ij.plugin.FITS_Writer Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of ij Show documentation
Show all versions of ij Show documentation
ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
package ij.plugin;
import java.io.*;
import java.util.Properties;
import ij.*;
import ij.io.*;
import ij.process.*;
import ij.measure.*;
/**
* This plugin saves a 16 or 32 bit image in FITS format. It is a stripped-down version of the SaveAs_FITS
* plugin from the collection of astronomical image processing plugins by Jennifer West at
* http://www.umanitoba.ca/faculties/science/astronomy/jwest/plugins.html.
*
*
Version 2010-11-23 : corrects 16-bit writing, adds BZERO & BSCALE updates (K.A. Collins, Univ. Louisville).
*
Version 2008-09-07 : preserves non-minimal FITS header if already present (F.V. Hessman, Univ. Goettingen).
*
Version 2008-12-15 : fixed END card recognition bug (F.V. Hessman, Univ. Goettingen).
*
Version 2019-11-03 : various updates (K.A. Collins, CfA-Harvard and Smithsonian).
*/
public class FITS_Writer implements PlugIn {
private int numCards = 0;
private Calibration cal;
private boolean unsigned16 = false;
private double bZero = 0.0;
private double bScale = 1.0;
public void run(String path) {
ImagePlus imp = IJ.getImage();
ImageProcessor ip = imp.getProcessor();
int numImages = imp.getImageStackSize();
int bitDepth = imp.getBitDepth();
if (bitDepth==24) {
IJ.error("RGB images are not supported");
return;
}
// GET PATH
if (path == null || path.trim().length() == 0) {
String title = "image.fits";
SaveDialog sd = new SaveDialog("Write FITS image",title,".fits");
path = sd.getDirectory()+sd.getFileName();
}
// GET FILE
File f = new File(path);
String directory = f.getParent()+File.separator;
String name = f.getName();
if (f.exists()) f.delete();
int numBytes = 0;
cal = imp.getCalibration();
unsigned16 = (bitDepth==16 && cal.getFunction()==Calibration.NONE && cal.getCoefficients()==null);
// GET IMAGE
if (bitDepth==8) {
numBytes = 1;
if (cal.getFunction()!=Calibration.NONE && cal.getCoefficients()!=null) {
bZero = cal.getCoefficients()[0];
if (cal.getCoefficients()[1] != 0) bScale = cal.getCoefficients()[1];
}
} else if (ip instanceof ShortProcessor) {
numBytes = 2;
if (unsigned16) {
bZero = 32768.0;
bScale = 1.0;
} else {
if (cal.getCoefficients()[1] != 0) bScale = cal.getCoefficients()[1];
bZero = cal.getCoefficients()[0] + (32768.0*bScale);
}
} else if (ip instanceof FloatProcessor) {
numBytes = 4; //float processor does not support calibration - data values are shifted and scaled in FITS_Reader
bZero = 0.0; //float values are written back out without shifting
bScale = 1.0; //and without scaling
}
int fillerLength = 2880 - ( (numBytes * imp.getWidth() * imp.getHeight()) % 2880 );
// WRITE FITS HEADER
String[] hdr = getHeader(imp);
// if (hdr == null)
// createHeader(path, ip, numBytes);
// else
createHeader(hdr, path, ip, numBytes);
// WRITE DATA
writeData(path, ip);
char[] endFiller = new char[fillerLength];
appendFile(endFiller, path);
}
// /**
// * Creates a FITS header for an image which doesn't have one already.
