//
// TrestleReader.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.io.IOException;
import java.util.ArrayList;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import loci.common.DataTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.ImageReader;
import loci.formats.MetadataTools;
import loci.formats.codec.BitWriter;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.PhotoInterp;
import loci.formats.tiff.TiffParser;
/**
* TrestleReader is the file format reader for Trestle slide datasets.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/TrestleReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/TrestleReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class TrestleReader extends BaseTiffReader {
// -- Constants --
/** Logger for this class. */
private static final Logger LOGGER =
LoggerFactory.getLogger(TrestleReader.class);
// -- Fields --
private ArrayList<String> files;
private String roiFile;
private String roiDrawFile;
private int[] overlaps;
// -- Constructor --
/** Constructs a new Trestle reader. */
public TrestleReader() {
super("Trestle", new String[] {"tif"});
domains = new String[] {FormatTools.HISTOLOGY_DOMAIN};
suffixSufficient = false;
suffixNecessary = false;
hasCompanionFiles = true;
datasetDescription = "One .tif file plus several other similarly-named " +
"files (e.g. *.FocalPlane-*, .sld, .slx, .ROI)";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
if (super.isThisType(name, open)) return true;
if (!checkSuffix(name, "tif") && open) {
Location current = new Location(name).getAbsoluteFile();
Location parent = current.getParentFile();
String tiff = current.getName();
int index = tiff.lastIndexOf(".");
if (index >= 0) {
tiff = tiff.substring(0, index);
}
tiff += ".tif";
Location tiffFile = new Location(parent, tiff);
return tiffFile.exists() && isThisType(tiffFile.getAbsolutePath(), open);
}
return false;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
TiffParser parser = new TiffParser(stream);
IFD ifd = parser.getFirstIFD();
if (ifd == null) return false;
String copyright = ifd.getIFDTextValue(IFD.COPYRIGHT);
if (copyright == null) return false;
return copyright.indexOf("Trestle Corp.") >= 0;
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return files.toArray(new String[files.size()]);
}
String[] allFiles = new String[files.size() + 1];
files.toArray(allFiles);
allFiles[allFiles.length - 1] = currentId;
return allFiles;
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
if (getSeriesCount() == 1) {
return super.openBytes(no, buf, x, y, w, h);
}
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
tiffParser.getSamples(ifds.get(series), buf, x, y, w, h,
overlaps[getSeries() * 2], overlaps[getSeries() * 2 + 1]);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
files = null;
}
}
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
try {
return (int) ifds.get(getSeries()).getTileWidth();
}
catch (FormatException e) {
LOGGER.debug("", e);
}
return super.getOptimalTileWidth();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
try {
return (int) ifds.get(getSeries()).getTileLength();
}
catch (FormatException e) {
LOGGER.debug("", e);
}
return super.getOptimalTileHeight();
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "tif")) {
Location parent = new Location(id).getAbsoluteFile().getParentFile();
String[] list = parent.list(true);
for (String f : list) {
if (checkSuffix(f, "tif")) {
String path = new Location(parent, f).getAbsolutePath();
if (isThisType(path)) {
id = path;
break;
}
}
}
}
super.initFile(id);
}
// -- Internal BaseTiffReader API methods --
/* @see loci.formats.in.BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
ifds = tiffParser.getIFDs();
for (IFD ifd : ifds) {
