XML Schema Documentation

Table of Contents

Master schema documentation file: ome.xsd.html

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Schema Document Properties

Target Namespace http://www.openmicroscopy.org/XMLschemas/CLI/RC1/CLI.xsd
Version RC1
Element and Attribute Namespaces
  • Global element and attribute declarations belong to this schema's target namespace.
  • By default, local element declarations belong to this schema's target namespace.
  • By default, local attribute declarations have no namespace.
Schema Composition
Documentation Open Microscopy Environment Command Line Interface XML Schema Author: Josiah Johnston

Declared Namespaces

Prefix Namespace
Default namespace http://www.w3.org/2001/XMLSchema
xml http://www.w3.org/XML/1998/namespace
CLI http://www.openmicroscopy.org/XMLschemas/CLI/RC1/CLI.xsd
Schema Component Representation
<schema targetNamespace="http://www.openmicroscopy.org/XMLschemas/CLI/RC1/CLI.xsd" version="RC1" elementFormDefault="qualified">
<import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/xml.xsd"/>
...
</schema>
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Global Declarations

Element: AutoIterate

Name AutoIterate
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Iterates a dimension over its entire range. Produces outputs.
Logical Diagram
element_OutputTo
XML Instance Representation
<CLI:AutoIterate>
<CLI:OutputTo> ... </CLI:OutputTo> [1..*]
</CLI:AutoIterate>
Diagram
element_OutputTo
Schema Component Representation
<element name="AutoIterate">
<complexType>
<sequence>
<element ref=" CLI:OutputTo " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: BitsPerPixel

Name BitsPerPixel
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:BitsPerPixel
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="BitsPerPixel">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: CommandLine

Name CommandLine
Type Locally-defined complex type
Nillable no
Abstract no
Documentation This describes the string that will be passed to a command line program via command line parameters. The command line handler will perform basic variable substitution on sub elements of this. Example: when you use the program, you type: /OME/bin/OME_Image_XYZ_stats Path=[path to repository file] Dims=[X],[Y],[Z],[W],[T],[BytesPerPix] XML specification of the command line parameters is: <CommandLine>Path=<RawImageFilePath/> Dims=<sizeX/>,<sizeY/>,<sizeZ/>,<sizeW/>,<sizeT/>,<BPP/></CommandLine>
Logical Diagram
element_Parameter
XML Instance Representation
<CLI:CommandLine>
<!--
Uniqueness Constraint - CommandLine_XYPlaneID
Selector - .//CLI:XYPlane
Field(s) - @XYPlaneID
-->
<!--
Key Reference Constraint - CommandLine_XYPlaneID_Ref
Selector - .//CLI:Match
Field(s) - @XYPlaneID
Refers to - CLI:CommandLine_XYPlaneID
-->

<CLI:Parameter> ... </CLI:Parameter> [0..*]
</CLI:CommandLine>
Diagram
element_Parameter
Schema Component Representation
<element name="CommandLine">
<complexType>
<sequence>
<element ref=" CLI:Parameter " minOccurs="0" maxOccurs="unbounded"/>
</sequence>
</complexType>
<unique name="CommandLine_XYPlaneID">
<selector xpath=".//CLI:XYPlane"/>
<field xpath="@XYPlaneID"/>
</unique>
<keyref name="CommandLine_XYPlaneID_Ref" refer=" CLI:CommandLine_XYPlaneID ">
<selector xpath=".//CLI:Match"/>
<field xpath="@XYPlaneID"/>
</keyref>
</element>
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Element: CustomRecord

Name CustomRecord
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Used to construct an arbitrarily formatted record. Not currently supported. email Josiah <siah@nih.gov> if you need this implemented.
Logical Diagram
element_InputSubString
XML Instance Representation
<CLI:CustomRecord>
<CLI:InputSubString> ... </CLI:InputSubString> [1..*]
</CLI:CustomRecord>
Diagram
element_InputSubString
Schema Component Representation
<element name="CustomRecord">
<complexType>
<sequence>
<element ref=" CLI:InputSubString " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: DelimitedRecord

Name DelimitedRecord
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Use this to construct a Delimited Record. (i.e. tab delimitted, comma delimitted, etc). At some point this will be expanded to include XYPlanes and RawImageFilePath.
Logical Diagram
element_Input
XML Instance Representation
<CLI:DelimitedRecord
FieldDelimiter="string [1]

'This string will be used to separate fields in this record.'

