Example 31 with Time
use of ome.units.quantity.Time 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);
}
}
Also used :
ServiceFactory(loci.common.services.ServiceFactory)
ArrayList(java.util.ArrayList)
Image(java.awt.Image)
BufferedImage(java.awt.image.BufferedImage)
CompositeImage(ij.CompositeImage)
OMEXMLService(loci.formats.services.OMEXMLService)
Index16ColorModel(loci.formats.gui.Index16ColorModel)
ImageProcessor(ij.process.ImageProcessor)
RecordedImageProcessor(loci.plugins.util.RecordedImageProcessor)
IMetadata(loci.formats.meta.IMetadata)
FileInfo(ij.io.FileInfo)
List(java.util.List)
ArrayList(java.util.ArrayList)
ImageStack(ij.ImageStack)
FloatProcessor(ij.process.FloatProcessor)
DependencyException(loci.common.services.DependencyException)
ROI(ome.xml.model.ROI)
FormatException(loci.formats.FormatException)
IFormatWriter(loci.formats.IFormatWriter)
JFileChooser(javax.swing.JFileChooser)
ServiceException(loci.common.services.ServiceException)
OMEXMLMetadataRoot(ome.xml.meta.OMEXMLMetadataRoot)
File(java.io.File)
ExtensionFileFilter(loci.formats.gui.ExtensionFileFilter)
EnumerationException(ome.xml.model.enums.EnumerationException)
ByteProcessor(ij.process.ByteProcessor)
ImageWriter(loci.formats.ImageWriter)
Time(ome.units.quantity.Time)
ColorProcessor(ij.process.ColorProcessor)
CompositeImage(ij.CompositeImage)
GenericDialog(ij.gui.GenericDialog)
RecordedImageProcessor(loci.plugins.util.RecordedImageProcessor)
ExtensionFileFilter(loci.formats.gui.ExtensionFileFilter)
FileFilter(javax.swing.filechooser.FileFilter)
PositiveInteger(ome.xml.model.primitives.PositiveInteger)
LUT(ij.process.LUT)
Calibration(ij.measure.Calibration)
IOException(java.io.IOException)
ImagePlus(ij.ImagePlus)
ServiceException(loci.common.services.ServiceException)
DependencyException(loci.common.services.DependencyException)
EnumerationException(ome.xml.model.enums.EnumerationException)
FormatException(loci.formats.FormatException)
IOException(java.io.IOException)
ShortProcessor(ij.process.ShortProcessor)
PositiveInteger(ome.xml.model.primitives.PositiveInteger)
Example 32 with Time
use of ome.units.quantity.Time in project bioformats by openmicroscopy.
the class ICSReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
LOGGER.info("Finding companion file");
String icsId = id, idsId = id;
int dot = id.lastIndexOf(".");
String ext = dot < 0 ? "" : id.substring(dot + 1).toLowerCase();
if (ext.equals("ics")) {
// convert C to D regardless of case
char[] c = idsId.toCharArray();
c[c.length - 2]++;
idsId = new String(c);
} else if (ext.equals("ids")) {
// convert D to C regardless of case
char[] c = icsId.toCharArray();
c[c.length - 2]--;
icsId = new String(c);
}
if (icsId == null)
throw new FormatException("No ICS file found.");
Location icsFile = new Location(icsId);
if (!icsFile.exists())
throw new FormatException("ICS file not found.");
LOGGER.info("Checking file version");
// check if we have a v2 ICS file - means there is no companion IDS file
RandomAccessInputStream f = new RandomAccessInputStream(icsId);
if (f.readString(17).trim().equals("ics_version\t2.0")) {
in = new RandomAccessInputStream(icsId);
versionTwo = true;
} else {
if (idsId == null) {
f.close();
throw new FormatException("No IDS file found.");
}
Location idsFile = new Location(idsId);
if (!idsFile.exists()) {
f.close();
throw new FormatException("IDS file not found.");
}
currentIdsId = idsId;
in = new RandomAccessInputStream(currentIdsId);
}
f.close();
currentIcsId = icsId;
LOGGER.info("Reading metadata");
CoreMetadata m = core.get(0);
Double[] scales = null;
Double[] timestamps = null;
String[] units = null;
String[] axes = null;
int[] axisLengths = null;
String byteOrder = null, rFormat = null, compression = null;
// parse key/value pairs from beginning of ICS file
RandomAccessInputStream reader = new RandomAccessInputStream(icsId);
reader.seek(0);
reader.readString(NL);
String line = reader.readString(NL);
boolean signed = false;
final StringBuilder textBlock = new StringBuilder();
double[] sizes = null;
Double[] emWaves = null, exWaves = null;
Length[] stagePos = null;
String imageName = null, date = null, description = null;
Double magnification = null, lensNA = null, workingDistance = null;
String objectiveModel = null, immersion = null, lastName = null;
Hashtable<Integer, Double> gains = new Hashtable<Integer, Double>();
Hashtable<Integer, Double> pinholes = new Hashtable<Integer, Double>();
Hashtable<Integer, Double> wavelengths = new Hashtable<Integer, Double>();
Hashtable<Integer, String> channelNames = new Hashtable<Integer, String>();
String laserModel = null;
String laserManufacturer = null;
Double laserPower = null;
Double laserRepetitionRate = null;
String detectorManufacturer = null;
String detectorModel = null;
String microscopeModel = null;
String microscopeManufacturer = null;
String experimentType = null;
Time exposureTime = null;
String filterSetModel = null;
String dichroicModel = null;
String excitationModel = null;
String emissionModel = null;
while (line != null && !line.trim().equals("end") && reader.getFilePointer() < reader.length() - 1) {
line = line.trim();
if (line.length() > 0) {
// split the line into tokens
String[] tokens = tokenize(line);
String token0 = tokens[0].toLowerCase();
String[] keyValue = null;
// version category
if (token0.equals("ics_version")) {
String value = concatenateTokens(tokens, 1, tokens.length);
addGlobalMeta(token0, value);
} else // filename category
if (token0.equals("filename")) {
imageName = concatenateTokens(tokens, 1, tokens.length);
addGlobalMeta(token0, imageName);
} else // layout category
if (token0.equals("layout")) {
keyValue = findKeyValue(tokens, LAYOUT_KEYS);
String key = keyValue[0];
String value = keyValue[1];
addGlobalMeta(key, value);
if (key.equalsIgnoreCase("layout sizes")) {
StringTokenizer t = new StringTokenizer(value);
axisLengths = new int[t.countTokens()];
for (int n = 0; n < axisLengths.length; n++) {
try {
axisLengths[n] = Integer.parseInt(t.nextToken().trim());
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse axis length", e);
}
}
} else if (key.equalsIgnoreCase("layout order")) {
StringTokenizer t = new StringTokenizer(value);
axes = new String[t.countTokens()];
for (int n = 0; n < axes.length; n++) {
axes[n] = t.nextToken().trim();
}
} else if (key.equalsIgnoreCase("layout significant_bits")) {
m.bitsPerPixel = Integer.parseInt(value);
}
} else // representation category
if (token0.equals("representation")) {
keyValue = findKeyValue(tokens, REPRESENTATION_KEYS);
String key = keyValue[0];
String value = keyValue[1];
addGlobalMeta(key, value);
if (key.equalsIgnoreCase("representation byte_order")) {
byteOrder = value;
} else if (key.equalsIgnoreCase("representation format")) {
rFormat = value;
} else if (key.equalsIgnoreCase("representation compression")) {
compression = value;
} else if (key.equalsIgnoreCase("representation sign")) {
signed = value.equals("signed");
}
} else // parameter category
if (token0.equals("parameter")) {
keyValue = findKeyValue(tokens, PARAMETER_KEYS);
String key = keyValue[0];
String value = keyValue[1];
addGlobalMeta(key, value);
if (key.equalsIgnoreCase("parameter scale")) {
// parse physical pixel sizes and time increment
scales = splitDoubles(value);
} else if (key.equalsIgnoreCase("parameter t")) {
// parse explicit timestamps
timestamps = splitDoubles(value);
} else if (key.equalsIgnoreCase("parameter units")) {
// parse units for scale
units = value.split("\\s+");
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (key.equalsIgnoreCase("parameter ch")) {
String[] names = value.split(" ");
for (int n = 0; n < names.length; n++) {
channelNames.put(new Integer(n), names[n].trim());
}
}
}
} else // history category
if (token0.equals("history")) {
keyValue = findKeyValue(tokens, HISTORY_KEYS);
String key = keyValue[0];
String value = keyValue[1];
addGlobalMeta(key, value);
