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mesh2vtk.py
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mesh2vtk.py
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'''
########################################################################################################
# Copyright 2019 F4E | European Joint Undertaking for ITER and the Development #
# of Fusion Energy (‘Fusion for Energy’). Licensed under the EUPL, Version 1.1 #
# or - as soon they will be approved by the European Commission - subsequent versions #
# of the EUPL (the “Licence”). You may not use this work except in compliance #
# with the Licence. You may obtain a copy of the Licence at: http://ec.europa.eu/idabc/eupl.html #
# Unless required by applicable law or agreed to in writing, software distributed #
# under the Licence is distributed on an “AS IS” basis, WITHOUT WARRANTIES #
# OR CONDITIONS OF ANY KIND, either express or implied. See the Licence permissions #
# and limitations under the Licence. #
########################################################################################################
'''
##----------------------------------------------------------------------------##
## ******** ** ******** ##
## ******** *** ******** ##
## ** ** * ** ##
## ****** ****** ****** ##
## ****** ****** ****** ##
## ** ** *** ##
## ** ** ******** ##
## ** ** ******** ##
## ##
##----------------------------------------------------------------------------##
## TSS / A&C / Nuclear Section ##
##----------------------------------------------------------------------------##
## ##
## Fusion for Energy ##
## c/ Josep Pla, n2 ##
## Torres Diagonal Litoral B3 ##
## Barcelona (Spain) ##
## +34 93 320 1800 ##
## http://fusionforenergy.europa.eu/ ##
## ##
##----------------------------------------------------------------------------##
# CODE: mesh2vtk
# LANGUAGE: PYTHON 3.6
# AUTHOR/S: Patrick Sauvan, Francisco Ogando, Marco Fabbri
# e-MAIL/S: psauvan@ind.uned.es, fogando@ind.uned.es, marco.fabbri@f4e.europa.eu
# DATE: 30/30/2021
# Copyright F4E 2019
# IDM: F4E_D_2R2H62 v1.0
# DESCRIPTION: It converts the meshes produced by MCNP and D1S-UNED into a VTK format has been developed.
# The tool is a python 3.6 based script able to read any mesh format in meshtally files produced by D1SUNED, MCNP5 or MCNP6.
# Mesh format includes usual MCNP column or matrix format and also specific D1SUNED format including cell or isotope contribution
# binning and source mesh importance format. Both Cartesian and cylindrical meshes can be read. The tool incorporates also simple
# functions to operate with meshes (add, scale, compare).
# The tool is used through a text based interactive menu, and it can be run under Windows or Linus systems.
# USAGE: python –m mesh2vtk.py
# OUTPUT: meshtalfiles + NoTally + .vtk/.vtr
# VERSIONS:
# 0.0 [2018-05-25] ---> Developed by Francisco Ogando & Patricl Sauvan (UNED) under the F4E EXP-263,https://idm.f4e.europa.eu/?uid=2BLKNA
