//
// NRRDReader.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.*;
import java.util.StringTokenizer;
import loci.formats.*;
/**
* File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/NRRDReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/NRRDReader.java">SVN</a></dd></dl>
*/
public class NRRDReader extends FormatReader {
// -- Fields --
/** Helper reader. */
private ImageReader helper;
/** Name of data file, if the current extension is 'nhdr'. */
private String dataFile;
/** Data encoding. */
private String encoding;
/** Offset to pixel data. */
private long offset;
// -- Constructor --
/** Constructs a new NRRD reader. */
public NRRDReader() { super("NRRD", new String[] {"nrrd", "nhdr"}); }
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
if (block.length < 4) return false;
return new String(block).startsWith("NRRD");
}
/* @see loci.formats.IFormatReader#getUsedFiles() */
public String[] getUsedFiles() {
if (dataFile == null) return new String[] {currentId};
return new String[] {currentId, dataFile};
}
/* @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);
// TODO : add support for additional encoding types
if (dataFile == null) {
if (encoding.equals("raw")) {
in.seek(offset + no * buf.length);
in.read(buf);
return buf;
}
else throw new FormatException("Unsupported encoding: " + encoding);
}
return helper.openBytes(no, buf);
}
/* @see loci.formats.IFormatReader#close() */
public void close() throws IOException {
super.close();
if (helper != null) helper.close();
}
// -- 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);
helper = new ImageReader();
boolean finished = false;
String line, key, v;
int numDimensions = 0;
core.sizeX[0] = 1;
core.sizeY[0] = 1;
core.sizeZ[0] = 1;
core.sizeC[0] = 1;
core.sizeT[0] = 1;
core.currentOrder[0] = "XYCZT";
while (!finished) {
line = in.readLine().trim();
if (!line.startsWith("#") && line.length() > 0 &&
!line.startsWith("NRRD"))
{
// parse key/value pair
key = line.substring(0, line.indexOf(":")).trim();
v = line.substring(line.indexOf(":") + 1).trim();
addMeta(key, v);
if (key.equals("type")) {
if (v.indexOf("char") != -1 || v.indexOf("8") != -1) {
core.pixelType[0] = FormatTools.UINT8;
}
else if (v.indexOf("short") != -1 || v.indexOf("16") != -1) {
core.pixelType[0] = FormatTools.UINT16;
}
else if (v.equals("int") || v.equals("signed int") ||
v.equals("int32") || v.equals("int32_t") || v.equals("uint") ||
v.equals("unsigned int") || v.equals("uint32") ||
v.equals("uint32_t"))
{
core.pixelType[0] = FormatTools.UINT32;
}
else if (v.equals("float")) core.pixelType[0] = FormatTools.FLOAT;
else if (v.equals("double")) core.pixelType[0] = FormatTools.DOUBLE;
else throw new FormatException("Unsupported data type: " + v);
}
else if (key.equals("dimension")) {
numDimensions = Integer.parseInt(v);
}
else if (key.equals("sizes")) {
StringTokenizer tokens = new StringTokenizer(v, " ");
for (int i=0; i<numDimensions; i++) {
String t = tokens.nextToken();
int size = Integer.parseInt(t);
if (numDimensions >= 3 && i == 0 && size > 1 && size <= 4) {
core.sizeC[0] = size;
}
else if (i == 0 || (core.sizeC[0] > 1 && i == 1)) {
core.sizeX[0] = size;
}
else if (i == 1 || (core.sizeC[0] > 1 && i == 2)) {
core.sizeY[0] = size;
}
else if (i == 2 || (core.sizeC[0] > 1 && i == 3)) {
core.sizeZ[0] = size;
}
else if (i == 3 || (core.sizeC[0] > 1 && i == 4)) {
core.sizeT[0] = size;
}
}
}
else if (key.equals("data file") || key.equals("datafile")) {
dataFile = v;
}
else if (key.equals("encoding")) encoding = v;
else if (key.equals("endian")) {
core.littleEndian[0] = v.equals("little");
}
}
if ((line.length() == 0 && dataFile == null) || line == null) {
finished = true;
}
if (dataFile != null && (in.length() - in.getFilePointer() < 2)) {
finished = true;
}
}
if (dataFile == null) offset = in.getFilePointer();
else {
File f = new File(currentId);
if (f.exists() && f.getParentFile() != null) {
dataFile =
f.getParentFile().getAbsolutePath() + File.separator + dataFile;
}
helper.setId(dataFile);
}
core.rgb[0] = core.sizeC[0] > 1;
core.interleaved[0] = true;
core.imageCount[0] = core.sizeZ[0] * core.sizeT[0];
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);
for (int i=0; i<core.sizeC[0]; i++) {
store.setLogicalChannel(i, null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null, null);
}
}
}