loci.formats.OMETools
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java.lang.Object
A utility class for constructing and manipulating OME-XML DOMs. It uses reflection to access the loci.ome.xml package so that the class compiles if the loci.ome.xml package is unavailable.
| Constructor Summary | |
OMETools()
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| Method Summary | |
static Object |
createRoot()
Constructs a new OME-XML root node. |
static Object |
createRoot(String xml)
Constructs a new OME-XML root node with the given XML block. |
static String |
dumpXML(Object root)
Dumps the given OME-XML DOM tree to a string. |
static Boolean |
getBigEndian(Object root)
Gets the first OME/Image/CA/Pixels element's BigEndian attribute. |
static String |
getCreationDate(Object root)
Gets the first OME/Image element's CreationDate attribute. |
static String |
getDescription(Object root,
String description)
Gets the first OME/Image element's Description attribute. |
static String |
getDimensionOrder(Object root)
Gets the first OME/Image/CA/Pixels element's DimensionOrder attribute. |
static String |
getImageName(Object root)
Gets the first OME/Image element's Name attribute. |
static Float |
getPixelSizeC(Object root)
Gets the first OME/Image/CA/Dimensions element's PixelSizeC attribute. |
static Float |
getPixelSizeT(Object root)
Gets the first OME/Image/CA/Dimensions element's PixelSizeT attribute. |
static Float |
getPixelSizeX(Object root)
Gets the first OME/Image/CA/Dimensions element's PixelSizeX attribute. |
static Float |
getPixelSizeY(Object root)
Gets the first OME/Image/CA/Dimensions element's PixelSizeY attribute. |
static Float |
getPixelSizeZ(Object root)
Gets the first OME/Image/CA/Dimensions element's PixelSizeZ attribute. |
static String |
getPixelType(Object root)
Gets the first OME/Image/CA/Pixels element's PixelType attribute. |
static Integer |
getSizeC(Object root)
Gets the first OME/Image/CA/Pixels element's SizeC attribute. |
static Integer |
getSizeT(Object root)
Gets the first OME/Image/CA/Pixels element's SizeT attribute. |
static Integer |
getSizeX(Object root)
Gets the first OME/Image/CA/Pixels element's SizeX attribute. |
static Integer |
getSizeY(Object root)
Gets the first OME/Image/CA/Pixels element's SizeY attribute. |
static Integer |
getSizeZ(Object root)
Gets the first OME/Image/CA/Pixels element's SizeZ attribute. |
static String |
getStageName(Object root,
String name)
Gets the first OME/Image/CA/StageLabel element's Name attribute. |
static Float |
getStageX(Object root)
Gets the first OME/Image/CA/StageLabel element's X attribute. |
static Float |
getStageY(Object root)
Gets the first OME/Image/CA/StageLabel element's Y attribute. |
static Float |
getStageZ(Object root)
Gets the first OME/Image/CA/StageLabel element's Z attribute. |
static Object |
setBigEndian(Object root,
boolean bigEndian)
Populates the first OME/Image/CA/Pixels element's BigEndian attribute. |
static Object |
setCreationDate(Object root,
String creationDate)
Populates the first OME/Image element's CreationDate attribute. |
static Object |
setDescription(Object root,
String description)
Populates the first OME/Image element's Description attribute. |
static Object |
setDimensionOrder(Object root,
String dimensionOrder)
Populates the first OME/Image/CA/Pixels element's DimensionOrder attribute. |
static Object |
setDimensions(Object root,
Float pixelSizeX,
Float pixelSizeY,
Float pixelSizeZ,
Float pixelSizeC,
Float pixelSizeT)
Populates the first OME/Image/CA/Dimensions element. |
static Object |
setDisplayROI(Object root,
Integer x0,
Integer y0,
Integer z0,
Integer x1,
Integer y1,
Integer z1,
Integer t0,
Integer t1,
Object displayOptions)
Populates the first OME/Image/CA/DisplayROI element. |
static Object |
setExperimenter(Object root,
String firstName,
String lastName,
String email,
String institution,
String dataDirectory,
Object group)
Populates the first OME/CA/Experimenter element. |
static Object |
setGroup(Object root,
String name,
Object leader,
Object contact)
Populates the first OME/CA/Group element. |
static Object |
setImage(Object root,
String name,
String creationDate,
String description)
Populates the first OME/Image element. |
static Object |
setImageName(Object root,
String name)
Populates the first OME/Image element's Name attribute. |
static Object |
setInstrument(Object root,
String manufacturer,
String model,
String serialNumber,
String type)
Populates the first OME/CA/Instrument element. |
static Object |
setPixels(Object root,
Integer sizeX,
Integer sizeY,
Integer sizeZ,
Integer sizeC,
Integer sizeT,
String pixelType,
Boolean bigEndian,
String dimensionOrder)
Populates the first OME/Image/CA/Pixels element. |
static Object |
setPixelSizeC(Object root,
float pixelSizeC)
Populates the first OME/Image/CA/Dimensions element's PixelSizeC attribute. |
static Object |
setPixelSizeT(Object root,
float pixelSizeT)
Populates the first OME/Image/CA/Dimensions element's PixelSizeT attribute. |
static Object |
setPixelSizeX(Object root,
float pixelSizeX)
Populates the first OME/Image/CA/Dimensions element's PixelSizeX attribute. |