"
RecordDelimiter="string [0..1]

'This will be used to separate Records. Defaults to a newline (a newline as interpretted by perl).'

">
<CLI:Input> ... </CLI:Input> [1..*]
</CLI:DelimitedRecord>
Diagram
element_Input
Schema Component Representation
<element name="DelimitedRecord">
<complexType>
<sequence>
<element ref=" CLI:Input " maxOccurs="unbounded"/>
</sequence>
<attribute name="FieldDelimiter" type=" string " use="required"/>
<attribute name="RecordDelimiter" type=" string " default="\n"/>
</complexType>
</element>
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Element: End

Name End
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an end point of iteration. Not currently supported.
Logical Diagram
XML Instance Representation
<CLI:End
Location="string [1]

'This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Input \'foo\', Location=\"foo.bar\"'

"/>
Diagram
attributeGroup_InputLocation
Schema Component Representation
<element name="End">
<complexType>
<attributeGroup ref=" CLI:InputLocation "/>
</complexType>
</element>
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Element: ExecutionInstructions

Name ExecutionInstructions
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Tied to DB. Table PROGRAMS Column EXECUTION
Logical Diagram
element_CommandLine element_STDIN element_STDOUT
XML Instance Representation
<CLI:ExecutionInstructions
ExecutionPoint=" string (value comes from list: {'executeGlobal'|'startDataset'|'startImage'|'startFeature'|'finishFeature'|'finishImage'|'finishDataset'}) [1]

'Assigns a execution point for the analysis.'

"
MakesNewFeature="boolean [0..1]">
<CLI:CommandLine> ... </CLI:CommandLine> [0..1]
<CLI:STDIN> ... </CLI:STDIN> [0..1]
<CLI:STDOUT> ... </CLI:STDOUT> [0..1]
</CLI:ExecutionInstructions>
Diagram
element_CommandLine element_STDIN element_STDOUT
Schema Component Representation
<element name="ExecutionInstructions">
<complexType>
<sequence>
<element ref=" CLI:CommandLine " minOccurs="0"/>
<element ref=" CLI:STDIN " minOccurs="0"/>
<element ref=" CLI:STDOUT " minOccurs="0"/>
</sequence>
<attribute name="ExecutionPoint" use="required">
<simpleType>
<restriction base=" string ">
<enumeration value="executeGlobal"/>
<enumeration value="startDataset"/>
<enumeration value="startImage"/>
<enumeration value="startFeature"/>
<enumeration value="finishFeature"/>
<enumeration value="finishImage"/>
<enumeration value="finishDataset"/>
</restriction>
</simpleType>
</attribute>
<attribute name="MakesNewFeature" type=" boolean " default="false"/>
</complexType>
</element>
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Element: Index

Name Index
Type Locally-defined complex type
Nillable no
Abstract no
Documentation This specifies what semantic elements of the attributes should be used to merge them into records. Every formalInput in a record should be included in this. For records with multiple indexes, (Stack Statistics for example has theT and theC), specify two indexes. The records will be sorted based on the index order. This means a stack statistics record that specifies theC as an index before theT will be sorted first on theC, then on theT.
Logical Diagram
element_Input
XML Instance Representation
<CLI:Index>
<CLI:Input> ... </CLI:Input> [1..*]
</CLI:Index>
Diagram
element_Input
Schema Component Representation
<element name="Index">
<complexType>
<sequence>
<element ref=" CLI:Input " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: Input

