Examples with EnumerationException ome.xml.model.enums.EnumerationException used on opensource projects

Example 11 with EnumerationException

use of ome.xml.model.enums.EnumerationException in project bioformats by openmicroscopy.

the class FakeReader method parseLength.

private Length parseLength(String value, String defaultUnit) {
    Matcher m = Pattern.compile("\\s*([\\d.]+)\\s*([^\\d\\s].*?)?\\s*").matcher(value);
    if (!m.matches()) {
        throw new RuntimeException(String.format("%s does not match a physical size!", value));
    }
    String number = m.group(1);
    String unit = m.group(2);
    if (unit == null || unit.trim().length() == 0) {
        unit = defaultUnit;
    }
    double d = Double.valueOf(number);
    Unit<Length> l = null;
    try {
        l = UnitsLengthEnumHandler.getBaseUnit(UnitsLength.fromString(unit));
    } catch (EnumerationException e) {
        LOGGER.warn("{} does not match a length unit!", unit);
    }
    if (l != null && d > Constants.EPSILON) {
        return new Length(d, l);
    }
    return null;
}

Example 12 with EnumerationException

use of ome.xml.model.enums.EnumerationException in project bioformats by openmicroscopy.

the class MakeTestOmeTiff method createWriter.

private OMETiffWriter createWriter(final String name, final CoreMetadata info, final String id) throws FormatException, IOException {
    final OMETiffWriter out = new OMETiffWriter();
    try {
        out.setMetadataRetrieve(createMetadata(name, info));
    } catch (final DependencyException e) {
        throw new FormatException(e);
    } catch (final ServiceException e) {
        throw new FormatException(e);
    } catch (final EnumerationException e) {
        throw new FormatException(e);
    }
    ensureNonExisting(id);
    out.setId(id);
    return out;
}

Example 13 with EnumerationException

use of ome.xml.model.enums.EnumerationException in project bioformats by openmicroscopy.

the class LeicaHandler method startElement.

