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
|
package ij.plugin.filter;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.plugin.frame.ThresholdAdjuster;
import java.awt.*;
/** Implements the Erode, Dilate, Open, Close, Outline, Skeletonize
and Fill Holes commands in the Process/Binary submenu.
Gabriel Landini contributed the clever binary fill algorithm
that fills holes in objects by filling the background.
Version 2009-06-23 preview added, interations can be aborted by escape (Michael Schmid)
*/
public class Binary implements ExtendedPlugInFilter, DialogListener {
static final int MAX_ITERATIONS = 100;
static final String NO_OPERATION = "Nothing";
static final String[] outputTypes = {"Overwrite", "8-bit", "16-bit", "32-bit"};
static final String[] operations = {NO_OPERATION, "Erode", "Dilate", "Open", "Close", "Outline", "Fill Holes", "Skeletonize"};
//parameters / options
static int iterations = 1; //iterations for erode, dilate, open, close
static int count = 1; //nearest neighbor count for erode, dilate, open, close
String operation = NO_OPERATION; //for dialog; will be copied to 'arg' for actual previewing
String arg;
ImagePlus imp; //null if only setting options with no preview possibility
PlugInFilterRunner pfr;
boolean doOptions; //whether options dialog is required
boolean previewing;
boolean escapePressed;
int foreground, background;
int flags = DOES_8G | DOES_8C | SUPPORTS_MASKING | PARALLELIZE_STACKS | KEEP_PREVIEW | KEEP_THRESHOLD;
int nPasses;
public int setup(String arg, ImagePlus imp) {
this.arg = arg;
IJ.register(Binary.class);
doOptions = arg.equals("options");
if (doOptions) {
if (imp == null) return NO_IMAGE_REQUIRED; //options dialog does not need a (suitable) image
ImageProcessor ip = imp.getProcessor();
if (!(ip instanceof ByteProcessor)) return NO_IMAGE_REQUIRED;
if (!((ByteProcessor)ip).isBinary()) return NO_IMAGE_REQUIRED;
}
return flags;
}
public int showDialog (ImagePlus imp, String command, PlugInFilterRunner pfr) {
if (doOptions) {
this.imp = imp;
this.pfr = pfr;
GenericDialog gd = new GenericDialog("Binary Options");
gd.addNumericField("Iterations (1-"+MAX_ITERATIONS+"):", iterations, 0, 3, "");
gd.addNumericField("Count (1-8):", count, 0, 3, "");
gd.addCheckbox("Black background", Prefs.blackBackground);
gd.addCheckbox("Pad edges when eroding", Prefs.padEdges);
gd.addChoice("EDM output:", outputTypes, outputTypes[EDM.getOutputType()]);
if (imp != null) {
gd.addChoice("Do:", operations, operation);
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
previewing = true;
}
gd.addHelp(IJ.URL+"/docs/menus/process.html#options");
gd.showDialog();
previewing = false;
if (gd.wasCanceled()) return DONE;
if (imp==null) { //options dialog only, no do/preview
dialogItemChanged(gd, null); //read dialog result
return DONE;
}
return operation.equals(NO_OPERATION) ? DONE : IJ.setupDialog(imp, flags);
} else { //no dialog, 'arg' is operation type
if (!((ByteProcessor)imp.getProcessor()).isBinary()) {
IJ.error("8-bit binary (black and white only) image required.");
return DONE;
}
return IJ.setupDialog(imp, flags);
}
}
public boolean dialogItemChanged (GenericDialog gd, AWTEvent e) {
iterations = (int)gd.getNextNumber();
count = (int)gd.getNextNumber();
boolean bb = Prefs.blackBackground;
Prefs.blackBackground = gd.getNextBoolean();
if ( Prefs.blackBackground!=bb)
ThresholdAdjuster.update();
Prefs.padEdges = gd.getNextBoolean();
gd.setSmartRecording(EDM.getOutputType()==0);
EDM.setOutputType(gd.getNextChoiceIndex());
gd.setSmartRecording(false);
boolean isInvalid = gd.invalidNumber();
if (iterations<1) {iterations = 1; isInvalid = true;}
if (iterations>MAX_ITERATIONS) {iterations = MAX_ITERATIONS; isInvalid = true;}