Name Input
Type Locally-defined complex type
Nillable no
Abstract no
Documentation References a particular column in a FormalInput. Used for variable substitution.
Logical Diagram
XML Instance Representation
<CLI:Input
Location="string [1]

'This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Input \'foo\', Location=\"foo.bar\"'

"
DivideBy="string [0..1]"
MultiplyBy="string [0..1]"/>
Diagram
attributeGroup_InputLocation
Schema Component Representation
<element name="Input">
<complexType>
<attributeGroup ref=" CLI:InputLocation "/>
<attribute name="DivideBy" type=" string "/>
<attribute name="MultiplyBy" type=" string "/>
</complexType>
</element>
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Element: InputRecord

Name InputRecord
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Groups a set of inputs into records.
Logical Diagram
element_Index
XML Instance Representation
<CLI:InputRecord>
<!--
Uniqueness Constraint - InputRecord_XYPlaneID
Selector - .//CLI:XYPlane
Field(s) - @XYPlaneID
-->
<!--
Key Reference Constraint - InputRecord_XYPlaneID_Ref
Selector - .//CLI:Match
Field(s) - @XYPlaneID
Refers to - CLI:InputRecord_XYPlaneID
-->

<CLI:Index> ... </CLI:Index> [1..*]
Start Choice [1]
<CLI:DelimitedRecord> ... </CLI:DelimitedRecord> [1]
<CLI:CustomRecord> ... </CLI:CustomRecord> [1]
End Choice
</CLI:InputRecord>
Diagram
element_Index element_DelimitedRecord element_CustomRecord
Schema Component Representation
<element name="InputRecord">
<complexType>
<sequence>
<element ref=" CLI:Index " maxOccurs="unbounded"/>
<choice>
<element ref=" CLI:DelimitedRecord "/>
<element ref=" CLI:CustomRecord "/>
</choice>
</sequence>
</complexType>
<unique name="InputRecord_XYPlaneID">
<selector xpath=".//CLI:XYPlane"/>
<field xpath="@XYPlaneID"/>
</unique>
<keyref name="InputRecord_XYPlaneID_Ref" refer=" CLI:InputRecord_XYPlaneID ">
<selector xpath=".//CLI:Match"/>
<field xpath="@XYPlaneID"/>
</keyref>
</element>
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Element: InputSubString

Name InputSubString
Type Locally-defined complex type
Nillable no
Abstract no
Logical Diagram
element_Input element_XYPlane element_RawImageFilePath element_RawText
XML Instance Representation
<CLI:InputSubString>
Start Choice [1]
<CLI:Input> ... </CLI:Input> [1]
<CLI:XYPlane> ... </CLI:XYPlane> [1]
<CLI:RawImageFilePath> ... </CLI:RawImageFilePath> [1]
<CLI:RawText> ... </CLI:RawText> [1]
End Choice
</CLI:InputSubString>
Diagram
element_Input element_XYPlane element_RawImageFilePath element_RawText
Schema Component Representation
<element name="InputSubString">
<complexType>
<choice>
<element ref=" CLI:Input "/>
<element ref=" CLI:XYPlane "/>
<element ref=" CLI:RawImageFilePath "/>
<element ref=" CLI:RawText "/>
</choice>
</complexType>
</element>
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Element: IterateRange

Name IterateRange
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Iterate this dimension over a range of values. Produces outputs.
Logical Diagram
element_Start element_End element_OutputTo
XML Instance Representation
<CLI:IterateRange>
<CLI:Start> ... </CLI:Start> [1]
<CLI:End> ... </CLI:End> [1]
<CLI:OutputTo> ... </CLI:OutputTo> [1..*]
</CLI:IterateRange>
Diagram
element_Start element_End element_OutputTo
Schema Component Representation
<element name="IterateRange">
<complexType>
<sequence>
<element ref=" CLI:Start "/>
<element ref=" CLI:End "/>
<element ref=" CLI:OutputTo " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: Match

Name Match
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Used to reference the index method used by another XYplane. Effectively syncs the planes on certain dimensions. Use with caution. Unsynced dimensions need to be compatible.
Logical Diagram
XML Instance Representation
<CLI:Match
XYPlaneID="string [1]

'References another Plane.'

