Changeset 172 for Xml/Release/ome.xsd
- Timestamp:
- 05/14/08 16:07:43 (7 months ago)
- Files:
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- 1 modified
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Xml/Release/ome.xsd (modified) (25 diffs)
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Xml/Release/ome.xsd
r106 r172 3 3 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 4 # 5 # Copyright (C) 2002-200 7Open Microscopy Environment5 # Copyright (C) 2002-2008 Open Microscopy Environment 6 6 # Massachusetts Institute of Technology, 7 7 # National Institutes of Health, … … 16 16 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 17 17 --> 18 <xsd:schema xmlns="http://www.openmicroscopy.org/Schemas/OME/200 7-06"19 targetNamespace="http://www.openmicroscopy.org/Schemas/OME/200 7-06"18 <xsd:schema xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-02" 19 targetNamespace="http://www.openmicroscopy.org/Schemas/OME/2008-02" 20 20 xmlns:xsd="http://www.w3.org/2001/XMLSchema" 21 xmlns:AML="http://www.openmicroscopy.org/Schemas/AnalysisModule/2007-06" 22 xmlns:STD="http://www.openmicroscopy.org/Schemas/STD/2007-06" 23 xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2007-06" 24 xmlns:CA="http://www.openmicroscopy.org/Schemas/CA/2007-06" 25 xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2007-06" 21 xmlns:AML="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02" 22 xmlns:STD="http://www.openmicroscopy.org/Schemas/STD/2008-02" 23 xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02" 24 xmlns:CA="http://www.openmicroscopy.org/Schemas/CA/2008-02" 25 xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2008-02" 26 xmlns:xml="http://www.w3.org/XML/1998/namespace" 26 27 version="2" 27 28 elementFormDefault="qualified"> 28 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/AnalysisModule/2007-06" schemaLocation="http://www.openmicroscopy.org/Schemas/AnalysisModule/2007-06/AnalysisModule.xsd"/> 29 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/STD/2007-06" schemaLocation="http://www.openmicroscopy.org/Schemas/STD/2007-06/STD.xsd"/> 30 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/BinaryFile/2007-06" schemaLocation="http://www.openmicroscopy.org/Schemas/BinaryFile/2007-06/BinaryFile.xsd"/> 31 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/CA/2007-06" schemaLocation="http://www.openmicroscopy.org/Schemas/CA/2007-06/CA.xsd"/> 32 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/SPW/2007-06" schemaLocation="http://www.openmicroscopy.org/Schemas/SPW/2007-06/SPW.xsd"/> 29 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02" schemaLocation="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02/AnalysisModule.xsd"/> 30 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/STD/2008-02" schemaLocation="http://www.openmicroscopy.org/Schemas/STD/2008-02/STD.xsd"/> 31 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02" schemaLocation="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02/BinaryFile.xsd"/> 32 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/CA/2008-02" schemaLocation="http://www.openmicroscopy.org/Schemas/CA/2008-02/CA.xsd"/> 33 <xsd:import namespace="http://www.openmicroscopy.org/Schemas/SPW/2008-02" schemaLocation="http://www.openmicroscopy.org/Schemas/SPW/2008-02/SPW.xsd"/> 34 <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/xml.xsd"/> 33 35 <xsd:annotation> 34 36 <xsd:documentation> 35 37 Open Microscopy Environment 36 OME XML Schema June 2007 - Update Version 2 September 200738 OME XML Schema February 2008 - Update Version 2 May 2008 37 39 Author: Ilya G. Goldberg, Andrew J Patterson 38 Copyright 2002 - 200 7OME. All rights reserved.40 Copyright 2002 - 2008 OME. All rights reserved. 