/** * Checks the original metadata table for ImageJ-specific information * to propagate into the metadata store. */ private void populateMetadataStoreImageJ(MetadataStore store) { // TODO: Perhaps we should only populate the physical Z size if the unit is // a known, physical quantity such as "micron" rather than "pixel". // e.g.: if (calibrationUnit.equals("micron")) if (physicalSizeZ != null) { double zDepth = physicalSizeZ.doubleValue(); if (zDepth < 0) zDepth = -zDepth; Length z = FormatTools.getPhysicalSizeZ(zDepth); if (z != null) { store.setPixelsPhysicalSizeZ(z, 0); } } if (timeIncrement != null) { store.setPixelsTimeIncrement(timeIncrement, 0); } }
/** * Checks the original metadata table for ImageJ-specific information * to propagate into the metadata store. */ private void populateMetadataStoreImageJ(MetadataStore store) { // TODO: Perhaps we should only populate the physical Z size if the unit is // a known, physical quantity such as "micron" rather than "pixel". // e.g.: if (calibrationUnit.equals("micron")) if (physicalSizeZ != null) { double zDepth = physicalSizeZ.doubleValue(); if (zDepth < 0) zDepth = -zDepth; Length z = FormatTools.getPhysicalSizeZ(zDepth); if (z != null) { store.setPixelsPhysicalSizeZ(z, 0); } } if (timeIncrement != null) { store.setPixelsTimeIncrement(timeIncrement, 0); } }
private void fillPhysicalSizes(MetadataStore store) { if (physicalSizeX == null && physicalSizeY == null && physicalSizeZ == null) return; for (int s=0; s<getSeriesCount(); s++) { store.setPixelsPhysicalSizeX(physicalSizeX, s); store.setPixelsPhysicalSizeY(physicalSizeY, s); store.setPixelsPhysicalSizeZ(physicalSizeZ, s); } }
private void fillPhysicalSizes(MetadataStore store) { if (physicalSizeX == null && physicalSizeY == null && physicalSizeZ == null) return; for (int s=0; s<getSeriesCount(); s++) { store.setPixelsPhysicalSizeX(physicalSizeX, s); store.setPixelsPhysicalSizeY(physicalSizeY, s); store.setPixelsPhysicalSizeZ(physicalSizeZ, s); } }
zStep = FormatTools.createLength(size, UNITS.MICROMETER); for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeZ(zStep, series);
zStep = FormatTools.createLength(size, UNITS.MICROMETER); for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeZ(zStep, series);
store.setPixelsPhysicalSizeZ(sizeZ, 0);
private void populateCalibrations(final MetadataStore store, final int imageIndex, final double calX, final double calY, final double calZ, final double calC, final double calT) { store.setPixelsPhysicalSizeX(// new Length(calX, UNITS.MICROMETER), imageIndex); store.setPixelsPhysicalSizeY(// new Length(calY, UNITS.MICROMETER), imageIndex); store.setPixelsPhysicalSizeZ(// new Length(calZ, UNITS.MICROMETER), imageIndex); store.setPixelsTimeIncrement(new Time(calT, UNITS.SECOND), imageIndex); }
store.setPixelsPhysicalSizeZ(FormatTools.createLength(dims_pixelSize[2], UNITS.MICROMETER), 0);
store.setPixelsPhysicalSizeZ(FormatTools.createLength(dims_pixelSize[2], UNITS.MICROMETER), 0);
store.setPixelsPhysicalSizeZ(sizeZ, 0);
store.setPixelsPhysicalSizeZ(sizeZ, 0);
if (physicalSizeZ != null && physicalSizeZ.value() != null) { physicalSizeZ = FormatTools.getPhysicalSize(physicalSizeZ.value().doubleValue(), physicalSizeZ.unit().getSymbol()); dest.setPixelsPhysicalSizeZ(physicalSizeZ, image);
if (physicalSizeZ != null && physicalSizeZ.value() != null) { physicalSizeZ = FormatTools.getPhysicalSize(physicalSizeZ.value().doubleValue(), physicalSizeZ.unit().getSymbol()); dest.setPixelsPhysicalSizeZ(physicalSizeZ, image);
store.setPixelsPhysicalSizeZ(sizeZ, 0);
store.setPixelsPhysicalSizeZ(sizeZ, 0);
store.setPixelsPhysicalSizeY(sizeY, 0); store.setPixelsPhysicalSizeZ(null, 0);
store.setPixelsPhysicalSizeX(FormatTools.createLength(x, UNITS.MICROMETER), 0); store.setPixelsPhysicalSizeY(FormatTools.createLength(y, UNITS.MICROMETER), 0); store.setPixelsPhysicalSizeZ(FormatTools.createLength(z, UNITS.MICROMETER), 0); store.setStageLabelName(wlz.getWlzOrgLabelName(), 0); store.setStageLabelX(new Length(wlz.getOrgX(), UNITS.REFERENCEFRAME), 0);
store.setPixelsPhysicalSizeX(FormatTools.createLength(x, UNITS.MICROMETER), 0); store.setPixelsPhysicalSizeY(FormatTools.createLength(y, UNITS.MICROMETER), 0); store.setPixelsPhysicalSizeZ(FormatTools.createLength(z, UNITS.MICROMETER), 0); store.setStageLabelName(wlz.getWlzOrgLabelName(), 0); store.setStageLabelX(new Length(wlz.getOrgX(), UNITS.REFERENCEFRAME), 0);
store.setPixelsPhysicalSizeZ(makeLengthXML(pz, getPhysicalSizeZUnitXsdDefault()), 0);