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
|
package ij.plugin;
import java.awt.*;
import java.awt.image.*;
import java.util.Vector;
import java.io.*;
import ij.*;
import ij.process.*;
import ij.io.*;
import ij.gui.*;
import ij.measure.ResultsTable;
/** Writes the XY coordinates and pixel values of all non-background
pixels to a tab-delimited text file. Backround is assumed to be the
value of the pixel in the upper left corner of the image. */
public class XYCoordinates implements PlugIn {
private static boolean processStack;
private static boolean invertY;
private static boolean suppress;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
Roi roi = imp.getRoi();
String options = Macro.getOptions();
boolean legacyMacro = IJ.isMacro() && options!=null && options.contains("background=");
if (roi!=null && roi.isArea() && !legacyMacro) {
saveSelectionCoordinates(imp);
return;
}
ImageProcessor ip = imp.getProcessor();
int width = imp.getWidth();
int height = imp.getHeight();
double background = ip.getPixelValue(0,0);
String bg = " \n";
boolean rgb = imp.getBitDepth()==24;
if (rgb) {
int c = ip.getPixel(0,0);
int r = (c&0xff0000)>>16;
int g = (c&0xff00)>>8;
int b = c&0xff;
bg = r+","+g+","+b;
bg = " \n Background value: " + bg + "\n";
}
imp.deleteRoi();
int slices = imp.getStackSize();
String msg =
"This plugin writes to a text file the XY coordinates and\n"
+ "pixel value of all non-background pixels. Backround\n"
+ "defaults to be the value of the pixel in the upper\n"
+ "left corner of the image.\n \n"
+ "If there is a selection, this dialog is skipped and the\n"
+ "coordinates and values of pixels in the selection are saved.\n";
GenericDialog gd = new GenericDialog("Save XY Coordinates");
gd.setInsets(0, 20, 0);
gd.addMessage(msg, null, Color.darkGray);
int digits = (int)background==background?0:4;
if (!rgb) {
gd.setInsets(5, 35, 3);
gd.addNumericField("Background value:", background, digits);
}
gd.setInsets(10, 35, 0);
gd.addCheckbox("Invert y coordinates off (0 at top of image)", invertY);
gd.setInsets(0, 35, 0);
gd.addCheckbox("Suppress Log output", suppress);
if (slices>1) {
gd.setInsets(0, 35, 0);
gd.addCheckbox("Process all "+slices+" images", processStack);
}
gd.showDialog();
if (gd.wasCanceled())
return;
if (!rgb)
background = gd.getNextNumber();
invertY = gd.getNextBoolean();
suppress = gd.getNextBoolean();
if (slices>1)
processStack = gd.getNextBoolean();
else
processStack = false;
if (!processStack) slices = 1;
SaveDialog sd = new SaveDialog("Save Coordinates as Text...", imp.getTitle(), ".txt");
String name = sd.getFileName();
if (name == null)
return;
String directory = sd.getDirectory();
PrintWriter pw = null;
try {
FileOutputStream fos = new FileOutputStream(directory+name);
BufferedOutputStream bos = new BufferedOutputStream(fos);
pw = new PrintWriter(bos);
}
catch (IOException e) {
IJ.error("Save XY Coordinates", "Error saving coordinates:\n "+e.getMessage());
return;
}
IJ.showStatus("Saving coordinates...");
int count = 0;
float v;
int c,r,g,b;
int type = imp.getType();
ImageStack stack = imp.getStack();
boolean nanBackground = Double.isNaN(background);
for (int z=0; z<slices; z++) {
if (slices>1) ip = stack.getProcessor(z+1);
String zstr = slices>1?z+"\t":"";
for (int i=0; i<height; i++) {
int y = invertY?i:height-1-i;
for (int x=0; x<width; x++) {
v = ip.getPixelValue(x,y);
if (v!=background && !(nanBackground&&Double.isNaN(v))) {
if (type==ImagePlus.GRAY32)
pw.println(x+"\t"+(invertY?y:height-1-y)+"\t"+zstr+v);
else if (rgb) {
c = ip.getPixel(x,y);
r = (c&0xff0000)>>16;
g = (c&0xff00)>>8;
b = c&0xff;
pw.println(x+"\t"+(invertY?y:height-1-y)+"\t"+zstr+r+"\t"+g+"\t"+b);
} else
pw.println(x+"\t"+(invertY?y:height-1-y)+"\t"+zstr+(int)v);
count++;
}
} // x
if (slices==1&&y%10==0) IJ.showProgress((double)(height-y)/height);
} // y
if (slices>1) IJ.showProgress(z+1, slices);
String img = slices>1?"-"+(z+1):"";
if (!suppress)
IJ.log(imp.getTitle() + img+": " + count + " pixels (" + IJ.d2s(count*100.0/(width*height)) + "%)\n");
count = 0;
} // z
IJ.showProgress(1.0);
IJ.showStatus("");
pw.close();
}
private void saveSelectionCoordinates(ImagePlus imp) {
SaveDialog sd = new SaveDialog("Save Coordinates as Text...", imp.getTitle(), ".csv");
String name = sd.getFileName();
if (name == null)
return;
String dir = sd.getDirectory();
Roi roi = imp.getRoi();
ImageProcessor ip = imp.getProcessor();
ImageProcessor mask = roi.getMask();
Rectangle r = roi.getBounds();
ResultsTable rt = new ResultsTable();
boolean rgb = imp.getBitDepth()==24;
for (int y=0; y<r.height; y++) {
for (int x=0; x<r.width; x++) {
if (mask==null || mask.getPixel(x,y)!=0) {
rt.incrementCounter();
rt.addValue("X", r.x+x);
rt.addValue("Y", r.y+y);
if (rgb) {
int c = ip.getPixel(r.x+x,r.y+y);
rt.addValue("Red", (c&0xff0000)>>16);
rt.addValue("Green", (c&0xff00)>>8);
rt.addValue("Blue", c&0xff);
} else
rt.addValue("Value", ip.getPixelValue(r.x+x,r.y+y));
}
}
}
rt.save(dir+name);
}
}
|