39 41 </xsd:documentation> 40 42 </xsd:annotation> … … 63 65 <xsd:element ref="CA:CustomAttributes" minOccurs="0"/> 64 66 </xsd:sequence> 67 <xsd:attribute name="UUID" type="UniversallyUniqueIdentifier"/> 65 68 </xsd:complexType> 66 69 </xsd:element> … … 92 95 <xsd:element ref="DatasetRef" minOccurs="0" maxOccurs="unbounded"/> 93 96 <xsd:element ref="InstrumentRef" minOccurs="0"/> 94 <xsd:element ref="Objective SettingsRef" minOccurs="0"/>97 <xsd:element ref="ObjectiveRef" minOccurs="0"/> 95 98 <xsd:element ref="ImagingEnvironment" minOccurs="0"/> 96 99 <xsd:element ref="Thumbnail" minOccurs="0"/> … … 99 102 <xsd:element ref="StageLabel" minOccurs="0"/> 100 103 <xsd:element ref="Pixels" maxOccurs="unbounded"/> 101 <xsd:element ref="AcquiredPixelsRef" minOccurs="0" maxOccurs="1"/>102 104 <xsd:element ref="Region" minOccurs="0" maxOccurs="unbounded"/> 103 105 <xsd:element ref="CA:CustomAttributes" minOccurs="0"/> … … 109 111 <xsd:attribute name="DefaultPixels" use="required" type="PixelsID"> 110 112 <xsd:annotation> 111 <xsd:documentation>More than one Pixels attribute may be associated with an Image. An Image will however have one "primary" set of Pixels. If a PixelsID is specified with this attribute, then that will be the "primary" pixels for this image. If this attribute 112 is not specified, then the FIRST <Pixels> element under <Image> will be assumed to be the "primary" set. 113 <xsd:documentation> 114 More than one Pixels element may be associated with an Image. 115 An Image will however have one "primary" set of Pixels specified with this attribute. 116 </xsd:documentation> 117 </xsd:annotation> 118 </xsd:attribute> 119 <xsd:attribute name="AcquiredPixels" type="PixelsID"> 120 <xsd:annotation> 121 <xsd:documentation> 122 Optional. 123 More than one Pixels element may be associated with an Image. 124 This attribute indicates the original acquired pixels. 113 125 </xsd:documentation> 114 126 </xsd:annotation> … … 155 167 </xsd:simpleType> 156 168 </xsd:attribute> 157 <xsd:attribute name="PixelType" use="required"> 158 <xsd:simpleType> 159 <xsd:restriction base="PixelTypes"> 160 <xsd:enumeration value = "int8"/> 161 <xsd:enumeration value = "int16"/> 162 <xsd:enumeration value = "int32"/> 163 <xsd:enumeration value = "uint8"/> 164 <xsd:enumeration value = "uint16"/> 165 <xsd:enumeration value = "uint32"/> 166 <xsd:enumeration value = "float"/> 167 </xsd:restriction> 168 </xsd:simpleType> 169 </xsd:attribute> 169 <xsd:attribute name="PixelType" use="required" type="PixelTypes"/> 170 170 <xsd:attribute name="BigEndian" use="required" type="xsd:boolean"> 171 171 <xsd:annotation> … … 218 218 </xsd:complexType> 219 219 </xsd:element> 220 221 <xsd:element name="AcquiredPixelsRef">222 <xsd:complexType>223 <xsd:complexContent>224 <xsd:extension base="Reference">225 <xsd:attribute name="ID" use="required" type="PixelsID"/>226 </xsd:extension>227 </xsd:complexContent>228 </xsd:complexType>229 </xsd:element>230 231 220 <xsd:element name="TiffData"> 232 221 <xsd:annotation> 233 222 <xsd:documentation> 234 </xsd:documentation> 235 </xsd:annotation> 236 <xsd:complexType> 223 This described the location of the pixel data in a tiff file. 224 </xsd:documentation> 225 </xsd:annotation> 226 <xsd:complexType> 227 <xsd:sequence> 228 <xsd:element name="UUID" minOccurs="0"> 229 <xsd:annotation> 230 <xsd:documentation> 231 This must be used when the IFDs are located in another file. 232 Note: It is permissible for this to be self referential. 