Examples with Length ome.units.quantity.Length used on opensource projects

Example 36 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class ZeissLSMReader method parseOverlays.

/**
 * Parses overlay-related fields.
 */
protected void parseOverlays(int series, long data, String suffix, MetadataStore store) throws IOException {
    if (data == 0)
        return;
    String prefix = "Series " + series + " ";
    in.seek(data);
    int numberOfShapes = in.readInt();
    int size = in.readInt();
    if (size <= 194)
        return;
    in.skipBytes(20);
    boolean valid = in.readInt() == 1;
    in.skipBytes(164);
    for (int i = totalROIs; i < totalROIs + numberOfShapes; i++) {
        long offset = in.getFilePointer();
        int type = in.readInt();
        int blockLength = in.readInt();
        double lineWidth = in.readInt();
        int measurements = in.readInt();
        double textOffsetX = in.readDouble();
        double textOffsetY = in.readDouble();
        int color = in.readInt();
        boolean validShape = in.readInt() != 0;
        int knotWidth = in.readInt();
        int catchArea = in.readInt();
        int fontHeight = in.readInt();
        int fontWidth = in.readInt();
        int fontEscapement = in.readInt();
        int fontOrientation = in.readInt();
        int fontWeight = in.readInt();
        boolean fontItalic = in.readInt() != 0;
        boolean fontUnderlined = in.readInt() != 0;
        boolean fontStrikeout = in.readInt() != 0;
        int fontCharSet = in.readInt();
        int fontOutputPrecision = in.readInt();
        int fontClipPrecision = in.readInt();
        int fontQuality = in.readInt();
        int fontPitchAndFamily = in.readInt();
        String fontName = DataTools.stripString(in.readString(64));
        boolean enabled = in.readShort() == 0;
        boolean moveable = in.readInt() == 0;
        in.skipBytes(34);
        String roiID = MetadataTools.createLSID("ROI", i);
        String shapeID = MetadataTools.createLSID("Shape", i, 0);
        Length fontSize = FormatTools.getFontSize(fontHeight);
        Length line = new Length(lineWidth, UNITS.PIXEL);
        switch(type) {
            case TEXT:
                double x = in.readDouble();
                double y = in.readDouble();
                String text = DataTools.stripString(in.readCString());
                store.setROIID(roiID, i);
                store.setLabelID(shapeID, i, 0);
                store.setLabelX(x, i, 0);
                store.setLabelY(y, i, 0);
                store.setLabelText(text, i, 0);
                if (fontSize != null) {
                    store.setLabelFontSize(fontSize, i, 0);
                }
                store.setLabelStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case LINE:
                in.skipBytes(4);
                double startX = in.readDouble();
                double startY = in.readDouble();
                double endX = in.readDouble();
                double endY = in.readDouble();
                store.setROIID(roiID, i);
                store.setLineID(shapeID, i, 0);
                store.setLineX1(startX, i, 0);
                store.setLineY1(startY, i, 0);
                store.setLineX2(endX, i, 0);
                store.setLineY2(endY, i, 0);
                if (fontSize != null) {
                    store.setLineFontSize(fontSize, i, 0);
                }
                store.setLineStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case SCALE_BAR:
            case OPEN_ARROW:
            case CLOSED_ARROW:
            case PALETTE:
                in.skipBytes(36);
                i--;
                numberOfShapes--;
                break;
            case RECTANGLE:
                in.skipBytes(4);
                double topX = in.readDouble();
                double topY = in.readDouble();
                double bottomX = in.readDouble();
                double bottomY = in.readDouble();
                double width = Math.abs(bottomX - topX);
                double height = Math.abs(bottomY - topY);
                topX = Math.min(topX, bottomX);
                topY = Math.min(topY, bottomY);
                store.setROIID(roiID, i);
                store.setRectangleID(shapeID, i, 0);
                store.setRectangleX(topX, i, 0);
                store.setRectangleY(topY, i, 0);
                store.setRectangleWidth(width, i, 0);
                store.setRectangleHeight(height, i, 0);
                if (fontSize != null) {
                    store.setRectangleFontSize(fontSize, i, 0);
                }
                store.setRectangleStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case ELLIPSE:
