private void parseCellObjects() { String rootObject = CellH5Constants.DEFINITION + CellH5Constants.OBJECT; List<String> allObjects = jhdf.getMember(rootObject); for (String objectName : allObjects) { String objectType = (String) jhdf.readCompoundArrayDataMap( rootObject + objectName)[0].get("type"); if (objectType.equals("region")) { cellObjectNames.add(objectName); LOGGER.debug("CellH5Reader: Found cell object {}", objectName); } } }
private void parseCellObjects() { String rootObject = CellH5Constants.DEFINITION + CellH5Constants.OBJECT; List<String> allObjects = jhdf.getMember(rootObject); for (String objectName : allObjects) { String objectType = (String) jhdf.readCompoundArrayDataMap( rootObject + objectName)[0].get("type"); if (objectType.equals("region")) { cellObjectNames.add(objectName); LOGGER.debug("CellH5Reader: Found cell object {}", objectName); } } }
private int getChannelIndexOfCellObjectName(String cellObjectName) { HDF5CompoundDataMap[] allImageRegions = jhdf.readCompoundArrayDataMap( CellH5Constants.DEFINITION + CellH5Constants.SEGMENTATION_PATH); for (int regionIdx = 0; regionIdx < allImageRegions.length; regionIdx++) { String regionName = (String) allImageRegions[regionIdx].get("region_name"); Integer channelIdx = (Integer) allImageRegions[regionIdx].get("channel_idx"); if (regionName.endsWith(cellObjectName)) { return channelIdx.intValue(); } } return -1; }
private int getChannelIndexOfCellObjectName(String cellObjectName) { HDF5CompoundDataMap[] allImageRegions = jhdf.readCompoundArrayDataMap( CellH5Constants.DEFINITION + CellH5Constants.SEGMENTATION_PATH); for (int regionIdx = 0; regionIdx < allImageRegions.length; regionIdx++) { String regionName = (String) allImageRegions[regionIdx].get("region_name"); Integer channelIdx = (Integer) allImageRegions[regionIdx].get("channel_idx"); if (regionName.endsWith(cellObjectName)) { return channelIdx.intValue(); } } return -1; }
if (jhdf.exists(pathToClassDefinition)) { String classColorHexString; HDF5CompoundDataMap[] classDef = jhdf.readCompoundArrayDataMap(pathToClassDefinition); for (int cls = 0; cls < classDef.length; cls++) { classColorHexString = (String) classDef[cls].get("color"); classes = jhdf.readCompoundArrayDataMap(coord.pathToPosition + featureName + CellH5Constants.PREDICTED_CLASS_LABELS); bbox = jhdf.readCompoundArrayDataMap(pathToBoundingBox); times = jhdf.readCompoundArrayDataMap( coord.pathToPosition + CellH5Constants.OBJECT + cellObjectName); int roiChannel = getChannelIndexOfCellObjectName(cellObjectName);
if (jhdf.exists(pathToClassDefinition)) { String classColorHexString; HDF5CompoundDataMap[] classDef = jhdf.readCompoundArrayDataMap(pathToClassDefinition); for (int cls = 0; cls < classDef.length; cls++) { classColorHexString = (String) classDef[cls].get("color"); classes = jhdf.readCompoundArrayDataMap(coord.pathToPosition + featureName + CellH5Constants.PREDICTED_CLASS_LABELS); bbox = jhdf.readCompoundArrayDataMap(pathToBoundingBox); times = jhdf.readCompoundArrayDataMap( coord.pathToPosition + CellH5Constants.OBJECT + cellObjectName); int roiChannel = getChannelIndexOfCellObjectName(cellObjectName);