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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 imageMap;
public final Map> objectCountMap = new ConcurrentHashMap<>();
public final Map orbitDataMap = new ConcurrentHashMap<>();
private final Random random = new Random();
private String path;
private OrbitModel model;
private String pipeline;
private String orbitUser = "";
public CpParser(String orbitUser) {
this.orbitUser = orbitUser;
}
private Map parseImages() throws Exception {
Map imageMap = new ConcurrentHashMap<>();
//File file = new File(path + File.separator + imageName + ending);
File file = null;
for (File f : new File(path).listFiles()) {
if (f.getName().toLowerCase().endsWith("image.csv")) {
file = f;
break;
}
}
if (file == null) {
throw new Exception("no *Image.csv found. Please configure your CP pipeline so that CP produces an *Image.csv file.");
}
try (
FileReader fr = new FileReader(file);
BufferedReader reader = new BufferedReader(fr);
) {
imageMap.clear();
String line;
reader.readLine(); // header
while ((line = reader.readLine()) != null) {
String[] split = line.split(sep);
int id = Integer.parseInt(split[0]);
CpImage img = new CpImage(id, Integer.parseInt(split[1]), Integer.parseInt(split[2]), Integer.parseInt(split[3]));
imageMap.put(id, img);
//System.out.println("img: "+img);
}
}
return imageMap;
}
private void parseObject(String objName, boolean writeDB, List objectNames) throws Exception {
log.info("parseObj " + objName + " start");
Map objNameMap = new HashMap<>();
for (int i = 0; i < objectNames.size(); i++) {
objNameMap.put(objectNames.get(i), i);
}
//if (model.getExclusionModel() == null) throw new Exception("no exclusion model available");
File file = new File(path + File.separator + objName + ending);
try (
FileReader fr = new FileReader(file);
BufferedReader reader = new BufferedReader(fr);
) {
String line;
reader.readLine(); // header
int lastImageId = -1;
int lastOrbitId = -1;
CpImage img = null;
OrbitData orbitData = null;
int cnt = 0;
while ((line = reader.readLine()) != null) {
cnt++;
String[] split = line.split(sep);
int imgId = Integer.parseInt(split[0]);
if (imgId != lastImageId) {
if (!imageMap.containsKey(imgId))
throw new IllegalArgumentException("Image with id " + imgId + " not found in image map");
img = imageMap.get(imgId);
lastImageId = imgId;
if (img.getOrbitId() != lastOrbitId) {
if (!orbitDataMap.containsKey(img.getOrbitId())) {
RawDataFile rdf = DALConfig.getImageProvider().LoadRawDataFile(img.getOrbitId());
RecognitionFrame rf = new RecognitionFrame(rdf);
Shape roi = OrbitUtils.loadAnnotationROI(img.getOrbitId(),/*model.getAnnotationGroup()*/0);
ExclusionMapGen exMapGen = ExclusionMapGen.constructExclusionMap(rdf, rf, model, (IScaleableShape) roi);
if (exMapGen != null)
exMapGen.generateMap();
OrbitData od = new OrbitData(img.getOrbitId(), exMapGen, rdf, roi, rf.bimg.getTileWidth(), rf.bimg.getTileHeight());
orbitDataMap.put(img.getOrbitId(), od);
}
orbitData = orbitDataMap.get(img.getOrbitId());
lastOrbitId = img.getOrbitId();
log.trace("cpImgId:" + imgId + ", orbitId:" + img.getOrbitId());
}
}
double centerX = Double.parseDouble(split[2]);
double centerY = Double.parseDouble(split[3]);
int x = (int) (img.getTileX() * orbitData.getTileWidth() + centerX);
int y = (int) (img.getTileY() * orbitData.getTileHeight() + centerY);
if (OrbitUtils.isInROI(x, y, orbitData.getRoi(), orbitData.getExMapGen())) {
if (!objectCountMap.containsKey(img.orbitId)) {
objectCountMap.put(img.getOrbitId(), new ConcurrentHashMap());
}
Map counts = objectCountMap.get(img.getOrbitId());
if (!counts.containsKey(objName)) {
counts.put(objName, 0);
}
int objCnt = counts.get(objName);
objCnt++;
counts.put(objName, objCnt);
// save as special annotation (but not nuclei - too many...)