                int knots = in.readInt();
                double[] xs = new double[knots];
                double[] ys = new double[knots];
                for (int j = 0; j < xs.length; j++) {
                    xs[j] = in.readDouble();
                    ys[j] = in.readDouble();
                }
                double rx = 0, ry = 0, centerX = 0, centerY = 0;
                store.setROIID(roiID, i);
                store.setEllipseID(shapeID, i, 0);
                if (knots == 4) {
                    double r1x = Math.abs(xs[2] - xs[0]) / 2;
                    double r1y = Math.abs(ys[2] - ys[0]) / 2;
                    double r2x = Math.abs(xs[3] - xs[1]) / 2;
                    double r2y = Math.abs(ys[3] - ys[1]) / 2;
                    if (r1x > r2x) {
                        ry = r1y;
                        rx = r2x;
                        centerX = Math.min(xs[3], xs[1]) + rx;
                        centerY = Math.min(ys[2], ys[0]) + ry;
                    } else {
                        ry = r2y;
                        rx = r1x;
                        centerX = Math.min(xs[2], xs[0]) + rx;
                        centerY = Math.min(ys[3], ys[1]) + ry;
                    }
                } else if (knots == 3) {
                    // we are given the center point and one cut point for each axis
                    centerX = xs[0];
                    centerY = ys[0];
                    rx = Math.sqrt(Math.pow(xs[1] - xs[0], 2) + Math.pow(ys[1] - ys[0], 2));
                    ry = Math.sqrt(Math.pow(xs[2] - xs[0], 2) + Math.pow(ys[2] - ys[0], 2));
                    // calculate rotation angle
                    double slope = (ys[2] - centerY) / (xs[2] - centerX);
                    double theta = Math.toDegrees(Math.atan(slope));
                    store.setEllipseTransform(getRotationTransform(theta), i, 0);
                }
                store.setEllipseX(centerX, i, 0);
                store.setEllipseY(centerY, i, 0);
                store.setEllipseRadiusX(rx, i, 0);
                store.setEllipseRadiusY(ry, i, 0);
                if (fontSize != null) {
                    store.setEllipseFontSize(fontSize, i, 0);
                }
                store.setEllipseStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case CIRCLE:
                in.skipBytes(4);
                centerX = in.readDouble();
                centerY = in.readDouble();
                double curveX = in.readDouble();
                double curveY = in.readDouble();
                double radius = Math.sqrt(Math.pow(curveX - centerX, 2) + Math.pow(curveY - centerY, 2));
                store.setROIID(roiID, i);
                store.setEllipseID(shapeID, i, 0);
                store.setEllipseX(centerX, i, 0);
                store.setEllipseY(centerY, i, 0);
                store.setEllipseRadiusX(radius, i, 0);
                store.setEllipseRadiusY(radius, i, 0);
                if (fontSize != null) {
                    store.setEllipseFontSize(fontSize, i, 0);
                }
                store.setEllipseStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case CIRCLE_3POINT:
                in.skipBytes(4);
                // given 3 points on the perimeter of the circle, we need to
                // calculate the center and radius
                double[][] points = new double[3][2];
                for (int j = 0; j < points.length; j++) {
                    for (int k = 0; k < points[j].length; k++) {
                        points[j][k] = in.readDouble();
                    }
                }
                double s = 0.5 * ((points[1][0] - points[2][0]) * (points[0][0] - points[2][0]) - (points[1][1] - points[2][1]) * (points[2][1] - points[0][1]));
                double div = (points[0][0] - points[1][0]) * (points[2][1] - points[0][1]) - (points[1][1] - points[0][1]) * (points[0][0] - points[2][0]);
                s /= div;
                double cx = 0.5 * (points[0][0] + points[1][0]) + s * (points[1][1] - points[0][1]);
                double cy = 0.5 * (points[0][1] + points[1][1]) + s * (points[0][0] - points[1][0]);
                double r = Math.sqrt(Math.pow(points[0][0] - cx, 2) + Math.pow(points[0][1] - cy, 2));
                store.setROIID(roiID, i);
                store.setEllipseID(shapeID, i, 0);
                store.setEllipseX(cx, i, 0);
                store.setEllipseY(cy, i, 0);
                store.setEllipseRadiusX(r, i, 0);
                store.setEllipseRadiusY(r, i, 0);
                if (fontSize != null) {
                    store.setEllipseFontSize(fontSize, i, 0);
