//
// FitsReader.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;
/**
* FitsReader is the file format reader for
* Flexible Image Transport System (FITS) images.
*
* Much of this code was adapted from ImageJ (http://rsb.info.nih.gov/ij).
*
* <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/FitsReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/FitsReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class FitsReader extends FormatReader {
// -- Constants --
private static final int LINE_LENGTH = 80;
// -- Fields --
private long pixelOffset;
// -- Constructor --
/** Constructs a new FitsReader. */
public FitsReader() {
super("Flexible Image Transport System", new String[] {"fits", "fts"});
domains =
new String[] {FormatTools.ASTRONOMY_DOMAIN, FormatTools.UNKNOWN_DOMAIN};
}
// -- IFormatReader API methods --
/**
* @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(pixelOffset + no * FormatTools.getPlaneSize(this));
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) pixelOffset = 0;
}
// -- 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);
String line = in.readString(LINE_LENGTH);
if (!line.startsWith("SIMPLE")) {
throw new FormatException("Unsupported FITS file.");
}
String key = "", value = "";
while (true) {
line = in.readString(LINE_LENGTH);
// parse key/value pair
int ndx = line.indexOf("=");
int comment = line.indexOf("/", ndx);
if (comment < 0) comment = line.length();
if (ndx >= 0) {
key = line.substring(0, ndx).trim();
value = line.substring(ndx + 1, comment).trim();
}
else key = line.trim();
// if the file has an extended header, "END" will appear twice
// the first time marks the end of the extended header
// the second time marks the end of the standard header
// image dimensions are only populated by the standard header
if (key.equals("END") && getSizeX() > 0) break;
if (key.equals("BITPIX")) {
int bits = Integer.parseInt(value);
boolean fp = bits < 0;
boolean signed = bits != 8;
bits = Math.abs(bits) / 8;
core[0].pixelType = FormatTools.pixelTypeFromBytes(bits, signed, fp);
}
else if (key.equals("NAXIS1")) core[0].sizeX = Integer.parseInt(value);
else if (key.equals("NAXIS2")) core[0].sizeY = Integer.parseInt(value);
else if (key.equals("NAXIS3")) core[0].sizeZ = Integer.parseInt(value);
addGlobalMeta(key, value);
}
while (in.read() == 0x20);
pixelOffset = in.getFilePointer() - 1;
core[0].sizeC = 1;
core[0].sizeT = 1;
if (getSizeZ() == 0) core[0].sizeZ = 1;
core[0].imageCount = core[0].sizeZ;
core[0].rgb = false;
core[0].littleEndian = false;
core[0].interleaved = false;
core[0].dimensionOrder = "XYZCT";
core[0].indexed = false;
core[0].falseColor = false;
core[0].metadataComplete = true;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
}
}