"/>
Diagram
Schema Component Representation
<element name="Match">
<complexType>
<attribute name="XYPlaneID" type=" string " use="required"/>
</complexType>
</element>
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Element: Output

Name Output
Type Locally-defined complex type
Nillable no
Abstract no
Documentation References a particular column of a FormalOutput.
Logical Diagram
element_OutputTo
XML Instance Representation
<CLI:Output
AccessBy="integer [1]

'Describes how to access information extracted using a regular expression. Examples are 1, 2, 3, ...'

">
<CLI:OutputTo> ... </CLI:OutputTo> [1..*]
</CLI:Output>
Diagram
element_OutputTo
Schema Component Representation
<element name="Output">
<complexType>
<sequence>
<element ref=" CLI:OutputTo " maxOccurs="unbounded"/>
</sequence>
<attribute name="AccessBy" type=" integer " use="required"/>
</complexType>
</element>
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Element: OutputRecord

Name OutputRecord
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Groups a set of outputs into records.
Logical Diagram
XML Instance Representation
<CLI:OutputRecord
RepeatCount="positiveInteger [0..1]

'RepeatCount specifies how many times to read a record. If it is not specified, reading will continue until it reaches the end of the output stream. If used in conjuction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first.'

"
TerminateAt="string [0..1]

'TerminateAt specifies a regular expression. When a match to this is found, reading will stop. If used in conjuction with RepeatCount, reading will stop after RepeatCount or TerminateAt, whichever comes first.'

"/>
Diagram
Schema Component Representation
<element name="OutputRecord">
<complexType>
<attribute name="RepeatCount" type=" positiveInteger "/>
<attribute name="TerminateAt" type=" string "/>
</complexType>
</element>
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Element: OutputTo

Name OutputTo
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies location to write output. One data chunk that the Output element references may be written to one or more places.
Logical Diagram
XML Instance Representation
<CLI:OutputTo
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
attributeGroup_OutputLocation
Schema Component Representation
<element name="OutputTo">
<complexType>
<attributeGroup ref=" CLI:OutputLocation "/>
</complexType>
</element>
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Element: Parameter

Name Parameter
Type Locally-defined complex type
Nillable no
Abstract no
Documentation All Formal Inputs referenced within this scope should have a count of 0 or 1.
Logical Diagram
element_InputSubString
XML Instance Representation
<CLI:Parameter>
<CLI:InputSubString> ... </CLI:InputSubString> [1..*]
</CLI:Parameter>
Diagram
element_InputSubString
Schema Component Representation
<element name="Parameter">
<complexType>
<sequence>
<element ref=" CLI:InputSubString " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: Path

Name Path
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies a data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:Path
FileID="string [0..1]

'Refers to a TempFile'

"/>
Diagram
Schema Component Representation
<element name="Path">
<complexType>
<attribute name="FileID" type=" string "/>
</complexType>
</element>
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Element: PixelOutput

Name PixelOutput
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Allows SemanticTypes Pixels and PixelsPlane to be outputs. The subelements specify locations for the population of data. This data population is useful for a Plane projection algorithm that has the same X and Y dimensions as the Pixels it is operating on. Alternately, these fields may be filled by ouput from STDOUT. The FileSHA1 subelement is automatically calculated for the pixel dump file.
Logical Diagram
element_SizeX element_SizeY element_SizeZ element_SizeC element_SizeT element_PixelType element_BitsPerPixel element_Repository element_Path
XML Instance Representation
<CLI:PixelOutput
type=" string (value comes from list: {'Pixels'|'PixelsPlane'}) [0..1]"
FormalOutput="string [0..1]"
UseBase="string [0..1]

'Unimplemented. Will subsume all subelements except <Repository> and <Path>. This will reference a formal input. That input be used for copying all possible data that has not been filled by other means.'

