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
256
257
258
259
260
261
262
263
264
|
package ij.plugin;
import java.awt.*;
import java.io.*;
import java.text.DecimalFormat;
import java.util.*;
import ij.*;
import ij.io.*;
import ij.gui.*;
import ij.measure.Calibration;
import ij.process.*;
import ij.plugin.frame.Recorder;
import ij.macro.Interpreter;
import ij.util.Tools;
/** This plugin, which saves the images in a stack as separate files,
implements the File/Save As/Image Sequence command. */
public class StackWriter implements PlugIn {
private static final String DIR_KEY = "save.sequence.dir";
private static String[] choices = {"BMP", "FITS", "GIF", "JPEG", "PGM", "PNG", "Raw", "Text", "TIFF", "ZIP"};
private static String staticFileType = "TIFF";
private String fileType = "TIFF";
private int ndigits = 4;
private boolean useLabels;
private boolean firstTime = true;
private int startAt;
private boolean hyperstack;
private int[] dim;
private ImagePlus imp;
private String directory;
private String format = "tiff";
private String name;
/** Saves the specified image as a sequence of images. */
public static void save(ImagePlus imp, String directoryPath, String options) {
StackWriter sw = new StackWriter();
sw.imp = imp;
sw.format = Tools.getStringFromList(options, "format=", sw.format);
sw.name = Tools.getStringFromList(options, "name=");
sw.ndigits = (int)Tools.getNumberFromList(options, "digits=", sw.ndigits);
sw.useLabels = options.contains(" use");
sw.run(directoryPath);
}
public void run(String arg) {
if (imp==null)
imp = WindowManager.getCurrentImage();
if (imp==null || (imp!=null && imp.getStackSize()<2&&!IJ.isMacro())) {
IJ.error("Stack Writer", "This command requires a stack.");
return;
}
int stackSize = imp.getStackSize();
if (name==null) {
name = imp.getTitle();
int dotIndex = name.lastIndexOf(".");
if (dotIndex>=0)
name = name.substring(0, dotIndex);
}
hyperstack = imp.isHyperStack();
LUT[] luts = null;
int lutIndex = 0;
int nChannels = imp.getNChannels();
if (hyperstack) {
dim = imp.getDimensions();
if (imp.isComposite())
luts = ((CompositeImage)imp).getLuts();
if (firstTime && ndigits==4) {
ndigits = 3;
firstTime = false;
}
}
if (arg!=null && arg.length()>0)
directory = arg;
else {
if (!showDialog(imp))
return;
}
File d = new File(directory);
if (d==null || !d.isDirectory()) {
IJ.error("File>Save As>Image Sequence", "Directory not found: "+directory);
return;
}
int number = 0;
if (ndigits<1) ndigits = 1;
if (ndigits>8) ndigits = 8;
int maxImages = (int)Math.pow(10,ndigits);
if (stackSize>maxImages && !useLabels && !hyperstack) {
IJ.error("Stack Writer", "More than " + ndigits
+" digits are required to generate \nunique file names for "+stackSize+" images.");
return;
}
if (format.equals("fits") && !FileSaver.okForFits(imp))
return;
if (format.equals("text"))
format = "text image";
String extension = "." + format;
if (format.equals("tiff"))
extension = ".tif";
else if (format.equals("text image"))
extension = ".txt";
Overlay overlay = imp.getOverlay();
boolean isOverlay = overlay!=null && !imp.getHideOverlay();
if (!(format.equals("jpeg")||format.equals("png")))
isOverlay = false;
ImageStack stack = imp.getStack();
ImagePlus imp2 = new ImagePlus();
imp2.setTitle(imp.getTitle());
Calibration cal = imp.getCalibration();
int nSlices = stack.size();
String path,label=null;
imp.lock();
for (int i=1; i<=nSlices; i++) {
IJ.showStatus("writing: "+i+"/"+nSlices);
IJ.showProgress(i, nSlices);
ImageProcessor ip = stack.getProcessor(i);
if (isOverlay) {
imp.setSliceWithoutUpdate(i);
ip = imp.flatten().getProcessor();
} else if (luts!=null && nChannels>1 && hyperstack) {
ip.setColorModel(luts[lutIndex++]);
if (lutIndex>=luts.length) lutIndex = 0;
