/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#getTimepoint(Integer) */ public PixelData getTimepoint(Integer t) throws IOException, DimensionsOutOfBoundsException { Long offset = getTimepointOffset(t); Integer size = safeLongToInteger(getTimepointSize()); return getRegion(size, offset); }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#getStack(Integer, Integer) */ public PixelData getStack(Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { Long offset = getStackOffset(c, t); Integer size = safeLongToInteger(getStackSize()); return getRegion(size, offset); }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#getHypercube(List, List, List) */ public PixelData getHypercube(List<Integer> offset, List<Integer> size, List<Integer> step) throws IOException, DimensionsOutOfBoundsException { byte[] buffer = new byte[ safeLongToInteger(getHypercubeSize(offset,size,step))]; getHypercubeDirect(offset,size,step,buffer); return new PixelData(pixels.getPixelsType().getValue(), ByteBuffer.wrap(buffer)); }
public byte[] getRow(Integer y, Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { checkBounds(null, y, z, c, t); try { if (buffer.length != getRowSize()) throw new RuntimeException("Buffer size incorrect."); int size = RomioPixelBuffer.safeLongToInteger(getPlaneSize()); byte[] plane = new byte[size]; getWholePlane(z,c,t,plane); System.arraycopy(plane, y*getRowSize(), buffer, 0, getRowSize()); } catch (FormatException e) { throw new RuntimeException(e); } return buffer; }
public byte[] getTimepoint(Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { checkBounds(null, null, null, null, t); if (buffer.length != getTimepointSize()) throw new RuntimeException("Buffer size incorrect."); int size = RomioPixelBuffer.safeLongToInteger(getStackSize()); byte[] stack = new byte[size]; int sizeC = getSizeC(); for(int c = 0; c < sizeC; c++) { getStack(c, t, stack); System.arraycopy(stack, 0, buffer, c*size, size); } return buffer; }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#setPlane(ByteBuffer, Integer, Integer, Integer) */ public void setPlane(ByteBuffer buffer, Integer z, Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { throwIfReadOnly(); Long offset = getPlaneOffset(z, c, t); Integer size = safeLongToInteger(getPlaneSize()); if (buffer.limit() != size) { // Handle the size mismatch. if (buffer.limit() < size) throw new BufferUnderflowException(); throw new BufferOverflowException(); } setRegion(size, offset, buffer); }
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; }
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 void getTimepoint_async(AMD_RawPixelsStore_getTimepoint __cb, int t, Current __current) throws ServerError { try { int size = RomioPixelBuffer.safeLongToInteger(reader.getTimepointSize()); byte[] timepoint = new byte[size]; reader.getTimepoint(t,timepoint); reader.swapIfRequired(timepoint); __cb.ice_response(timepoint); } catch (Exception e) { __cb.ice_exception(e); } }
public void getStack_async(AMD_RawPixelsStore_getStack __cb, int c, int t, Current __current) throws ServerError { try { int size = RomioPixelBuffer.safeLongToInteger( reader.getStackSize()); byte[] stack = new byte[size]; reader.getStack(c,t,stack); reader.swapIfRequired(stack); __cb.ice_response(stack); } catch (Exception e) { __cb.ice_exception(e); } }
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 void getPlane_async(AMD_RawPixelsStore_getPlane __cb, int z, int c, int t, Current __current) throws ServerError { try { int size = RomioPixelBuffer.safeLongToInteger( reader.getPlaneSize()); byte[] plane = new byte[size]; reader.getPlane(z,c,t,plane); reader.swapIfRequired(plane); __cb.ice_response(plane); } catch (Exception e) { __cb.ice_exception(e); } }
public PixelData getHypercube(List<Integer> offset, List<Integer> size, List<Integer> step) throws IOException, DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); PixelData d; int hypercubeSize = RomioPixelBuffer.safeLongToInteger( getHypercubeSize(offset,size,step)); byte[] buffer = new byte[hypercubeSize]; reader.getHypercube(offset,size,step,buffer); d = new PixelData(reader.getPixelsType(), ByteBuffer.wrap(buffer)); d.setOrder(isLittleEndian()? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN); return d; }
@RolesAllowed("user") public synchronized byte[] getPlane(int arg0, int arg1, int arg2) { errorIfNotLoaded(); int size = RomioPixelBuffer.safeLongToInteger(buffer.getPlaneSize()); if (readBuffer == null || readBuffer.length != size) { readBuffer = new byte[size]; } try { readBuffer = buffer.getPlaneDirect(arg0, arg1, arg2, readBuffer); } catch (Exception e) { handleException(e); } return readBuffer; }
@RolesAllowed("user") public synchronized byte[] getStack(int arg0, int arg1) { errorIfNotLoaded(); int size = RomioPixelBuffer.safeLongToInteger(buffer.getStackSize()); if (readBuffer == null || readBuffer.length != size) { readBuffer = new byte[size]; } try { readBuffer = buffer.getStackDirect(arg0, arg1, readBuffer); } catch (Exception e) { handleException(e); } return readBuffer; }
@RolesAllowed("user") public synchronized byte[] getPlaneRegion(int z, int c, int t, int count, int offset) { errorIfNotLoaded(); int size = RomioPixelBuffer.safeLongToInteger( buffer.getByteWidth() * (long) count); if (readBuffer == null || readBuffer.length != size) { readBuffer = new byte[size]; } try { readBuffer = buffer.getPlaneRegionDirect(z, c, t, count, offset, readBuffer); } catch (Exception e) { handleException(e); } return readBuffer; }
public void getHypercube_async(AMD_RawPixelsStore_getHypercube __cb, List<Integer> offset, List<Integer> size, List<Integer> step, Current __current) throws ServerError { try { int hypercubeSize = RomioPixelBuffer.safeLongToInteger( reader.getHypercubeSize(offset,size,step)); byte[] cube = new byte[hypercubeSize]; reader.getHypercube(offset,size,step,cube); reader.swapIfRequired(cube); __cb.ice_response(cube); } catch (Exception e) { __cb.ice_exception(e); } }
@RolesAllowed("user") public synchronized byte[] getTimepoint(int arg0) { errorIfNotLoaded(); int size = RomioPixelBuffer.safeLongToInteger( buffer.getTimepointSize()); if (readBuffer == null || readBuffer.length != size) { readBuffer = new byte[size]; } try { readBuffer = buffer.getTimepointDirect(arg0, readBuffer); } catch (Exception e) { handleException(e); } return readBuffer; }
@RolesAllowed("user") public synchronized byte[] getHypercube(List<Integer> offset, List<Integer> size, List<Integer> step) { errorIfNotLoaded(); int cubeSize = RomioPixelBuffer.safeLongToInteger( buffer.getHypercubeSize(offset, size, step)); if (readBuffer == null || readBuffer.length != cubeSize) { readBuffer = new byte[cubeSize]; } try { readBuffer = buffer.getHypercubeDirect(offset, size, step, readBuffer); } catch (Exception e) { handleException(e); } return readBuffer; }
@RolesAllowed("user") public synchronized byte[] getTile(int z, int c, int t, int x, int y, int w, int h) { errorIfNotLoaded(); int size = RomioPixelBuffer.safeLongToInteger( (long) w * (long) h * buffer.getByteWidth()); if (readBuffer == null || readBuffer.length != size) { readBuffer = new byte[size]; } try { readBuffer = buffer.getTileDirect(z, c, t, x, y, w, h, readBuffer); } catch (Exception e) { handleException(e); } return readBuffer; }