DAMASK_EICMD/processing/pre/patchFromReconstructedBoundaries

#!/usr/bin/env python

import sys,os,math,re
#import sys,os,pwd,math,re
try:
  import Image,ImageDraw
  ImageCapability = True
except:
  ImageCapability = False

from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP

# -----------------------------
class extendedOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
    
    ACTIONS = Option.ACTIONS + ("extend",)
    STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
    TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
    ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)

    def take_action(self, action, dest, opt, value, values, parser):
        if action == "extend":
            lvalue = value.split(",")
            values.ensure_value(dest, []).extend(lvalue)
        else:
            Option.take_action(self, action, dest, opt, value, values, parser)


releases = {'2010':['linux64',''],
            '2008r1':[''],
            '2007r1':[''],
            '2005r3':[''],
           }

try:
  file = open('%s/../MSCpath'%os.path.dirname(os.path.realpath(sys.argv[0])))
  MSCpath = os.path.normpath(file.readline().strip())
  file.close()
except:
  MSCpath = '/msc'

for release,subdirs in sorted(releases.items(),reverse=True):
  for subdir in subdirs:
    libPath = '%s/mentat%s/shlib/%s'%(MSCpath,release,subdir)
    if os.path.exists(libPath):
      sys.path.append(libPath)
      break
    else:
      continue
  break

try:
  from py_mentat import *
  MentatCapability = True
except:
  print('error: no valid Mentat release found in %s'%MSCpath)
  MentatCapability = False



def outMentat(cmd,locals):
  if cmd[0:3] == '(!)':
    exec(cmd[3:])
  elif cmd[0:3] == '(?)':
    cmd = eval(cmd[3:])
    py_send(cmd)
    if 'log' in locals: locals['log'].append(cmd)
  else:
    py_send(cmd)
    if 'log' in locals: locals['log'].append(cmd)
  return

def outStdout(cmd,locals):
  if cmd[0:3] == '(!)':
    exec(cmd[3:])
  elif cmd[0:3] == '(?)':
    cmd = eval(cmd[3:])
    print cmd
  else:
    print cmd
  return


def output(cmds,locals,dest):
  for cmd in cmds:
    if isinstance(cmd,list):
      output(cmd,locals,dest)
    else:
      {\
      'Mentat': outMentat,\
      'Stdout': outStdout,\
      }[dest](cmd,locals)
  return


def rcbOrientationParser(content):

  grains = []
  myOrientation = [0.0,0.0,0.0]
  for line in content:
    if line[0] != '#':                      # skip comments
      for grain in range(2):
        myID = int(line.split()[12+grain])          # get grain id
        myOrientation = map(float,line.split())[3*grain:3+3*grain]  # get orientation
        if len(grains) < myID:
          for i in range(myID-len(grains)):       # extend list to necessary length
            grains.append([0.0,0.0,0.0])
        grains[myID-1] = myOrientation            # store Euler angles
  
  return grains

def rcbParser(content,M,size,tolerance):                      # parser for TSL-OIM reconstructed boundary files

# find bounding box

  boxX = [1.*sys.maxint,-1.*sys.maxint]
  boxY = [1.*sys.maxint,-1.*sys.maxint]
  x = [0.,0.]
  y = [0.,0.]
  for line in content:
    if line[0] != '#':                                          # skip comments
      (x[0],y[0],x[1],y[1]) = map(float,line.split())[8:12]     # get start and end coordinates of each segment.
      (x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0])   # apply transformation to coordinates
      (x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1])   # to get rcb --> Euler system
      boxX[0] = min(boxX[0],x[0],x[1])
      boxX[1] = max(boxX[1],x[0],x[1])
      boxY[0] = min(boxY[0],y[0],y[1])
      boxY[1] = max(boxY[1],y[0],y[1])
  dX = boxX[1]-boxX[0]
  dY = boxY[1]-boxY[0]
  
  scalePatch = size/dX


# read segments
  segment = 0
  connectivityXY = {"0": {"0":[],"%g"%dY:[],},\
          "%g"%dX: {"0":[],"%g"%dY:[],},}
  connectivityYX = {"0": {"0":[],"%g"%dX:[],},\
          "%g"%dY: {"0":[],"%g"%dX:[],},}
  grainNeighbors = []
  
  for line in content:
    if line[0] != '#':                                          # skip comments
      (x[0],y[0],x[1],y[1]) = map(float,line.split())[8:12]     # get start and end coordinates of each segment
      (x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0])   # apply transformation to coordinates
      (x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1])   # to get rcb --> Euler system

