//
// SlidebookReader.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.Vector;
import loci.formats.*;
/**
* SlidebookReader is the file format reader for 3I Slidebook files.
* The strategies employed by this reader are highly suboptimal, as we
* have very little information on the Slidebook format.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/SlidebookReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/SlidebookReader.java">SVN</a></dd></dl>
*
* @author Melissa Linkert linkert at wisc.edu
*/
public class SlidebookReader extends FormatReader {
// -- Fields --
private Vector metadataOffsets;
private Vector pixelOffsets;
private Vector pixelLengths;
// -- Constructor --
/** Constructs a new Slidebook reader. */
public SlidebookReader() { super("Olympus Slidebook", "sld"); }
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
if (block.length < 8) return false;
return block[0] == 0x6c && block[1] == 0 && block[2] == 0 &&
block[3] == 1 && block[4] == 0x49 && block[5] == 0x49 && block[6] == 0;
}
/* @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 plane = core.sizeX[series] * core.sizeY[series] * 2;
long offset = ((Long) pixelOffsets.get(series)).longValue() + plane * no;
in.seek(offset);
in.read(buf);
return buf;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (debug) debug("SlidebookReader.initFile(" + id + ")");
super.initFile(id);
in = new RandomAccessStream(id);
in.order(true);
status("Finding offsets to pixel data");
in.skipBytes(4);
core.littleEndian[0] = in.read() == 0x49;
metadataOffsets = new Vector();
pixelOffsets = new Vector();
pixelLengths = new Vector();
in.seek(0);
while (in.getFilePointer() < in.length() - 8) {
in.skipBytes(4);
int checkOne = in.read();
int checkTwo = in.read();
if (checkOne == 'I' && checkTwo == 'I') {
metadataOffsets.add(new Long(in.getFilePointer() - 6));
if (in.read() == 0) in.skipBytes(249);
else in.skipBytes(121);
}
else {
String s = null;
long fp = in.getFilePointer() - 6;
in.seek(fp);
int len = in.read();
if (len > 0 && len <= 32) {
byte[] b = new byte[len];
in.read(b);
s = new String(b);
}
if (s != null && s.indexOf("Annotation") != -1) {
if (s.equals("CTimelapseAnnotation")) {
in.skipBytes(41);
if (in.read() == 0) in.skipBytes(10);
else in.seek(in.getFilePointer() - 1);
}
else if (s.equals("CIntensityBarAnnotation")) {
in.skipBytes(56);
int n = in.read();
while (n == 0 || n < 6 || n > 0x80) n = in.read();
in.seek(in.getFilePointer() - 1);
}
else if (s.equals("CCubeAnnotation")) {
in.skipBytes(66);
int n = in.read();
if (n != 0) in.seek(in.getFilePointer() - 1);
}
else if (s.equals("CScaleBarAnnotation")) {
in.skipBytes(52);
}
}
else if (s != null && s.indexOf("Decon") != -1) {
in.seek(fp);
while (in.read() != ']');
}
else {
in.seek(fp);
pixelOffsets.add(new Long(fp));
try {
byte[] buf = new byte[8192];
boolean found = false;
int n = in.read(buf);
while (!found && in.getFilePointer() < in.length()) {
for (int i=0; i<buf.length-6; i++) {
if (buf[i] == 'h' && buf[i+4] == 'I' && buf[i+5] == 'I') {
found = true;
in.seek(in.getFilePointer() - n + i - 20);
break;
}
}
if (!found) {
byte[] tmp = buf;
buf = new byte[8192];
System.arraycopy(tmp, tmp.length - 20, buf, 0, 20);
n = in.read(buf, 20, buf.length - 20);
}
}
if (in.getFilePointer() <= in.length()) {
pixelLengths.add(new Long(in.getFilePointer() - fp));
}
else pixelOffsets.remove(pixelOffsets.size() - 1);
