//
// CoreMetadata.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 3 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;

import java.util.Hashtable;

/**
 * Encompasses core metadata values.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/CoreMetadata.java">Trac</a>,
 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/CoreMetadata.java">SVN</a></dd></dl>
 */
public class CoreMetadata {
  public int[] sizeX, sizeY, sizeZ, sizeC, sizeT;
  public int[] thumbSizeX, thumbSizeY;
  public int[] pixelType;
  public int[] imageCount;
  public int[][] cLengths;
  public String[][] cTypes;
  public String[] currentOrder;
  public boolean[] orderCertain, rgb, littleEndian, interleaved;
  public boolean[] indexed, falseColor, metadataComplete;
  public Hashtable[] seriesMetadata;

  public CoreMetadata(int series) {
    sizeX = new int[series];
    sizeY = new int[series];
    sizeZ = new int[series];
    sizeC = new int[series];
    sizeT = new int[series];
    thumbSizeX = new int[series];
    thumbSizeY = new int[series];
    pixelType = new int[series];
    imageCount = new int[series];
    cLengths = new int[series][];
    cTypes = new String[series][];
    currentOrder = new String[series];
    orderCertain = new boolean[series];
    rgb = new boolean[series];
    littleEndian = new boolean[series];
    interleaved = new boolean[series];
    indexed = new boolean[series];
    falseColor = new boolean[series];
    metadataComplete = new boolean[series];
    seriesMetadata = new Hashtable[series];
    for (int i=0; i<series; i++) seriesMetadata[i] = new Hashtable();
  }

}

//
// CoreMetadata.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 3 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;

import java.util.Hashtable;

/**
 * Encompasses core metadata values.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/CoreMetadata.java">Trac</a>,
 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/CoreMetadata.java">SVN</a></dd></dl>
 */
public class CoreMetadata {
  // TODO - Refactor this class to encapsulate core metadata for only one
  // series at a time, and use an array of CoreMetadata objects in FormatReader
  // instead. This approach is cleaner than the parallel arrays approach below.

  // We may also want to consider refactoring the FormatReader getter methods
  // that populate missing CoreMetadata fields on the fly
  // (getChannelDimLengths, getChannelDimTypes, getThumbSizeX, getThumbSizeY)
  // to avoid doing so -- one alternate approach would be to have this class
  // use getter methods instead of public fields.

  // Lastly, we should add javadoc comments to the fields in this class.

  public int[] sizeX, sizeY, sizeZ, sizeC, sizeT;
  public int[] thumbSizeX, thumbSizeY;
  public int[] pixelType;
  public int[] imageCount;
  public int[][] cLengths;
  public String[][] cTypes;
  public String[] currentOrder;
  public boolean[] orderCertain, rgb, littleEndian, interleaved;
  public boolean[] indexed, falseColor, metadataComplete;
  public Hashtable[] seriesMetadata;

  public CoreMetadata(int series) {
    sizeX = new int[series];
    sizeY = new int[series];
    sizeZ = new int[series];
    sizeC = new int[series];
    sizeT = new int[series];
    thumbSizeX = new int[series];
    thumbSizeY = new int[series];
    pixelType = new int[series];
    imageCount = new int[series];
    cLengths = new int[series][];
    cTypes = new String[series][];
    currentOrder = new String[series];
    orderCertain = new boolean[series];
    rgb = new boolean[series];
    littleEndian = new boolean[series];
    interleaved = new boolean[series];
    indexed = new boolean[series];
    falseColor = new boolean[series];
    metadataComplete = new boolean[series];
    seriesMetadata = new Hashtable[series];
    for (int i=0; i<series; i++) seriesMetadata[i] = new Hashtable();
  }

}

Add some "to do" notes.