      x[0] -= boxX[0]                                           # make relative to origin of bounding box
      x[1] -= boxX[0]
      y[0] -= boxY[0]
      y[1] -= boxY[0]
      grainNeighbors.append(map(int,line.split()[12:14]))     # remember right and left grain per segment
      for i in range(2):                                      # store segment to both points
        match = False                                         # check whether point is already known (within a small range)
        for posX in connectivityXY.keys():
          if (abs(float(posX)-x[i])<dX*tolerance):
            for posY in connectivityXY[posX].keys():
              if (abs(float(posY)-y[i])<dY*tolerance):
                keyX = posX
                keyY = posY
                match = True
                break
            break
        if (not match):
        # force to boundary if inside tolerance to it
          if (abs(x[i])<dX*tolerance):
            x[i] = 0
          if (abs(dX-x[i])<dX*tolerance):
            x[i] = dX
          if (abs(y[i])<dY*tolerance):
            y[i] = 0
          if (abs(dY-y[i])<dY*tolerance):
            y[i] = dY
          keyX = "%g"%x[i]
          keyY = "%g"%y[i]
          if keyX not in connectivityXY: # create new hash entry for so far unknown point
            connectivityXY[keyX] = {}
          if keyY not in connectivityXY[keyX]: # create new hash entry for so far unknown point
            connectivityXY[keyX][keyY] = []
          if keyY not in connectivityYX: # create new hash entry for so far unknown point
            connectivityYX[keyY] = {}
          if keyX not in connectivityYX[keyY]: # create new hash entry for so far unknown point
            connectivityYX[keyY][keyX] = []
        connectivityXY[keyX][keyY].append(segment)
        connectivityYX[keyY][keyX].append(segment)
      segment += 1
      

# top border
  keyId = "0"
  boundary = connectivityYX[keyId].keys()
  boundary.sort(key=float)
  for indexBdy in range(len(boundary)-1):
    connectivityXY[boundary[indexBdy]][keyId].append(segment)
    connectivityXY[boundary[indexBdy+1]][keyId].append(segment)
    connectivityYX[keyId][boundary[indexBdy]].append(segment)
    connectivityYX[keyId][boundary[indexBdy+1]].append(segment)
    segment += 1

# right border
  keyId = "%g"%(boxX[1]-boxX[0])
  boundary = connectivityXY[keyId].keys()
  boundary.sort(key=float)
  for indexBdy in range(len(boundary)-1):
    connectivityYX[boundary[indexBdy]][keyId].append(segment)
    connectivityYX[boundary[indexBdy+1]][keyId].append(segment)
    connectivityXY[keyId][boundary[indexBdy]].append(segment)
    connectivityXY[keyId][boundary[indexBdy+1]].append(segment)
    segment += 1

# bottom border
  keyId = "%g"%(boxY[1]-boxY[0])
  boundary = connectivityYX[keyId].keys()
  boundary.sort(key=float,reverse=True)
  for indexBdy in range(len(boundary)-1):
    connectivityXY[boundary[indexBdy]][keyId].append(segment)
    connectivityXY[boundary[indexBdy+1]][keyId].append(segment)
    connectivityYX[keyId][boundary[indexBdy]].append(segment)
    connectivityYX[keyId][boundary[indexBdy+1]].append(segment)
    segment += 1

# left border
  keyId = "0"
  boundary = connectivityXY[keyId].keys()
  boundary.sort(key=float,reverse=True)
  for indexBdy in range(len(boundary)-1):
    connectivityYX[boundary[indexBdy]][keyId].append(segment)
    connectivityYX[boundary[indexBdy+1]][keyId].append(segment)
    connectivityXY[keyId][boundary[indexBdy]].append(segment)
    connectivityXY[keyId][boundary[indexBdy+1]].append(segment)
    segment += 1


  allkeysX = connectivityXY.keys()
  allkeysX.sort()
  points = []
  segments = [[] for i in range(segment)]
  pointId = 0
  for keyX in allkeysX:
    allkeysY = connectivityXY[keyX].keys()
    allkeysY.sort()
    for keyY in allkeysY:
      points.append({'coords': [float(keyX)*scalePatch,float(keyY)*scalePatch], 'segments': connectivityXY[keyX][keyY]})
      for segment in connectivityXY[keyX][keyY]:
        if (segments[segment] == None):
          segments[segment] = pointId
        else:
          segments[segment].append(pointId)
      pointId += 1

  grains = {'draw': [], 'legs': []}
  pointId = 0
  for point in points:
    while point['segments']:
      myStart = pointId
      grainDraw = [points[myStart]['coords']]
      innerAngleSum = 0.0
      myWalk = point['segments'].pop()
      grainLegs = [myWalk]
      if segments[myWalk][0] == myStart:
        myEnd = segments[myWalk][1]
      else:
        myEnd = segments[myWalk][0]