                }
                store.setEllipseStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case ANGLE:
                in.skipBytes(4);
                points = new double[3][2];
                for (int j = 0; j < points.length; j++) {
                    for (int k = 0; k < points[j].length; k++) {
                        points[j][k] = in.readDouble();
                    }
                }
                StringBuilder p = new StringBuilder();
                for (int j = 0; j < points.length; j++) {
                    p.append(points[j][0]);
                    p.append(",");
                    p.append(points[j][1]);
                    if (j < points.length - 1)
                        p.append(" ");
                }
                store.setROIID(roiID, i);
                store.setPolylineID(shapeID, i, 0);
                store.setPolylinePoints(p.toString(), i, 0);
                if (fontSize != null) {
                    store.setPolylineFontSize(fontSize, i, 0);
                }
                store.setPolylineStrokeWidth(line, i, 0);
                store.setImageROIRef(roiID, series, i);
                break;
            case CLOSED_POLYLINE:
            case OPEN_POLYLINE:
            case POLYLINE_ARROW:
                int nKnots = in.readInt();
                points = new double[nKnots][2];
                for (int j = 0; j < points.length; j++) {
                    for (int k = 0; k < points[j].length; k++) {
                        points[j][k] = in.readDouble();
                    }
                }
                p = new StringBuilder();
                for (int j = 0; j < points.length; j++) {
                    p.append(points[j][0]);
                    p.append(",");
                    p.append(points[j][1]);
                    if (j < points.length - 1)
                        p.append(" ");
                }
                store.setROIID(roiID, i);
                if (type != CLOSED_POLYLINE) {
                    store.setPolylinePoints(p.toString(), i, 0);
                    if (fontSize != null) {
                        store.setPolylineFontSize(fontSize, i, 0);
                    }
                    store.setPolylineStrokeWidth(line, i, 0);
                    store.setPolylineID(shapeID, i, 0);
                } else {
                    store.setPolygonPoints(p.toString(), i, 0);
                    if (fontSize != null) {
                        store.setPolygonFontSize(fontSize, i, 0);
                    }
                    store.setPolygonStrokeWidth(line, i, 0);
                    store.setPolygonID(shapeID, i, 0);
                }
                store.setImageROIRef(roiID, series, i);
                break;
            case CLOSED_BEZIER:
            case OPEN_BEZIER:
            case BEZIER_WITH_ARROW:
                nKnots = in.readInt();
                points = new double[nKnots][2];
                for (int j = 0; j < points.length; j++) {
                    for (int k = 0; k < points[j].length; k++) {
                        points[j][k] = in.readDouble();
                    }
                }
                p = new StringBuilder();
                for (int j = 0; j < points.length; j++) {
                    p.append(points[j][0]);
                    p.append(",");
                    p.append(points[j][1]);
                    if (j < points.length - 1)
                        p.append(" ");
                }
                store.setROIID(roiID, i);
                if (type == OPEN_BEZIER) {
                    store.setPolylineID(shapeID, i, 0);
                    store.setPolylinePoints(p.toString(), i, 0);
                    if (fontSize != null) {
                        store.setPolylineFontSize(fontSize, i, 0);
                    }
                    store.setPolylineStrokeWidth(line, i, 0);
                } else {
                    store.setPolygonID(shapeID, i, 0);
                    store.setPolygonPoints(p.toString(), i, 0);
                    if (fontSize != null) {
                        store.setPolygonFontSize(fontSize, i, 0);
                    }
                    store.setPolygonStrokeWidth(line, i, 0);
                }
                store.setImageROIRef(roiID, series, i);
                break;
            default:
                i--;
                numberOfShapes--;
                continue;
        }
        // populate shape attributes
        in.seek(offset + blockLength);
    }
    totalROIs += numberOfShapes;
}

Example 37 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class VarianFDFReader method parseFDF.