// */
// void createHeader(String path, ImageProcessor ip, int numBytes) {
//
// String bitperpix = "";
// if (numBytes==2) {bitperpix = " 16";}
// else if (numBytes==4) {bitperpix = " -32";}
// else if (numBytes==1) {bitperpix = " 8";}
// appendFile(writeCard("SIMPLE", " T", "Created by ImageJ FITS_Writer"), path);
// appendFile(writeCard("BITPIX", bitperpix, "number of bits per data pixel"), path);
// appendFile(writeCard("NAXIS", " 2", "number of data axes"), path);
// appendFile(writeCard("NAXIS1", " "+ip.getWidth(), "length of data axis 1"), path);
// appendFile(writeCard("NAXIS2", " "+ip.getHeight(), "length of data axis 2"), path);
// if (bZero != 0 || bScale != 1.0)
// {
// appendFile(writeCard("BZERO", ""+bZero, "data range offset"), path);
// appendFile(writeCard("BSCALE", ""+bScale, "scaling factor"), path);
// }
//
// int fillerSize = 2880 - ((numCards*80+3) % 2880);
// char[] end = new char[3];
// end[0] = 'E'; end[1] = 'N'; end[2] = 'D';
// char[] filler = new char[fillerSize];
// for (int i = 0; i < fillerSize; i++)
// filler[i] = ' ';
// appendFile(end, path);
// appendFile(filler, path);
// }
/**
* Writes one line of a FITS header
*/
char[] writeCard(String title, String value, String comment) {
char[] card = new char[80];
for (int i = 0; i < 80; i++)
card[i] = ' ';
s2ch(title, card, 0);
card[8] = '=';
s2ch(value, card, 10);
card[31] = '/';
card[32] = ' ';
s2ch(comment, card, 33);
numCards++;
return card;
}
void writeCard(char[] line, String path) {
appendFile(line, path);
numCards++;
}
/**
* Converts a String to a char[]
*/
void s2ch (String str, char[] ch, int offset) {
int j = 0;
for (int i = offset; i < 80 && i < str.length()+offset; i++)
ch[i] = str.charAt(j++);
}
/**
* Appends 'line' to the end of the file specified by 'path'.
*/
void appendFile(char[] line, String path) {
try {
FileWriter output = new FileWriter(path, true);
output.write(line);
output.close();
} catch (IOException e) {
IJ.showStatus("Error writing file!");
return;
}
}
/**
* Appends the data of the current image to the end of the file specified by path.
*/
void writeData(String path, ImageProcessor ip) {
int w = ip.getWidth();
int h = ip.getHeight();
if (ip instanceof ByteProcessor) {
byte[] pixels = (byte[])ip.getPixels();
try {
DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path,true)));
for (int i = h - 1; i >= 0; i-- )
for (int j = i*w; j < w*(i+1); j++)
dos.writeByte(pixels[j]);
dos.close();
} catch (IOException e) {
IJ.showStatus("Error writing file!");
return;
}
} else if (ip instanceof ShortProcessor) {
short[] pixels = (short[])ip.getPixels();
try {
DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path,true)));
for (int i = h - 1; i >= 0; i-- )
for (int j = i*w; j < w*(i+1); j++)
dos.writeShort(pixels[j]^0x8000);
dos.close();
} catch (IOException e) {
IJ.showStatus("Error writing file!");
return;
}
} else if (ip instanceof FloatProcessor) {
float[] pixels = (float[])ip.getPixels();
try {
DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path,true)));
for (int i = h - 1; i >= 0; i-- )
for (int j = i*w; j < w*(i+1); j++)
dos.writeFloat(pixels[j]);
dos.close();
} catch (IOException e) {
IJ.showStatus("Error writing file!");
return;
}
}
}
/**
* Extracts the original FITS header from the Properties object of the
* ImagePlus image (or from the current slice label in the case of an ImageStack)
* and returns it as an array of String objects representing each card.
*
* Taken from the ImageJ astroj package (www.astro.physik.uni-goettingen.de/~hessman/ImageJ/Astronomy)
*
* @param img The ImagePlus image which has the FITS header in it's "Info" property.