Double doubleValue = null;
try {
doubleValue = new Double(value);
} catch (NumberFormatException e) {
// ARG this happens a lot; spurious error in most cases
LOGGER.debug("Could not parse double value '{}'", value, e);
}
if (key.equalsIgnoreCase("history software") && value.indexOf("SVI") != -1) {
// ICS files written by SVI Huygens are inverted on the Y axis
invertY = true;
} else if (key.equalsIgnoreCase("history date") || key.equalsIgnoreCase("history created on")) {
if (value.indexOf(' ') > 0) {
date = value.substring(0, value.lastIndexOf(" "));
date = DateTools.formatDate(date, DATE_FORMATS);
}
} else if (key.equalsIgnoreCase("history creation date")) {
date = DateTools.formatDate(value, DATE_FORMATS);
} else if (key.equalsIgnoreCase("history type")) {
// HACK - support for Gray Institute at Oxford's ICS lifetime data
if (value.equalsIgnoreCase("time resolved") || value.equalsIgnoreCase("FluorescenceLifetime")) {
lifetime = true;
}
experimentType = value;
} else if (key.equalsIgnoreCase("history labels")) {
// HACK - support for Gray Institute at Oxford's ICS lifetime data
labels = value;
} else if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (key.equalsIgnoreCase("history") || key.equalsIgnoreCase("history text")) {
textBlock.append(value);
textBlock.append("\n");
metadata.remove(key);
} else if (key.startsWith("history gain")) {
Integer n = 0;
try {
n = new Integer(key.substring(12).trim());
n = new Integer(n.intValue() - 1);
} catch (NumberFormatException e) {
}
if (doubleValue != null) {
gains.put(n, doubleValue);
}
} else if (key.startsWith("history laser") && key.endsWith("wavelength")) {
int laser = Integer.parseInt(key.substring(13, key.indexOf(" ", 13))) - 1;
value = value.replaceAll("nm", "").trim();
try {
wavelengths.put(new Integer(laser), new Double(value));
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse wavelength", e);
}
} else if (key.equalsIgnoreCase("history Wavelength*")) {
String[] waves = value.split(" ");
for (int i = 0; i < waves.length; i++) {
wavelengths.put(new Integer(i), new Double(waves[i]));
}
} else if (key.equalsIgnoreCase("history laser manufacturer")) {
laserManufacturer = value;
} else if (key.equalsIgnoreCase("history laser model")) {
laserModel = value;
} else if (key.equalsIgnoreCase("history laser power")) {
try {
// TODO ARG i.e. doubleValue
laserPower = new Double(value);
} catch (NumberFormatException e) {
}
} else if (key.equalsIgnoreCase("history laser rep rate")) {
String repRate = value;
if (repRate.indexOf(' ') != -1) {
repRate = repRate.substring(0, repRate.lastIndexOf(" "));
}
laserRepetitionRate = new Double(repRate);
} else if (key.equalsIgnoreCase("history objective type") || key.equalsIgnoreCase("history objective")) {
objectiveModel = value;
} else if (key.equalsIgnoreCase("history objective immersion")) {
immersion = value;
} else if (key.equalsIgnoreCase("history objective NA")) {
lensNA = doubleValue;
} else if (key.equalsIgnoreCase("history objective WorkingDistance")) {
workingDistance = doubleValue;
} else if (key.equalsIgnoreCase("history objective magnification") || key.equalsIgnoreCase("history objective mag")) {
magnification = doubleValue;
} else if (key.equalsIgnoreCase("history camera manufacturer")) {
detectorManufacturer = value;
} else if (key.equalsIgnoreCase("history camera model")) {
detectorModel = value;
} else if (key.equalsIgnoreCase("history author") || key.equalsIgnoreCase("history experimenter")) {
lastName = value;
} else if (key.equalsIgnoreCase("history extents")) {
String[] lengths = value.split(" ");
sizes = new double[lengths.length];
for (int n = 0; n < sizes.length; n++) {
try {
sizes[n] = Double.parseDouble(lengths[n].trim());
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse axis length", e);
}
}
} else if (key.equalsIgnoreCase("history stage_xyzum")) {
String[] positions = value.split(" ");
stagePos = new Length[positions.length];
for (int n = 0; n < stagePos.length; n++) {
try {
final Double number = Double.valueOf(positions[n]);
stagePos[n] = new Length(number, UNITS.REFERENCEFRAME);
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse stage position", e);
}
}
} else if (key.equalsIgnoreCase("history stage positionx")) {
if (stagePos == null) {
stagePos = new Length[3];
}
final Double number = Double.valueOf(value);
stagePos[0] = new Length(number, UNITS.REFERENCEFRAME);
} else if (key.equalsIgnoreCase("history stage positiony")) {
if (stagePos == null) {
stagePos = new Length[3];
}
final Double number = Double.valueOf(value);
stagePos[1] = new Length(number, UNITS.REFERENCEFRAME);
} else if (key.equalsIgnoreCase("history stage positionz")) {
if (stagePos == null) {
stagePos = new Length[3];
}
final Double number = Double.valueOf(value);
stagePos[2] = new Length(number, UNITS.REFERENCEFRAME);
} else if (key.equalsIgnoreCase("history other text")) {
description = value;
} else if (key.startsWith("history step") && key.endsWith("name")) {
Integer n = new Integer(key.substring(12, key.indexOf(" ", 12)));
channelNames.put(n, value);
} else if (key.equalsIgnoreCase("history cube")) {
channelNames.put(new Integer(channelNames.size()), value);
} else if (key.equalsIgnoreCase("history cube emm nm")) {
if (emWaves == null) {
emWaves = new Double[1];
}
emWaves[0] = new Double(value.split(" ")[1].trim());
} else if (key.equalsIgnoreCase("history cube exc nm")) {
if (exWaves == null) {
exWaves = new Double[1];
}
exWaves[0] = new Double(value.split(" ")[1].trim());
} else if (key.equalsIgnoreCase("history microscope")) {
microscopeModel = value;
} else if (key.equalsIgnoreCase("history manufacturer")) {
microscopeManufacturer = value;
} else if (key.equalsIgnoreCase("history Exposure")) {
String expTime = value;
if (expTime.indexOf(' ') != -1) {
expTime = expTime.substring(0, expTime.indexOf(' '));
}
Double expDouble = new Double(expTime);
if (expDouble != null) {
exposureTime = new Time(expDouble, UNITS.SECOND);
}
} else if (key.equalsIgnoreCase("history filterset")) {
filterSetModel = value;
} else if (key.equalsIgnoreCase("history filterset dichroic name")) {
dichroicModel = value;
} else if (key.equalsIgnoreCase("history filterset exc name")) {
excitationModel = value;
} else if (key.equalsIgnoreCase("history filterset emm name")) {
emissionModel = value;
}
}
} else // document category
if (token0.equals("document")) {
keyValue = findKeyValue(tokens, DOCUMENT_KEYS);
String key = keyValue[0];
String value = keyValue[1];
addGlobalMeta(key, value);
} else // sensor category
if (token0.equals("sensor")) {
keyValue = findKeyValue(tokens, SENSOR_KEYS);
String key = keyValue[0];
String value = keyValue[1];
addGlobalMeta(key, value);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (key.equalsIgnoreCase("sensor s_params LambdaEm")) {
String[] waves = value.split(" ");
emWaves = new Double[waves.length];
for (int n = 0; n < emWaves.length; n++) {
try {
emWaves[n] = new Double(Double.parseDouble(waves[n]));
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse emission wavelength", e);
}
}
} else if (key.equalsIgnoreCase("sensor s_params LambdaEx")) {
String[] waves = value.split(" ");
exWaves = new Double[waves.length];
for (int n = 0; n < exWaves.length; n++) {
try {
exWaves[n] = new Double(Double.parseDouble(waves[n]));
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse excitation wavelength", e);
}
}
} else if (key.equalsIgnoreCase("sensor s_params PinholeRadius")) {
String[] pins = value.split(" ");
int channel = 0;
for (int n = 0; n < pins.length; n++) {
if (pins[n].trim().equals(""))
continue;
try {
pinholes.put(new Integer(channel++), new Double(pins[n]));
} catch (NumberFormatException e) {
LOGGER.debug("Could not parse pinhole", e);
}
}
}
}
} else // view category
if (token0.equals("view")) {
keyValue = findKeyValue(tokens, VIEW_KEYS);
String key = keyValue[0];
String value = keyValue[1];
// handle "view view color lib lut Green Fire green", etc.
