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

Example 56 with Length

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

the class ROIHandler method storeText.

/**
 * Stores the text ROI into the metadata stored.
 *
 * @param roi The roi to convert.
 * @param store The store to handle.
 * @param roiNum The roi number
 * @param shape The index of the shape.
 * @param c The selected channel.
 * @param z The selected slice.
 * @param t The selected timepoint.
 */
private static void storeText(TextRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) {
    store.setLabelX(roi.getPolygon().getBounds().getX(), roiNum, shape);
    store.setLabelY(roi.getPolygon().getBounds().getY(), roiNum, shape);
    store.setLabelText(roi.getText().trim(), roiNum, shape);
    store.setLabelFontSize(new Length(roi.getCurrentFont().getSize(), UNITS.PIXEL), roiNum, shape);
    if (c >= 0) {
        store.setLabelTheC(unwrap(c), roiNum, shape);
    }
    if (z >= 0) {
        store.setLabelTheZ(unwrap(z), roiNum, shape);
    }
    if (t >= 0) {
        store.setLabelTheT(unwrap(t), roiNum, shape);
    }
    if (roi.getStrokeWidth() > 0) {
        store.setLabelStrokeWidth(new Length((roi.getStrokeWidth()), UNITS.PIXEL), roiNum, shape);
    }
    if (roi.getStrokeColor() != null) {
        store.setLabelStrokeColor(toOMExmlColor(roi.getStrokeColor()), roiNum, shape);
    }
    if (roi.getFillColor() != null) {
        store.setLabelFillColor(toOMExmlColor(roi.getFillColor()), roiNum, shape);
    }
}

Example 57 with Length

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

the class ROIHandler method storePolygon.

/**
 * Stores the Polygon ROI into the specified metadata store.
 *
 * @param roi The roi to convert.
 * @param store The store to handle.
 * @param roiNum The roi number
 * @param shape The index of the shape.
 * @param c The selected channel.
 * @param z The selected slice.
 * @param t The selected timepoint.
 */
private static void storePolygon(PolygonRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) {
    int[] xCoordinates = roi.getPolygon().xpoints;
    int[] yCoordinates = roi.getPolygon().ypoints;
    String st1 = roi.getTypeAsString();
    String points = "1";
    for (int i = 0; i < xCoordinates.length; i++) {
        if (i == 0) {
            points = (xCoordinates[i] + "," + yCoordinates[i]);
        } else {
            points = (points + " " + xCoordinates[i] + "," + yCoordinates[i]);
        }
    }
    if (st1.matches("Polyline") || st1.matches("Freeline") || st1.matches("Angle")) {
        store.setPolylinePoints(points.toString(), roiNum, shape);
        store.setPolylineText(roi.getName(), roiNum, shape);
        if (c >= 0) {
            store.setPolylineTheC(unwrap(c), roiNum, shape);
        }
        if (z >= 0) {
            store.setPolylineTheZ(unwrap(z), roiNum, shape);
        }
        if (t >= 0) {
            store.setPolylineTheT(unwrap(t), roiNum, shape);
        }
        if (roi.getStrokeWidth() > 0) {
            store.setPolylineStrokeWidth(new Length((roi.getStrokeWidth()), UNITS.PIXEL), roiNum, shape);
        }
        if (roi.getStrokeColor() != null) {
            store.setPolylineStrokeColor(toOMExmlColor(roi.getStrokeColor()), roiNum, shape);
        }
        if (roi.getFillColor() != null) {
            store.setPolylineFillColor(toOMExmlColor(roi.getFillColor()), roiNum, shape);
        }
    } else if (st1.matches("Polygon") || st1.matches("Freehand") || st1.matches("Traced")) {
        store.setPolygonPoints(points.toString(), roiNum, shape);
        store.setPolygonText(roi.getName(), roiNum, shape);
        if (c >= 0) {
            store.setPolygonTheC(unwrap(c), roiNum, shape);
        }
        if (z >= 0) {
            store.setPolygonTheZ(unwrap(z), roiNum, shape);
        }
        if (t >= 0) {
            store.setPolygonTheT(unwrap(t), roiNum, shape);
        }
        if (roi.getStrokeWidth() > 0) {
            store.setPolygonStrokeWidth(new Length((roi.getStrokeWidth()), UNITS.PIXEL), roiNum, shape);
        }
        if (roi.getStrokeColor() != null) {
            store.setPolygonStrokeColor(toOMExmlColor(roi.getStrokeColor()), roiNum, shape);
        }
        if (roi.getFillColor() != null) {
            store.setPolygonFillColor(toOMExmlColor(roi.getFillColor()), roiNum, shape);
        }
    }
}

Example 58 with Length

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

the class ROIHandler method storeOval.