static Object |
setPixelSizeY(Object root,
float pixelSizeY)
Populates the first OME/Image/CA/Dimensions element's PixelSizeY attribute. |
static Object |
setPixelSizeZ(Object root,
float pixelSizeZ)
Populates the first OME/Image/CA/Dimensions element's PixelSizeZ attribute. |
static Object |
setPixelType(Object root,
String pixelType)
Populates the first OME/Image/CA/Pixels element's PixelType attribute. |
static Object |
setSizeC(Object root,
int sizeC)
Populates the first OME/Image/CA/Pixels element's SizeC attribute. |
static Object |
setSizeT(Object root,
int sizeT)
Populates the first OME/Image/CA/Pixels element's SizeT attribute. |
static Object |
setSizeX(Object root,
int sizeX)
Populates the first OME/Image/CA/Pixels element's SizeX attribute. |
static Object |
setSizeY(Object root,
int sizeY)
Populates the first OME/Image/CA/Pixels element's SizeY attribute. |
static Object |
setSizeZ(Object root,
int sizeZ)
Populates the first OME/Image/CA/Pixels element's SizeZ attribute. |
static Object |
setStageLabel(Object root,
String name,
Float x,
Float y,
Float z)
Populates the first OME/Image/CA/StageLabel element. |
static Object |
setStageName(Object root,
String name)
Populates the first OME/Image/CA/StageLabel element's Name attribute. |
static Object |
setStageX(Object root,
float x)
Populates the first OME/Image/CA/StageLabel element's X attribute. |
static Object |
setStageY(Object root,
float y)
Populates the first OME/Image/CA/StageLabel element's Y attribute. |
static Object |
setStageZ(Object root,
float z)
Populates the first OME/Image/CA/StageLabel element's Z attribute. |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Constructor Detail |
public OMETools()
| Method Detail |
public static Object createRoot()
public static Object createRoot(String xml)
public static String dumpXML(Object root)
public static Object setImage(Object root,
String name,
String creationDate,
String description)
public static Object setExperimenter(Object root,
String firstName,
String lastName,
String email,
String institution,
String dataDirectory,
Object group)
public static Object setGroup(Object root,
String name,
Object leader,
Object contact)
public static Object setInstrument(Object root,
String manufacturer,
String model,
String serialNumber,
String type)
public static Object setDimensions(Object root,
Float pixelSizeX,
Float pixelSizeY,
Float pixelSizeZ,
Float pixelSizeC,
Float pixelSizeT)
public static Object setDisplayROI(Object root,
Integer x0,
Integer y0,
Integer z0,
Integer x1,
Integer y1,
Integer z1,
Integer t0,
Integer t1,
Object displayOptions)
public static Object setPixels(Object root,
Integer sizeX,
Integer sizeY,
Integer sizeZ,
Integer sizeC,
Integer sizeT,
String pixelType,
Boolean bigEndian,
String dimensionOrder)
public static Object setStageLabel(Object root,
String name,
Float x,
Float y,
Float z)
public static Object setImageName(Object root,
String name)
public static Object setCreationDate(Object root,
String creationDate)
public static Object setDescription(Object root,
String description)
public static Object setPixelSizeX(Object root,
float pixelSizeX)
public static Object setPixelSizeY(Object root,
float pixelSizeY)
public static Object setPixelSizeZ(Object root,
float pixelSizeZ)
public static Object setPixelSizeC(Object root,
float pixelSizeC)
public static Object setPixelSizeT(Object root,
float pixelSizeT)
public static Object setSizeX(Object root,
int sizeX)
public static Object setSizeY(Object root,
int sizeY)
public static Object setSizeZ(Object root,
int sizeZ)
public static Object setSizeC(Object root,
int sizeC)
public static Object setSizeT(Object root,
int sizeT)
public static Object setPixelType(Object root,
String pixelType)
public static Object setBigEndian(Object root,
boolean bigEndian)
public static Object setDimensionOrder(Object root,
String dimensionOrder)
public static Object setStageName(Object root,
String name)
public static Object setStageX(Object root,
float x)
public static Object setStageY(Object root,
float y)
public static Object setStageZ(Object root,
float z)
public static String getImageName(Object root)
public static String getCreationDate(Object root)
public static String getDescription(Object root,
String description)
public static Float getPixelSizeX(Object root)
public static Float getPixelSizeY(Object root)
public static Float getPixelSizeZ(Object root)
public static Float getPixelSizeC(Object root)
public static Float getPixelSizeT(Object root)
public static Integer getSizeX(Object root)
public static Integer getSizeY(Object root)
public static Integer getSizeZ(Object root)
public static Integer getSizeC(Object root)
public static Integer getSizeT(Object root)
public static String getPixelType(Object root)
public static Boolean getBigEndian(Object root)
public static String getDimensionOrder(Object root)
public static String getStageName(Object root,
String name)
public static Float getStageX(Object root)
public static Float getStageY(Object root)
public static Float getStageZ(Object root)
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