@Override
public void startElement(String uri, String localName, String qName, Attributes attributes) {
    if (attributes.getLength() > 0 && !qName.equals("Element") && !qName.equals("Attachment") && !qName.equals("LMSDataContainerHeader")) {
        nameStack.push(qName);
    }
    int oldSeriesCount = numDatasets;
    Hashtable h = getSeriesHashtable(numDatasets);
    if (qName.equals("LDM_Block_Sequential_Master")) {
        canParse = false;
    } else if (qName.startsWith("LDM")) {
        linkedInstruments = true;
    }
    if (!canParse)
        return;
    final StringBuilder key = new StringBuilder();
    final Iterator<String> nameStackIterator = nameStack.descendingIterator();
    while (nameStackIterator.hasNext()) {
        final String k = nameStackIterator.next();
        key.append(k);
        key.append("|");
    }
    String suffix = attributes.getValue("Identifier");
    String value = attributes.getValue("Variant");
    if (suffix == null)
        suffix = attributes.getValue("Description");
    if (level != MetadataLevel.MINIMUM) {
        if (suffix != null && value != null) {
            storeKeyValue(h, key.toString() + suffix, value);
        } else {
            for (int i = 0; i < attributes.getLength(); i++) {
                String name = attributes.getQName(i);
                storeKeyValue(h, key.toString() + name, attributes.getValue(i));
            }
        }
    }
    if (qName.equals("Element")) {
        elementName = attributes.getValue("Name");
    } else if (qName.equals("Collection")) {
        collection = elementName;
    } else if (qName.equals("Image")) {
        if (!linkedInstruments && level != MetadataLevel.MINIMUM) {
            int c = 0;
            for (Detector d : detectors) {
                String id = MetadataTools.createLSID("Detector", numDatasets, detectorChannel);
                store.setDetectorID(id, numDatasets, detectorChannel);
                try {
                    DetectorTypeEnumHandler handler = new DetectorTypeEnumHandler();
                    store.setDetectorType((DetectorType) handler.getEnumeration(d.type), numDatasets, detectorChannel);
                } catch (EnumerationException e) {
                }
                store.setDetectorModel(d.model, numDatasets, detectorChannel);
                store.setDetectorZoom(d.zoom, numDatasets, detectorChannel);
                store.setDetectorOffset(d.offset, numDatasets, detectorChannel);
                store.setDetectorVoltage(new ElectricPotential(d.voltage, UNITS.VOLT), numDatasets, detectorChannel);
                if (c < numChannels) {
                    if (d.active) {
                        store.setDetectorSettingsOffset(d.offset, numDatasets, c);
                        store.setDetectorSettingsID(id, numDatasets, c);
                        c++;
                    }
                }
                detectorChannel++;
            }
            int filter = 0;
            for (int i = 0; i < nextFilter; i++) {
                while (filter < detectors.size() && !detectors.get(filter).active) {
                    filter++;
                }
                if (filter >= detectors.size() || filter >= nextFilter)
                    break;
                String id = MetadataTools.createLSID("Filter", numDatasets, filter);
                if (i < numChannels && detectors.get(filter).active) {
                    String lsid = MetadataTools.createLSID("Channel", numDatasets, i);
                    store.setChannelID(lsid, numDatasets, i);
                    store.setLightPathEmissionFilterRef(id, numDatasets, i, 0);
                }
                filter++;
            }
        }
        core.add(new CoreMetadata());
        numDatasets++;
        laserCount = 0;
        linkedInstruments = false;
        detectorChannel = 0;
        detectors.clear();
        lasers.clear();
        nextFilter = 0;
        String name = elementName;
        if (collection != null)
            name = collection + "/" + name;
        store.setImageName(name, numDatasets);
        h = getSeriesHashtable(numDatasets);
        storeKeyValue(h, "Image name", name);
        storeSeriesHashtable(numDatasets, h);
        String instrumentID = MetadataTools.createLSID("Instrument", numDatasets);
        store.setInstrumentID(instrumentID, numDatasets);
        store.setImageInstrumentRef(instrumentID, numDatasets);
        numChannels = 0;
        extras = 1;
    } else if (qName.equals("Attachment") && level != MetadataLevel.MINIMUM) {
        if ("ContextDescription".equals(attributes.getValue("Name"))) {
            store.setImageDescription(attributes.getValue("Content"), numDatasets);
        }
    } else if (qName.equals("ChannelDescription")) {
        count++;
        numChannels++;
        lutNames.add(attributes.getValue("LUTName"));
        String bytesInc = attributes.getValue("BytesInc");
        int bytes = bytesInc == null ? 0 : Integer.parseInt(bytesInc);
        if (bytes > 0) {
            bytesPerAxis.put(new Integer(bytes), "C");
        }
    } else if (qName.equals("DimensionDescription")) {
        int len = Integer.parseInt(attributes.getValue("NumberOfElements"));
        int id = Integer.parseInt(attributes.getValue("DimID"));
        double physicalLen = Double.parseDouble(attributes.getValue("Length"));
        String unit = attributes.getValue("Unit");
        int nBytes = Integer.parseInt(attributes.getValue("BytesInc"));
        physicalLen /= len;
        if (unit.equals("Ks")) {
            physicalLen /= 1000;