if (count < 1) {count = 1; isInvalid = true;}
if (count > 8) {count = 8; isInvalid = true;}
if (isInvalid) return false;
if (imp != null) {
operation = gd.getNextChoice();
arg = operation.toLowerCase();
}
return true;
}
public void setNPasses (int nPasses) {
this.nPasses = nPasses;
}
public void run (ImageProcessor ip) {
int fg = Prefs.blackBackground ? 255 : 0;
foreground = ip.isInvertedLut() ? 255-fg : fg;
background = 255 - foreground;
ip.setSnapshotCopyMode(true);
if (arg.equals("outline"))
outline(ip);
else if (arg.startsWith("fill"))
fill(ip, foreground, background);
else if (arg.startsWith("skel")) {
ip.resetRoi(); skeletonize(ip);
} else if (arg.equals("erode") || arg.equals("dilate"))
doIterations((ByteProcessor)ip, arg);
else if (arg.equals("open")) {
doIterations(ip, "erode");
doIterations(ip, "dilate");
} else if (arg.equals("close")) {
doIterations(ip, "dilate");
doIterations(ip, "erode");
}
ip.setSnapshotCopyMode(false);
ip.setBinaryThreshold();
}
void doIterations (ImageProcessor ip, String mode) {
if (escapePressed) return;
if (!previewing && iterations>1)
IJ.showStatus(arg+"... press ESC to cancel");
for (int i=0; i<iterations; i++) {
if (Thread.currentThread().isInterrupted()) return;
if (IJ.escapePressed()) {
escapePressed = true;
ip.reset();
return;
}
if (mode.equals("erode"))
((ByteProcessor)ip).erode(count, background);
else
((ByteProcessor)ip).dilate(count, background);
}
}
void outline(ImageProcessor ip) {
if (Prefs.blackBackground) ip.invert();
((ByteProcessor)ip).outline();
if (Prefs.blackBackground) ip.invert();
}
void skeletonize(ImageProcessor ip) {
if (Prefs.blackBackground) ip.invert();
boolean edgePixels = hasEdgePixels(ip);
ImageProcessor ip2 = expand(ip, edgePixels);
((ByteProcessor)ip2).skeletonize();
ip = shrink(ip, ip2, edgePixels);
if (Prefs.blackBackground) ip.invert();
}
boolean hasEdgePixels(ImageProcessor ip) {
int width = ip.getWidth();
int height = ip.getHeight();
boolean edgePixels = false;
for (int x=0; x<width; x++) { // top edge
if (ip.getPixel(x, 0)==foreground)
edgePixels = true;
}
for (int x=0; x<width; x++) { // bottom edge
if (ip.getPixel(x, height-1)==foreground)
edgePixels = true;
}
for (int y=0; y<height; y++) { // left edge
if (ip.getPixel(0, y)==foreground)
edgePixels = true;
}
for (int y=0; y<height; y++) { // right edge
if (ip.getPixel(width-1, y)==foreground)
edgePixels = true;
}
return edgePixels;
}
ImageProcessor expand(ImageProcessor ip, boolean hasEdgePixels) {
if (hasEdgePixels) {
ImageProcessor ip2 = ip.createProcessor(ip.getWidth()+2, ip.getHeight()+2);
if (foreground==0) {
ip2.setColor(255);
ip2.fill();
}
ip2.insert(ip, 1, 1);
//new ImagePlus("ip2", ip2).show();
return ip2;
} else
return ip;
}
ImageProcessor shrink(ImageProcessor ip, ImageProcessor ip2, boolean hasEdgePixels) {
if (hasEdgePixels) {
int width = ip.getWidth();
int height = ip.getHeight();
for (int y=0; y<height; y++)
for (int x=0; x<width; x++)
ip.putPixel(x, y, ip2.getPixel(x+1, y+1));
}
return ip;
}
// Binary fill by Gabriel Landini, G.Landini at bham.ac.uk
// 21/May/2008
void fill(ImageProcessor ip, int foreground, int background) {
int width = ip.getWidth();
int height = ip.getHeight();
FloodFiller ff = new FloodFiller(ip);
ip.setColor(127);
for (int y=0; y<height; y++) {
if (ip.getPixel(0,y)==background) ff.fill(0, y);
if (ip.getPixel(width-1,y)==background) ff.fill(width-1, y);
}
for (int x=0; x<width; x++){
if (ip.getPixel(x,0)==background) ff.fill(x, 0);
if (ip.getPixel(x,height-1)==background) ff.fill(x, height-1);
}
byte[] pixels = (byte[])ip.getPixels();
int n = width*height;
for (int i=0; i<n; i++) {
if (pixels[i]==127)
pixels[i] = (byte)background;
else
pixels[i] = (byte)foreground;
}
}
}
|
