private int getExternalSeries() { return getExternalSeries(getCoreIndex()); }
private int getExternalSeries() { return getExternalSeries(getCoreIndex()); }
/** * Gets the reader that should be used with the given series and image plane. */ public DimensionSwapper getReader(int series, int no) { if (noStitch) return (DimensionSwapper) reader; DimensionSwapper r = externals[getExternalSeries(series)].getReader(no); initReader(series, no); return r; }
/** * Gets the reader that should be used with the given series and image plane. */ public DimensionSwapper getReader(int series, int no) { if (noStitch) return (DimensionSwapper) reader; DimensionSwapper r = externals[getExternalSeries(series)].getReader(no); initReader(series, no); return r; }
/** * Gets the axis guesser object used to guess * which dimensional axes are which. */ public AxisGuesser getAxisGuesser() { FormatTools.assertId(getCurrentFile(), true, 2); return externals[getExternalSeries()].getAxisGuesser(); }
/** * Gets the axis guesser object used to guess * which dimensional axes are which. */ public AxisGuesser getAxisGuesser() { FormatTools.assertId(getCurrentFile(), true, 2); return externals[getExternalSeries()].getAxisGuesser(); }
/** * Gets the axis type for each dimensional block. * @return An array containing values from the enumeration: * <ul> * <li>AxisGuesser.Z_AXIS: focal planes</li> * <li>AxisGuesser.T_AXIS: time points</li> * <li>AxisGuesser.C_AXIS: channels</li> * <li>AxisGuesser.S_AXIS: series</li> * </ul> */ public int[] getAxisTypes() { FormatTools.assertId(getCurrentFile(), true, 2); return externals[getExternalSeries()].getAxisGuesser().getAxisTypes(); }
/** * Gets the axis type for each dimensional block. * @return An array containing values from the enumeration: * <ul> * <li>AxisGuesser.Z_AXIS: focal planes</li> * <li>AxisGuesser.T_AXIS: time points</li> * <li>AxisGuesser.C_AXIS: channels</li> * <li>AxisGuesser.S_AXIS: series</li> * </ul> */ public int[] getAxisTypes() { FormatTools.assertId(getCurrentFile(), true, 2); return externals[getExternalSeries()].getAxisGuesser().getAxisTypes(); }
/** Gets the file pattern object used to build the list of files. */ public FilePattern getFilePattern() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? findPattern(getCurrentFile()) : externals[getExternalSeries()].getFilePattern(); }
/** Gets the file pattern object used to build the list of files. */ public FilePattern getFilePattern() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? findPattern(getCurrentFile()) : externals[getExternalSeries()].getFilePattern(); }
/** * Sets the axis type for each dimensional block. * @param axes An array containing values from the enumeration: * <ul> * <li>AxisGuesser.Z_AXIS: focal planes</li> * <li>AxisGuesser.T_AXIS: time points</li> * <li>AxisGuesser.C_AXIS: channels</li> * <li>AxisGuesser.S_AXIS: series</li> * </ul> */ public void setAxisTypes(int[] axes) throws FormatException { FormatTools.assertId(getCurrentFile(), true, 2); externals[getExternalSeries()].getAxisGuesser().setAxisTypes(axes); computeAxisLengths(); }
/** * Sets the axis type for each dimensional block. * @param axes An array containing values from the enumeration: * <ul> * <li>AxisGuesser.Z_AXIS: focal planes</li> * <li>AxisGuesser.T_AXIS: time points</li> * <li>AxisGuesser.C_AXIS: channels</li> * <li>AxisGuesser.S_AXIS: series</li> * </ul> */ public void setAxisTypes(int[] axes) throws FormatException { FormatTools.assertId(getCurrentFile(), true, 2); externals[getExternalSeries()].getAxisGuesser().setAxisTypes(axes); computeAxisLengths(); }
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); } }
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); IFormatReader r = getReader(no); int ino = getAdjustedIndex(no); if (ino < r.getImageCount()) return r.openThumbBytes(ino); // return a blank image to cover for the fact that // this file does not contain enough image planes return externals[getExternalSeries()].getBlankThumbBytes(); }
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); IFormatReader r = getReader(no); int ino = getAdjustedIndex(no); if (ino < r.getImageCount()) return r.openThumbBytes(ino); // return a blank image to cover for the fact that // this file does not contain enough image planes return externals[getExternalSeries()].getBlankThumbBytes(); }
if (noStitch) return new int[] {0, no}; int sno = getCoreIndex(); ExternalSeries s = externals[getExternalSeries()];
if (noStitch) return new int[] {0, no}; int sno = getCoreIndex(); ExternalSeries s = externals[getExternalSeries()];
int sno = getCoreIndex(); CoreMetadata ms = core.get(sno); ExternalSeries s = externals[getExternalSeries()]; FilePattern p = s.getFilePattern();
int sno = getCoreIndex(); CoreMetadata ms = core.get(sno); ExternalSeries s = externals[getExternalSeries()]; FilePattern p = s.getFilePattern();