hclust.main Namespace Reference

Functions
def	Hierarchical (raw_tractography, MatrixDist_output, affinities_graph_output, MaxDistance_Threshold, dendogram_output)
def	Particional_Hierarchical (maxdist, var, arbfile, afffile, partfile)
def	Write_Retrieve_clusters (d_result, wfv)

Variables
	pathname = os.path.dirname(__file__)
	exepath = os.path.join(pathname, "hierarchical")
	dir_raw_tractography = sys.argv[1]
	Path to the .bundles file that corresponds to the raw tractography. More...
	MatrixDist_output = os.path.join(pathname, "data","hierarch","matrixd.bin")
	affinities_graph_output = os.path.join(pathname, "data","hierarch","affin.txt")
	MaxDistance_Threshold = sys.argv[2]
	Maximum threshold of euclidian distance between pairs of fibers, 40 is recommended. More...
	dendogram_output = os.path.join(pathname, "data","hierarch","dendogram.txt")
	t0 = time.time()
	maxdist = float(sys.argv[3])
	Maximum threshold of affinity, 30 is recommended. More...
	var = float(sys.argv[4])
	Value related with the scale of similarity used, 3600 is recommended. More...
	result_path = sys.argv[5]
	Output directory path. More...
	arbfile = dendogram_output
	afffile = affinities_graph_output
string	partfile = os.path.join(pathname, "data","hierarch","particion_")+str(maxdist)+".txt"
	d_result = result_path
	wfv = CT.wforest_partition_maxdist_from_graph( arbfile,maxdist,True,afffile,var)

Detailed Description

How to run

The segmentation code is ran like this:

python3 -m hclust <dir_raw_tractography> <MaxDistance_Threshold> <maxdist> <result_path>

Function Documentation

Hierarchical()

def hclust.main.Hierarchical	(		raw_tractography,
			MatrixDist_output,
			affinities_graph_output,
			MaxDistance_Threshold,
			dendogram_output
	)

Run to Hierarchical clustering.

Particional_Hierarchical()

def hclust.main.Particional_Hierarchical	(		maxdist,
			var,
			arbfile,
			afffile,
			partfile
	)

   Returns a ".txt" file with the detected clusters, where each list is a cluster.    
   maxdist, 30 or 40mmm is recommended
   var = 3600 ##minimum affinity within a cluster => #  N.exp( -max_cldist * max_cldist / var)

Write_Retrieve_clusters()

def hclust.main.Write_Retrieve_clusters	(		d_result,
			wfv
	)

Return the clusters in the directory, d_result    

Variable Documentation

dir_raw_tractography

hclust.main.dir_raw_tractography = sys.argv[1]

Path to the .bundles file that corresponds to the raw tractography.

Ruta al archivo .bundles que corresponde a la tractografía.

maxdist

hclust.main.maxdist = float(sys.argv[3])

Maximum threshold of affinity, 30 is recommended.

Máximo umbral de afinidad, se recomienda 30.

MaxDistance_Threshold

hclust.main.MaxDistance_Threshold = sys.argv[2]

Maximum threshold of euclidian distance between pairs of fibers, 40 is recommended.

Máximo umbral de distancia euclidiana entre pares de fibras, se recomienda 40.

result_path

hclust.main.result_path = sys.argv[5]

Output directory path.

Ruta del directorio de salida.

var

hclust.main.var = float(sys.argv[4])

Value related with the scale of similarity used, 3600 is recommended.

Valor relacionado con la escala de similitud utilizada, se recomienda 3600.