/** * Get the ROI of the selected object, if available, or null * @return */ public ROI getSelectedROI() { if (pathObjectSelected != null) return pathObjectSelected.getROI(); return null; }
@Override public String getMetadataString(final String key) { Object value = getMetadataValue(key); if (value instanceof String) return (String)value; return null; }
public MeasurementList getMeasurementList() { if (measurements == null) measurements = createEmptyMeasurementList(); return measurements; }
/** * Get the ROI for a PathObject, with a preference for the nucleus ROI of a cell. * * @param pathObject * @param preferNucleus * @return */ public static ROI getROI(final PathObject pathObject, final boolean preferNucleus) { if (preferNucleus && pathObject instanceof PathCellObject) { ROI roi = ((PathCellObject)pathObject).getNucleusROI(); if (roi != null) return roi; } return pathObject.getROI(); }
@Override public String toString() { return getDisplayedName() + objectCountPostfix(); // if (getROI() != null) // return getROI().getName() + objectCountPostfix(); // return "Unnamed TMA core"; // Entire image }
public static boolean containsPointObject(Collection<PathObject> pathObjects) { for (PathObject pathObject : pathObjects) { if (pathObject.isPoint()) return true; } return false; }
public PathROIObject(ROI pathROI, PathClass pc) { super(); this.pathROI = pathROI; setPathClass(pc); }
/** * Get a metadata value. * * @param key * @param value * @return the metadata value if set, or null if not * * @see storeMetadataValue */ protected Object retrieveMetadataValue(final String key) { return metadata == null ? null : metadata.get(key); }
public int getNMissingCores() { int missing = 0; for (TMACoreObject core : cores) if (core.isMissing()) missing++; return missing; }
/** * The level of the object in a hierarchy. * If the object has no parent, this is 0. * Otherwise, it is equal to parent.getLevel() + 1. * * @return */ public int getLevel() { if (parent == null) return 0; return parent.getLevel() + 1; }
@Override public Object putMetadataValue(final String key, final String value) { return storeMetadataValue(key, value); }
private void tryToSetObjectLock(final PathObject pathObject, final boolean locked) { if (pathObject instanceof PathROIObject) ((PathROIObject)pathObject).setLocked(locked); }
protected void clearMetadataMap() { if (metadata != null) metadata.clear(); }
@Override public Object getMetadataValue(final String key) { return super.retrieveMetadataValue(key); }
@Override public Set<String> getMetadataKeys() { return super.retrieveMetadataKeys(); }
@Override public Map<String, String> getMetadataMap() { return super.getUnmodifiableMetadataMap(); }
@Override public boolean containsValue(Object value) { return containsValue(value); }
public void addPathObjects(Collection<? extends PathObject> pathObjects) { addPathObjectsImpl(pathObjects); }
@Override public boolean containsMetadataString(final String key) { return getMetadataValue(key) instanceof String; }
public PathROIObject(ROI pathROI, PathClass pc, MeasurementList measurements) { super(measurements); this.pathROI = pathROI; setPathClass(pc); }