<segmentation schemaVersion="0.6.0a4">
  <version>{1,1}</version>
  <name>{1,1}</name>
  <software>{0,1}</software>
  <transformList>{0,1}</transformList>
  <filePath>{1,1}</filePath>
  <primaryDescriptor>{1,1}</primaryDescriptor>
  <boundingBox xmax="" xmin="0" ymax="" ymin="0" zmax="" zmin="0">{0,1}</boundingBox>
  <globalExternalReferences id="" otherType="" type="" value="">{0,1}</globalExternalReferences>
  <segmentList>{1,1}</segmentList>
  <details>{0,1}</details>
</segmentation>

<xs:element name="segmentation">
  <xs:annotation>
    <xs:documentation>Link to assembly or component id.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="version" type="xs:string"/>
      <xs:element name="name" type="xs:string"/>
      <xs:element name="software" type="softwareType" minOccurs="0"/>
      <xs:element name="transformList" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element ref="transform" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="filePath" type="xs:token">
        <xs:annotation>
          <xs:documentation>Specifies the location of file containing referenced data. Applies to 'threeDVolume' and 'subtomogramAverage'. If its value is an empty string then the full path is assumed to be contained in the 'file' attribute that refers to the data ('threeDVolume' or 'subtomogramAverage'). Otherwise it is assumed to be a full path excluding the filename. This is consistent with concatenating the 'filePath' content with the 'file' content.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="primaryDescriptor">
        <xs:annotation>
          <xs:documentation>Mandatory field. Designates the element type within 'segmentList' that contains the primary description of the segments. Constrained to be either 'threeDVolume', 'shapePrimitiveList', 'contourList' or 'meshList'.</xs:documentation>
        </xs:annotation>
        <xs:simpleType>
          <xs:restriction base="xs:string">
            <xs:enumeration value="threeDVolume"/>
            <xs:enumeration value="shapePrimitiveList"/>
            <xs:enumeration value="contourList"/>
            <xs:enumeration value="meshList"/>
          </xs:restriction>
        </xs:simpleType>
      </xs:element>
      <xs:element name="boundingBox" type="boundingBoxType" minOccurs="0"/>
      <xs:element name="globalExternalReferences" type="externalReferenceType" minOccurs="0"/>
      <xs:element name="segmentList">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="segment" type="segmentType" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="details" type="xs:string" minOccurs="0"/>
    </xs:sequence>
    <xs:attribute name="schemaVersion" type="xs:token" default="0.6.0a4">
      <xs:annotation>
        <xs:documentation>
          <![CDATA[
                        Version History
                        0.2, 2015/3/15, Ardan Patwardhan: 
                        1) Added support for color 
                        2) Added support for triangle representation of segment - this is in support of Amira segmentations 
                        
                        0.3, 2015/10/21, Paul Korir: 
                        1) Added voxelTransform 
                        2) Added filePath for segmentLinks to HDF5 (Segger) segmentations 
                        3) Added segmentObjects with contours and meshes for IMOD 
                        
                        0.4, 2015/11/04, Paul Korir: 
                        1) Added alpha for rgb color (transparency) 
                        
                        0.5, 2015/12/14, Paul Korir: 
                        1) Removed 'voxelTransform'
                        2) Moved 'numberOfCopies' as 'numberOfInstances' to  be a sequence element within 'biologicalAnnotation'
                        3) Made 'color' a choice between 'name' (X11/HTML4 sRGB colour space names) and 'rgba'
                        4) Added a 'transform' element, which is a possibly empty list of transformation matrices referenced within the document by a non-negative identifier
                        5) Renamed 'segmentLink' to 'voxelSegmentation' and added a 'transformId' element
                        6) Renamed 'color' element to 'colour' and 'colorType' to 'colourType'
                        7) Structured 'shapePrimitive' to a list of 'shapePrimitive' (substitution group for 'ellipsoid', 'cuboid', 'pyramid', 'cylinder')
                        8) Identified and labeled deprecated data types
                        9) Renamed shapePrimitive 'pyramid' to 'cone' and added tentative definition
                        10) Removed 'origin' and 'viewVectorRotation' elements from shape primitives (cuboid, ellipsoid, cone, cylinder) and replaced with 'transformId' element
                        11) Renamed references to 'triangles' to 'polygons' e.g. 'triangleListType' now 'polygonListType'
                        
                        0.5.1, 2015/12/23, Paul Korir:
                        1) Change colourType to have rgbaType minOccurs=1
                        2) Added 'attribute' element (e.g. for FOM) to shapePrimitive
                        3) Deleted comment: 'Are the CCP4 format masks going to be allowed? If so, we could represent the information of the mask (mapType) here.' from 'voxelSegmentation'.
                        4) Added segment 'format' element to 'voxelSegmentation' restricted to values 'runLengthEncoding', 'MRC', or 'Segger'
                        5) Renamed 'voxelSegmentation' to 'threeDVolume' and deprecated 'subTomogramAverage'.
                        6) Restructured 'transforms' into a list ('transformList') of 'transform', which is a substitutionGroup of 'transformationMatrix', 'canonicalEulerAngles' or 'viewVectorRotation'. 
                        7) Added an 'angleDegreeType' to restrict angle range in degrees [0,360].
                        
