String order = swap.getDimensionOrder();
String order = swap.getDimensionOrder();
protected void initReader(int sno, int fno) { int external = getExternalSeries(sno); DimensionSwapper r = externals[external].getReader(fno); try { if (r.getCurrentFile() == null) { r.setGroupFiles(false); } r.setId(externals[external].getFiles()[fno]); r.setCoreIndex(reader.getCoreMetadataList().size() > 1 ? sno : 0); String newOrder = ((DimensionSwapper) reader).getInputOrder(); if ((externals[external].getFiles().length > 1 || !r.isOrderCertain()) && (r.getRGBChannelCount() == 1 || newOrder.indexOf('C') == r.getDimensionOrder().indexOf('C'))) { r.swapDimensions(newOrder); } r.setOutputOrder(newOrder); } catch (FormatException e) { LOGGER.debug("", e); } catch (IOException e) { LOGGER.debug("", e); } }
protected void initReader(int sno, int fno) { int external = getExternalSeries(sno); DimensionSwapper r = externals[external].getReader(fno); try { if (r.getCurrentFile() == null) { r.setGroupFiles(false); } r.setId(externals[external].getFiles()[fno]); r.setCoreIndex(reader.getCoreMetadataList().size() > 1 ? sno : 0); String newOrder = ((DimensionSwapper) reader).getInputOrder(); if ((externals[external].getFiles().length > 1 || !r.isOrderCertain()) && (r.getRGBChannelCount() == 1 || newOrder.indexOf('C') == r.getDimensionOrder().indexOf('C'))) { r.swapDimensions(newOrder); } r.setOutputOrder(newOrder); } catch (FormatException e) { LOGGER.debug("", e); } catch (IOException e) { LOGGER.debug("", e); } }
protected int reorder(int no) { if (getInputOrder() == null) return no; return FormatTools.getReorderedIndex(getInputOrder(), getDimensionOrder(), getSizeZ(), getEffectiveSizeC(), getSizeT(), getImageCount(), no); }
protected int reorder(int no) { if (getInputOrder() == null) return no; return FormatTools.getReorderedIndex(getInputOrder(), getDimensionOrder(), getSizeZ(), getEffectiveSizeC(), getSizeT(), getImageCount(), no); }
/** * Tests the results of setting the output order. */ @Test(dataProvider="swapper") public void testOutputOrdering(DimensionSwapper swapper) { // set output order swapper.setOutputOrder(NEW_ORDER); // output order should be updated assertEquals(swapper.getDimensionOrder().equals(NEW_ORDER), true); // dimension sizes should be unchanged assertEquals(swapper.getSizeZ(), SIZE_Z); assertEquals(swapper.getSizeC(), SIZE_C); assertEquals(swapper.getSizeT(), SIZE_T); }
/** * Tests the results of setting the input order. */ @Test(dataProvider="swapper") public void testInputOrdering(DimensionSwapper swapper) { // set input (storage) order swapper.swapDimensions(NEW_ORDER); // output order should be unchanged assertEquals(swapper.getDimensionOrder().equals(OUTPUT_ORDER), true); // dimension sizes should be updated assertEquals(swapper.getSizeZ(), SIZE_T); assertEquals(swapper.getSizeC(), SIZE_Z); assertEquals(swapper.getSizeT(), SIZE_C); }
/** * Tests the interactions of setting output and input orders. */ @Test(dataProvider="swapper") public void testInputOutputOrdering(DimensionSwapper swapper) { swapper.setOutputOrder(NEW_ORDER); swapper.swapDimensions(NEW_ORDER); // output order should be updated assertEquals(swapper.getDimensionOrder().equals(NEW_ORDER), true); // dimension sizes should be updated assertEquals(swapper.getSizeZ(), SIZE_T); assertEquals(swapper.getSizeC(), SIZE_Z); assertEquals(swapper.getSizeT(), SIZE_C); }
public ExternalSeries(FilePattern pattern) throws FormatException, IOException { this.pattern = pattern; files = this.pattern.getFiles(); int nReaders = files.length > MAX_READERS ? 1 : files.length; readers = new DimensionSwapper[nReaders]; for (int i=0; i<readers.length; i++) { if (classList != null) { readers[i] = new DimensionSwapper(new ImageReader(classList)); } else readers[i] = new DimensionSwapper(); readers[i].setMetadataOptions(getMetadataOptions()); readers[i].setGroupFiles(false); } readers[0].setId(files[0]); ag = new AxisGuesser(this.pattern, readers[0].getDimensionOrder(), readers[0].getSizeZ(), readers[0].getSizeT(), readers[0].getSizeC(), readers[0].isOrderCertain()); blankThumbBytes = new byte[FormatTools.getPlaneSize(readers[0], readers[0].getThumbSizeX(), readers[0].getThumbSizeY())]; originalOrder = readers[0].getDimensionOrder(); imagesPerFile = readers[0].getImageCount(); }
public ExternalSeries(FilePattern pattern) throws FormatException, IOException { this.pattern = pattern; files = this.pattern.getFiles(); int nReaders = files.length > MAX_READERS ? 1 : files.length; readers = new DimensionSwapper[nReaders]; for (int i=0; i<readers.length; i++) { if (classList != null) { readers[i] = new DimensionSwapper(new ImageReader(classList)); } else readers[i] = new DimensionSwapper(); readers[i].setMetadataOptions(getMetadataOptions()); readers[i].setGroupFiles(false); } readers[0].setId(files[0]); ag = new AxisGuesser(this.pattern, readers[0].getDimensionOrder(), readers[0].getSizeZ(), readers[0].getSizeT(), readers[0].getSizeC(), readers[0].isOrderCertain()); blankThumbBytes = new byte[FormatTools.getPlaneSize(readers[0], readers[0].getThumbSizeX(), readers[0].getThumbSizeY())]; originalOrder = readers[0].getDimensionOrder(); imagesPerFile = readers[0].getImageCount(); }
final String stackOrder = dimSwapper.getDimensionOrder(); final int zSize = imp.getNSlices(); final int cSize = imp.getNChannels();
final String stackOrder = dimSwapper.getDimensionOrder(); final int zSize = imp.getNSlices(); final int cSize = imp.getNChannels();