// -- Helper methods --
private void parseFDF(String file) throws FormatException, IOException {
    in = new RandomAccessInputStream(file);
    CoreMetadata m = core.get(0);
    boolean storedFloats = false;
    boolean multifile = false;
    String data = in.readString(Character.toString((char) 0x0c));
    String[] lines = data.split("\n");
    for (String line : lines) {
        line = line.trim();
        if (line.length() == 0)
            break;
        if (line.startsWith("#"))
            continue;
        int space = line.indexOf(' ');
        int eq = line.indexOf('=');
        String type = line.substring(0, space).trim();
        String var = line.substring(space, eq).trim();
        String value = line.substring(eq + 1, line.indexOf(';')).trim();
        if (var.equals("*storage")) {
            storedFloats = value.equals("\"float\"");
        }
        if (var.equals("bits")) {
            m.bitsPerPixel = Integer.parseInt(value);
            if (value.equals("8")) {
                m.pixelType = FormatTools.UINT8;
            } else if (value.equals("16")) {
                m.pixelType = FormatTools.UINT16;
            } else if (value.equals("32")) {
                if (storedFloats) {
                    m.pixelType = FormatTools.FLOAT;
                } else
                    m.pixelType = FormatTools.UINT32;
            } else
                throw new FormatException("Unsupported bits: " + value);
        } else if (var.equals("matrix[]")) {
            String[] values = parseArray(value);
            m.sizeX = (int) Double.parseDouble(values[0]);
            m.sizeY = (int) Double.parseDouble(values[1]);
            if (values.length > 2) {
                m.sizeZ = (int) Double.parseDouble(values[2]);
            }
        } else if (var.equals("slices")) {
            m.sizeZ = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("echoes")) {
            m.sizeT = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("span[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                pixelSizeX = computePhysicalSize(getSizeX(), values[0], units[0]);
            }
            if (values.length > 1) {
                pixelSizeY = computePhysicalSize(getSizeY(), values[1], units[1]);
            }
            if (values.length > 2) {
                pixelSizeZ = computePhysicalSize(getSizeZ(), values[2], units[2]);
            }
        } else if (var.equals("origin[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                final double size = computePhysicalSize(1, values[0], units[0]);
                originX = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("X position for position #1", originX);
            }
            if (values.length > 1) {
                final double size = computePhysicalSize(1, values[1], units[1]);
                originY = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Y position for position #1", originY);
            }
            if (values.length > 2) {
                final double size = computePhysicalSize(1, values[2], units[2]);
                originZ = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Z position for position #1", originZ);
            }
        } else if (var.equals("*abscissa[]")) {
            units = parseArray(value);
        } else if (var.equals("bigendian")) {
            m.littleEndian = value.equals("0");
            in.order(isLittleEndian());
        }
        addGlobalMeta(var, value);
    }
    if (multifile && files.isEmpty()) {
        Location thisFile = new Location(file).getAbsoluteFile();
        Location parent = thisFile.getParentFile();
        String[] list = parent.list(true);
        Arrays.sort(list);
        for (String f : list) {
            if (checkSuffix(f, "fdf") && f.length() == thisFile.getName().length()) {
                files.add(new Location(parent, f).getAbsolutePath());
            }
        }
    }
}

Example 38 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class VarianFDFReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    CoreMetadata m = core.get(0);
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    parseFDF(id);
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    m.dimensionOrder = "XYTZC";
    if (files.size() > getImageCount()) {
        int rem = files.size() / getImageCount();
        m.sizeT *= rem;
        m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    }
    pixelOffsets = new long[getImageCount()];
    int planeSize = FormatTools.getPlaneSize(this);
    for (int i = 0; i < pixelOffsets.length; i++) {
        if (files.size() > 1) {
            in.close();
            in = new RandomAccessInputStream(files.get(i));
            pixelOffsets[i] = in.length() - planeSize;
        } else {
            pixelOffsets[i] = in.length() - (planeSize * (getImageCount() - i));
        }
    }
    boolean minMetadata = getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, !minMetadata);
    if (!minMetadata) {
        Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
        Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
        Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
        for (int i = 0; i < getImageCount(); i++) {
            store.setPlanePositionX(originX, 0, i);
            store.setPlanePositionY(originY, 0, i);
            store.setPlanePositionZ(originZ, 0, i);