      while (myEnd != pointId):
        myV = [points[myEnd]['coords'][0]-points[myStart]['coords'][0],\
          points[myEnd]['coords'][1]-points[myStart]['coords'][1]]
        myLen = math.sqrt(myV[0]**2+myV[1]**2)
        best = {'product': -2.0, 'peek': -1, 'len': -1, 'point': -1}
        for peek in points[myEnd]['segments']:
          if peek == myWalk:
            continue
          if segments[peek][0] == myEnd:
            peekEnd = segments[peek][1]
          else:
            peekEnd = segments[peek][0]
          peekV = [points[myEnd]['coords'][0]-points[peekEnd]['coords'][0],\
              points[myEnd]['coords'][1]-points[peekEnd]['coords'][1]]
          peekLen = math.sqrt(peekV[0]**2+peekV[1]**2)
          crossproduct = (myV[0]*peekV[1]-myV[1]*peekV[0])/myLen/peekLen
          dotproduct = (myV[0]*peekV[0]+myV[1]*peekV[1])/myLen/peekLen
          if crossproduct*(dotproduct+1.0) >= best['product']:
            best['product'] = crossproduct*(dotproduct+1.0)
            best['peek'] = peek
            best['point'] = peekEnd
        innerAngleSum += best['product']
        myWalk = best['peek']
        myStart = myEnd
        myEnd = best['point']
        if myWalk in points[myStart]['segments']:
          points[myStart]['segments'].remove(myWalk)
        else:
          sys.stderr.write(str(myWalk)+' not in segments of '+str(myStart))
        grainDraw.append(points[myStart]['coords'])
        grainLegs.append(myWalk)
      if innerAngleSum > 0.0:
        grains['draw'].append(grainDraw)
        grains['legs'].append(grainLegs)
      else:
        grains['box'] = grainLegs
    pointId += 1


# build overall data structure

  rcData = {'dimension':[dX,dY], 'point': [],'segment': [], 'grain': [], 'grainMapping': []}

  for point in points:
    rcData['point'].append(point['coords'])
  print "found %i points"%(len(rcData['point']))

  for segment in segments:  
    rcData['segment'].append(segment)
  print "built %i segments"%(len(rcData['segment']))

  for grain in grains['legs']:  
    rcData['grain'].append(grain)
    myNeighbors = {}
    for leg in grain:
      if leg < len(grainNeighbors):
        for side in range(2):
          if grainNeighbors[leg][side] in myNeighbors:
            myNeighbors[grainNeighbors[leg][side]] += 1
          else:
            myNeighbors[grainNeighbors[leg][side]] = 1
    if myNeighbors:   # do I have any neighbors
      rcData['grainMapping'].append(sorted(myNeighbors.iteritems(), key=lambda (k,v): (v,k), reverse=True)[0][0])   # most frequent grain is me
  print "found %i grains"%(len(rcData['grain']))

  rcData['box'] = grains['box']


  
  return rcData


def init():
    return ["*new_model yes",
      "*select_clear",
      "*reset",
      "*set_nodes off",
      "*elements_solid",
      "*show_view 4",
      "*reset_view",
      "*view_perspective",
      "*redraw",
      ]


def sample(size,aspect,n,xmargin,ymargin):

  cmds = [\
# gauge
    "*add_points %f %f %f"%(-size*(0.5+xmargin), size*(0.5*aspect+ymargin),0),
    "*add_points %f %f %f"%( size*(0.5+xmargin), size*(0.5*aspect+ymargin),0),
    "*add_points %f %f %f"%( size*(0.5+xmargin),-size*(0.5*aspect+ymargin),0),
    "*add_points %f %f %f"%(-size*(0.5+xmargin),-size*(0.5*aspect+ymargin),0),
    "*set_curve_type line",
    "*add_curves %i %i"%(1,2),
    "*add_curves %i %i"%(3,4),
    "*set_curve_div_type_fix_ndiv",
    "*set_curve_div_num %i"%n,
    "*apply_curve_divisions",
    "1 2 #",
    "*add_curves %i %i"%(2,3),  # right side
    "*add_curves %i %i"%(4,1),  # left side
    "*set_curve_div_type_fix_ndiv",
    "*set_curve_div_num %i"%n,
    "*apply_curve_divisions",
    "3 4 #",
    ]

  return cmds
  

def patch(a,n,mesh,rcData):
  cmds = []
  for l in range(len(rcData['point'])):           # generate all points
    cmds.append("*add_points %f %f %f"%(rcData['point'][l][0]-a/2.0,rcData['point'][l][1]-a/rcData['dimension'][0]*rcData['dimension'][1]/2.0,0))

  cmds.append(["*set_curve_type line",
         "*set_curve_div_type_fix_ndiv",
        ])
  for m in range(len(rcData['segment'])):           # generate all curves and subdivide them for overall balanced piece length
    start = rcData['segment'][m][0]
    end   = rcData['segment'][m][1]
    cmds.append([\
      "*add_curves %i %i" %(start+rcData['offsetPoints'],
                  end  +rcData['offsetPoints']),
      "*set_curve_div_num %i"%(max(1,round(math.sqrt((rcData['point'][start][0]-rcData['point'][end][0])**2+\
                               (rcData['point'][start][1]-rcData['point'][end][1])**2)/a*n))),
      "*apply_curve_divisions",
      "%i #"%(m+rcData['offsetSegments']),
      ])

