Merge branch 'grid-filters' into MiscImprovements

processing/post/addCalculation.py

@@ -4,7 +4,7 @@ import os
 import sys
 from optparse import OptionParser
 import re
-import collections
+from collections.abc import Iterable
 import math                                                                                         # noqa
 
 import scipy                                                                                        # noqa
@@ -18,7 +18,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 def listify(x):
-  return x if isinstance(x, collections.Iterable) else [x]
+  return x if isinstance(x, Iterable) else [x]
 
 
 # --------------------------------------------------------------------
@@ -65,9 +65,10 @@ for i in range(len(options.formulas)):
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try: 
-                                    buffered = False)
+    table = damask.ASCIItable(name = name, buffered = False)
-  except: continue
+  except IOError: 
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header -------------------------------------------  

processing/post/addCumulative.py

@@ -41,9 +41,9 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name, buffered = False)
-                              buffered = False)
+  except IOError: 
-  except IOError: continue
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------  

processing/post/addCurl.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
 import numpy as np
@@ -12,48 +13,6 @@ import damask
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
-def merge_dicts(*dict_args):
-  """Given any number of dicts, shallow copy and merge into a new dict, with precedence going to key value pairs in latter dicts."""
-  result = {}
-  for dictionary in dict_args:
-      result.update(dictionary)
-  return result
-
-def curlFFT(geomdim,field):
-  """Calculate curl of a vector or tensor field by transforming into Fourier space."""
-  shapeFFT    = np.array(np.shape(field))[0:3]
-  grid = np.array(np.shape(field)[2::-1])
-  N = grid.prod()                                                                                    # field size
-  n = np.array(np.shape(field)[3:]).prod()                                                           # data size
-
-  field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
-  curl_fourier  = np.empty(field_fourier.shape,'c16')
-
-  # differentiation in Fourier space
-  TWOPIIMG = 2.0j*np.pi
-  einsums = { 
-              3:'slm,ijkl,ijkm->ijks',                                                               # vector, 3 -> 3
-              9:'slm,ijkl,ijknm->ijksn',                                                             # tensor, 3x3 -> 3x3
-            }
-  k_sk = np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2]))/geomdim[0]
-  if grid[2]%2 == 0: k_sk[grid[2]//2] = 0                                                            # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
-
-  k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/geomdim[1]
-  if grid[1]%2 == 0: k_sj[grid[1]//2] = 0                                                            # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
-
-  k_si = np.arange(grid[0]//2+1)/geomdim[2]
-
-  kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
-  k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')
-
-  e = np.zeros((3, 3, 3))
-  e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = 1.0                                                         # Levi-Civita symbols 
-  e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
-
-  curl_fourier = np.einsum(einsums[n],e,k_s,field_fourier)*TWOPIIMG
-
-  return np.fft.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
-
 
 # --------------------------------------------------------------------
 #                                MAIN
@@ -61,8 +20,7 @@ def curlFFT(geomdim,field):
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing curl of requested column(s).
-Operates on periodic ordered three-dimensional data sets
+Operates on periodic ordered three-dimensional data sets of vector and tensor fields.
-of vector and tensor fields.
 """, version = scriptID)
 
 parser.add_option('-p','--pos','--periodiccellcenter',
@@ -70,93 +28,30 @@ parser.add_option('-p','--pos','--periodiccellcenter',
                   type = 'string', metavar = 'string',
                   help = 'label of coordinates [%default]')
 parser.add_option('-l','--label',
-                  dest = 'data',
+                  dest = 'labels',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'label(s) of field values')
 
 parser.set_defaults(pos = 'pos',
                    )
 
-
 (options,filenames) = parser.parse_args()
-
-if options.data is None: parser.error('no data column specified.')
-
-# --- define possible data types -------------------------------------------------------------------
-
-datatypes = {
-              3: {'name': 'vector',
-                  'shape': [3],
-                 },
-              9: {'name': 'tensor',
-                  'shape': [3,3],
-                 },
-            }
-
-# --- loop over input files ------------------------------------------------------------------------
-
 if filenames == []: filenames = [None]
 
+if options.labels is None: parser.error('no data column specified.')
+
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,buffered = False)
+    damask.util.report(scriptName,name)
-  except: continue
-  damask.util.report(scriptName,name)
 
-# --- interpret header ----------------------------------------------------------------------------
+    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
 
-  table.head_read()
+    for label in options.labels:
-
+        field = table.get(label)
-  remarks = []
+        shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3)                         # vector or tensor
-  errors  = []
+        field = field.reshape(np.append(grid[::-1],shape))
-  active = []
+        table.add('curlFFT({})'.format(label),
-
+                  damask.grid_filters.curl(size[::-1],field).reshape((-1,np.prod(shape))),
-  coordDim = table.label_dimension(options.pos)
+                  scriptID+' '+' '.join(sys.argv[1:]))
-  if coordDim != 3:
+    
-    errors.append('coordinates "{}" must be three-dimensional.'.format(options.pos))
+    table.to_ASCII(sys.stdout if name is None else name)
-  else: coordCol = table.label_index(options.pos)
-
-  for me in options.data:
-    dim = table.label_dimension(me)
-    if dim in datatypes:
-      active.append(merge_dicts({'label':me},datatypes[dim]))
-      remarks.append('differentiating {} "{}"...'.format(datatypes[dim]['name'],me))
-    else:
-      remarks.append('skipping "{}" of dimension {}...'.format(me,dim) if dim != -1 else \
-                     '"{}" not found...'.format(me) )
-
-  if remarks != []: damask.util.croak(remarks)
-  if errors  != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-
-# ------------------------------------------ assemble header --------------------------------------
-
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  for data in active:
-    table.labels_append(['{}_curlFFT({})'.format(i+1,data['label']) 
-                        for i in range(np.prod(np.array(data['shape'])))])                         # extend ASCII header with new labels
-  table.head_write()
-
-# --------------- figure out size and grid ---------------------------------------------------------
-
-  table.data_readArray()
-  grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
-
-# ------------------------------------------ process value field -----------------------------------
-
-  stack = [table.data]
-  for data in active:
-    # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
-    stack.append(curlFFT(size[::-1],
-                         table.data[:,table.label_indexrange(data['label'])].
-                         reshape(grid[::-1].tolist()+data['shape'])))
-
-# ------------------------------------------ output result -----------------------------------------
-
-  if len(stack) > 1: table.data = np.hstack(tuple(stack))
-  table.data_writeArray('%.12g')
-
-# ------------------------------------------ output finalization -----------------------------------
-
-  table.close()                                                                                     # close input ASCII table (works for stdin)

processing/post/addDisplacement.py

@@ -2,10 +2,10 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
 import numpy as np
-import scipy.ndimage
 
