/** * Delegates to {@link IFormatReader#isLittleEndian()}. * @return See above. */ public boolean isLittleEndian() { // Ensure the reader has been initialized reader(); return bfReader.isLittleEndian(); }
public Long getTimepointOffset(Integer t) throws DimensionsOutOfBoundsException { return reader().getTimepointOffset(t); }
public void checkBounds(Integer x, Integer y, Integer z, Integer c, Integer t) throws DimensionsOutOfBoundsException { reader().checkBounds(x, y, z, c, t); }
public Long getStackOffset(Integer c, Integer t) throws DimensionsOutOfBoundsException { return reader().getStackOffset(c,t); }
public int getResolutionLevels() { // Ensure the reader has been initialized reader(); return bfReader.getResolutionCount(); }
/** * Sets the current series in the underlying Bio-Formats reader. * @param series The series to set. */ public void setSeries(int series) { // Ensure the reader has been initialized reader(); bfReader.setSeries(series); seriesIndex = series; }
/** * Retrieves the current series of the underlying Bio-Formats reader. * @return The series. */ public int getSeries() { // Ensure the reader has been initialized reader(); return bfReader.getSeries(); }
public Long getHypercubeSize(List<Integer> offset, List<Integer> size, List<Integer> step) throws DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); return reader.getHypercubeSize(offset,size,step); }
public byte[] getRowDirect(Integer y, Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { try { final BfPixelsWrapper reader = reader(); reader.getRow(y,z,c,t,buffer); reader.swapIfRequired(buffer); } catch (FormatException e) { throw new RuntimeException(e); } return buffer; }
public byte[] getHypercubeDirect(List<Integer> offset, List<Integer> size, List<Integer> step, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { try { final BfPixelsWrapper reader = reader(); reader.getHypercube(offset,size,step,buffer); reader.swapIfRequired(buffer); } catch (FormatException e) { throw new RuntimeException(e); } return buffer; }
public byte[] getPlaneDirect(Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { try { final BfPixelsWrapper reader = reader(); reader.getPlane(z,c,t,buffer); reader.swapIfRequired(buffer); } catch (FormatException e) { throw new RuntimeException(e); } return buffer; }
public Dimension getTileSize() { // Ensure the reader has been initialized reader(); return new Dimension(bfReader.getOptimalTileWidth(), bfReader.getOptimalTileHeight()); }
public byte[] getColDirect(Integer x, Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { try { final BfPixelsWrapper reader = reader(); reader.getCol(x,z,c,t,buffer); reader.swapIfRequired(buffer); } catch (FormatException e) { throw new RuntimeException(e); } return buffer; }
public byte[] getStackDirect(Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { try { final BfPixelsWrapper reader = reader(); reader.getStack(c,t,buffer); reader.swapIfRequired(buffer); } catch (FormatException e) { throw new RuntimeException(e); } return buffer; }
public void setResolutionLevel(int resolutionLevel) { // Ensure the reader has been initialized reader(); // The highest resolution level (100%) is actually the first series bfReader.setResolution(Math.abs( resolutionLevel - (getResolutionLevels() - 1))); }
public int getResolutionLevel() { // Ensure the reader has been initialized reader(); // The highest resolution level (100%) is actually the first series return Math.abs( bfReader.getResolution() - (getResolutionLevels() - 1)); }
public PixelData getCol(Integer x, Integer z, Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); PixelData d; byte[] buffer = new byte[reader.getColSize()]; reader.getCol(x,z,c,t,buffer); d = new PixelData(reader.getPixelsType(), ByteBuffer.wrap(buffer)); d.setOrder(isLittleEndian()? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN); return d; }
public PixelData getStack(Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); PixelData d; int size = RomioPixelBuffer.safeLongToInteger(reader.getStackSize()); byte[] buffer = new byte[size]; reader.getStack(c,t,buffer); d = new PixelData(reader.getPixelsType(), ByteBuffer.wrap(buffer)); d.setOrder(isLittleEndian()? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN); return d; }
public PixelData getTimepoint(Integer t) throws IOException, DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); PixelData d; int size = RomioPixelBuffer.safeLongToInteger( reader.getTimepointSize()); byte[] buffer = new byte[size]; reader.getTimepoint(t,buffer); d = new PixelData(reader.getPixelsType(), ByteBuffer.wrap(buffer)); d.setOrder(isLittleEndian()? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN); return d; }
public PixelData getPlane(Integer z, Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); PixelData d; int size = RomioPixelBuffer.safeLongToInteger(reader.getPlaneSize()); byte[] buffer = new byte[size]; reader.getPlane(z,c,t,buffer); d = new PixelData(reader.getPixelsType(), ByteBuffer.wrap(buffer)); d.setOrder(isLittleEndian()? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN); return d; }