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#############################################################################*/
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import string
from . import string_six
import traceback
import sys
import numpy
import math
import time
from os.path import basename
import os.path
import mpi4py.MPI as MPI
from . import setCpuSet
from . import segment_cy
def segmenta():
myrank = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
mypname = MPI.Get_processor_name()
comm = MPI.COMM_WORLD
maxnargs = 8
mygpus, MemPerProc,coresperproc,ncpusperproc =setCpuSet.setCpuSet(maxnargs)
print( " PROCESS :mypname, myrank, nprocs, coresperproc, mygpus, MemPerProc , argv " , mypname, myrank, nprocs, coresperproc, mygpus, MemPerProc, sys.argv)
pagbone_outputfile = sys.argv[2]
threshold = string.atof(sys.argv[3])
medianR = string.atof(sys.argv[4])
maskbone_outputfile = sys.argv[5]
dilatation = string.atoi(sys.argv[6])
from xml.dom import minidom
xmldoc = minidom.parse(pagbone_outputfile+'.xml')
SIZEZ = string.atoi(xmldoc.getElementsByTagName('SIZEZ')[0].firstChild.data)
SIZEY = string.atoi(xmldoc.getElementsByTagName('SIZEY')[0].firstChild.data)
SIZEX = string.atoi(xmldoc.getElementsByTagName('SIZEX')[0].firstChild.data)
if myrank==0 :
size = SIZEZ*SIZEY*SIZEX
f=open(maskbone_outputfile,"w")
f.seek(size*4-1)
f.write(" ")
f.close()
comm.Barrier()
print( " chiamo cython ", myrank)
segment_cy.pysegment( pagbone_outputfile,
threshold,
medianR,
maskbone_outputfile,
myrank,
nprocs,
coresperproc,
MemPerProc ,
SIZEZ, SIZEY, SIZEX, dilatation)
def spilla():
myrank = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
mypname = MPI.Get_processor_name()
comm = MPI.COMM_WORLD
maxnargs = 8
mygpus, MemPerProc,coresperproc,ncpusperproc=setCpuSet.setCpuSet(maxnargs)
print( " PROCESS :mypname, myrank, nprocs, coresperproc, mygpus, MemPerProc , argv " , mypname, myrank, nprocs, coresperproc, mygpus, MemPerProc, sys.argv)
pagbone_outputfile = sys.argv[2]
absbone_outputfile = sys.argv[3]
maskbone_outputfile = sys.argv[4]
threshold = string.atof(sys.argv[5])
corrbone_outputfile = sys.argv[6]
from xml.dom import minidom
xmldoc = minidom.parse(absbone_outputfile+'.xml')
SIZEZ = string.atoi(xmldoc.getElementsByTagName('SIZEZ')[0].firstChild.data)
SIZEY = string.atoi(xmldoc.getElementsByTagName('SIZEY')[0].firstChild.data)
SIZEX = string.atoi(xmldoc.getElementsByTagName('SIZEX')[0].firstChild.data)
if myrank==0 :
size = SIZEZ*SIZEY*SIZEX
f=open(corrbone_outputfile,"w")
f.seek(size*4-1)
f.write(" ")
f.close()
comm.Barrier()
print( absbone_outputfile, pagbone_outputfile, maskbone_outputfile,threshold,corrbone_outputfile)
segment_cy.pyspilla( pagbone_outputfile,
absbone_outputfile,
maskbone_outputfile ,
threshold,
corrbone_outputfile,
myrank,
nprocs,
coresperproc,
MemPerProc ,
SIZEZ, SIZEY, SIZEX)
def incolla():
myrank = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
mypname = MPI.Get_processor_name()
comm = MPI.COMM_WORLD
maxnargs = 7
mygpus, MemPerProc,coresperproc,ncpusperproc =setCpuSet.setCpuSet(maxnargs)
print( " PROCESS :mypname, myrank, nprocs, coresperproc, mygpus, MemPerProc , argv " , mypname, myrank, nprocs, coresperproc, mygpus, MemPerProc, sys.argv)
pagbone_outputfile = sys.argv[2]
maskbone_outputfile = sys.argv[3]
correctedvol_outputfile = sys.argv[4]
outputfile = sys.argv[5]
from xml.dom import minidom
xmldoc = minidom.parse(pagbone_outputfile+'.xml')
SIZEZ = string.atoi(xmldoc.getElementsByTagName('SIZEZ')[0].firstChild.data)
SIZEY = string.atoi(xmldoc.getElementsByTagName('SIZEY')[0].firstChild.data)
SIZEX = string.atoi(xmldoc.getElementsByTagName('SIZEX')[0].firstChild.data)
if myrank==0 :
size = SIZEZ*SIZEY*SIZEX
f=open(outputfile,"w")
f.seek(size*4-1)
f.write(" ")
f.close()
comm.Barrier()
if myrank==0 :
name1 = correctedvol_outputfile+".info"
name2 = outputfile+".info"
open(name2,"w").write(open(name1,"r").read())
name1 = correctedvol_outputfile+".xml"
name2 = outputfile+".xml"
name2_base = os.path.basename(outputfile)
s = open(name1,"r").read()
pos1=s.find("<SUBVOLUME_NAME>")
pos2=s.find("<SIZEX>")
s = s[:pos1] + "<SUBVOLUME_NAME>%s</SUBVOLUME_NAME>"%name2_base + s[pos2:]
open(name2,"w").write(s)
comm.Barrier()
segment_cy.pyincolla( pagbone_outputfile,
maskbone_outputfile,
correctedvol_outputfile,
outputfile,
myrank,
nprocs,
coresperproc,
MemPerProc ,
SIZEZ, SIZEY, SIZEX)
if(sys.argv[1]=="segmenta") :
segmenta()
if(sys.argv[1]=="spilla") :
spilla()
if(sys.argv[1]=="incolla") :
incolla()
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