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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 dateFormatHMS = new ThreadLocal() {
@Override
protected SimpleDateFormat initialValue() {
return new SimpleDateFormat("dd.MM.yyyy HH.mm.ss");
}
};
public static synchronized Map>> enhanceResults(final Map>> rdfResults) throws Exception {
Map>> resutlMap = new HashMap>>();
if (rdfResults != null && rdfResults.size() > 0) {
for (Integer rdfId : rdfResults.keySet()) {
RawDataFile rdf = DALConfig.getImageProvider().LoadRawDataFile(rdfId);
RawData rd = DALConfig.getImageProvider().LoadRawData(rdf.getRawDataId());
List> vals = new ArrayList>();
vals.add(new KeyValue(FILENAME, rdf.getFileName()));
vals.add(new KeyValue("OrbitId", rdf.getRawDataFileId()));
if (rd != null)
vals.add(new KeyValue("ELB", rd.getBioLabJournal()));
// add LIMS meta data (if available)
if (rdf.getBioSampleId() > 0) {
LIMSBioSample bioSample = DALConfig.getImageProvider().getLIMSBiosample(rdf);
if (bioSample != null) {
vals.add(new KeyValue("Study-IVV", bioSample.getStudyIVV())); // invivo name
vals.add(new KeyValue("Study-ID", bioSample.getStudyId()));
vals.add(new KeyValue("Study-Phase", bioSample.getStudyPhase()));
vals.add(new KeyValue("Study-Group", bioSample.getStudyGroup()));
vals.add(new KeyValue("Biosample", bioSample.getParentName()));
//vals.add(new KeyValue("Type", bioSample.getBiotype()));
}
}
// add well-based data (if available)
try {
HCSMetaData hcsMetaData = DALConfig.getImageProvider().LoadHCSMetaData(rdfId);
if (hcsMetaData != null) { // well-based meta data available
vals.add(new KeyValue("BatchNr", hcsMetaData.getBtachNr()));
vals.add(new KeyValue("PlateName", hcsMetaData.getPlateName()));
vals.add(new KeyValue("WellName", hcsMetaData.getWellName()));
vals.add(new KeyValue("SiteX", hcsMetaData.getSiteX()));
vals.add(new KeyValue("SiteY", hcsMetaData.getSiteY()));
vals.add(new KeyValue("SiteZ", hcsMetaData.getSiteZ()));
vals.add(new KeyValue("Channel", hcsMetaData.getChannel()));
}
} catch (Exception e) {
e.printStackTrace();
}
vals.addAll(rdfResults.get(rdfId));
resutlMap.put(rdfId, vals);
}
}
//System.out.println("size rdfresults: "+rdfResults.get(rdfResults.keySet().toArray(new Integer[0])[0]).get(9).getValue());
return resutlMap;
}
public static synchronized Map>> enhanceROIArea(final OrbitModel model, final Map>> rdfResults) throws Exception {
if (ScaleoutMode.SCALEOUTMODE.get()) DALConfig.getImageProvider().authenticateUserScaleout();
try {
List rdfList = new ArrayList(rdfResults.size());
for (Integer rdfId : rdfResults.keySet()) {
rdfList.add(DALConfig.getImageProvider().LoadRawDataFile(rdfId));
}
String modelNew = OrbitUtils.generateUniqueFilename("orbit", OrbitUtils.MODEL_ENDING);
// if (useScaleout) {
// modelNew = DALConfig.getScaleOut().getRemoteContextStore().generateUniqueFilename("orbit", OrbitUtils.MODEL_ENDING);
// }
ImageTile.modelCache.put(modelNew, model); // for local execution we just keep it in memory
//DALConfig.getScaleOut().getRemoteContextStore().copyToRemote(model.getAsByteArray(), OrbitUtils.remoteNameSpace, modelNew);
List imageTiles = OrbitHelper.EncodeImageTiles(modelNew, -1, model.getMipLayer(), rdfList);
ROIAreaMapReduce mr = new ROIAreaMapReduce();
mr.setModel(new OrbitModel(model));
Map areas = null;
IMapReduceExecutor executor = new MapReduceExecutorLocalMultiCore();
areas = executor.execute(imageTiles, mr);
for (Integer rdfId : areas.keySet()) {
OrbitUtils.ScaleAndUnit scaleAndUnit = OrbitUtils.getImageScaleAndUnit(DALConfig.getImageProvider().LoadRawDataFile(rdfId));
double area = areas.get(rdfId);
String unit = scaleAndUnit.getUnit();
if (scaleAndUnit.getUnit().equals(OrbitUtils.muMeterUnicode)) {
unit = "mm" + (char) 178;
area /= 1000000d;
}
rdfResults.get(rdfId).add(new KeyValue("ROIArea[" + unit + "]", area));
rdfResults.get(rdfId).add(new KeyValue("ROI-Group", model.getAnnotationGroup()));
}
} finally {
try {
if (ScaleoutMode.SCALEOUTMODE.get()) DALConfig.getImageProvider().close();
} catch (IOException e) {
e.printStackTrace();
}
}
return rdfResults;
}
private static void addMeta(List> vals, int rdfId, String metaName, String outName, Object defValue) throws Exception {