233 </xsd:documentation> 234 </xsd:annotation> 235 <xsd:complexType> 236 <xsd:simpleContent> 237 <xsd:extension base = "UniversallyUniqueIdentifier"> 238 <xsd:attribute name="FileName" type="xsd:string"> 239 <xsd:annotation> 240 <xsd:documentation> 241 This can be used when the IFDs are located in another file. 242 The / (forward slash) is used as the path separator. 243 A relative path is recommended. However an absolute path can be specified. 244 Default is to use the file the ome-xml data has been pulled from. 245 Note: It is permissible for this to be self referential. The file image1.tiff 246 may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff" 247 </xsd:documentation> 248 </xsd:annotation> 249 </xsd:attribute> 250 </xsd:extension> 251 </xsd:simpleContent> 252 </xsd:complexType> 253 </xsd:element> 254 </xsd:sequence> 237 255 <xsd:attribute name="IFD" type="xsd:integer" default="0"> 238 256 <xsd:annotation> … … 288 306 <xsd:element name="PlaneTiming" type="PlaneTiming" minOccurs="0" maxOccurs="1"/> 289 307 <xsd:element name="StagePosition" type="StagePosition" minOccurs="0" maxOccurs="1"/> 308 <xsd:choice minOccurs="0" maxOccurs="1"> 309 <xsd:annotation> 310 <xsd:documentation> 311 This optional element is a hash of the plane's image data. 312 It is a choice between all the support hash types. 313 Currently the only method supported is SHA1. 314 </xsd:documentation> 315 </xsd:annotation> 316 <xsd:element name="HashSHA1" type="Hex40"/> 317 </xsd:choice> 290 318 </xsd:sequence> 291 319 <xsd:attribute name="TheZ" use="required" type="xsd:integer"/> … … 443 471 The PhotometricInterpretation attribute is used to describe how to display a multi-component channel. This attribute may be set to: 444 472 'monochrome', 'RGB', 'ARGB', 'CMYK', 'HSV'. The default for single-component channels is 'monochrome'. 445 The Mode lattribute describes the type of microscopy performed for each channel. This may be set to:473 The Mode attribute describes the type of microscopy performed for each channel. This may be set to: 446 474 'Wide-field','Wide-field','Laser Scanning Microscopy','Laser Scanning Confocal','Spinning Disk Confocal','Slit Scan Confocal','Multi-Photon Microscopy', 447 475 'Structured Illumination','Single Molecule Imaging','Total Internal Reflection','Fluorescence-Lifetime','Spectral Imaging', … … 778 806 <xsd:documentation> 779 807 A description of the microscope's objective lens. 780 Required elements include the lens numerical aperture, and the magnification, both of which a floating point (real) numbers. 808 Required elements include the lens numerical aperture, 809 and the magnification, both of which a floating 810 point (real) numbers. 811 The values are those that are fixed for a particular 812 objective: either because it has been manufactured to 813 this specification or the value has been measured on 814 this particular objective. 815 Correction: This is the type of correction coating applied to this lens. 816 Immersion: This is the types of immersion medium the lens is designed to 817 work with. It is not the same as 'Medium' in ObjectiveRef (a 818 single type) as here Immersion can have compound values like 'Multi'. 