  grain = 0
  cmds.append('(!)locals["last"] = py_get_int("nelements()")')
  for g in rcData['grain']:
    cmds.append([\
      '(!)locals["first"] = locals["last"]+1',
      "*%s "%mesh+" ".join([str(rcData['offsetSegments']+x) for x in g])+" #",
      '(!)locals["last"] = py_get_int("nelements()")',
      "*select_elements",
      '(?)"%i to %i #"%(locals["first"],locals["last"])',
      "*store_elements grain_%i"%rcData['grainMapping'][grain],
      "all_selected",
      "*select_clear",
      ])
    grain += 1

  return cmds


def gage(mesh,rcData):

  return([\
    "*%s "%mesh + 
    " ".join([str(x) for x in range(1,rcData['offsetSegments'])]) +
    " " +
    " ".join([str(rcData['offsetSegments']+x)for x in rcData['box']]) +
    " #",
    "*select_reset",
    "*select_clear",
    "*select_elements",
    "all_existing",
    "*select_mode_except",
    ['grain_%i'%rcData['grainMapping'][i] for i in range(len(rcData['grain']))],
    "#",
    "*store_elements matrix",
    "all_selected",
    "*select_mode_invert",
    "*select_elements",
    "all_existing",
    "*store_elements _grains",
    "all_selected",
    "*select_clear",
    "*select_reset",
    ])


def expand3D(thickness,steps):
  return([\
    "*set_expand_translation z %f"%(thickness/steps),
    "*set_expand_repetitions %i"%steps,
    "*expand_elements",
    "all_existing",
    ])


def initial_conditions(grainNumber,grainMapping):
  cmds = [\
    "*new_icond",
    "*icond_name _temperature",
    "*icond_type state_variable",
    "*icond_param_value state_var_id 1",
    "*icond_dof_value var 300",
    "*add_icond_elements",
    "all_existing",
    "*new_icond",
    "*icond_name _homogenization",
    "*icond_type state_variable",
    "*icond_param_value state_var_id 2",
    "*icond_dof_value var 1",
    "*add_icond_elements",
    "all_existing",
    ]
  
  for grain in range(grainNumber):
    cmds.append([\
    "*new_icond",
    "*icond_name grain_%i"%grainMapping[grain],
    "*icond_type state_variable",
    "*icond_param_value state_var_id 3",
    "*icond_dof_value var %i"%(grain+1),
    "*add_icond_elements",
    "grain_%i"%grainMapping[grain],
    "",
          ])
  cmds.append([\
    "*new_icond",
    "*icond_name rim",
    "*icond_type state_variable",
    "*icond_param_value state_var_id 3",
    "*icond_dof_value var %i"%(grainNumber+1),
    "*add_icond_elements",
    "matrix",
    ])
  return cmds


def boundary_conditions(rate,thickness, size,aspect,xmargin,ymargin):

  inner = (1 - 1.0e-4) * size*(0.5+xmargin)
  outer = (1 + 1.0e-4) * size*(0.5+xmargin)
  lower = (1 - 1.0e-4) * size*(0.5*aspect+ymargin)
  upper = (1 + 1.0e-4) * size*(0.5*aspect+ymargin)
  
  return [\
  "*new_md_table 1 1",
  "*table_name linear",
  "*set_md_table_type 1 time",
  "*table_add",
  "0 0",
  "1 1",
  "*select_method_box",
  "*new_apply",
  "*apply_name pull_bottom",
  "*apply_type fixed_displacement",
  "*apply_dof y",
  "*apply_dof_value y %f"%(-rate*(inner+outer)/2.0),
  "*apply_dof_table y linear",
  "*select_clear_nodes",
  "*select_nodes",
  "%f %f"%(-outer,outer),
  "%f %f"%(-upper,-lower),
  "%f %f"%(-.0001*thickness,1.0001*thickness),
  "*add_apply_nodes",
  "all_selected",
  "*new_apply",
  "*apply_name pull_top",
  "*apply_type fixed_displacement",
  "*apply_dof y",
  "*apply_dof_value y %f"%(rate*(inner+outer)/2.0),
  "*apply_dof_table y linear",
  "*select_clear_nodes",
  "*select_nodes",
  "%f %f"%(-outer,outer),
  "%f %f"%(lower,upper),
  "%f %f"%(-.0001*thickness,1.0001*thickness),
  "*add_apply_nodes",
  "all_selected",
  "*new_apply",
  "*apply_name fix_x",
  "*apply_type fixed_displacement",
  "*apply_dof x",
  "*apply_dof_value x 0",
  "*select_clear_nodes",
  "*select_nodes",
  "%f %f"%(-outer,-inner),
  "%f %f"%(lower,upper),
  "%f %f"%(-.0001*thickness,.0001*thickness),
  "%f %f"%(-outer,-inner),
  "%f %f"%(lower,upper),
  "%f %f"%(0.9999*thickness,1.0001*thickness),
  "%f %f"%(-outer,-inner),
  "%f %f"%(-upper,-lower),
  "%f %f"%(-.0001*thickness,.0001*thickness),
  "%f %f"%(-outer,-inner),
  "%f %f"%(-upper,-lower),
  "%f %f"%(0.9999*thickness,1.0001*thickness),
  "*add_apply_nodes",
  "all_selected",
  "*new_apply",
  "*apply_name fix_z",
  "*apply_type fixed_displacement",
  "*apply_dof z",
  "*apply_dof_value z 0",
  "*select_clear_nodes",
  "*select_nodes",
  "%f %f"%(-outer,-inner),
  "%f %f"%(lower,upper),
  "%f %f"%(-.0001*thickness,.0001*thickness),
  "%f %f"%(-outer,-inner),
  "%f %f"%(-upper,-lower),
  "%f %f"%(-.0001*thickness,.0001*thickness),
  "%f %f"%(inner,outer),
  "%f %f"%(lower,upper),
  "%f %f"%(-.0001*thickness,.0001*thickness),
  "%f %f"%(inner,outer),
  "%f %f"%(-upper,-lower),
  "%f %f"%(-.0001*thickness,.0001*thickness),
  "*add_apply_nodes",
  "all_selected",
  "*select_clear",
  "*select_reset",
  ]

