//
// SBIGReader.java
//

/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

package loci.formats.in;

import java.io.IOException;

import loci.common.DataTools;
import loci.common.DateTools;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;

/**
 * SBIGReader is the file format reader for SBIG files.
 * See the specification at http://www.sbig.com/pdffiles/file.format.pdf.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/SBIGReader.java">Trac</a>,
 * <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/SBIGReader.java;hb=HEAD">Gitweb</a></dd></dl>
 */
public class SBIGReader extends FormatReader {

  // -- Constants --

  private static final long HEADER_SIZE = 2048;
  private static final String DATE_FORMAT = "MM/dd/yy HH:mm:ss";

  // -- Fields --

  private boolean compressed;

  // -- Constructor --

  /** Constructs a new SBIG reader. */
  public SBIGReader() {
    super("SBIG", "");
    domains = new String[] {FormatTools.ASTRONOMY_DOMAIN};
    suffixSufficient = false;
    suffixNecessary = false;
  }

  // -- IFormatReader API methods --

  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = (int) HEADER_SIZE;
    final int checkLen = 32;
    if (!FormatTools.validStream(stream, blockLen, false)) return false;
    return stream.readString(checkLen).indexOf("Image") > 0;
  }

  /**
   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
   */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
    throws FormatException, IOException
  {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    in.seek(HEADER_SIZE);
    int width = getSizeX() * 2;

    if (compressed) {
      for (int row=0; row<h; row++) {
        int rowLen = in.readShort();
        if (rowLen == width) {
          in.read(buf, row * width, rowLen);
        }
        else {
          int bufferPointer = row * width;
          in.read(buf, bufferPointer, 2);
          while (bufferPointer - row * width < width - 2) {
            short prevPixel =
              DataTools.bytesToShort(buf, bufferPointer, isLittleEndian());
            bufferPointer += 2;
            byte check = in.readByte();
            if (check == -128) {
              in.read(buf, bufferPointer, 2);
            }
            else {
              prevPixel += check;
              DataTools.unpackBytes(prevPixel, buf, bufferPointer, 2,
                isLittleEndian());
            }
          }
        }
      }
    }
    else readPlane(in, x, y, w, h, buf);
    return buf;
  }

  /* @see loci.formats.IFormatReader#close(boolean) */
  public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (!fileOnly) {
      compressed = false;
    }
  }

  // -- Internal FormatReader API methods --

  /* @see loci.formats.FormatReader#initFile(String) */
  protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);

    Double temperature = null;
    Double sizeX = null, sizeY = null;
    String date = null, description = null;

    String[] lines = DataTools.readFile(currentId).split("\n");
    for (String line : lines) {
      line = line.trim();
      int eq = line.indexOf("=");
      if (eq != -1) {
        String key = line.substring(0, eq).trim();
        String value = line.substring(eq + 1).trim();
        addGlobalMeta(key, value);

        if (key.equals("Width")) {
          core[0].sizeX = Integer.parseInt(value);
        }
        else if (key.equals("Height")) {
          core[0].sizeY = Integer.parseInt(value);
        }
        else if (key.equals("Note")) {
          description = value;
        }
        else if (key.equals("X_pixel_size")) {
          sizeX = new Double(value) * 1000;
        }
        else if (key.equals("Y_pixel_size")) {
          sizeY = new Double(value) * 1000;
        }
        else if (key.equals("Date")) {
          date = value;
        }
        else if (key.equals("Time")) {
          date += " " + value;
        }
      }
      else if (line.indexOf("Compressed") != -1) {
        compressed = true;
      }
      else if (line.equals("End")) break;
    }

    core[0].pixelType = FormatTools.UINT16;
    core[0].littleEndian = true;
    core[0].rgb = false;
    core[0].sizeZ = 1;
    core[0].sizeC = 1;
    core[0].sizeT = 1;
    core[0].imageCount = 1;
    core[0].dimensionOrder = "XYZCT";

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);

    if (date != null) {
      store.setImageAcquiredDate(DateTools.formatDate(date, DATE_FORMAT), 0);
    }
    else MetadataTools.setDefaultCreationDate(store, currentId, 0);

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      store.setPixelsPhysicalSizeX(sizeX, 0);
      store.setPixelsPhysicalSizeY(sizeY, 0);
      store.setImageDescription(description, 0);
    }
  }

}

@@ -2525,16 +2525,32 @@
 ndexOf(%22
+ST-7 Compressed 
 Image%22) 
@@ -2550,16 +2550,17 @@
 mage%22) %3E
+=
  0;%0A  %7D%0A

Make isThisType(...) more strict.