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.
 *
 * <br>Version 2010-11-23 : corrects 16-bit writing, adds BZERO & BSCALE updates (K.A. Collins, Univ. Louisville).
 * <br>Version 2008-09-07 : preserves non-minimal FITS header if already present (F.V. Hessman, Univ. Goettingen).
 * <br>Version 2008-12-15 : fixed END card recognition bug (F.V. Hessman, Univ. Goettingen).
 * <br>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);
        }

    }