tiffParser.fillInIFD(ifd);
}
String comment = ifds.get(0).getComment();
String[] values = comment.split(";");
for (String v : values) {
int eq = v.indexOf("=");
if (eq < 0) continue;
String key = v.substring(0, eq).trim();
String value = v.substring(eq + 1).trim();
addGlobalMeta(key, value);
if (key.equals("OverlapsXY")) {
String[] overlapValues = value.split(" ");
overlaps = new int[ifds.size() * 2];
for (int i=0; i<overlapValues.length; i++) {
overlaps[i] = Integer.parseInt(overlapValues[i]);
}
}
}
core = new CoreMetadata[ifds.size()];
for (int i=0; i<core.length; i++) {
setSeries(i);
core[i] = new CoreMetadata();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
}
}
setSeries(0);
// repopulate core metadata
for (int s=0; s<core.length; s++) {
IFD ifd = ifds.get(s);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
long numTileRows = ifd.getTilesPerColumn() - 1;
long numTileCols = ifd.getTilesPerRow() - 1;
int overlapX = overlaps[s * 2];
int overlapY = overlaps[s * 2 + 1];
core[s].sizeX = (int) (ifd.getImageWidth() - (numTileCols * overlapX));
core[s].sizeY = (int) (ifd.getImageLength() - (numTileRows * overlapY));
core[s].sizeZ = 1;
core[s].sizeT = 1;
core[s].sizeC = core[s].rgb ? samples : 1;
core[s].littleEndian = ifd.isLittleEndian();
core[s].indexed = p == PhotoInterp.RGB_PALETTE &&
(get8BitLookupTable() != null || get16BitLookupTable() != null);
core[s].imageCount = 1;
core[s].pixelType = ifd.getPixelType();
core[s].metadataComplete = true;
core[s].interleaved = false;
core[s].falseColor = false;
core[s].dimensionOrder = "XYCZT";
core[s].thumbnail = s > 0;
}
// look for all of the other associated metadata files
files = new ArrayList<String>();
Location baseFile = new Location(currentId).getAbsoluteFile();
Location parent = baseFile.getParentFile();
String name = baseFile.getName();
if (name.indexOf(".") >= 0) {
name = name.substring(0, name.indexOf(".") + 1);
}
roiFile = new Location(parent, name + "ROI").getAbsolutePath();
roiDrawFile = new Location(parent, name + "ROI-draw").getAbsolutePath();
String[] list = parent.list(true);
for (String f : list) {
if (!f.equals(baseFile.getName())) {
files.add(new Location(parent, f).getAbsolutePath());
}
}
}
/* @see loci.formats.BaseTiffReader#initMetadataStore() */
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
for (int i=0; i<getSeriesCount(); i++) {
store.setImageName("Series " + (i + 1), i);
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
if (level != MetadataLevel.NO_OVERLAYS) {
try {
parseROIs(store);
}
catch (IOException e) {
LOGGER.debug("Could not parse ROIs", e);
}
}
}
}
// -- Helper methods --
private void parseROIs(MetadataStore store)
throws FormatException, IOException
{
if (MetadataTools.isOMEXMLMetadata(store) ||
MetadataTools.isOMEXMLRoot(store.getRoot()))
{
return;
}
String roiID = MetadataTools.createLSID("ROI", 0, 0);
String maskID = MetadataTools.createLSID("Shape", 0, 0);
store.setROIID(roiID, 0);
store.setMaskID(maskID, 0, 0);
String positionData = DataTools.readFile(roiDrawFile);
String[] coordinates = positionData.split("[ ,]");
double x1 = Double.parseDouble(coordinates[1]);
double y1 = Double.parseDouble(coordinates[2]);
double x2 = Double.parseDouble(coordinates[3]);
double y2 = Double.parseDouble(coordinates[5]);
store.setMaskX(x1, 0, 0);
store.setMaskY(y1, 0, 0);
store.setMaskWidth(x2 - x1, 0, 0);
store.setMaskHeight(y2 - y1, 0, 0);
store.setImageROIRef(roiID, 0, 0);
ImageReader roiReader = new ImageReader();
roiReader.setId(roiFile);
byte[] roiPixels = roiReader.openBytes(0);
roiReader.close();
BitWriter bits = new BitWriter(roiPixels.length / 8);
for (int i=0; i<roiPixels.length; i++) {
bits.write(roiPixels[i] == 0 ? 0 : 1, 1);
}
store.setMaskBinData(bits.toByteArray(), 0, 0);
}
}