if (key.equalsIgnoreCase("view view color lib lut")) {
int index;
int redIndex = value.toLowerCase().lastIndexOf("red");
int greenIndex = value.toLowerCase().lastIndexOf("green");
int blueIndex = value.toLowerCase().lastIndexOf("blue");
if (redIndex > 0 && redIndex > greenIndex && redIndex > blueIndex) {
index = redIndex + "red".length();
} else if (greenIndex > 0 && greenIndex > redIndex && greenIndex > blueIndex) {
index = greenIndex + "green".length();
} else if (blueIndex > 0 && blueIndex > redIndex && blueIndex > greenIndex) {
index = blueIndex + "blue".length();
} else {
index = value.indexOf(' ');
}
if (index > 0) {
key = key + ' ' + value.substring(0, index);
value = value.substring(index + 1);
}
} else // "view view color mode rgb set blue-green-red", etc.
if (key.equalsIgnoreCase("view view color mode rgb set")) {
int index = value.toLowerCase().lastIndexOf("colors");
if (index > 0) {
index += "colors".length();
} else {
index = value.indexOf(' ');
}
if (index > 0) {
key = key + ' ' + value.substring(0, index);
value = value.substring(index + 1);
}
}
addGlobalMeta(key, value);
} else {
LOGGER.debug("Unknown category " + token0);
}
}
line = reader.readString(NL);
}
reader.close();
hasInstrumentData = emWaves != null || exWaves != null || lensNA != null || stagePos != null || magnification != null || workingDistance != null || objectiveModel != null || immersion != null;
addGlobalMeta("history text", textBlock.toString());
LOGGER.info("Populating core metadata");
m.rgb = false;
m.dimensionOrder = "XY";
// find axis sizes
channelLengths = new Vector<Integer>();
channelTypes = new Vector<String>();
int bitsPerPixel = 0;
for (int i = 0; i < axes.length; i++) {
if (i >= axisLengths.length)
break;
if (axes[i].equals("bits")) {
bitsPerPixel = axisLengths[i];
while (bitsPerPixel % 8 != 0) bitsPerPixel++;
if (bitsPerPixel == 24 || bitsPerPixel == 48)
bitsPerPixel /= 3;
} else if (axes[i].equals("x")) {
m.sizeX = axisLengths[i];
} else if (axes[i].equals("y")) {
m.sizeY = axisLengths[i];
} else if (axes[i].equals("z")) {
m.sizeZ = axisLengths[i];
if (getDimensionOrder().indexOf('Z') == -1) {
m.dimensionOrder += 'Z';
}
} else if (axes[i].equals("t")) {
if (getSizeT() == 0)
m.sizeT = axisLengths[i];
else
m.sizeT *= axisLengths[i];
if (getDimensionOrder().indexOf('T') == -1) {
m.dimensionOrder += 'T';
}
} else {
if (m.sizeC == 0)
m.sizeC = axisLengths[i];
else
m.sizeC *= axisLengths[i];
channelLengths.add(new Integer(axisLengths[i]));
storedRGB = getSizeX() == 0;
m.rgb = getSizeX() == 0 && getSizeC() <= 4 && getSizeC() > 1;
if (getDimensionOrder().indexOf('C') == -1) {
m.dimensionOrder += 'C';
}
if (axes[i].startsWith("c")) {
channelTypes.add(FormatTools.CHANNEL);
} else if (axes[i].equals("p")) {
channelTypes.add(FormatTools.PHASE);
} else if (axes[i].equals("f")) {
channelTypes.add(FormatTools.FREQUENCY);
} else
channelTypes.add("");
}
}
if (channelLengths.isEmpty()) {
channelLengths.add(1);
channelTypes.add(FormatTools.CHANNEL);
}
if (isRGB() && emWaves != null && emWaves.length == getSizeC()) {
m.rgb = false;
storedRGB = true;
}
m.dimensionOrder = MetadataTools.makeSaneDimensionOrder(getDimensionOrder());
if (getSizeZ() == 0)
m.sizeZ = 1;
if (getSizeC() == 0)
m.sizeC = 1;
if (getSizeT() == 0)
m.sizeT = 1;
// length and type.