*/
public static String[] getHeader (ImagePlus img) {
String content = null;
int depth = img.getStackSize();
if (depth == 1) {
Properties props = img.getProperties();
if (props == null)
return null;
content = (String)props.getProperty ("Info");
}
else if (depth > 1) {
int slice = img.getCurrentSlice();
ImageStack stack = img.getStack();
content = stack.getSliceLabel(slice);
if (content == null) {
Properties props = img.getProperties();
if (props == null)
return null;
content = (String)props.getProperty ("Info");
}
}
if (content == null)
return null;
// PARSE INTO LINES
String[] lines = content.split("\n");
// FIND "SIMPLE" AND "END" KEYWORDS
int istart = 0;
for (; istart < lines.length; istart++) {
if (lines[istart].startsWith("SIMPLE") ) break;
}
if (istart == lines.length) return null;
int iend = istart+1;
for (; iend < lines.length; iend++) {
String s = lines[iend].trim();
if ( s.equals ("END") || s.startsWith ("END ") ) break;
}
if (iend >= lines.length) return null;
int l = iend-istart+1;
String header = "";
for (int i=0; i < l; i++)
header += lines[istart+i]+"\n";
return header.split("\n");
}
/**
* Converts a string into an 80-char array.
*/
char[] eighty(String s) {
char[] c = new char[80];
int l=s.length();
for (int i=0; i < l && i < 80; i++)
c[i]=s.charAt(i);
if (l < 80) {
for (; l < 80; l++) c[l]=' ';
}
return c;
}
/**
* Copies the image header contained in the image's Info property.
*/
void createHeader(String[] hdr, String path, ImageProcessor ip, int numBytes) {
String bitperpix = "";
int imw=ip.getWidth();
int imh=ip.getHeight();
String wbuf = " ";
String hbuf = " ";
if (imw < 10000)
wbuf = wbuf + " ";
if (imw < 1000)
wbuf = wbuf + " ";
if (imw < 100)
wbuf = wbuf + " ";
if (imw < 10)
wbuf = wbuf + " ";
if (imh < 10000)
hbuf = hbuf + " ";
if (imh < 1000)
hbuf = hbuf + " ";
if (imh < 100)
hbuf = hbuf + " ";
if (imh < 10)
hbuf = hbuf + " ";
// THESE KEYWORDS NEED TO BE MADE CONFORMAL WITH THE PRESENT IMAGE
if (numBytes==2) {bitperpix = " 16";}
else if (numBytes==4) {bitperpix = " -32";}
else if (numBytes==1) {bitperpix = " 8";}
appendFile(writeCard("SIMPLE", " T", "Created by ImageJ FITS_Writer"), path);
appendFile(writeCard("BITPIX", bitperpix, "number of bits per data pixel"), path);
appendFile(writeCard("NAXIS", " 2", "number of data axes"), path);
appendFile(writeCard("NAXIS1", wbuf + imw, "length of data axis 1"), path);
appendFile(writeCard("NAXIS2", hbuf + imh, "length of data axis 2"), path);
if (bZero != 0 || bScale != 1.0) {
appendFile(writeCard("BZERO", ""+bZero, "data range offset"), path);
appendFile(writeCard("BSCALE", ""+bScale, "scaling factor"), path);
}
if (hdr != null) {
// APPEND THE REST OF THE HEADER IF ONE EXISTS
char[] card;
for (int i=0; i < hdr.length; i++) {
String s = hdr[i];
card = eighty(s);
if (!s.startsWith("SIMPLE") &&
!s.startsWith("BITPIX") &&
!s.startsWith("NAXIS") &&
!s.startsWith("BZERO") &&
!s.startsWith("BSCALE") &&
!s.startsWith("END") &&
s.trim().length() > 1) {
writeCard(card, path);
}
}
}
// FINISH OFF THE HEADER
int fillerSize = 2880 - ((numCards*80+3) % 2880);
char[] end = new char[3];
end[0] = 'E'; end[1] = 'N'; end[2] = 'D';
char[] filler = new char[fillerSize];
for (int i = 0; i < fillerSize; i++)
filler[i] = ' ';
appendFile(end, path);
appendFile(filler, path);
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy