//
// SBIGReader.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.DataTools;
import loci.common.DateTools;
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;
/**
* SBIGReader is the file format reader for SBIG files.
* See the specification at http://www.sbig.com/pdffiles/file.format.pdf.
*
* <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/SBIGReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/SBIGReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class SBIGReader extends FormatReader {
// -- Constants --
private static final long HEADER_SIZE = 2048;
private static final String DATE_FORMAT = "MM/dd/yy HH:mm:ss";
// -- Fields --
private boolean compressed;
// -- Constructor --
/** Constructs a new SBIG reader. */
public SBIGReader() {
super("SBIG", "");
domains = new String[] {FormatTools.ASTRONOMY_DOMAIN};
suffixSufficient = false;
suffixNecessary = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = (int) HEADER_SIZE;
final int checkLen = 32;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(checkLen).indexOf("ST-7 Compressed Image") >= 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);
in.seek(HEADER_SIZE);
int width = getSizeX() * 2;
if (compressed) {
byte[] b = new byte[FormatTools.getPlaneSize(this)];
for (int row=0; row<getSizeY(); row++) {
int rowLen = in.readShort();
if (rowLen == width) {
in.read(b, row * width, rowLen);
}
else {
int bufferPointer = row * width;
in.read(b, bufferPointer, 2);
while (bufferPointer - row * width < width - 2) {
short prevPixel =
DataTools.bytesToShort(b, bufferPointer, isLittleEndian());
bufferPointer += 2;
byte check = in.readByte();
if (check == -128) {
in.read(b, bufferPointer, 2);
}
else {
prevPixel += check;
DataTools.unpackBytes(prevPixel, b, bufferPointer, 2,
isLittleEndian());
}
}
}
}
RandomAccessInputStream stream = new RandomAccessInputStream(b);
readPlane(stream, x, y, w, h, buf);
stream.close();
}
else 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) {
compressed = false;
}
}
// -- 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);
Double temperature = null;
Double sizeX = null, sizeY = null;
String date = null, description = null;
String[] lines = DataTools.readFile(currentId).split("\n");
for (String line : lines) {
line = line.trim();
int eq = line.indexOf("=");
if (eq != -1) {
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1).trim();
addGlobalMeta(key, value);
if (key.equals("Width")) {
core[0].sizeX = Integer.parseInt(value);
}
else if (key.equals("Height")) {
core[0].sizeY = Integer.parseInt(value);
}
else if (key.equals("Note")) {
description = value;
}
else if (key.equals("X_pixel_size")) {
sizeX = new Double(value) * 1000;
}
else if (key.equals("Y_pixel_size")) {
sizeY = new Double(value) * 1000;
}
else if (key.equals("Date")) {
date = value;
}
else if (key.equals("Time")) {
date += " " + value;
}
}
else if (line.indexOf("Compressed") != -1) {
compressed = true;
}
else if (line.equals("End")) break;
}
core[0].pixelType = FormatTools.UINT16;
core[0].littleEndian = true;
core[0].rgb = false;
core[0].sizeZ = 1;
core[0].sizeC = 1;
core[0].sizeT = 1;
core[0].imageCount = 1;
core[0].dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
store.setImageAcquiredDate(DateTools.formatDate(date, DATE_FORMAT), 0);
}
else MetadataTools.setDefaultCreationDate(store, currentId, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setPixelsPhysicalSizeX(new PositiveFloat(sizeX), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(sizeY), 0);
store.setImageDescription(description, 0);
}
}
}