My Project
Functions | Variables
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.