//
// AnalyzeReader.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.Location;
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;
/**
* AnalyzeReader is the file format reader for Analyze 7.5 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/AnalyzeReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/AnalyzeReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class AnalyzeReader extends FormatReader {
// -- Constants --
private static final int MAGIC = 0x15c;
// -- Fields --
/** Offset to the pixel data in the .img file. */
private int pixelOffset;
/** File containing the pixel data. */
private RandomAccessInputStream pixelFile;
private String pixelsFilename;
// -- Constructor --
/** Constructs a new Analyze reader. */
public AnalyzeReader() {
super("Analyze 7.5", new String[] {"img", "hdr"});
domains = new String[] {FormatTools.MEDICAL_DOMAIN};
hasCompanionFiles = true;
datasetDescription = "One .img file and one similarly-named .hdr file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
if (!super.isThisType(name, open)) return false;
if (!open) return false;
String headerFile = checkSuffix(name, "hdr") ? name : null;
String extension = name.substring(name.lastIndexOf(".") + 1);
name = name.substring(0, name.lastIndexOf("."));
if (extension.equals("img")) extension = "hdr";
else if (extension.equals("IMG")) extension = "HDR";
else if (extension.equals("hdr")) extension = "img";
else if (extension.equals("HDR")) extension = "IMG";
if (extension.equalsIgnoreCase("hdr")) {
headerFile = name + "." + extension;
}
boolean validHeader = false;
try {
RandomAccessInputStream headerStream =
new RandomAccessInputStream(headerFile);
validHeader = isThisType(headerStream);
headerStream.close();
}
catch (IOException e) { }
return new Location(name + "." + extension).exists() && validHeader;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
stream.order(true);
int checkLittleEndian = stream.readInt();
stream.seek(stream.getFilePointer() - 4);
stream.order(false);
int checkBigEndian = stream.readInt();
return checkLittleEndian == MAGIC || checkBigEndian == MAGIC;
}
/* @see loci.formats.IFormatReader#isSingleFile(String) */
public boolean isSingleFile(String id) throws FormatException, IOException {
return 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);
int planeSize = FormatTools.getPlaneSize(this);
pixelFile.seek(pixelOffset + no * planeSize);
readPlane(pixelFile, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
return noPixels ? new String[] {currentId} :
new String[] {currentId, pixelsFilename};
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (pixelFile != null) pixelFile.close();
if (!fileOnly) {
pixelOffset = 0;
pixelFile = null;
pixelsFilename = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
// the dataset has two files - we want the one ending in '.hdr'
if (id.endsWith(".img")) {
LOGGER.info("Looking for header file");
String header = id.substring(0, id.lastIndexOf(".")) + ".hdr";
if (new Location(header).exists()) {
setId(header);
return;
}
else throw new FormatException("Header file not found.");
}
super.initFile(id);
in = new RandomAccessInputStream(id);
pixelsFilename = id.substring(0, id.lastIndexOf(".")) + ".img";
pixelFile = new RandomAccessInputStream(pixelsFilename);
LOGGER.info("Reading header");
int fileSize = in.readInt();
boolean little = fileSize != in.length();
in.order(little);
pixelFile.order(little);
in.skipBytes(10);
String imageName = in.readString(18);
in.skipBytes(8);
int ndims = in.readShort();
int x = in.readShort();
int y = in.readShort();
int z = in.readShort();
int t = in.readShort();
in.skipBytes(20);
int dataType = in.readShort();
int nBitsPerPixel = in.readShort();
String description = null;
double voxelWidth = 0d, voxelHeight = 0d, sliceThickness = 0d, deltaT = 0d;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
in.skipBytes(6);
voxelWidth = in.readFloat();
voxelHeight = in.readFloat();
sliceThickness = in.readFloat();
deltaT = in.readFloat();
in.skipBytes(12);
pixelOffset = (int) in.readFloat();
in.skipBytes(12);
float calibratedMax = in.readFloat();
float calibratedMin = in.readFloat();
float compressed = in.readFloat();
float verified = in.readFloat();
float pixelMax = in.readFloat();
float pixelMin = in.readFloat();
description = in.readString(80);
String auxFile = in.readString(24);
char orient = (char) in.readByte();
String originator = in.readString(10);
String generated = in.readString(10);
String scannum = in.readString(10);
String patientID = in.readString(10);
String expDate = in.readString(10);
String expTime = in.readString(10);
in.skipBytes(3);
int views = in.readInt();
int volsAdded = in.readInt();
int startField = in.readInt();
int fieldSkip = in.readInt();
int omax = in.readInt();
int omin = in.readInt();
int smax = in.readInt();
int smin = in.readInt();
addGlobalMeta("Database name", imageName);
addGlobalMeta("Number of dimensions", ndims);
addGlobalMeta("Data type", dataType);
addGlobalMeta("Number of bits per pixel", nBitsPerPixel);
addGlobalMeta("Voxel width", voxelWidth);
addGlobalMeta("Voxel height", voxelHeight);
addGlobalMeta("Slice thickness", sliceThickness);
addGlobalMeta("Exposure time", deltaT);
addGlobalMeta("Pixel offset", pixelOffset);
addGlobalMeta("Calibrated maximum", calibratedMax);
addGlobalMeta("Calibrated minimum", calibratedMin);
addGlobalMeta("Compressed", compressed);
addGlobalMeta("Verified", verified);
addGlobalMeta("Pixel maximum", pixelMax);
addGlobalMeta("Pixel minimum", pixelMin);
addGlobalMeta("Description", description);
addGlobalMeta("Auxiliary file", auxFile);
addGlobalMeta("Orientation", orient);
addGlobalMeta("Originator", originator);
addGlobalMeta("Generated", generated);
addGlobalMeta("Scan Number", scannum);
addGlobalMeta("Patient ID", patientID);
addGlobalMeta("Acquisition Date", expDate);
addGlobalMeta("Acquisition Time", expTime);
}
else {
in.skipBytes(34);
pixelOffset = (int) in.readFloat();
}
LOGGER.info("Populating core metadata");
core[0].sizeX = x;
core[0].sizeY = y;
core[0].sizeZ = z;
core[0].sizeT = t;
core[0].sizeC = 1;
if (getSizeZ() == 0) core[0].sizeZ = 1;
if (getSizeT() == 0) core[0].sizeT = 1;
core[0].imageCount = getSizeZ() * getSizeT();
core[0].rgb = false;
core[0].interleaved = false;
core[0].indexed = false;
core[0].dimensionOrder = "XYZTC";
switch (dataType) {
case 1:
case 2:
core[0].pixelType = FormatTools.UINT8;
break;
case 4:
core[0].pixelType = FormatTools.INT16;
break;
case 8:
core[0].pixelType = FormatTools.INT32;
break;
case 16:
core[0].pixelType = FormatTools.FLOAT;
break;
case 64:
core[0].pixelType = FormatTools.DOUBLE;
break;
case 128:
core[0].pixelType = FormatTools.UINT8;
core[0].sizeC = 3;
core[0].rgb = true;
core[0].interleaved = true;
core[0].dimensionOrder = "XYCZT";
default:
throw new FormatException("Unsupported data type: " + dataType);
}
LOGGER.info("Populating MetadataStore");
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
store.setImageName(imageName, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(description, 0);
store.setPixelsPhysicalSizeX(new PositiveFloat(voxelWidth * 0.001), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(voxelHeight * 0.001), 0);
store.setPixelsPhysicalSizeZ(
new PositiveFloat(sliceThickness * 0.001), 0);
store.setPixelsTimeIncrement(new Double(deltaT * 1000), 0);
}
}
}