/**
 * Stores the Oval ROI into the specified metadata store.
 *
 * @param roi The roi to convert.
 * @param store The store to handle.
 * @param roiNum The roi number
 * @param shape The index of the shape.
 * @param c The selected channel.
 * @param z The selected slice.
 * @param t The selected timepoint.
 */
private static void storeOval(OvalRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) {
    Rectangle vnRectBounds = roi.getPolygon().getBounds();
    int x = vnRectBounds.x;
    int y = vnRectBounds.y;
    double rx = vnRectBounds.getWidth();
    double ry = vnRectBounds.getHeight();
    store.setEllipseX(((double) x + rx / 2), roiNum, shape);
    store.setEllipseY(((double) y + ry / 2), roiNum, shape);
    store.setEllipseRadiusX((double) rx / 2, roiNum, shape);
    store.setEllipseRadiusY((double) ry / 2, roiNum, shape);
    store.setEllipseText(roi.getName(), roiNum, shape);
    if (c >= 0) {
        store.setEllipseTheC(unwrap(c), roiNum, shape);
    }
    if (z >= 0) {
        store.setEllipseTheZ(unwrap(z), roiNum, shape);
    }
    if (t >= 0) {
        store.setEllipseTheT(unwrap(t), roiNum, shape);
    }
    if (roi.getStrokeWidth() > 0) {
        store.setEllipseStrokeWidth(new Length((roi.getStrokeWidth()), UNITS.PIXEL), roiNum, shape);
    }
    if (roi.getStrokeColor() != null) {
        store.setEllipseStrokeColor(toOMExmlColor(roi.getStrokeColor()), roiNum, shape);
    }
    if (roi.getFillColor() != null) {
        store.setEllipseFillColor(toOMExmlColor(roi.getFillColor()), roiNum, shape);
    }
}

Example 59 with Length

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

the class FormatTools method getPhysicalSize.

public static Length getPhysicalSize(Double value, String unit) {
    if (value != null && value != 0 && value < Double.POSITIVE_INFINITY) {
        if (unit != null) {
            try {
                UnitsLength ul = UnitsLength.fromString(unit);
                int ordinal = ul.ordinal();
                Length returnLength = UnitsLength.create(value, ul);
                if (returnLength.value().doubleValue() > Constants.EPSILON && returnLength.value().doubleValue() < Double.POSITIVE_INFINITY) {
                    return returnLength;
                }
                // Using UnitsLength.values().length - 2 as a boundary so as not to include Pixel and Reference Frame as convertible units
                while (returnLength.value().doubleValue() < Constants.EPSILON && ordinal < (UnitsLength.values().length - 3)) {
                    ordinal++;
                    ul = UnitsLength.values()[ordinal];
                    Length tempLength = UnitsLength.create(0, ul);
                    returnLength = UnitsLength.create(returnLength.value(tempLength.unit()), ul);
                }
                if (returnLength.value().doubleValue() > Constants.EPSILON && returnLength.value().doubleValue() < Double.POSITIVE_INFINITY) {
                    return returnLength;
                } else {
                    LOGGER.debug("Expected positive value for PhysicalSize; got {}", value);
                    return null;
                }
            } catch (EnumerationException e) {
            }
        }
        return new Length(value, UNITS.MICROMETER);
    }
    LOGGER.debug("Expected positive value for PhysicalSize; got {}", value);
    return null;
}

Example 60 with Length

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

the class LociFunctions method getPixelsPhysicalSizeX.

public void getPixelsPhysicalSizeX(Double[] sizeX) {
    int imageIndex = r.getSeries();
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Length x = retrieve.getPixelsPhysicalSizeX(imageIndex);
    if (x != null) {
        sizeX[0] = x.value(UNITS.MICROMETER).doubleValue();
    }
    if (sizeX[0] == null)
        sizeX[0] = new Double(Double.NaN);
}