        } else if (unit.equals("m")) {
            physicalLen *= 1000000;
        }
        Double physicalSize = new Double(physicalLen);
        CoreMetadata coreMeta = core.get(core.size() - 1);
        switch(id) {
            case // X axis
            1:
                coreMeta.sizeX = len;
                coreMeta.rgb = (nBytes % 3) == 0;
                if (coreMeta.rgb)
                    nBytes /= 3;
                switch(nBytes) {
                    case 1:
                        coreMeta.pixelType = FormatTools.UINT8;
                        break;
                    case 2:
                        coreMeta.pixelType = FormatTools.UINT16;
                        break;
                    case 4:
                        coreMeta.pixelType = FormatTools.FLOAT;
                        break;
                }
                physicalSizeX = physicalSize.doubleValue();
                Length sizeX = FormatTools.getPhysicalSizeX(physicalSize);
                if (sizeX != null) {
                    store.setPixelsPhysicalSizeX(sizeX, numDatasets);
                }
                break;
            case // Y axis
            2:
                if (coreMeta.sizeY != 0) {
                    if (coreMeta.sizeZ == 1) {
                        coreMeta.sizeZ = len;
                        bytesPerAxis.put(new Integer(nBytes), "Z");
                    } else if (coreMeta.sizeT == 1) {
                        coreMeta.sizeT = len;
                        bytesPerAxis.put(new Integer(nBytes), "T");
                    }
                } else {
                    coreMeta.sizeY = len;
                    physicalSizeY = physicalSize.doubleValue();
                    Length sizeY = FormatTools.getPhysicalSizeY(physicalSize);
                    if (sizeY != null) {
                        store.setPixelsPhysicalSizeY(sizeY, numDatasets);
                    }
                }
                break;
            case // Z axis
            3:
                if (coreMeta.sizeY == 0) {
                    // XZ scan - swap Y and Z
                    coreMeta.sizeY = len;
                    coreMeta.sizeZ = 1;
                    physicalSizeY = physicalSize.doubleValue();
                    Length sizeY = FormatTools.getPhysicalSizeY(physicalSize);
                    if (sizeY != null) {
                        store.setPixelsPhysicalSizeY(sizeY, numDatasets);
                    }
                    bytesPerAxis.put(new Integer(nBytes), "Y");
                } else {
                    coreMeta.sizeZ = len;
                    bytesPerAxis.put(new Integer(nBytes), "Z");
                }
                break;
            case // T axis
            4:
                if (coreMeta.sizeY == 0) {
                    // XT scan - swap Y and T
                    coreMeta.sizeY = len;
                    coreMeta.sizeT = 1;
                    physicalSizeY = physicalSize.doubleValue();
                    Length sizeY = FormatTools.getPhysicalSizeY(physicalSize);
                    if (sizeY != null) {
                        store.setPixelsPhysicalSizeY(sizeY, numDatasets);
                    }
                    bytesPerAxis.put(new Integer(nBytes), "Y");
                } else {
                    coreMeta.sizeT = len;
                    bytesPerAxis.put(new Integer(nBytes), "T");
                }
                break;
            default:
                extras *= len;
        }
        count++;
    } else if (qName.equals("ScannerSettingRecord") && level != MetadataLevel.MINIMUM) {
        String id = attributes.getValue("Identifier");
        if (id == null)
            id = "";
        if (id.equals("SystemType")) {
            store.setMicroscopeModel(value, numDatasets);
            store.setMicroscopeType(MicroscopeType.OTHER, numDatasets);
        } else if (id.equals("dblPinhole")) {
            pinhole = new Double(Double.parseDouble(value) * 1000000);
        } else if (id.equals("dblZoom")) {
            zoom = new Double(value);
        } else if (id.equals("dblStepSize")) {
            double zStep = Double.parseDouble(value) * 1000000;
            Length sizeZ = FormatTools.getPhysicalSizeZ(zStep);
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, numDatasets);
            }
        } else if (id.equals("nDelayTime_s")) {
            Double timeIncrement = new Double(value);
            if (timeIncrement != null) {
                store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.SECOND), numDatasets);
            }
        } else if (id.equals("CameraName")) {
            store.setDetectorModel(value, numDatasets, 0);
        } else if (id.indexOf("WFC") == 1) {
            int c = 0;
            try {
                c = Integer.parseInt(id.replaceAll("\\D", ""));
            } catch (NumberFormatException e) {
            }
            Channel channel = channels.get(numDatasets + "-" + c);
            if (channel == null)
                channel = new Channel();
            if (id.endsWith("ExposureTime") && c < numChannels) {
                try {
                    Double exposureTime = new Double(value);
                    if (exposureTime != null) {
                        store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), numDatasets, c);
                    }
                } catch (IndexOutOfBoundsException e) {
                }
            } else if (id.endsWith("Gain")) {
                channel.gain = new Double(value);
                String detectorID = MetadataTools.createLSID("Detector", numDatasets, 0);
