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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 dateFormat = new ThreadLocal() {
@Override
protected SimpleDateFormat initialValue() {
return new SimpleDateFormat("HH:mm:ss");
}
};
public static final int ANNOTATION_GROUPS = 20;
public static final String muMeter = (char) 181 + "m";
public static final String muMeterUnicode = "\u00B5";
public static final String squareMuMeter = muMeter + (char) 178;
private static boolean w32_ = System.getProperty("os.name").toLowerCase().startsWith("windows");
private static boolean linux_ = System.getProperty("os.name").toLowerCase().startsWith("linux");
private static boolean mac_ = System.getProperty("os.name").toLowerCase().contains("mac");
public static final String MODEL_ENDING = ".omo"; // filename ending of orbit models
public static final String remoteNameSpace = "orbit/temp";
public static final String orbitHelpURL = "http://www.orbit.bio/help";
public static final String orbitTutorialsURL = "http://www.orbit.bio/tutorials";
public static final String orbitImageProviderURL = "http://www.orbit.bio/setup";
public static final String CHANNEL_NAME_ALL = "";
public static final String CHANNEL_NAME2HUE = "channel_name2hue_";
static {
Logger root = LoggerFactory.getLogger("com.actelion.research");
if (root instanceof ch.qos.logback.classic.Logger) // can only set if logback implementation
((ch.qos.logback.classic.Logger) root).setLevel(DEVELOPMENTMODE ? Level.DEBUG : Level.INFO);
if (ScaleoutMode.SCALEOUTMODE.get()) {
DALConfig.getImageProvider().setPooledConnectionEnabled(false);
DALConfig.getImageProvider().setDBConnectionName("OrbitGridJob");
}
}
public final static double getVersion() {
try (InputStreamReader in = new InputStreamReader(OrbitUtils.class.getResourceAsStream("/version.txt"));
BufferedReader reader = new BufferedReader(in);) {
String s = reader.readLine();
s = s.trim();
double version = Double.parseDouble(s);
return version;
} catch (Exception e) {
e.printStackTrace();
return 0;
}
}
public static boolean isOME_TIFF(String filename) {
if (filename==null) return false;
String fn = filename.toLowerCase();
if (fn.endsWith("ome.tiff")||fn.endsWith("ome.tif")||fn.endsWith("ome.tf2")||fn.endsWith("ome.tf8")||fn.endsWith("ome.btf")) return true;
else return false;
}
/**
* replaces " " by "_" in channelName
* @param channelName
* @return
*/
public static String cleanChannelName(String channelName) {
if (channelName==null) return null;
channelName = channelName.trim();
channelName = channelName.replaceAll(";","_");
//channelName = channelName.replaceAll(" ","_");
return channelName;
}
/**
* returns the hueMap merged with the user defined custom hue map (priority)
*/
public static Map getMergedHueMap() {
Map hm = new HashMap<>(ChannelToHue.hueMap);
hm.putAll(ChannelToHue.userHueMap);
return hm;
}
public static float[] getHues(final String[] channelNames, final Map hueMap) {
if (channelNames==null) return null;
if (hueMap==null) return null;
float[] hues = new float[channelNames.length];
for (int c=0; c0) {
float[] hueMap = new float[multiChannelImage.getChannelNames().length];
for (int c=0; c0 && multiChannelImage.getChannelNames()!=null && multiChannelImage.getChannelNames().length>0) {
HashSet activeChannelLookup = new HashSet<>(Arrays.asList(featureDescription.getActiveFluoChannels()));
float[] channelContributions = new float[multiChannelImage.getChannelNames().length];
for (int c=0; c rmList = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(rdfId, RawUtilsCommon.STR_META_IMAGE_SCALE);
scale = Double.parseDouble(rmList.get(0).getValue());
} catch (Exception e) {
logger.info("could not load image scale for image " + rdfId);
}
return scale;
}
public static ScaleAndUnit getImageScaleAndUnit(RawDataFile rdf) {
double scale = 0d;
String unit = "pixel";
if (rdf != null) {
scale = loadImageScale(rdf.getRawDataFileId());
}
if (scale == 0d) {
scale = 1d;
unit = "pixel";
} else {
unit = OrbitUtils.muMeterUnicode;
}
ScaleAndUnit sau = new ScaleAndUnit(scale, scale * scale, unit, unit + (char) 178);
return sau;
}
public static boolean isInROI(int x, int y, Shape ROI, ExclusionMapGen exclusionMapGen) {
if ((ROI == null) || (ROI.contains(x, y))) {
if ((exclusionMapGen == null) || /*(exclusionMapGen.useForSegmentation()) ||*/ (!exclusionMapGen.isExcluded(x, y) || ((ROI != null) && (ROI instanceof ShapeAnnotationList) && (((ShapeAnnotationList) ROI)).containsExplicit(x, y)))) {
return true;
}
}
return false;
}
/**
* Fuzzy check if a tile is inside the ROI. It only checks if one corner or the center of the tile is inside the ROI.
