private void updateLabels(String pattern) { try { swap.setId(pattern); String z = zLabel.getText(); z = z.substring(0, z.indexOf('<')); z += "<1-" + swap.getSizeZ() + ">"; zLabel.setText(z); String t = tLabel.getText(); t = t.substring(0, t.indexOf('<')); t += "<1-" + swap.getSizeT() + ">"; tLabel.setText(t); String c = cLabel.getText(); c = c.substring(0, c.indexOf('<')); c += "<1-" + swap.getEffectiveSizeC() + ">"; cLabel.setText(c); includeZ.setEnabled(true); includeT.setEnabled(true); includeC.setEnabled(true); } catch (FormatException exc) { LOGGER.info("", exc); } catch (IOException exc) { LOGGER.info("", exc); } }
private void updateLabels(String pattern) { try { swap.setId(pattern); String z = zLabel.getText(); z = z.substring(0, z.indexOf('<')); z += "<1-" + swap.getSizeZ() + ">"; zLabel.setText(z); String t = tLabel.getText(); t = t.substring(0, t.indexOf('<')); t += "<1-" + swap.getSizeT() + ">"; tLabel.setText(t); String c = cLabel.getText(); c = c.substring(0, c.indexOf('<')); c += "<1-" + swap.getEffectiveSizeC() + ">"; cLabel.setText(c); includeZ.setEnabled(true); includeT.setEnabled(true); includeC.setEnabled(true); } catch (FormatException exc) { LOGGER.info("", exc); } catch (IOException exc) { LOGGER.info("", exc); } }
swap.setId(pattern);
swap.setId(pattern);
for (int i=0; i<readers.length; i++) { try { readers[i].setId(f[i]); String[] used = readers[i].getUsedFiles(); for (String file : used) {
for (int i=0; i<readers.length; i++) { try { readers[i].setId(f[i]); String[] used = readers[i].getUsedFiles(); for (String file : used) {
@DataProvider(name = "swapper") public Object[][] createDimSwapper() { Location.mapId(TEST_FILE, TEST_FILE); DimensionSwapper swapper = new DimensionSwapper(); try { swapper.setId(TEST_FILE); } catch (FormatException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } swapper.setOutputOrder(OUTPUT_ORDER); return new Object[][]{{swapper}}; }
swap.setId(in); if (series != null) { swap.setSeries(((Integer) series.getValue()).intValue() - 1);
swap.setId(in); if (series != null) { swap.setSeries(((Integer) series.getValue()).intValue() - 1);
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); } }
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(); }