                channel.detector = detectorID;
                store.setDetectorID(detectorID, numDatasets, 0);
                store.setDetectorType(DetectorType.CCD, numDatasets, 0);
            } else if (id.endsWith("WaveLength")) {
                Double exWave = new Double(value);
                Length ex = FormatTools.getExcitationWavelength(exWave);
                if (ex != null) {
                    channel.exWave = ex;
                }
            } else // NB: "UesrDefName" is not a typo.
            if (id.endsWith("UesrDefName") && !value.equals("None")) {
                channel.name = value;
            }
            channels.put(numDatasets + "-" + c, channel);
        }
    } else if (qName.equals("FilterSettingRecord") && level != MetadataLevel.MINIMUM) {
        String object = attributes.getValue("ObjectName");
        String attribute = attributes.getValue("Attribute");
        String objectClass = attributes.getValue("ClassName");
        String variant = attributes.getValue("Variant");
        CoreMetadata coreMeta = core.get(numDatasets);
        if (attribute.equals("NumericalAperture")) {
            store.setObjectiveLensNA(new Double(variant), numDatasets, 0);
        } else if (attribute.equals("OrderNumber")) {
            store.setObjectiveSerialNumber(variant, numDatasets, 0);
        } else if (objectClass.equals("CDetectionUnit")) {
            if (attribute.equals("State")) {
                Detector d = new Detector();
                String data = attributes.getValue("data");
                if (data == null)
                    data = attributes.getValue("Data");
                d.channel = data == null ? 0 : Integer.parseInt(data);
                d.type = "PMT";
                d.model = object;
                d.active = variant.equals("Active");
                d.zoom = zoom;
                detectors.add(d);
            } else if (attribute.equals("HighVoltage")) {
                Detector d = detectors.get(detectors.size() - 1);
                d.voltage = new Double(variant);
            } else if (attribute.equals("VideoOffset")) {
                Detector d = detectors.get(detectors.size() - 1);
                d.offset = new Double(variant);
            }
        } else if (attribute.equals("Objective")) {
            StringTokenizer tokens = new StringTokenizer(variant, " ");
            boolean foundMag = false;
            final StringBuilder model = new StringBuilder();
            while (!foundMag) {
                String token = tokens.nextToken();
                int x = token.indexOf('x');
                if (x != -1) {
                    foundMag = true;
                    Double mag = Double.parseDouble(token.substring(0, x));
                    String na = token.substring(x + 1);
                    store.setObjectiveNominalMagnification(mag, numDatasets, 0);
                    store.setObjectiveLensNA(new Double(na), numDatasets, 0);
                } else {
                    model.append(token);
                    model.append(" ");
                }
            }
            String immersion = "Other";
            if (tokens.hasMoreTokens()) {
                immersion = tokens.nextToken();
                if (immersion == null || immersion.trim().equals("")) {
                    immersion = "Other";
                }
            }
            try {
                ImmersionEnumHandler handler = new ImmersionEnumHandler();
                store.setObjectiveImmersion((Immersion) handler.getEnumeration(immersion), numDatasets, 0);
            } catch (EnumerationException e) {
            }
            String correction = "Other";
            if (tokens.hasMoreTokens()) {
                correction = tokens.nextToken();
                if (correction == null || correction.trim().equals("")) {
                    correction = "Other";
                }
            }
            try {
                CorrectionEnumHandler handler = new CorrectionEnumHandler();
                store.setObjectiveCorrection((Correction) handler.getEnumeration(correction), numDatasets, 0);
            } catch (EnumerationException e) {
            }
            store.setObjectiveModel(model.toString().trim(), numDatasets, 0);
        } else if (attribute.equals("RefractionIndex")) {
            String id = MetadataTools.createLSID("Objective", numDatasets, 0);
            store.setObjectiveID(id, numDatasets, 0);
            store.setObjectiveSettingsID(id, numDatasets);
            store.setObjectiveSettingsRefractiveIndex(new Double(variant), numDatasets);
        } else if (attribute.equals("XPos")) {
            int c = coreMeta.rgb || coreMeta.sizeC == 0 ? 1 : coreMeta.sizeC;
            int nPlanes = coreMeta.imageCount;
            final Double posXn = Double.valueOf(variant);
            final Length posXl = new Length(posXn, UNITS.REFERENCEFRAME);
            for (int image = 0; image < nPlanes; image++) {
                store.setPlanePositionX(posXl, numDatasets, image);
            }
            if (numChannels == 0)
                xPos.add(posXl);
        } else if (attribute.equals("YPos")) {
            int c = coreMeta.rgb || coreMeta.sizeC == 0 ? 1 : coreMeta.sizeC;
            int nPlanes = coreMeta.imageCount;
            final Double posYn = Double.valueOf(variant);
            final Length posYl = new Length(posYn, UNITS.REFERENCEFRAME);
            for (int image = 0; image < nPlanes; image++) {
                store.setPlanePositionY(posYl, numDatasets, image);
            }
            if (numChannels == 0)
