use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.
the class Exporter method run.
// -- Exporter API methods --
/**
* Executes the plugin.
*/
public void run() {
String outfile = null;
Boolean splitZ = null;
Boolean splitC = null;
Boolean splitT = null;
Boolean padded = null;
Boolean saveRoi = null;
String compression = null;
Boolean windowless = Boolean.FALSE;
if (plugin.arg != null) {
outfile = Macro.getValue(plugin.arg, "outfile", null);
String z = Macro.getValue(plugin.arg, "splitZ", null);
String c = Macro.getValue(plugin.arg, "splitC", null);
String t = Macro.getValue(plugin.arg, "splitT", null);
String zeroPad = Macro.getValue(plugin.arg, "padded", null);
String sr = Macro.getValue(plugin.arg, "saveRoi", null);
compression = Macro.getValue(plugin.arg, "compression", null);
String id = Macro.getValue(plugin.arg, "imageid", null);
splitZ = z == null ? null : Boolean.valueOf(z);
splitC = c == null ? null : Boolean.valueOf(c);
splitT = t == null ? null : Boolean.valueOf(t);
padded = zeroPad == null ? null : Boolean.valueOf(zeroPad);
saveRoi = sr == null ? null : Boolean.valueOf(sr);
if (id != null) {
try {
int imageID = Integer.parseInt(id);
ImagePlus plus = WindowManager.getImage(imageID);
if (plus != null)
imp = plus;
} catch (Exception e) {
// nothing to do, we use the current imagePlus
}
}
String w = Macro.getValue(plugin.arg, "windowless", null);
if (w != null) {
windowless = Boolean.valueOf(w);
}
plugin.arg = null;
}
if (outfile == null) {
String options = Macro.getOptions();
if (options != null) {
String save = Macro.getValue(options, "save", null);
if (save != null)
outfile = save;
}
}
// create a temporary file if window less
if (windowless && (outfile == null || outfile.length() == 0)) {
File tmp = null;
try {
String name = removeExtension(imp.getTitle());
String n = name + ".ome.tif";
tmp = File.createTempFile(name, ".ome.tif");
File p = tmp.getParentFile();
File[] list = p.listFiles();
// make sure we delete a previous tmp file with same name if any
if (list != null) {
File toDelete = null;
for (int i = 0; i < list.length; i++) {
if (list[i].getName().equals(n)) {
toDelete = list[i];
break;
}
}
if (toDelete != null) {
toDelete.delete();
}
}
outfile = new File(p, n).getAbsolutePath();
if (Recorder.record)
Recorder.recordPath("outputfile", outfile);
IJ.log("exporter outputfile " + outfile);
} catch (Exception e) {
// fall back to window mode.
} finally {
if (tmp != null)
tmp.delete();
}
}
File f = null;
if (outfile == null || outfile.length() == 0) {
// open a dialog prompting for the filename to save
// NB: Copied and adapted from ij.io.SaveDIalog.jSaveDispatchThread,
// so that the save dialog has a file filter for choosing output format.
