/**
*
*/
package fr.unistra.pelican.algorithms.io;
import java.io.IOException;
import fr.unistra.pelican.Algorithm;
import fr.unistra.pelican.AlgorithmException;
import fr.unistra.pelican.BooleanImage;
import fr.unistra.pelican.ByteImage;
import fr.unistra.pelican.Image;
import fr.unistra.pelican.IntegerImage;
import fr.unistra.pelican.util.jFits.Fits;
import fr.unistra.pelican.util.jFits.FitsException;
import fr.unistra.pelican.util.jFits.FitsFile;
import fr.unistra.pelican.util.jFits.FitsHDUnit;
import fr.unistra.pelican.util.jFits.FitsHeader;
import fr.unistra.pelican.util.jFits.FitsKeyword;
import fr.unistra.pelican.util.jFits.FitsMatrix;
/**
* Save an image in fits file format.
* Can handle x,y and b dim.
* In case of multiband image, each band is saved in a standard fits image extension.
*
* If a header is provided, its correctness is NOT verified.
* If no header is provided, a suitable header is searched in image properties.
* If no header is found at all, a minimal header is generated automatically.
*
*
* @author Benjamin Perret
*
*/
public class FitsImageSave extends Algorithm {
/**
* File path, destination of saved image
*/
public String filename;
/**
* Image to save
*/
public Image inputImage;
/**
* Optional header
*/
public FitsHeader header;
/**
* Force to use a special bit per pixel as specified in {@link Fits}
*/
public int bitPix=-1;
/**
*
*/
public FitsImageSave() {
super.inputs="filename,inputImage";
super.options="bitPix,header";
super.outputs="";
}
/* (non-Javadoc)
* @see fr.unistra.pelican.Algorithm#launch()
*/
@Override
public void launch() throws AlgorithmException {
try{
FitsHDUnit [] hdus=new FitsHDUnit[inputImage.bdim];
for(int b=0;b<inputImage.bdim;b++)
{
FitsMatrix data=null;
switch (bitPix)
{
case Fits.BYTE:
data=getMatrixByte(inputImage,b);
break;
case Fits.SHORT:
data=getMatrixShort(inputImage,b);
break;
case Fits.INT:
data=getMatrixInt(inputImage,b);
break;
case Fits.FLOAT:
data=getMatrixFloat(inputImage,b);
break;
case Fits.DOUBLE:
data=getMatrixDouble(inputImage,b);
break;
default:
if(inputImage instanceof BooleanImage || inputImage instanceof ByteImage)
data=getMatrixByte(inputImage,b);
else if(inputImage instanceof IntegerImage)
data=getMatrixInt(inputImage,b);
else data=getMatrixDouble(inputImage,b);
}
FitsHeader head;
if(b==0)
{
if(header == null)
{
Object o = inputImage.properties.get(LoadFitsWithExtensions.HEADER_KEYWORD + b);
if (o!= null && o instanceof FitsHeader)
{
head=mergeHeader(data.getHeader(),(FitsHeader)o);
//System.out.println("Head found in properties for band " +b);
} else {
//System.out.println("Headder generated for " +b + " " +o);
head=data.getHeader();
}
} else {
head=header;
}
if(inputImage.bdim!=1)
head.insertKeywordAt(new FitsKeyword("EXTEND", true,"File may contain standard extension"), 5);
head.addKeyword(new FitsKeyword("COMMENT","Generated from PELICAN"));
}
else {
if(header == null)
{
Object o = inputImage.properties.get(LoadFitsWithExtensions.HEADER_KEYWORD + b);
if (o!= null && o instanceof FitsHeader)
{
head=mergeHeader(data.getHeader(),(FitsHeader)o);
//System.out.println("Head found in properties for band " +b);
} else {
//System.out.println("Headder generated for " +b + " " +o);
head=data.getHeader();
}
} else {
head=header;
}
head.setExtension(Fits.IMAGE);
}
if(b==0)
filterHeader(head);
hdus[b]=new FitsHDUnit(head,data);
}
FitsFile file = new FitsFile();
for(int b=0;b<inputImage.bdim;b++)
file.addHDUnit(hdus[b]);
file.writeFile(filename);
file.closeFile();}
catch (FitsException e)
{
throw new AlgorithmException("Fits Save error: " +e);
} catch (IOException e)
{
throw new AlgorithmException("Fits Save error: " +e);
}
}
private FitsHeader filterHeader(FitsHeader header)
{
String [] remove={"PCOUNT","GCOUNT"};
for(int i=0;i < header.getNoKeywords(); i++)
{
FitsKeyword kw= header.getKeyword(i);
boolean flag=true;
