.. _scil_connectivity_hdf5_average_density_map:

scil_connectivity_hdf5_average_density_map
==========================================

::

	usage: __main__.py [-h] [--binary] [--processes NBR]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_hdf5 [in_hdf5 ...] out_dir
	
	Compute a density map for each connection from a hdf5 file.
	Typically use after scil_tractogram_segment_connections_from_labels in
	order to obtain the average density map of each connection to allow the use
	of --similarity in scil_connectivity_compute_matrices.
	
	This script is parallelized, but will run much slower on non-SSD if too many
	processes are used. The output is a directory containing the thousands of
	connections:
	out_dir/
	    |-- LABEL1_LABEL1.nii.gz
	    |-- LABEL1_LABEL2.nii.gz
	    |-- [...]
	    |-- LABEL90_LABEL90.nii.gz
	
	positional arguments:
	  in_hdf5               List of HDF5 filenames (.h5) from scil_tractogram_segment_connections_from_labels.
	  out_dir               Path of the output directory.
	
	options:
	  -h, --help            show this help message and exit
	  --binary              Binarize density maps before the population average.
	  --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.
	
	2.2.2