/*
* #%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 loci.common.DateTools;
import loci.common.RandomAccessInputStream;
import loci.common.xml.BaseHandler;
import loci.common.xml.XMLTools;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.PhotoInterp;
import loci.formats.tiff.TiffParser;
import ome.xml.model.primitives.Timestamp;
import org.xml.sax.Attributes;
/**
* ImaconReader is the file format reader for Imacon .fff (TIFF) files.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class ImaconReader extends BaseTiffReader {
// -- Constants --
private static final int CREATOR_TAG = 34377;
private static final int XML_TAG = 50457;
private static final int PIXELS_TAG = 46275;
// -- Fields --
private String experimenterName;
private String creationDate;
private String imageName;
// -- Constructor --
/** Constructs a new Imacon reader. */
public ImaconReader() {
super("Imacon", new String[] {"fff"});
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
TiffParser parser = new TiffParser(stream);
parser.setDoCaching(false);
IFD ifd = parser.getFirstIFD();
if (ifd == null) return false;
return ifd.containsKey(XML_TAG);
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
experimenterName = null;
creationDate = null;
imageName = null;
}
}
/**
* @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 (tiffParser == null) {
initTiffParser();
}
tiffParser.getSamples(ifds.get(getSeries()), buf, x, y, w, h);
return buf;
}
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
ifds = tiffParser.getIFDs();
core.clear();
for (int i=0; i<ifds.size(); i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
ms.imageCount = 1;
IFD ifd = ifds.get(i);
ifd.remove(PIXELS_TAG);
tiffParser.fillInIFD(ifd);
PhotoInterp photo = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
ms.rgb = samples > 1 || photo == PhotoInterp.RGB ||
photo == PhotoInterp.CFA_ARRAY;
if (photo == PhotoInterp.CFA_ARRAY) samples = 3;
ms.sizeX = (int) ifd.getImageWidth();
ms.sizeY = (int) ifd.getImageLength();
ms.sizeZ = 1;
ms.sizeC = isRGB() ? samples : 1;
ms.sizeT = 1;
ms.pixelType = ifd.getPixelType();
ms.indexed = photo == PhotoInterp.RGB_PALETTE;
ms.dimensionOrder = "XYCZT";
ms.interleaved = false;
}
IFD firstIFD = ifds.get(0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
String xml = firstIFD.getIFDTextValue(XML_TAG).trim();
xml = xml.substring(xml.indexOf("<"));
XMLTools.parseXML(xml, new ImaconHandler());
}
String[] creationInfo = firstIFD.getIFDTextValue(CREATOR_TAG).split("\n");
if (creationInfo.length > 4) {
experimenterName = creationInfo[4].trim();
}
if (creationInfo.length > 6) {
imageName = creationInfo[6].trim();
}
if (creationInfo.length > 8) {
creationDate = creationInfo[8].trim();
}
if (creationInfo.length > 10) {
creationDate += " " + creationInfo[10].trim();
}
}
/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
if (creationDate != null) {
creationDate = DateTools.formatDate(creationDate, "yyyyMMdd HHmmSSZ");
}
for (int i=0; i<getSeriesCount(); i++) {
String name = imageName;
if (imageName.length() == 0) {
name = "#" + (i + 1);
}
else {
name += " #" + (i + 1);
}
store.setImageName(name, i);
if (creationDate != null) {
store.setImageAcquisitionDate(new Timestamp(creationDate), i);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (experimenterName == null) experimenterName = "";
int nameSpace = experimenterName.indexOf(" ");
String firstName =
nameSpace == -1 ? "" : experimenterName.substring(0, nameSpace);
String lastName = nameSpace == -1 ? experimenterName :
experimenterName.substring(nameSpace + 1);
String experimenter = MetadataTools.createLSID("Experimenter", 0);
store.setExperimenterID(experimenter, 0);
store.setExperimenterFirstName(firstName, 0);
store.setExperimenterLastName(lastName, 0);
for (int i=0; i<getSeriesCount(); i++) {
store.setImageExperimenterRef(experimenter, i);
}
}
}
// -- Helper class --
class ImaconHandler extends BaseHandler {
private String key, value;
private String qName;
// -- DefaultHandler API methods --
@Override
public void characters(char[] data, int start, int len) {
if (qName.equals("key")) {
key = new String(data, start, len);
value = null;
}
else value = new String(data, start, len);
if (key != null && value != null) {
addGlobalMeta(key, value);
}
}
@Override
public void startElement(String uri, String localName, String qName,
Attributes attributes)
{
this.qName = qName;
}
}
}