/** * Parse masks into a separate overlay-specific MetadataStore. */ public void parseMasks(MetadataStore overlayStore) throws FormatException, IOException { boolean originalMaskParsing = parseMasks; int roi = 0; parseMasks = true; for (AnalysisFile roiFile : roiFiles) { roi += parseMasks(overlayStore, roiFile.well, roi, roiFile.filename); } parseMasks = originalMaskParsing; }
/** * Parse masks into a separate overlay-specific MetadataStore. */ public void parseMasks(MetadataStore overlayStore) throws FormatException, IOException { boolean originalMaskParsing = parseMasks; int roi = 0; parseMasks = true; for (AnalysisFile roiFile : roiFiles) { roi += parseMasks(overlayStore, roiFile.well, roi, roiFile.filename); } parseMasks = originalMaskParsing; }
/** * If available, populates overlays for a given set of pixels objects. * @param pixelsList Pixels objects to populate overlays for. * @param plateIds Plate object IDs to populate overlays for. */ private void importOverlays( List<Pixels> pixelsList, List<Long> plateIds) throws FormatException, IOException { IFormatReader baseReader = reader.getImageReader().getReader(); if (baseReader instanceof MIASReader) { try { MIASReader miasReader = (MIASReader) baseReader; ServiceFactoryPrx sf = store.getServiceFactory(); OverlayMetadataStore s = new OverlayMetadataStore(); s.initialize(sf, pixelsList, plateIds); miasReader.parseMasks(s); s.complete(); } catch (ServerError e) { log.warn("Error while populating MIAS overlays.", e); } } }
nextROI += parseMasks(store, well, nextROI, file); nextROI += parseMasks(store, well, nextROI, file);
nextROI += parseMasks(store, well, nextROI, file); nextROI += parseMasks(store, well, nextROI, file);