}
catch (EOFException e) {
pixelOffsets.remove(pixelOffsets.size() - 1);
}
}
}
}
core = new CoreMetadata(pixelOffsets.size() - 1);
status("Determining dimensions");
// determine total number of pixel bytes
long pixelBytes = 0;
for (int i=0; i<pixelLengths.size(); i++) {
pixelBytes += ((Long) pixelLengths.get(i)).longValue();
}
// try to find the width and height
int iCount = 0;
int hCount = 0;
int uCount = 0;
for (int i=0; i<metadataOffsets.size(); i++) {
long off = ((Long) metadataOffsets.get(i)).longValue();
in.seek(off);
int n = in.read();
if (n == 'i') {
in.skipBytes(79);
core.sizeX[0] = in.readShort();
core.sizeY[0] = in.readShort();
iCount++;
}
else if (n == 'h') hCount++;
else if (n == 'u') uCount++;
}
core.rgb[0] = false;
core.sizeC[0] = iCount < 5 ? iCount : 1;
if (core.sizeC[0] == 0) core.sizeC[0] = 1;
if (core.sizeZ[0] == 0) core.sizeZ[0] = 1;
if (core.sizeT[0] == 0) core.sizeT[0] = 1;
if (core.sizeX[0] * core.sizeY[0] * 2 * core.sizeC[0] *
core.sizeZ[0] * core.sizeT[0] != pixelBytes && hCount > 0)
{
core.sizeZ[0] = hCount / core.sizeC[0];
}
int n = core.sizeZ[0] * core.sizeC[0] * core.sizeT[0];
if (uCount == core.sizeZ[0] * core.sizeT[0]) uCount = n;
if (uCount < core.sizeZ[0] * core.sizeT[0] * core.sizeC[0]) {
int planesPerMontage = (n * 2) / uCount;
while (planesPerMontage > 1) {
core.sizeY[0] /= 2;
planesPerMontage /= 2;
if (planesPerMontage > 1) {
core.sizeX[0] /= 2;
planesPerMontage /= 2;
}
}
if (core.sizeC[0] == 1) core.sizeC[0] = 2;
else core.sizeT[0] *= 2;
}
else if (uCount > core.sizeZ[0] * core.sizeT[0] * core.sizeC[0]) {
int planesPerMontage =
(int) ((core.sizeX[0] * core.sizeY[0] * 2) / (pixelBytes / uCount));
if (planesPerMontage % 2 != 0) planesPerMontage++;
if (planesPerMontage == 2) planesPerMontage += 2;
if (planesPerMontage == 0) planesPerMontage++;
int plane = core.sizeX[0] * core.sizeY[0];
while (uCount * core.sizeC[0] * (plane*2 / planesPerMontage) <
(pixelBytes - plane))
{
uCount++;
}
while (planesPerMontage > 1 &&
core.sizeX[0] * core.sizeY[0] * 2 * uCount > pixelBytes)
{
core.sizeY[0] /= 2;
planesPerMontage /= 2;
if (planesPerMontage > 1 &&
core.sizeX[0] * core.sizeY[0] * 2 * uCount > pixelBytes)
{
core.sizeX[0] /= 2;
planesPerMontage /= 2;
}
else planesPerMontage = 1;
}
core.sizeZ[0] = uCount;
}
// couldn't find the dimensions; these are reasonable guesses
if (core.sizeX[0] == 0) core.sizeX[0] = 512;
if (core.sizeY[0] == 0) core.sizeY[0] = 512;
for (int i=0; i<core.sizeX.length; i++) {
core.sizeX[i] = core.sizeX[0];
core.sizeY[i] = core.sizeY[0];
core.currentOrder[i] = "XYZCT";
core.pixelType[i] = FormatTools.UINT16;
core.littleEndian[i] = true;
core.sizeC[i] = core.sizeC[0];
core.sizeT[i] = core.sizeT[0];
long len = ((Long) pixelLengths.get(i)).longValue();
core.sizeZ[i] =
(int) (len / (core.sizeX[i] * core.sizeY[i] * 2 * core.sizeC[i]));
core.imageCount[i] = core.sizeC[i] * core.sizeZ[i] * core.sizeT[i];
core.indexed[i] = false;
core.falseColor[i] = false;
core.metadataComplete[i] = true;
}
MetadataStore store = getMetadataStore();
FormatTools.populatePixels(store, this);
for (int i=0; i<core.sizeX.length; i++) {
Integer ii = new Integer(i);
store.setImage(currentId, null, null, ii);
for (int j=0; j<core.sizeC[i]; j++) {
store.setLogicalChannel(j, null, null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null, null, null,
null, null, null, null, null, ii);
}
}
}
}