//
// UBMReader.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.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;

/**
 * UBMReader is the file format reader for UBM .pr3 files.
 *
 * <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/UBMReader.java">Trac</a>,
 * <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/UBMReader.java;hb=HEAD">Gitweb</a></dd></dl>
 */
public class UBMReader extends FormatReader {

  // -- Constants --

  public static final int HEADER_SIZE = 128;

  // -- Fields --

  private int padding;

  // -- Constructor --

  /** Constructs a new UBM reader. */
  public UBMReader() {
    super("UBM", "pr3");
    domains = new String[] {FormatTools.SEM_DOMAIN};
  }

  // -- IFormatReader API methods --

  /**
   * @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);
    readPlane(in, x, y, w, h, padding, buf);
    return buf;
  }

  /* @see loci.formats.IFormatReader#close(boolean) */
  public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (!fileOnly) {
      padding = 0;
    }
  }

  // -- 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);

    core[0].littleEndian = true;
    in.order(isLittleEndian());

    in.seek(44);

    core[0].sizeX = in.readInt();
    core[0].sizeY = in.readInt();

    core[0].pixelType = FormatTools.UINT32;
    core[0].sizeZ = 1;
    core[0].sizeC = 1;
    core[0].sizeT = 1;
    core[0].imageCount = 1;
    core[0].dimensionOrder = "XYZCT";

    padding =
      (int) ((in.length() - FormatTools.getPlaneSize(this)) / (getSizeY() * 4));
    addGlobalMeta("Padding bytes", padding);

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    MetadataTools.setDefaultCreationDate(store, id, 0);
  }

}