">
<CLI:SizeX> ... </CLI:SizeX> [0..1]
<CLI:SizeY> ... </CLI:SizeY> [0..1]
<CLI:SizeZ> ... </CLI:SizeZ> [0..1]
<CLI:SizeC> ... </CLI:SizeC> [0..1]
<CLI:SizeT> ... </CLI:SizeT> [0..1]
<CLI:PixelType> ... </CLI:PixelType> [0..1]
<CLI:BitsPerPixel> ... </CLI:BitsPerPixel> [0..1]
<CLI:Repository> ... </CLI:Repository> [0..1]
<CLI:Path> ... </CLI:Path> [0..1]
</CLI:PixelOutput>
Diagram
element_SizeX element_SizeY element_SizeZ element_SizeC element_SizeT element_PixelType element_BitsPerPixel element_Repository element_Path
Schema Component Representation
<element name="PixelOutput">
<complexType>
<sequence>
<element ref=" CLI:SizeX " minOccurs="0"/>
<element ref=" CLI:SizeY " minOccurs="0"/>
<element ref=" CLI:SizeZ " minOccurs="0"/>
<element ref=" CLI:SizeC " minOccurs="0"/>
<element ref=" CLI:SizeT " minOccurs="0"/>
<element ref=" CLI:PixelType " minOccurs="0"/>
<element ref=" CLI:BitsPerPixel " minOccurs="0"/>
<element ref=" CLI:Repository " minOccurs="0"/>
<element ref=" CLI:Path " minOccurs="0"/>
</sequence>
<attribute name="type">
<simpleType>
<restriction base=" string ">
<enumeration value="Pixels"/>
<enumeration value="PixelsPlane"/>
</restriction>
</simpleType>
</attribute>
<attribute name="FormalOutput" type=" string "/>
<attribute name="UseBase" type=" string "/>
</complexType>
</element>
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Element: PixelType

Name PixelType
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:PixelType
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="PixelType">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: PixelsInput

Name PixelsInput
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Grants file path to Pixels input. Future plans include dumping pixel file contents as well.
Logical Diagram
XML Instance Representation
<CLI:PixelsInput
Location="string [1]

'This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Input \'foo\', Location=\"foo.bar\"'

"
SubstituteWith=" string (value comes from list: {'path'}) [1]"/>
Diagram
attributeGroup_InputLocation
Schema Component Representation
<element name="PixelsInput">
<complexType>
<attributeGroup ref=" CLI:InputLocation "/>
<attribute name="SubstituteWith" use="required">
<simpleType>
<restriction base=" string ">
<enumeration value="path"/>
</restriction>
</simpleType>
</attribute>
</complexType>
</element>
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Element: RawImageFilePath

Name RawImageFilePath
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Used with variable substitution. This will be substituted with the path and file of the raw pixel dump image file. e.g. /OME/repository/1-tinyTest.ori
Logical Diagram
XML Instance Representation
<CLI:RawImageFilePath
Pixels="string [1]

'References a formal input of semantic type \'Pixels\''

"/>
Diagram
Schema Component Representation
<element name="RawImageFilePath">
<complexType>
<attribute name="Pixels" type=" string " use="required"/>
</complexType>
</element>
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Element: RawText

Name RawText
Type string
Nillable no
Abstract no
Logical Diagram
XML Instance Representation
<CLI:RawText> string </CLI:RawText>
Diagram
Schema Component Representation
<element name="RawText" type=" string "/>
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Element: Repository

Name Repository
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:Repository
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="Repository">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: STDIN

Name STDIN
Type Locally-defined complex type
Nillable no
Abstract no
Documentation This specifies what and how to write to STDIN. Currently this is still in development. I would STRONGLY recommend contacting Josiah <siah@nih.gov> before coding against it.
Logical Diagram
element_InputRecord
XML Instance Representation
<CLI:STDIN>
<CLI:InputRecord> ... </CLI:InputRecord> [1..*]
</CLI:STDIN>
Diagram
element_InputRecord
Schema Component Representation
<element name="STDIN">
<complexType>
<sequence>
<element ref=" CLI:InputRecord " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: STDOUT