* Might return false if a few pixels of the tile are inside the ROI!
*/
public static boolean isTileInROI(int tileX, int tileY, final PlanarImage image, Shape ROI, ExclusionMapGen exclusionMapGen) {
Rectangle rect = image.getTileRect(tileX,tileY);
if (isInROI((int)rect.getMinX(),(int)rect.getMinY(),ROI,exclusionMapGen)) return true; // top-left
if (isInROI((int)rect.getMaxX(),(int)rect.getMinY(),ROI,exclusionMapGen)) return true; // top-right
if (isInROI((int)rect.getMinX(),(int)rect.getMaxY(),ROI,exclusionMapGen)) return true; // bottom-left
if (isInROI((int)rect.getMaxX(),(int)rect.getMaxY(),ROI,exclusionMapGen)) return true; // bottom-right
if (isInROI((int)rect.getCenterX(),(int)rect.getCenterY(),ROI,exclusionMapGen)) return true; // bottom-right
return false;
}
/**
* Loads the combined annotation ROI. Set annotationGroup to 0 to load the annotations of all annotation groups.
*
* @param rdfId
* @param annotationGroup
* @return
* @throws SQLException
*/
public static IScaleableShape loadAnnotationROI(int rdfId, int annotationGroup) throws Exception {
return loadAnnotationROI(rdfId, annotationGroup, false);
}
/**
* Loads the combined annotation ROI. Set annotationGroup to 0 to load the annotations of all annotation groups.
*
* @param rdfId
* @param annotationGroup
* @return
* @throws SQLException
*/
public static IScaleableShape loadAnnotationROI(int rdfId, int annotationGroup, boolean otherGroupROIAsExclusion) throws Exception {
return loadAnnotationROI(rdfId, annotationGroup, otherGroupROIAsExclusion, false);
}
/**
* Loads the combined annotation ROI. Set annotationGroup to 0 to load the annotations of all annotation groups.
*
* @param rdfId
* @param annotationGroup
* @return
* @throws SQLException
*/
public static IScaleableShape loadAnnotationROI(int rdfId, int annotationGroup, boolean otherGroupROIAsExclusion, boolean exclusionsForAllGroups) throws Exception {
List annotations = DALConfig.getImageProvider().LoadRawAnnotationsByRawDataFile(rdfId, RawAnnotation.ANNOTATION_TYPE_IMAGE);
if (annotations != null && annotations.size() > 0) {
IScaleableShape roi = new ShapeAnnotationList(annotations, annotationGroup, null, otherGroupROIAsExclusion, exclusionsForAllGroups);
return roi; // bounds can be null - this is explicitely allowed!
} else return null;
}
public static double getROISize(RecognitionFrame rf, ExclusionMapGen exclMapGen) {
double mumPP = rf.getMuMeterPerPixel() > 0 ? rf.getMuMeterPerPixel() : 1d;
return OrbitUtils.getROISize(rf.bimg.getImage(), rf.getROI(), exclMapGen, mumPP);
}
public static double getROISize(OrbitTiledImage2 img, Shape roi, ExclusionMapGen exclusionMapGen, double mumPerPixel) {
Rectangle bounds = img.getBounds();
if (roi != null) {
if (roi instanceof IScaleableShape) {
roi = ((IScaleableShape) roi).getScaledInstance(100d, new Point(0, 0));
}
Rectangle roiBounds = roi.getBounds();
if (roiBounds != null && roiBounds.getMinX() > 0 && roiBounds.getMinY() > 0)
bounds.setLocation(roiBounds.x, roiBounds.y);
if (roiBounds != null && roiBounds.getMaxX() < bounds.getMaxX() && roiBounds.getMaxY() < bounds.getMaxY())
bounds.setSize(roiBounds.getSize());
}
return getROISize(img.getWidth(), img.getHeight(), bounds, roi, exclusionMapGen, mumPerPixel);
}
/**
* Computes the ROI area in square mu meter. If bounds is null imgWidth*imgHeight*mumPerPixel*mumPerPixel will be returned.