# Starting version.
# 1.0 [2021-03-30] ---> Improved by Marco Fabbri (F4E) & Alvaro Cubi (F4E-EXT)for further usage. Changes implemented:
# 1) Conversion to PY3.6
# 2) Capability to deal with cylindrical mesh not aligned with Z axis added
# 3) CuV mesh treatment added
# IMPROVEMENTS:
# -->
# -->
dep_path='./' # adjust this path to the location of the meshtal_mod.py module
import os
import re
from sys import path
path.append(dep_path)
from meshtal_mod import *
principal_menu="""
***********************************************
Process meshtally to VTK
***********************************************
* Append meshtally file (open)
* Display mesh information (info)
* Write VTK file (write)
* Mesh operation (operate)
* Exit (end)
"""
info_menu="""
* Mesh information (meshinfo)
* Tally information (tallyinfo)
* Exit (end)
"""
operate_menu="""
* Mesh scale (scale)
* Mesh sum (sum)
* Mesh difference (diff)
* Energy bin sum (binsum)
* Check identical mesh (identical)
* Change correlation (corr)"""
def answer_loop(menu):
pkeys = ['open','info','write','operate','end']
ikeys = ['meshinfo','tallyinfo','end']
okeys = ['scale','sum','diff','binsum','identical','corr']
menulist = {'principal':pkeys, 'info':ikeys, 'operate':okeys}
while True:
ans = input(" enter action :")
ans = ans.split()
ans0 = None
ans1 = None
if len(ans) > 0:
ans0 = ans[0]
if len(ans) > 1 :
ans1 = ans[1]
if menu == 'operate' and (ans1 == None and ans0 not in ['identical','corr']):
if ans0 not in okeys:
print(' bad operation keyword')
else:
print(' name of the result mesh is missing')
elif ans0 in menulist[menu] :
break
else:
print(' not expected keyword')
return ans0,ans1
def display_meshlist(opmesh=True):
# display mesh list
if opmesh :
nfiles = len(meshfiles) + len(newmesh)
else:
nfiles = len(meshfiles)
if nfiles > 1 :
onefile = False
for i,f in enumerate(meshfiles):
print(" - {}".format(f))
tallylist = list(meshtally[i].mesh.keys())
tallylist.sort()
for tally in tallylist:
print(" - {}".format(tally))
else:
onefile = True
tallylist = list(meshtally[0].mesh.keys())
tallylist.sort()
for tally in tallylist:
print(" - {}".format(tally))
if opmesh and len(newmesh) > 0 :
print(" - Result mesh (result)")
for rmesh in newmesh.keys():
print(" - {}".format(rmesh))
return onefile
def answer_meshlist(menu,answer,onefile=True):
label_00 = ' select mesh, finish "end":'
label_01 = ' tally and scaling factor "tally factor":'
label_02 = ' mesh and scaling factor "tally factor", finish "end":'
label_03 = ' first mesh "tally":'
label_04 = ' second mesh "tally":'
label_05 = ' select mesh :'
label_10 = ' select mesh "file tally", finish "end":'
label_11 = ' meshtally file, tally and scaling factor "file tally factor":'
label_12 = ' meshtally file, tally and scaling factor "file tally factor", finish "end":'
label_13 = ' first mesh "file tally":'
label_14 = ' second mesh "file tally":'
label_15 = ' select mesh "file tally":'
label_one = [label_00,label_01,label_02,label_03,label_04,label_05]
label = [label_10,label_11,label_12,label_13,label_14,label_05]
if menu == '3' :
labelindex = 0
nans = 2
nvalues = -1
elif menu == '4' :
if answer == 'scale' :
labelindex = 1
nans = 3
nvalues = 1
elif answer == 'sum' :
labelindex = 2
nans = 3
nvalues = -1
elif answer == 'diff' :
labelindex = 3
nans = 2
nvalues = 2
elif answer == 'binsum' :
labelindex = 5
nans = 2
nvalues = 1
else:
labelindex = 3
nans = 2
nvalues = 2
finish = False
mlist = []
f1 = 1.