def materials():
  return [\
  "*new_material",
  "*material_name patch",
  "*material_type mechanical:hypoelastic",
  "*material_option hypoelastic:method:hypela2",
  "*material_option hypoelastic:pass:def_rot",
  "*add_material_elements",
  "all_existing",
  ]
  

def loadcase(time,incs,Ftol): 
  return [\
  "*new_loadcase",
  "*loadcase_name puller",
  "*loadcase_type static",
  "*loadcase_value time",
  "%g"%time,
  "*loadcase_value nsteps",
  "%i"%incs,
  "*loadcase_value maxrec",
  "20",
  "*loadcase_value ntime_cuts",
  "30",
  "*loadcase_value force",
  "%g"%Ftol,
  ]


def job(grainNumber,grainMapping,twoD):  
  return [\
  "*new_job",
  "*job_name pull",
  "*job_class mechanical",
  "*add_job_loadcases puller",
  "*add_job_iconds homogenization",
  ["*add_job_iconds grain_%i"%i for i in grainMapping[:grainNumber]],
  "*add_job_iconds rim",
  "*job_option dimen:%s                     | analysis dimension"%({True:'two',False:'three'}[twoD]),
  "*job_option strain:large                 | finite strains",
  "*job_option large_strn_proc:upd_lagrange | updated Lagrange framework",
  "*job_option plas_proc:multiplicative     | multiplicative decomp of F",
  "*job_option solver_nonsym:on             | nonsymmetrical solution",
  "*job_option solver:mfront_sparse         | multi-frontal sparse",
  "*job_param stef_boltz 5.670400e-8",
  "*job_param univ_gas_const 8.314472",
  "*job_param planck_radiation_2 1.4387752e-2",
  "*job_param speed_light_vacuum 299792458",
#  "*job_usersub_file /san/%s/FEM/DAMASK/code/mpie_cpfem_marc2010.f90  | subroutine definition"%(pwd.getpwuid(os.geteuid())[0].rpartition("\\")[2]),
  "*job_option user_source:compile_save",
  ]

# "*job_option large:on                  | large displacement",
# "*job_option plasticity:l_strn_mn_add  | large strain additive",
# "*job_option cdilatation:on            | constant dilatation",
# "*job_option update:on                 | updated lagrange procedure",
# "*job_option finite:on                 | large strains",
# "*job_option restart_mode:write        | enable restarting",


def postprocess():
  return [\
  "*add_post_tensor stress",
  "*add_post_tensor strain",
  "*add_post_var von_mises",
  "",
  ]



def cleanUp(a):
  return [\
  "*remove_curves",
  "all_existing",
  "*remove_points",
  "all_existing",
  "*set_sweep_tolerance %f"%(1e-5*a),
  "*sweep_all",
  "*renumber_all",
  ]


# -------------------------
def image(name,imgsize,marginX,marginY,rcData):
# -------------------------

  dX = max([coords[0] for coords in rcData['point']])
  dY = max([coords[1] for coords in rcData['point']])
  offsetX = imgsize*marginX
  offsetY = imgsize*marginY
  sizeX = int(imgsize*(1    +2*marginX))
  sizeY = int(imgsize*(dY/dX+2*marginY))

  scaleImg = imgsize/dX            # rescale from max x coord

  img = Image.new("RGB",(sizeX,sizeY),(255,255,255))
  draw = ImageDraw.Draw(img)

  for id,point in enumerate(rcData['point']):
    draw.text([offsetX+point[0]*scaleImg,sizeY-(offsetY+point[1]*scaleImg)],"%i"%id,fill=(0,0,0))

