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
|
package ij.plugin;
import java.awt.*;
import java.io.*;
import java.util.zip.GZIPInputStream;
import ij.*;
import ij.io.*;
import ij.process.*;
import ij.measure.*;
/** Opens and displays FITS images. The FITS format is
* described at "http://fits.gsfc.nasa.gov/fits_standard.html".
* Add setOption("FlipFitsImages",false) to the
* Edit/Options/Startup dialog to have FITS images not
* flipped vertically.
*/
public class FITS_Reader extends ImagePlus implements PlugIn {
private static boolean flipImages = true;
public void run(String arg) {
OpenDialog od = new OpenDialog("Open FITS...", arg);
String directory = od.getDirectory();
String fileName = od.getFileName();
if (fileName==null)
return;
IJ.showStatus("Opening: " + directory + fileName);
FitsDecoder fd = new FitsDecoder(directory, fileName);
FileInfo fi = null;
try {
fi = fd.getInfo();
} catch (IOException e) {}
if (fi!=null && fi.width>0 && fi.height>0 && fi.offset>0) {
FileOpener fo = new FileOpener(fi);
ImagePlus imp = fo.openImage();
if (flipImages) {
if (fi.nImages==1) {
ImageProcessor ip = imp.getProcessor();
ip.flipVertical(); // origin is at bottom left corner
setProcessor(fileName, ip);
} else {
ImageStack stack = imp.getStack(); // origin is at bottom left corner
for(int i=1; i<=stack.getSize(); i++)
stack.getProcessor(i).flipVertical();
setStack(fileName, stack);
}
}
setStack(fileName, imp.getStack());
Calibration cal = imp.getCalibration();
if (fi.fileType==FileInfo.GRAY16_SIGNED && fd.bscale==1.0 && fd.bzero==32768.0)
cal.setFunction(Calibration.NONE, null, "Gray Value");
setCalibration(cal);
setProperty("Info", fd.getHeaderInfo());
setFileInfo(fi); // needed for File->Revert
if (arg.equals("")) show();
} else
IJ.error("This does not appear to be a FITS file.");
IJ.showStatus("");
}
public static void flipImages(boolean flip) {
flipImages = flip;
}
}
class FitsDecoder {
private String directory, fileName;
private DataInputStream f;
private StringBuffer info = new StringBuffer(512);
double bscale, bzero;
public FitsDecoder(String directory, String fileName) {
this.directory = directory;
this.fileName = fileName;
}
FileInfo getInfo() throws IOException {
FileInfo fi = new FileInfo();
fi.fileFormat = FileInfo.FITS;
fi.fileName = fileName;
fi.directory = directory;
fi.width = 0;
fi.height = 0;
fi.offset = 0;
InputStream is = new FileInputStream(directory + fileName);
if (fileName.toLowerCase().endsWith(".gz")) is = new GZIPInputStream(is);
f = new DataInputStream(is);
String line = getString(80);
info.append(line+"\n");
if (!line.startsWith("SIMPLE"))
{f.close(); return null;}
int count = 1;
while ( true ) {
count++;
line = getString(80);
info.append(line+"\n");
// Cut the key/value pair
int index = line.indexOf ( "=" );
// Strip out comments
int commentIndex = line.indexOf ( "/", index );
if ( commentIndex < 0 )
commentIndex = line.length ();
// Split that values
String key;
String value;
if ( index >= 0 ) {
key = line.substring ( 0, index ).trim ();
value = line.substring ( index + 1, commentIndex ).trim ();
} else {
key = line.trim ();
value = "";
}
// Time to stop ?
if (key.equals ("END") ) break;
// Look for interesting information
if (key.equals("BITPIX")) {
int bitsPerPixel = Integer.parseInt ( value );
if (bitsPerPixel==8)
fi.fileType = FileInfo.GRAY8;
else if (bitsPerPixel==16)
fi.fileType = FileInfo.GRAY16_SIGNED;
else if (bitsPerPixel==32)
fi.fileType = FileInfo.GRAY32_INT;
else if (bitsPerPixel==-32)
fi.fileType = FileInfo.GRAY32_FLOAT;
else if (bitsPerPixel==-64)
fi.fileType = FileInfo.GRAY64_FLOAT;
else {
IJ.error("BITPIX must be 8, 16, 32, -32 (float) or -64 (double).");
f.close();
return null;
}
} else if (key.equals("NAXIS1"))
fi.width = Integer.parseInt ( value );
else if (key.equals("NAXIS2"))
fi.height = Integer.parseInt( value );
else if (key.equals("NAXIS3")) //for multi-frame fits
fi.nImages = Integer.parseInt ( value );
else if (key.equals("BSCALE"))
bscale = parseDouble ( value );
else if (key.equals("BZERO"))
bzero = parseDouble ( value );
else if (key.equals("CDELT1"))
fi.pixelWidth = parseDouble ( value );
else if (key.equals("CDELT2"))
fi.pixelHeight = parseDouble ( value );
else if (key.equals("CDELT3"))
fi.pixelDepth = parseDouble ( value );
else if (key.equals("CTYPE1"))
fi.unit = value;
if (count>360 && fi.width==0)
{f.close(); return null;}
}
if (fi.pixelWidth==1.0 && fi.pixelDepth==1)
fi.unit = "pixel";
f.close();
fi.offset = 2880+2880*(((count*80)-1)/2880);
return fi;
}
String getString(int length) throws IOException {
byte[] b = new byte[length];
f.readFully(b);
if (IJ.debugMode)
IJ.log(new String(b));
return new String(b);
}
int getInteger(String s) {
s = s.substring(10, 30);
s = s.trim();
return Integer.parseInt(s);
}
double parseDouble(String s) throws NumberFormatException {
Double d = Double.valueOf(s);
return d.doubleValue();
}
String getHeaderInfo() {
return new String(info);
}
}
|
