Merge branch 'development' into new-ASCII

VERSION

@@ -1 +1 @@
-v2.0.3-957-gccbcc0d0
+v2.0.3-1097-ga7fca4df

examples/ConfigFiles/Phase_Dislotwin_Tungsten.config

@@ -14,7 +14,7 @@ SolidSolutionStrength 1.5e8         # Strength due to elements in solid solution
 
 ### Dislocation glide parameters ###
 #per family
-Nslip               12 0 
+Nslip               12 
 slipburgers         2.72e-10        # Burgers vector of slip system [m]
 rhoedge0            1.0e12          # Initial edge dislocation density [m/m**3]
 rhoedgedip0         1.0             # Initial edged dipole dislocation density [m/m**3]

processing/post/DADF5_postResults.py

@@ -65,7 +65,7 @@ for filename in options.filenames:
           x = results.get_dataset_location(label)
           if len(x) == 0:
             continue
-          array = results.read_dataset(x,0)
+          array = results.read_dataset(x,0,plain=True)
           d = int(np.product(np.shape(array)[1:]))
           data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
           
@@ -80,7 +80,7 @@ for filename in options.filenames:
           x = results.get_dataset_location(label)
           if len(x) == 0:
             continue
-          array = results.read_dataset(x,0)
+          array = results.read_dataset(x,0,plain=True)
           d = int(np.product(np.shape(array)[1:]))
           data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
           

processing/pre/geom_addPrimitive.py

@@ -132,7 +132,4 @@ for name in filenames:
   damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_canvas.py

@@ -61,7 +61,7 @@ for name in filenames:
   canvas = np.full(new,options.fill if options.fill is not None
                   else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
 
-  l = np.clip( offset,    0,np.minimum(old  +offset,new))
+  l = np.clip( offset,    0,np.minimum(old  +offset,new))                                           # noqa
   r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
   L = np.clip(-offset,    0,np.minimum(new  -offset,old))
   R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
@@ -71,7 +71,4 @@ for name in filenames:
   damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_clean.py

@@ -5,9 +5,6 @@ import sys
 from io import StringIO
 from optparse import OptionParser
 
-from scipy import ndimage
-import numpy as np
-
 import damask
 
 
@@ -15,11 +12,6 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 
-def mostFrequent(arr):
-  unique, inverse = np.unique(arr, return_inverse=True)
-  return unique[np.argmax(np.bincount(inverse))]
-
-
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
@@ -45,13 +37,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
+  damask.util.croak(geom.clean(options.stencil))
-  damask.util.croak(geom.update(ndimage.filters.generic_filter(
-                                  geom.microstructure,mostFrequent,
-                                  size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_fromDREAM3D.py

@@ -86,7 +86,7 @@ for name in filenames:
            * inFile[os.path.join(group_geom,'SPACING')][...]
     grid   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
     origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
-  except:
+  except KeyError:
     errors.append('Geometry data ({}) not found'.format(group_geom))
 
 
@@ -98,13 +98,13 @@ for name in filenames:
     try:
       quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
       rot   = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
-    except:
+    except KeyError:
       errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
 
     dataset = os.path.join(group_pointwise,options.phase)
     try:
       phase = np.reshape(inFile[dataset][...],(np.product(grid)))
-    except:
+    except KeyError:
       errors.append('Pointwise phase data ({}) not readable'.format(dataset))
 
     microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
@@ -116,7 +116,7 @@ for name in filenames:
     dataset = os.path.join(group_pointwise,options.microstructure)
     try:
       microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0))               # convert from C ordering
-    except:
+    except KeyError:
       errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
 
     group_average = os.path.join(rootDir,options.basegroup,options.average)
@@ -124,13 +124,13 @@ for name in filenames:
     dataset = os.path.join(group_average,options.quaternion)
     try:
       rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]         # skip first entry (unindexed)
-    except:
+    except KeyError:
       errors.append('Average orientation data ({}) not readable'.format(dataset))
 
     dataset = os.path.join(group_average,options.phase)
     try:
       phase = [i[0] for i in inFile[dataset][...]][1:]                                              # skip first entry (unindexed)
-    except:
+    except KeyError:
       errors.append('Average phase data ({}) not readable'.format(dataset))
 
   if errors != []:
@@ -155,4 +155,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  geom.to_file(os.path.splitext(name)[0]+'.geom')
+  geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False)

processing/pre/geom_fromMinimalSurface.py

@@ -89,7 +89,4 @@ geom=damask.Geom(microstructure,options.size,
                  comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromOsteonGeometry.py

@@ -145,7 +145,4 @@ geom = damask.Geom(microstructure.reshape(grid),
                    homogenization=options.homogenization,comments=header)
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromScratch.py

@@ -63,7 +63,4 @@ geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype)
                    comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromTable.py

@@ -152,7 +152,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_fromVoronoiTessellation.py

@@ -302,7 +302,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_grainGrowth.py

@@ -172,7 +172,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_mirror.py

@@ -5,8 +5,6 @@ import sys
 from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
-
 import damask
 
