<segmentation schema_version="0.8.0.dev1">
  <version>{1,1}</version>
  <name>{1,1}</name>
  <software_list>{0,1}</software_list>
  <transform_list>{1,1}</transform_list>
  <primary_descriptor>{1,1}</primary_descriptor>
  <bounding_box xmax="" xmin="0" ymax="" ymin="0" zmax="" zmin="0">{0,1}</bounding_box>
  <global_external_references>{0,1}</global_external_references>
  <segment_list>{1,1}</segment_list>
  <lattice_list>{0,1}</lattice_list>
  <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_list" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="software" type="software_type" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="transform_list" minOccurs="1">
        <xs:annotation>
          <xs:documentation>Mandatory field. The first 'transformation_matrix' must be the image-to-physical transform with scale parameters (diagonal elements) in angstroms (Å). The right-most column consists of the translation applied and is the physical distance from the physical origin in anstroms (Å).</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="transformation_matrix" type="transformation_matrix_type" minOccurs="1" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="primary_descriptor">
        <xs:annotation>
          <xs:documentation>Mandatory field. Designates the element type within 'segment_list' that contains the primary description of the segments. Constrained to be either 'three_d_volume', 'shape_primitive_list', or 'mesh_list'.</xs:documentation>
        </xs:annotation>
        <xs:simpleType>
          <xs:restriction base="xs:string">
            <xs:enumeration value="three_d_volume"/>
            <xs:enumeration value="shape_primitive_list"/>
            <xs:enumeration value="mesh_list"/>
          </xs:restriction>
        </xs:simpleType>
      </xs:element>
      <xs:element name="bounding_box" type="bounding_box_type" minOccurs="0"/>
      <xs:element name="global_external_references" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="ref" type="external_reference_type" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="segment_list">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="segment" type="segment_type" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="lattice_list" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="lattice" type="lattice_type" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="details" type="xs:string" minOccurs="0"/>
    </xs:sequence>
    <xs:attribute name="schema_version" type="xs:string" default="0.8.0.dev1">
      <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

0.6.0a4, 2017/09/25, Paul Korir:
3) Restructured global external references to have the form <ref [attrs]/>
4) Now externalReferenceType has attributes: type (required), otherType (required), value (required), label (new, optional), description (new, optional)

0.6.0a4, 2017/11/23, Paul Korir:
5) Replaced all active 'token' to 'string' types

0.7.0.dev0, 2017/11/09, Paul Korir:
1) new 3D volume type: 'threeDVolumeType' (previous one is 'oldThreeDVolumeType'
    supports both byte/integer lattices and density volumes (for subtomogram averages)
2) embedded volume as base64 string using new 'latticeType'
3) removed contour representation

0.7.0.dev0, 2018/05/04, Paul Korir:
4) segment name added
5) removed filePath
6) removed viewVectorRotation and canonicalEulerAngles
7) colour has rgbaType now

0.7.0.dev0, 2018/07/18, Paul Korir:
8) vertex designation now 'surface' or 'normal'

0.8.0.dev0, 2019/11/08, Paul Korir:
1) converted all camelCase names to underscore_case
2) 'polygon' is now 'triangle'
3) changed 'transformation_matrix' from being a subsitution group
4) external_reference (ref): attributes changed to 'resource', 'url', 'accession' from
'type', 'otherType' and 'value', respectively
5) renamed 'macromolecules_and_complexes_type' to 'complexes_and_macromolecules_type'
6) restructured 'macromolecules' to 'macromolecule_list' (same for 'complexes')
7) now 'macromolecule_list' contains 'macromolecule' with 'id' and text value for accession

0.8.0.dev0, 2019/12/18, Paul Korir:
8) now 'transform_list' is mandatory with at least one 'transformation_matrix' for the image-to-physical transform
9) changed 'software' to be a 'software_list' of zero or more 'software' items; software 'version' now required if 'software' is defined
10) 'complexes_and_macromolecules' are deprecated (were for annotation; 'external_references' are sufficient)
11) overhaul of 'mesh' field to have 'vertices', 'normals' (optional) and 'triangles' which are base64-encoded strings of actual data
12) 'xmax', 'ymax' and 'zmax' of 'bounding_box' are mandatory 