if (writeDB /*&& !objName.equals("Nuclei")*/ && cnt <= MAX_CNT_WRITEDB) {
Color col = Color.yellow;
int classNum = 0;
// different colors per class
// switch (objName) {
// case "FilteredCD4": col=Color.red; classNum=0; break;
// case "FilteredFoxp3": col=Color.green; classNum=1; break;
// case "CD4_FOXP3": col=Color.yellow; classNum=2; break;
// }
classNum = objNameMap.get(objName);
col = RecognitionFrame.getColorByNum(classNum);
final double w = 10d;
final double h = 10d;
double xj = x + ((random.nextDouble() - 0.5d) * 3d);
double yj = y + ((random.nextDouble() - 0.5d) * 3d);
ClassShape cs = new ClassShape(objName, col, ClassShape.SHAPETYPE_ARC);
cs.getShapeList().add(new Arc2DExt(xj - (w / 2d), yj - (h / 2d), 10, 10, 0, 360, Arc2DFixed.CHORD));
CellDetectionAnnotation anno = new CellDetectionAnnotation(objName, cs);
anno.setRawDataFileId(img.getOrbitId());
anno.setUserId(orbitUser);
anno.setClassNum(classNum);
DALConfig.getImageProvider().InsertRawAnnotation(anno);
}
}
}
}
log.info("parseObj " + objName + " end");
}
public Map> processObjects(String path, String pipeline, String exclModelFilename, boolean writeDB) throws Exception {
final OrbitModel model = exclModelFilename == null ? null : OrbitModel.LoadFromFile(exclModelFilename);
return processObjects(path, pipeline, model, writeDB);
}
public Map> processObjects(String path, String pipeline, final OrbitModel exclModel, boolean writeDB) throws Exception {
this.path = path;
this.model = exclModel;
this.imageMap = parseImages();
this.pipeline = pipeline;
List objectNames = parseOutputObjects(pipeline);
for (String objectName : objectNames) {
parseObject(objectName, writeDB, objectNames);
}
StringBuilder sb = new StringBuilder();
sb.append("OrbitId,ImageName");
for (String objName : objectNames) sb.append("," + objName);
sb.append("\n");
try (BufferedWriter writer = new BufferedWriter(new FileWriter(path + File.separator + "objectcounts.csv"))) {
writer.write(sb.toString());
for (int orbitId : objectCountMap.keySet()) {
RawDataFile rdf = DALConfig.getImageProvider().LoadRawDataFile(orbitId);
String s = orbitId + sep + "\"" + rdf.getFileName() + "\"";
for (String objName : objectNames) {
s += sep + objectCountMap.get(orbitId).get(objName);
}
s += "\n";
sb.append(s);
writer.write(s);
}
writer.flush();
}
System.out.println("\n" + sb.toString());
return objectCountMap;
}
public List parseOutputObjects(String pipeline) throws IOException {
List objectNames = new ArrayList<>();
try (BufferedReader reader = new BufferedReader(new FileReader(pipeline))) {
String line;
while ((line = reader.readLine()) != null) {
if (line.trim().startsWith(Data_OUT_IDENTIFIER)) {
String objectName = line.replaceAll(Data_OUT_IDENTIFIER, "").trim();
if (!objectName.equals(imageName)) {
log.debug("object name found in pipeline: " + objectName);
objectNames.add(objectName);
}
}
}
}
return objectNames;
}
class OrbitData {
private int orbitId;
private RawDataFile rdf;
private ExclusionMapGen exMapGen;
private Shape roi;
private int tileWidth;
private int tileHeight;
public OrbitData(int orbitId, ExclusionMapGen exMapGen, RawDataFile rdf, Shape roi, int tileWidth, int tileHeight) {
this.orbitId = orbitId;
this.exMapGen = exMapGen;
this.rdf = rdf;
this.roi = roi;
this.tileWidth = tileWidth;
this.tileHeight = tileHeight;
}
public int getTileHeight() {
return tileHeight;
}
public void setTileHeight(int tileHeight) {
this.tileHeight = tileHeight;
}
public int getTileWidth() {
return tileWidth;
}
public void setTileWidth(int tileWidth) {
this.tileWidth = tileWidth;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
OrbitData orbitData = (OrbitData) o;
return orbitId == orbitData.orbitId;
}
@Override
public int hashCode() {
return orbitId;
}
@Override
public String toString() {
return "OrbitData{" +
"orbitId=" + orbitId +
", rdf=" + rdf +
", roi=" + roi +
'}';
}
public ExclusionMapGen getExMapGen() {
return exMapGen;
}
public void setExMapGen(ExclusionMapGen exMapGen) {
this.exMapGen = exMapGen;
}
public int getOrbitId() {
return orbitId;
}
public void setOrbitId(int orbitId) {
this.orbitId = orbitId;
}
public RawDataFile getRdf() {
return rdf;
}
public void setRdf(RawDataFile rdf) {
this.rdf = rdf;
}
public Shape getRoi() {
return roi;
}
public void setRoi(Shape roi) {
this.roi = roi;
}
}
class CpImage implements Serializable {
private int id;
private int orbitId;
private int tileX;
private int tileY;
public CpImage(int id, int orbitId, int tileX, int tileY) {
this.id = id;
this.orbitId = orbitId;
this.tileX = tileX;
this.tileY = tileY;
}
@Override
public String toString() {
return "CpImage{" +
"id=" + id +
", orbitId=" + orbitId +
", tileX=" + tileX +
", tileY=" + tileY +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
CpImage cpImage = (CpImage) o;
if (id != cpImage.id) return false;
if (orbitId != cpImage.orbitId) return false;
if (tileX != cpImage.tileX) return false;
return tileY == cpImage.tileY;
}
@Override
public int hashCode() {
int result = id;
result = 31 * result + orbitId;
result = 31 * result + tileX;
result = 31 * result + tileY;
return result;
}
public int getId() {
return id;
}
public void setId(int id) {
this.id = id;
}
public int getOrbitId() {
return orbitId;
}
public void setOrbitId(int orbitId) {
this.orbitId = orbitId;
}
public int getTileX() {
return tileX;
}
public void setTileX(int tileX) {
this.tileX = tileX;
}
public int getTileY() {
return tileY;
}
public void setTileY(int tileY) {
this.tileY = tileY;
}
}
}