 import damask
 
@@ -14,79 +14,6 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 
-#--------------------------------------------------------------------------------------------------
-def cell2node(cellData,grid):
-
-  nodeData = 0.0
-  datalen = np.array(cellData.shape[3:]).prod()
-  
-  for i in range(datalen):
-    node = scipy.ndimage.convolve(cellData.reshape(tuple(grid[::-1])+(datalen,))[...,i],
-                                  np.ones((2,2,2))/8.,                                              # 2x2x2 neighborhood of cells
-                                  mode = 'wrap',
-                                  origin = -1,                                                      # offset to have cell origin as center
-                                 )                                                                  # now averaged at cell origins
-    node = np.append(node,node[np.newaxis,0,:,:,...],axis=0)                                        # wrap along z
-    node = np.append(node,node[:,0,np.newaxis,:,...],axis=1)                                        # wrap along y
-    node = np.append(node,node[:,:,0,np.newaxis,...],axis=2)                                        # wrap along x
-
-    nodeData = node[...,np.newaxis] if i==0 else np.concatenate((nodeData,node[...,np.newaxis]),axis=-1)
-
-  return nodeData
-
-#--------------------------------------------------------------------------------------------------
-def displacementAvgFFT(F,grid,size,nodal=False,transformed=False):
-  """Calculate average cell center (or nodal) displacement for deformation gradient field specified in each grid cell"""
-  if nodal:
-    x, y, z = np.meshgrid(np.linspace(0,size[2],1+grid[2]),
-                          np.linspace(0,size[1],1+grid[1]),
-                          np.linspace(0,size[0],1+grid[0]),
-                          indexing = 'ij')
-  else:
-    delta = size/grid*0.5
-    x, y, z = np.meshgrid(np.linspace(delta[2],size[2]-delta[2],grid[2]),
-                          np.linspace(delta[1],size[1]-delta[1],grid[1]),
-                          np.linspace(delta[0],size[0]-delta[0],grid[0]),
-                          indexing = 'ij')
-
-  origCoords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) 
-
-  F_fourier = F if transformed else np.fft.rfftn(F,axes=(0,1,2))                                    # transform or use provided data
-  Favg = np.real(F_fourier[0,0,0,:,:])/grid.prod()                                                  # take zero freq for average
-  avgDisplacement = np.einsum('ml,ijkl->ijkm',Favg-np.eye(3),origCoords)                            # dX = Favg.X
-
-  return avgDisplacement
-
-#--------------------------------------------------------------------------------------------------
-def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
-  """Calculate cell center (or nodal) displacement for deformation gradient field specified in each grid cell"""
-  integrator = 0.5j * size / np.pi
-
-  kk, kj, ki = np.meshgrid(np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2])),
-                           np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1])),
-                                    np.arange(grid[0]//2+1),
-                           indexing = 'ij')
-  k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3) 
-  k_sSquared = np.einsum('...l,...l',k_s,k_s)
-  k_sSquared[0,0,0] = 1.0                                                                           # ignore global average frequency
-
-#--------------------------------------------------------------------------------------------------
-# integration in Fourier space
-
-  displacement_fourier = -np.einsum('ijkml,ijkl,l->ijkm',
-                                    F if transformed else np.fft.rfftn(F,axes=(0,1,2)),
-                                    k_s,
-                                    integrator,
-                                   ) / k_sSquared[...,np.newaxis]
-
-#--------------------------------------------------------------------------------------------------
-# backtransformation to real space
-
-  displacement = np.fft.irfftn(displacement_fourier,grid[::-1],axes=(0,1,2))
-
-  return cell2node(displacement,grid) if nodal else displacement
-
-
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
@@ -100,7 +27,7 @@ Outputs at cell centers or cell nodes (into separate file).
 
 parser.add_option('-f',
                   '--defgrad',
-                  dest    = 'defgrad',
+                  dest    = 'f',
                   metavar = 'string',
                   help    = 'label of deformation gradient [%default]')
 parser.add_option('-p',
@@ -113,108 +40,34 @@ parser.add_option('--nodal',
                   action  = 'store_true',
                   help    = 'output nodal (instead of cell-centered) displacements')
 
-parser.set_defaults(defgrad = 'f',
+parser.set_defaults(f   = 'f',
-                    pos     = 'pos',
+                    pos = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
 
-# --- loop over input files -------------------------------------------------------------------------
-
-if filenames == []: filenames = [None]
-
 for name in filenames:
-  outname = (os.path.splitext(name)[0] +
+    damask.util.report(scriptName,name)
-             '_nodal' +
-             os.path.splitext(name)[1]) if (options.nodal and name) else None
-  try:    table = damask.ASCIItable(name = name,
-                                    outname = outname,
-                                    buffered = False)
-  except: continue
-  damask.util.report(scriptName,'{}{}'.format(name if name else '',
-                                              ' --> {}'.format(outname) if outname else ''))
 
-# ------------------------------------------ read header ------------------------------------------
+    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
+    grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
-  table.head_read()
+    
-
+    F = table.get(options.f).reshape(np.append(grid[::-1],(3,3)))
-# ------------------------------------------ sanity checks ----------------------------------------
+    if options.nodal:
-
+        table = damask.Table(damask.grid_filters.node_coord0(grid[::-1],size[::-1]).reshape((-1,3)),
-  errors  = []
+                             {'pos':(3,)})
-  remarks = []
+        table.add('avg({}).{}'.format(options.f,options.pos),
-  
+                  damask.grid_filters.node_displacement_avg(size[::-1],F).reshape((-1,3)),
-  if table.label_dimension(options.defgrad) != 9:
+                  scriptID+' '+' '.join(sys.argv[1:]))
-    errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad))
+        table.add('fluct({}).{}'.format(options.f,options.pos),
-
+                  damask.grid_filters.node_displacement_fluct(size[::-1],F).reshape((-1,3)),
-  coordDim = table.label_dimension(options.pos)
+                  scriptID+' '+' '.join(sys.argv[1:]))
-  if not 3 >= coordDim >= 1:
+        table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
-    errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
+    else:
-  elif coordDim < 3:
+        table.add('avg({}).{}'.format(options.f,options.pos),
-    remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
+                  damask.grid_filters.cell_displacement_avg(size[::-1],F).reshape((-1,3)),
-                                                                            's' if coordDim < 2 else '',
+                  scriptID+' '+' '.join(sys.argv[1:]))
-                                                                            options.pos))
+        table.add('fluct({}).{}'.format(options.f,options.pos),
-
+                  damask.grid_filters.cell_displacement_fluct(size[::-1],F).reshape((-1,3)),
-  if remarks != []: damask.util.croak(remarks)
+                  scriptID+' '+' '.join(sys.argv[1:]))
-  if errors  != []:
+        table.to_ASCII(sys.stdout if name is None else name)
-    damask.util.croak(errors)
-    table.close(dismiss=True)
-    continue
-
-# --------------- figure out size and grid ---------------------------------------------------------
-
-  table.data_readArray([options.defgrad,options.pos])
-  table.data_rewind()
-
-  if len(table.data.shape) < 2: table.data.shape += (1,)                                            # expand to 2D shape
-  if table.data[:,9:].shape[1] < 3:
-    table.data = np.hstack((table.data,
-                            np.zeros((table.data.shape[0],
-                                      3-table.data[:,9:].shape[1]),dtype='f')))                     # fill coords up to 3D with zeros
-
-  grid,size = damask.util.coordGridAndSize(table.data[:,9:12])
-  N = grid.prod()
-
-  if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid))
-  if errors  != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-  
-# ------------------------------------------ process data ------------------------------------------
-
-  F_fourier = np.fft.rfftn(table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),axes=(0,1,2))      # perform transform only once...
-
-  fluctDisplacement = displacementFluctFFT(F_fourier,grid,size,options.nodal,transformed=True)
-  avgDisplacement   = displacementAvgFFT  (F_fourier,grid,size,options.nodal,transformed=True)
-
-# ------------------------------------------ assemble header ---------------------------------------
-
-  if options.nodal:
-    table.info_clear()
-    table.labels_clear()
-
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  table.labels_append((['{}_pos'         .format(i+1)   for i in range(3)] if options.nodal else []) +
-                       ['{}_avg({}).{}'  .format(i+1,options.defgrad,options.pos) for i in range(3)] +
-                       ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.pos) for i in range(3)] )
-  table.head_write()
-
-# ------------------------------------------ output data -------------------------------------------
-
-  Zrange = np.linspace(0,size[2],1+grid[2]) if options.nodal else range(grid[2])
-  Yrange = np.linspace(0,size[1],1+grid[1]) if options.nodal else range(grid[1])
-  Xrange = np.linspace(0,size[0],1+grid[0]) if options.nodal else range(grid[0])
-
-  for i,z     in enumerate(Zrange):
-    for j,y   in enumerate(Yrange):
-      for k,x in enumerate(Xrange):
-        if options.nodal: table.data_clear()
-        else:             table.data_read()
-        table.data_append([x,y,z] if options.nodal else [])
-        table.data_append(list(  avgDisplacement[i,j,k,:]))
-        table.data_append(list(fluctDisplacement[i,j,k,:]))
-        table.data_write()                       
-
-# ------------------------------------------ output finalization -----------------------------------
-
-  table.close()                                                                                     # close ASCII tables

