com.actelion.research.orbit.imageAnalysis.models.ImageAnnotation Maven / Gradle / Ivy
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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 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 convertToImageAnnotations(List rawAnnotations) {
if (rawAnnotations == null) return null;
List iaList = new ArrayList(rawAnnotations.size());
try {
for (RawAnnotation ra : rawAnnotations) {
if (ra.getRawAnnotationType() == RawAnnotation.ANNOTATION_TYPE_IMAGE) {
ImageAnnotation ia = new ImageAnnotation(ra);
iaList.add(ia);
}
}
} catch (IOException e) {
e.printStackTrace();
} catch (ClassNotFoundException e) {
e.printStackTrace();
}
return iaList;
}
public Shape getFirstShape() {
Shape cs = shape.getShapeList().get(0);
return cs;
}
public ClassShape getShape() {
return shape;
}
public void setShape(ClassShape shape) {
this.shape = shape;
}
/**
* sRGB color in int encoding
*
* @return
*/
public int getColor() {
return color;
}
/**
* sRGB color in int encoding
*
* @param color
*/
public void setColor(int color) {
this.color = color;
if (getShape() != null) {
getShape().setColor(new Color(color));
}
}
public int getSubType() {
return subType;
}
public void setSubType(int subType) {
this.subType = subType;
}
public int getGroup() {
return group;
}
public void setGroup(int group) {
this.group = group;
}
@Override
public byte[] getData() {
IScaleableShape p = ((IScaleableShape) shape.getShapeList().get(0));
//p.setClosed(true);
data = null;
ByteArrayOutputStream os = null;
ObjectOutputStream oos = null;
try {
os = new ByteArrayOutputStream();
oos = new ObjectOutputStream(os);
oos.writeInt(color);
oos.writeObject(p);
oos.writeInt(subType);
oos.writeInt(group);
oos.flush();
oos.close();
data = os.toByteArray();
} catch (Exception ex) {
} finally {
if (oos != null) try {
oos.close();
} catch (IOException e) {
}
if (os != null) try {
os.close();
} catch (IOException e) {
}
}
return data;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equalsInherited(o)) return false;
ImageAnnotation that = (ImageAnnotation) o;
if (color != that.color) return false;
if (group != that.group) return false;
if (subType != that.subType) return false;
if (description != null && !description.equals(that.getDescription())) return false;
return shape != null ? shape.equals(that.shape) : that.shape == null;
}
@Override
public int hashCode() {
int result = super.hashCodeInherited();
result = 31 * result + (shape != null ? shape.hashCode() : 0);
result = 31 * result + color;
result = 31 * result + subType;
result = 31 * result + group;
result = 31 * result + (description != null ? description.hashCode() : 0);
return result;
}
public String getSubTypeName() {
return ImageAnnotation.getSubTypeName(subType);
}
public static String getSubTypeName(int subType) {
switch (subType) {
case SUBTYPE_NORMAL: {
return "normal";
}
case SUBTYPE_ROI: {
return "ROI";
}
case SUBTYPE_INCLUSION: {
return "inclusion";
}
case SUBTYPE_EXCLUSION: {
return "exclusion";
}
default: {
return "normal";
}
}
}
public static int getSubTypeNum(String name) {
if (name.equalsIgnoreCase("normal")) return SUBTYPE_NORMAL;
else if (name.equalsIgnoreCase("ROI")) return SUBTYPE_ROI;
else if (name.equalsIgnoreCase("inclusion")) return SUBTYPE_INCLUSION;
else if (name.equalsIgnoreCase("exclusion")) return SUBTYPE_EXCLUSION;
else
return SUBTYPE_NORMAL;
}
@Override
public int getRawAnnotationType() {
return ANNOTATION_TYPE_IMAGE;
}
@Override
public String toString() {
return "ImageAnnotation [hash=" + hashCode() + ", shape=" + shape + ", color=" + color + ", subType=" + getSubTypeName() + ", group=" + group + ", rawAnnotationId=" + rawAnnotationId + ", rawDataFileId=" + rawDataFileId
+ ", rawAnnotationType=" + rawAnnotationType + ", description=" + description + ", userId=" + userId + ", modifyDate=" + modifyDate + "]";
}
@Override
public ImageAnnotation clone() {
return SerialClone.clone(this);
}
public boolean isSelected() {
return selected;
}
public void setSelected(boolean selected) {
this.selected = selected;
}
public static class SubType {
private int subType = SUBTYPE_NORMAL;
public SubType(int subType) {
this.subType = subType;
}
public int getSubType() {
return subType;
}
public void setSubType(int subType) {
this.subType = subType;
}
@Override
public String toString() {
return ImageAnnotation.getSubTypeName(subType);
}
}
}