819 LensNA: The numerical aperture of the lens (as a float) 820 NominalMagnification: The specified magnification e.g. x10 821 CalibratedMagnification: The measured magnification e.g. x10.3 822 WorkingDistance: WorkingDistance of the lense. The Units are um. 781 823 </xsd:documentation> 782 824 </xsd:annotation> … … 799 841 </xsd:complexType> 800 842 </xsd:element> 801 <xsd:element name="ObjectiveSettings">802 <xsd:annotation>803 <xsd:documentation>804 A description of the user settings on a microscope's objective lens.805 </xsd:documentation>806 </xsd:annotation>807 <xsd:complexType>808 <xsd:sequence>809 <xsd:element ref="ObjectiveRef"/>810 </xsd:sequence>811 <xsd:attribute name="CorrectionCollar" type="xsd:float"/>812 <xsd:attribute name="Medium" type="Medium"/>813 <xsd:attribute name="RefractiveIndex" type="xsd:float"/>814 </xsd:complexType>815 </xsd:element>816 843 <xsd:simpleType name="Medium"> 817 844 <xsd:annotation> 818 845 <xsd:documentation> 819 A description of a Medium used either for the sampleor the lens.846 A description of a Medium used for the lens. 820 847 </xsd:documentation> 821 848 </xsd:annotation> … … 897 924 </xsd:annotation> 898 925 </xsd:element> 899 <xsd:element name="Correction" type="Correction">926 <xsd:element name="Correction"> 900 927 <xsd:annotation> 901 928 <xsd:documentation>The coating applied to the lens</xsd:documentation> 902 929 </xsd:annotation> 903 </xsd:element>904 <xsd:simpleType name="Correction">905 <xsd:restriction base="xsd:string">906 <xsd:enumeration value="UV"/>907 <xsd:enumeration value="PlanApo"/>908 <xsd:enumeration value="PlanFluor"/>909 <xsd:enumeration value="SuperFluor"/>910 < xsd:enumeration value="VioletCorrected"/>911 </xsd: restriction>912 </xsd: simpleType>913 <xsd:element name="Immersion" type="Immersion">930 <xsd:simpleType> 931 <xsd:restriction base="xsd:string"> 932 <xsd:enumeration value="UV"/> 933 <xsd:enumeration value="PlanApo"/> 934 <xsd:enumeration value="PlanFluor"/> 935 <xsd:enumeration value="SuperFluor"/> 936 <xsd:enumeration value="VioletCorrected"/> 937 </xsd:restriction> 938 </xsd:simpleType> 939 </xsd:element> 940 <xsd:element name="Immersion"> 914 941 <xsd:annotation> 915 942 <xsd:documentation>The immersion medium the lens is designed for</xsd:documentation> 916 943 </xsd:annotation> 917 </xsd:element>918 <xsd:simpleType name="Immersion">919 <xsd:restriction base="xsd:string">920 <xsd:enumeration value="Oil"/>921 <xsd:enumeration value="Water"/>922 <xsd:enumeration value="WaterDipping"/>923 <xsd:enumeration value="Air"/>924 <xsd:enumeration value="Multi"/>925 <xsd:enumeration value="Glycerol"/>926 < xsd:enumeration value="Other"/>927 </xsd: restriction>928 </xsd: simpleType>944 <xsd:simpleType> 945 <xsd:restriction base="xsd:string"> 946 <xsd:enumeration value="Oil"/> 947 <xsd:enumeration value="Water"/> 948 <xsd:enumeration value="WaterDipping"/> 949 <xsd:enumeration value="Air"/> 950 <xsd:enumeration value="Multi"/> 951 <xsd:enumeration value="Glycerol"/> 952 <xsd:enumeration value="Other"/> 953 </xsd:restriction> 954 </xsd:simpleType> 955 </xsd:element> 929 956 <xsd:element name="WorkingDistance" type="xsd:float"> 930 957 <xsd:annotation> … … 993 1020 </xsd:complexType> 994 1021 </xsd:element> 995 <xsd:element name ="Description">1022 <xsd:element name = "Description"> 996 1023 <xsd:annotation> 997 1024 <xsd:documentation> 998 1025 Just some free-form text to describe Images, Screens and Projects. 