if onefile :
nans = nans - 1
# select mesh
ishft = 0
tallylist = meshtally[0].mesh.keys()
while not finish:
while True:
error = False
if onefile :
sfile = input(label_one[labelindex + ishft])
sfile = sfile.split()
if len(sfile) == 1 and sfile[0] == 'end':
finish = True
break
if len(sfile) == nans :
m1 = 0
if len(sfile) == 1 and sfile[0] == 'all':
for tally in tallylist:
mlist.append([m1,tally,f1])
finish = True
break
try :
tally = int(sfile[0])
except :
tally = -1
if tally in tallylist :
if nans == 2 :
try :
f1 = float(sfile[1])
except:
error = True
print(' factor value should be float')
else:
error = True
print(' bad tally values')
else :
error = True
print(' {} values are entered,{} are expected'.format(len(sfile),nans))
else :
sfile = input(label[labelindex + ishft])
sfile = sfile.split()
if len(sfile) == 1 and sfile[0] == 'end':
finish = True
break
if len(sfile) == nans :
if ( sfile[0] in meshfiles or sfile[0] == 'result'):
if (sfile[0] == 'result'):
tallylist = newmesh.keys()
m1 = -1
if len(sfile) == 2 and sfile[1] == 'all':
for tally in tallylist:
tl = [m1,tally,f1]
if tl not in mlist:
mlist.append([m1,tally,f1])
break
tally = sfile[1]
else:
m1 = meshfiles.index(sfile[0])
tallylist = meshtally[m1].mesh.keys()
if len(sfile) == 2 and sfile[1] == 'all':
for tally in tallylist:
tl = [m1,tally,f1]
if tl not in mlist:
mlist.append([m1,tally,f1])
break
try:
tally = int(sfile[1])
except:
tally = -1
if tally in tallylist :
if nans == 3 :
try :
f1 = float(sfile[2])
except:
error = True
print(' factor value should be float')
else:
error = True
print(' bad tally values')
else:
error = True
print(' {} meshtally not found'.format(sfile[0]))
else:
error = True
print(' {} values are entered,{} are expected'.format(len(sfile),nans))
if not error :
mlist.append([m1,tally,f1])
if (menu == '4' and answer in ['diff','identical'] ) : ishft = 1
if nvalues == len(mlist) : finish = True
break
return mlist
def enterfilename(name):
if name is None:
fname = input(' enter Meshtally file name:')
else:
fname = name
if fname != '' and fname not in meshfiles :
if os.path.isfile(fname):
meshfiles.append(fname)
else:
print (' {} not found'.format(fname))
print('\n Input files :')
for f in meshfiles:
print(" - {}".format(f))
def mltf_option(meshtal):
normopt=['none','vtot','celf','']
askSameNorm = True
repeatNorm = False
askSameFilter = True
repeatFilter = False
keys = list(meshtal.mesh.keys())
keys.sort()
for k in keys:
m = meshtal.mesh[k]
if m.__format__ in ['mltf','cuv'] :
if not repeatNorm :
print (' Tally mesh {} is cell-under-voxel, set normalization.'.format(k))
else:
print (' Tally mesh {} is cell-under-voxel, normalization set to {}.'.format(k,normtype))
while True and not repeatNorm:
ans=input(' {lab[0]}(default), {lab[1]}, {lab[2]}:'.format(lab=normopt))
if ans in normopt:
if ans == '':
m.__mltopt__ = normopt[0]
else:
m.__mltopt__ = ans
print(' Normalization set to {}'.format(m.__mltopt__))
break
else:
print ('bad normalization option')
if repeatNorm :
m.__mltopt__ = normtype
if len(meshtal.mesh) > 1 and askSameNorm:
askSameNorm = False
ans = input('Apply same normalization options for all meshes (Yes/No) ?')
if ans.upper() in ['YES','Y']:
repeatNorm = True
normtype = m.__mltopt__
# Inquire cell filtering
while True and not repeatFilter:
ans=input(' Enter cell filename (no filename no filtering):')
anslist=ans.split()
if ans == '':
m.__mltflt__ = None
break
else :
fname = ans
if os.path.isfile(fname):
m.__mltflt__ = fname
break
else:
print (' File {} not found.'.format(fname))
if repeatFilter :
m.__mltflt__ = filterFile
if len(meshtal.mesh) > 1 and askSameFilter:
askSameFilter = False
ans = input('Use the same file filter for all meshes (Yes/No) ?')
