//
// AliconaReader.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 loci.formats.*;
/**
* AliconaReader is the file format reader for Alicona AL3D files.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/AliconaReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/AliconaReader.java">SVN</a></dd></dl>
*/
public class AliconaReader extends FormatReader {
// -- Fields --
/** Image offset. */
private int textureOffset;
/** Number of bytes per pixel (either 1 or 2). */
private int numBytes;
// -- Constructor --
/** Constructs a new Alicona reader. */
public AliconaReader() { super("Alicona AL3D", "al3d"); }
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
return (new String(block)).indexOf("Alicona") != -1;
}
/* @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);
int pad = (8 - (core.sizeX[0] % 8)) % 8;
for (int i=0; i<numBytes; i++) {
in.seek(textureOffset + (no * (core.sizeX[0] + pad)*core.sizeY[0]*(i+1)));
for (int j=0; j<core.sizeX[0] * core.sizeY[0]; j++) {
buf[j*numBytes + i] = in.readByte();
if (j % core.sizeX[0] == core.sizeX[0] - 1) in.skipBytes(pad);
}
}
return buf;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (debug) debug("AliconaReader.initFile(" + id + ")");
super.initFile(id);
in = new RandomAccessStream(id);
// check that this is a valid AL3D file
status("Verifying Alicona format");
String magicString = in.readString(17);
if (!magicString.trim().equals("AliconaImaging")) {
throw new FormatException("Invalid magic string : " +
"expected 'AliconaImaging', got " + magicString);
}
// now we read a series of tags
// each one is 52 bytes - 20 byte key + 30 byte value + 2 byte CRLF
status("Reading tags");
int count = 2;
boolean hasC = false;
String voltage = null, magnification = null;
String pntX = null, pntY = null, pntZ = null;
for (int i=0; i<count; i++) {
String key = in.readString(20).trim();
String value = in.readString(30).trim();
addMeta(key, value);
in.skipBytes(2);
if (key.equals("TagCount")) count += Integer.parseInt(value);
else if (key.equals("Rows")) core.sizeY[0] = Integer.parseInt(value);
else if (key.equals("Cols")) core.sizeX[0] = Integer.parseInt(value);
else if (key.equals("NumberOfPlanes")) {
core.imageCount[0] = Integer.parseInt(value);
}
else if (key.equals("TextureImageOffset")) {
textureOffset = Integer.parseInt(value);
}
else if (key.equals("TexturePtr") && !value.equals("7")) hasC = true;
else if (key.equals("Voltage")) voltage = value;
else if (key.equals("Magnification")) magnification = value;
else if (key.equals("PlanePntX")) pntX = value;
else if (key.equals("PlanePntY")) pntY = value;
else if (key.equals("PlanePntZ")) pntZ = value;
}
status("Populating metadata");
numBytes = (int) (in.length() - textureOffset) /
(core.sizeX[0] * core.sizeY[0] * core.imageCount[0]);
core.sizeC[0] = hasC ? 3 : 1;
core.sizeZ[0] = 1;
core.sizeT[0] = core.imageCount[0] / core.sizeC[0];
core.rgb[0] = false;
core.interleaved[0] = false;
core.littleEndian[0] = true;
core.pixelType[0] = numBytes == 2 ? FormatTools.UINT16 : FormatTools.UINT8;
core.currentOrder[0] = "XYCTZ";
core.metadataComplete[0] = true;
core.indexed[0] = false;
core.falseColor[0] = false;
MetadataStore store = getMetadataStore();
store.setImage(currentId, null, null, null);
FormatTools.populatePixels(store, this);
if (voltage != null) {
store.setDetector(null, null, null, null, null, new Float(voltage),
null, null, null);
}
if (magnification != null) {
store.setObjective(null, null, null, null, new Float(magnification),
null, null);
}
if (pntX != null && pntY != null && pntZ != null) {
store.setDimensions(new Float(pntX.trim()), new Float(pntY.trim()),
new Float(pntZ.trim()), null, null, null);
}
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);
}
}
}