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# Usage: salome -t define_groups.py

import sys
import os
import adapt_mesh_from_image

import salome
import GEOM
from salome.geom import geomBuilder
import SMESH, SALOMEDS
from salome.smesh import smeshBuilder


def CloseSalome():
    """Try to close out of Salome gracefully"""
    # there is nothing graceful about this
    try:
        sys.stdout = 'redirect to nowhere...'  # so I don't see the junk it prints
        from killSalomeWithPort import killMyPort
        killMyPort(2810)
    except:
        pass

# try:
# Create directory for mesh adaptation files
Directory = '/home/morrile2/Documents/MULTISData/MULTIS_invitro/CMULTIS008-1/AdaptiveMeshing/'
CaseName = "CMULTIS008-1_UL_quad"
case_dir = os.path.join(Directory, CaseName)

if not os.path.exists(case_dir): os.makedirs(case_dir)
os.chdir(case_dir)

# Get filenames needed for mesh adaptation
img_path = os.path.join(case_dir, 'CMULTIS008-1_UL_CT_seg_02.nii')
trgVolpath = os.path.join(case_dir, 'leg_1.med')
MedName = os.path.split(trgVolpath)[1]

import time
start = time.time()
print "Mapping image to original mesh................."
trg_field = adapt_mesh_from_image.MapImageToOriginalMesh(case_dir, img_path, trgVolpath, MedName)
end = time.time()-start
start = end
print "Time = %f" %end

print "Adapting mesh using image field................"
n_iter = 3
for i in range(n_iter):
    # if i &gt; 1:
    print
    print "Iteration %i of %i" % ( i +1, n_iter)
    print case_dir
    adapt_mesh_from_image.AdaptMeshFromImage(case_dir, MedName, 'FieldRefineValue', i+ 1)
    adapt_mesh_from_image.create_groups_from_field(case_dir, Directory, MedName, i + 1)

    # adapt_mesh_from_image.AdaptMeshFromImage(case_dir, MedName, 'UnrefineNeighbor', i + 1)
    # adapt_mesh_from_image.create_groups_from_field(case_dir, Directory, MedName, i + 1)

    end = time.time()-start
    start = time.time()
    print "Time = %f" %end
print "Mesh Adaptation Complete"
adapt_mesh_from_image.create_groups_from_field(case_dir, Directory, MedName, i + 2)
CloseSalome()

# except:
#     CloseSalome()</pre></body></html>