int previousCoreIndex = getCoreIndex(); setCoreIndex(coreIndex); plane.col = dimension.start; if ((prestitched == null || prestitched) && getSizeX() > 0 && dimension.size != getSizeX() && allowAutostitching()) if (allowAutostitching() || ms0.sizeX == 0 || dimension.size == dimension.storedSize) { ms0.sizeX = dimension.size; plane.row = dimension.start; if ((prestitched == null || prestitched) && getSizeY() > 0 && dimension.size != getSizeY() && allowAutostitching()) if (allowAutostitching() || ms0.sizeY == 0 || dimension.size == dimension.storedSize) { ms0.sizeY = dimension.size; if (dimension.start >= getSizeC()) { ms0.sizeC = dimension.start + 1; if (dimension.start > 0 && dimension.start >= getSizeZ()) { ms0.sizeZ = dimension.start + 1; else if (dimension.size > getSizeZ()) { ms0.sizeZ = dimension.size; if (dimension.size > getSizeT()) { ms0.sizeT = dimension.size;
private void calculateDimensions() { calculateDimensions(0, false); }
if (base.endsWith(")") && isGroupFiles()) { LOGGER.info("Checking for master file"); int lastFileSeparator = base.lastIndexOf(File.separator); if (new Location(base).exists()) { LOGGER.info("Initializing master file {}", base); initFile(base); return; readSegments(id); Arrays.sort(keys); for (Integer key : keys) { readSegments(pixels.get(key)); calculateDimensions(); if (getSizeC() == 0) { ms0.sizeC = 1; if (getSizeZ() == 0) { ms0.sizeZ = 1; if (getSizeT() == 0) { ms0.sizeT = 1; if (getImageCount() == 0) { ms0.imageCount = ms0.sizeZ * ms0.sizeT;
private void readAttachments() throws FormatException, IOException { if (!canReadAttachments()) { return; ZeissCZIReader thumbReader = new ZeissCZIReader(); thumbReader.setMetadataOptions(getMetadataOptions()); ByteArrayHandle stream = new ByteArrayHandle(((Attachment) segment).attachmentData); Location.mapFile("image.czi", stream); thumbReader.setId("image.czi"); CoreMetadata c = thumbReader.getCoreMetadataList().get(0); ((Attachment) segment).attachmentData = thumbReader.openBytes(0); thumbReader.close();
case 'M': if (dimension.start > prevM) { if (!extraDimOrder.contains('M') && mosaics <= getSeriesCount() && (prestitched == null || !prestitched || !allowAutostitching())) case 'Z': z = dimension.start; if (z >= getSizeZ()) { z = getSizeZ() - 1; if (t >= getSizeT()) { t = getSizeT() - 1; p / (getImageCount() * (getSeriesCount() / angles)); z = r * (getSizeZ() / rotations) + z; c = i * (getSizeC() / illuminations) + c; t = phase * (getSizeT() / phases) + t; plane.planeIndex = getIndex(z, c, t); int seriesIndex = FormatTools.positionToRaster(extraLengths, extra); plane.resolutionIndex = plane.coreIndex;
addGlobalMeta(s, value); addGlobalMetaList(s, value); addGlobalMeta(keyString + attrName, attrValue); addGlobalMetaList(keyString + attrName, attrValue); Object child = children.item(i); if (child instanceof Element) { populateOriginalMetadata((Element) child, nameStack);
if (base.endsWith(")") && isGroupFiles()) { LOGGER.info("Checking for master file"); int lastFileSeparator = base.lastIndexOf(File.separator); if (new Location(base).exists()) { LOGGER.info("Initializing master file {}", base); initFile(base); return; readSegments(id); Arrays.sort(keys); for (Integer key : keys) { readSegments(pixels.get(key)); calculateDimensions(); if (getSizeC() == 0) { ms0.sizeC = 1; if (getSizeZ() == 0) { ms0.sizeZ = 1; if (getSizeT() == 0) { ms0.sizeT = 1; if (getImageCount() == 0) { ms0.imageCount = ms0.sizeZ * ms0.sizeT;
private void readAttachments() throws FormatException, IOException { if (!canReadAttachments()) { return; ZeissCZIReader thumbReader = new ZeissCZIReader(); thumbReader.setMetadataOptions(getMetadataOptions()); ByteArrayHandle stream = new ByteArrayHandle(((Attachment) segment).attachmentData); Location.mapFile("image.czi", stream); thumbReader.setId("image.czi"); CoreMetadata c = thumbReader.getCoreMetadataList().get(0); ((Attachment) segment).attachmentData = thumbReader.openBytes(0); thumbReader.close();
case 'M': if (dimension.start > prevM) { if (!extraDimOrder.contains('M') && mosaics <= getSeriesCount() && (prestitched == null || !prestitched || !allowAutostitching())) case 'Z': z = dimension.start; if (z >= getSizeZ()) { z = getSizeZ() - 1; if (t >= getSizeT()) { t = getSizeT() - 1; p / (getImageCount() * (getSeriesCount() / angles)); z = r * (getSizeZ() / rotations) + z; c = i * (getSizeC() / illuminations) + c; t = phase * (getSizeT() / phases) + t; plane.planeIndex = getIndex(z, c, t); int seriesIndex = FormatTools.positionToRaster(extraLengths, extra); plane.resolutionIndex = plane.coreIndex;
addGlobalMeta(s, value); addGlobalMetaList(s, value); addGlobalMeta(keyString + attrName, attrValue); addGlobalMetaList(keyString + attrName, attrValue); Object child = children.item(i); if (child instanceof Element) { populateOriginalMetadata((Element) child, nameStack);
int previousCoreIndex = getCoreIndex(); setCoreIndex(coreIndex); plane.col = dimension.start; if ((prestitched == null || prestitched) && getSizeX() > 0 && dimension.size != getSizeX() && allowAutostitching()) if (allowAutostitching() || ms0.sizeX == 0 || dimension.size == dimension.storedSize) { ms0.sizeX = dimension.size; plane.row = dimension.start; if ((prestitched == null || prestitched) && getSizeY() > 0 && dimension.size != getSizeY() && allowAutostitching()) if (allowAutostitching() || ms0.sizeY == 0 || dimension.size == dimension.storedSize) { ms0.sizeY = dimension.size; if (dimension.start >= getSizeC()) { ms0.sizeC = dimension.start + 1; if (dimension.start > 0 && dimension.start >= getSizeZ()) { ms0.sizeZ = dimension.start + 1; else if (dimension.size > getSizeZ()) { ms0.sizeZ = dimension.size; if (dimension.size > getSizeT()) { ms0.sizeT = dimension.size;
private void calculateDimensions() { calculateDimensions(0, false); }