if (channelLengths.size() > 0) {
int clen0 = channelLengths.get(0);
String ctype0 = channelTypes.get(0);
boolean same = true;
for (Integer len : channelLengths) {
if (clen0 != len)
same = false;
}
for (String type : channelTypes) {
if (!ctype0.equals(type))
same = false;
}
if (same) {
m.moduloC.type = ctype0;
if (FormatTools.LIFETIME.equals(ctype0)) {
m.moduloC.parentType = FormatTools.SPECTRA;
}
m.moduloC.typeDescription = "TCSPC";
m.moduloC.start = 0;
m.moduloC.step = 1;
m.moduloC.end = clen0 - 1;
}
}
m.interleaved = isRGB();
m.indexed = false;
m.falseColor = false;
m.metadataComplete = true;
m.littleEndian = true;
// HACK - support for Gray Institute at Oxford's ICS lifetime data
if (lifetime && labels != null) {
int binCount = 0;
String newOrder = null;
if (labels.equalsIgnoreCase("t x y")) {
// nominal X Y Z is actually C X Y (which is X Y C interleaved)
newOrder = "XYCZT";
m.interleaved = true;
binCount = m.sizeX;
m.sizeX = m.sizeY;
m.sizeY = m.sizeZ;
m.sizeZ = 1;
} else if (labels.equalsIgnoreCase("x y t")) {
// nominal X Y Z is actually X Y C
newOrder = "XYCZT";
binCount = m.sizeZ;
m.sizeZ = 1;
} else {
LOGGER.debug("Lifetime data, unexpected 'history labels' " + labels);
}
if (newOrder != null) {
m.dimensionOrder = newOrder;
m.sizeC = binCount;
m.moduloC.parentType = FormatTools.LIFETIME;
}
}
// do not modify the Z, T, or channel counts after this point
m.imageCount = getSizeZ() * getSizeT();
if (!isRGB())
m.imageCount *= getSizeC();
if (byteOrder != null) {
String firstByte = byteOrder.split(" ")[0];
int first = Integer.parseInt(firstByte);
m.littleEndian = rFormat.equals("real") ? first == 1 : first != 1;
}
gzip = (compression == null) ? false : compression.equals("gzip");
if (versionTwo) {
String s = in.readString(NL);
while (!s.trim().equals("end")) s = in.readString(NL);
}
offset = in.getFilePointer();
int bytes = bitsPerPixel / 8;
if (bitsPerPixel < 32)
m.littleEndian = !isLittleEndian();
boolean fp = rFormat.equals("real");
m.pixelType = FormatTools.pixelTypeFromBytes(bytes, signed, fp);
LOGGER.info("Populating OME metadata");
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
// populate Image data
store.setImageName(imageName, 0);
if (date != null)
store.setImageAcquisitionDate(new Timestamp(date), 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(description, 0);
// link Instrument and Image
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
store.setMicroscopeModel(microscopeModel, 0);
store.setMicroscopeManufacturer(microscopeManufacturer, 0);
store.setImageInstrumentRef(instrumentID, 0);
store.setExperimentID(MetadataTools.createLSID("Experiment", 0), 0);
store.setExperimentType(getExperimentType(experimentType), 0);
if (scales != null) {
if (units != null && units.length == scales.length - 1) {
// correct for missing units
// sometimes, the units for the C axis are missing entirely
ArrayList<String> realUnits = new ArrayList<String>();
int unitIndex = 0;
for (int i = 0; i < axes.length; i++) {
if (axes[i].toLowerCase().equals("ch")) {
realUnits.add("nm");
} else {
realUnits.add(units[unitIndex++]);
}
}
units = realUnits.toArray(new String[realUnits.size()]);
}
for (int i = 0; i < scales.length; i++) {
Double scale = scales[i];
if (scale == null) {
continue;
}
String axis = axes != null && axes.length > i ? axes[i] : "";
String unit = units != null && units.length > i ? units[i] : "";
if (axis.equals("x")) {
if (checkUnit(unit, "um", "microns", "micrometers")) {
Length x = FormatTools.getPhysicalSizeX(scale);
if (x != null) {
store.setPixelsPhysicalSizeX(x, 0);
}
}
} else if (axis.equals("y")) {
if (checkUnit(unit, "um", "microns", "micrometers")) {
Length y = FormatTools.getPhysicalSizeY(scale);
if (y != null) {
store.setPixelsPhysicalSizeY(y, 0);
}
}
} else if (axis.equals("z")) {
if (checkUnit(unit, "um", "microns", "micrometers")) {
Length z = FormatTools.getPhysicalSizeZ(scale);
if (z != null) {
store.setPixelsPhysicalSizeZ(z, 0);
}
}
} else if (axis.equals("t") && scale != null) {
if (checkUnit(unit, "ms")) {
store.setPixelsTimeIncrement(new Time(scale, UNITS.MILLISECOND), 0);
} else if (checkUnit(unit, "seconds") || checkUnit(unit, "s")) {
store.setPixelsTimeIncrement(new Time(scale, UNITS.SECOND), 0);
}
}
}
} else if (sizes != null) {
if (sizes.length > 0) {
Length x = FormatTools.getPhysicalSizeX(sizes[0]);
if (x != null) {
store.setPixelsPhysicalSizeX(x, 0);
}
}
if (sizes.length > 1) {
sizes[1] /= getSizeY();
Length y = FormatTools.getPhysicalSizeY(sizes[1]);
if (y != null) {
store.setPixelsPhysicalSizeY(y, 0);
}
}
}
if (timestamps != null) {
for (int t = 0; t < timestamps.length; t++) {
// ignore superfluous timestamps
if (t >= getSizeT())
break;
// ignore missing timestamp
if (timestamps[t] == null)
continue;
Time deltaT = new Time(timestamps[t], UNITS.SECOND);
// ignore invalid timestamp
if (Double.isNaN(deltaT.value().doubleValue()))
continue;
// assign timestamp to all relevant planes
for (int z = 0; z < getSizeZ(); z++) {
for (int c = 0; c < getEffectiveSizeC(); c++) {
int index = getIndex(z, c, t);
store.setPlaneDeltaT(deltaT, 0, index);
}
}
}
}
for (int i = 0; i < getEffectiveSizeC(); i++) {
if (channelNames.containsKey(i)) {
store.setChannelName(channelNames.get(i), 0, i);
}
if (pinholes.containsKey(i)) {
store.setChannelPinholeSize(new Length(pinholes.get(i), UNITS.MICROMETER), 0, i);
}
if (emWaves != null && i < emWaves.length) {
Length em = FormatTools.getEmissionWavelength(emWaves[i]);
if (em != null) {
store.setChannelEmissionWavelength(em, 0, i);
}
}
if (exWaves != null && i < exWaves.length) {
Length ex = FormatTools.getExcitationWavelength(exWaves[i]);
if (ex != null) {
store.setChannelExcitationWavelength(ex, 0, i);
}
}
}
// populate Laser data
Integer[] lasers = wavelengths.keySet().toArray(new Integer[0]);
Arrays.sort(lasers);
for (int i = 0; i < lasers.length; i++) {
store.setLaserID(MetadataTools.createLSID("LightSource", 0, i), 0, i);
Length wave = FormatTools.getWavelength(wavelengths.get(lasers[i]));
if (wave != null) {
store.setLaserWavelength(wave, 0, i);
}
store.setLaserType(getLaserType("Other"), 0, i);
store.setLaserLaserMedium(getLaserMedium("Other"), 0, i);
store.setLaserManufacturer(laserManufacturer, 0, i);
store.setLaserModel(laserModel, 0, i);
Power theLaserPower = FormatTools.createPower(laserPower, UNITS.MILLIWATT);
if (theLaserPower != null) {
store.setLaserPower(theLaserPower, 0, i);
}
Frequency theLaserRepetitionRate = FormatTools.createFrequency(laserRepetitionRate, UNITS.HERTZ);
if (theLaserRepetitionRate != null) {
store.setLaserRepetitionRate(theLaserRepetitionRate, 0, i);
}
}
if (lasers.length == 0 && laserManufacturer != null) {
store.setLaserID(MetadataTools.createLSID("LightSource", 0, 0), 0, 0);
store.setLaserType(getLaserType("Other"), 0, 0);
store.setLaserLaserMedium(getLaserMedium("Other"), 0, 0);
store.setLaserManufacturer(laserManufacturer, 0, 0);
store.setLaserModel(laserModel, 0, 0);
Power theLaserPower = FormatTools.createPower(laserPower, UNITS.MILLIWATT);
if (theLaserPower != null) {
store.setLaserPower(theLaserPower, 0, 0);