String dir = null, name = null;
JFileChooser fc = GUITools.buildFileChooser(new ImageWriter(), false);
fc.setDialogTitle("Bio-Formats Exporter");
String defaultDir = OpenDialog.getDefaultDirectory();
if (defaultDir != null)
fc.setCurrentDirectory(new File(defaultDir));
// set OME-TIFF as the default output format
FileFilter[] ff = fc.getChoosableFileFilters();
FileFilter defaultFilter = null;
for (int i = 0; i < ff.length; i++) {
if (ff[i] instanceof ExtensionFileFilter) {
ExtensionFileFilter eff = (ExtensionFileFilter) ff[i];
if (i == 0 || eff.getExtension().equals("ome.tif")) {
defaultFilter = eff;
break;
}
}
}
if (defaultFilter != null)
fc.setFileFilter(defaultFilter);
int returnVal = fc.showSaveDialog(IJ.getInstance());
if (returnVal != JFileChooser.APPROVE_OPTION) {
Macro.abort();
return;
}
f = fc.getSelectedFile();
dir = fc.getCurrentDirectory().getPath() + File.separator;
name = fc.getName(f);
if (f.exists()) {
int ret = JOptionPane.showConfirmDialog(fc, "The file " + f.getName() + " already exists. \n" + "Would you like to replace it?", "Replace?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
if (ret != JOptionPane.OK_OPTION)
f = null;
} else {
// ensure filename matches selected filter
FileFilter filter = fc.getFileFilter();
if (filter instanceof ExtensionFileFilter) {
ExtensionFileFilter eff = (ExtensionFileFilter) filter;
String[] ext = eff.getExtensions();
String lName = name.toLowerCase();
boolean hasExtension = false;
for (int i = 0; i < ext.length; i++) {
if (lName.endsWith("." + ext[i])) {
hasExtension = true;
break;
}
}
if (!hasExtension && ext.length > 0) {
// append chosen extension
name = name + "." + ext[0];
}
f = fc.getSelectedFile();
String filePath = f.getAbsolutePath();
if (!filePath.endsWith("." + ext[0])) {
f = new File(filePath + '.' + ext[0]);
}
if (f.exists()) {
int ret1 = JOptionPane.showConfirmDialog(fc, "The file " + f.getName() + " already exists. \n" + "Would you like to replace it?", "Replace?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
if (ret1 != JOptionPane.OK_OPTION)
f = null;
}
}
}
if (f == null)
Macro.abort();
else {
// do some ImageJ bookkeeping
OpenDialog.setDefaultDirectory(dir);
if (Recorder.record)
Recorder.recordPath("save", dir + name);
}
if (dir == null || name == null)
return;
outfile = new File(dir, name).getAbsolutePath();
if (outfile == null)
return;
}
if (windowless) {
if (splitZ == null)
splitZ = Boolean.FALSE;
if (splitC == null)
splitC = Boolean.FALSE;
if (splitT == null)
splitT = Boolean.FALSE;
if (padded == null)
padded = Boolean.FALSE;
}
if (splitZ == null || splitC == null || splitT == null) {
// ask if we want to export multiple files
GenericDialog multiFile = new GenericDialog("Bio-Formats Exporter - Multiple Files");
multiFile.addCheckbox("Write_each_Z_section to a separate file", false);
multiFile.addCheckbox("Write_each_timepoint to a separate file", false);
multiFile.addCheckbox("Write_each_channel to a separate file", false);
multiFile.addCheckbox("Use zero padding for filename indexes", false);
multiFile.showDialog();
splitZ = multiFile.getNextBoolean();
splitT = multiFile.getNextBoolean();
splitC = multiFile.getNextBoolean();
padded = multiFile.getNextBoolean();
if (multiFile.wasCanceled())
return;
}
try (IFormatWriter w = new ImageWriter().getWriter(outfile)) {
int ptype = 0;
int channels = 1;
switch(imp.getType()) {
case ImagePlus.GRAY8:
case ImagePlus.COLOR_256:
ptype = FormatTools.UINT8;
break;
case ImagePlus.COLOR_RGB:
channels = 3;
ptype = FormatTools.UINT8;
break;
case ImagePlus.GRAY16:
ptype = FormatTools.UINT16;
break;
case ImagePlus.GRAY32:
ptype = FormatTools.FLOAT;
break;
}
String title = imp.getTitle();
w.setWriteSequentially(true);
FileInfo fi = imp.getOriginalFileInfo();
String xml = fi == null ? null : fi.description == null ? null : fi.description.indexOf("xml") == -1 ? null : fi.description;
OMEXMLService service = null;
IMetadata store = null;
try {
ServiceFactory factory = new ServiceFactory();
service = factory.getInstance(OMEXMLService.class);
store = service.createOMEXMLMetadata(xml);
} catch (DependencyException de) {
} catch (ServiceException se) {
}
if (store == null)
IJ.error("OME-XML Java library not found.");
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) store.getRoot();
if (root.sizeOfROIList() > 0) {
while (root.sizeOfROIList() > 0) {
ROI roi = root.getROI(0);
root.removeROI(roi);
}
store.setRoot(root);
}
if (xml == null) {
store.createRoot();
} else if (store.getImageCount() > 1) {
// the original dataset had multiple series
// we need to modify the IMetadata to represent the correct series