  for id,vertex in enumerate(rcData['segment']):
      start = rcData['point'][vertex[0]]
      end   = rcData['point'][vertex[1]]
      draw.text([offsetX+(start[0]+end[0])/2.0*scaleImg,sizeY-(offsetY+(start[1]+end[1])/2.0*scaleImg)],"%i"%id,fill=(0,0,128))
      draw.line([offsetX+start[0]*scaleImg,sizeY-(offsetY+start[1]*scaleImg),
                 offsetX+  end[0]*scaleImg,sizeY-(offsetY+  end[1]*scaleImg)],width=1,fill=(128,128,128))

  for id,segment in enumerate(rcData['box']):
        start = rcData['point'][rcData['segment'][segment][0]]
        end   = rcData['point'][rcData['segment'][segment][1]]
        draw.line([offsetX+start[0]*scaleImg,sizeY-(offsetY+start[1]*scaleImg),
                   offsetX+  end[0]*scaleImg,sizeY-(offsetY+  end[1]*scaleImg)],width=3,fill=(128,128*(id%2),0))

  for grain,origGrain in enumerate(rcData['grainMapping']):
    center = [0.0,0.0]
    for segment in rcData['grain'][grain]:                    # loop thru segments around grain
      for point in rcData['segment'][segment]:                # take start and end points
        center[0] += rcData['point'][point][0]                # build vector sum
        center[1] += rcData['point'][point][1]

    center[0] /= len(rcData['grain'][grain])*2                 # normalize by two times segment count, i.e. point count
    center[1] /= len(rcData['grain'][grain])*2

    draw.text([offsetX+center[0]*scaleImg,sizeY-(offsetY+center[1]*scaleImg)],'%i -> %i'%(grain,origGrain),fill=(128,32,32))

    img.save(name+'.png',"PNG")

# -------------------------
def inside(x,y,points):                                                     # tests whether point(x,y) is within polygon described by points
# -------------------------
 inside = False
 npoints=len(points)
 (x1,y1) = points[npoints-1]                                                # start with last point of points
 startover = (y1 >= y)                                                      # am I above testpoint?
 for i in range(npoints):                                                   # loop through all points
   (x2,y2) = points[i]                                                      # next point
   endover = (y2 >= y)                                                      # am I above testpoint?
   if (startover != endover):                                               # one above one below testpoint?
     if((y2 - y)*(x2 - x1) <= (y2 - y1)*(x2 - x)):                          # check for intersection
       if (endover):
         inside = not inside                                                # found intersection
     else:
       if (not endover):
         inside = not inside                                                # found intersection
   startover = endover                                                      # make second point first point
   (x1,y1) = (x2,y2)
   
 return inside
  
# -------------------------
def fftbuild(rcData, height,xframe,yframe,resolution,extrusion):            # build array of grain numbers
# -------------------------
 maxX = -1.*sys.maxint
 maxY = -1.*sys.maxint
 for line in rcData['point']:                                               # find data range
   (x,y) = line
   maxX = max(maxX, x)
   maxY = max(maxY, y)
 xsize = maxX+2*xframe                                                      # add framsize
 ysize = maxY+2*yframe
 xres=round(resolution/2.0)*2                                               # use only even resolution
 yres=round(xres/xsize*ysize/2.0)*2                                         # calculate other resolutions
 zres=round(extrusion/2.0)*2
 zsize = xsize/xres*zres                                                    # calculate z size
 
 fftdata = {'fftpoints':[], \
            'resolution':(xres,yres,zres), \
            'dimension':(xsize,ysize,zsize)}
 
 frameindex=len(rcData['grain'])+1                                          # calculate frame index as largest grain index plus one 
 dx = xsize/(xres+1)                                                        # calculate step sizes
 dy = ysize/(yres+1)

 grainpoints = []
 for segments in rcData['grain']:                                           # get segments of each grain
   points = {}
   for i,segment in enumerate(segments[:-1]):                               # loop thru segments except last (s=[start,end])
     points[rcData['segment'][segment][0]] = i                              # assign segment index to start point
     points[rcData['segment'][segment][1]] = i                              # assigne segment index to endpoint
   for i in range(2):                                                       # check points of last segment
     if points[rcData['segment'][segments[-1]][i]] != 0:                    # not on first segment
       points[rcData['segment'][segments[-1]][i]] = len(segments)-1         # assign segment index to last point
   
   grainpoints.append([])                                                   # start out blank for current grain
   for p in sorted(points, key=points.get):                                 # loop thru set of sorted points
     grainpoints[-1].append([rcData['point'][p][0],rcData['point'][p][1]])  # append x,y of point