}
Frequency theLaserRepetitionRate = FormatTools.createFrequency(laserRepetitionRate, UNITS.HERTZ);
if (theLaserRepetitionRate != null) {
store.setLaserRepetitionRate(theLaserRepetitionRate, 0, 0);
}
}
if (filterSetModel != null) {
store.setFilterSetID(MetadataTools.createLSID("FilterSet", 0, 0), 0, 0);
store.setFilterSetModel(filterSetModel, 0, 0);
String dichroicID = MetadataTools.createLSID("Dichroic", 0, 0);
String emFilterID = MetadataTools.createLSID("Filter", 0, 0);
String exFilterID = MetadataTools.createLSID("Filter", 0, 1);
store.setDichroicID(dichroicID, 0, 0);
store.setDichroicModel(dichroicModel, 0, 0);
store.setFilterSetDichroicRef(dichroicID, 0, 0);
store.setFilterID(emFilterID, 0, 0);
store.setFilterModel(emissionModel, 0, 0);
store.setFilterSetEmissionFilterRef(emFilterID, 0, 0, 0);
store.setFilterID(exFilterID, 0, 1);
store.setFilterModel(excitationModel, 0, 1);
store.setFilterSetExcitationFilterRef(exFilterID, 0, 0, 0);
}
if (objectiveModel != null)
store.setObjectiveModel(objectiveModel, 0, 0);
if (immersion == null)
immersion = "Other";
store.setObjectiveImmersion(getImmersion(immersion), 0, 0);
if (lensNA != null)
store.setObjectiveLensNA(lensNA, 0, 0);
if (workingDistance != null) {
store.setObjectiveWorkingDistance(new Length(workingDistance, UNITS.MICROMETER), 0, 0);
}
if (magnification != null) {
store.setObjectiveCalibratedMagnification(magnification, 0, 0);
}
store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
// link Objective to Image
String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objectiveID, 0, 0);
store.setObjectiveSettingsID(objectiveID, 0);
// populate Detector data
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detectorID, 0, 0);
store.setDetectorManufacturer(detectorManufacturer, 0, 0);
store.setDetectorModel(detectorModel, 0, 0);
store.setDetectorType(getDetectorType("Other"), 0, 0);
for (Integer key : gains.keySet()) {
int index = key.intValue();
if (index < getEffectiveSizeC()) {
store.setDetectorSettingsGain(gains.get(key), 0, index);
store.setDetectorSettingsID(detectorID, 0, index);
}
}
if (lastName != null) {
String experimenterID = MetadataTools.createLSID("Experimenter", 0);
store.setExperimenterID(experimenterID, 0);
store.setExperimenterLastName(lastName, 0);
}
if (stagePos != null) {
for (int i = 0; i < getImageCount(); i++) {
if (stagePos.length > 0) {
store.setPlanePositionX(stagePos[0], 0, i);
addGlobalMeta("X position for position #1", stagePos[0]);
}
if (stagePos.length > 1) {
store.setPlanePositionY(stagePos[1], 0, i);
addGlobalMeta("Y position for position #1", stagePos[1]);
}
if (stagePos.length > 2) {
store.setPlanePositionZ(stagePos[2], 0, i);
addGlobalMeta("Z position for position #1", stagePos[2]);
}
}
}
if (exposureTime != null) {
for (int i = 0; i < getImageCount(); i++) {
store.setPlaneExposureTime(exposureTime, 0, i);
}
}
}
}
Also used :
ArrayList(java.util.ArrayList)
Time(ome.units.quantity.Time)
Timestamp(ome.xml.model.primitives.Timestamp)
Hashtable(java.util.Hashtable)
CoreMetadata(loci.formats.CoreMetadata)
FormatException(loci.formats.FormatException)
MetadataStore(loci.formats.meta.MetadataStore)
StringTokenizer(java.util.StringTokenizer)
Length(ome.units.quantity.Length)
Frequency(ome.units.quantity.Frequency)
RandomAccessInputStream(loci.common.RandomAccessInputStream)
Power(ome.units.quantity.Power)
Location(loci.common.Location)
Example 33 with Time
use of ome.units.quantity.Time in project bioformats by openmicroscopy.
the class MicromanagerReader method parsePosition.
private void parsePosition(String jsonData, int posIndex) throws IOException, FormatException {
Position p = positions.get(posIndex);
CoreMetadata ms = core.get(posIndex);
String parent = new Location(p.metadataFile).getParent();
// now parse the rest of the metadata
// metadata.txt looks something like this:
//
// {
// "Section Name": {
// "Key": "Value",
// "Array key": [
// first array value, second array value
// ]
// }
//
// }
LOGGER.info("Populating metadata");
Vector<Double> stamps = new Vector<Double>();
p.voltage = new Vector<Double>();
StringTokenizer st = new StringTokenizer(jsonData, "\n");
int[] slice = new int[3];
while (st.hasMoreTokens()) {
String token = st.nextToken().trim();
boolean open = token.indexOf('[') != -1;
boolean closed = token.indexOf(']') != -1;
if (open || (!open && !closed && !token.equals("{") && !token.startsWith("}"))) {
int quote = token.indexOf("\"") + 1;
String key = token.substring(quote, token.indexOf("\"", quote));
String value = null;
if (open == closed) {
value = token.substring(token.indexOf(':') + 1);
} else if (!closed) {
final StringBuilder valueBuffer = new StringBuilder();
while (!closed) {
token = st.nextToken();
closed = token.indexOf(']') != -1;
valueBuffer.append(token);
}
value = valueBuffer.toString();
value = value.replaceAll("\n", "");
}
if (value == null)
continue;
int startIndex = value.indexOf('[');
int endIndex = value.indexOf(']');
if (endIndex == -1)
endIndex = value.length();
value = value.substring(startIndex + 1, endIndex).trim();
if (value.length() == 0) {
continue;
}
value = value.substring(0, value.length() - 1);
value = value.replaceAll("\"", "");
if (value.endsWith(","))
value = value.substring(0, value.length() - 1);
addSeriesMeta(key, value);
if (key.equals("Channels")) {
ms.sizeC = Integer.parseInt(value);
} else if (key.equals("ChNames")) {
p.channels = value.split(",");
for (int q = 0; q < p.channels.length; q++) {
p.channels[q] = p.channels[q].replaceAll("\"", "").trim();
}
} else if (key.equals("Frames")) {
ms.sizeT = Integer.parseInt(value);
} else if (key.equals("Slices")) {
ms.sizeZ = Integer.parseInt(value);
} else if (key.equals("SlicesFirst")) {
if (value.equals("false")) {
ms.dimensionOrder = "XYCZT";
} else {
ms.dimensionOrder = "XYZCT";
}
} else if (key.equals("PixelSize_um")) {
p.pixelSize = new Double(value);
} else if (key.equals("z-step_um")) {
p.sliceThickness = new Double(value);
} else if (key.equals("Time")) {
p.time = value;
} else if (key.equals("Comment")) {
p.comment = value;
} else if (key.equals("FileName")) {
p.fileNameMap.put(new Index(slice), value);
if (p.baseTiff == null) {
p.baseTiff = value;
}
} else if (key.equals("Width")) {
ms.sizeX = Integer.parseInt(value);
} else if (key.equals("Height")) {
ms.sizeY = Integer.parseInt(value);
} else if (key.equals("IJType")) {
int type = Integer.parseInt(value);
switch(type) {
case 0:
ms.pixelType = FormatTools.UINT8;
break;
case 1:
ms.pixelType = FormatTools.UINT16;
break;
default:
throw new FormatException("Unknown type: " + type);
}
}
}
if (token.startsWith("\"FrameKey")) {
int dash = token.indexOf('-') + 1;
int nextDash = token.indexOf("-", dash);
slice[2] = Integer.parseInt(token.substring(dash, nextDash));
dash = nextDash + 1;
nextDash = token.indexOf("-", dash);
slice[1] = Integer.parseInt(token.substring(dash, nextDash));
dash = nextDash + 1;
slice[0] = Integer.parseInt(token.substring(dash, token.indexOf("\"", dash)));
token = st.nextToken().trim();
String key = "";
StringBuilder valueBuffer = new StringBuilder();