                yPos.add(posYl);
        } else if (attribute.equals("ZPos")) {
            int c = coreMeta.rgb || coreMeta.sizeC == 0 ? 1 : coreMeta.sizeC;
            int nPlanes = coreMeta.imageCount;
            final Double posZn = Double.valueOf(variant);
            final Length posZl = new Length(posZn, UNITS.REFERENCEFRAME);
            for (int image = 0; image < nPlanes; image++) {
                store.setPlanePositionZ(posZl, numDatasets, image);
            }
            if (numChannels == 0)
                zPos.add(posZl);
        } else if (objectClass.equals("CSpectrophotometerUnit")) {
            Double v = null;
            try {
                v = Double.parseDouble(variant);
            } catch (NumberFormatException e) {
            }
            if (attributes.getValue("Description").endsWith("(left)")) {
                String id = MetadataTools.createLSID("Filter", numDatasets, nextFilter);
                store.setFilterID(id, numDatasets, nextFilter);
                store.setFilterModel(object, numDatasets, nextFilter);
                Length in = FormatTools.getCutIn(v);
                if (in != null) {
                    store.setTransmittanceRangeCutIn(in, numDatasets, nextFilter);
                }
            } else if (attributes.getValue("Description").endsWith("(right)")) {
                Length out = FormatTools.getCutOut(v);
                if (out != null) {
                    store.setTransmittanceRangeCutOut(out, numDatasets, nextFilter);
                    nextFilter++;
                }
            }
        }
    } else if (qName.equals("Detector") && level != MetadataLevel.MINIMUM) {
        String v = attributes.getValue("Gain");
        Double gain = v == null ? null : new Double(v);
        v = attributes.getValue("Offset");
        Double offset = v == null ? null : new Double(v);
        boolean active = "1".equals(attributes.getValue("IsActive"));
        if (active) {
            // find the corresponding MultiBand and Detector
            MultiBand m = null;
            Detector detector = null;
            Laser laser = lasers.isEmpty() ? null : lasers.get(lasers.size() - 1);
            String c = attributes.getValue("Channel");
            int channel = c == null ? 0 : Integer.parseInt(c);
            for (MultiBand mb : multiBands) {
                if (mb.channel == channel) {
                    m = mb;
                    break;
                }
            }
            for (Detector d : detectors) {
                if (d.channel == channel) {
                    detector = d;
                    break;
                }
            }
            String id = MetadataTools.createLSID("Detector", numDatasets, nextChannel);
            if (m != null) {
                String channelID = MetadataTools.createLSID("Channel", numDatasets, nextChannel);
                store.setChannelID(channelID, numDatasets, nextChannel);
                store.setChannelName(m.dyeName, numDatasets, nextChannel);
                String filter = MetadataTools.createLSID("Filter", numDatasets, nextFilter);
                store.setFilterID(filter, numDatasets, nextFilter);
                Length in = FormatTools.getCutIn(m.cutIn);
                Length out = FormatTools.getCutOut(m.cutOut);
                if (in != null) {
                    store.setTransmittanceRangeCutIn(in, numDatasets, nextFilter);
                }
                if (out != null) {
                    store.setTransmittanceRangeCutOut(out, numDatasets, nextFilter);
                }
                store.setLightPathEmissionFilterRef(filter, numDatasets, nextChannel, 0);
                nextFilter++;
                store.setDetectorID(id, numDatasets, nextChannel);
                store.setDetectorType(DetectorType.PMT, numDatasets, nextChannel);
                store.setDetectorSettingsGain(gain, numDatasets, nextChannel);
                store.setDetectorSettingsOffset(offset, numDatasets, nextChannel);
                store.setDetectorSettingsID(id, numDatasets, nextChannel);
            }
            store.setDetectorID(id, numDatasets, nextChannel);
            if (detector != null) {
                store.setDetectorSettingsGain(gain, numDatasets, nextChannel);
                store.setDetectorSettingsOffset(offset, numDatasets, nextChannel);
                store.setDetectorSettingsID(id, numDatasets, nextChannel);
                try {
                    DetectorTypeEnumHandler handler = new DetectorTypeEnumHandler();
                    store.setDetectorType((DetectorType) handler.getEnumeration(detector.type), numDatasets, nextChannel);
                } catch (EnumerationException e) {
                }
                store.setDetectorModel(detector.model, numDatasets, nextChannel);
                store.setDetectorZoom(detector.zoom, numDatasets, nextChannel);
                store.setDetectorOffset(detector.offset, numDatasets, nextChannel);
                store.setDetectorVoltage(new ElectricPotential(detector.voltage, UNITS.VOLT), numDatasets, nextChannel);
            }
            if (laser != null && laser.intensity < 100) {
                store.setChannelLightSourceSettingsID(laser.id, numDatasets, nextChannel);
                store.setChannelLightSourceSettingsAttenuation(new PercentFraction((float) laser.intensity / 100f), numDatasets, nextChannel);
                Length wavelength = FormatTools.getExcitationWavelength(laser.wavelength);
                if (wavelength != null) {
                    store.setChannelExcitationWavelength(wavelength, numDatasets, nextChannel);
