/*
* #%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.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.ome.OMEXMLMetadata;
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.
*/
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) */
@Override
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) */
@Override
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) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
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)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
if (core.size() == 1) {
return super.openBytes(no, buf, x, y, w, h);
}
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
tiffParser.getSamples(ifds.get(getCoreIndex()), buf, x, y, w, h,
overlaps[getCoreIndex() * 2], overlaps[getCoreIndex() * 2 + 1]);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
files = null;
}
}
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
try {
return (int) ifds.get(getCoreIndex()).getTileWidth();
}
catch (FormatException e) {
LOGGER.debug("", e);
}
return super.getOptimalTileWidth();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
try {
return (int) ifds.get(getCoreIndex()).getTileLength();
}
catch (FormatException e) {
LOGGER.debug("", e);
}
return super.getOptimalTileHeight();
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
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() */
@Override
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]);
}
}
}
int seriesCount = ifds.size();
core.clear();
for (int i=0; i<seriesCount; i++) {
CoreMetadata c = new CoreMetadata();
if (i == 0 && !hasFlattenedResolutions()) {
c.resolutionCount = seriesCount;
}
core.add(c);
}
// repopulate core metadata
for (int s=0; s<core.size(); s++) {
CoreMetadata ms = core.get(s);
IFD ifd = ifds.get(s);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
ms.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];
ms.sizeX = (int) (ifd.getImageWidth() - (numTileCols * overlapX));
ms.sizeY = (int) (ifd.getImageLength() - (numTileRows * overlapY));
ms.sizeZ = 1;
ms.sizeT = 1;
ms.sizeC = ms.rgb ? samples : 1;
ms.littleEndian = ifd.isLittleEndian();
ms.indexed = p == PhotoInterp.RGB_PALETTE &&
(get8BitLookupTable() != null || get16BitLookupTable() != null);
ms.imageCount = 1;
ms.pixelType = ifd.getPixelType();
ms.metadataComplete = true;
ms.interleaved = false;
ms.falseColor = false;
ms.dimensionOrder = "XYCZT";
ms.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() */
@Override
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) {
// do not store the mask data in OME-XML MetadataStores
// doing so would guarantee invalid OME-XML, since the required BinData
// will not be stored with the mask dimensions
if (level != MetadataLevel.NO_OVERLAYS &&
!(getMetadataStore() instanceof OMEXMLMetadata))
{
try {
parseROIs(store);
}
catch (IOException e) {
LOGGER.debug("Could not parse ROIs", e);
}
}
}
}
// -- Helper methods --
private void parseROIs(MetadataStore store)
throws FormatException, IOException
{
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);
}
}