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common objects for orbit image analysis
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2016 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
*
* 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 3 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 {
public static final DateFormat HCSdateFormat = new SimpleDateFormat("dd.MM.yyyy HH:mm:ss,SSS Z");
public static final char HCSSeparator = '\t';
private static final long serialVersionUID = 1L;
private String containerName = "";
private String wellName = "";
private int siteX = 0;
private int siteY = 0;
private double siteZ = 0;
private String objectId = "";
private int objectX = 0;
private int objectY = 0;
private Date dateTime = new Date();
private double[] values = null;
public HCSRow() {
}
public HCSRow(String containerName, String wellName, int siteX, int siteY, double siteZ, String objectId, int objectX, int objectY, Date dateTime,
double[] values) {
this.containerName = containerName;
this.wellName = wellName;
this.siteX = siteX;
this.siteY = siteY;
this.siteZ = siteZ;
this.objectId = objectId;
this.objectX = objectX;
this.objectY = objectY;
this.dateTime = dateTime;
this.values = values;
}
/**
* Parses a HCSRow.toString() string and create a HCSRow instance.
* Returns null if s is null.
*
* @param s
* @return
* @throws ParseException
*/
public static HCSRow parseHCSRow(String s) throws ParseException {
if (s == null) return null;
String[] split = s.split(String.valueOf(HCSSeparator), -1);
if (split == null || split.length < 9)
throw new ParseException("argument is not a valid HCSRow (null or length<9)", 0);
Date dateTime = HCSdateFormat.parse(split[8]);
double[] values = null;
if (split.length > 9) {
values = new double[split.length - 9];
double d = Double.NaN;
for (int i = 0; i < split.length - 9; i++) {
try {
d = Double.parseDouble(split[i + 9]);
} catch (Exception e) {
d = Double.NaN;
}
values[i] = d;
}
}
return new HCSRow(split[0], split[1], Integer.parseInt(split[2]), Integer.parseInt(split[3]), Double.parseDouble(split[4]),
split[5], Integer.parseInt(split[6]), Integer.parseInt(split[7]), dateTime, values);
}
/**
* Returns one data line as a string with respect to HCSSeparator and HCSDateFormat.
* Remark: No StringBuilder is used because in most cases values.length will be around 4.
* If length is >> 4 a StringBuilder should be considered.
*/
@Override
public String toString() {
String s = containerName + HCSSeparator + wellName + HCSSeparator + siteX + HCSSeparator + siteY + HCSSeparator + siteZ + HCSSeparator + objectId + HCSSeparator + objectX + HCSSeparator + objectY + HCSSeparator + HCSdateFormat.format(dateTime);
if (values != null) {
for (double v : values) {
String ds = Double.isNaN(v) ? "" : Double.toString(v);
s += HCSSeparator + ds;
}
}
return s;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((containerName == null) ? 0 : containerName.hashCode());
result = prime * result + ((dateTime == null) ? 0 : dateTime.hashCode());
result = prime * result + ((objectId == null) ? 0 : objectId.hashCode());
result = prime * result + objectX;
result = prime * result + objectY;
result = prime * result + siteX;
result = prime * result + siteY;
long temp;
temp = Double.doubleToLongBits(siteZ);
result = prime * result + (int) (temp ^ (temp >>> 32));
result = prime * result + Arrays.hashCode(values);
result = prime * result + ((wellName == null) ? 0 : wellName.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (!(obj instanceof HCSRow))
return false;
HCSRow other = (HCSRow) obj;
if (containerName == null) {
if (other.containerName != null)
return false;
} else if (!containerName.equals(other.containerName))
return false;
if (dateTime == null) {
if (other.dateTime != null)
return false;
} else if (!dateTime.equals(other.dateTime))
return false;
if (objectId == null) {
if (other.objectId != null)
return false;
} else if (!objectId.equals(other.objectId))
return false;
if (objectX != other.objectX)
return false;
if (objectY != other.objectY)
return false;
if (siteX != other.siteX)
return false;
if (siteY != other.siteY)
return false;
if (Double.doubleToLongBits(siteZ) != Double.doubleToLongBits(other.siteZ))
return false;
if (!Arrays.equals(values, other.values))
return false;
if (wellName == null) {
if (other.wellName != null)
return false;
} else if (!wellName.equals(other.wellName))
return false;
return true;
}
public String getContainerName() {
return containerName;
}
public void setContainerName(String containerName) {
this.containerName = containerName;
}
public String getWellName() {
return wellName;
}
public void setWellName(String wellName) {
this.wellName = wellName;
}
public int getSiteX() {
return siteX;
}
public void setSiteX(int siteX) {
this.siteX = siteX;
}
public int getSiteY() {
return siteY;
}
public void setSiteY(int siteY) {
this.siteY = siteY;
}
public double getSiteZ() {
return siteZ;
}
public void setSiteZ(double siteZ) {
this.siteZ = siteZ;
}
public String getObjectId() {
return objectId;
}
public void setObjectId(String objectId) {
this.objectId = objectId;
}
public int getObjectX() {
return objectX;
}
public void setObjectX(int objectX) {
this.objectX = objectX;
}
public int getObjectY() {
return objectY;
}
public void setObjectY(int objectY) {
this.objectY = objectY;
}
public Date getDateTime() {
return dateTime;
}
public void setDateTime(Date dateTime) {
this.dateTime = dateTime;
}
public double[] getValues() {
return values;
}
public void setValues(double[] values) {
this.values = values;
}
public static DateFormat getHcsdateformat() {
return HCSdateFormat;
}
public int compareTo(HCSRow o) {
if (o == null) return -1;
if (this == o) return 0;
int comp;
// containerName
if (containerName != null && o.getContainerName() != null) {
comp = containerName.compareTo(o.getContainerName());
if (comp != 0) return comp;
}
// wellName
if (wellName != null && o.getWellName() != null) {
comp = wellName.compareTo(o.getWellName());
if (comp != 0) return comp;
}
// siteX,Y,Z
if (siteX != o.getSiteX()) return siteX - o.getSiteX();
if (siteY != o.getSiteY()) return siteY - o.getSiteY();
if (siteZ != o.getSiteZ()) return (int) Math.signum(siteZ - o.getSiteZ());
// objectId
if (objectId != null && o.getObjectId() != null) {
comp = objectId.compareTo(o.getObjectId());
if (comp != 0) return comp;
}
// objectX,Y
if (objectX != o.getObjectX()) return objectX - o.getObjectX();
if (objectY != o.getObjectY()) return objectY - o.getObjectY();
return dateTime.compareTo(o.getDateTime());
}
}