*
* @param imgWidth
* @param imgHeight
* @param bounds
* @param roi
* @param exclusionMapGen
* @param mumPerPixel
* @return
*/
public static double getROISize(int imgWidth, int imgHeight, Rectangle bounds, Shape roi, ExclusionMapGen exclusionMapGen, double mumPerPixel) {
double mumPPSquare = mumPerPixel * mumPerPixel;
if (bounds == null) {
return (double) imgWidth * imgHeight * mumPPSquare;
}
if (roi == null && exclusionMapGen == null) {
return bounds.getWidth() * bounds.getHeight() * mumPPSquare;
}
//System.out.println("minX:"+bounds.getMinX()+" maxX:"+bounds.getMaxX()+" minY:"+bounds.getMinY()+" maxY:"+bounds.getMaxY());
if (roi != null) {
if (roi instanceof IScaleableShape) {
roi = ((IScaleableShape) roi).getScaledInstance(100d, new Point(0, 0));
}
}
long pixelInROI = 0;
double size = bounds.getWidth() * bounds.getHeight();
final int inc = size < (5000 * 5000d) ? 1 : 3;
for (int y = (int) bounds.getMinY(); y < bounds.getMaxY(); y += inc) {
for (int x = (int) bounds.getMinX(); x < bounds.getMaxX(); x += inc) {
if ((isInROI(x, y, roi, exclusionMapGen))) {
pixelInROI++;
}
}
//System.out.println("y: "+y);
}
pixelInROI *= inc * inc;
double area = (double) pixelInROI * mumPPSquare;
//System.out.println("roiBB: "+roi.getBounds()+" pixel: "+pixelInROI+" mumPP: "+mumPerPixel+" mumPPSquare: "+mumPPSquare);
return area;
}
/**
* formats time in seconds.
*
* @param s
* @return
*/
public static String formatTime(double s) {
String d = "";
if (s > 3600 * 24) {
d = Integer.toString((int) (s / (3600 * 24))) + "d +";
s -= 3600 * 24;
}
return d + dateFormat.get().format(new Date((long) s * 1000L - 3600000));
}
public static List buildDefaultClassShapes() {
List classShapes = new ArrayList(3);
classShapes.add(new ClassShape("Background", Color.darkGray, ClassShape.SHAPETYPE_POLYGONEXT));
classShapes.add(new ClassShape("Celltype 1", RecognitionFrame.getColorByNum(1), ClassShape.SHAPETYPE_POLYGONEXT));
classShapes.add(new ClassShape("Celltype 2", RecognitionFrame.getColorByNum(2), ClassShape.SHAPETYPE_POLYGONEXT));
return classShapes;
}
public static List buildCellCountClassShapes() {
List classShapes = new ArrayList(3);
classShapes.add(new ClassShape("Background", Color.darkGray, ClassShape.SHAPETYPE_POLYGONEXT));
classShapes.add(new ClassShape("Border", RecognitionFrame.getColorByNum(1), ClassShape.SHAPETYPE_POLYGONEXT));
classShapes.add(new ClassShape("Cells", RecognitionFrame.getColorByNum(2), ClassShape.SHAPETYPE_POLYGONEXT));
return classShapes;
}
/**
* creates a new list of classShapes with cloned classShapes. The shapeList will be an empty list.
*
* @param classShapes
* @return
*/
public static List cloneClassShapes(List classShapes) {
return cloneClassShapes(classShapes, false);
}
/**
* creates a new list of classShapes with cloned classShapes.
*
* @param classShapes
* @return
*/
public static List cloneClassShapes(List classShapes, boolean keepShapes) {
if (classShapes == null) return null;
List csList = Collections.synchronizedList(new ArrayList(classShapes.size()));
for (ClassShape cs : classShapes) {
ClassShape newShape = cs.clone();
if (!keepShapes)
newShape.setShapeList(Collections.synchronizedList(new ArrayList())); // store empty list to save memory
csList.add(newShape);
}
return csList;
}
/*
* returns the available temp disk space in byte.