 
@@ -38,35 +36,12 @@ parser.set_defaults(reflect = False)
 
 (options, filenames) = parser.parse_args()
 
-if options.directions is None:
-  parser.error('no direction given.')
-
-if not set(options.directions).issubset(validDirections):
-  invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
-  parser.error('invalid directions {}. '.format(*invalidDirections))
-
-limits = [None,None] if options.reflect else [-2,0]
-
-
 if filenames == []: filenames = [None]
 
 for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
+  damask.util.croak(geom.mirror(options.directions,options.reflect))
-  microstructure = geom.get_microstructure()
-  if 'z' in options.directions:
-    microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2)
-  if 'y' in options.directions:
-    microstructure = np.concatenate([microstructure,microstructure[:,limits[0]:limits[1]:-1,:]],1)
-  if 'x' in options.directions:
-    microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0)
-
-  damask.util.croak(geom.update(microstructure,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_pack.py

@@ -34,41 +34,4 @@ for name in filenames:
   damask.util.croak(geom)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
  
-  compressType = None
+  geom.to_file(sys.stdout if name is None else name,pack=True)
-  former = start = -1
-  reps = 0
-
-  if name is None:
-    f = sys.stdout
-  else:
-    f= open(name,'w')
-
-  for current in geom.microstructure.flatten('F'):
-    if abs(current - former) == 1 and (start - current) == reps*(former - current):
-      compressType = 'to'
-      reps += 1
-    elif current == former and start == former:
-      compressType = 'of'
-      reps += 1
-    else:
-      if   compressType is None:
-        f.write('\n'.join(geom.get_header())+'\n')
-      elif compressType == '.':
-        f.write('{}\n'.format(former))
-      elif compressType == 'to':
-        f.write('{} to {}\n'.format(start,former))
-      elif compressType == 'of':
-        f.write('{} of {}\n'.format(reps,former))
-
-      compressType = '.'
-      start = current
-      reps = 1
-
-    former = current
-
-  if compressType == '.':
-    f.write('{}\n'.format(former))
-  elif compressType == 'to':
-    f.write('{} to {}\n'.format(start,former))
-  elif compressType == 'of':
-    f.write('{} of {}\n'.format(reps,former))

processing/pre/geom_renumber.py

@@ -5,8 +5,6 @@ import sys
 from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
-
 import damask
 
 
@@ -32,15 +30,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
+  damask.util.croak(geom.renumber())
-  renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
-  for i, oldID in enumerate(np.unique(geom.microstructure)):
-    renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)
-
-  damask.util.croak(geom.update(renumbered))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_rescale.py

@@ -2,11 +2,10 @@
 
 import os
 import sys
-import numpy as np
-
 from io import StringIO
 from optparse import OptionParser
-from scipy import ndimage
+
+import numpy as np
 
 import damask
 
@@ -55,20 +54,7 @@ for name in filenames:
              np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \
                   else float(n) for o,n in zip(size,options.size)],dtype=float)
 
-  damask.util.croak(geom.update(microstructure =
+  geom.scale(new_grid)
-                                ndimage.interpolation.zoom(
+  damask.util.croak(geom.update(microstructure = None,size = new_size))
-                                    geom.microstructure,
-                                    new_grid/grid,
-                                    output=geom.microstructure.dtype,
-                                    order=0,
-                                    mode='nearest',
-                                    prefilter=False,
-                                 ) if np.any(new_grid != grid) \
-                                 else None,
-                                 size = new_size))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_rotate.py

@@ -95,7 +95,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_translate.py

@@ -58,7 +58,4 @@ for name in filenames:
   damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_unpack.py

@@ -34,7 +34,4 @@ for name in filenames:
   damask.util.croak(geom)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_vicinityOffset.py

@@ -82,7 +82,4 @@ for name in filenames:
                                            geom.microstructure + offset,geom.microstructure)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

python/damask/asciitable.py

@@ -2,7 +2,7 @@ import os
 import sys
 import re
 import shlex
-from collections import Iterable
+from collections.abc import Iterable
 
 import numpy as np
 
@@ -15,7 +15,7 @@ except NameError:
 
 # ------------------------------------------------------------------
 class ASCIItable():
-  """Read and write to ASCII tables"""
+  """Read and write to ASCII tables."""
 
   tmpext = '_tmp'                                                                                   # filename extension for in-place access
   
