/*
* #%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.DateTools;
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.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
/**
* BioRadGelReader is the file format reader for Bio-Rad gel files.
*/
public class BioRadGelReader extends FormatReader {
// -- Constants --
private static final int MAGIC_BYTES = 0xafaf;
private static final long PIXEL_OFFSET = 59654;
private static final long START_OFFSET = 160;
private static final long BASE_OFFSET = 352;
// -- Fields --
private long offset;
private long diff;
// -- Constructor --
/** Constructs a new Bio-Rad gel reader. */
public BioRadGelReader() {
super("Bio-Rad GEL", "1sc");
domains = new String[] {FormatTools.GEL_DOMAIN};
suffixNecessary = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 2;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readShort() & 0xffff) == MAGIC_BYTES;
}
/**
* @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);
int planeSize = FormatTools.getPlaneSize(this);
if (PIXEL_OFFSET + planeSize < in.length()) {
// offsets were determined by trial and error, and may not be 100% correct
if (diff < 0) {
in.seek(0x379d1);
}
else if (diff == 0) {
in.seek(PIXEL_OFFSET);
}
else if (in.length() - planeSize > 61000) {
in.seek(PIXEL_OFFSET - 196);
while (!in.readString(3).equals("scn")) {
in.seek(in.getFilePointer() - 2);
}
in.skipBytes(91);
int len = in.readShort();
in.skipBytes(len);
in.skipBytes(32);
}
else in.seek(in.length() - planeSize);
}
else in.seek(in.length() - planeSize);
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int pixel = bpp * getSizeC();
in.skipBytes(pixel * getSizeX() * (getSizeY() - h - y));
for (int row=h-1; row>=0; row--) {
in.skipBytes(x * pixel);
in.read(buf, row * w * pixel, w * pixel);
in.skipBytes(pixel * (getSizeX() - w - x));
}
return buf;
}
// -- 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);
String check = in.readString(48);
if (check.indexOf("Intel Format") != -1) {
in.order(true);
}
in.seek(START_OFFSET);
boolean codeFound = false;
int skip = 0;
while (!codeFound) {
short code = in.readShort();
if (code == 0x81) codeFound = true;
short length = in.readShort();
in.skipBytes(2 + 2 * length);
if (codeFound) {
skip = (in.readShort() & 0xffff) - 32;
}
else {
if (length == 1) in.skipBytes(12);
else if (length == 2) in.skipBytes(10);
}
}
long baseFP = in.getFilePointer();
diff = BASE_OFFSET - baseFP;
skip += diff;
double physicalWidth = 0d, physicalHeight = 0d;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (baseFP + skip - 8187 > 0) {
in.seek(baseFP + skip - 8187);
String scannerName = in.readCString();
in.skipBytes(8);
in.readCString();
in.skipBytes(8);
String imageArea = in.readCString();
imageArea = imageArea.substring(imageArea.indexOf(":") + 1).trim();
int xIndex = imageArea.indexOf("x");
if (xIndex > 0) {
int space = imageArea.indexOf(" ");
if (space >= 0) {
String width = imageArea.substring(1, space);
int nextSpace = imageArea.indexOf(" ", xIndex + 2);
if (nextSpace > xIndex) {
String height = imageArea.substring(xIndex + 1, nextSpace);
physicalWidth = Double.parseDouble(width.trim()) * 1000;
physicalHeight = Double.parseDouble(height.trim()) * 1000;
}
}
}
}
}
in.seek(baseFP + skip - 298);
String date = in.readString(17);
date = DateTools.formatDate(date, "dd-MMM-yyyy HH:mm");
in.skipBytes(73);
String scannerName = in.readCString();
addGlobalMeta("Scanner name", scannerName);
in.seek(baseFP + skip);
CoreMetadata m = core.get(0);
m.sizeX = in.readShort() & 0xffff;
m.sizeY = in.readShort() & 0xffff;
if (getSizeX() * getSizeY() > in.length()) {
in.order(true);
in.seek(in.getFilePointer() - 4);
m.sizeX = in.readShort();
m.sizeY = in.readShort();
}
in.skipBytes(2);
int bpp = in.readShort();
m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
offset = in.getFilePointer();
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYCZT";
m.rgb = false;
m.interleaved = false;
m.indexed = false;
m.littleEndian = in.isLittleEndian();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Length sizeX =
FormatTools.getPhysicalSizeX(physicalWidth / getSizeX());
Length sizeY =
FormatTools.getPhysicalSizeY(physicalHeight / getSizeY());
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
}