boolean valueArray = false;
int nestedCount = 0;
while (!token.startsWith("}") || nestedCount > 0) {
if (token.trim().endsWith("{")) {
nestedCount++;
token = st.nextToken().trim();
continue;
} else if (token.trim().startsWith("}")) {
nestedCount--;
token = st.nextToken().trim();
continue;
}
if (valueArray || token.trim().equals("],")) {
if (token.trim().equals("],")) {
valueArray = false;
} else {
valueBuffer.append(token.trim().replaceAll("\"", ""));
token = st.nextToken().trim();
continue;
}
} else {
int colon = token.indexOf(':');
key = token.substring(1, colon).trim();
valueBuffer.setLength(0);
valueBuffer.append(token.substring(colon + 1, token.length() - 1).trim().replaceAll("\"", ""));
key = key.replaceAll("\"", "");
if (token.trim().endsWith("[")) {
valueArray = true;
token = st.nextToken().trim();
continue;
}
}
String value = valueBuffer.toString();
addSeriesMeta(key, value);
if (key.equals("Exposure-ms")) {
p.exposureTime = new Time(Double.valueOf(value), UNITS.MILLISECOND);
} else if (key.equals("ElapsedTime-ms")) {
stamps.add(Double.valueOf(value));
} else if (key.equals("Core-Camera"))
p.cameraRef = value;
else if (key.equals(p.cameraRef + "-Binning")) {
if (value.indexOf('x') != -1)
p.binning = value;
else
p.binning = value + "x" + value;
} else if (key.equals(p.cameraRef + "-CameraID"))
p.detectorID = value;
else if (key.equals(p.cameraRef + "-CameraName")) {
p.detectorModel = value;
} else if (key.equals(p.cameraRef + "-Gain")) {
p.gain = (int) Double.parseDouble(value);
} else if (key.equals(p.cameraRef + "-Name")) {
p.detectorManufacturer = value;
} else if (key.equals(p.cameraRef + "-Temperature")) {
p.temperature = Double.parseDouble(value);
} else if (key.equals(p.cameraRef + "-CCDMode")) {
p.cameraMode = value;
} else if (key.startsWith("DAC-") && key.endsWith("-Volts")) {
p.voltage.add(new Double(value));
} else if (key.equals("FileName")) {
p.fileNameMap.put(new Index(slice), value);
Location realFile = new Location(parent, value);
if (realFile.exists()) {
if (p.tiffs == null) {
p.tiffs = new Vector<String>();
}
p.tiffs.add(realFile.getAbsolutePath());
}
if (p.baseTiff == null) {
p.baseTiff = value;
}
}
token = st.nextToken().trim();
}
} else if (token.startsWith("\"Coords-")) {
String path = token.substring(token.indexOf('-') + 1, token.lastIndexOf("\""));
int[] zct = new int[3];
int position = 0;
while (!token.startsWith("}")) {
int sep = token.indexOf(':');
if (sep > 0) {
String key = token.substring(0, sep);
String value = token.substring(sep + 1);
key = key.replaceAll("\"", "").trim();
value = value.replaceAll(",", "").trim();
if (key.equals("position")) {
position = Integer.parseInt(value);
} else if (key.equals("time")) {
zct[2] = Integer.parseInt(value);
} else if (key.equals("z")) {
zct[0] = Integer.parseInt(value);
} else if (key.equals("channel")) {
zct[1] = Integer.parseInt(value);
}
}
token = st.nextToken().trim();
}
Index idx = new Index(zct);
idx.position = position;
p.fileNameMap.put(idx, path);
}
}
p.timestamps = stamps.toArray(new Double[stamps.size()]);
Arrays.sort(p.timestamps);
if (new Location(parent, XML).exists()) {
p.xmlFile = new Location(parent, XML).getAbsolutePath();
parseXMLFile();
}
if (getSizeZ() == 0)
ms.sizeZ = 1;
if (getSizeT() == 0)
ms.sizeT = 1;
if (ms.dimensionOrder == null)
ms.dimensionOrder = "XYZCT";
ms.interleaved = false;
ms.rgb = false;
ms.littleEndian = false;
ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
ms.indexed = false;
ms.falseColor = false;
ms.metadataComplete = true;
}
Also used :
Time(ome.units.quantity.Time)
CoreMetadata(loci.formats.CoreMetadata)
FormatException(loci.formats.FormatException)
StringTokenizer(java.util.StringTokenizer)
Vector(java.util.Vector)
Location(loci.common.Location)
Example 34 with Time
use of ome.units.quantity.Time in project bioformats by openmicroscopy.
the class BaseTiffReader method initMetadataStore.
/**
* Populates the metadata store using the data parsed in
* {@link #initStandardMetadata()} along with some further parsing done in
* the method itself.
*
* All calls to the active <code>MetadataStore</code> should be made in this
* method and <b>only</b> in this method. This is especially important for
* sub-classes that override the getters for pixel set array size, etc.
*/
protected void initMetadataStore() throws FormatException {
LOGGER.info("Populating OME metadata");
// the metadata store we're working with
MetadataStore store = makeFilterMetadata();
IFD firstIFD = ifds.get(0);
IFD exif = null;
if (ifds.get(0).containsKey(IFD.EXIF)) {
try {
IFDList exifIFDs = tiffParser.getExifIFDs();
if (exifIFDs.size() > 0) {
exif = exifIFDs.get(0);
}
tiffParser.fillInIFD(exif);
} catch (IOException e) {
LOGGER.debug("Could not read EXIF IFDs", e);
}
}
MetadataTools.populatePixels(store, this, exif != null);
// format the creation date to ISO 8601
String creationDate = getImageCreationDate();
String date = DateTools.formatDate(creationDate, DATE_FORMATS, ".");
if (creationDate != null && date == null) {
LOGGER.warn("unknown creation date format: {}", creationDate);
}
creationDate = date;
if (creationDate != null) {
store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
// populate Experimenter
String artist = firstIFD.getIFDTextValue(IFD.ARTIST);
if (artist != null) {
String firstName = null, lastName = null;
int ndx = artist.indexOf(' ');
if (ndx < 0)
lastName = artist;
else {
firstName = artist.substring(0, ndx);
lastName = artist.substring(ndx + 1);
}
String email = firstIFD.getIFDStringValue(IFD.HOST_COMPUTER);
store.setExperimenterFirstName(firstName, 0);
store.setExperimenterLastName(lastName, 0);
store.setExperimenterEmail(email, 0);
store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
}
store.setImageDescription(firstIFD.getComment(), 0);
// set the X and Y pixel dimensions
double pixX = firstIFD.getXResolution();
double pixY = firstIFD.getYResolution();
String unit = getResolutionUnitFromComment(firstIFD);
Length sizeX = FormatTools.getPhysicalSizeX(pixX, unit);
Length sizeY = FormatTools.getPhysicalSizeY(pixY, unit);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
store.setPixelsPhysicalSizeZ(null, 0);
if (exif != null) {
if (exif.containsKey(IFD.EXPOSURE_TIME)) {
Object exp = exif.get(IFD.EXPOSURE_TIME);
if (exp instanceof TiffRational) {
Time exposure = new Time(((TiffRational) exp).doubleValue(), UNITS.SECOND);
for (int i = 0; i < getImageCount(); i++) {
store.setPlaneExposureTime(exposure, 0, i);
}
}
}
}
}
}
Also used :
MetadataStore(loci.formats.meta.MetadataStore)
Length(ome.units.quantity.Length)
IFD(loci.formats.tiff.IFD)
IFDList(loci.formats.tiff.IFDList)
TiffRational(loci.formats.tiff.TiffRational)
Time(ome.units.quantity.Time)
IOException(java.io.IOException)
Timestamp(ome.xml.model.primitives.Timestamp)
Example 35 with Time
use of ome.units.quantity.Time in project bioformats by openmicroscopy.
the class CellVoyagerReader method readInfo.
private void readInfo(final Document msDocument, final Document omeDocument) throws FormatException {
/*
* Magnification.