999 The content model is currently ANY, but this is going to change to String in 1000 the near future. This is no longer the correct place for an XML sub-document 1001 - use CustomAttributes instead. 1002 </xsd:documentation> 1003 </xsd:annotation> 1026 The content model is now String. 1027 This is no longer the correct place for an XML sub-document 1028 Either 1029 - use CustomAttributes instead 1030 Or 1031 - define your own xml tree outside the OME node and link to the OME objects using references to the IDs 1032 </xsd:documentation> 1033 </xsd:annotation> 1034 <xsd:complexType> 1035 <xsd:simpleContent> 1036 <xsd:extension base = "xsd:string"> 1037 <xsd:attribute ref = "xml:lang" default = "en"/> 1038 </xsd:extension> 1039 </xsd:simpleContent> 1040 </xsd:complexType> 1004 1041 </xsd:element> 1005 1042 <xsd:element name="Microscope"> … … 1153 1190 </xsd:restriction> 1154 1191 </xsd:simpleType> 1192 <xsd:simpleType name="UniversallyUniqueIdentifier"> 1193 <xsd:annotation> 1194 <xsd:documentation> 1195 This is a unique ID for the file but does not conform to the ID pattern used in the rest of the file. 1196 The rest of the IDs are either an full LSID or an internal ID which is a string that is simply unique in this file. 1197 As the UniversallyUniqueIdentifier is used from outside this file to identify it having the same ID in another file could cause problems. 1198 A UUID is 32 hexadecimal digits, in 5 groups, 8-4-4-4-12, separated by hyphens 1199 e.g. urn:uuid:3e450fae-b8f2-4d35-aa54-702168b2487f 1200 There are methods to generate these in most modern languages. 1201 http://www.ietf.org/rfc/rfc4122.txt 1202 </xsd:documentation> 1203 </xsd:annotation> 1204 <xsd:restriction base="xsd:anyURI"> 1205 <xsd:pattern value="(urn:uuid:[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12})"/> 1206 </xsd:restriction> 1207 </xsd:simpleType> 1155 1208 <xsd:simpleType name="ProjectID"> 1156 1209 <xsd:restriction base="LSID"> … … 1206 1259 <xsd:restriction base="LSID"> 1207 1260 <xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Objective:\S+)|(Objective:\S+)"/> 1208 </xsd:restriction>1209 </xsd:simpleType>1210 <xsd:simpleType name="ObjectiveSettingsID">1211 <xsd:restriction base="LSID">1212 <xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:ObjectiveSettings:\S+)|(ObjectiveSettings:\S+)"/>1213 1261 </xsd:restriction> 1214 1262 </xsd:simpleType> … … 1260 1308 <xsd:simpleType name="PixelTypes"> 1261 1309 <xsd:restriction base="xsd:string"> 1262 <xsd:enumeration value="bit"/> 1263 <xsd:enumeration value="int8"/> 1264 <xsd:enumeration value="int16"/> 1265 <xsd:enumeration value="int32"/> 1266 <xsd:enumeration value="uint8"/> 1267 <xsd:enumeration value="uint16"/> 1268 <xsd:enumeration value="uint32"/> 1269 <xsd:enumeration value ="float"/> 1270 <xsd:enumeration value ="double"/> 1271 <xsd:enumeration value ="complex"/> 1272 <xsd:enumeration value ="double-complex"/> 1273 </xsd:restriction> 1310 <xsd:enumeration value = "int8"/> 1311 <xsd:enumeration value = "int16"/> 1312 <xsd:enumeration value = "int32"/> 1313 <xsd:enumeration value = "uint8"/> 1314 <xsd:enumeration value = "uint16"/> 1315 <xsd:enumeration value = "uint32"/> 1316 <xsd:enumeration value = "float"/> 1317 </xsd:restriction> 1318 </xsd:simpleType> 1319 <xsd:simpleType name="ExtendedPixelTypes"> 1320 <xsd:union memberTypes="PixelTypes"> 1321 <xsd:simpleType> 1322 <xsd:restriction base="xsd:string"> 1323 <xsd:enumeration value = "bit"/> 1324 <xsd:enumeration