/*
* #%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.util.Hashtable;
import java.util.Vector;
import loci.common.xml.BaseHandler;
import ome.units.UNITS;
import ome.units.quantity.Length;
import org.xml.sax.Attributes;
/**
* MetamorphTiffReader is the file format reader for TIFF files produced by
* Metamorph software version 7.5 and above.
*
* @author Melissa Linkert melissa at glencoesoftware.com
* @author Thomas Caswell tcaswell at uchicago.edu
*/
public class MetamorphHandler extends BaseHandler {
// -- Fields --
private Hashtable metadata;
private Vector<String> timestamps;
private String imageName;
private String date;
private Vector<Integer> wavelengths;
private Vector<Double> zPositions;
private double pixelSizeX, pixelSizeY;
private double temperature;
private double lensNA;
private String binning;
private double readOutRate, zoom;
private Length positionX, positionY;
private Vector<Double> exposures;
private String channelName;
private String stageLabel;
private Double gain;
// -- Constructor --
public MetamorphHandler() {
this(null);
}
public MetamorphHandler(Hashtable metadata) {
super();
this.metadata = metadata;
timestamps = new Vector<String>();
wavelengths = new Vector<Integer>();
zPositions = new Vector<Double>();
exposures = new Vector<Double>();
}
// -- MetamorphHandler API methods --
public Double getGain() { return gain; }
public String getChannelName() { return channelName; }
public String getStageLabel() { return stageLabel; }
public Vector<String> getTimestamps() { return timestamps; }
public Vector<Integer> getWavelengths() { return wavelengths; }
public Vector<Double> getZPositions() { return zPositions; }
public String getDate() { return date; }
public String getImageName() { return imageName; }
public double getPixelSizeX() { return pixelSizeX; }
public double getPixelSizeY() { return pixelSizeY; }
public double getTemperature() { return temperature; }
public String getBinning() { return binning; }
public double getReadOutRate() { return readOutRate; }
public double getZoom() { return zoom; }
public Length getStagePositionX() { return positionX; }
public Length getStagePositionY() { return positionY; }
public double getLensNA() { return lensNA; }
public Vector<Double> getExposures() { return exposures; }
// -- DefaultHandler API methods --
@Override
public void startElement(String uri, String localName, String qName,
Attributes attributes)
{
String id = attributes.getValue("id");
String value = attributes.getValue("value");
String delim = " #13; #10;";
if (value != null && value.indexOf(delim) < 0) {
delim = "
";
}
if (id != null && value != null) {
if (id.equals("Description")) {
if (metadata != null) metadata.remove("Comment");
String k = null, v = null;
if (value.indexOf(delim) != -1) {
int currentIndex = -delim.length();
while (currentIndex != -1) {
currentIndex += delim.length();
int nextIndex = value.indexOf(delim, currentIndex);
String line = null;
if (nextIndex == -1) {
line = value.substring(currentIndex, value.length());
}
else {
line = value.substring(currentIndex, nextIndex);
}
currentIndex = nextIndex;
int colon = line.indexOf(":");
if (colon != -1) {
k = line.substring(0, colon).trim();
v = line.substring(colon + 1).trim();
if (metadata != null) metadata.put(k, v);
checkKey(k, v);
}
}
}
else {
int colon = value.indexOf(":");
while (colon != -1) {
k = value.substring(0, colon);
int space = value.lastIndexOf(" ", value.indexOf(":", colon + 1));
if (space == -1) space = value.length();
v = value.substring(colon + 1, space).trim();
if (metadata != null) metadata.put(k, v);
value = value.substring(space).trim();
colon = value.indexOf(":");
checkKey(k, v);
}
}
}
else {
if (metadata != null) metadata.put(id, value);
checkKey(id, value);
}
}
}
// -- Helper methods --
/** Check if the value needs to be saved. */
private void checkKey(String key, String value) {
if (key.equals("Temperature")) {
temperature = Double.parseDouble(value);
}
else if (key.equals("spatial-calibration-x")) {
pixelSizeX = Double.parseDouble(value);
}
else if (key.equals("spatial-calibration-y")) {
pixelSizeY = Double.parseDouble(value);
}
else if (key.equals("z-position")) {
zPositions.add(new Double(value));
}
else if (key.equals("wavelength")) {
wavelengths.add(new Integer(value));
}
else if (key.equals("acquisition-time-local")) {
date = value;
timestamps.add(date);
}
else if (key.equals("image-name")) imageName = value;
else if (key.equals("Binning")) {
binning = value;
}
else if (key.equals("Readout Frequency")) {
readOutRate = Double.parseDouble(value);
}
else if (key.equals("zoom-percent")) {
zoom = Double.parseDouble(value);
}
else if (key.equals("stage-position-x")) {
final Double number = Double.valueOf(value);
positionX = new Length(number, UNITS.REFERENCEFRAME);
if (metadata != null) {
metadata.put("X position for position #1", positionX);
}
}
else if (key.equals("stage-position-y")) {
final Double number = Double.valueOf(value);
positionY = new Length(number, UNITS.REFERENCEFRAME);
if (metadata != null) {
metadata.put("Y position for position #1", positionY);
}
}
else if (key.equals("Speed")) {
int space = value.indexOf(" ");
if (space > 0) {
value = value.substring(0, space);
}
try {
readOutRate = Double.parseDouble(value.trim());
}
catch (NumberFormatException e) { }
}
else if (key.equals("Exposure")) {
if (value.indexOf(" ") != -1) {
value = value.substring(0, value.indexOf(" "));
}
// exposure times are stored in milliseconds, we want them in seconds
try {
exposures.add(new Double(Double.parseDouble(value) / 1000));
}
catch (NumberFormatException e) { }
}
else if (key.equals("_IllumSetting_")) {
channelName = value;
}
else if (key.equals("stage-label")) {
stageLabel = value;
}
else if (key.endsWith("Gain") && gain == null) {
try {
gain = new Double(value.replaceAll("[xX]", ""));
}
catch (NumberFormatException e) { }
}
else if (key.equals("_MagNA_")) {
lensNA = Double.parseDouble(value);
}
}
}