swin = (StackWindow) win;
if (swin!=null)
swin.updateSliceSelector();
}
ImagePlus impSubstack = imp.createImagePlus();
impSubstack.setStack(stackTitle, stack2);
if (virtualStack)
impSubstack.setDisplayRange(min, max);
return impSubstack;
}
// extract range of slices
ImagePlus stackRange(ImagePlus imp, int first, int last, int inc, String title) throws Exception {
ImageStack stack = imp.getStack();
ImageStack stack2 = null;
boolean virtualStack = stack.isVirtual();
double min = imp.getDisplayRangeMin();
double max = imp.getDisplayRangeMax();
Roi roi = imp.getRoi();
boolean showProgress = stack.getSize()>400 || stack.isVirtual();
for (int i= first, j=0; i<= last; i+=inc) {
if (showProgress) IJ.showProgress(i,last);
int currSlice = i-j;
ImageProcessor ip2 = stack.getProcessor(currSlice);
ip2.setRoi(roi);
ip2 = ip2.crop();
if (stack2==null)
stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(stack.getSliceLabel(currSlice), ip2);
if (delete) {
stack.deleteSlice(currSlice);
j++;
}
}
if (delete) {
imp.setStack(stack);
// next three lines for updating the scroll bar
ImageWindow win = imp.getWindow();
StackWindow swin = (StackWindow) win;
if (swin!=null)
swin.updateSliceSelector();
}
ImagePlus substack = imp.createImagePlus();
substack.setStack(title, stack2);
substack.setCalibration(imp.getCalibration());
if (virtualStack)
substack.setDisplayRange(min, max);
return substack;
}
}
|
