My Project
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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) | |
The segmentation code is ran like this:
python3 -m hclust <dir_raw_tractography> <MaxDistance_Threshold> <maxdist> <result_path>
def hclust.main.Hierarchical | ( | raw_tractography, | |
MatrixDist_output, | |||
affinities_graph_output, | |||
MaxDistance_Threshold, | |||
dendogram_output | |||
) |
Run to Hierarchical clustering.
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)
def hclust.main.Write_Retrieve_clusters | ( | d_result, | |
wfv | |||
) |
Return the clusters in the directory, d_result
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.
hclust.main.maxdist = float(sys.argv[3]) |
Maximum threshold of affinity, 30 is recommended.
Máximo umbral de afinidad, se recomienda 30.
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.
hclust.main.result_path = sys.argv[5] |
Output directory path.
Ruta del directorio de salida.
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.