.. _scil_tractogram_compute_ae:

scil_tractogram_compute_ae
==========================

::

	usage: __main__.py [-h] [--dpp_key DPP_KEY] [--save_as_color]
	                   [--save_mean_map filename] [--cmap CMAP]
	                   [--cmap_max [CMAP_MAX]] [--processes NBR]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f] [--no_bbox_check]
	                   in_tractogram in_peaks out_tractogram
	
	Compute the angular error (AE) for each segment of the streamlines.
	
	For each segment of each streamline, the direction is compared with the
	underlying peak (for single peak files, e.g. the first eigen-vector of tensors
	for DTI) or with the closest peak (ex, with fODF peaks). AE is computed as the
	cosine difference.
	
	Currently, interpolation is not supported: peaks of the closest voxel are used
	(nearest neighbor).
	
	The AE is added as data_per_point (dpp) for each point, using the first point
	of the segment. The last point of each streamline has an AE of zero.
	Optionnally, you may also save it as a color.
	
	When using --save_mean_map, if you want to be sure that your streamlines have
	points in most voxels that they touch, you could resample your tractogram
	first, with a small step size. See scil_tractogram_resample_nb_points.
	
	Hints:
	  - If you want to see which streamlines have the best AE / worst AE, explore
	    the script scil_tractogram_filter_by_streamlines_properties.
	  - If you want to average the DPP into a mean DPS over each streamline, see
	    the script scil_tractogram_dpp_math.
	
	positional arguments:
	  in_tractogram         Path of the input tractogram file (trk or tck).
	  in_peaks              Path of the input peaks file.
	  out_tractogram        Path of the output tractogram file (trk or tck) with AE in dpp.
	
	options:
	  -h, --help            show this help message and exit
	  --dpp_key DPP_KEY     Name of the dpp key containg the AE in the output. Default: AE
	  --processes NBR       Number of sub-processes to start. 
	                        Default: [1]
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  -f                    Force overwriting of the output files.
	  --no_bbox_check       Activate to ignore validity of the bounding box during loading / saving of 
	                        tractograms (ignores the presence of invalid streamlines).
	
	Optional outputs:
	  --save_as_color       Save the AE as a color. Colors will range between black (0) and yellow (--cmap_max) 
	                        See also scil_tractogram_assign_custom_color, option --use_dpp.
	  --save_mean_map filename
	                        If set, save the mean value of each streamline per voxel. Name of the map file (nifti).
	                        See also scil_tractogram_project_streamlines_to_map.
	
	Coloring options:
	  --cmap CMAP           Choice of matplotlib colormap. Default: jet.
	  --cmap_max [CMAP_MAX]
	                        If set, the maximum color on the colormap (yellow) will be associated 
	                        to this value. If not set, the maxium value found in the data will be used instead.
	                        Default if set: 180 degrees.
	
	2.3.0