processing/post/addDivergence.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
 import numpy as np
@@ -12,53 +13,14 @@ import damask
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
-def merge_dicts(*dict_args):
-  """Given any number of dicts, shallow copy and merge into a new dict, with precedence going to key value pairs in latter dicts."""
-  result = {}
-  for dictionary in dict_args:
-      result.update(dictionary)
-  return result
-
-def divFFT(geomdim,field):
-  """Calculate divergence of a vector or tensor field by transforming into Fourier space."""
-  shapeFFT    = np.array(np.shape(field))[0:3]
-  grid = np.array(np.shape(field)[2::-1])
-  N = grid.prod()                                                                                    # field size
-  n = np.array(np.shape(field)[3:]).prod()                                                           # data size
-
-  field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
-  div_fourier   = np.empty(field_fourier.shape[0:len(np.shape(field))-1],'c16')
-
-  # differentiation in Fourier space
-  TWOPIIMG = 2.0j*np.pi
-  einsums = { 
-              3:'ijkl,ijkl->ijk',                                                               # vector, 3 -> 1
-              9:'ijkm,ijklm->ijkl',                                                             # tensor, 3x3 -> 3
-            }
-  k_sk = np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2]))/geomdim[0]
-  if grid[2]%2 == 0: k_sk[grid[2]//2] = 0                                                            # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
-
-  k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/geomdim[1]
-  if grid[1]%2 == 0: k_sj[grid[1]//2] = 0                                                            # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
-
-  k_si = np.arange(grid[0]//2+1)/geomdim[2]
-
-  kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
-  k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')                           
-
-  div_fourier = np.einsum(einsums[n],k_s,field_fourier)*TWOPIIMG
-
-  return np.fft.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n//3])
-
 
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Add column(s) containing curl of requested column(s).
+Add column(s) containing divergence of requested column(s).
-Operates on periodic ordered three-dimensional data sets
+Operates on periodic ordered three-dimensional data sets of vector and tensor fields.
-of vector and tensor fields.
 """, version = scriptID)
 
 parser.add_option('-p','--pos','--periodiccellcenter',
@@ -66,95 +28,30 @@ parser.add_option('-p','--pos','--periodiccellcenter',
                   type = 'string', metavar = 'string',
                   help = 'label of coordinates [%default]')
 parser.add_option('-l','--label',
-                  dest = 'data',
+                  dest = 'labels',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'label(s) of field values')
 
 parser.set_defaults(pos = 'pos',
                    )
 
-
 (options,filenames) = parser.parse_args()
-
-if options.data is None: parser.error('no data column specified.')
-
-# --- define possible data types -------------------------------------------------------------------
-
-datatypes = {
-              3: {'name': 'vector',
-                  'shape': [3],
-                 },
-              9: {'name': 'tensor',
-                  'shape': [3,3],
-                 },
-            }
-
-# --- loop over input files ------------------------------------------------------------------------
-
 if filenames == []: filenames = [None]
 
+if options.labels is None: parser.error('no data column specified.')
+
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,buffered = False)
+    damask.util.report(scriptName,name)
-  except: continue
-  damask.util.report(scriptName,name)
 
-# --- interpret header ----------------------------------------------------------------------------
+    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
 
-  table.head_read()
+    for label in options.labels:
-
+        field = table.get(label)
-  remarks = []
+        shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3)                         # vector or tensor
-  errors  = []
+        field = field.reshape(np.append(grid[::-1],shape))
-  active = []
+        table.add('divFFT({})'.format(label),
-
+                  damask.grid_filters.divergence(size[::-1],field).reshape((-1,np.prod(shape)//3)),
-  coordDim = table.label_dimension(options.pos)
+                  scriptID+' '+' '.join(sys.argv[1:]))
-  if coordDim != 3:
+    
-    errors.append('coordinates "{}" must be three-dimensional.'.format(options.pos))
+    table.to_ASCII(sys.stdout if name is None else name)
-  else: coordCol = table.label_index(options.pos)
-
-  for me in options.data:
-    dim = table.label_dimension(me)
-    if dim in datatypes:
-      active.append(merge_dicts({'label':me},datatypes[dim]))
-      remarks.append('differentiating {} "{}"...'.format(datatypes[dim]['name'],me))
-    else:
-      remarks.append('skipping "{}" of dimension {}...'.format(me,dim) if dim != -1 else \
-                     '"{}" not found...'.format(me) )
-
-  if remarks != []: damask.util.croak(remarks)
-  if errors  != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-
-# ------------------------------------------ assemble header --------------------------------------
-
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  for data in active:
-    table.labels_append(['divFFT({})'.format(data['label']) if data['shape'] == [3] \
-                 else '{}_divFFT({})'.format(i+1,data['label']) 
-                 for i in range(np.prod(np.array(data['shape']))//3)])                              # extend ASCII header with new labels
-  table.head_write()
-
-# --------------- figure out size and grid ---------------------------------------------------------
-
-  table.data_readArray()
-
-  grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
-
-# ------------------------------------------ process value field -----------------------------------
-
-  stack = [table.data]
-  for data in active:
-    # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
-    stack.append(divFFT(size[::-1],
-                        table.data[:,table.label_indexrange(data['label'])].
-                        reshape(grid[::-1].tolist()+data['shape'])))
-
-# ------------------------------------------ output result -----------------------------------------
-
-  if len(stack) > 1: table.data = np.hstack(tuple(stack))
-  table.data_writeArray('%.12g')
-
-# ------------------------------------------ output finalization -----------------------------------
-
-  table.close()                                                                                     # close input ASCII table (works for stdin)

processing/post/addGradient.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
 import numpy as np
@@ -12,44 +13,6 @@ import damask
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
-def merge_dicts(*dict_args):
-  """Given any number of dicts, shallow copy and merge into a new dict, with precedence going to key value pairs in latter dicts."""
-  result = {}
-  for dictionary in dict_args:
-      result.update(dictionary)
-  return result
-
-def gradFFT(geomdim,field):
-  """Calculate gradient of a vector or scalar field by transforming into Fourier space."""
-  shapeFFT = np.array(np.shape(field))[0:3]
-  grid     = np.array(np.shape(field)[2::-1])
-  N = grid.prod()                                                                                    # field size
-  n = np.array(np.shape(field)[3:]).prod()                                                           # data size
-
-  field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
-  grad_fourier  = np.empty(field_fourier.shape+(3,),'c16')
-
-  # differentiation in Fourier space
-  TWOPIIMG = 2.0j*np.pi
-  einsums = { 
-              1:'ijkl,ijkm->ijkm',                                                                   # scalar, 1 -> 3
-              3:'ijkl,ijkm->ijklm',                                                                  # vector, 3 -> 3x3
-            }
-
-  k_sk = np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2]))/geomdim[0]
-  if grid[2]%2 == 0: k_sk[grid[2]//2] = 0                                                            # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
-
-  k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/geomdim[1]
-  if grid[1]%2 == 0: k_sj[grid[1]//2] = 0                                                            # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
-
-  k_si = np.arange(grid[0]//2+1)/geomdim[2]
-
-  kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
-  k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')                           
-  grad_fourier = np.einsum(einsums[n],field_fourier,k_s)*TWOPIIMG
-
-  return np.fft.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
-
 