 bestGuess = 0                                                              # assume grain 0 as best guess
 for i in range(int(xres*yres)):                                            # walk through all points in xy plane
   xtest = -xframe+((i%xres)+0.5)*dx                                        # calculate coordinates
   ytest = -yframe+(int(i/xres)+0.5)*dy
   if(xtest < 0 or xtest > maxX):                                           # check wether part of frame
     if( ytest < 0 or ytest > maxY):                                        # part of edges
       fftdata['fftpoints'].append(frameindex+2)                            # append frameindex to result array
     else:                                                                  # part of xframe
       fftdata['fftpoints'].append(frameindex)                              # append frameindex to result array
   elif( ytest < 0 or ytest > maxY):                                        # part of yframe
       fftdata['fftpoints'].append(frameindex+1)                            # append frameindex to result array
   else:
      if inside(xtest,ytest,grainpoints[bestGuess]):                        # check best guess first
        fftdata['fftpoints'].append(bestGuess+1)
      else:                                                                 # no success
        for g in range(len(grainpoints)):                                   # test all
          if inside(xtest,ytest,grainpoints[g]):
            fftdata['fftpoints'].append(g+1)
            bestGuess = g
            break
        
 return fftdata  


# ----------------------- MAIN -------------------------------
  
parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile[s]', description = """
what I do...
""")

parser.add_option("-o", "--output", action='extend', dest='output', type='string', \
        help="type of output [image,mentat,procedure,spectral]")
parser.add_option("-p", "--port", type="int",\
        dest="port",\
        help="Mentat connection port")
parser.add_option("-2", "--twodimensional", action="store_true",\
        dest="twoD",\
        help="twodimensional model [%default]")
parser.add_option("-s","--patchsize", type="float",\
        dest="size",\
        help="height of patch [%default]")
parser.add_option("-e", "--strain", type="float",\
        dest="strain",\
        help="final strain to reach in simulation [%default]")
parser.add_option("--rate", type="float",\
        dest="strainrate",\
        help="(engineering) strain rate to simulate")
parser.add_option("-N", "--increments", type="int",\
        dest="increments",\
        help="number of increments to take")
parser.add_option("-t", "--tolerance", type="float",\
        dest="tolerance",\
        help="relative tolerance of pixel positions to be swept")
parser.add_option("-m", "--mesh", choices=['dt_planar_trimesh','af_planar_trimesh','af_planar_quadmesh'],\
        dest="mesh",\
        help="algorithm and element type for automeshing [%default]")
parser.add_option("-x", "--xmargin", type="float",\
        dest="xmargin",\
        help="margin in x in units of patch size [%default]")
parser.add_option("-y", "--ymargin", type="float",\
        dest="ymargin",\
        help="margin in y in units of patch size [%default]")
parser.add_option("-r", "--resolution", type="int",\
        dest="resolution",\
        help="number of Fourier points/Finite Elements across patch size + x_margin [%default]")
parser.add_option("-z", "--extrusion", type="int",\
        dest="extrusion",\
        help="number of repetitions in z-direction [%default]")
parser.add_option("-i", "--imagesize", type="int",\
        dest="imgsize",\
        help="size of PNG image")
parser.add_option("-M", "--coordtransformation", type="float", nargs=4, \
        dest="M",\
        help="2x2 transformation from rcb to Euler coords ( = M . [x_rcb,y_rcb])")
parser.add_option("--scatter", type="float",\
        dest="scatter",\
        help="orientation scatter [%default]")

parser.set_defaults(output = [])
parser.set_defaults(size = 1.0)
parser.set_defaults(xmargin = 0.0)
parser.set_defaults(ymargin = 0.0)
parser.set_defaults(resolution = 64)
parser.set_defaults(extrusion = 2)
parser.set_defaults(imgsize = 512)
parser.set_defaults(M = [0.0,1.0,1.0,0])  # M_11, M_12, M_21, M_22.  x,y in RCB is y,x of Eulers!!
parser.set_defaults(tolerance = 1.0e-3)
parser.set_defaults(scatter = 0.0)
parser.set_defaults(strain = 0.2)
parser.set_defaults(strainrate = 1.0e-3)
parser.set_defaults(increments = 200)
parser.set_defaults(mesh = 'dt_planar_trimesh')
parser.set_defaults(twoD = False)

(options, args) = parser.parse_args()
if not len(args):
  parser.error('no boundary file specified')

try:
  boundaryFile = open(args[0])
  boundarySegments = boundaryFile.readlines()
  boundaryFile.close()
except:
  print 'unable to read boundary file "%s"'%args[0]
  sys.exit(-1)

options.output = [s.lower() for s in options.output]                        # lower case

myName = os.path.splitext(args[0])[0]
print "\n",myName

orientationData = rcbOrientationParser(boundarySegments)
rcData = rcbParser(boundarySegments,options.M,options.size,options.tolerance)

# ----- write image -----

if ImageCapability and 'image' in options.output and options.imgsize > 0:
  image(myName,options.imgsize,options.xmargin,options.ymargin,rcData)