        }
    }
}

Example 39 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class ScanrReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (metadataFiles.size() > 0) {
        // this dataset has already been initialized
        return;
    }
    // make sure we have the .xml file
    if (!checkSuffix(id, "xml") && isGroupFiles()) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        if (checkSuffix(id, "tif") && parent.getName().equalsIgnoreCase("Data")) {
            parent = parent.getParentFile();
        }
        String[] list = parent.list();
        for (String file : list) {
            if (file.equals(XML_FILE)) {
                id = new Location(parent, file).getAbsolutePath();
                super.initFile(id);
                break;
            }
        }
        if (!checkSuffix(id, "xml")) {
            throw new FormatException("Could not find " + XML_FILE + " in " + parent.getAbsolutePath());
        }
    } else if (!isGroupFiles() && checkSuffix(id, "tif")) {
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(id);
        core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
        metadataStore = r.getMetadataStore();
        final Map<String, Object> globalMetadata = r.getGlobalMetadata();
        for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
            addGlobalMeta(entry.getKey(), entry.getValue());
        }
        r.close();
        tiffs = new String[] { id };
        reader = new MinimalTiffReader();
        return;
    }
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    String[] list = dir.list(true);
    for (String file : list) {
        Location f = new Location(dir, file);
        if (checkSuffix(file, METADATA_SUFFIXES) && !f.isDirectory()) {
            metadataFiles.add(f.getAbsolutePath());
        }
    }
    // parse XML metadata
    String xml = DataTools.readFile(id).trim();
    if (xml.startsWith("<?")) {
        xml = xml.substring(xml.indexOf("?>") + 2);
    }
    xml = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + xml;
    XMLTools.parseXML(xml, new ScanrHandler());
    final List<String> uniqueRows = new ArrayList<String>();
    final List<String> uniqueColumns = new ArrayList<String>();
    if (wellRows == 0 || wellColumns == 0) {
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            String row = well.substring(0, 1).trim();
            String column = well.substring(1).trim();
            if (!uniqueRows.contains(row) && row.length() > 0)
                uniqueRows.add(row);
            if (!uniqueColumns.contains(column) && column.length() > 0) {
                uniqueColumns.add(column);
            }
        }
        wellRows = uniqueRows.size();
        wellColumns = uniqueColumns.size();
        if (wellRows * wellColumns != wellCount) {
            adjustWellDimensions();
        }
    }
    int nChannels = getSizeC() == 0 ? channelNames.size() : (int) Math.min(channelNames.size(), getSizeC());
    if (nChannels == 0)
        nChannels = 1;
    int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
    int nTimepoints = getSizeT();
    int nWells = wellCount;
    int nPos = 0;
    if (foundPositions)
        nPos = fieldPositionX.length;
    else
        nPos = fieldRows * fieldColumns;
    if (nPos == 0)
        nPos = 1;
    // get list of TIFF files
    Location dataDir = new Location(dir, "data");
    list = dataDir.list(true);
    if (list == null) {
        // try to find the TIFFs in the current directory
        list = dir.list(true);
    } else
        dir = dataDir;
    if (nTimepoints == 0 || list.length < nTimepoints * nChannels * nSlices * nWells * nPos) {
        nTimepoints = list.length / (nChannels * nWells * nPos * nSlices);
        if (nTimepoints == 0)
            nTimepoints = 1;
    }
    tiffs = new String[nChannels * nWells * nPos * nTimepoints * nSlices];
    Arrays.sort(list, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            int lastSeparator1 = s1.lastIndexOf(File.separator) + 1;
            int lastSeparator2 = s2.lastIndexOf(File.separator) + 1;
            String dir1 = s1.substring(0, lastSeparator1);
            String dir2 = s2.substring(0, lastSeparator2);
            if (!dir1.equals(dir2)) {
                return dir1.compareTo(dir2);
            }
            int dash1 = s1.indexOf("-", lastSeparator1);
            int dash2 = s2.indexOf("-", lastSeparator2);
            String label1 = dash1 < 0 ? "" : s1.substring(lastSeparator1, dash1);
            String label2 = dash2 < 0 ? "" : s2.substring(lastSeparator2, dash2);
            if (label1.equals(label2)) {
                String remainder1 = dash1 < 0 ? s1 : s1.substring(dash1);
                String remainder2 = dash2 < 0 ? s2 : s2.substring(dash2);
                return remainder1.compareTo(remainder2);
            }
            Integer index1 = wellLabels.get(label1);
            Integer index2 = wellLabels.get(label2);
            if (index1 == null && index2 != null) {
                return 1;
            } else if (index1 != null && index2 == null) {
                return -1;
            }
            return index1.compareTo(index2);
        }
    });
    int lastListIndex = 0;
    int next = 0;
    String[] keys = wellLabels.keySet().toArray(new String[wellLabels.size()]);
    Arrays.sort(keys, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            char row1 = s1.charAt(0);
