= Command-line reconstruction interface =


Apart from GUI, the 3D Brain Atlas Reconstructor comes with command line interface (or shorter: CLI) allowing the user to perform batch reconstructions without configured graphics environment. After invoking the batch interface, following information will appear:

{{{

  $./batchinterface.sh
  
  Usage: ./batchinterface.sh [options] <CAF index> [<structure 1> [<structure 2> ...]]

  3d Brain Atlas Reconstructor ver.ver. 0.1 Batch reconstruction interface

  Options:
    --version             show program's version number and exit
    -h, --help            show this help message and exit
    -g GENERATESUBSTRUCTURES, --generateSubstructures=GENERATESUBSTRUCTURES
                          maximum level of substructures (in the structure tree)
                          to be generated; defaults to 0
    -d VOXELDIMENSIONS, --voxelDimensions=VOXELDIMENSIONS
                          voxel size [mm] (in coronal plane, along anterior-
                          posterior axis)
    -e EXPORTDIR, --exportDir=EXPORTDIR
                          the path to a directory for reconstructions
    -p PIPELINE, --usePipeline=PIPELINE
                          the path to a custom pipeline definition
    -a CAMERAMOVEMENTANGLES, --cameraMovementAngles=CAMERAMOVEMENTANGLES
                          camera movement angles (azimuth, elevation, roll)
    -b BACKGROUND, --background=BACKGROUND
                          RGB background colourcomponents (within 0.0-255.0
                          range)
    --exportToWindow, --show
                          the reconstruction is displayed to the user
    --composite           perform a reconstruction of the structure as a scene
                          composed of the reconstructions of the basic
                          substructures in the hierarchy tree (up to the maximum
                          given level)
    --includeBrainOutline
                          Includes additional translucent brain outline to the
                          reconstructions. Applies only when exporting to VRML,
                          X3D or thumbnail.
    --ignoreBoundingBox   Overrides bounding box calculation - bounding
                          box will be always equal to hierarchy root element
                          bounding box. Volumes for all structures will always
                          have the same size and origin. This feature increases
                          memory usage and reconstruction time.

    Output Format Options:
      --exportToX3d       exports as X3D scene
      --exportToVRML      exports as VRML scene
      --exportToPOVRay    exports to POV-Ray
      --exportToVTKPolydata
                          exports as VTKpolyMesh
      --exportToVolume    exports as VTKstructGrid
      --exportToNiftii    exports as Niftii file
      --exportToNumpy     exports as Numpy array
      --exportScreenshot  saves screenshot as an PNG image
      --exportThumbnail   saves scaled screenshot as an PNG image
}}}

The `<CAF index>` is a location of the index file of the given CAF dataset while the `[<structure 1> [<structure 2> ...]]` is space-separated list of all structures to reconstruction contained in the CAF dataset.

The simplest usage of the CLI is to generate reconstruction of a single structure from provided CAF dataset using default settings. Assume that our CAF dataset is located in the `~/atlases/mouse/caf/` directory and we would like to reconstruct the ''Thalamus'' and save a nifti volume with the reconstruction:

{{{
$./batchinterface.sh ~/atlases/mouse/caf/index.xml Thalamus --exportToNiftii
}}}

By default, reconstructions of requested structures generated with predefined voxel dimensions, pipeline and camera position are stored in directory parallel to the CAF dataset directory (in this example it would be `~/atlases/mouse/reconstructions/`). However, this behavior can be customized with commandline options.