ArrayList<Integer> matchingSeries = new ArrayList<Integer>();
for (int series = 0; series < store.getImageCount(); series++) {
String type = store.getPixelsType(series).toString();
int pixelType = FormatTools.pixelTypeFromString(type);
if (pixelType == ptype) {
String imageName = store.getImageName(series);
if (title.indexOf(imageName) >= 0) {
matchingSeries.add(series);
}
}
}
int series = 0;
if (matchingSeries.size() > 1) {
for (int i = 0; i < matchingSeries.size(); i++) {
int index = matchingSeries.get(i);
String name = store.getImageName(index);
boolean valid = true;
for (int j = 0; j < matchingSeries.size(); j++) {
if (i != j) {
String compName = store.getImageName(matchingSeries.get(j));
if (compName.indexOf(name) >= 0) {
valid = false;
break;
}
}
}
if (valid) {
series = index;
break;
}
}
} else if (matchingSeries.size() == 1)
series = matchingSeries.get(0);
ome.xml.model.Image exportImage = root.getImage(series);
List<ome.xml.model.Image> allImages = root.copyImageList();
for (ome.xml.model.Image img : allImages) {
if (!img.equals(exportImage)) {
root.removeImage(img);
}
}
store.setRoot(root);
}
store.setPixelsSizeX(new PositiveInteger(imp.getWidth()), 0);
store.setPixelsSizeY(new PositiveInteger(imp.getHeight()), 0);
store.setPixelsSizeZ(new PositiveInteger(imp.getNSlices()), 0);
store.setPixelsSizeC(new PositiveInteger(channels * imp.getNChannels()), 0);
store.setPixelsSizeT(new PositiveInteger(imp.getNFrames()), 0);
if (store.getImageID(0) == null) {
store.setImageID(MetadataTools.createLSID("Image", 0), 0);
}
if (store.getPixelsID(0) == null) {
store.setPixelsID(MetadataTools.createLSID("Pixels", 0), 0);
}
// reset the pixel type, unless the only change is signedness
// this prevents problems if the user changed the bit depth of the image
boolean applyCalibrationFunction = false;
try {
int originalType = -1;
if (store.getPixelsType(0) != null) {
originalType = FormatTools.pixelTypeFromString(store.getPixelsType(0).toString());
}
if (ptype != originalType && (store.getPixelsType(0) == null || !FormatTools.isSigned(originalType) || FormatTools.getBytesPerPixel(originalType) != FormatTools.getBytesPerPixel(ptype))) {
store.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(ptype)), 0);
} else if (FormatTools.isSigned(originalType)) {
applyCalibrationFunction = true;
}
} catch (EnumerationException e) {
}
if (store.getPixelsBinDataCount(0) == 0 || store.getPixelsBinDataBigEndian(0, 0) == null) {
store.setPixelsBinDataBigEndian(Boolean.FALSE, 0, 0);
}
if (store.getPixelsDimensionOrder(0) == null) {
try {
store.setPixelsDimensionOrder(DimensionOrder.fromString(ORDER), 0);
} catch (EnumerationException e) {
}
}
LUT[] luts = new LUT[imp.getNChannels()];
for (int c = 0; c < imp.getNChannels(); c++) {
if (c >= store.getChannelCount(0) || store.getChannelID(0, c) == null) {
String lsid = MetadataTools.createLSID("Channel", 0, c);
store.setChannelID(lsid, 0, c);
}
store.setChannelSamplesPerPixel(new PositiveInteger(channels), 0, 0);
if (imp instanceof CompositeImage) {
luts[c] = ((CompositeImage) imp).getChannelLut(c + 1);
}
}
Calibration cal = imp.getCalibration();
store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(cal.pixelWidth), 0);
store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(cal.pixelHeight), 0);
store.setPixelsPhysicalSizeZ(FormatTools.getPhysicalSizeZ(cal.pixelDepth), 0);
store.setPixelsTimeIncrement(new Time(new Double(cal.frameInterval), UNITS.SECOND), 0);
if (imp.getImageStackSize() != imp.getNChannels() * imp.getNSlices() * imp.getNFrames()) {
if (!windowless) {
IJ.showMessageWithCancel("Bio-Formats Exporter Warning", "The number of planes in the stack (" + imp.getImageStackSize() + ") does not match the number of expected planes (" + (imp.getNChannels() * imp.getNSlices() * imp.getNFrames()) + ")." + "\nIf you select 'OK', only " + imp.getImageStackSize() + " planes will be exported. If you wish to export all of the " + "planes,\nselect 'Cancel' and convert the Image5D window " + "to a stack.");
}
store.setPixelsSizeZ(new PositiveInteger(imp.getImageStackSize()), 0);
store.setPixelsSizeC(new PositiveInteger(1), 0);
store.setPixelsSizeT(new PositiveInteger(1), 0);
}
Object info = imp.getProperty("Info");
if (info != null) {
String imageInfo = info.toString();
if (imageInfo != null) {
String[] lines = imageInfo.split("\n");
for (String line : lines) {
int eq = line.lastIndexOf("=");
if (eq > 0) {
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1).trim();
if (key.endsWith("BitsPerPixel")) {
w.setValidBitsPerPixel(Integer.parseInt(value));
break;
}
}
}
}
}
// NB: Animation rate code copied from ij.plugin.Animator#doOptions().