            char row2 = s2.charAt(0);
            final Integer col1 = new Integer(s1.substring(1));
            final Integer col2 = new Integer(s2.substring(1));
            if (row1 < row2) {
                return -1;
            } else if (row1 > row2) {
                return 1;
            }
            return col1.compareTo(col2);
        }
    });
    int realPosCount = 0;
    for (int well = 0; well < nWells; well++) {
        int missingWellFiles = 0;
        int wellIndex = wellNumbers.get(well);
        String wellPos = getBlock(wellIndex, "W");
        int originalIndex = next;
        for (int pos = 0; pos < nPos; pos++) {
            String posPos = getBlock(pos + 1, "P");
            int posIndex = next;
            for (int z = 0; z < nSlices; z++) {
                String zPos = getBlock(z, "Z");
                for (int t = 0; t < nTimepoints; t++) {
                    String tPos = getBlock(t, "T");
                    for (int c = 0; c < nChannels; c++) {
                        for (int i = lastListIndex; i < list.length; i++) {
                            String file = list[i];
                            if (file.indexOf(wellPos) != -1 && file.indexOf(zPos) != -1 && file.indexOf(posPos) != -1 && file.indexOf(tPos) != -1 && file.indexOf(channelNames.get(c)) != -1) {
                                tiffs[next++] = new Location(dir, file).getAbsolutePath();
                                if (c == nChannels - 1) {
                                    lastListIndex = i;
                                }
                                break;
                            }
                        }
                        if (next == originalIndex) {
                            missingWellFiles++;
                        }
                    }
                }
            }
            if (posIndex != next)
                realPosCount++;
        }
        if (next == originalIndex && well < keys.length) {
            wellLabels.remove(keys[well]);
        }
        if (next == originalIndex && missingWellFiles == nSlices * nTimepoints * nChannels * nPos) {
            wellNumbers.remove(well);
        }
    }
    nWells = wellNumbers.size();
    if (wellLabels.size() > 0 && wellLabels.size() != nWells) {
        uniqueRows.clear();
        uniqueColumns.clear();
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            String row = well.substring(0, 1).trim();
            String column = well.substring(1).trim();
            if (!uniqueRows.contains(row) && row.length() > 0)
                uniqueRows.add(row);
            if (!uniqueColumns.contains(column) && column.length() > 0) {
                uniqueColumns.add(column);
            }
        }
        nWells = uniqueRows.size() * uniqueColumns.size();
        adjustWellDimensions();
    }
    if (realPosCount < nPos) {
        nPos = realPosCount;
    }
    reader = new MinimalTiffReader();
    reader.setId(tiffs[0]);
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int pixelType = reader.getPixelType();
    tileWidth = reader.getOptimalTileWidth();
    tileHeight = reader.getOptimalTileHeight();
    switch(pixelType) {
        case FormatTools.INT8:
            pixelType = FormatTools.UINT8;
            break;
        case FormatTools.INT16:
            pixelType = FormatTools.UINT16;
            break;
    }
    boolean rgb = reader.isRGB();
    boolean interleaved = reader.isInterleaved();
    boolean indexed = reader.isIndexed();
    boolean littleEndian = reader.isLittleEndian();
    reader.close();
    int seriesCount = nWells * nPos;
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeC = nChannels;
        ms.sizeZ = nSlices;
        ms.sizeT = nTimepoints;
        ms.sizeX = sizeX;
        ms.sizeY = sizeY;
        ms.pixelType = pixelType;
        ms.rgb = rgb;
        ms.interleaved = interleaved;
        ms.indexed = indexed;
        ms.littleEndian = littleEndian;
        ms.dimensionOrder = "XYCTZ";
        ms.imageCount = nSlices * nTimepoints * nChannels;
        ms.bitsPerPixel = 12;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateColumns(new PositiveInteger(wellColumns), 0);
    store.setPlateRows(new PositiveInteger(wellRows), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    int nFields = 0;
    if (foundPositions) {
        nFields = fieldPositionX.length;
    } else {
        nFields = fieldRows * fieldColumns;
    }
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(nFields);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int field = i % nFields;
        int well = i / nFields;
        int index = well;
        while (wellNumbers.get(index) == null && index < wellNumbers.size()) {
            index++;
        }
        int wellIndex = wellNumbers.get(index) == null ? index : wellNumbers.get(index) - 1;
        int wellRow = wellIndex / wellColumns;
        int wellCol = wellIndex % wellColumns;
        if (field == 0) {
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellColumn(new NonNegativeInteger(wellCol), 0, well);
            store.setWellRow(new NonNegativeInteger(wellRow), 0, well);
        }
        String wellSample = MetadataTools.createLSID("WellSample", 0, well, field);
        store.setWellSampleID(wellSample, 0, well, field);