value = "double"/> 1325 <xsd:enumeration value = "complex"/> 1326 <xsd:enumeration value = "double-complex"/> 1327 </xsd:restriction> 1328 </xsd:simpleType> 1329 </xsd:union> 1274 1330 </xsd:simpleType> 1275 1331 <xsd:simpleType name="ModuleID"> … … 1489 1545 </xsd:sequence> 1490 1546 <xsd:attribute name="ID" use="required" type="OTFID"/> 1491 <xsd:attribute name="PixelType" use="required" type=" PixelTypes"/>1547 <xsd:attribute name="PixelType" use="required" type="ExtendedPixelTypes"/> 1492 1548 <xsd:attribute name="OpticalAxisAveraged" use="required" type="xsd:boolean"/> 1493 1549 <xsd:attribute name="SizeX" use="required" type="xsd:positiveInteger"/> … … 1600 1656 Laser types are specified using two attributes - the Type and the lasing medium (Medium). Type is a string which may be set to: 1601 1657 'Excimer','Gas','Metal Vapor','Solid State','Dye','Semiconductor', or 'Free Electron'. The Medium attribute specifies the actual lasing medium 1602 for a given laser type (for example, 'Nd-YAG'). Additionally, the Wavelength (in nm), whether or not the laser is FrequencyDoubled or Tuneablemay be specified.1658 for a given laser type (for example, 'Nd-YAG'). Additionally, the Wavelength (in nm), whether or not the laser is Tuneable, and any FrequencyMultiplication that may be specified. 1603 1659 The Pulse attribute can be set to 'CW' (Continuous Wave),','Single','Q-Switched','Repetitive','Mode-Locked'. 1604 1660 The Power attribute specifies the nominal laser power in watts. … … 1655 1711 <xsd:documentation> 1656 1712 The Arc element is used to describe various kinds of Arc lamps - Hg, Xe, HgXe. 1657 The Power attribute is the lamp's nominal power in watts.1713 The Power of the Arc is now stored in the LightSource. 1658 1714 </xsd:documentation> 1659 1715 </xsd:annotation> … … 1668 1724 </xsd:simpleType> 1669 1725 </xsd:attribute> 1670 <xsd:attribute name="Power" type="xsd:float"/>1671 1726 </xsd:complexType> 1672 1727 </xsd:element> … … 1675 1730 <xsd:documentation> 1676 1731 The Filament element is used to describe various kinds of filament bulbs such as Incadescent or Halogen. 1677 The Power attribute is the bulb's nominal power in watts.1732 The Power of the Filament is now stored in the LightSource. 1678 1733 </xsd:documentation> 1679 1734 </xsd:annotation> … … 1687 1742 </xsd:simpleType> 1688 1743 </xsd:attribute> 1689 <xsd:attribute name="Power" type="xsd:float"/>1690 1744 </xsd:complexType> 1691 1745 </xsd:element> … … 1771 1825 </xsd:element> 1772 1826 <xsd:element name="ObjectiveRef"> 1827 <xsd:annotation> 1828 <xsd:documentation> 1829 This holds the setting applied to an objective as well as a 1830 reference to the objective. 1831 The ID is the objective used in this case. 1832 The CorrectionCollar is it normal an adjustable ring on the 1833 objective. Each has an arbitrary scale on it so the values 1834 is unit-less. 1835 The Medium is the actual immersion medium used in this case. 1836 The RefractiveIndex is that of the immersion medium. This is 1837 a ratio so it also unit-less. 1838 </xsd:documentation> 1839 </xsd:annotation> 1773 1840 <xsd:complexType> 1774 1841 <xsd:complexContent> … … 1780 1847 <xsd:annotation><xsd:documentation>This is unit-less, it is a ratio.</xsd:documentation></xsd:annotation> 1781 1848 </xsd:attribute> 1782 </xsd:extension>1783 </xsd:complexContent>1784 </xsd:complexType>1785 </xsd:element>1786 <xsd:element name="ObjectiveSettingsRef">1787 <xsd:complexType>1788 &n
