/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.in;
import java.io.File;
import java.io.IOException;
import java.util.Vector;
import loci.common.DataTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
/**
* VisitechReader is the file format reader for Visitech XYS files.
*/
public class VisitechReader extends FormatReader {
// -- Constants --
public static final String[] HTML_SUFFIX = {"html"};
public static final String HEADER_MARKER = "[USE SAME FILE]";
public static final byte[] PIXELS_MARKER = new byte[] {
0, 0, 0, 0, 0, 0, (byte) 0xf0, 0x3f, 0, 0, 0, 0, 0, 0, (byte) 0xf0, 0x3f
};
// -- Fields --
/** Files in this dataset. */
private Vector<String> files;
private long[] pixelOffsets;
// -- Constructor --
public VisitechReader() {
super("Visitech XYS", new String[] {"xys", "html"});
suffixSufficient = false;
domains = new String[] {FormatTools.LM_DOMAIN};
hasCompanionFiles = true;
datasetDescription = "One .html file plus one or more .xys files";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
return getSizeY();
}
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (checkSuffix(name, "xys")) return true;
// verify that there is an .xys file in the same directory
if (name.indexOf(" ") == -1) return false;
if (!open) return false;
String prefix = name.substring(0, name.lastIndexOf(" "));
Location xys = new Location(prefix + " 1.xys");
return xys.exists();
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int plane = FormatTools.getPlaneSize(this);
int div = getSizeZ() * getSizeT();
int fileIndex = (getSeries() * getSizeC()) + no / div;
int planeIndex = no % div;
if (fileIndex >= files.size() || fileIndex >= pixelOffsets.length) {
return buf;
}
String file = files.get(fileIndex);
RandomAccessInputStream s = new RandomAccessInputStream(file);
s.order(isLittleEndian());
s.seek(pixelOffsets[fileIndex]);
int paddingBytes =
(int) (s.length() - s.getFilePointer() - div * plane) / (div - 1);
if (planeIndex > 0) {
s.skipBytes((plane + paddingBytes) * planeIndex);
}
readPlane(s, x, y, w, h, buf);
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
Vector<String> v = new Vector<String>();
v.add(currentId);
if (!noPixels && files != null) {
int nFiles = getSizeC();
for (int i=0; i<nFiles; i++) {
int index = getSeries() * nFiles + i;
if (index < files.size()) {
v.add(files.get(index));
}
}
}
return v.toArray(new String[v.size()]);
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
files = null;
pixelOffsets = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
CoreMetadata ms0 = core.get(0);
// first, make sure we have the HTML file
if (!checkSuffix(id, HTML_SUFFIX)) {
String base = id.substring(0, id.lastIndexOf(" "));
currentId = null;
initFile(base + " Report.html");
return;
}
// parse the HTML file
String s = DataTools.readFile(id);
// 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]>", "");
String key = null, value = null;
int numSeries = 0;
String[] tokens = s.split("\n");
int estimatedSeriesCount = 0, estimatedSizeC = 0;
for (String token : tokens) {
token = token.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")) {
ms0.sizeZ = Integer.parseInt(value);
}
else if (key.equals("Image bit depth")) {
int bits = Integer.parseInt(value);
while ((bits % 8) != 0) bits++;
bits /= 8;
ms0.pixelType =
FormatTools.pixelTypeFromBytes(bits, false, false);
}
else if (key.equals("Image dimensions")) {
int n = value.indexOf(",");
ms0.sizeX = Integer.parseInt(value.substring(1, n).trim());
ms0.sizeY = Integer.parseInt(value.substring(n + 1,
value.length() - 1).trim());
}
else if (key.startsWith("Channel Selection")) {
ms0.sizeC++;
}
else if (key.startsWith("Microscope XY")) {
numSeries++;
}
addGlobalMeta(key, value);
}
if (token.indexOf("pixels") != -1) {
ms0.sizeC++;
ms0.imageCount +=
Integer.parseInt(token.substring(0, token.indexOf(" ")));
}
else if (token.startsWith("Time Series")) {
int idx = token.indexOf(";") + 1;
String ss = token.substring(idx, token.indexOf(" ", idx)).trim();
ms0.sizeT = Integer.parseInt(ss);
}
}
else if (token.indexOf("Document created") != -1) {
estimatedSeriesCount++;
estimatedSizeC++;
}
}
if (numSeries == 0) {
numSeries = estimatedSeriesCount;
ms0.sizeC *= estimatedSizeC;
}
if (getSizeC() == 0) ms0.sizeC = estimatedSizeC;
if (getSizeC() == 0) ms0.sizeC = 1;
if (getSizeZ() == 0) ms0.sizeZ = 1;
// find pixels files - we think there is one channel per file
files = new Vector<String>();
int ndx = currentId.lastIndexOf(File.separator) + 1;
String base = currentId.substring(ndx, currentId.lastIndexOf(" "));
Location f = new Location(currentId).getAbsoluteFile();
String file = f.exists() ? f.getParent() + File.separator : "";
if (numSeries == 0) numSeries = 1;
for (int i=0; i<getSizeC(); i++) {
String pixelsFile = file + base + " " + (i + 1) + ".xys";
Location p = new Location(pixelsFile);
if (p.exists()) files.add(p.getAbsolutePath());
else {
if (numSeries > 1) {
ms0.sizeC -= (getSizeC() / numSeries);
numSeries--;
}
else if (getSizeC() > 1) ms0.sizeC--;
}
}
files.add(currentId);
if (getSizeT() == 0) {
ms0.sizeT = getImageCount() / (getSizeZ() * getSizeC());
if (getSizeT() == 0) ms0.sizeT = 1;
}
if (getImageCount() == 0) {
ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
}
if (numSeries > 1) {
int x = getSizeX();
int y = getSizeY();
int z = getSizeZ();
int c = getSizeC() / numSeries;
int t = getSizeT();
int count = z * c * t;
int ptype = getPixelType();
core.clear();
for (int i=0; i<numSeries; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
ms.sizeX = x;
ms.sizeY = y;
ms.sizeZ = z;
ms.sizeC = c;
ms.sizeT = t;
ms.imageCount = count;
ms.pixelType = ptype;
}
}
for (int i=0; i<getSeriesCount(); i++) {
CoreMetadata ms = core.get(i);
ms.rgb = false;
ms.dimensionOrder = "XYZTC";
ms.interleaved = false;
ms.littleEndian = true;
ms.indexed = false;
ms.falseColor = false;
ms.metadataComplete = true;
}
pixelOffsets = new long[files.size() - 1];
for (int i=0; i<pixelOffsets.length; i++) {
pixelOffsets[i] = findPixelsOffset(i);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
for (int i=0; i<numSeries; i++) {
store.setImageName("Position " + (i + 1), i);
}
}
// -- Helper methods --
private long findPixelsOffset(int fileIndex) throws IOException {
String file = files.get(fileIndex);
RandomAccessInputStream s = new RandomAccessInputStream(file);
s.order(isLittleEndian());
s.findString(false, HEADER_MARKER);
int plane = FormatTools.getPlaneSize(this);
int planeCount = getSizeZ() * getSizeT();
long skip =
(s.length() - s.getFilePointer() - (planeCount * plane)) / planeCount;
long fp = s.getFilePointer() + skip - HEADER_MARKER.length();
s.seek(fp);
if (s.readByte() == PIXELS_MARKER[PIXELS_MARKER.length - 1]) {
fp++;
}
s.close();
return fp;
}
}