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Open Microscopy Environment
Command Line Interface XML Schema
Author: Josiah Johnston, Andrew J Patterson
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"Tied to DB. Table PROGRAMS Column EXECUTION
Assigns a execution point for the analysis.
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>
This specifies what and how to write to STDIN.
Currently this is still in development. I would STRONGLY recommend contacting Josiah <[email protected]> before coding against it.
This specifies what and how to read STDOUT.
References a particular column in a FormalInput. Used for variable substitution.References a particular column of a FormalOutput.Describes how to access information extracted using a regular expression. Examples are 1, 2, 3, ...Describes how the Z constraints of the XY plane should be produced or acquired.Describes how the wavenumber constraints of the XY plane should be produced or acquired.Describes how the time constraints of the XY plane should be produced or acquired.Describes an XY plane. Used with variable substitution. This will be substituted with a dynamically generated plane.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.
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.
Needed if you need another plane to match indexes. Referenced by the Match element.Specifies whether to the program needs the FilePath or the FileContents. Currently, only the FilePath is supported.References a formal input of semantic type 'Pixels'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
References a formal input of semantic type 'Pixels'Groups a set of inputs into records.Groups a set of outputs into records.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.
Contains a regular expression. Checked for compilation when the module is imported.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.References another Plane.Use an input value. References an input, does not produce an output.Iterates a dimension over its entire range. Produces outputs.Iterate this dimension over a range of values. Produces outputs.Specifies an end point of iteration.
Not currently supported.
Specifies a starting point of iteration.
Not currently supported.
Specifies location to write output. One data chunk that the Output element references may be written to one or more places.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.
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 string will be used to separate fields in this record.This will be used to separate Records. Defaults to a newline (a newline as interpretted by perl).Used to construct an arbitrarily formatted record. Not currently supported. email Josiah <[email protected]> if you need this implemented.All Formal Inputs referenced within this scope should have a count of 0 or 1.Will be substituted with the full path of the file created. The OutputTo feature is not implemented yet.Should uniquely identify this tempFile. It is used to retrieve the path as a variable.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"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.
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. Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies an input data location for populating the semantic elementThis 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"Specifies a data location for populating the semantic elementRefers to a TempFileGrants file path to Pixels input. Future plans include dumping pixel file contents as well.