final int rate;
if (cal.fps != 0.0) {
rate = (int) cal.fps;
} else if (cal.frameInterval != 0.0 && cal.getTimeUnit().equals("sec")) {
rate = (int) (1.0 / cal.frameInterval);
} else {
// NB: Code from ij.plugin.Animator#animationRate initializer.
// The value is 7 by default in ImageJ, so must be 7 here as well.
rate = (int) Prefs.getDouble(Prefs.FPS, 7.0);
}
if (rate > 0)
w.setFramesPerSecond(rate);
String[] outputFiles = new String[] { outfile };
int sizeZ = store.getPixelsSizeZ(0).getValue();
int sizeC = store.getPixelsSizeC(0).getValue();
int sizeT = store.getPixelsSizeT(0).getValue();
if (splitZ || splitC || splitT) {
int nFiles = 1;
if (splitZ) {
nFiles *= sizeZ;
}
if (splitC) {
nFiles *= sizeC;
}
if (splitT) {
nFiles *= sizeT;
}
outputFiles = new String[nFiles];
int dot = outfile.indexOf(".", outfile.lastIndexOf(File.separator));
String base = outfile.substring(0, dot);
String ext = outfile.substring(dot);
int nextFile = 0;
for (int z = 0; z < (splitZ ? sizeZ : 1); z++) {
for (int c = 0; c < (splitC ? sizeC : 1); c++) {
for (int t = 0; t < (splitT ? sizeT : 1); t++) {
int index = FormatTools.getIndex(ORDER, sizeZ, sizeC, sizeT, sizeZ * sizeC * sizeT, z, c, t);
String pattern = base + (splitZ ? "_Z%z" : "") + (splitC ? "_C%c" : "") + (splitT ? "_T%t" : "") + ext;
outputFiles[nextFile++] = FormatTools.getFilename(0, index, store, pattern, padded);
}
}
}
}
if (!w.getFormat().startsWith("OME")) {
if (splitZ) {
store.setPixelsSizeZ(new PositiveInteger(1), 0);
}
if (splitC) {
store.setPixelsSizeC(new PositiveInteger(1), 0);
}
if (splitT) {
store.setPixelsSizeT(new PositiveInteger(1), 0);
}
}
// prompt for options
String[] codecs = w.getCompressionTypes();
ImageProcessor proc = imp.getImageStack().getProcessor(1);
Image firstImage = proc.createImage();
firstImage = AWTImageTools.makeBuffered(firstImage, proc.getColorModel());
int thisType = AWTImageTools.getPixelType((BufferedImage) firstImage);
if (proc instanceof ColorProcessor) {
thisType = FormatTools.UINT8;
} else if (proc instanceof ShortProcessor) {
thisType = FormatTools.UINT16;
}
boolean notSupportedType = !w.isSupportedType(thisType);
if (notSupportedType) {
IJ.error("Pixel type (" + FormatTools.getPixelTypeString(thisType) + ") not supported by this format.");
return;
}
if (codecs != null && codecs.length > 1) {
boolean selected = false;
if (compression != null) {
for (int i = 0; i < codecs.length; i++) {
if (codecs[i].equals(compression)) {
selected = true;
break;
}
}
}
if (!selected && !windowless) {
GenericDialog gd = new GenericDialog("Bio-Formats Exporter Options");
gd.addChoice("Compression type: ", codecs, codecs[0]);
if (saveRoi != null) {
gd.addCheckbox("Export ROIs", saveRoi.booleanValue());
} else {
gd.addCheckbox("Export ROIs", true);
}
gd.showDialog();
saveRoi = gd.getNextBoolean();
if (gd.wasCanceled())
return;
compression = gd.getNextChoice();
}
}
boolean in = false;
if (outputFiles.length > 1) {
for (int i = 0; i < outputFiles.length; i++) {
if (new File(outputFiles[i]).exists()) {
in = true;
break;
}
}
}
if (in && !windowless) {
int ret1 = JOptionPane.showConfirmDialog(null, "Some files already exist. \n" + "Would you like to replace them?", "Replace?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
if (ret1 != JOptionPane.OK_OPTION) {
return;
}
// Delete the files overwrite does not correctly work
for (int i = 0; i < outputFiles.length; i++) {
new File(outputFiles[i]).delete();
}
}
// delete the file.
