//
// VisitechReader.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.*;
import loci.formats.*;
/**
* VisitechReader is the file format reader for Visitech XYS files.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/VisitechReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/VisitechReader.java">SVN</a></dd></dl>
*/
public class VisitechReader extends FormatReader {
// -- Fields --
/** Files in this dataset. */
private Vector files;
// -- Constructor --
public VisitechReader() {
super("Visitech XYS", new String[] {"xys", "html"});
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
return false;
}
/* @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[0] * core.sizeY[0] *
FormatTools.getBytesPerPixel(core.pixelType[0]);
int div = core.sizeZ[0] * core.sizeT[0];
int fileIndex = no / div;
int planeIndex = no % div;
String file = (String) files.get(fileIndex);
RandomAccessStream s = new RandomAccessStream(file);
s.skipBytes(374);
while (s.read() != (byte) 0xf0);
s.skipBytes((plane + 164) * planeIndex + 1);
s.read(buf);
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#getUsedFiles() */
public String[] getUsedFiles() {
if (files == null) return new String[0];
return (String[]) files.toArray(new String[0]);
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
// first, make sure we have the HTML file
if (!id.toLowerCase().endsWith("html")) {
Location file = new Location(id).getAbsoluteFile();
String path = file.exists() ? file.getPath() : id;
int ndx = path.lastIndexOf(File.separator);
String base = path.substring(ndx + 1, path.indexOf(" ", ndx));
String suffix = " Report.html";
currentId = null;
initFile(file.exists() ? new Location(file.getParent(),
base + suffix).getAbsolutePath() : base + suffix);
return;
}
// parse the HTML file
in = new RandomAccessStream(id);
String s = in.readString((int) in.length());
// strip out "style", "a", and "script" tags
s = s.replaceAll("<[bB][rR]>", "\n");
s = s.replaceAll("<[sS][tT][yY][lL][eE]\\p{ASCII}*?" +
"[sS][tT][yY][lL][eE]>", "");
s = s.replaceAll("<[sS][cC][rR][iI][pP][tT]\\p{ASCII}*?" +
"[sS][cC][rR][iI][pP][tT]>", "");
StringTokenizer st = new StringTokenizer(s, "\n");
String token = null, key = null, value = null;
while (st.hasMoreTokens()) {
token = st.nextToken().trim();
if ((token.startsWith("<") && !token.startsWith("</")) ||
token.indexOf("pixels") != -1)
{
token = token.replaceAll("<.*?>", "");
int ndx = token.indexOf(":");
if (ndx != -1) {
key = token.substring(0, ndx).trim();
value = token.substring(ndx + 1).trim();
if (key.equals("Number of steps")) {
core.sizeZ[0] = Integer.parseInt(value);
}
else if (key.equals("Image bit depth")) {
int bits = Integer.parseInt(value);
while ((bits % 8) != 0) bits++;
switch (bits) {
case 16:
core.pixelType[0] = FormatTools.UINT16;
break;
case 32:
core.pixelType[0] = FormatTools.UINT32;
break;
default: core.pixelType[0] = FormatTools.UINT8;
}
}
else if (key.equals("Image dimensions")) {
int n = value.indexOf(",");
core.sizeX[0] = Integer.parseInt(value.substring(1, n).trim());
core.sizeY[0] = Integer.parseInt(value.substring(n + 1,
value.length() - 1).trim());
}
addMeta(key, value);
}
if (token.indexOf("pixels") != -1) {
core.sizeC[0]++;
core.imageCount[0] +=
Integer.parseInt(token.substring(0, token.indexOf(" ")));
}
}
}
core.sizeT[0] = core.imageCount[0] / (core.sizeZ[0] * core.sizeC[0]);
core.rgb[0] = false;
core.currentOrder[0] = "XYZTC";
core.interleaved[0] = false;
core.littleEndian[0] = true;
core.indexed[0] = false;
core.falseColor[0] = false;
core.metadataComplete[0] = true;
// find pixels files - we think there is one channel per file
files = new Vector();
int ndx = currentId.lastIndexOf(File.separator);
String base = currentId.substring(ndx + 1, currentId.indexOf(" ", ndx));
File f = new File(currentId).getAbsoluteFile();
for (int i=0; i<core.sizeC[0]; i++) {
files.add((f.exists() ? f.getParent() + File.separator : "") + base +
" " + (i + 1) + ".xys");
}
files.add(currentId);
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);
}
}
}