public void configureReaderPostInit() { if (swapOrder != null) dimSwapper.swapDimensions(swapOrder); if (shuffleOrder != null) dimSwapper.setOutputOrder(shuffleOrder); }
swap.swapDimensions(order);
swap.swapDimensions(order);
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); } }
/** * 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); }
/** Performed following ImportStep.DIM_ORDER notification. */ private void initializeDimOrder() { final int seriesCount = getSeriesCount(); final String stackOrder = getStackOrder(); for (int s=0; s<seriesCount; s++) { reader.setSeries(s); // set input order String dimOrder = options.getInputOrder(s); if (dimOrder != null) dimensionSwapper.swapDimensions(dimOrder); // set output order getDimensionSwapper().setOutputOrder(stackOrder); try { DimensionOrder order = DimensionOrder.fromString(stackOrder); getOMEMetadata().setPixelsDimensionOrder(order, s); } catch (EnumerationException e) { } } }
/** Performed following ImportStep.DIM_ORDER notification. */ private void initializeDimOrder() { final int seriesCount = getSeriesCount(); final String stackOrder = getStackOrder(); for (int s=0; s<seriesCount; s++) { reader.setSeries(s); // set input order String dimOrder = options.getInputOrder(s); if (dimOrder != null) dimensionSwapper.swapDimensions(dimOrder); // set output order getDimensionSwapper().setOutputOrder(stackOrder); try { DimensionOrder order = DimensionOrder.fromString(stackOrder); getOMEMetadata().setPixelsDimensionOrder(order, s); } catch (EnumerationException e) { } } }
/** * 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); }
((DimensionSwapper) reader).swapDimensions(guesser.getAdjustedOrder());
((DimensionSwapper) reader).swapDimensions(guesser.getAdjustedOrder());