if (f != null)
f.delete();
if (compression != null) {
w.setCompression(compression);
}
// Save ROI's
if (saveRoi != null && saveRoi.booleanValue()) {
ROIHandler.saveROIs(store);
}
w.setMetadataRetrieve(store);
// convert and save slices
int size = imp.getImageStackSize();
ImageStack is = imp.getImageStack();
boolean doStack = w.canDoStacks() && size > 1;
int start = doStack ? 0 : imp.getCurrentSlice() - 1;
int end = doStack ? size : start + 1;
boolean littleEndian = false;
if (w.getMetadataRetrieve().getPixelsBigEndian(0) != null) {
littleEndian = !w.getMetadataRetrieve().getPixelsBigEndian(0).booleanValue();
} else if (w.getMetadataRetrieve().getPixelsBinDataCount(0) == 0) {
littleEndian = !w.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
}
byte[] plane = null;
w.setInterleaved(false);
int[] no = new int[outputFiles.length];
for (int i = start; i < end; i++) {
if (doStack) {
BF.status(false, "Saving plane " + (i + 1) + "/" + size);
BF.progress(false, i, size);
} else
BF.status(false, "Saving image");
proc = is.getProcessor(i + 1);
if (proc instanceof RecordedImageProcessor) {
proc = ((RecordedImageProcessor) proc).getChild();
}
int x = proc.getWidth();
int y = proc.getHeight();
if (proc instanceof ByteProcessor) {
if (applyCalibrationFunction) {
// don't alter 'pixels' directly as that will
// affect the open ImagePlus
byte[] pixels = (byte[]) proc.getPixels();
plane = new byte[pixels.length];
float[] calibration = proc.getCalibrationTable();
for (int pixel = 0; pixel < pixels.length; pixel++) {
plane[pixel] = (byte) calibration[pixels[pixel] & 0xff];
}
} else {
plane = (byte[]) proc.getPixels();
}
} else if (proc instanceof ShortProcessor) {
short[] pixels = (short[]) proc.getPixels();
if (applyCalibrationFunction) {
// don't alter 'pixels' directly as that will
// affect the open ImagePlus
plane = new byte[pixels.length * 2];
float[] calibration = proc.getCalibrationTable();
for (int pixel = 0; pixel < pixels.length; pixel++) {
short v = (short) calibration[pixels[pixel] & 0xffff];
DataTools.unpackBytes(v, plane, pixel * 2, 2, littleEndian);
}
} else {
plane = DataTools.shortsToBytes(pixels, littleEndian);
}
} else if (proc instanceof FloatProcessor) {
plane = DataTools.floatsToBytes((float[]) proc.getPixels(), littleEndian);
} else if (proc instanceof ColorProcessor) {
byte[][] pix = new byte[3][x * y];
((ColorProcessor) proc).getRGB(pix[0], pix[1], pix[2]);
plane = new byte[3 * x * y];
System.arraycopy(pix[0], 0, plane, 0, x * y);
System.arraycopy(pix[1], 0, plane, x * y, x * y);
System.arraycopy(pix[2], 0, plane, 2 * x * y, x * y);
if (i == start) {
sizeC /= 3;
}
}
int fileIndex = 0;
if (doStack) {
int[] coords = FormatTools.getZCTCoords(ORDER, sizeZ, sizeC, sizeT, size, i);
int realZ = sizeZ;
int realC = sizeC;
int realT = sizeT;
if (!splitZ) {
coords[0] = 0;
realZ = 1;
}
if (!splitC) {
coords[1] = 0;
realC = 1;
}
if (!splitT) {
coords[2] = 0;
realT = 1;
}
fileIndex = FormatTools.getIndex(ORDER, realZ, realC, realT, realZ * realC * realT, coords[0], coords[1], coords[2]);
}
if (notSupportedType) {
IJ.error("Pixel type not supported by this format.");
} else {
w.changeOutputFile(outputFiles[fileIndex]);
int currentChannel = FormatTools.getZCTCoords(ORDER, sizeZ, sizeC, sizeT, imp.getStackSize(), i)[1];