Name STDOUT
Type Locally-defined complex type
Nillable no
Abstract no
Documentation This specifies what and how to read STDOUT.
Logical Diagram
element_OutputRecord
XML Instance Representation
<CLI:STDOUT>
<CLI:OutputRecord> ... </CLI:OutputRecord> [1..*]
</CLI:STDOUT>
Diagram
element_OutputRecord
Schema Component Representation
<element name="STDOUT">
<complexType>
<sequence>
<element ref=" CLI:OutputRecord " maxOccurs="unbounded"/>
</sequence>
</complexType>
</element>
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Element: SizeC

Name SizeC
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:SizeC
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="SizeC">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: SizeT

Name SizeT
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:SizeT
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="SizeT">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: SizeX

Name SizeX
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:SizeX
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="SizeX">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: SizeY

Name SizeY
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:SizeY
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="SizeY">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: SizeZ

Name SizeZ
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies an input data location for populating the semantic element
Logical Diagram
XML Instance Representation
<CLI:SizeZ
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"/>
Diagram
Schema Component Representation
<element name="SizeZ">
<complexType>
<attribute name="Location" type=" string " use="required"/>
</complexType>
</element>
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Element: Start

Name Start
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Specifies a starting point of iteration. Not currently supported.
Logical Diagram
XML Instance Representation
<CLI:Start
Location="string [1]

'This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Input \'foo\', Location=\"foo.bar\"'

"/>
Diagram
attributeGroup_InputLocation
Schema Component Representation
<element name="Start">
<complexType>
<attributeGroup ref=" CLI:InputLocation "/>
</complexType>
</element>
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Element: TempFile

Name TempFile
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Will be substituted with the full path of the file created. The OutputTo feature is not implemented yet.
Logical Diagram
element_OutputTo
XML Instance Representation
<CLI:TempFile
FileID="string [0..1]

'Should uniquely identify this tempFile. It is used to retrieve the path as a variable.'

"
Repository="string [0..1]

'If specified, the temporary file will be located in the repository. This specifies where to find a repository attribute by FormalInputName and SemanticElementName(s). Following references is valid. e.g. Location=\"PixelInput.Repository\"'

">
<CLI:OutputTo> ... </CLI:OutputTo> [0..*]
</CLI:TempFile>
Diagram
element_OutputTo
Schema Component Representation
<element name="TempFile">
<complexType>
<sequence>
<element ref=" CLI:OutputTo " minOccurs="0" maxOccurs="unbounded"/>
</sequence>
<attribute name="FileID" type=" string "/>
<attribute name="Repository" type=" string "/>
</complexType>
</element>
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Element: UseValue

Name UseValue
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Use an input value. References an input, does not produce an output.
Logical Diagram
XML Instance Representation
<CLI:UseValue
Location="string [1]

'This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Input \'foo\', Location=\"foo.bar\"'

"/>
Diagram
attributeGroup_InputLocation
Schema Component Representation
<element name="UseValue">
<complexType>
<attributeGroup ref=" CLI:InputLocation "/>
</complexType>
</element>
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Element: XYPlane

Name XYPlane
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Describes an XY plane. Used with variable substitution. This will be substituted with a dynamically generated plane.
Logical Diagram
element_theZ element_theT element_theW
XML Instance Representation
<CLI:XYPlane
BPP=" integer (value comes from list: {'8'|'16'}) [0..1]

'Specifies bits per pixel (BPP) the module is expecting. If the program can deal with either 8 or 16 bit images, leave this out or specify 16. Both of these result in the BPP of the image being used. That is, if the image is 8 bits, the module will get an 8 bits per pixel. If the image is 16 bits, the module will get 16 bits per pixel. Currently, only native image pixels are supported.'