0.8.0.dev1, 2020/01/29, Paul Korir:
Bugfix: 'software' elements should have an 'id' attribute; 'id' attribute erroneously placed in 'software_list' and should be a list of 0 or more 'software' elements

0.8.0.dev1, 2023/01/30, Paul Korir:
Clarified that transform units are in angstroms (Å).
]]>
        </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_list>
  <software id="">{0,unbounded}</software>
</software_list>

<xs:element name="software_list" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="software" type="software_type" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<software id="">
  <name>{1,1}</name>
  <version>{1,1}</version>
  <processing_details>{0,1}</processing_details>
</software>

<xs:element name="software" type="software_type" minOccurs="0" maxOccurs="unbounded"/>

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

<xs:element name="version" type="xs:string" minOccurs="1"/>

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

<transform_list>
  <transformation_matrix id="">{1,unbounded}</transformation_matrix>
</transform_list>

<xs:element name="transform_list" minOccurs="1">
  <xs:annotation>
    <xs:documentation>Mandatory field. The first 'transformation_matrix' must be the image-to-physical transform with scale parameters (diagonal elements) in angstroms (Å). The right-most column consists of the translation applied and is the physical distance from the physical origin in anstroms (Å).</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="transformation_matrix" type="transformation_matrix_type" minOccurs="1" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<transformation_matrix id="">
  <rows>{1,1}</rows>
  <cols>{1,1}</cols>
  <data>{1,1}</data>
</transformation_matrix>

<xs:element name="transformation_matrix" type="transformation_matrix_type" minOccurs="1" maxOccurs="unbounded"/>

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

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

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

<xs:element name="primary_descriptor">
  <xs:annotation>
    <xs:documentation>Mandatory field. Designates the element type within 'segment_list' that contains the primary description of the segments. Constrained to be either 'three_d_volume', 'shape_primitive_list', or 'mesh_list'.</xs:documentation>
  </xs:annotation>
  <xs:simpleType>
    <xs:restriction base="xs:string">
      <xs:enumeration value="three_d_volume"/>
      <xs:enumeration value="shape_primitive_list"/>
      <xs:enumeration value="mesh_list"/>
    </xs:restriction>
  </xs:simpleType>
</xs:element>

<xs:element name="bounding_box" type="bounding_box_type" minOccurs="0"/>

<global_external_references>
  <ref accession="" description="" id="" label="" resource="" url="">{0,unbounded}</ref>
</global_external_references>

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

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

<segment_list>
  <segment id="" parent_id="">{1,unbounded}</segment>
</segment_list>

<xs:element name="segment_list">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="segment" type="segment_type" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<segment id="" parent_id="">
  <biological_annotation>{0,1}</biological_annotation>
  <colour>{0,1}</colour>
  <three_d_volume>{0,1}</three_d_volume>
  <shape_primitive_list>{0,1}</shape_primitive_list>
  <mesh_list>{0,1}</mesh_list>
</segment>

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

<biological_annotation>
  <name>{0,1}</name>
  <description>{0,1}</description>
  <external_references>{0,1}</external_references>
  <number_of_instances>{0,1}</number_of_instances>
</biological_annotation>

<xs:element name="biological_annotation" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="name" type="xs:string" minOccurs="0"/>
      <xs:element name="description" type="xs:string" minOccurs="0"/>
      <xs:element name="external_references" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="ref" type="external_reference_type" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="number_of_instances" 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="name" type="xs:string" minOccurs="0"/>

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

<external_references>
  <ref accession="" description="" id="" label="" resource="" url="">{0,unbounded}</ref>
</external_references>

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

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

<xs:element name="number_of_instances" 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>

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

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

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

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

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

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

<three_d_volume>
  <lattice_id>{1,1}</lattice_id>
  <value>{1,1}</value>
  <transform_id>{0,1}</transform_id>
</three_d_volume>

<xs:element name="three_d_volume" type="three_d_volume_type" minOccurs="0"/>

<xs:element name="lattice_id" type="xs:nonNegativeInteger">
  <xs:annotation>
    <xs:documentation>The ID of the lattice in 'latticeList' that contains the data referred to by this 3D volume.</xs:documentation>
  </xs:annotation>
</xs:element>