                }
            }
            nextChannel++;
        }
    } else if (qName.equals("LaserLineSetting") && level != MetadataLevel.MINIMUM) {
        Laser l = new Laser();
        String lineIndex = attributes.getValue("LineIndex");
        String qual = attributes.getValue("Qualifier");
        l.index = lineIndex == null ? 0 : Integer.parseInt(lineIndex);
        int qualifier = qual == null ? 0 : Integer.parseInt(qual);
        l.index += (2 - (qualifier / 10));
        if (l.index < 0)
            l.index = 0;
        l.id = MetadataTools.createLSID("LightSource", numDatasets, l.index);
        l.wavelength = new Double(attributes.getValue("LaserLine"));
        while (l.index > laserCount) {
            String lsid = MetadataTools.createLSID("LightSource", numDatasets, laserCount);
            store.setLaserID(lsid, numDatasets, laserCount);
            laserCount++;
        }
        store.setLaserID(l.id, numDatasets, l.index);
        laserCount++;
        Length wavelength = FormatTools.getWavelength(l.wavelength);
        if (wavelength != null) {
            store.setLaserWavelength(wavelength, numDatasets, l.index);
        }
        store.setLaserType(LaserType.OTHER, numDatasets, l.index);
        store.setLaserLaserMedium(LaserMedium.OTHER, numDatasets, l.index);
        String intensity = attributes.getValue("IntensityDev");
        l.intensity = intensity == null ? 0d : Double.parseDouble(intensity);
        if (l.intensity > 0) {
            l.intensity = 100d - l.intensity;
            lasers.add(l);
        }
    } else if (qName.equals("TimeStamp") && numDatasets >= 0) {
        String stampHigh = attributes.getValue("HighInteger");
        String stampLow = attributes.getValue("LowInteger");
        long high = stampHigh == null ? 0 : Long.parseLong(stampHigh);
        long low = stampLow == null ? 0 : Long.parseLong(stampLow);
        long ms = DateTools.getMillisFromTicks(high, low);
        if (count == 0) {
            String date = DateTools.convertDate(ms, DateTools.COBOL);
            Timestamp timestamp = Timestamp.valueOf(date);
            if (timestamp != null && timestamp.asInstant().getMillis() < System.currentTimeMillis()) {
                store.setImageAcquisitionDate(new Timestamp(date), numDatasets);
            }
            firstStamp = ms;
            store.setPlaneDeltaT(new Time(0.0, UNITS.SECOND), numDatasets, count);
        } else if (level != MetadataLevel.MINIMUM) {
            CoreMetadata coreMeta = core.get(numDatasets);
            int nImages = coreMeta.sizeZ * coreMeta.sizeT * coreMeta.sizeC;
            if (count < nImages) {
                ms -= firstStamp;
                store.setPlaneDeltaT(new Time(ms / 1000.0, UNITS.SECOND), numDatasets, count);
            }
        }
        count++;
    } else if (qName.equals("RelTimeStamp") && level != MetadataLevel.MINIMUM) {
        CoreMetadata coreMeta = core.get(numDatasets);
        int nImages = coreMeta.sizeZ * coreMeta.sizeT * coreMeta.sizeC;
        if (count < nImages) {
            Double time = new Double(attributes.getValue("Time"));
            if (time != null) {
                store.setPlaneDeltaT(new Time(time, UNITS.SECOND), numDatasets, count++);
            }
        }
    } else if (qName.equals("Annotation") && level != MetadataLevel.MINIMUM) {
        roi = new ROI();
        String type = attributes.getValue("type");
        if (type != null)
            roi.type = Integer.parseInt(type);
        String color = attributes.getValue("color");
        if (color != null)
            roi.color = Integer.parseInt(color);
        roi.name = attributes.getValue("name");
        roi.fontName = attributes.getValue("fontName");
        roi.fontSize = attributes.getValue("fontSize");
        roi.transX = parseDouble(attributes.getValue("transTransX"));
        roi.transY = parseDouble(attributes.getValue("transTransY"));
        roi.scaleX = parseDouble(attributes.getValue("transScalingX"));
        roi.scaleY = parseDouble(attributes.getValue("transScalingY"));
        roi.rotation = parseDouble(attributes.getValue("transRotation"));
        String linewidth = attributes.getValue("linewidth");
        if (linewidth != null)
            roi.linewidth = Integer.parseInt(linewidth);
        roi.text = attributes.getValue("text");
    } else if (qName.equals("Vertex") && level != MetadataLevel.MINIMUM) {
        String x = attributes.getValue("x");
        String y = attributes.getValue("y");
        if (x != null) {
            x = x.replaceAll(",", ".");
            roi.x.add(new Double(x));
        }
        if (y != null) {
            y = y.replaceAll(",", ".");
            roi.y.add(new Double(y));
        }
    } else if (qName.equals("ROI")) {
        alternateCenter = true;
    } else if (qName.equals("MultiBand") && level != MetadataLevel.MINIMUM) {
        MultiBand m = new MultiBand();
        m.dyeName = attributes.getValue("DyeName");
        m.channel = Integer.parseInt(attributes.getValue("Channel"));
        m.cutIn = (double) Math.round(Double.parseDouble(attributes.getValue("LeftWorld")));
        m.cutOut = (double) Math.round(Double.parseDouble(attributes.getValue("RightWorld")));
        multiBands.add(m);
    } else if (qName.equals("ChannelInfo")) {
        int index = Integer.parseInt(attributes.getValue("Index"));
        channels.remove(numDatasets + "-" + index);
    } else
        count = 0;
    if (numDatasets == oldSeriesCount)
        storeSeriesHashtable(numDatasets, h);
}