"
Format=" string (value comes from list: {'RAW'|'TIFF'}) [0..1]

'Specifies the expected format of the plane. RAW corrosponds to OME repository format of pixel dump. TIFF corrosponds to TIFF files. Currently only TIFF is supported.'

"
XYPlaneID="string [0..1]

'Needed if you need another plane to match indexes. Referenced by the Match element.'

"
Return=" string (value comes from list: {'FilePath'|'File'}) [0..1]

'Specifies whether to the program needs the FilePath or the FileContents. Currently, only the FilePath is supported.'

"
Pixels="string [1]

'References a formal input of semantic type \'Pixels\''

">
<CLI:theZ> ... </CLI:theZ> [1]
<CLI:theT> ... </CLI:theT> [1]
<CLI:theW> ... </CLI:theW> [1]
</CLI:XYPlane>
Diagram
element_theZ element_theT element_theW
Schema Component Representation
<element name="XYPlane">
<complexType>
<sequence>
<element ref=" CLI:theZ "/>
<element ref=" CLI:theT "/>
<element ref=" CLI:theW "/>
</sequence>
<attribute name="BPP">
<simpleType>
<restriction base=" integer ">
<enumeration value="8"/>
<enumeration value="16"/>
</restriction>
</simpleType>
</attribute>
<attribute name="Format">
<simpleType>
<restriction base=" string ">
<enumeration value="RAW"/>
<enumeration value="TIFF"/>
</restriction>
</simpleType>
</attribute>
<attribute name="XYPlaneID" type=" string "/>
<attribute name="Return">
<simpleType>
<restriction base=" string ">
<enumeration value="FilePath"/>
<enumeration value="File"/>
</restriction>
</simpleType>
</attribute>
<attribute name="Pixels" type=" string " use="required"/>
</complexType>
</element>
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Element: pat

Name pat
Type string
Nillable no
Abstract no
Documentation Contains a regular expression. Checked for compilation when the module is imported.
Logical Diagram
XML Instance Representation
<CLI:pat> string </CLI:pat>
Diagram
Schema Component Representation
<element name="pat" type=" string "/>
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Element: theT

Name theT
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Describes how the time constraints of the XY plane should be produced or acquired.
Logical Diagram
element_AutoIterate element_UseValue element_IterateRange element_Match
XML Instance Representation
<CLI:theT>
Start Choice [1]
<CLI:AutoIterate> ... </CLI:AutoIterate> [1]
<CLI:UseValue> ... </CLI:UseValue> [1]
<CLI:IterateRange> ... </CLI:IterateRange> [1]
<CLI:Match> ... </CLI:Match> [1]
End Choice
</CLI:theT>
Diagram
element_AutoIterate element_UseValue element_IterateRange element_Match
Schema Component Representation
<element name="theT">
<complexType>
<choice>
<element ref=" CLI:AutoIterate "/>
<element ref=" CLI:UseValue "/>
<element ref=" CLI:IterateRange "/>
<element ref=" CLI:Match "/>
</choice>
</complexType>
</element>
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Element: theW

Name theW
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Describes how the wavenumber constraints of the XY plane should be produced or acquired.
Logical Diagram
element_AutoIterate element_UseValue element_IterateRange element_Match
XML Instance Representation
<CLI:theW>
Start Choice [1]
<CLI:AutoIterate> ... </CLI:AutoIterate> [1]
<CLI:UseValue> ... </CLI:UseValue> [1]
<CLI:IterateRange> ... </CLI:IterateRange> [1]
<CLI:Match> ... </CLI:Match> [1]
End Choice
</CLI:theW>
Diagram
element_AutoIterate element_UseValue element_IterateRange element_Match
Schema Component Representation
<element name="theW">
<complexType>
<choice>
<element ref=" CLI:AutoIterate "/>
<element ref=" CLI:UseValue "/>
<element ref=" CLI:IterateRange "/>
<element ref=" CLI:Match "/>
</choice>
</complexType>
</element>
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Element: theZ