 # --------------------------------------------------------------------
 #                                MAIN
@@ -57,9 +20,7 @@ def gradFFT(geomdim,field):
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing gradient of requested column(s).
-Operates on periodic ordered three-dimensional data sets
+Operates on periodic ordered three-dimensional data sets of scalar and vector fields.
-of vector and scalar fields.
-
 """, version = scriptID)
 
 parser.add_option('-p','--pos','--periodiccellcenter',
@@ -67,7 +28,7 @@ parser.add_option('-p','--pos','--periodiccellcenter',
                   type = 'string', metavar = 'string',
                   help = 'label of coordinates [%default]')
 parser.add_option('-l','--label',
-                  dest = 'data',
+                  dest = 'labels',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'label(s) of field values')
 
@@ -75,85 +36,22 @@ parser.set_defaults(pos = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
-
-if options.data is None: parser.error('no data column specified.')
-
-# --- define possible data types -------------------------------------------------------------------
-
-datatypes = {
-              1: {'name': 'scalar',
-                  'shape': [1],
-                 },
-              3: {'name': 'vector',
-                  'shape': [3],
-                 },
-            }
-
-# --- loop over input files ------------------------------------------------------------------------
-
 if filenames == []: filenames = [None]
 
+if options.labels is None: parser.error('no data column specified.')
+
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,buffered = False)
+    damask.util.report(scriptName,name)
-  except: continue
-  damask.util.report(scriptName,name)
 
-# --- interpret header ----------------------------------------------------------------------------
+    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
 
-  table.head_read()
+    for label in options.labels:
-
+        field = table.get(label)
-  remarks = []
+        shape = (1,) if np.prod(field.shape)//np.prod(grid) == 1 else (3,)                          # scalar or vector
-  errors  = []
+        field = field.reshape(np.append(grid[::-1],shape))
-  active = []
+        table.add('gradFFT({})'.format(label),
-
+                  damask.grid_filters.gradient(size[::-1],field).reshape((-1,np.prod(shape)*3)),
-  coordDim = table.label_dimension(options.pos)
+                  scriptID+' '+' '.join(sys.argv[1:]))
-  if coordDim != 3:
+    
-    errors.append('coordinates "{}" must be three-dimensional.'.format(options.pos))
+    table.to_ASCII(sys.stdout if name is None else name)
-  else: coordCol = table.label_index(options.pos)
-
-  for me in options.data:
-    dim = table.label_dimension(me)
-    if dim in datatypes:
-      active.append(merge_dicts({'label':me},datatypes[dim]))
-      remarks.append('differentiating {} "{}"...'.format(datatypes[dim]['name'],me))
-    else:
-      remarks.append('skipping "{}" of dimension {}...'.format(me,dim) if dim != -1 else \
-                     '"{}" not found...'.format(me) )
-
-  if remarks != []: damask.util.croak(remarks)
-  if errors  != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-
-# ------------------------------------------ assemble header --------------------------------------
-
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  for data in active:
-    table.labels_append(['{}_gradFFT({})'.format(i+1,data['label']) 
-                        for i in range(coordDim*np.prod(np.array(data['shape'])))])                 # extend ASCII header with new labels
-  table.head_write()
-
-# --------------- figure out size and grid ---------------------------------------------------------
-
-  table.data_readArray()
-
-  grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
-
-# ------------------------------------------ process value field -----------------------------------
-
-  stack = [table.data]
-  for data in active:
-    # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
-    stack.append(gradFFT(size[::-1],
-                         table.data[:,table.label_indexrange(data['label'])].
-                         reshape(grid[::-1].tolist()+data['shape'])))
-
-# ------------------------------------------ output result -----------------------------------------
-
-  if len(stack) > 1: table.data = np.hstack(tuple(stack))
-  table.data_writeArray('%.12g')
-
-# ------------------------------------------ output finalization -----------------------------------
-
-  table.close()                                                                                     # close input ASCII table (works for stdin)

processing/post/addOrientations.py

@@ -125,9 +125,10 @@ R = damask.Rotation.fromAxisAngle(np.array(options.labrotation),options.degrees,
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try: 
-                                    buffered = False)
+    table = damask.ASCIItable(name = name, buffered = False)
-  except Exception: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/pre/geom_fromTable.py

@@ -78,36 +78,15 @@ for name in filenames:
   table = damask.ASCIItable(name = name,readonly=True)
   table.head_read()                                                                                 # read ASCII header info
 
-# ------------------------------------------ sanity checks ---------------------------------------
-
-  coordDim = table.label_dimension(options.pos)
-
-  errors = []
-  if not 3 >= coordDim >= 2:
-    errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.pos))
-  if not np.all(table.label_dimension(label) == dim):
-    errors.append('input "{}" needs to have dimension {}.'.format(label,dim))
-  if options.phase and table.label_dimension(options.phase) != 1:
-    errors.append('phase column "{}" is not scalar.'.format(options.phase))
-
-  if errors != []:
-    damask.util.croak(errors)
-    continue
 
   table.data_readArray([options.pos] \
                        + (label if isinstance(label, list) else [label]) \
                        + ([options.phase] if options.phase else []))
 
-  if coordDim == 2:
-    table.data = np.insert(table.data,2,np.zeros(len(table.data)),axis=1)                           # add zero z coordinate for two-dimensional input
   if options.phase is None:
     table.data = np.column_stack((table.data,np.ones(len(table.data))))                             # add single phase if no phase column given
 
-  grid,size = damask.util.coordGridAndSize(table.data[:,0:3])
+  grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.data[:,0:3])
-  coords = [np.unique(table.data[:,i]) for i in range(3)]
-  mincorner = np.array(list(map(min,coords)))
-  origin = mincorner - 0.5*size/grid                                                                # shift from cell center to corner
-
 
   indices  = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2]))                          # indices of position when sorting x fast, z slow
   microstructure = np.empty(grid,dtype = int)                                                       # initialize empty microstructure
@@ -142,7 +121,6 @@ for name in filenames:
     config_header += ['<microstructure>']
     for i,data in enumerate(unique):
       config_header += ['[Grain{}]'.format(i+1),
-                        'crystallite 1',
                         '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(int(data[4]),i+1),
                        ]
 

processing/pre/geom_toTable.py

@@ -2,10 +2,8 @@
 
 import os
 import sys
-from optparse import OptionParser
 from io import StringIO
-
+from optparse import OptionParser
-import numpy as np
 
 import damask
 
@@ -24,38 +22,25 @@ Translate geom description into ASCIItable containing position and microstructur
 """, version = scriptID)
 