*
* We need it early, because the file format reports only un-magnified
* sizes. So if we are to put proper metadata, we need to make the
* conversion to size measured at the sample level ourselves. I feel
* like this is fragile and most likely to change in a future version of
* the file format.
*/
final Element msRoot = msDocument.getDocumentElement();
final double objectiveMagnification = Double.parseDouble(getChildText(msRoot, new String[] { "ObjectiveLens", "Magnification" }));
// final double zoomLensMagnification = Double.parseDouble(
// getChildText( msRoot, new String[] { "ZoomLens", "Magnification",
// "Value" } ) );
// *
final double magnification = objectiveMagnification;
// zoomLensMagnification;
/*
* Read the ome.xml file. Since it is malformed, we need to parse all
* nodes, and add an "ID" attribute to those who do not have it.
*/
final NodeList nodeList = omeDocument.getElementsByTagName("*");
for (int i = 0; i < nodeList.getLength(); i++) {
final Node node = nodeList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
final NamedNodeMap atts = node.getAttributes();
final Node namedItem = atts.getNamedItem("ID");
if (namedItem == null) {
final String name = node.getNodeName();
final String id = name + ":" + i;
if (!node.getParentNode().getNodeName().equals("LightSource")) {
((Element) node).setAttribute("ID", id);
}
}
}
}
/*
* For single-slice image, the PhysicalSizeZ can be 0, which will make
* the metadata read fail. Correct that.
*/
final Element pszEl = getChild(omeDocument.getDocumentElement(), new String[] { "Image", "Pixels" });
final double physicalSizeZ = Double.parseDouble(pszEl.getAttribute("PhysicalSizeZ"));
if (physicalSizeZ <= 0) {
// default to 1 whatever
pszEl.setAttribute("PhysicalSizeZ", "" + 1);
}
/*
* Now that the XML document is properly formed, we can build a metadata
* object from it.
*/
OMEXMLService service = null;
String xml = null;
try {
xml = XMLTools.getXML(omeDocument);
} catch (final TransformerConfigurationException e2) {
LOGGER.debug("", e2);
} catch (final TransformerException e2) {
LOGGER.debug("", e2);
}
try {
service = new ServiceFactory().getInstance(OMEXMLService.class);
} catch (final DependencyException e1) {
LOGGER.debug("", e1);
}
OMEXMLMetadata omeMD = null;
try {
omeMD = service.createOMEXMLMetadata(xml);
} catch (final ServiceException e) {
LOGGER.debug("", e);
} catch (final NullPointerException npe) {
LOGGER.debug("", npe);
throw npe;
}
// Correct pixel size for magnification
omeMD.setPixelsPhysicalSizeX(FormatTools.createLength(omeMD.getPixelsPhysicalSizeX(0).value().doubleValue() / magnification, omeMD.getPixelsPhysicalSizeX(0).unit()), 0);
omeMD.setPixelsPhysicalSizeY(FormatTools.createLength(omeMD.getPixelsPhysicalSizeY(0).value().doubleValue() / magnification, omeMD.getPixelsPhysicalSizeY(0).unit()), 0);
// Time interval
if (Double.valueOf(readFrameInterval(msDocument)) != null) {
omeMD.setPixelsTimeIncrement(new Time(Double.valueOf(readFrameInterval(msDocument)), UNITS.SECOND), 0);
}
/*
* Channels
*/
final Element channelsEl = getChild(msRoot, "Channels");
final List<Element> channelEls = getChildren(channelsEl, "Channel");
channelInfos = new ArrayList<ChannelInfo>();
for (final Element channelEl : channelEls) {
final boolean isEnabled = Boolean.parseBoolean(getChildText(channelEl, "IsEnabled"));
if (!isEnabled) {
continue;
}
final ChannelInfo ci = readChannel(channelEl);
channelInfos.add(ci);
}
/*
* Fix missing IDs.
*
* Some IDs are missing in the malformed OME.XML file. We must put them
* back manually. Some are fixed here
*/
omeMD.setProjectID(MetadataTools.createLSID("Project", 0), 0);
omeMD.setScreenID(MetadataTools.createLSID("Screen", 0), 0);
omeMD.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
omeMD.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
// Read pixel sizes from OME metadata.
final double pixelWidth = omeMD.getPixelsPhysicalSizeX(0).value().doubleValue();
final double pixelHeight = omeMD.getPixelsPhysicalSizeY(0).value().doubleValue();
/*
* Read tile size from channel info. This is weird, but it's like that.
* Since we build a multi-C image, we have to assume that all channels
* have the same dimension, even if the file format allows for changing
* the size, binning, etc. from channel to channel. Failure to load
* datasets that have this exoticity is to be sought here.
*/
final int tileWidth = channelInfos.get(0).tileWidth;
final int tileHeight = channelInfos.get(0).tileHeight;
/*
* Handle multiple wells.
*
* The same kind of remark apply: We assume that a channel setting can
* be applied to ALL wells. So this file reader will fail for dataset
* that have one well that has a different dimension that of others.
*/
/*
* First remark: there can be two modes to store Areas in the xml file:
* Either we define different areas for each well, and in that case, the
* areas are found as a child element of the well element. Either the
* definition of areas is common to all wells, and in that case they
* area defined in a separate element.
*/
final boolean sameAreaPerWell = Boolean.parseBoolean(getChildText(msRoot, "UsesSameAreaParWell"));
List<AreaInfo> areas = null;
if (sameAreaPerWell) {
final Element areasEl = getChild(msRoot, new String[] { "SameAreaUsingWell", "Areas" });
final List<Element> areaEls = getChildren(areasEl, "Area");
int areaIndex = 0;
areas = new ArrayList<AreaInfo>(areaEls.size());
int fieldIndex = 1;
for (final Element areaEl : areaEls) {
final AreaInfo area = readArea(areaEl, fieldIndex, pixelWidth, pixelHeight, tileWidth, tileHeight);
area.index = areaIndex++;
areas.add(area);
// Continue incrementing field index across areas.
fieldIndex = area.fields.get(area.fields.size() - 1).index + 1;
}
}
final Element wellsEl = getChild(msRoot, "Wells");
final List<Element> wellEls = getChildren(wellsEl, "Well");
wells = new ArrayList<WellInfo>();
for (final Element wellEl : wellEls) {
final boolean isWellEnabled = Boolean.parseBoolean(getChild(wellEl, "IsEnabled").getTextContent());
if (isWellEnabled) {
final WellInfo wi = readWellInfo(wellEl, pixelWidth, pixelHeight, tileWidth, tileHeight);
if (sameAreaPerWell) {
wi.areas = areas;
}
wells.add(wi);
}
}
/*
* Z range.
*
* In this file format, the Z range appears to be general: it applies to
* all fields of all wells.
*/
final int nZSlices = Integer.parseInt(getChildText(msRoot, new String[] { "ZStackConditions", "NumberOfSlices" }));
/*
* Time points. They are general as well. Which just makes sense.
*/
timePoints = readTimePoints(msDocument);
/*
* Populate CORE metadata for each area.
*
* This reader takes to convention that state that 1 area = 1 series. So
* if you have 10 wells with 2 areas in each well, and each area is made
* of 20 fields, you will get 20 series, and each series will be
* stitched from 20 fields.
