@Override public void setOriginalMetadataPopulated(boolean populate) { FormatTools.assertId(currentId, false, 1); saveOriginalMetadata = populate; }
@Override public String[] getDomains() { FormatTools.assertId(currentId, true, 1); return isHCS ? new String[] {FormatTools.HCS_DOMAIN} : new String[] {FormatTools.LM_DOMAIN}; }
@Override public String[] getSeriesUsedFiles(boolean noPixels) { FormatTools.assertId(currentId, true, 1); List<String> files = new ArrayList<String>(); fakeSeries.clear(); if (!noPixels) files.addAll(listFakeSeries(currentId)); if (iniFile != null) files.add(iniFile); return files.toArray(new String[files.size()]); }
@Override public int getSizeX() { FormatTools.assertId(currentId, true, 1); return getCurrentCore().sizeX; }
@Override public int getSizeY() { FormatTools.assertId(currentId, true, 1); return getCurrentCore().sizeY; }
@Override public Modulo getModuloC() { FormatTools.assertId(currentId, true, 1); return getCurrentCore().moduloC; }
@Override public int getIndex(int z, int c, int t) { FormatTools.assertId(currentId, true, 1); return FormatTools.getIndex(this, z, c, t); }
@Override public int getOptimalTileWidth() { FormatTools.assertId(currentId, true, 1); return getSizeX(); }
@Override public void setNormalized(boolean normalize) { FormatTools.assertId(currentId, false, 2); for (int i=0; i<readers.length; i++) readers[i].setNormalized(normalize); }
public byte[][] get8BitLookupTable() { FormatTools.assertId(currentId, true, 1); if (isIndexed()) { return lut; } return null; }
@Override public int getSeriesCount() { FormatTools.assertId(currentId, true, 1); if (hasFlattenedResolutions()) { return core.size(); } return coreIndexToSeries(core.size() - 1) + 1; }
@Override public boolean isThumbnailSeries() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isThumbnailSeries() : core.get(getCoreIndex()).thumbnail; }
@Override public Hashtable<String, Object> getSeriesMetadata() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.getSeriesMetadata() : core.get(getCoreIndex()).seriesMetadata; }
@Override public int getOptimalTileWidth() { FormatTools.assertId(currentId, true, 1); try { return (int) ifds.get(0).getTileWidth(); } catch (FormatException e) { LOGGER.debug("Could not retrieve tile width", e); } return super.getOptimalTileWidth(); }
@Override public int getOptimalTileWidth() { FormatTools.assertId(currentId, true, 1); if (tiffReader.getCurrentFile() == null) { setupReader(); } return tiffReader.getOptimalTileWidth(); }
@Override public int getOptimalTileWidth() { FormatTools.assertId(currentId, true, 1); try { return (int) ifds[getSeries()].get(0).getTileWidth(); } catch (FormatException e) { LOGGER.debug("Could not retrieve tile width", e); } return super.getOptimalTileWidth(); }
@Override public void setSeries(int no) { FormatTools.assertId(getCurrentFile(), true, 2); int n = reader.getCoreMetadataList().size(); if (n > 1 || noStitch) { reader.setSeries(no); } setCoreIndex(seriesToCoreIndex(no)); reader.setResolution(0); }
@Override public int getThumbSizeX() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.getThumbSizeX() : getReader(getCoreIndex(), 0).getThumbSizeX(); }
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); int source = getOriginalIndex(no); byte[] thumb = reader.openThumbBytes(source); int c = getSizeC() / reader.getEffectiveSizeC(); int channel = no % c; int bpp = FormatTools.getBytesPerPixel(getPixelType()); return ImageTools.splitChannels(thumb, channel, c, bpp, false, reader.isInterleaved()); }
@Override public int[] getZCTModuloCoords(int index) { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.getZCTModuloCoords(index) : FormatTools.getZCTCoords(core.get(getCoreIndex()).dimensionOrder, getSizeZ(), getEffectiveSizeC(), getSizeT(), getModuloZ().length(), getModuloC().length(), getModuloT().length(), getImageCount(), index); }