*/
public static long getTempDiskSpace() {
if (ScaleoutMode.SCALEOUTMODE.get()) return 100 * 1024 * 1024L;
long space = -1L;
try {
File f = File.createTempFile("orbit", null);
File tmpDir = f.getParentFile();
space = tmpDir.getFreeSpace();
f.delete();
} catch (Exception e) {
e.printStackTrace();
}
return space;
}
public static String getTempDir() {
String s = null;
try {
File f = File.createTempFile("orbit", null);
s = f.getParentFile().getAbsolutePath();
f.delete();
} catch (Exception e) {
e.printStackTrace();
}
return s;
}
public static void cleanUpTemp() {
if (DiskMemImageOrbit.getCommonTileCache() != null)
DiskMemImageOrbit.getCommonTileCache().flush();
//DiskMemImage.getCommonTileCache().removeNullTiles();
//manually remove existing temp files
try {
File f = File.createTempFile(DiskCachedTile.FILE_PREFIX, DiskCachedTile.FILE_SUFFIX, DiskCachedTile.getCacheFolder());
File tmpDir = f.getParentFile();
f.delete();
logger.debug("Cleaning up tile temp folder: " + tmpDir + "... ");
if (tmpDir != null) {
FilenameFilter filter = new FilenameFilter() {
public boolean accept(File dir, String name) {
return name.startsWith(DiskCachedTile.FILE_PREFIX) ||
name.startsWith("jai-FCSS-");
}
};
File[] files = tmpDir.listFiles(filter);
if ((files != null) && (files.length > 0)) {
for (File tf : files) {
if (tf.isFile()) tf.deleteOnExit(); // delete file when vm terminates
//System.out.println(tf);
}
}
}
logger.trace("done.");
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Parses the params for key and returns value. The params have to be in the form
* -key1 value1 -key2 value2 ...
* Everything is treated as string.
* If the key is not found or params is null or params.length<2 null will be returned.
*
* @param key
* @param params
* @return
*/
public static String parseParams(String key, String[] params) {
if (params == null) return null;
if (params.length < 2) return null;
for (int i = 0; i < params.length - 1; i++) {
if (params[i].equalsIgnoreCase("-" + key) && (!params[i + 1].startsWith("-"))) {
return params[i + 1];
}
}
return null;
}
public static double parseDouble(String s, double NanValue) {
double d = NanValue;
try {
d = Double.parseDouble(s.replaceAll(",", "\\."));
} catch (Exception e) {
d = NanValue;
}
return d;
}
public static int parseInt(String s, int NanValue) {
int i = NanValue;
try {
i = Integer.parseInt(s);
} catch (Exception e) {
i = NanValue;
}
return i;
}
/**
* returns the position (starting from 0) of a wellname with leading 0, e.g. A01 -> 0,0 (A1 also works)
*
* @param wellName
* @return
*/
public static Point getWellPos(String wellName) throws IllegalArgumentException {
if (wellName == null || wellName.length() < 2)
throw new IllegalArgumentException("not a valid wellname: " + wellName);
int y = wellName.charAt(0) - (byte) ('A');
String s = String.valueOf(wellName.charAt(1));
if (wellName.length() > 2) {
s += wellName.charAt(2);
}
try {
int x = Integer.parseInt(s);
return new Point(x - 1, y);
} catch (Exception e) {
throw new IllegalArgumentException("not a valid wellname: " + wellName);
}
}
/**
* returns the well name (e.g. A01) based on the well position (x,y) (x and y starting from 0)
*
* @param x
* @param y
* @return
*/
public static String getWellName(int x, int y) {
char wy = ((char) (y + (byte) ('A')));
String wellName = wy + "" + String.format("%1$02d", x + 1);
return wellName;
}
/**
* returns the well name (e.g. A1) based on the well position (x,y) (x and y starting from 0)
*
* @param x
* @param y
* @return
*/
public static String getWellNameShort(int x, int y) {
char wy = ((char) (y + (byte) ('A')));
String wellName = wy + "" + String.format("%1$01d", x + 1);
return wellName;
}
/**
* waits until worker.isDone or worker.isCancelled is true
*
* @param worker
*/
public static void waitForWorker(OrbitWorker worker) {
while ((!worker.isDone()) || worker.isCancelled()) {
try {
Thread.sleep(100);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
}
/**
* creates a html document, lines beginning with # are headings and lines with multi tabs are table blocks.
*
* @return
*/
public static String text2SmartHtml(String text) {
final String sep = "\t";
String color = OrbitUtils.DARKUI ? " color=white" : "";
StringBuilder sb = new StringBuilder();
sb.append("");
boolean tableBlock = false;
String s;
String lines[] = text.split("\\r?\\n");
for (String line : lines) {
if (line.trim().startsWith("#")) {
if (tableBlock) {
tableBlock = false;
sb.append("");
}
s = line.trim().replaceFirst("#", "") + "
";
sb.append(s);
} else {
String[] tabs = line.split(sep);
if (tabs != null && tabs.length > 1) {
// table block
if (!tableBlock) { // header
tableBlock = true;
sb.append("");
for (String col : tabs) {
sb.append("" + col + " ");
}
sb.append(" ");
} else { // data
sb.append("");
for (String col : tabs) {
sb.append("" + col + " ");
}
sb.append(" ");
}
} else {
if (tableBlock) {
tableBlock = false;
sb.append("
");
}
sb.append(line + "
");
}
}
}
sb.append("