        store.setWellSampleIndex(new NonNegativeInteger(i), 0, well, field);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setWellSampleImageRef(imageID, 0, well, field);
        store.setImageID(imageID, i);
        String name = "Well " + (well + 1) + ", Field " + (field + 1) + " (Spot " + (i + 1) + ")";
        store.setImageName(name, i);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < getSeriesCount(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                store.setChannelName(channelNames.get(c), i, c);
            }
            Length x = FormatTools.getPhysicalSizeX(pixelSize);
            Length y = FormatTools.getPhysicalSizeY(pixelSize);
            if (x != null) {
                store.setPixelsPhysicalSizeX(x, i);
            }
            if (y != null) {
                store.setPixelsPhysicalSizeY(y, i);
            }
            if (fieldPositionX != null && fieldPositionY != null) {
                int field = i % nFields;
                int well = i / nFields;
                final Length posX = fieldPositionX[field];
                final Length posY = fieldPositionY[field];
                store.setWellSamplePositionX(posX, 0, well, field);
                store.setWellSamplePositionY(posY, 0, well, field);
                for (int c = 0; c < getSizeC(); c++) {
                    int image = getIndex(0, c, 0);
                    store.setPlaneTheZ(new NonNegativeInteger(0), i, image);
                    store.setPlaneTheC(new NonNegativeInteger(c), i, image);
                    store.setPlaneTheT(new NonNegativeInteger(0), i, image);
                    store.setPlanePositionX(fieldPositionX[field], i, image);
                    store.setPlanePositionY(fieldPositionY[field], i, image);
                    // exposure time is stored in milliseconds
                    // convert to seconds before populating MetadataStore
                    Double time = exposures.get(c);
                    if (time != null) {
                        time /= 1000;
                        store.setPlaneExposureTime(new Time(time, UNITS.SECOND), i, image);
                    }
                    if (deltaT != null) {
                        store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), i, image);
                    }
                }
            }
        }
        String row = wellRows > 26 ? "Number" : "Letter";
        String col = wellRows > 26 ? "Letter" : "Number";
        store.setPlateRowNamingConvention(getNamingConvention(row), 0);
        store.setPlateColumnNamingConvention(getNamingConvention(col), 0);
        store.setPlateName(plateName, 0);
    }
}

Example 40 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class ColumbusReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
    Location xml = findXML(id);
    if (null == xml) {
        throw new FormatException("Could not find " + XML_FILE);
    }
    id = xml.getAbsolutePath();
    super.initFile(id);
    Location parent = new Location(currentId).getAbsoluteFile().getParentFile();
    // parse plate layout and image dimensions from the XML files
    String xmlData = DataTools.readFile(id);
    MeasurementHandler handler = new MeasurementHandler();
    XMLTools.parseXML(xmlData, handler);
    String[] parentDirectories = parent.list(true);
    Arrays.sort(parentDirectories);
    ArrayList<String> timepointDirs = new ArrayList<String>();
    for (String file : parentDirectories) {
        Location absFile = new Location(parent, file);
        if (absFile.isDirectory()) {
            timepointDirs.add(absFile.getAbsolutePath());
            for (String f : absFile.list(true)) {
                if (!checkSuffix(f, "tif")) {
                    if (!metadataFiles.contains(file + File.separator + f)) {
                        metadataFiles.add(file + File.separator + f);
                    }
                }
            }
        }
    }
    for (int i = 0; i < metadataFiles.size(); i++) {
        String metadataFile = metadataFiles.get(i);
        int end = metadataFile.indexOf(File.separator);
        String timepointPath = end < 0 ? "" : parent + File.separator + metadataFile.substring(0, end);
        Location f = new Location(parent + File.separator + metadataFile);
        if (!f.exists()) {
            metadataFile = metadataFile.substring(end + 1);
            f = new Location(parent, metadataFile);
        }
        String path = f.getAbsolutePath();
        metadataFiles.set(i, path);
        if (checkSuffix(path, "columbusidx.xml")) {
            int timepoint = timepointDirs.indexOf(timepointPath);
            if (timepointDirs.size() == 0) {
                timepoint = 0;
            }
            parseImageXML(path, timepoint);
        }
    }
    // process plane list to determine plate size
    Comparator<Plane> planeComp = new Comparator<Plane>() {

        public int compare(Plane p1, Plane p2) {
            if (p1.row != p2.row) {
                return p1.row - p2.row;
            }
            if (p1.col != p2.col) {
                return p1.col - p2.col;
            }
            if (p1.field != p2.field) {
                return p1.field - p2.field;
            }
            if (p1.timepoint != p2.timepoint) {
                return p1.timepoint - p2.timepoint;
            }
            if (p1.channel != p2.channel) {
                return p1.channel - p2.channel;
            }
