private static double getPosition( final Length planePos, final Length stageLabel, final boolean invert ) { // check plane position if ( planePos != null ) return invert ? -planePos.value().doubleValue() : planePos.value().doubleValue(); // check global stage label if ( stageLabel != null ) return invert ? -stageLabel.value().doubleValue() : stageLabel.value().doubleValue(); return 0; }
/** * Helper method to extract values out of {@link PositiveFloat}s, for * physical pixel sizes (calibration values). Returns 1.0 if given a null or * invalid (< 0) calibration. */ private double getValue(final Length pixelPhysicalSize) { if (pixelPhysicalSize == null) return 1.0; final Double physSize = pixelPhysicalSize.value().doubleValue(); return physSize < 0 ? 1.0 : physSize; }
private double checkValue(final Length l) { return l == null ? 1.0 : l.value().doubleValue(); } }
/** * Calibrates the given axis if the physical pixel size is non-null * @param stageLabel */ private static void calibrate(Length pixelsPhysicalSize, CalibratedAxis axis, Length stageLabel) { if (pixelsPhysicalSize != null) { FormatTools.calibrate(axis, pixelsPhysicalSize.value().doubleValue(), stageLabel == null ? 0.0 : stageLabel.value().doubleValue()); } }
/** * Check quantities for equality. * * Unit conversion will be performed when required to convert into * the unit system of this quantity in order to perform the * comparison. * * Note that floating point comparison is dangerous. Do not use * this method. * * @return true if equal, false if not equal. */ @Override public int compareTo(Length other) { if (this == other) { return 0; } return Double.compare(value.doubleValue(), other.value(unit).doubleValue()); }
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); }
public void getPixelsPhysicalSizeY(Double[] sizeY) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length y = retrieve.getPixelsPhysicalSizeY(imageIndex); if (y != null) { sizeY[0] = y.value(UNITS.MICROMETER).doubleValue(); } if (sizeY[0] == null) sizeY[0] = new Double(Double.NaN); }
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); }
public void getPixelsPhysicalSizeY(Double[] sizeY) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length y = retrieve.getPixelsPhysicalSizeY(imageIndex); if (y != null) { sizeY[0] = y.value(UNITS.MICROMETER).doubleValue(); } if (sizeY[0] == null) sizeY[0] = new Double(Double.NaN); }
public void getPixelsPhysicalSizeZ(Double[] sizeZ) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length z = retrieve.getPixelsPhysicalSizeZ(imageIndex); if (z != null) { sizeZ[0] = z.value(UNITS.MICROMETER).doubleValue(); } if (sizeZ[0] == null) sizeZ[0] = new Double(Double.NaN); }
public void getPixelsPhysicalSizeZ(Double[] sizeZ) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length z = retrieve.getPixelsPhysicalSizeZ(imageIndex); if (z != null) { sizeZ[0] = z.value(UNITS.MICROMETER).doubleValue(); } if (sizeZ[0] == null) sizeZ[0] = new Double(Double.NaN); }
public void getPlanePositionX(Double[] positionX, Double no) { int imageIndex = r.getSeries(); int planeIndex = getPlaneIndex(r, no.intValue()); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length val = null; if (planeIndex >= 0) { val = retrieve.getPlanePositionX(imageIndex, planeIndex); } positionX[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue(); }
public void getPlanePositionX(Double[] positionX, Double no) { int imageIndex = r.getSeries(); int planeIndex = getPlaneIndex(r, no.intValue()); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length val = null; if (planeIndex >= 0) { val = retrieve.getPlanePositionX(imageIndex, planeIndex); } positionX[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue(); }
public Length(ome.units.quantity.Length value) { this(value.value().doubleValue(), UnitsLength.bySymbol(value.unit().getSymbol())); }
public void getPlanePositionZ(Double[] positionZ, Double no) { int imageIndex = r.getSeries(); int planeIndex = getPlaneIndex(r, no.intValue()); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length val = null; if (planeIndex >= 0) { val = retrieve.getPlanePositionZ(imageIndex, planeIndex); } if (val == null) { val = new Length(Double.NaN, UNITS.REFERENCEFRAME); } positionZ[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue(); }
public void getPlanePositionY(Double[] positionY, Double no) { int imageIndex = r.getSeries(); int planeIndex = getPlaneIndex(r, no.intValue()); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length val = null; if (planeIndex >= 0) { val = retrieve.getPlanePositionY(imageIndex, planeIndex); } if (val == null) { val = new Length(Double.NaN, UNITS.REFERENCEFRAME); } positionY[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue(); }
public void getPlanePositionY(Double[] positionY, Double no) { int imageIndex = r.getSeries(); int planeIndex = getPlaneIndex(r, no.intValue()); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length val = null; if (planeIndex >= 0) { val = retrieve.getPlanePositionY(imageIndex, planeIndex); } if (val == null) { val = new Length(Double.NaN, UNITS.REFERENCEFRAME); } positionY[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue(); }
public void getPlanePositionZ(Double[] positionZ, Double no) { int imageIndex = r.getSeries(); int planeIndex = getPlaneIndex(r, no.intValue()); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length val = null; if (planeIndex >= 0) { val = retrieve.getPlanePositionZ(imageIndex, planeIndex); } if (val == null) { val = new Length(Double.NaN, UNITS.REFERENCEFRAME); } positionZ[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue(); }
/** * Convert a Bio-Formats {@link Length} to an OMERO Length. A null will be * returned if the input is null. */ public static Length convertLength(ome.units.quantity.Length value) { if (value == null) return null; String internal = xmlLengthEnumToOMERO(value.unit().getSymbol()); UnitsLength ul = UnitsLength.valueOf(internal); return new omero.model.LengthI(value.value().doubleValue(), ul); }
/** * Convert a Bio-Formats {@link Length} to an OMERO Length. */ public LengthI(ome.units.quantity.Length value) { ome.model.enums.UnitsLength internal = ome.model.enums.UnitsLength.bySymbol(value.unit().getSymbol()); UnitsLength ul = UnitsLength.valueOf(internal.toString()); setValue(value.value().doubleValue()); setUnit(ul); }