Name theZ
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Describes how the Z constraints of the XY plane should be produced or acquired.
Logical Diagram
element_AutoIterate element_UseValue element_IterateRange element_Match
XML Instance Representation
<CLI:theZ>
Start Choice [1]
<CLI:AutoIterate> ... </CLI:AutoIterate> [1]
<CLI:UseValue> ... </CLI:UseValue> [1]
<CLI:IterateRange> ... </CLI:IterateRange> [1]
<CLI:Match> ... </CLI:Match> [1]
End Choice
</CLI:theZ>
Diagram
element_AutoIterate element_UseValue element_IterateRange element_Match
Schema Component Representation
<element name="theZ">
<complexType>
<choice>
<element ref=" CLI:AutoIterate "/>
<element ref=" CLI:UseValue "/>
<element ref=" CLI:IterateRange "/>
<element ref=" CLI:Match "/>
</choice>
</complexType>
</element>
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Global Definitions

Attribute Group: InputLocation

Name InputLocation
XML Instance Representation
Location="string [1]

'This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Input \'foo\', Location=\"foo.bar\"'

"
Diagram
Schema Component Representation
<attributeGroup name="InputLocation">
<attribute name="Location" type=" string " use="required"/>
</attributeGroup>
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Attribute Group: OutputLocation

Name OutputLocation
XML Instance Representation
Location="string [1]

'This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element \'bar\' from Formal Output \'foo\', Location=\"foo.bar\"'

"
Diagram
Schema Component Representation
<attributeGroup name="OutputLocation">
<attribute name="Location" type=" string " use="required"/>
</attributeGroup>
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Legend

Complex Type:

Schema Component Type

AusAddress

Schema Component Name
Super-types: Address < AusAddress (by extension)
Sub-types:
  • QLDAddress (by restriction)
If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.
Name AusAddress
Abstract no
The table above displays the properties of this schema component.
XML Instance Representation
<... country="Australia" >
<unitNo> string </unitNo> [0..1]
<houseNo> string </houseNo> [1]
<street> string </street> [1]
Start Choice [1]
<city> string </city> [1]
<town> string </town> [1]
End Choice
<state> AusStates </state> [1]
<postcode> string <<pattern = [1-9][0-9]{3}>> </postcode> [1] ?
</...>

The XML Instance Representation table above shows the schema component's content as an XML instance.

Schema Component Representation
<complexType name="AusAddress">
<complexContent>
<extension base=" Address ">
<sequence>
<element name="state" type=" AusStates "/>
<element name="postcode">
<simpleType>
<restriction base=" string ">
<pattern value="[1-9][0-9]{3}"/>
</restriction>
</simpleType>
</element>
</sequence>
<attribute name="country" type=" string " fixed="Australia"/>
</extension>
</complexContent>
</complexType>
The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)
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Glossary

Abstract (Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.

All Model Group Child elements can be provided in any order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-all.

Choice Model Group Only one from the list of child elements and model groups can be provided in instances. See: http://www.w3.org/TR/xmlschema-1/#element-choice.

Collapse Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.

Disallowed Substitutions (Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an xsi:type attribute.

Key Constraint Like Uniqueness Constraint, but additionally requires that the specified value(s) must be provided. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Key Reference Constraint Ensures that the specified value(s) must match value(s) from a Key Constraint or Uniqueness Constraint. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Model Group Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: http://www.w3.org/TR/xmlschema-1/#Model_Groups.

Nillable (Applies to element declarations). If an element declaration is nillable, instances can use the xsi:nil attribute. The xsi:nil attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an xsi:nil attribute set to true, it can be left empty, even though its element declaration may have required content.

Notation A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations.

Preserve Whitespace Policy Preserve whitespaces exactly as they appear in instances.

Prohibited Derivations (Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.

Prohibited Substitutions (Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.

Replace Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32).

Sequence Model Group Child elements and model groups must be provided in the specified order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-sequence.

Substitution Group Elements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.

Substitution Group Exclusions (Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.

Target Namespace The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.

Uniqueness Constraint Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

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