//
// FitsReader.java
//
/*
LOCI Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan,
Eric Kjellman and Brian Loranger.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU Library 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 Library General Public License for more details.
You should have received a copy of the GNU Library 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.formats.*;
/**
* 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="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/FitsReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/FitsReader.java">SVN</a></dd></dl>
*/
public class FitsReader extends FormatReader {
// -- Fields --
/** Number of lines in the header. */
private int count;
// -- Constructor --
/** Constructs a new FitsReader. */
public FitsReader() { super("Flexible Image Transport System", "fits"); }
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
return true;
}
/* @see loci.formats.IFormatReader#openBytes(int, byte[]) */
public byte[] openBytes(int no, byte[] buf)
throws FormatException, IOException
{
FormatTools.assertId(currentId, true, 1);
FormatTools.checkPlaneNumber(this, no);
FormatTools.checkBufferSize(this, buf.length);
in.seek(2880 + 2880 * (((count * 80) - 1) / 2880));
int line = core.sizeX[0] * FormatTools.getBytesPerPixel(core.pixelType[0]);
for (int y=core.sizeY[0]-1; y>=0; y--) {
in.read(buf, y*line, line);
}
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 RandomAccessStream(id);
count = 1;
String line = in.readString(80);
if (!line.startsWith("SIMPLE")) {
throw new FormatException("Unsupported FITS file.");
}
while (true) {
count++;
line = in.readString(80);
// parse key/value pair
int ndx = line.indexOf("=");
int comment = line.indexOf("/", ndx);
if (comment < 0) comment = line.length();
String key = "", value = "";
if (ndx >= 0) {
key = line.substring(0, ndx).trim();
value = line.substring(ndx + 1, comment).trim();
}
else key = line.trim();
if (key.equals("END")) break;
if (key.equals("BITPIX")) {
int bits = Integer.parseInt(value);
switch (bits) {
case 8: core.pixelType[0] = FormatTools.UINT8; break;
case 16: core.pixelType[0] = FormatTools.UINT16; break;
case 32: core.pixelType[0] = FormatTools.UINT32; break;
case -32: core.pixelType[0] = FormatTools.FLOAT; break;
default: throw new FormatException("Unsupported pixel type: " + bits);
}
}
else if (key.equals("NAXIS1")) core.sizeX[0] = Integer.parseInt(value);
else if (key.equals("NAXIS2")) core.sizeY[0] = Integer.parseInt(value);
else if (key.equals("NAXIS3")) core.sizeZ[0] = Integer.parseInt(value);
addMeta(key, value);
}
core.sizeC[0] = 1;
core.sizeT[0] = 1;
if (core.sizeZ[0] == 0) core.sizeZ[0] = 1;
core.imageCount[0] = core.sizeZ[0];
core.rgb[0] = false;
core.littleEndian[0] = false;
core.interleaved[0] = false;
core.currentOrder[0] = "XYZCT";
core.indexed[0] = false;
core.falseColor[0] = false;
core.metadataComplete[0] = true;
MetadataStore store = getMetadataStore();
store.setImage(currentId, null, null, null);
FormatTools.populatePixels(store, this);
store.setLogicalChannel(0, null, null, null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null, null, null,
null, null, null, null, null);
}
}