*/
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omeMD.getRoot();
Image firstImage = root.getImage(0);
core.clear();
for (final WellInfo well : wells) {
for (final AreaInfo area : well.areas) {
final CoreMetadata ms = new CoreMetadata();
core.add(ms);
if (core.size() > 1) {
root.addImage(firstImage);
}
ms.sizeX = area.width;
ms.sizeY = area.height;
ms.sizeZ = nZSlices;
ms.sizeC = channelInfos.size();
ms.sizeT = timePoints.size();
ms.dimensionOrder = "XYCZT";
ms.rgb = false;
ms.imageCount = nZSlices * channelInfos.size() * timePoints.size();
// Bit depth.
switch(omeMD.getPixelsType(0)) {
case UINT8:
ms.pixelType = FormatTools.UINT8;
ms.bitsPerPixel = 8;
break;
case UINT16:
ms.pixelType = FormatTools.UINT16;
ms.bitsPerPixel = 16;
break;
case UINT32:
ms.pixelType = FormatTools.UINT32;
ms.bitsPerPixel = 32;
break;
default:
throw new FormatException("Cannot read image with pixel type = " + omeMD.getPixelsType(0));
}
// Determined manually on sample data. Check here is the image
// you get is weird.
ms.littleEndian = true;
}
}
omeMD.setRoot(root);
/*
* Populate the MetadataStore.
*/
final MetadataStore store = makeFilterMetadata();
MetadataConverter.convertMetadata(omeMD, store);
MetadataTools.populatePixels(store, this, true);
/*
* Pinhole disk
*/
final double pinholeSize = Double.parseDouble(getChildText(msRoot, new String[] { "PinholeDisk", "PinholeSize_um" }));
/*
* MicroPlate specific stuff
*/
final Element containerEl = getChild(msRoot, new String[] { "Attachment", "HolderInfoList", "HolderInfo", "MountedSampleContainer" });
final String type = containerEl.getAttribute("xsi:type");
boolean plateMetadata = false;
if (type.equals("WellPlate")) {
plateMetadata = true;
final int nrows = Integer.parseInt(getChildText(containerEl, "RowCount"));
final int ncols = Integer.parseInt(getChildText(containerEl, "ColumnCount"));
store.setPlateRows(new PositiveInteger(nrows), 0);
store.setPlateColumns(new PositiveInteger(ncols), 0);
final String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
store.setPlateAcquisitionID(plateAcqID, 0, 0);
final Element dimInfoEl = getChild(msRoot, "DimensionsInfo");
final int maxNFields = Integer.parseInt(getChild(dimInfoEl, "F").getAttribute("Max"));
final PositiveInteger fieldCount = FormatTools.getMaxFieldCount(maxNFields);
if (fieldCount != null) {
store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
}
// Plate acquisition time
final String beginTime = getChildText(msRoot, "BeginTime");
final String endTime = getChildText(msRoot, "EndTime");
store.setPlateAcquisitionStartTime(new Timestamp(beginTime), 0, 0);
store.setPlateAcquisitionEndTime(new Timestamp(endTime), 0, 0);
store.setPlateName(beginTime, 0);
} else if (!type.equals("PreparedSlide")) {
LOGGER.warn("Unexpected acquisition type: {}", type);
}
// Wells position on the plate
int seriesIndex = -1;
int wellIndex = -1;
for (final WellInfo well : wells) {
wellIndex++;
final int wellNumber = well.number;
if (plateMetadata) {
store.setWellID(MetadataTools.createLSID("Well", 0, wellIndex), 0, wellIndex);
store.setWellRow(new NonNegativeInteger(well.row), 0, wellIndex);
store.setWellColumn(new NonNegativeInteger(well.col), 0, wellIndex);
}
int areaIndex = -1;
for (final AreaInfo area : well.areas) {
seriesIndex++;
areaIndex++;
String imageID = MetadataTools.createLSID("Image", seriesIndex);
store.setImageID(imageID, seriesIndex);
final String imageName = "Well " + wellNumber + " (UID=" + well.UID + ", r=" + well.row + ", c=" + well.col + ") - Area " + areaIndex;
store.setImageName(imageName, seriesIndex);
if (plateMetadata) {
Length posX = new Length(Double.valueOf(well.centerX), UNITS.REFERENCEFRAME);
Length posY = new Length(Double.valueOf(well.centerY), UNITS.REFERENCEFRAME);
String wellSample = MetadataTools.createLSID("WellSample", 0, wellIndex, areaIndex);
store.setWellSampleID(wellSample, 0, wellIndex, areaIndex);
store.setWellSampleImageRef(imageID, 0, wellIndex, areaIndex);
store.setWellSampleIndex(new NonNegativeInteger(area.index), 0, wellIndex, areaIndex);
store.setWellSamplePositionX(posX, 0, wellIndex, areaIndex);
store.setWellSamplePositionY(posY, 0, wellIndex, areaIndex);
store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, seriesIndex);
}
store.setImageInstrumentRef(MetadataTools.createLSID("Instrument", 0), seriesIndex);
for (int i = 0; i < channelInfos.size(); i++) {
store.setChannelPinholeSize(new Length(pinholeSize, UNITS.MICROMETER), seriesIndex, i);
store.setChannelName(channelInfos.get(i).name, seriesIndex, i);
store.setChannelColor(channelInfos.get(i).color, seriesIndex, i);
}
}
}
}
Also used :
TransformerConfigurationException(javax.xml.transform.TransformerConfigurationException)
ServiceFactory(loci.common.services.ServiceFactory)
Element(org.w3c.dom.Element)
Node(org.w3c.dom.Node)
Time(ome.units.quantity.Time)
Image(ome.xml.model.Image)
Timestamp(ome.xml.model.primitives.Timestamp)
OMEXMLService(loci.formats.services.OMEXMLService)
TransformerException(javax.xml.transform.TransformerException)
PositiveInteger(ome.xml.model.primitives.PositiveInteger)
NamedNodeMap(org.w3c.dom.NamedNodeMap)
NonNegativeInteger(ome.xml.model.primitives.NonNegativeInteger)
NodeList(org.w3c.dom.NodeList)
DependencyException(loci.common.services.DependencyException)
CoreMetadata(loci.formats.CoreMetadata)
FormatException(loci.formats.FormatException)
MetadataStore(loci.formats.meta.MetadataStore)
ServiceException(loci.common.services.ServiceException)
Length(ome.units.quantity.Length)
OMEXMLMetadata(loci.formats.ome.OMEXMLMetadata)
OMEXMLMetadataRoot(ome.xml.meta.OMEXMLMetadataRoot)
Aggregations
Time (ome.units.quantity.Time)74
Length (ome.units.quantity.Length)46
MetadataStore (loci.formats.meta.MetadataStore)41
Timestamp (ome.xml.model.primitives.Timestamp)33
CoreMetadata (loci.formats.CoreMetadata)30
FormatException (loci.formats.FormatException)24
RandomAccessInputStream (loci.common.RandomAccessInputStream)21
Location (loci.common.Location)20
ArrayList (java.util.ArrayList)17
PositiveInteger (ome.xml.model.primitives.PositiveInteger)13
NonNegativeInteger (ome.xml.model.primitives.NonNegativeInteger)12
IOException (java.io.IOException)10
Temperature (ome.units.quantity.Temperature)9
IFD (loci.formats.tiff.IFD)8
ElectricPotential (ome.units.quantity.ElectricPotential)7
Color (ome.xml.model.primitives.Color)7
IMetadata (loci.formats.meta.IMetadata)6
File (java.io.File)5
DependencyException (loci.common.services.DependencyException)5
ServiceException (loci.common.services.ServiceException)5
