/*
* #%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.ArrayList;
import loci.common.Constants;
import loci.common.DataTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.common.xml.BaseHandler;
import loci.common.xml.XMLTools;
import loci.formats.ChannelSeparator;
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;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.PositiveInteger;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
import ome.units.quantity.Time;
import ome.units.UNITS;
import org.xml.sax.Attributes;
/**
* AFIReader is the file format reader for Aperio AFI files.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class AFIReader extends FormatReader {
// -- Constants --
private static final int EXTRA_IMAGES = 3;
// -- Fields --
private ArrayList<String> pixels = new ArrayList<String>();
private ChannelSeparator[] reader;
// -- Constructor --
/** Constructs a new AFI reader. */
public AFIReader() {
super("Aperio AFI", "afi");
domains = new String[] {FormatTools.HISTOLOGY_DOMAIN};
hasCompanionFiles = true;
datasetDescription = "One .afi file and several similarly-named .svs files";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return true;
}
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
return reader[0].getOptimalTileWidth();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
return reader[0].getOptimalTileHeight();
}
/* @see loci.formats.IFormatReader#openThumbBytes(int) */
@Override
public byte[] openThumbBytes(int no) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
if (getCoreIndex() >= core.size() - EXTRA_IMAGES) {
reader[0].setCoreIndex(getCoreIndex());
return reader[0].openThumbBytes(no);
}
int coreIndex = getCoreIndex();
setCoreIndex(core.size() - EXTRA_IMAGES - 1);
byte[] thumb = FormatTools.openThumbBytes(this, no);
setCoreIndex(coreIndex);
return thumb;
}
/**
* @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);
if (getCoreIndex() >= core.size() - EXTRA_IMAGES) {
reader[0].setCoreIndex(getCoreIndex());
return reader[0].openBytes(no, buf, x, y, w, h);
}
int[] coords = getZCTCoords(no);
int channel = coords[1];
int index = getIndex(coords[0], 0, coords[2]);
reader[channel].setCoreIndex(getCoreIndex());
return reader[channel].openBytes(index, buf, x, y, w, h);
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return new String[] {currentId};
}
String[] files = new String[pixels.size() + 1];
files[0] = currentId;
for (int i=0; i<pixels.size(); i++) {
files[i + 1] = pixels.get(i);
}
return files;
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
if (reader != null) {
for (ChannelSeparator r : reader) {
if (r != null) {
r.close();
}
}
}
reader = null;
pixels.clear();
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
// The AFI file is just simple XML that lists the .svs files from
// which to read pixel data. Each .svs corresponds to a single channel;
// we assemble the channels in the order in which they are stored in
// the XML.
//
// Note that the last two series are identical across the .svs files,
// so we just use the ones from the first listed file.
String xml = DataTools.readFile(id);
XMLTools.parseXML(xml, new AFIHandler());
String parent = new Location(id).getAbsoluteFile().getParent();
String[] channelNames = new String[pixels.size()];
reader = new ChannelSeparator[pixels.size()];
for (int i=0; i<pixels.size(); i++) {
String file = pixels.get(i);
int underscore = file.indexOf("_");
int fullStop = file.indexOf(".");
if (underscore >= 0 && fullStop > underscore) {
channelNames[i] = file.substring(underscore + 1, fullStop);
}
pixels.set(i, new Location(parent, file).getAbsolutePath());
reader[i] = new ChannelSeparator(new SVSReader());
reader[i].setFlattenedResolutions(hasFlattenedResolutions());
reader[i].setId(pixels.get(i));
}
core = reader[0].getCoreMetadataList();
for (int i=0; i<core.size() - EXTRA_IMAGES; i++) {
CoreMetadata c = core.get(i);
c.sizeC = pixels.size();
c.imageCount = c.sizeC * c.sizeZ * c.sizeT;
c.rgb = false;
if (i == 0) {
c.resolutionCount = core.size() - EXTRA_IMAGES;
}
}
MetadataStore store = makeFilterMetadata();
boolean minimalMetadata =
getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
MetadataTools.populatePixels(store, this, !minimalMetadata);
String fileID = currentId.substring(
currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
for (int i=0; i<getSeriesCount(); i++) {
store.setImageName(fileID + " - image #" + (i + 1), i);
}
if (!minimalMetadata) {
Length[] emission = new Length[pixels.size()];
Length[] excitation = new Length[pixels.size()];
Double[] exposure = new Double[pixels.size()];
Timestamp[] datestamp = new Timestamp[pixels.size()];
Length[] physicalSizes = null;
double magnification = Double.NaN;
for (int c=0; c<pixels.size(); c++) {
SVSReader baseReader = (SVSReader) reader[c].getReader();
emission[c] = baseReader.getEmission();
excitation[c] = baseReader.getExcitation();
exposure[c] = baseReader.getExposureTime();
datestamp[c] = baseReader.getDatestamp();
physicalSizes = baseReader.getPhysicalSizes();
if (c == 0) {
magnification = baseReader.getMagnification();
}
}
String instrument = MetadataTools.createLSID("Instrument", 0);
String objective = MetadataTools.createLSID("Objective", 0, 0);
store.setInstrumentID(instrument, 0);
store.setObjectiveID(objective, 0, 0);
store.setObjectiveNominalMagnification(magnification, 0, 0);
for (int i=0; i<getSeriesCount() - EXTRA_IMAGES; i++) {
if (datestamp[0] != null) {
store.setImageAcquisitionDate(datestamp[0], i);
}
store.setImageInstrumentRef(instrument, i);
store.setObjectiveSettingsID(objective, i);
if (i < physicalSizes.length &&
physicalSizes[i] != null &&
physicalSizes[i].value(UNITS.MICROM).doubleValue() - Constants.EPSILON > 0)
{
Length size = physicalSizes[i];
store.setPixelsPhysicalSizeX(size, i);
store.setPixelsPhysicalSizeY(size, i);
}
for (int c=0; c<channelNames.length; c++) {
store.setChannelName(channelNames[c], i, c);
if (emission[c] != null) {
store.setChannelEmissionWavelength(emission[c], i, c);
}
if (excitation[c] != null) {
store.setChannelExcitationWavelength(excitation[c], i, c);
}
store.setPlaneExposureTime(FormatTools.createTime(exposure[c], UNITS.S), i, c);
}
}
}
}
// -- Helper class --
class AFIHandler extends BaseHandler {
private String currentElement;
@Override
public void characters(char[] ch, int start, int length) {
String value = new String(ch, start, length);
if (currentElement.equals("Path") && value.trim().length() > 0) {
pixels.add(value);
}
}
@Override
public void startElement(String uri, String localName, String qName,
Attributes attributes)
{
currentElement = qName;
}
}
}