| | 101 | Apart from GUI, |3dBAR| comes with command line interface (or shorter: CLI) allowing the user to perform batch reconstructions without configured graphics environment. |
| | 102 | |
| | 103 | :: |
| | 104 | |
| | 105 | $./batchreconstructor.sh |
| | 106 | |
| | 107 | Usage: ./batchinterface.sh [options] <CAF index> [<structure 1> [<structure 2> ...]] |
| | 108 | 3d Brain Atlas Reconstructor ver.0.1 Batch reconstruction interface |
| | 109 | |
| | 110 | Options: |
| | 111 | -h, --help show this help message and exit |
| | 112 | -g GENERATESUBSTRUCTURES, --generateSubstructures=GENERATESUBSTRUCTURES |
| | 113 | maximum level of substructures (in the structure tree) |
| | 114 | to be generated; default: 0 |
| | 115 | -d VOXELDIMENSIONS, --voxelDimensions=VOXELDIMENSIONS |
| | 116 | voxel size (in units defined in given dataset) in slide plane |
| | 117 | and in plane perpendicular to the slides, consecutively. |
| | 118 | -e EXPORTDIR, --exportDir=EXPORTDIR |
| | 119 | the path to a directory for reconstructions |
| | 120 | -p PIPELINE, --usePipeline=PIPELINE |
| | 121 | the path to a custom pipeline definition |
| | 122 | -v CAMERA, --useViewport=CAMERA |
| | 123 | the direction vector from the center of the scene to |
| | 124 | the camera position |
| | 125 | --exportToWindow, --show |
| | 126 | the reconstruction is displayed to the user |
| | 127 | --composite perform a reconstruction of the structure as a scene |
| | 128 | composed of the reconstructions of the basic |
| | 129 | substructures in the hierarchy tree (up to the maximum |
| | 130 | given level) |
| | 131 | --includeBrainOutline |
| | 132 | Includes additional translucent brain outline to the |
| | 133 | reconstructions. Applies only when exporting to VRML, |
| | 134 | X3D, screenshot or thumbnail. |
| | 135 | |
| | 136 | Output Format Options: |
| | 137 | --exportToX3d exports as X3D scene |
| | 138 | --exportToVRML exports as VRML scene |
| | 139 | --exportToPOVRay exports to POV-Ray |
| | 140 | --exportToVTKPolydata |
| | 141 | exports as VTKpolyMesh |
| | 142 | --exportToVolume exports as VTKstructGrid |
| | 143 | --exportToNiftii exports as Niftii file |
| | 144 | --exportToNumpy exports as Numpy array |
| | 145 | --exportScreenshot saves screenshot as an PNG image |
| | 146 | --exportThumbnail saves scaled screenshot as an PNG image |
| | 147 | |
| | 148 | |
| | 149 | |
