BrainVISA Processes

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BrainVISA Processes
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Plan

• What is BrainVISA ?
• Writing a process
• Simple process
• Database ontology
• Viewer
• Creating a toolbox
• Documentation
• Advanced use

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What is BrainVISA ?

• Modular and customizable software platform built
  to host heterogeneous tools dedicated to
  neuroimaging research
• Keywords process, toolbox, data ontology
• Visualization with Anatomist

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Writing a process

• Writing a process
• Simple process
• Database ontology
• Viewer

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Simple process

• Script python
• Contains
• Imports
• Declarative part name, userLevel, role
• Signature input and output parameters
• Functions validation, initialization, execution
• Example Concatenate grey and white hemispheres
  mesh

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Simple process

• Mandatory import
• from neuroProcesses import
• Process name
• name string
• Visibility level
• userLevel integer
• Role
• roles ( role, ...)
• role lt- viewer editor converter importer

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Simple process

• Signature
• signature Signature( parameter_list )
• parameter_list lt- parameter_name, parameter_type,
  ...
• Parameter types
• String()
• Number()
• Integer()
• Float()
• Choice( value1, ... )
• ReadDiskItem( type, formats)
• WriteDiskItem( type, formats )

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Simple process

• DiskItem data, can be stored in several files.
• Type data meaning (T1 MRI, Brain Mask...)
• Format file format for storage (NIFTI image,
  GIS Image, BMP Image, ...)
• Types and formats used in processes must exists
  in BrainVISA.
• Documentation about existing types

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Simple process

• Functions
• Validation
• def validation()
• if ltconditiongt
• raise ValidationError( "error message" )
• Initialization
• def initialization( self )
• self.parameter_name value
• self.setOptional( parameter_name )
• self.linkParameters( destination, source )
• self.addLink( destination, sources , function )
• Execution
• def execution(self, context)
• function_body

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Simple process

• Execution context interactions with BrainVISA,
  system commands call...
• write, warning, error prints a message.
• log writes a message in the BrainVISA log
  file.
• ask, dialog asks a question to the user.
• temporary creates a temporary file.
• system call a system command.
• runProcess runs a process.
• matlab calls a Matlab command.
• checkInterruption defines a breakpoint.

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Examples

• Ex1 process using existing types, no database
• -gt iterations, default viewer
• Ex2 add-hoc link between output and inputs
• Ex3 specific types for inputs, link between
  inputs, database
• Ex4 New type for output -gt udpate types and
  hierarchy

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Database ontology

• Ontology BrainVISA
• Data types and formats
• Hierarchy organization of data in the
  database file system
• Filenames
• Files places in database directory
• filename and place ltgt type and attributes
• gt allows linking parameters
• Example type Hemisphere whitegrey Mesh

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Viewer

• Special process callable by clicking on
• One mandatory input parameter
• Uses pyanatomist
• Examples
• Viewer for Hemisphere whitegrey Mesh
• Ex5 importance of referentials

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Toolbox

• Groups processes that are related to a same
  domain
• Contains processes and data ontology
• Each toolbox can be developped, maintained and
  distributed by a different group / lab
• Examples
• T1 MRI
• Diffusion tracking
• Sulci
• FMRI
• MEG-EEG, ...
• My Processes is also a toolbox (in
  home/.brainvisa)

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Toolbox

• File organization (T1 MRI toolbox)

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Toolbox

• Configuration file
• userName the name that will be displayed in
  BrainVISA interface.
• icon file path of the icon that will reprensent
  the toolbox in graphical interface. Optional,
  there is a default icon.
• description tooltip for the toolbox, that will
  be displayed when the mouse pass on the toolbox
  name. Optional, default tooltip is the name of
  the toolbox.

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Toolbox

• Links with other toolboxes
• Link on a process can appear in several toolboxes
• Links are stored in a minf file named
  lttoolbox_namegt.minf
• Example
• diffusion importation processes in Diffusion
  tracking toolbox
• Links on these processes in Data management
  toolbox

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Documentation

• Displayed in BrainVISAs right panel
• Documentation on
• Process ltprocess file namegt.procdoc
• -gt Interface for editing process documentation
• Category (processes sub-directories)
  category_documentation.minf in the directory
• Toolbox category_documentation.minf in
  processes directory
• Can include
• HTML tags
• Links to processes, category
• images

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Advanced use

• Pipelines
• Other special processes converters, editors
• Changing graphical interface
• Running in batch mode
• Translations
• ...

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Where can I find documentation ?

• Index of all docs
• file///i2bm/research/share/doc/index.html
• http//brainvisa.info/doc/index.html
• BrainVISA programming manual
• file///i2bm/research/share/doc/brainvisa-3.1/bv_p
  g/en/html/index.html
• BrainVISA epydoc
• file///i2bm/research/share/doc/brainvisa-3.1/bv_p
  g/en/html/index.html
• Pyanatomist epydoc
• file///i2bm/research/share/doc/pyanatomist-3.1/ep
  ydoc/index.html

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Summary

• Process
• Types and Formats
• Hierarchy
• Toolbox
• Documentation

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BrainVISA processes

• Thank you !