 (options, filenames) = parser.parse_args()
-
-
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  damask.util.report(scriptName,name)
+    damask.util.report(scriptName,name)
 
-  geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    damask.util.croak(geom)
 
-  damask.util.croak(geom)
+    coord0 = damask.grid_filters.cell_coord0(geom.grid,geom.size,geom.origin).reshape((-1,3),order='F')
 
-# --- generate grid --------------------------------------------------------------------------------
+    comments = geom.comments \
+             + [scriptID + ' ' + ' '.join(sys.argv[1:]),
+                "grid\ta {}\tb {}\tc {}".format(*geom.grid),
+                "size\tx {}\ty {}\tz {}".format(*geom.size),
+                "origin\tx {}\ty {}\tz {}".format(*geom.origin),
+                "homogenization\t{}".format(geom.homogenization)]
 
-  grid   = geom.get_grid()
+    table = damask.Table(coord0,{'pos':(3,)},comments)
-  size   = geom.get_size()
+    table.add('microstructure',geom.microstructure.reshape((-1,1)))
-  origin = geom.get_origin()
 
-  x = (0.5 + np.arange(grid[0],dtype=float))/grid[0]*size[0]+origin[0]
+    table.to_ASCII(sys.stdout if name is None else \
-  y = (0.5 + np.arange(grid[1],dtype=float))/grid[1]*size[1]+origin[1]
+                   os.path.splitext(name)[0]+'.txt')
-  z = (0.5 + np.arange(grid[2],dtype=float))/grid[2]*size[2]+origin[2]
-
-  xx = np.tile(          x,        grid[1]* grid[2])
-  yy = np.tile(np.repeat(y,grid[0]        ),grid[2])
-  zz =         np.repeat(z,grid[0]*grid[1])
-
-# ---  create ASCII table --------------------------------------------------------------------------
-
-  table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt' if name else name)
-  table.info_append(geom.get_comments() + [scriptID + '\t' + ' '.join(sys.argv[1:])])
-  table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure'])
-  table.head_write()
-  table.output_flush()
-  table.data = np.squeeze(np.dstack((xx,yy,zz,geom.microstructure.flatten('F'))),axis=0)
-  table.data_writeArray()
-  table.close()

processing/pre/mentat_spectralBox.py

@@ -1,9 +1,10 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
-import os,sys
+import os
-import numpy as np
+import sys
+from io import StringIO
 from optparse import OptionParser
+
 import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
@@ -191,78 +192,45 @@ parser.add_option('-p', '--port',
                   dest = 'port',
                   type = 'int', metavar = 'int',
                   help = 'Mentat connection port [%default]')
-parser.add_option('--homogenization',
-                  dest = 'homogenization',
-                  type = 'int', metavar = 'int',
-                  help = 'homogenization index to be used [auto]')
 
-parser.set_defaults(port           = None,
+parser.set_defaults(port = None,
-                    homogenization = None,
+                   )
-)
 
 (options, filenames) = parser.parse_args()
 
-if options.port:
+if options.port is not None:
-  try:
+    try:
-    import py_mentat
+        import py_mentat
-  except:
+    except ImportError:
-    parser.error('no valid Mentat release found.')
+        parser.error('no valid Mentat release found.')
 
 # --- loop over input files ------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:
+    damask.util.report(scriptName,name)
-    table = damask.ASCIItable(name    = name,
-                              outname = os.path.splitext(name)[0]+'.proc' if name else name,
-                              buffered = False, labeled = False)
-  except: continue
-  damask.util.report(scriptName,name)
-
-# --- interpret header ----------------------------------------------------------------------------
-
-  table.head_read()
-  info,extra_header = table.head_getGeom()
-  if options.homogenization: info['homogenization'] = options.homogenization
     
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
+    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-                     'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
+    microstructure = geom.get_microstructure().flatten(order='F')
-                     'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-                     'homogenization:  %i'%info['homogenization'],
-                     'microstructures: %i'%info['microstructures'],
-              ])
 
-  errors = []
+    cmds = [\
-  if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
+      init(),
-  if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
+      mesh(geom.grid,geom.size),
-  if errors != []:
+      material(),
-    damask.util.croak(errors)
+      geometry(),
-    table.close(dismiss = True)
+      initial_conditions(geom.homogenization,microstructure),
-    continue
+      '*identify_sets',
-
+      '*show_model',
-# --- read data ------------------------------------------------------------------------------------
+      '*redraw',
-
+      '*draw_automatic',
-  microstructure = table.microstructure_read(info['grid']).reshape(info['grid'].prod(),order='F')   # read microstructure
+    ]
-
+    
-  cmds = [\
+    outputLocals = {}
-    init(),
+    if options.port:
-    mesh(info['grid'],info['size']),
+        py_mentat.py_connect('',options.port)
-    material(),
+        output(cmds,outputLocals,'Mentat')
-    geometry(),
+        py_mentat.py_disconnect()
-    initial_conditions(info['homogenization'],microstructure),
+    else:
-    '*identify_sets',
+        with sys.stdout if name is None else open(os.path.splitext(name)[0]+'.proc','w') as f:
-    '*show_model',
+            output(cmds,outputLocals,f)
-    '*redraw',
-    '*draw_automatic',
-  ]
-  
-  outputLocals = {}
-  if options.port:
-    py_mentat.py_connect('',options.port)
-    output(cmds,outputLocals,'Mentat')
-    py_mentat.py_disconnect()
-  else:
-    output(cmds,outputLocals,table.__IO__['out'])                                                   # bad hack into internals of table class...
-
-  table.close()

processing/pre/seeds_fromGeom.py

@@ -1,9 +1,12 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
-import os,sys
+import os
-import numpy as np
+import sys
+from io import StringIO
 from optparse import OptionParser
+
+import numpy as np
+
 import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
@@ -29,88 +32,39 @@ parser.add_option('-b',
                   action = 'extend', metavar = '<int LIST>',
                   dest   = 'blacklist',
                   help   = 'blacklist of grain IDs')
-parser.add_option('-p',
-                  '--pos', '--seedposition',
-                  dest = 'pos',
-                  type = 'string', metavar = 'string',
-                  help = 'label of coordinates [%default]')
 
 parser.set_defaults(whitelist = [],
                     blacklist = [],
-                    pos       = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
-
-options.whitelist = list(map(int,options.whitelist))
-options.blacklist = list(map(int,options.blacklist))
-
-# --- loop over output files -------------------------------------------------------------------------
-
 if filenames == []: filenames = [None]
 
+options.whitelist = [int(i) for i in options.whitelist]
+options.blacklist = [int(i) for i in options.blacklist]
+
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+    damask.util.report(scriptName,name)
-                                    outname = os.path.splitext(name)[0]+'.seeds' if name else name,
+    
-                                    buffered = False,
+    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-                                    labeled = False)
+    microstructure = geom.get_microstructure().reshape((-1,1),order='F')
-  except: continue
-  damask.util.report(scriptName,name)
 
