.. _scil_fibertube_compute_density:

scil_fibertube_compute_density
==============================

::

	usage: __main__.py [-h] [--out_density_map OUT_DENSITY_MAP]
	                   [--out_density_measures OUT_DENSITY_MEASURES]
	                   [--out_collision_map OUT_COLLISION_MAP]
	                   [--out_collision_measures OUT_COLLISION_MEASURES]
	                   [--samples_per_voxel_axis SAMPLES_PER_VOXEL_AXIS] [-f]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [--indent INDENT]
	                   [--sort_keys]
	                   in_fibertubes
	
	Estimates the per-voxel volumetric density of a set of fibertubes. In other
	words, how much space is occupied by fibertubes and how much is emptiness.
	
	1. Segments voxels that contain at least a single fibertube.
	2. Valid voxels are finely sampled and we count the number of samples that
	landed within a fibertube. For each voxel, this number is then divided by
	its total amount of samples.
	3. By doing the same steps for samples that landed within 2 or more
	fibertubes, we can create a density map of the fibertube collisions.
	
	To form fibertubes from a set of streamlines, you can use the scripts:
	- scil_tractogram_filter_collisions to assign a diameter to each streamline
	  and remove all colliding fibertubes.
	- scil_tractogram_dps_math to assign a diameter without filtering.
	
	See also:
	    - docs/source/documentation/fibertube_tracking.rst
	
	positional arguments:
	  in_fibertubes         Path to the tractogram (must be .trk) file 
	                        containing fibertubes. They must have their 
	                        respective diameter saved as data_per_streamline.
	
	options:
	  -h, --help            show this help message and exit
	  --out_density_map OUT_DENSITY_MAP
	                        Path of the density Nifti image.
	  --out_density_measures OUT_DENSITY_MEASURES
	                        Path of the output file containing central 
	                        tendency measures about volumetric density. 
	                        (Must be .json)
	  --out_collision_map OUT_COLLISION_MAP
	                        Path of the collision Nifti image.
	  --out_collision_measures OUT_COLLISION_MEASURES
	                        Path of the output file containing central 
	                        tendency measures about collision density. 
	                        (Must be .json)
	  --samples_per_voxel_axis SAMPLES_PER_VOXEL_AXIS
	                        Number of samples to be created along a single 
	                        axis of a voxel. The total number of samples in the 
	                        voxel will be this number cubed. [10]
	  -f                    Force overwriting of the output files.
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	
	Json options:
	  --indent INDENT       Indent for json pretty print.
	  --sort_keys           Sort keys in output json.