                        0.5.2, 2016/01/04, Paul Korir:
                        1) Made 'transformList' optional
                        2) Added 'id' attributes for 'canonicalEulerAngle' and 'viewVectorRotation'
                        3) Annotations for 'filePath'
                        4) Added 'other' to types for 'externalReference' and optional 'otherTypes' attribute
                        5) Changed type of 'name' element in 'colour' from 'xs:string' to 'xs:token'
                        6) Created 'threeDVolumeType' to be used by 'threeDVolume' and 'subtomogramAverage'
                        7) Added 'id' attributes for 'shapePrimitive' and 'threeDVolumeType'
                        8) Renamed 'contours' to 'contourList'
                        9) Created 'meshList' as a sequence of 'mesh'. Each 'mesh' has an 'id'
                        
                        0.5.3, 2016/01/06, Paul Korir:
                        1) Renamed 'transformationMatrixType' attribute from 'transformId' to 'id'
                        2) Created 'dimensionType' for all 'shapePrimitive' dimensions
                        
                        0.5.4, 2016/01/06, Paul Korir:
                        1) Added element 'primaryDescriptor' of type restricted string to 'threeDVolume', 'shapePrimitiveList', 'contourList', 'meshList'
                        
                        0.5.5, 2016/01/22, Paul Korir:
                        1) Changed 'vertices' and 'polygons' to 'vertexList' and 'polygonList', respectively.
                        2) Added attribute 'designation' restricted to string 'vertex' (default) and 'normal' to 'vertex' element.
                        
                        0.5.6, 2016/01/25, Paul Korir:
                        1) Changed attribute 'polygonID' from 'positiveInteger' to 'nonNegativeInteger'
                        
                        0.5.7, 2016/01/26, Paul Korir:
                        1) Change element names to save disk space: 'vertex' to 'v', 'vertexID' to 'vID', 'point' to 'p', 'polygon' to 'P', 'polygonID' to 'PID'
                        2) Changed 'vertexType' to have ID of type 'xs:nonNegativeInteger' (from 'xs:positiveInteger')
                        
                        0.5.8, 2016/04/26, Paul Korir:
                        1) Added 'version' element at the root.
                        
                        0.5.8, 2016/08/08, Paul Korir:
                        2) Made 'shapePrimitive' element 'attribute (not present in 'subtomogramAverage' optional (minOccurs=0)
                        
                        0.5.8, 2016/08/17, Paul Korir:
                        3) Added a 'transformId' element to 'contourList' and to 'mesh'.
                        
                        0.5.8, 2016/10/04, Paul Korir:
                        4) Simplified shape primitives by eliminating internal layering e.g. cone/dimensions/height to cone/height
                        
                        0.5.8, 2016/10/14, Paul Korir:
                        5) (Finally) renamed 'surfaceType' to 'meshType' for consistency.
                        
                        0.5.8, 2016/10/20, Paul Korir:
                        6) 'macromolecule' and 'complex' changed from 'positiveInteger' to 'string'
                        
                        0.6.0a1, 2017/02/28, Paul Korir:
                        1) Added 'EMAN' as a 'threeDVolume' format
                        
                        0.6.0a2, 2017/05/15, Paul Korir:
                        1) Restructured 'externalReferences' from simpleType to complexType
                        2) Changed 'externalReference' to 'externalReferenceType' and replaced elements with attributes
                        
                        0.6.0a3, 2017/05/25, Paul Korir:
                        1) Added element 'boundingBox' taking six integers: xmin, xmax, ymin, ymax, zmin, zmax; minimums default to 0
                        
                        0.6.0a4, 2017/07/31, Paul Korir:
                        1) Added global (optional) external references
                        
                        0.6.0a4, 2017/09/20, Paul Korir:
                        2) Renamed global external references to globalExternalReferences
                        ]]>
        </xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

<xs:element name="version" type="xs:string"/>

<xs:element name="name" type="xs:string"/>

<software>
  <name>{1,1}</name>
  <version>{0,1}</version>
  <processingDetails>{0,1}</processingDetails>
</software>