if ans.upper() in ['YES','Y']:
repeatFilter = True
filterFile = m.__mltflt__
def meshinfo():
im = 0
print(info_menu)
ans0,ans1 = answer_loop('info')
if len(meshfiles) > 1 :
print(' Input files :')
for f in meshfiles:
print(" - {}".format(f))
while True:
sfile = input(' Select file #:')
if sfile in meshfiles:
im = meshfiles.index(sfile)
break
else:
print (' bad filename')
tallylist = list(meshtally[im].mesh.keys())
tallylist.sort()
# print tally list
if ans0 == 'meshinfo' :
meshtally[im].print_info()
# print tally information
elif ans0 == 'tallyinfo' :
try:
tally = int(ans1)
except:
tally = 0
if tally not in tallylist:
if ans1 is not None :
print(' bad tally value')
print(' Tallies :')
for f in tallylist:
print(" - tally {}".format(f))
while True:
tally = input(' Select tally #:')
if tally.isdigit():
tally = int(tally)
if tally in tallylist:
break
else:
print (' bad tally number')
print(' Meshtally file : {}'.format(meshfiles[im]))
meshtally[im].mesh[tally].print_info()
def vtkwrite():
print(' select mesh to write to VTK :')
# display mesh list
onefile = display_meshlist(True)
finish = False
wlist = []
mlist = answer_meshlist('3',None,onefile)
print ('')
for mid in mlist:
m1 = mid[0]
tally = mid[1]
tallyname = tally
if (m1 != -1) :
if ( not meshtally[m1].mesh[tally].filled ) :
meshtally[m1].readMesh([tally])
meshname = meshfiles[m1]
meshobj = meshtally[m1].mesh[tally]
else:
if len(meshtally) == 1 :
meshname = meshfiles[m1]
else:
meshname = 'result'
meshobj = newmesh[tally]
# write mesh into VTK
if meshobj.cart:
name = '{}_{}.vtr'.format(meshname,tallyname)
else:
name = '{}_{}.vts'.format(meshname,tallyname)
print ( ' Write mesh {}'.format(name))
meshobj.writeVTK(name)
def operate():
global idadd,corr
print(operate_menu)
print(' correlation : {}'.format(corr))
ans,meshname = answer_loop('operate')
if ans != 'corr':
# display mesh list
onefile = display_meshlist(True)
if ans == 'scale' :
mlist = answer_meshlist('4',ans,onefile)
if len(mlist) > 0 :
m1 = mlist[0][0]
tally = mlist[0][1]
sfact = mlist[0][2]
if m1 == -1 :
smesh = scalemesh(newmesh[tally],sfact)
else:
if not meshtally[m1].mesh[tally].filled :
meshtally[m1].readMesh([tally])
smesh = scalemesh(meshtally[m1].mesh[tally],sfact)
smesh.filled = True
newmesh[meshname]=smesh
elif ans == 'sum' :
idadd += 1
mlist = answer_meshlist('4',ans,onefile)
if len(mlist) > 1 :
smesh = AddMesh(mlist)
if smesh is not None: newmesh[meshname]=smesh
elif ans == 'diff' :
mlist = answer_meshlist('4',ans,onefile)
if len(mlist) == 2 :
smesh = DiffMesh(mlist[0],mlist[1])
if smesh is not None: newmesh[meshname]=smesh
elif ans == 'binsum' :
mlist = answer_meshlist('4',ans,onefile)
if len(mlist) > 0 :
m1 = mlist[0][0]
tally = mlist[0][1]
if m1 == -1 :
mesh = newmesh[tally]
else:
if not meshtally[m1].mesh[tally].filled :
meshtally[m1].readMesh([tally])
mesh = meshtally[m1].mesh[tally]
mesh.print_EbinRange()
while True:
ans=input(' Enter bin index list:' )
if ans == 'all':
binlist = range(len(mesh.ener))
break
elif re.search(r'[^\d +-]',ans) is None:
binlist=ans.split()