String name=kw.getName();
for(int j=0;j<remove.length;j++)
if(name.compareTo(remove[j])==0)
{
header.removeKeywordAt(i);
i--;
continue;
}
}
return header;
}
private FitsHeader mergeHeader(FitsHeader minimalHeader, FitsHeader complete)
{
String [] forbidden={"NAXIS","BITPIX","SIMPLE","EXTEND","NAXIS1","NAXIS2","NAXIS3"};
for(int i=0;i < complete.getNoKeywords(); i++)
{
FitsKeyword kw= complete.getKeyword(i);
boolean flag=true;
String name=kw.getName();
for(int j=0;j<forbidden.length;j++)
if(name.compareTo(forbidden[j])==0)
flag=false;
if(flag){
minimalHeader.addKeyword(kw);
//System.out.println("accept " + kw + " name : '"+kw.getName()+"'");
}
}
return minimalHeader;
}
private FitsMatrix getMatrixShort(Image im, int b) throws FitsException, IOException
{
int xdim=im.xdim;
int ydim=im.ydim;
int nax[]={xdim,ydim}; // dimensions
short dat [] =new short[xdim*ydim]; //donnï¿œes
for(int j=0;j<ydim;j++) // conversion des donnees et mise sous forme lineaire
for (int i=0;i<xdim;i++)
dat[j*im.xdim + i]=(short)im.getPixelXYBInt(i, ydim-j-1, b);
FitsMatrix data=new FitsMatrix(Fits.SHORT,nax); // fits matrix des bonnes dims
data.setShortValues(0, dat); // remplissage sans offset
return data;
}
private FitsMatrix getMatrixDouble(Image im, int b) throws FitsException, IOException
{
int xdim=im.xdim;
int ydim=im.ydim;
int nax[]={xdim,ydim}; // dimensions
double dat [] =new double[xdim*ydim]; //donnï¿œes
for(int j=0;j<ydim;j++) // conversion des donnees et mise sous forme lineaire
for (int i=0;i<xdim;i++)
dat[j*im.xdim + i]=im.getPixelXYBDouble(i, ydim-j-1, b);
FitsMatrix data=new FitsMatrix(Fits.DOUBLE,nax); // fits matrix des bonnes dims
data.setDoubleValues(0, dat); // remplissage sans offset
return data;
}
private FitsMatrix getMatrixFloat(Image im, int b) throws FitsException, IOException
{
int xdim=im.xdim;
int ydim=im.ydim;
int nax[]={xdim,ydim}; // dimensions
float dat [] =new float[xdim*ydim]; //donnï¿œes
for(int j=0;j<ydim;j++) // conversion des donnees et mise sous forme lineaire
for (int i=0;i<xdim;i++)
dat[j*im.xdim + i]=(float)im.getPixelXYBDouble(i, ydim-j-1, b);
FitsMatrix data=new FitsMatrix(Fits.FLOAT,nax); // fits matrix des bonnes dims
data.setFloatValues(0, dat); // remplissage sans offset
return data;
}
private FitsMatrix getMatrixByte(Image im, int b) throws FitsException, IOException
{
int xdim=im.xdim;
int ydim=im.ydim;
int nax[]={xdim,ydim}; // dimensions
short dat [] =new short[xdim*ydim]; //donnees
for(int j=0;j<ydim;j++) // conversion des donnees et mise sous forme lineaire
for (int i=0;i<xdim;i++)
dat[ j*im.xdim + i]=(short)im.getPixelXYBByte(i, ydim-j-1, b);
FitsMatrix data=new FitsMatrix(Fits.SHORT,nax); // fits matrix des bonnes dims
data.setShortValues(0, dat); // remplissage sans offset
return data;
}
private FitsMatrix getMatrixInt(Image im, int b) throws FitsException, IOException
{
int xdim=im.xdim;
int ydim=im.ydim;
int nax[]={xdim,ydim}; // dimensions
int dat [] =new int[xdim*ydim]; //donnees
for(int j=0;j<ydim;j++) // conversion des donnees et mise sous forme lineaire
for (int i=0;i<xdim;i++)
dat[j*im.xdim + i]=(short)im.getPixelXYBInt(i, ydim-j-1, b);
FitsMatrix data=new FitsMatrix(Fits.SHORT,nax); // fits matrix des bonnes dims
data.setIntValues(0, dat); // remplissage sans offset
return data;
}
public static void exec(String filename, Image inputImage)
{
(new FitsImageSave()).process(filename,inputImage);
}
public static void exec(String filename, Image inputImage, int bitPix)
{
(new FitsImageSave()).process(filename,inputImage,bitPix);
}
public static void exec(String filename, Image inputImage, FitsHeader header)
{
(new FitsImageSave()).process(filename,inputImage,-1,header) ;
}
public static void exec(String filename, Image inputImage, int bitPix,FitsHeader header)
{
(new FitsImageSave()).process(filename,inputImage,bitPix,header) ;
}
}