# ----- write spectral geom -----

if 'spectral' in options.output:
  fftdata = fftbuild(rcData, options.size, options.xmargin, options.ymargin, options.resolution, options.extrusion)
  
  geomFile = open(myName+'_'+str(int(fftdata['resolution'][0]))+'.geom','w')  # open geom file for writing
  geomFile.write('resolution a %i b %i c %i\n'%(fftdata['resolution']))       # write resolution
  geomFile.write('dimension x %f y %f z %f\n'%(fftdata['dimension']))         # write size
  geomFile.write('homogenization 1\n')                                        # write homogenization
  for i in range(int(fftdata['resolution'][2])):                              # repetitions according to z resolution, i.e. extrude 2D to 3D
   geomFile.write('\n'.join(map(str,fftdata['fftpoints']))+'\n')              # write grain indexes, one per line
  geomFile.close()                                                            # close geom file
  
  print('assigned %i out of %i Fourier points'%(len(fftdata['fftpoints']), int(fftdata['resolution'][0])*int(fftdata['resolution'][1])))
  

# ----- write Mentat procedure -----

if MentatCapability and 'mentat' in options.output:
  rcData['offsetPoints']   = 1+4                # gage definition generates 4 points
  rcData['offsetSegments'] = 1+4                # gage definition generates 4 segments
  
  cmds = [\
    init(),
    sample(options.size,rcData['dimension'][1]/rcData['dimension'][0],12,options.xmargin,options.ymargin),
    patch(options.size,options.resolution,options.mesh,rcData),
    gage(options.mesh,rcData),
    ]
  
  if not options.twoD:
    cmds += [expand3D(options.size*(1.0+2.0*options.xmargin)/options.resolution*options.extrusion,options.extrusion),]
  
  cmds += [\
    cleanUp(options.size),
    materials(),
    initial_conditions(len(rcData['grain']),rcData['grainMapping']),
    boundary_conditions(options.strainrate,options.size*(1.0+2.0*options.xmargin)/options.resolution*options.extrusion,\
                        options.size,rcData['dimension'][1]/rcData['dimension'][0],options.xmargin,options.ymargin),
    loadcase(options.strain/options.strainrate,options.increments,0.01),
    job(len(rcData['grain']),rcData['grainMapping'],options.twoD),
    postprocess(),
    ["*identify_sets","*regen","*fill_view","*save_as_model %s yes"%(myName)],
  ]
  
  outputLocals = {'log':[]}
  if (options.port != None):
    py_connect('',options.port)
    output(cmds,outputLocals,'Mentat')
    py_disconnect()
    if 'procedure' in options.output:
      output(outputLocals['log'],outputLocals,'Stdout')
    

# ----- write config data to file -----

if 'mentat' in options.output or 'spectral' in options.output:
  output = ''
  output += '\n\n<homogenization>\n' + \
            '\n[SX]\n' + \
            'type\tisostrain\n' + \
            'Ngrains\t1\n' + \
            '\n\n<microstructure>\n'
  
  for i,grain in enumerate(rcData['grainMapping']):
    output += '\n[grain %i]\n'%grain + \
              'crystallite\t1\n' + \
              '(constituent)\tphase 1\ttexture %i\tfraction 1.0\n'%(i+1)
  if (options.xmargin > 0.0):
      output += '\n[x-margin]\n' + \
                'crystallite\t1\n' + \
                '(constituent)\tphase 2\ttexture %i\tfraction 1.0\n'%(len(rcData['grainMapping'])+1)
  if (options.ymargin > 0.0):
      output += '\n[y-margin]\n' + \
                'crystallite\t1\n' + \
                '(constituent)\tphase 2\ttexture %i\tfraction 1.0\n'%(len(rcData['grainMapping'])+1)
  if (options.xmargin > 0.0 and options.ymargin > 0.0):
      output += '\n[margin edge]\n' + \
                'crystallite\t1\n' + \
                '(constituent)\tphase 2\ttexture %i\tfraction 1.0\n'%(len(rcData['grainMapping'])+1)
  
  output += '\n\n<crystallite>\n' + \
            '\n[fillMeIn]\n' + \
            '\n\n<phase>\n' + \
            '\n[patch]\n'
  if (options.xmargin > 0.0 or options.ymargin > 0.0):
    output += '\n[margin]\n'
  
  output += '\n\n<texture>\n\n'
  for grain in rcData['grainMapping']:
    output += '\n[grain %i]\n'%grain + \
              '(gauss)\tphi1\t%f\tphi\t%f\tphi2\t%f\tscatter\t%f\tfraction\t1.0\n'\
              %(math.degrees(orientationData[grain-1][0]),math.degrees(orientationData[grain-1][1]),math.degrees(orientationData[grain-1][2]),options.scatter)
  if (options.xmargin > 0.0 or options.ymargin > 0.0):
    output += '\n[margin]\n' + \
              '(random)\t\tscatter\t0.0\tfraction\t1.0\n'
  
  configFile = open(myName+'.config','w')
  configFile.write(output)
  configFile.close()