-# --- interpret header ----------------------------------------------------------------------------
+    mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist else \
+                          np.full(geom.grid.prod(),True,dtype=bool),
+                          np.in1d(microstructure,options.blacklist,invert=True)  if options.blacklist else \
+                          np.full(geom.grid.prod(),True,dtype=bool))
+   
+    seeds = np.concatenate((damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape((-1,3)),
+                            microstructure),
+                            axis=1)[mask]
+    
+    comments = geom.comments \
+             + [scriptID + ' ' + ' '.join(sys.argv[1:]),
+                "grid\ta {}\tb {}\tc {}".format(*geom.grid),
+                "size\tx {}\ty {}\tz {}".format(*geom.size),
+                "origin\tx {}\ty {}\tz {}".format(*geom.origin),
+                "homogenization\t{}".format(geom.homogenization)]
 
-  table.head_read()
+    table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
-  info,extra_header = table.head_getGeom()
+    table.to_ASCII(sys.stdout if name is None else \
-  damask.util.report_geom(info)
+                   os.path.splitext(name)[0]+'.seeds')
-
-  errors = []
-  if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
-  if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
-  if errors != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-
-# --- read data ------------------------------------------------------------------------------------
-
-  microstructure = table.microstructure_read(info['grid'])                                          # read (linear) microstructure
-
-# --- generate grid --------------------------------------------------------------------------------
-
-  x = (0.5 + np.arange(info['grid'][0],dtype=float))/info['grid'][0]*info['size'][0]+info['origin'][0]
-  y = (0.5 + np.arange(info['grid'][1],dtype=float))/info['grid'][1]*info['size'][1]+info['origin'][1]
-  z = (0.5 + np.arange(info['grid'][2],dtype=float))/info['grid'][2]*info['size'][2]+info['origin'][2]
-
-  xx = np.tile(          x,                info['grid'][1]* info['grid'][2])
-  yy = np.tile(np.repeat(y,info['grid'][0]                ),info['grid'][2])
-  zz =         np.repeat(z,info['grid'][0]*info['grid'][1])
-
-  mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist != []
-                                                                               else np.full_like(microstructure,True,dtype=bool), 
-                        np.in1d(microstructure,options.blacklist,invert=True ) if options.blacklist != []
-                                                                               else np.full_like(microstructure,True,dtype=bool))
-
-# ------------------------------------------ assemble header ---------------------------------------
-
-  table.info_clear()
-  table.info_append(extra_header+[
-    scriptID + ' ' + ' '.join(sys.argv[1:]),
-    "grid\ta {}\tb {}\tc {}".format(*info['grid']),
-    "size\tx {}\ty {}\tz {}".format(*info['size']),
-    "origin\tx {}\ty {}\tz {}".format(*info['origin']),
-    "homogenization\t{}".format(info['homogenization']),
-    "microstructures\t{}".format(info['microstructures']),
-    ])
-  table.labels_clear()
-  table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.pos) for i in range(3)]+['microstructure'])
-  table.head_write()
-  table.output_flush()
-  
-# --- write seeds information ------------------------------------------------------------
-
-  table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)))[mask]
-  table.data_writeArray()
-
-# ------------------------------------------ finalize output ---------------------------------------
-
-  table.close()

processing/pre/seeds_fromPokes.py

@@ -1,11 +1,14 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
-import os,math,sys
+import os
-import numpy as np
+import sys
-import damask
+from io import StringIO
 from optparse import OptionParser
 
+import numpy as np
+
+import damask
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -35,117 +38,58 @@ parser.add_option('-y',
                   action = 'store_true',
                   dest   = 'y',
                   help   = 'poke 45 deg along y')
-parser.add_option('-p','--position',
-                  dest = 'position',
-                  type = 'string', metavar = 'string',
-                  help = 'column label for coordinates [%default]')
 
 parser.set_defaults(x = False,
                     y = False,
                     box = [0.0,1.0,0.0,1.0,0.0,1.0],
                     N = 16,
-                    position = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
+if filenames == []: filenames = [None]
 
 options.box = np.array(options.box).reshape(3,2)
 
-# --- loop over output files -------------------------------------------------------------------------
-
-if filenames == []: filenames = [None]
-
 for name in filenames:
-  try:
+    damask.util.report(scriptName,name)
-    table = damask.ASCIItable(name = name,
+    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-                              outname = os.path.splitext(name)[-2]+'_poked_{}.seeds'.format(options.N) if name else name,
-                              buffered = False, labeled = False)
-  except: continue
-  damask.util.report(scriptName,name)
-
-# --- interpret header ----------------------------------------------------------------------------
-
-  table.head_read()
-  info,extra_header = table.head_getGeom()
-  
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-                     'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-                     'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-                     'homogenization:  %i'%info['homogenization'],
-                     'microstructures: %i'%info['microstructures'],
-                    ])
-
-  errors = []
-  if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
-  if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
-  if errors != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-
-# --- read data ------------------------------------------------------------------------------------
-
-  microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F')          # read microstructure
-
-# --- do work ------------------------------------------------------------------------------------
- 
-  newInfo = {
-             'microstructures': 0,
-            }
-  offset = (np.amin(options.box, axis=1)*info['grid']/info['size']).astype(int)
-  box = np.amax(options.box, axis=1) - np.amin(options.box, axis=1)
-
-  Nx = int(options.N/math.sqrt(options.N*info['size'][1]*box[1]/info['size'][0]/box[0]))
-  Ny = int(options.N/math.sqrt(options.N*info['size'][0]*box[0]/info['size'][1]/box[1]))
-  Nz = int(box[2]*info['grid'][2])
-
-  damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box))
-
-  seeds = np.zeros((Nx*Ny*Nz,4),'d')
-  grid = np.zeros(3,'i')
-
-  n = 0
-  for i in range(Nx):
-    for j in range(Ny):
-      grid[0] = round((i+0.5)*box[0]*info['grid'][0]/Nx-0.5)+offset[0]
-      grid[1] = round((j+0.5)*box[1]*info['grid'][1]/Ny-0.5)+offset[1]
-      for k in range(Nz):
-        grid[2] = k + offset[2]
-        grid %= info['grid']
-        seeds[n,0:3] = (0.5+grid)/info['grid']                                                     # normalize coordinates to box
-        seeds[n,  3] = microstructure[grid[0],grid[1],grid[2]]
-        if options.x: grid[0] += 1
-        if options.y: grid[1] += 1
-        n += 1
-      
-  newInfo['microstructures'] = len(np.unique(seeds[:,3]))
-
-# --- report ---------------------------------------------------------------------------------------
-  if (newInfo['microstructures'] != info['microstructures']): 
-    damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
-
-
-# ------------------------------------------ assemble header ---------------------------------------
-  table.info_clear()
-  table.info_append(extra_header+[
-    scriptID + ' ' + ' '.join(sys.argv[1:]),
-    "poking\ta {}\tb {}\tc {}".format(Nx,Ny,Nz),
-    "grid\ta {}\tb {}\tc {}".format(*info['grid']),
-    "size\tx {}\ty {}\tz {}".format(*info['size']),
-    "origin\tx {}\ty {}\tz {}".format(*info['origin']),
-    "homogenization\t{}".format(info['homogenization']),
-    "microstructures\t{}".format(newInfo['microstructures']),
-    ])
-  table.labels_clear()
-  table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in range(3)]+['microstructure'])
-  table.head_write()
-  table.output_flush()
-  
-# --- write seeds information ------------------------------------------------------------
-
-  table.data = seeds
-  table.data_writeArray()
     
