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JEOLReader.java
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JEOLReader.java
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/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2017 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.Location;
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;
/**
* JEOLReader is the file format reader for JEOL files.
*/
public class JEOLReader extends FormatReader {
// -- Fields --
private long pixelOffset;
private String parameterFile;
// -- Constructor --
/** Constructs a new JEOL reader. */
public JEOLReader() {
super("JEOL", new String[] {"dat", "img", "par"});
domains = new String[] {FormatTools.SEM_DOMAIN};
hasCompanionFiles = true;
suffixSufficient = false;
datasetDescription = "A single .dat file or an .img file with a " +
"similarly-named .par file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String) */
@Override
public boolean isThisType(String name, boolean open) {
if (checkSuffix(name, "par") && open) {
String base = new Location(name).getAbsoluteFile().getAbsolutePath();
base = base.substring(0, base.lastIndexOf("."));
String id = base + ".IMG";
if (!new Location(id).exists()) {
id = base + ".DAT";
}
if (!new Location(id).exists()) {
return false;
}
return true;
}
if (checkSuffix(name, "dat") && open) {
try (RandomAccessInputStream stream = new RandomAccessInputStream(name)) {
if (stream.length() == (1024 * 1024)) return true;
}
catch (IOException e) { }
return false;
}
return super.isThisType(name, open);
}
/* @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;
String magic = stream.readString(blockLen);
return magic.equals("MG") || magic.equals("IM");
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
if (noPixels) {
return parameterFile == null ? null : new String[] {parameterFile};
}
String id = new Location(currentId).getAbsolutePath();
return parameterFile == null ? new String[] {id} :
new String[] {id, parameterFile};
}
/**
* @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(pixelOffset);
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) {
pixelOffset = 0;
parameterFile = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (checkSuffix(id, "par")) {
String base = new Location(id).getAbsoluteFile().getAbsolutePath();
base = base.substring(0, base.lastIndexOf("."));
id = base + ".IMG";
if (!new Location(id).exists()) {
id = base + ".DAT";
}
if (!new Location(id).exists()) {
throw new FormatException("Could not find image file.");
}
}
super.initFile(id);
in = new RandomAccessInputStream(id);
CoreMetadata m = core.get(0);
m.littleEndian = true;
in.order(isLittleEndian());
parameterFile = id.substring(0, id.lastIndexOf(".")) + ".PAR";
parameterFile = new Location(parameterFile).getAbsolutePath();
if (!new Location(parameterFile).exists()) parameterFile = null;
String magic = in.readString(2);
if (magic.equals("MG")) {
in.seek(0x63c);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
pixelOffset = in.getFilePointer() + 540;
}
else if (magic.equals("IM")) {
int commentLength = in.readShort();
m.sizeX = 1024;
pixelOffset = in.getFilePointer() + commentLength + 56;
m.sizeY = (int) ((in.length() - pixelOffset) / getSizeX());
}
else {
m.sizeX = 1024;
m.sizeY = 1024;
pixelOffset = 0;
}
addGlobalMeta("Pixel data offset", pixelOffset);
m.pixelType = FormatTools.UINT8;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}