<xs:element name="value" type="xs:float">
  <xs:annotation>
    <xs:documentation>The 'value' can either be a contour level used to denote a boundary or the voxel value for this segmentation. The value of 'mode' will be used to cast this elements value.</xs:documentation>
  </xs:annotation>
</xs:element>

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

<shape_primitive_list>
  <shape_primitive>{1,unbounded}</shape_primitive>
</shape_primitive_list>

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

<xs:element name="shape_primitive"/>

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

<xs:element name="mesh_list" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="mesh" type="mesh_type" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<mesh id="">
  <vertices data="" endianness="little" mode="float32" num_vertices="">{1,1}</vertices>
  <normals data="" endianness="little" mode="float32" num_normals="">{0,1}</normals>
  <triangles data="" endianness="little" mode="uint32" num_triangles="">{1,1}</triangles>
  <transform_id>{0,1}</transform_id>
</mesh>

<xs:element name="mesh" type="mesh_type" maxOccurs="unbounded"/>

<xs:element name="vertices" type="vertices_type" minOccurs="1"/>

<xs:element name="normals" type="normals_type" minOccurs="0"/>

<xs:element name="triangles" type="triangles_type" minOccurs="1"/>

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

<lattice_list>
  <lattice id="">{1,unbounded}</lattice>
</lattice_list>

<xs:element name="lattice_list" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="lattice" type="lattice_type" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

<lattice id="">
  <mode>{1,1}</mode>
  <endianness>{1,1}</endianness>
  <size>{1,1}</size>
  <start>{1,1}</start>
  <data>{1,1}</data>
</lattice>

<xs:element name="lattice" type="lattice_type" maxOccurs="unbounded"/>

<xs:element name="mode" type="mode_type">
  <xs:annotation>
    <xs:documentation>Mode specifies the datatype of each voxel in the 3D volume</xs:documentation>
  </xs:annotation>
</xs:element>

<xs:element name="endianness" type="endian_type" default="little">
  <xs:annotation>
    <xs:documentation>The manner in which the binary data is read.</xs:documentation>
  </xs:annotation>
</xs:element>

<size>
  <cols>{1,1}</cols>
  <rows>{1,1}</rows>
  <sections>{1,1}</sections>
</size>

<xs:element name="size" type="volume_structure_type">
  <xs:annotation>
    <xs:documentation>The 3D volume size in voxels.</xs:documentation>
  </xs:annotation>
</xs:element>

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

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

<xs:element name="sections" type="xs:nonNegativeInteger"/>

<start>
  <cols>{1,1}</cols>
  <rows>{1,1}</rows>
  <sections>{1,1}</sections>
</start>

<xs:element name="start" type="volume_index_type">
  <xs:annotation>
    <xs:documentation>The index values for the start voxel.</xs:documentation>
  </xs:annotation>
</xs:element>

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

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

<xs:element name="sections" type="xs:integer"/>

<xs:element name="data" type="xs:string">
  <xs:annotation>
    <xs:documentation>Data is a base64 encoded string of zlib-compressed binary data.</xs:documentation>
  </xs:annotation>
</xs:element>

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

<cuboid id="">
  <x>{1,1}</x>
  <y>{1,1}</y>
  <z>{1,1}</z>
  <transform_id>{1,1}</transform_id>
  <attribute>{0,1}</attribute>
</cuboid>

<xs:element name="cuboid" substitutionGroup="shape_primitive">
  <xs:annotation>
    <xs:documentation>3D rectangle</xs:documentation>
    <xs:documentation>'attribute' could refer to figure of merit (FOM)</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="x" type="dimension_type"/>
      <xs:element name="y" type="dimension_type"/>
      <xs:element name="z" type="dimension_type"/>
      <xs:element name="transform_id" type="xs:nonNegativeInteger"/>
      <xs:element name="attribute" type="xs:float" minOccurs="0"/>
    </xs:sequence>
    <xs:attribute name="id" type="xs:nonNegativeInteger"/>
  </xs:complexType>
</xs:element>

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