| 94 | | ------------------------------- |
| 95 | | |3dBAR| CLI reconstruction tool |
| 96 | | ------------------------------- |
| 97 | | |
| 98 | | Apart from GUI, |3dBAR| 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:: |
| 99 | | |
| 100 | | $./batchinterface.sh |
| 101 | | |
| 102 | | Usage: ./batchinterface.sh [options] <CAF index> [<structure 1> [<structure 2> ...]] |
| 103 | | 3d Brain Atlas Reconstructor ver.0.1 Batch reconstruction interface |
| 104 | | |
| 105 | | Options: |
| 106 | | -h, --help show this help message and exit |
| 107 | | -g GENERATESUBSTRUCTURES, --generateSubstructures=GENERATESUBSTRUCTURES |
| 108 | | maximum level of substructures (in the structure tree) |
| 109 | | to be generated; default: 0 |
| 110 | | -d VOXELDIMENSIONS, --voxelDimensions=VOXELDIMENSIONS |
| 111 | | voxel size (in units defined in given dataset) in slide plane |
| 112 | | and in plane perpendicular to the slides, consecutively. |
| 113 | | -e EXPORTDIR, --exportDir=EXPORTDIR |
| 114 | | the path to a directory for reconstructions |
| 115 | | -p PIPELINE, --usePipeline=PIPELINE |
| 116 | | the path to a custom pipeline definition |
| 117 | | -v CAMERA, --useViewport=CAMERA |
| 118 | | the direction vector from the center of the scene to |
| 119 | | the camera position |
| 120 | | --exportToWindow, --show |
| 121 | | the reconstruction is displayed to the user |
| 122 | | --composite perform a reconstruction of the structure as a scene |
| 123 | | composed of the reconstructions of the basic |
| 124 | | substructures in the hierarchy tree (up to the maximum |
| 125 | | given level) |
| 126 | | --includeBrainOutline |
| 127 | | Includes additional translucent brain outline to the |
| 128 | | reconstructions. Applies only when exporting to VRML, |
| 129 | | X3D, screenshot or thumbnail. |
| 130 | | |
| 131 | | Output Format Options: |
| 132 | | --exportToX3d exports as X3D scene |
| 133 | | --exportToVRML exports as VRML scene |
| 134 | | --exportToVTKPolydata |
| 135 | | exports as vtkPolyData |
| 136 | | --exportToVolume exports as vtkStructuredPoints |
| 137 | | --exportToNifti exports as NIfTI file |
| 138 | | --exportToNumpy exports as NumPy array |
| 139 | | --exportScreenshot saves screenshot as an PNG image |
| 140 | | --exportThumbnail saves scaled screenshot as an PNG image |
| 141 | | |
| 142 | | |
| 143 | | 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. |
| 144 | | |
| 145 | | 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* as save a nifti volume with the reconstruction: :: |
| 146 | | |
| 147 | | $./batchinterface.sh ~/atlases/mouse/caf/index.xml Thalamus --exportToNiftii |
| 148 | | |
| 149 | | By default, the reconstructions generated using a predefined pipeline and stored in directory parallel to the CAF dataset directory (in this example it would be ``~/atlases/mouse/reconstructions/``). However, this behavior can be customized using various switches. |
| 150 | | |
| 151 | | |
