BurleighReader.java

/*
 * #%L
 * OME Bio-Formats package for reading and converting biological file formats.
 * %%
 * Copyright (C) 2005 - 2015 Open Microscopy Environment:
 *   - Board of Regents of the University of Wisconsin-Madison
 *   - Glencoe Software, Inc.
 *   - University of Dundee
 * %%
 * 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, see
 * <http://www.gnu.org/licenses/gpl-2.0.html>.
 * #L%
 */

package loci.formats.in;

import java.io.IOException;

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

import ome.xml.model.primitives.PositiveFloat;
import ome.units.quantity.Length;

/**
 * BurleighReader is the file format reader for Burleigh .img files.
 */
public class BurleighReader extends FormatReader {

  // -- Fields --

  private int pixelsOffset;

  // -- Constructor --

  /** Constructs a new Burleigh reader. */
  public BurleighReader() {
    super("Burleigh", "img");
    domains = new String[] {FormatTools.SEM_DOMAIN};
    suffixSufficient = false;
    suffixNecessary = false;
  }

  // -- IFormatReader API methods --

  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
  @Override
  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = 4;
    if (!FormatTools.validStream(stream, blockLen, false)) return false;
    byte[] magic = new byte[blockLen];
    stream.read(magic);
    return magic[0] == 0x66 && magic[1] == 0x66 && magic[3] == 0x40 &&
     (magic[2] == 0x46 || magic[2] == 0x06);
  }

  /**
   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
   */
  @Override
  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(pixelsOffset);
    readPlane(in, x, y, w, h, buf);
    return buf;
  }

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

  // -- Internal FormatReader API methods --

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

    CoreMetadata m = core.get(0);

    m.littleEndian = true;
    in.order(isLittleEndian());

    int version = (int) in.readFloat() - 1;

    m.sizeX = in.readShort();
    m.sizeY = in.readShort();

    double xSize = 0d, ySize = 0d, zSize = 0d;

    pixelsOffset = version == 1 ? 8 : 260;

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      double timePerPixel = 0d;
      int mode = 0, gain = 0, mag = 0;
      double sampleVolts = 0d, tunnelCurrent = 0d;
      if (version == 1) {
        in.seek(in.length() - 40);
        in.skipBytes(12);
        xSize = in.readInt();
        ySize = in.readInt();
        zSize = in.readInt();
        timePerPixel = in.readShort() * 50;
        mag = in.readShort();

        switch (mag) {
          case 3:
            mag = 10;
            break;
          case 4:
            mag = 50;
            break;
          case 5:
            mag = 250;
            break;
        }
        xSize /= mag;
        ySize /= mag;
        zSize /= mag;

        mode = in.readShort();
        gain = in.readShort();
        sampleVolts = in.readFloat() / 1000;
        tunnelCurrent = in.readFloat();
      }
      else if (version == 2) {
        in.skipBytes(14);
        xSize = in.readInt();
        ySize = in.readInt();
        zSize = in.readInt();
        mode = in.readShort();
        in.skipBytes(4);
        gain = in.readShort();
        timePerPixel = in.readShort() * 50;
        in.skipBytes(12);
        sampleVolts = in.readFloat();
        tunnelCurrent = in.readFloat();
        addGlobalMeta("Force", in.readFloat());
      }

      addGlobalMeta("Version", version);
      addGlobalMeta("Image mode", mode);
      addGlobalMeta("Z gain", gain);
      addGlobalMeta("Time per pixel (s)", timePerPixel);
      addGlobalMeta("Sample volts", sampleVolts);
      addGlobalMeta("Tunnel current", tunnelCurrent);
      addGlobalMeta("Magnification", mag);
    }

    m.pixelType = FormatTools.UINT16;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";

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

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      Length sizeX = FormatTools.getPhysicalSizeX(xSize / getSizeX());
      Length sizeY = FormatTools.getPhysicalSizeY(ySize / getSizeY());
      Length sizeZ = FormatTools.getPhysicalSizeZ(zSize / getSizeZ());
      if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
      }
      if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
      }
      if (sizeZ != null) {
        store.setPixelsPhysicalSizeZ(sizeZ, 0);
      }
    }
  }

}