# binlist = map(int,binlist)
# binlist.sort()
binlist = sorted(map(int,binlist))
if binlist[0] >= 0 and binlist[-1] < len(meshtally[m1].mesh[tally].ener) : break
print (' bad bin list values')
bmesh = addbin(mesh,binlist,corr=corr)
newmesh[meshname]=bmesh
elif ans == 'identical' :
mlist = answer_meshlist('4',ans,onefile)
if len(mlist) == 2 :
if mlist[0][0] == -1 :
m1 = newmesh[mlist[0][1]]
else :
m1 = meshtally[mlist[0][0]].mesh[mlist[0][1]]
if mlist[1][0] == -1 :
m2 = newmesh[mlist[1][1]]
else:
m2 = meshtally[mlist[1][0]].mesh[mlist[1][1]]
print_identical(m1,m2)
elif ans == 'corr' :
corr = not corr
print(' Correlation set to {}'.format(corr))
def print_identical(m1,m2):
part, mesh, mtyp = identical_mesh(m1,m2)
if False not in [part,mesh,mtyp]:
print (' Meshes are identical')
else:
if not mesh : print (' Meshes are different')
if not part : print (' Particles are different')
if not mtyp : print (' Mesh types are different')
def AddMesh(mlist):
noread = {}
for m in mlist:
if m[0] == -1 : continue
if not meshtally[m[0]].mesh[m[1]].filled:
if m[0] in noread.keys():
noread[m[0]].append(m[1])
else:
noread[m[0]] = [m[1]]
for k in noread.keys() :
meshtally[k].readMesh(noread[k])
if mlist[0][0] == -1 :
m1 = newmesh[mlist[0][1]]
else :
m1 = meshtally[mlist[0][0]].mesh[mlist[0][1]]
if mlist[1][0] == -1 :
m2 = newmesh[mlist[1][1]]
else:
m2 = meshtally[mlist[1][0]].mesh[mlist[1][1]]
f1 = mlist[0][2]
f2 = mlist[1][2]
msum = addmesh(m1,m2,f1,f2,corr=corr)
if msum is None: return
for m in mlist[2:]:
if m[0] == -1 :
mi = newmesh[m[1]]
else:
mi = meshtally[m[0]].mesh[m[1]]
fi = m[2]
msum = addmesh(msum,mi,1.,fi,corr=corr)
if msum is None: return
return msum
def DiffMesh(mlst1,mlst2):
if mlst1[0] == -1 :
m1 = newmesh[mlst1[1]]
else:
if not meshtally[mlst1[0]].mesh[mlst1[1]].filled:
meshtally[mlst1[0]].readMesh([mlst1[1]])
m1 = meshtally[mlst1[0]].mesh[mlst1[1]]
if mlst2[0] == -1 :
m2 = newmesh[mlst2[1]]
else:
if not meshtally[mlst2[0]].mesh[mlst2[1]].filled:
meshtally[mlst2[0]].readMesh([mlst2[1]])
m2 = meshtally[mlst2[0]].mesh[mlst2[1]]
print ('execute diff')
return diffmesh(m1,m2)
def clear_screen():
if os.name == 'nt':
os.system('cls')
else:
os.system('clear')
meshfiles = [] # list stroing filename
meshtally = [] # list storing meshtal objects
newmesh = {} # mesh produced after operation
idadd = 0
corr = False
if __name__ == "__main__":
clear_screen()
print(principal_menu)
ans,optname=answer_loop('principal')
while True:
# enter meshtally filename
if ans[0:4] == 'open' :
enterfilename(optname)
if len(meshfiles) > len(meshtally):
filetype='MCNP'
meshtally.append(Meshtal(meshfiles[-1],filetype))
mltf_option(meshtally[-1])
# Print meshtally information
elif ans == 'info' :
if len(meshfiles) == 0:
print(' No meshtally file')
else:
meshinfo()
# Write mesh to VTK
elif ans == 'write':
if len(meshfiles) == 0:
print(' No meshtally file')
else:
vtkwrite()
# operate on mesh
elif ans == 'operate':
if len(meshfiles) == 0:
print(' No meshtally file')
else:
operate()
else:
break
ans,optname=answer_loop('principal')
clear_screen()
print(principal_menu)