if (luts[currentChannel] != null) {
// expand to 16-bit LUT if necessary
int bpp = FormatTools.getBytesPerPixel(thisType);
if (bpp == 1) {
w.setColorModel(luts[currentChannel]);
} else if (bpp == 2) {
int lutSize = luts[currentChannel].getMapSize();
byte[][] lut = new byte[3][lutSize];
luts[currentChannel].getReds(lut[0]);
luts[currentChannel].getGreens(lut[1]);
luts[currentChannel].getBlues(lut[2]);
short[][] newLut = new short[3][65536];
int bins = newLut[0].length / lut[0].length;
for (int c = 0; c < newLut.length; c++) {
for (int q = 0; q < newLut[c].length; q++) {
int index = q / bins;
newLut[c][q] = (short) ((lut[c][index] * lut[0].length) + (q % bins));
}
}
w.setColorModel(new Index16ColorModel(16, newLut[0].length, newLut, littleEndian));
}
} else if (!proc.isDefaultLut()) {
w.setColorModel(proc.getColorModel());
}
w.saveBytes(no[fileIndex]++, plane);
}
}
w.close();
} catch (FormatException e) {
WindowTools.reportException(e);
} catch (IOException e) {
WindowTools.reportException(e);
}
}
use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.
the class OMEXMLServiceImpl method getOriginalMetadata.
/**
* @see OMEXMLService#getOriginalMetadata(loci.formats.ome.OMEXMLMetadata)
*/
@Override
public Hashtable getOriginalMetadata(OMEXMLMetadata omexmlMeta) {
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
StructuredAnnotations annotations = root.getStructuredAnnotations();
if (annotations == null) {
return null;
}
Hashtable metadata = new Hashtable();
for (int i = 0; i < annotations.sizeOfXMLAnnotationList(); i++) {
XMLAnnotation annotation = annotations.getXMLAnnotation(i);
if (annotation instanceof OriginalMetadataAnnotation) {
OriginalMetadataAnnotation original = (OriginalMetadataAnnotation) annotation;
metadata.put(original.getKey(), original.getValueForKey());
continue;
}
String xml = annotation.getValue();
try {
Document annotationRoot = XMLTools.parseDOM(xml);
NodeList metadataNodes = annotationRoot.getElementsByTagName("OriginalMetadata");
for (int meta = 0; meta < metadataNodes.getLength(); meta++) {
Element metadataNode = (Element) metadataNodes.item(meta);
NodeList keys = metadataNode.getElementsByTagName("Key");
NodeList values = metadataNode.getElementsByTagName("Value");
for (int q = 0; q < keys.getLength(); q++) {
Node key = keys.item(q);
Node value = values.item(q);
metadata.put(key.getTextContent(), value.getTextContent());
}
}
if (metadataNodes.getLength() == 0) {
metadataNodes = annotationRoot.getDocumentElement().getChildNodes();
for (int meta = 0; meta < metadataNodes.getLength(); meta++) {
// com.sun.org.apache.xerces.internal.dom.DeferredCommentImpl.
if (metadataNodes.item(meta) instanceof Element) {
Element node = (Element) metadataNodes.item(meta);
String name = node.getNodeName();
NamedNodeMap attrs = node.getAttributes();
Node value = attrs.getNamedItem("Value");
if (value != null) {
metadata.put(name, value.getNodeValue());
}
}
}
}
} catch (ParserConfigurationException e) {
LOGGER.debug("Failed to parse OriginalMetadata", e);
} catch (SAXException e) {
LOGGER.debug("Failed to parse OriginalMetadata", e);
} catch (IOException e) {
LOGGER.debug("Failed to parse OriginalMetadata", e);
}
}
return metadata;
}
use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.
the class OMEXMLServiceImpl method removeTiffData.