-# --- output finalization --------------------------------------------------------------------------
+    offset =(np.amin(options.box, axis=1)*geom.grid/geom.size).astype(int)
-
+    box    = np.amax(options.box, axis=1) \
-  table.close()                                                                                     # close ASCII table
+           - np.amin(options.box, axis=1)
+  
+    Nx = int(options.N/np.sqrt(options.N*geom.size[1]*box[1]/geom.size[0]/box[0]))
+    Ny = int(options.N/np.sqrt(options.N*geom.size[0]*box[0]/geom.size[1]/box[1]))
+    Nz = int(box[2]*geom.grid[2])
+  
+    damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box))
+  
+    seeds = np.zeros((Nx*Ny*Nz,4),'d')
+    g     = np.zeros(3,'i')
+  
+    n = 0
+    for i in range(Nx):
+        for j in range(Ny):
+            g[0] = round((i+0.5)*box[0]*geom.grid[0]/Nx-0.5)+offset[0]
+            g[1] = round((j+0.5)*box[1]*geom.grid[1]/Ny-0.5)+offset[1]
+            for k in range(Nz):
+                g[2] = k + offset[2]
+                g %= geom.grid
+                seeds[n,0:3] = (g+0.5)/geom.grid                                                    # normalize coordinates to box
+                seeds[n,  3] = geom.microstructure[g[0],g[1],g[2]]
+                if options.x: g[0] += 1
+                if options.y: g[1] += 1
+                n += 1
+        
+  
+    comments = geom.comments \
+             + [scriptID + ' ' + ' '.join(sys.argv[1:]),
+                "poking\ta {}\tb {}\tc {}".format(Nx,Ny,Nz),
+                "grid\ta {}\tb {}\tc {}".format(*geom.grid),
+                "size\tx {}\ty {}\tz {}".format(*geom.size),
+                "origin\tx {}\ty {}\tz {}".format(*geom.origin),
+                "homogenization\t{}".format(geom.homogenization)]
+  
+    table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
+    table.to_ASCII(sys.stdout if name is None else \
+                   os.path.splitext(name)[0]+'_poked_{}.seeds'.format(options.N))

python/damask/__init__.py

@@ -23,4 +23,5 @@ from .util        import extendableOption # noqa
 
 # functions in modules
 from . import mechanics                   # noqa
+from . import grid_filters                # noqa
 

python/damask/geom.py

@@ -205,6 +205,9 @@ class Geom():
             else:
                 self.homogenization = homogenization
 
+    @property
+    def grid(self):
+        return self.get_grid()
 
     def get_microstructure(self):
         """Return the microstructure representation."""

python/damask/grid_filters.py

@@ -0,0 +1,299 @@
+from scipy import spatial
+import numpy as np
+
+def __ks(size,grid,first_order=False):
+    """
+    Get wave numbers operator.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+
+    """
+    k_sk = np.where(np.arange(grid[0])>grid[0]//2,np.arange(grid[0])-grid[0],np.arange(grid[0]))/size[0]
+    if grid[0]%2 == 0 and first_order: k_sk[grid[0]//2] = 0                                         # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
+
+    k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/size[1]
+    if grid[1]%2 == 0 and first_order: k_sj[grid[1]//2] = 0                                         # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
+
+    k_si = np.arange(grid[2]//2+1)/size[2]
+
+    kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
+    return np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3)
+
+
+def curl(size,field):
+    """
+    Calculate curl of a vector or tensor field in Fourier space.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+
+    """
+    n = np.prod(field.shape[3:])
+    k_s = __ks(size,field.shape[:3],True)
+
+    e = np.zeros((3, 3, 3))
+    e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0                                                     # Levi-Civita symbol 
+    e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
+
+    field_fourier = np.fft.rfftn(field,axes=(0,1,2))
+    curl = (np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,field_fourier)*2.0j*np.pi if n == 3 else        # vector, 3   -> 3
+            np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*2.0j*np.pi)                      # tensor, 3x3 -> 3x3
+
+    return np.fft.irfftn(curl,axes=(0,1,2),s=field.shape[:3])
+
+
+def divergence(size,field):
+    """
+    Calculate divergence of a vector or tensor field in Fourier space.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+
+    """
+    n = np.prod(field.shape[3:])
+    k_s = __ks(size,field.shape[:3],True)
+
+    field_fourier = np.fft.rfftn(field,axes=(0,1,2))
+    divergence = (np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*np.pi if n == 3 else         # vector, 3   -> 1
+                  np.einsum('ijkm,ijklm->ijkl',k_s,field_fourier)*2.0j*np.pi)                       # tensor, 3x3 -> 3
+
+    return np.fft.irfftn(divergence,axes=(0,1,2),s=field.shape[:3])
+
+
+def gradient(size,field):
+    """
+    Calculate gradient of a vector or scalar field in Fourier space.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+
+    """
+    n = np.prod(field.shape[3:])
+    k_s = __ks(size,field.shape[:3],True)
+
+    field_fourier = np.fft.rfftn(field,axes=(0,1,2))
+    gradient = (np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*np.pi if n == 1 else           # scalar, 1 -> 3
+                np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*2.0j*np.pi)                         # vector, 3 -> 3x3
+
+    return np.fft.irfftn(gradient,axes=(0,1,2),s=field.shape[:3])
+
+
+def cell_coord0(grid,size,origin=np.zeros(3)):
+    """
+    Cell center positions (undeformed).
+
+    Parameters
+    ----------
+    grid : numpy.ndarray
+        number of grid points.
+    size : numpy.ndarray
+        physical size of the periodic field. 
+
+    """
+    start = origin + size/grid*.5
+    end   = origin - size/grid*.5 + size
+    x, y, z = np.meshgrid(np.linspace(start[2],end[2],grid[2]),
+                          np.linspace(start[1],end[1],grid[1]),
+                          np.linspace(start[0],end[0],grid[0]),
+                          indexing = 'ij')
+
+    return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) 
+
+def cell_displacement_fluct(size,F):
+    """
+    Cell center displacement field from fluctuation part of the deformation gradient field.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+
+    """
+    integrator = 0.5j*size/np.pi
+
+    k_s = __ks(size,F.shape[:3],False)
+    k_s_squared = np.einsum('...l,...l',k_s,k_s)
+    k_s_squared[0,0,0] = 1.0
+
+    displacement = -np.einsum('ijkml,ijkl,l->ijkm',
+                              np.fft.rfftn(F,axes=(0,1,2)),
+                              k_s,
+                              integrator,
+                             ) / k_s_squared[...,np.newaxis]
+
+    return np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
+
+def cell_displacement_avg(size,F):
+    """
+    Cell center displacement field from average part of the deformation gradient field.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+
+    """
+    F_avg = np.average(F,axis=(0,1,2))
+    return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3],size))
+
+def cell_coord0_2_DNA(coord0,ordered=True):
+    """
+    Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
+
+    Parameters
+    ----------
+    coord0 : numpy.ndarray
+        array of undeformed cell coordinates.
+    ordered : bool, optional
+        expect coord0 data to be ordered (x fast, z slow).
+
+    """
+    coords    = [np.unique(coord0[:,i]) for i in range(3)]
+    mincorner = np.array(list(map(min,coords)))
+    maxcorner = np.array(list(map(max,coords)))
+    grid      = np.array(list(map(len,coords)),'i')
+    size      = grid/np.maximum(grid-1,1) * (maxcorner-mincorner)
+    delta     = size/grid
+    origin    = mincorner - delta*.5
+   
+    if grid.prod() != len(coord0):
+        raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
+
+    start = origin + delta*.5
+    end   = origin - delta*.5 + size
+
+    if not np.allclose(coords[0],np.linspace(start[0],end[0],grid[0])) and \
+           np.allclose(coords[1],np.linspace(start[1],end[1],grid[1])) and \
+           np.allclose(coords[2],np.linspace(start[2],end[2],grid[2])):
+        raise ValueError('Regular grid spacing violated.')
+
+    if ordered and not np.allclose(coord0.reshape(tuple(grid[::-1])+(3,)),cell_coord0(grid,size,origin)):
+        raise ValueError('Input data is not a regular grid.')
+
+    return (grid,size,origin)
+
+
+def node_coord0(grid,size,origin=np.zeros(3)):
+    """
+    Nodal positions (undeformed).
+
+    Parameters
+    ----------
+    grid : numpy.ndarray
+        number of grid points.
+    size : numpy.ndarray
+        physical size of the periodic field. 
+
+    """
+    x, y, z = np.meshgrid(np.linspace(origin[2],size[2]+origin[2],1+grid[2]),
+                          np.linspace(origin[1],size[1]+origin[1],1+grid[1]),
+                          np.linspace(origin[0],size[0]+origin[0],1+grid[0]),
+                          indexing = 'ij')
+    
+    return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) 
+
+def node_displacement_fluct(size,F):
+    """
+    Nodal displacement field from fluctuation part of the deformation gradient field.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+
+    """
+    return cell_2_node(cell_displacement_fluct(size,F))
+
+def node_displacement_avg(size,F):
+    """
+    Nodal displacement field from average part of the deformation gradient field.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+
+    """
+    F_avg = np.average(F,axis=(0,1,2))
+    return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3],size))
+
+
+def cell_2_node(cell_data):
+    """Interpolate cell data to nodal data."""
+    n = (  cell_data + np.roll(cell_data,1,(0,1,2))
+         + np.roll(cell_data,1,(0,))  + np.roll(cell_data,1,(1,))  + np.roll(cell_data,1,(2,))
+         + np.roll(cell_data,1,(0,1)) + np.roll(cell_data,1,(1,2)) + np.roll(cell_data,1,(2,0)))*0.125
+  
+    return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
+
+def node_2_cell(node_data):
+    """Interpolate nodal data to cell data."""
+    c = (  node_data + np.roll(node_data,1,(0,1,2))
+         + np.roll(node_data,1,(0,))  + np.roll(node_data,1,(1,))  + np.roll(node_data,1,(2,))
+         + np.roll(node_data,1,(0,1)) + np.roll(node_data,1,(1,2)) + np.roll(node_data,1,(2,0)))*0.125
+  
+    return c[:-1,:-1,:-1]
+
+def node_coord0_2_DNA(coord0,ordered=False):
+    """
+    Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
+
+    Parameters
+    ----------
+    coord0 : numpy.ndarray
+        array of undeformed nodal coordinates
+    ordered : bool, optional
+        expect coord0 data to be ordered (x fast, z slow).
+
+    """
+    coords    = [np.unique(coord0[:,i]) for i in range(3)]
+    mincorner = np.array(list(map(min,coords)))
+    maxcorner = np.array(list(map(max,coords)))
+    grid      = np.array(list(map(len,coords)),'i') - 1
+    size      = maxcorner-mincorner
+    origin    = mincorner
+ 
+    if (grid+1).prod() != len(coord0):
+        raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
+
+    if not np.allclose(coords[0],np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \
+           np.allclose(coords[1],np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \
+           np.allclose(coords[2],np.linspace(mincorner[2],maxcorner[2],grid[2]+1)):
+        raise ValueError('Regular grid spacing violated.')
+
+    if ordered and not np.allclose(coord0.reshape(tuple((grid+1)[::-1])+(3,)),node_coord0(grid,size,origin)):
+        raise ValueError('Input data is not a regular grid.')
+
+    return (grid,size,origin)
+
+
+def regrid(size,F,new_grid):
+    """tbd."""
+    c = cell_coord0(F.shape[:3][::-1],size) \
+      + cell_displacement_avg(size,F) \
+      + cell_displacement_fluct(size,F)
+
+    outer = np.dot(np.average(F,axis=(0,1,2)),size)
+    for d in range(3):
+        c[np.where(c[:,:,:,d]<0)]        += outer[d]
+        c[np.where(c[:,:,:,d]>outer[d])] -= outer[d]
+
+    tree = spatial.cKDTree(c.reshape((-1,3)),boxsize=outer)
+    return tree.query(cell_coord0(new_grid,outer))[1]

