//
// MRCReader.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 java.math.BigInteger;
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;
import ome.xml.model.primitives.PositiveFloat;
/**
* MRCReader is the file format reader for MRC files.
* Specifications available at
* http://bio3d.colorado.edu/imod/doc/mrc_format.txt
*
* <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/MRCReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/MRCReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class MRCReader extends FormatReader {
// -- Constants --
private static final String[] TYPES =
{"mono", "tilt", "tilts", "lina", "lins"};
// NB: Unfortunately, we cannot just look for "MAP " at offset 0xd0, which
// works for modern .mrc files, because older IMOD versions did not put that
// there, according to: http://bio3d.colorado.edu/imod/doc/mrc_format.txt
private static final String[] MRC_SUFFIXES =
{"mrc", "st", "ali", "map", "rec"};
private static final int HEADER_SIZE = 1024;
private static final int ENDIANNESS_OFFSET = 212;
// -- Fields --
/** Size of extended header */
private int extHeaderSize = 0;
// -- Constructor --
/** Constructs a new MRC reader. */
public MRCReader() {
super("Medical Research Council", MRC_SUFFIXES);
domains = new String[] {FormatTools.MEDICAL_DOMAIN, FormatTools.LM_DOMAIN};
suffixSufficient = false;
}
// -- IFormatReader API methods --
/** @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
return FormatTools.validStream(stream, HEADER_SIZE, false);
}
/**
* @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);
long planeSize = FormatTools.getPlaneSize(this);
long offset = HEADER_SIZE + extHeaderSize + no * planeSize;
if (offset + planeSize <= in.length() && offset >= 0) {
in.seek(offset);
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) {
extHeaderSize = 0;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
public void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
MetadataLevel level = getMetadataOptions().getMetadataLevel();
LOGGER.info("Reading header");
// check endianness
in.seek(ENDIANNESS_OFFSET);
core[0].littleEndian = in.read() == 68;
// read dimension information from 1024 byte header
in.seek(0);
in.order(isLittleEndian());
core[0].sizeX = in.readInt();
core[0].sizeY = in.readInt();
core[0].sizeZ = in.readInt();
// We are using BigInteger here because of the very real possiblity
// of not just an int overflow but also a long overflow when multiplying
// sizeX * sizeY * sizeZ.
BigInteger v = BigInteger.valueOf(getSizeX());
v = v.multiply(BigInteger.valueOf(getSizeY()));
v = v.multiply(BigInteger.valueOf(getSizeZ()));
if (getSizeX() < 0 || getSizeY() < 0 || getSizeZ() < 0 ||
(v.compareTo(BigInteger.valueOf(in.length())) > 0))
{
LOGGER.debug("Detected endianness is wrong, swapping");
core[0].littleEndian = !isLittleEndian();
in.seek(0);
in.order(isLittleEndian());
core[0].sizeX = in.readInt();
core[0].sizeY = in.readInt();
core[0].sizeZ = in.readInt();
}
core[0].sizeC = 1;
int mode = in.readInt();
switch (mode) {
case 0:
core[0].pixelType = FormatTools.UINT8;
break;
case 1:
core[0].pixelType = FormatTools.INT16;
break;
case 6:
core[0].pixelType = FormatTools.UINT16;
break;
case 2:
core[0].pixelType = FormatTools.FLOAT;
break;
case 3:
core[0].pixelType = FormatTools.UINT32;
break;
case 4:
core[0].pixelType = FormatTools.DOUBLE;
break;
case 16:
core[0].sizeC = 3;
core[0].pixelType = FormatTools.UINT16;
break;
}
in.skipBytes(12);
// pixel size = xlen / mx
double xSize = 0d, ySize = 0d, zSize = 0d;
if (level != MetadataLevel.MINIMUM) {
int mx = in.readInt();
int my = in.readInt();
int mz = in.readInt();
xSize = in.readFloat() / mx;
ySize = in.readFloat() / my;
zSize = in.readFloat() / mz;
if (xSize == Double.POSITIVE_INFINITY) xSize = 1;
if (ySize == Double.POSITIVE_INFINITY) ySize = 1;
if (zSize == Double.POSITIVE_INFINITY) zSize = 1;
addGlobalMeta("Pixel size (X)", xSize);
addGlobalMeta("Pixel size (Y)", ySize);
addGlobalMeta("Pixel size (Z)", zSize);
addGlobalMeta("Alpha angle", in.readFloat());
addGlobalMeta("Beta angle", in.readFloat());
addGlobalMeta("Gamma angle", in.readFloat());
in.skipBytes(12);
// min, max and mean pixel values
}
else in.skipBytes(48);
double minValue = in.readFloat();
double maxValue = in.readFloat();
addGlobalMeta("Minimum pixel value", minValue);
addGlobalMeta("Maximum pixel value", maxValue);
addGlobalMeta("Mean pixel value", in.readFloat());
int bytes = FormatTools.getBytesPerPixel(getPixelType());
double range = Math.pow(2, bytes * 8) - 1;
double pixelTypeMin = 0;
boolean signed = FormatTools.isSigned(getPixelType());
if (signed) {
pixelTypeMin -= (range / 2);
}
double pixelTypeMax = pixelTypeMin + range;
if (pixelTypeMax < maxValue || pixelTypeMin > minValue && signed) {
// make the pixel type unsigned
switch (getPixelType()) {
case FormatTools.INT8:
core[0].pixelType = FormatTools.UINT8;
break;
case FormatTools.INT16:
core[0].pixelType = FormatTools.UINT16;
break;
case FormatTools.INT32:
core[0].pixelType = FormatTools.UINT32;
break;
}
}
in.skipBytes(4);
extHeaderSize = in.readInt();
if (level != MetadataLevel.MINIMUM) {
in.skipBytes(64);
int idtype = in.readShort();
String type = "unknown";
if (idtype >= 0 && idtype < TYPES.length) type = TYPES[idtype];
addGlobalMeta("Series type", type);
addGlobalMeta("Lens", in.readShort());
addGlobalMeta("ND1", in.readShort());
addGlobalMeta("ND2", in.readShort());
addGlobalMeta("VD1", in.readShort());
addGlobalMeta("VD2", in.readShort());
for (int i=0; i<6; i++) {
addGlobalMeta("Angle " + (i + 1), in.readFloat());
}
in.skipBytes(24);
addGlobalMeta("Number of useful labels", in.readInt());
for (int i=0; i<10; i++) {
addGlobalMeta("Label " + (i + 1), in.readString(80));
}
}
LOGGER.info("Populating metadata");
core[0].sizeT = 1;
core[0].dimensionOrder = "XYZTC";
core[0].imageCount = getSizeZ();
core[0].rgb = false;
core[0].interleaved = true;
core[0].indexed = false;
core[0].falseColor = false;
core[0].metadataComplete = true;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
if (level != MetadataLevel.MINIMUM) {
if (xSize > 0.0d) {
store.setPixelsPhysicalSizeX(new PositiveFloat(xSize), 0);
}
else {
LOGGER.warn("xSize {} not a positive float skipping", xSize);
}
if (ySize > 0.0d) {
store.setPixelsPhysicalSizeY(new PositiveFloat(ySize), 0);
}
else {
LOGGER.warn("ySize {} not a positive float skipping", ySize);
}
if (zSize > 0.0d) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(zSize), 0);
}
else {
LOGGER.warn("zSize {} not a positive float skipping", zSize);
}
}
}
}