//
// INRReader.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.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;
/**
* INRReader is the file format reader for INR 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/INRReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/INRReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class INRReader extends FormatReader {
// -- Constants --
private static final String INR_MAGIC = "#INRIMAGE";
private static final int HEADER_SIZE = 256;
// -- Constructor --
/** Constructs a new INR reader. */
public INRReader() {
super("INR", "inr");
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = INR_MAGIC.length();
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readString(blockLen)).indexOf(INR_MAGIC) == 0;
}
/**
* @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 = (long) FormatTools.getPlaneSize(this);
in.seek(HEADER_SIZE + no * planeSize);
readPlane(in, x, y, w, h, buf);
return buf;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
// read the fixed-size header
LOGGER.info("Reading header");
String header = in.readString(HEADER_SIZE);
String[] lines = header.split("\n");
Double physicalSizeX = null;
Double physicalSizeY = null;
Double physicalSizeZ = null;
boolean isSigned = false;
int nBits = 0;
for (String line : lines) {
int index = line.indexOf("=");
if (index >= 0) {
String key = line.substring(0, index);
String value = line.substring(index + 1);
addGlobalMeta(key, value);
if (key.equals("XDIM")) {
core[0].sizeX = Integer.parseInt(value);
}
else if (key.equals("YDIM")) {
core[0].sizeY = Integer.parseInt(value);
}
else if (key.equals("ZDIM")) {
core[0].sizeZ = Integer.parseInt(value);
}
else if (key.equals("VDIM")) {
core[0].sizeT = Integer.parseInt(value);
}
else if (key.equals("TYPE")) {
isSigned = value.toLowerCase().startsWith("signed");
}
else if (key.equals("PIXSIZE")) {
String bits = value.substring(0, value.indexOf(" "));
nBits = Integer.parseInt(bits);
}
else if (key.equals("VX")) {
physicalSizeX = new Double(value);
}
else if (key.equals("VY")) {
physicalSizeY = new Double(value);
}
else if (key.equals("VZ")) {
physicalSizeZ = new Double(value);
}
}
}
// finish populating core metadata
LOGGER.info("Populating metadata");
if (getSizeZ() == 0) {
core[0].sizeZ = 1;
}
if (getSizeT() == 0) {
core[0].sizeT = 1;
}
core[0].sizeC = 1;
core[0].imageCount = getSizeZ() * getSizeT() * getSizeC();
core[0].pixelType =
FormatTools.pixelTypeFromBytes(nBits / 8, isSigned, false);
core[0].dimensionOrder = "XYZTC";
// populate the metadata store
LOGGER.info("Populating OME metadata");
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (physicalSizeX != null) {
store.setPixelsPhysicalSizeX(new PositiveFloat(physicalSizeX), 0);
}
if (physicalSizeY != null) {
store.setPixelsPhysicalSizeY(new PositiveFloat(physicalSizeY), 0);
}
if (physicalSizeZ != null) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(physicalSizeZ), 0);
}
}
}
}