python/damask/table.py

@@ -97,7 +97,6 @@ class Table():
 
     @property
     def labels(self):
-        """Return the labels of all columns."""
         return list(self.shapes.keys())
 
 

python/tests/test_grid_filters.py

@@ -0,0 +1,54 @@
+import pytest
+import numpy as np
+
+from damask import grid_filters
+
+class TestGridFilters:
+   
+    def test_cell_coord0(self):
+         size = np.random.random(3)
+         grid = np.random.randint(8,32,(3))
+         coord = grid_filters.cell_coord0(grid,size)
+         assert np.allclose(coord[0,0,0],size/grid*.5) and coord.shape == tuple(grid[::-1]) + (3,)
+
+    def test_node_coord0(self):
+         size = np.random.random(3)
+         grid = np.random.randint(8,32,(3))
+         coord = grid_filters.node_coord0(grid,size)
+         assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(grid[::-1]+1) + (3,)
+
+    def test_coord0(self):
+         size = np.random.random(3)
+         grid = np.random.randint(8,32,(3))
+         c = grid_filters.cell_coord0(grid+1,size+size/grid)
+         n = grid_filters.node_coord0(grid,size) + size/grid*.5
+         assert np.allclose(c,n)
+
+    @pytest.mark.parametrize('mode',[('cell'),('node')])
+    def test_grid_DNA(self,mode):
+         """Ensure that xx_coord0_2_DNA is the inverse of xx_coord0."""
+         grid   = np.random.randint(8,32,(3))
+         size   = np.random.random(3)
+         origin = np.random.random(3)
+        
+         coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode))                     # noqa
+         _grid,_size,_origin = eval('grid_filters.{}_coord0_2_DNA(coord0.reshape((-1,3)))'.format(mode))
+         assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
+
+
+    @pytest.mark.parametrize('mode',[('cell'),('node')])
+    def test_displacement_avg_vanishes(self,mode):
+         """Ensure that random fluctuations in F do not result in average displacement."""
+         size = np.random.random(3)                                                                 # noqa
+         grid = np.random.randint(8,32,(3))
+         F    = np.random.random(tuple(grid)+(3,3))
+         F   += np.eye(3) - np.average(F,axis=(0,1,2))
+         assert np.allclose(eval('grid_filters.{}_displacement_avg(size,F)'.format(mode)),0.0)
+
+    @pytest.mark.parametrize('mode',[('cell'),('node')])
+    def test_displacement_fluct_vanishes(self,mode):
+         """Ensure that constant F does not result in fluctuating displacement."""
+         size = np.random.random(3)                                                                 # noqa
+         grid = np.random.randint(8,32,(3))
+         F    = np.broadcast_to(np.random.random((3,3)), tuple(grid)+(3,3))                         # noqa
+         assert np.allclose(eval('grid_filters.{}_displacement_fluct(size,F)'.format(mode)),0.0)