            return 0;
        }
    };
    Plane[] tmpPlanes = planes.toArray(new Plane[planes.size()]);
    Arrays.sort(tmpPlanes, planeComp);
    planes.clear();
    reader = new MinimalTiffReader();
    reader.setId(tmpPlanes[0].file);
    core = reader.getCoreMetadataList();
    CoreMetadata m = core.get(0);
    m.sizeC = 0;
    m.sizeT = 0;
    ArrayList<Integer> uniqueSamples = new ArrayList<Integer>();
    ArrayList<Integer> uniqueRows = new ArrayList<Integer>();
    ArrayList<Integer> uniqueCols = new ArrayList<Integer>();
    for (Plane p : tmpPlanes) {
        planes.add(p);
        int sampleIndex = p.row * handler.getPlateColumns() + p.col;
        if (!uniqueSamples.contains(sampleIndex)) {
            uniqueSamples.add(sampleIndex);
        }
        if (!uniqueRows.contains(p.row)) {
            uniqueRows.add(p.row);
        }
        if (!uniqueCols.contains(p.col)) {
            uniqueCols.add(p.col);
        }
        // counts are assumed to be non-sparse
        if (p.field >= nFields) {
            nFields = p.field + 1;
        }
        if (p.channel >= getSizeC()) {
            m.sizeC = p.channel + 1;
        }
        if (p.timepoint >= getSizeT()) {
            m.sizeT = p.timepoint + 1;
        }
    }
    m.sizeZ = 1;
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    m.dimensionOrder = "XYCTZ";
    m.rgb = false;
    int seriesCount = uniqueSamples.size() * nFields;
    for (int i = 1; i < seriesCount; i++) {
        core.add(m);
    }
    // populate the MetadataStore
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    store.setScreenID(MetadataTools.createLSID("Screen", 0), 0);
    store.setScreenName(handler.getScreenName(), 0);
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateName(handler.getPlateName(), 0);
    store.setPlateRows(new PositiveInteger(handler.getPlateRows()), 0);
    store.setPlateColumns(new PositiveInteger(handler.getPlateColumns()), 0);
    String imagePrefix = handler.getPlateName() + " Well ";
    int wellSample = 0;
    int nextWell = -1;
    Timestamp date = new Timestamp(acquisitionDate);
    long timestampSeconds = date.asInstant().getMillis() / 1000;
    for (Integer row : uniqueRows) {
        for (Integer col : uniqueCols) {
            if (!uniqueSamples.contains(row * handler.getPlateColumns() + col)) {
                continue;
            }
            nextWell++;
            store.setWellID(MetadataTools.createLSID("Well", 0, nextWell), 0, nextWell);
            store.setWellRow(new NonNegativeInteger(row), 0, nextWell);
            store.setWellColumn(new NonNegativeInteger(col), 0, nextWell);
            for (int field = 0; field < nFields; field++) {
                Plane p = lookupPlane(row, col, field, 0, 0);
                String wellSampleID = MetadataTools.createLSID("WellSample", 0, nextWell, field);
                store.setWellSampleID(wellSampleID, 0, nextWell, field);
                store.setWellSampleIndex(new NonNegativeInteger(wellSample), 0, nextWell, field);
                if (p != null) {
                    store.setWellSamplePositionX(new Length(p.positionX, UNITS.REFERENCEFRAME), 0, nextWell, field);
                    store.setWellSamplePositionY(new Length(p.positionY, UNITS.REFERENCEFRAME), 0, nextWell, field);
                }
                String imageID = MetadataTools.createLSID("Image", wellSample);
                store.setImageID(imageID, wellSample);
                store.setWellSampleImageRef(imageID, 0, nextWell, field);
                store.setImageName(imagePrefix + (char) (row + 'A') + (col + 1) + " Field #" + (field + 1), wellSample);
                store.setImageAcquisitionDate(date, wellSample);
                if (p != null) {
                    p.series = wellSample;
                    store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(p.sizeX), p.series);
                    store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(p.sizeY), p.series);
                    for (int c = 0; c < getSizeC(); c++) {
                        p = lookupPlane(row, col, field, 0, c);
                        if (p != null) {
                            p.series = wellSample;
                            store.setChannelName(p.channelName, p.series, p.channel);
                            if ((int) p.emWavelength > 0) {
                                store.setChannelEmissionWavelength(FormatTools.getEmissionWavelength(p.emWavelength), p.series, p.channel);
                            }
                            if ((int) p.exWavelength > 0) {
                                store.setChannelExcitationWavelength(FormatTools.getExcitationWavelength(p.exWavelength), p.series, p.channel);
                            }
                            store.setChannelColor(p.channelColor, p.series, p.channel);
                        }
                        for (int t = 0; t < getSizeT(); t++) {
                            p = lookupPlane(row, col, field, t, c);
                            if (p != null) {
                                p.series = wellSample;
                                store.setPlaneDeltaT(new Time(p.deltaT - timestampSeconds, UNITS.SECOND), p.series, getIndex(0, c, t));
                            }
                        }
                    }
                }
                wellSample++;
            }
        }
    }
}