List rmList = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(rdfId, metaName);
Object obj = defValue;
if (rmList != null && rmList.size() > 0) {
RawMeta rm = rmList.get(0);
String val = rm.getValue();
obj = val;
try {
if (rm.getRawTypeId() == RawDbTypes.RAW_TYPE_INTEGER)
obj = Integer.parseInt(val);
else if (rm.getRawTypeId() == RawDbTypes.RAW_TYPE_DOUBLE)
obj = Double.parseDouble(val);
else if (rm.getRawTypeId() == RawDbTypes.RAW_TYPE_DATE)
obj = RawMetaFactoryFile.dateFormat.parse(val);
} catch (Exception e) {
log.warn("ORBITERR00480: error parsing meta data", e);
}
}
vals.add(new KeyValue(outName, obj));
}
public static String toString(final Map>> result) {
if (result == null || result.size() == 0) {
log.warn("ORBITERR00450: no result available (result:{})", result);
}
// TODO
//String hcsResult = DALConfig.getImageProvider().getReplacementMetadata(result);
//if (hcsResult != null) return hcsResult;
// generate filename, list
List>>> imgList = new ArrayList>>>();
Collection>> valueList = result.values();
for (List> keyValues : valueList) {
String filename = "";
List> vals = new ArrayList>();
for (KeyValue kv : keyValues) {
if (kv.getKey().equals(FILENAME)) {
filename = obj2str(kv.getValue());
} else {
vals.add(kv);
}
}
imgList.add(new KeyValue>>(filename, vals));
}
Collections.sort(imgList, new Comparator>>>() {
@Override
public int compare(KeyValue>> o1, KeyValue>> o2) {
return o1.getKey().compareTo(o2.getKey());
}
});
// generate output
StringBuilder sb = new StringBuilder();
// header
List> firstRow = imgList.get(0).getValue();
List names = new ArrayList();
names.add(FILENAME);
for (KeyValue kv : firstRow) {
names.add(kv.getKey());
}
for (int i = 0; i < names.size(); i++) {
String name = names.get(i);
sb.append(name);
if (i < names.size() - 1) sb.append(SEP);
}
sb.append("\n");
// add values
for (KeyValue>> img : imgList) {
// generate map
Map map = new HashMap(img.getValue().size());
for (KeyValue kv : img.getValue()) {
map.put(kv.getKey(), kv.getValue());
}
sb.append(img.getKey() + SEP); // filename
for (int i = 0; i < names.size(); i++) {
String name = names.get(i);
if (!name.equals(FILENAME)) {
Object obj = map.get(name);
sb.append(obj2str(obj));
if (i < names.size() - 1) sb.append(SEP);
else sb.append("\n");
}
}
}
return sb.toString();
}
private static String obj2str(final Object obj) {
String res = "null";
if (obj != null) {
if (obj instanceof String) {
res = "\"" + obj.toString() + "\"";
} else if (obj instanceof Integer) {
res = obj.toString();
} else if (obj instanceof Long) {
res = obj.toString();
} else if (obj instanceof Byte) {
res = obj.toString();
} else if (obj instanceof Short) {
res = obj.toString();
} else if (obj instanceof Number) {
res = String.format("%1$.6f", (Number) obj);
} else if (obj instanceof Date) {
res = dateFormatHMS.get().format((Date) obj);
} else res = obj.toString();
}
return res;
}
private static String shortenStr(String str) {
String s = "";
if (str != null) {
s = str.replaceAll("\n", "").trim();
if (s.length() > 40) s = s.substring(0, 39);
}
return s;
}
public static Map>> convertToNamedMeasurement(final Map measurements, String measurementName) {
Map>> namedMap = new HashMap>>(measurements.size());
for (Integer rdfId : measurements.keySet()) {
List> valList = new ArrayList>(1);
Object measurement = measurements.get(rdfId);
if (measurements.get(rdfId) instanceof KeyValue)
measurement = ((KeyValue) measurements.get(rdfId)).getValue();
valList.add(new KeyValue(measurementName, measurement));
namedMap.put(rdfId, valList);
}
return namedMap;
}
public static void main(String[] args) throws Exception {
DALConfig.getImageProvider().authenticateUser("user1", "omero");
List rdfList = DALConfig.getImageProvider().LoadRawDataFilesSearchFast("3096-", 1000, Arrays.asList(RawUtilsCommon.DATA_TYPE_IMAGE_JPG));
Map>> rdfResults = new HashMap>>();
Map counts = new HashMap();
int number = 0;
for (RawDataFile rdf : rdfList) {
counts.put(rdf.getRawDataFileId(), number);
number++;
}
rdfResults = convertToNamedMeasurement(counts, "count");
rdfResults = enhanceResults(rdfResults);
String res = toString(rdfResults);
System.out.println("=== results ===");
System.out.println(res);
DALConfig.getImageProvider().close();
}
}