<xs:element name="software" type="softwareType" minOccurs="0"/>

<xs:element name="name" type="xs:token"/>

<xs:element name="version" type="xs:token" minOccurs="0"/>

<xs:element name="processingDetails" type="xs:string" minOccurs="0"/>

<transformList>
  <transform>{0,unbounded}</transform>
</transformList>

<xs:element name="transformList" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="transform" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<xs:element name="transform"/>

<xs:element name="filePath" type="xs:token">
  <xs:annotation>
    <xs:documentation>Specifies the location of file containing referenced data. Applies to 'threeDVolume' and 'subtomogramAverage'. If its value is an empty string then the full path is assumed to be contained in the 'file' attribute that refers to the data ('threeDVolume' or 'subtomogramAverage'). Otherwise it is assumed to be a full path excluding the filename. This is consistent with concatenating the 'filePath' content with the 'file' content.</xs:documentation>
  </xs:annotation>
</xs:element>

<xs:element name="primaryDescriptor">
  <xs:annotation>
    <xs:documentation>Mandatory field. Designates the element type within 'segmentList' that contains the primary description of the segments. Constrained to be either 'threeDVolume', 'shapePrimitiveList', 'contourList' or 'meshList'.</xs:documentation>
  </xs:annotation>
  <xs:simpleType>
    <xs:restriction base="xs:string">
      <xs:enumeration value="threeDVolume"/>
      <xs:enumeration value="shapePrimitiveList"/>
      <xs:enumeration value="contourList"/>
      <xs:enumeration value="meshList"/>
    </xs:restriction>
  </xs:simpleType>
</xs:element>

<xs:element name="boundingBox" type="boundingBoxType" minOccurs="0"/>

<xs:element name="globalExternalReferences" type="externalReferenceType" minOccurs="0"/>

<segmentList>
  <segment id="" parentID="">{1,unbounded}</segment>
</segmentList>

<xs:element name="segmentList">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="segment" type="segmentType" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<segment id="" parentID="">
  <biologicalAnnotation>{0,1}</biologicalAnnotation>
  <complexesAndMacromolecules>{0,1}</complexesAndMacromolecules>
  <colour>{0,1}</colour>
  <threeDVolume id="">{0,1}</threeDVolume>
  <shapePrimitiveList>{0,1}</shapePrimitiveList>
  <contourList>{0,1}</contourList>
  <meshList>{0,1}</meshList>
</segment>

<xs:element name="segment" type="segmentType" maxOccurs="unbounded"/>

<biologicalAnnotation>
  <description>{0,1}</description>
  <externalReferences>{0,1}</externalReferences>
  <numberOfInstances>{0,1}</numberOfInstances>
</biologicalAnnotation>

<xs:element name="biologicalAnnotation" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="description" type="xs:string" minOccurs="0"/>
      <xs:element name="externalReferences" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="ref" type="externalReferenceType" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="numberOfInstances" type="xs:positiveInteger" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Number of instances present of the basic structure (complex or macromolecule). For example it could be '7' for the upper ring of GroEL</xs:documentation>
        </xs:annotation>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<xs:element name="description" type="xs:string" minOccurs="0"/>

<externalReferences>
  <ref id="" otherType="" type="" value="">{0,unbounded}</ref>
</externalReferences>

<xs:element name="externalReferences" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="ref" type="externalReferenceType" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<xs:element name="ref" type="externalReferenceType" minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="numberOfInstances" type="xs:positiveInteger" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Number of instances present of the basic structure (complex or macromolecule). For example it could be '7' for the upper ring of GroEL</xs:documentation>
  </xs:annotation>
</xs:element>

<complexesAndMacromolecules>
  <macromolecule>{0,1}</macromolecule>
  <complex>{0,1}</complex>
</complexesAndMacromolecules>

<xs:element name="complexesAndMacromolecules" type="macromoleculesAndComplexesType" minOccurs="0">
  <xs:annotation>
    <xs:documentation>EMDB internal use</xs:documentation>
  </xs:annotation>
</xs:element>

<macromolecule>
  <id>{1,unbounded}</id>
</macromolecule>

<xs:element name="macromolecule" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="id" type="xs:string" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<xs:element name="id" type="xs:string" maxOccurs="unbounded"/>

<complex>
  <id>{1,unbounded}</id>
</complex>

<xs:element name="complex" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="id" type="xs:string" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<xs:element name="id" type="xs:string" maxOccurs="unbounded"/>

<colour>
  <name>{1,1}</name>
  <rgba>{1,1}</rgba>
</colour>

<xs:element name="colour" type="colourType" minOccurs="0"/>

<xs:element name="name" type="xs:token"/>

<rgba>
  <red>{1,1}</red>
  <green>{1,1}</green>
  <blue>{1,1}</blue>
  <alpha>{0,1}</alpha>
</rgba>