/**
* @see OMEXMLService#removeTiffData(OMEXMLMetadata)
*/
@Override
public void removeTiffData(OMEXMLMetadata omexmlMeta) {
omexmlMeta.resolveReferences();
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
List<Image> images = root.copyImageList();
for (Image img : images) {
Pixels pix = img.getPixels();
List<TiffData> tiffData = pix.copyTiffDataList();
for (TiffData tiff : tiffData) {
pix.removeTiffData(tiff);
}
pix.setMetadataOnly(null);
}
omexmlMeta.setRoot(root);
}
use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.
the class OMEXMLServiceImpl method removeChannels.
/**
* @see OMEXMLService#removeChannels(OMEXMLMetadata, int, int)
*/
@Override
public void removeChannels(OMEXMLMetadata omexmlMeta, int image, int sizeC) {
omexmlMeta.resolveReferences();
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
Pixels img = root.getImage(image).getPixels();
List<Channel> channels = img.copyChannelList();
for (int c = 0; c < channels.size(); c++) {
Channel channel = channels.get(c);
if (channel.getID() == null || c >= sizeC) {
img.removeChannel(channel);
}
}
omexmlMeta.setRoot(root);
}
use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.
the class OMEXMLServiceImpl method getModuloAlong.
/**
* Create a {@link loci.formats.Modulo} corresponding to the given ModuloAlong* tag.
* @param omexml the OMEXMLMetadata from which to retrieve the ModuloAlong* tag
* @param tag the tag name (e.g. "ModuloAlongC")
* @param image the Image index within the OMEXMLMetadata
* @return the corresponding Modulo object
*/
private Modulo getModuloAlong(OMEXMLMetadata omexml, String tag, int image) {
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
Image img = root.getImage(image);
if (img == null) {
return null;
}
for (int i = 0; i < img.sizeOfLinkedAnnotationList(); i++) {
Annotation annotation = img.getLinkedAnnotation(i);
if (!(annotation instanceof XMLAnnotation)) {
continue;
}
String xml = ((XMLAnnotation) annotation).getValue();
try {
Document annotationRoot = XMLTools.parseDOM(xml);
NodeList nodes = annotationRoot.getElementsByTagName(tag);
if (nodes.getLength() > 0) {
Element modulo = (Element) nodes.item(0);
NamedNodeMap attrs = modulo.getAttributes();
Modulo m = new Modulo(tag.substring(tag.length() - 1));
Node start = attrs.getNamedItem("Start");
Node end = attrs.getNamedItem("End");
Node step = attrs.getNamedItem("Step");
Node type = attrs.getNamedItem("Type");
Node typeDescription = attrs.getNamedItem("TypeDescription");
Node unit = attrs.getNamedItem("Unit");
if (start != null) {
m.start = Double.parseDouble(start.getNodeValue());
}
if (end != null) {
m.end = Double.parseDouble(end.getNodeValue());
}
if (step != null) {
m.step = Double.parseDouble(step.getNodeValue());
}
if (type != null) {
m.type = type.getNodeValue();
}
if (typeDescription != null) {
m.typeDescription = typeDescription.getNodeValue();
}
if (unit != null) {
m.unit = unit.getNodeValue();
}
NodeList labels = modulo.getElementsByTagName("Label");
if (labels != null && labels.getLength() > 0) {
m.labels = new String[labels.getLength()];
for (int q = 0; q < labels.getLength(); q++) {
m.labels[q] = labels.item(q).getTextContent();
}
}
return m;
}
} catch (ParserConfigurationException e) {
LOGGER.debug("Failed to parse ModuloAlong", e);
} catch (SAXException e) {
LOGGER.debug("Failed to parse ModuloAlong", e);
} catch (IOException e) {
LOGGER.debug("Failed to parse ModuloAlong", e);
}
}
return null;
}
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