Example 14 with EnumerationException

use of ome.xml.model.enums.EnumerationException in project bioformats by openmicroscopy.

the class Configuration method getPhysicalSizeY.

public Length getPhysicalSizeY() {
    String physicalSize = currentTable.get(PHYSICAL_SIZE_Y);
    String sizeYUnits = currentTable.get(PHYSICAL_SIZE_Y_UNIT);
    try {
        UnitsLength yUnits = sizeYUnits == null ? UnitsLength.MICROMETER : UnitsLength.fromString(sizeYUnits);
        return physicalSize == null ? null : UnitsLength.create(new Double(physicalSize), yUnits);
    } catch (NumberFormatException e) {
    } catch (EnumerationException e) {
    }
    return null;
}

Example 15 with EnumerationException

use of ome.xml.model.enums.EnumerationException in project bioformats by openmicroscopy.

the class Configuration method getPhysicalSizeZ.

public Length getPhysicalSizeZ() {
    String physicalSize = currentTable.get(PHYSICAL_SIZE_Z);
    String sizeZUnits = currentTable.get(PHYSICAL_SIZE_Z_UNIT);
    try {
        UnitsLength zUnits = sizeZUnits == null ? UnitsLength.MICROMETER : UnitsLength.fromString(sizeZUnits);
        return physicalSize == null ? null : UnitsLength.create(new Double(physicalSize), zUnits);
    } catch (NumberFormatException e) {
    } catch (EnumerationException e) {
    }
    return null;
}