'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\"'
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>
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.
'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\"'
<CLI:ExecutionInstructions ExecutionPoint="xsd:string (value comes from list: {'executeGlobal'|'startDataset'|'startImage'|'startRegion'|'finishRegion'|'finishImage'|'finishDataset'})[1]
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.
'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\"'
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.
'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 conjunction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first.'
'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.'
'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\"'
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
XML Instance Representation
<CLI:PixelOutput type="xsd:string (value comes from list: {'Pixels'|'PixelsPlane'})[0..1]" FormalOutput="xsd:string[0..1]" UseBase="xsd: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.'
'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\"'
'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="xsd:string (value comes from list: {'path'})[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\"'
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.
'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\"'
'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\"'
'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\"'
'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\"'
'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\"'
'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\"'
'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\"'
'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\"'
Describes an XY plane. Used with variable substitution. This will be substituted with a dynamically generated plane.
Logical Diagram
XML Instance Representation
<CLI:XYPlane BPP="xsd: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="xsd:string (value comes from list: {'RAW'|'TIFF'})[0..1]
'Specifies the expected format of the plane. RAW corresponds to OME repository format of pixel dump. TIFF corresponds to TIFF files. Currently only TIFF is supported.'
'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\"'
'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\"'
The XML Instance Representation table above shows the schema component's content as an XML instance.
The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].
Model group information are shown in gray, e.g. Start Choice ... End Choice.
For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in bold.
If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".
Otherwise, the type of the element/attribute is displayed.
If the element/attribute's type is in the schema, a link is provided to it.
For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<pattern = [1-9][0-9]{3}>>.
If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.
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.
Collapse Whitespace PolicyReplace 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.
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.
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 PolicyReplace tab, line feed, and carriage return characters with space character (Unicode character 32).
Substitution GroupElements 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 NamespaceThe 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.