<xs:element name="rgba" type="rgbaType" minOccurs="1"/>

<xs:element name="red" type="colourChannelType"/>

<xs:element name="green" type="colourChannelType"/>

<xs:element name="blue" type="colourChannelType"/>

<xs:element name="alpha" type="colourChannelType" default="1.0" minOccurs="0"/>

<threeDVolume id="">
  <file>{1,1}</file>
  <objectPath>{0,1}</objectPath>
  <contourLevel>{0,1}</contourLevel>
  <transformId>{0,1}</transformId>
  <format>{1,1}</format>
</threeDVolume>

<xs:element name="threeDVolume" type="threeDVolumeType" minOccurs="0"/>

<xs:element name="file" type="xs:token"/>

<xs:element name="objectPath" type="xs:token" minOccurs="0">
  <xs:annotation>
    <xs:documentation>This is particularly relevant if all the segments are stored in one file, like in HDF5.</xs:documentation>
  </xs:annotation>
</xs:element>

<xs:element name="contourLevel" type="xs:float" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Should be specified if map is non-binary</xs:documentation>
  </xs:annotation>
</xs:element>

<xs:element name="transformId" type="xs:nonNegativeInteger" minOccurs="0"/>

<xs:element name="format">
  <xs:simpleType>
    <xs:restriction base="xs:string">
      <xs:enumeration value="runLengthEncoding"/>
      <xs:enumeration value="MRC"/>
      <xs:enumeration value="Segger"/>
      <xs:enumeration value="EMAN"/>
    </xs:restriction>
  </xs:simpleType>
</xs:element>

<shapePrimitiveList>
  <shapePrimitive>{1,unbounded}</shapePrimitive>
</shapePrimitiveList>

<xs:element name="shapePrimitiveList" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="shapePrimitive" minOccurs="1" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<xs:element name="shapePrimitive"/>

<contourList>
  <contour id="">{1,unbounded}</contour>
  <transformId>{0,1}</transformId>
</contourList>

<xs:element name="contourList" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="contour" type="contourType" minOccurs="1" maxOccurs="unbounded"/>
      <xs:element name="transformId" type="xs:nonNegativeInteger" minOccurs="0"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<contour id="">
  <p x="" y="" z="">{1,unbounded}</p>
</contour>

<xs:element name="contour" type="contourType" minOccurs="1" maxOccurs="unbounded"/>

<xs:element name="p" type="floatVectorType" maxOccurs="unbounded"/>

<xs:element name="transformId" type="xs:nonNegativeInteger" minOccurs="0"/>

<meshList>
  <mesh id="">{1,unbounded}</mesh>
</meshList>

<xs:element name="meshList" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="mesh" type="meshType" minOccurs="1" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<mesh id="">
  <vertexList numVertices="">{1,1}</vertexList>
  <polygonList numPolygons="">{1,1}</polygonList>
  <transformId>{0,1}</transformId>
</mesh>

<xs:element name="mesh" type="meshType" minOccurs="1" maxOccurs="unbounded"/>

<vertexList numVertices="">
  <v designation="vertex" vID="">{3,unbounded}</v>
</vertexList>

<xs:element name="vertexList" type="vertexListType"/>

<v designation="vertex" vID="">
  <x>{1,1}</x>
  <y>{1,1}</y>
  <z>{1,1}</z>
</v>

<xs:element name="v" type="vertexType" minOccurs="3" maxOccurs="unbounded"/>

<xs:element name="x" type="xs:float"/>

<xs:element name="y" type="xs:float"/>

<xs:element name="z" type="xs:float"/>

<polygonList numPolygons="">
  <P PID="">{1,1}</P>
</polygonList>

<xs:element name="polygonList" type="polygonListType"/>

<P PID="">
  <v>{3,unbounded}</v>
</P>

<xs:element name="P" type="polygonType"/>

<xs:element name="v" type="xs:nonNegativeInteger" minOccurs="3" maxOccurs="unbounded"/>

<xs:element name="transformId" type="xs:nonNegativeInteger" minOccurs="0"/>

<xs:element name="details" type="xs:string" minOccurs="0"/>

<xs:element name="rows" type="xs:positiveInteger"/>

<xs:element name="cols" type="xs:positiveInteger"/>

<xs:element name="data" type="xs:string"/>

<xs:element name="phi" type="angleDegreeType"/>

<xs:element name="theta" type="angleDegreeType"/>

<xs:element name="psi" type="angleDegreeType"/>

<xs:element name="x" type="xs:float"/>

<xs:element name="y" type="xs:float"/>