}
imp2.setProcessor(null, ip);
String label2 = stack.getSliceLabel(i);
imp2.setProp("Slice_Label", null);
if (label2!=null) {
if (label2.contains("\n"))
imp2.setProperty("Info", label2);
else
imp2.setProp("Slice_Label", label2);;
} else {
Properties props = imp2.getProperties();
if (props!=null) props.remove("Info");
}
imp2.setCalibration(cal);
String digits = getDigits(number++);
if (useLabels) {
label = stack.getShortSliceLabel(i, 111);
if (label!=null && label.equals("")) label = null;
if (label!=null) label = label.replaceAll("/","-");
}
if (label==null)
path = directory+name+digits+extension;
else
path = directory+label+extension;
if (i==1) {
File f = new File(path);
if (f.exists()) {
if (!IJ.isMacro() && !IJ.showMessageWithCancel("Overwrite files?",
"One or more files will be overwritten if you click \"OK\".\n \n"+path)) {
imp.unlock();
IJ.showStatus("");
IJ.showProgress(1.0);
return;
}
}
}
if (Recorder.record)
Recorder.disablePathRecording();
imp2.setOverlay(null);
if (overlay!=null && format.equals("tiff")) {
Overlay overlay2 = overlay.duplicate();
overlay2.crop(i, i);
if (overlay2.size()>0) {
for (int j=0; j<overlay2.size(); j++) {
Roi roi = overlay2.get(j);
int pos = roi.getPosition();
if (pos==1)
roi.setPosition(i);
}
imp2.setOverlay(overlay2);
}
}
IJ.saveAs(imp2, format, path);
}
imp.unlock();
if (isOverlay) imp.setSlice(1);
IJ.showStatus("");
}
private boolean showDialog(ImagePlus imp) {
String options = Macro.getOptions();
if (options!=null && options.contains("save=")) //macro
Macro.setOptions(options.replaceAll("save=", "dir="));
directory = Prefs.get(DIR_KEY, IJ.getDir("downloads")+"stack2/");
GenericDialog gd = new GenericDialog("Save Image Sequence");
if (!IJ.isMacro())
fileType = staticFileType;
gd.setInsets(5, 0, 0);
gd.addDirectoryField("Dir:", directory);
gd.setInsets(2, 110, 5);
gd.addMessage("drag and drop target", IJ.font10, Color.darkGray);
gd.addChoice("Format:", choices, fileType);
gd.addStringField("Name:", name, 12);
if (!hyperstack)
gd.addNumericField("Start At:", startAt, 0);
gd.addNumericField("Digits (1-8):", ndigits, 0);
if (!hyperstack)
gd.addCheckbox("Use slice labels as file names", useLabels);
gd.showDialog();
if (gd.wasCanceled())
return false;
directory = gd.getNextString();
directory = IJ.addSeparator(directory);
Prefs.set(DIR_KEY, directory);
gd.setSmartRecording(true);
fileType = gd.getNextChoice();
format = fileType.toLowerCase(Locale.US);
if (!IJ.isMacro())
staticFileType = fileType;
String name2 = gd.getNextString();
boolean nameChanged = !name2.equals(name);
name = name2;
if (!hyperstack)
startAt = (int)gd.getNextNumber();
if (startAt<0) startAt = 0;
int ndigits2 = (int)gd.getNextNumber();
boolean ndigitsChanged = ndigits2!=ndigits;
ndigits = ndigits2;
if (!hyperstack)
useLabels = gd.getNextBoolean();
else
useLabels = false;
if (Recorder.record) {
String options2 = "format="+format;
if (nameChanged)
options2 += " name="+name;
if (ndigitsChanged)
options2 += " digits="+ndigits;
if (useLabels)
options2 += " use";
String dir = Recorder.fixPath(directory);
Recorder.recordCall("StackWriter.save(imp, \""+dir+"\", \""+options2+"\");");
}
return true;
}
String getDigits(int n) {
if (hyperstack) {
int c = (n%dim[2])+1;
int z = ((n/dim[2])%dim[3])+1;
int t = ((n/(dim[2]*dim[3]))%dim[4])+1;
String cs="", zs="", ts="";
if (dim[2]>1) {
cs = "00000000"+c;
cs = "_c"+cs.substring(cs.length()-ndigits);
}
if (dim[3]>1) {
zs = "00000000"+z;
zs = "_z"+zs.substring(zs.length()-ndigits);
}
if (dim[4]>1) {
ts = "00000000"+t;
ts = "_t"+ts.substring(ts.length()-ndigits);
}
return ts+zs+cs;
} else {
String digits = "00000000"+(startAt+n);
return digits.substring(digits.length()-ndigits);
}
}
}
|
