public PixelData getPlane(Integer z, Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { ByteBuffer buf = ByteBuffer.wrap(planes[z][c][t]); return new PixelData(pixels.getPixelsType().getValue(), buf); }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#getRegion(Integer, Long) */ public PixelData getRegion(Integer size, Long offset) throws IOException { FileChannel fileChannel = getFileChannel(); /* * fileChannel should not be "null" as it will throw an exception if * there happens to be an error. */ MappedByteBuffer b = fileChannel.map(MapMode.READ_ONLY, offset, size); return new PixelData(pixels.getPixelsType().getValue(), b); }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#isFloat() */ public boolean isFloat() { PixelData d = new PixelData(pixels.getPixelsType().getValue(), null); return d.isFloat(); }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#isSigned() */ public boolean isSigned() { PixelData d = new PixelData(pixels.getPixelsType().getValue(), null); return d.isSigned(); }
public boolean isFloat() { MappedByteBuffer b = null; PixelData d = new PixelData(pixels.getPixelsType().getValue(), b); return d.isFloat(); }
public boolean isSigned() { MappedByteBuffer b = null; PixelData d = new PixelData(pixels.getPixelsType().getValue(), b); return d.isSigned(); }
/** * 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 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 getRow(Integer y, Integer z, Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { final BfPixelsWrapper reader = reader(); PixelData d; byte[] buffer = new byte[reader.getRowSize()]; reader.getRow(y,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 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; }
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 getTile(Integer z, Integer c, Integer t, Integer x, Integer y, Integer w, Integer h) throws IOException { final BfPixelsWrapper reader = reader(); byte[] buffer = new byte[ w * h * FormatTools.getBytesPerPixel(reader.getPixelsType())]; try { // Call getTile on reader() rather than on this // so as not to swap the bytes twice. reader().getTile(z, c, t, x, y, w, h, buffer); PixelData d = new PixelData( reader.getPixelsType(), ByteBuffer.wrap(buffer)); d.setOrder(isLittleEndian()? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN); return d; } catch (FormatException e) { throw new RuntimeException(e); } }
new PixelData(PixelsType.VALUE_BIT, ByteBuffer.wrap(overlay)); wData.add(new Plane2D(pDef, metadata, data));
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#getColDirect(Integer, Integer, Integer, Integer, byte[]) */ public byte[] getColDirect(Integer x, Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException { PixelData plane = getPlane(z, c, t); Integer sizeY = getSizeY(); Integer sizeX = getSizeX(); ByteBuffer buf = ByteBuffer.wrap(buffer); PixelData column = new PixelData(pixels.getPixelsType().getValue(), buf); int offset; double value; for (int i = 0; i < sizeY; i++) { offset = (i * sizeX) + x; value = plane.getPixelValue(offset); column.setPixelValue(i, value); } plane.dispose(); return buffer; }
/** * Implemented as specified by {@link PixelBuffer} I/F. * @see PixelBuffer#getCol(Integer, Integer, Integer, Integer) */ public PixelData getCol(Integer x, Integer z, Integer c, Integer t) throws IOException, DimensionsOutOfBoundsException { //Dimension check in plane. PixelData plane = getPlane(z, c, t); Integer sizeY = getSizeY(); Integer sizeX = getSizeX(); Integer colSize = getColSize(); ByteBuffer buf = ByteBuffer.wrap(new byte[colSize]); PixelData column = new PixelData(pixels.getPixelsType().getValue(), buf); int offset; double value; for (int i = 0; i < sizeY; i++) { offset = (i * sizeX) + x; value = plane.getPixelValue(offset); column.setPixelValue(i, value); } plane.dispose(); return column; }
size = width*height*getByteWidth(); buf = ByteBuffer.wrap(new byte[size]); region = new PixelData(pixels.getPixelsType().getValue(), buf); for (int i = 0; i < height; i++) { for (int j = 0; j < width; j++) { size = width*height*getByteWidth()/(stride*stride); buf = ByteBuffer.wrap(new byte[size]); region = new PixelData(pixels.getPixelsType().getValue(), buf); int k = 0; int l = 0;
byte[] buf = new byte[planeSize]; ctx.from = pixelBuffer.getStack(channelIndex, timepoint); ctx.to = new PixelData(pixelsType.getValue(), ByteBuffer.wrap(buf));
ctx.planeSizeInPixels * (iPixels.getBitDepth(pixelsType) / 8); byte[] buf = new byte[planeSize]; ctx.to = new PixelData(pixelsType.getValue(), ByteBuffer.wrap(buf)); int newC = 0; for (Integer c : channels)