@@ -27,6 +27,7 @@ class ASCIItable():
                labeled   = True,                                                                    # assume table has labels
                readonly  = False,                                                                   # no reading from file
               ):
+    """Read and write to ASCII tables."""
     self.__IO__ = {'output': [],
                    'buffered': buffered,
                    'labeled':  labeled,                                                             # header contains labels
@@ -72,7 +73,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def _removeCRLF(self,
                   string):
-    """Delete any carriage return and line feed from string"""
+    """Delete any carriage return and line feed from string."""
     try:
       return string.replace('\n','').replace('\r','')
     except AttributeError:
@@ -82,7 +83,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def _quote(self,
              what):
-    """Quote empty or white space-containing output"""
+    """Quote empty or white space-containing output."""
     return '{quote}{content}{quote}'.format(
              quote   = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
              content = what)
@@ -103,7 +104,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def output_write(self,
                    what):
-    """Aggregate a single row (string) or list of (possibly containing further lists of) rows into output"""
+    """Aggregate a single row (string) or list of (possibly containing further lists of) rows into output."""
     if isinstance(what, (str, unicode)):
       self.__IO__['output'] += [what]
     else:
@@ -143,7 +144,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def head_read(self):
     """
-    Get column labels
+    Get column labels.
     
     by either reading the first row or,
     if keyword "head[*]" is present, the last line of the header
@@ -154,7 +155,7 @@ class ASCIItable():
       pass
 
     firstline = self.__IO__['in'].readline().strip()
-    m = re.search('(\d+)\s+head', firstline.lower())                                                # search for "head" keyword
+    m = re.search(r'(\d+)\s+head', firstline.lower())                                                # search for "head" keyword
     
     if m:                                                                                           # proper ASCIItable format
 
@@ -194,7 +195,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def head_write(self,
                  header = True):
-    """Write current header information (info + labels)"""
+    """Write current header information (info + labels)."""
     head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
     head.append(self.info)
     if self.__IO__['labeled']:
@@ -205,7 +206,7 @@ class ASCIItable():
 
 # ------------------------------------------------------------------
   def head_getGeom(self):
-    """Interpret geom header"""
+    """Interpret geom header."""
     identifiers = {
             'grid':    ['a','b','c'],
             'size':    ['x','y','z'],
@@ -247,7 +248,7 @@ class ASCIItable():
   def labels_append(self,
                     what,
                     reset = False):
-    """Add item or list to existing set of labels (and switch on labeling)"""
+    """Add item or list to existing set of labels (and switch on labeling)."""
     if isinstance(what, (str, unicode)):
       self.tags += [self._removeCRLF(what)]
     else:
@@ -261,7 +262,7 @@ class ASCIItable():
 
 # ------------------------------------------------------------------
   def labels_clear(self):
-    """Delete existing labels and switch to no labeling"""
+    """Delete existing labels and switch to no labeling."""
     self.tags = []
     self.__IO__['labeled'] = False
 
@@ -392,7 +393,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def info_append(self,
                   what):
-    """Add item or list to existing set of infos"""
+    """Add item or list to existing set of infos."""
     if isinstance(what, (str, unicode)):
       self.info += [self._removeCRLF(what)]
     else:
@@ -403,7 +404,7 @@ class ASCIItable():
 
 # ------------------------------------------------------------------
   def info_clear(self):
-    """Delete any info block"""
+    """Delete any info block."""
     self.info = []
 
 # ------------------------------------------------------------------
@@ -416,7 +417,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def data_skipLines(self,
                      count):
-    """Wind forward by count number of lines"""
+    """Wind forward by count number of lines."""
     for i in range(count):
       alive = self.data_read()
 
@@ -426,7 +427,7 @@ class ASCIItable():
   def data_read(self,
                 advance = True,
                 respectLabels = True):
-    """Read next line (possibly buffered) and parse it into data array"""
+    """Read next line (possibly buffered) and parse it into data array."""
     self.line = self.__IO__['readBuffer'].pop(0) if len(self.__IO__['readBuffer']) > 0 \
            else self.__IO__['in'].readline().strip()                                                # take buffered content or get next data row from file
 
@@ -446,9 +447,11 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def data_readArray(self,
                      labels = []):
-    """Read whole data of all (given) labels as numpy array"""
+    """Read whole data of all (given) labels as numpy array."""
-    try:      self.data_rewind()                                                                    # try to wind back to start of data
+    try:
-    except:   pass                                                                                  # assume/hope we are at data start already...
+      self.data_rewind()                                                                            # try to wind back to start of data
+    except IOError:
+      pass                                                                                          # assume/hope we are at data start already...
 
     if labels is None or labels == []:
       use = None                                                                                    # use all columns (and keep labels intact)
@@ -480,7 +483,7 @@ class ASCIItable():
 # ------------------------------------------------------------------
   def data_write(self,
                  delimiter = '\t'):
-    """Write current data array and report alive output back"""
+    """Write current data array and report alive output back."""
     if len(self.data) == 0: return True
 
     if isinstance(self.data[0],list):
@@ -492,16 +495,16 @@ class ASCIItable():
   def data_writeArray(self,
                       fmt = None,
                       delimiter = '\t'):
-    """Write whole numpy array data"""
+    """Write whole numpy array data."""
     for row in self.data:
       try:
         output = [fmt % value for value in row] if fmt else list(map(repr,row))
-      except:
+      except Exception:
         output = [fmt % row] if fmt else [repr(row)]
       
       try:
         self.__IO__['out'].write(delimiter.join(output) + '\n')
-      except:
+      except Exception:
         pass
 
 # ------------------------------------------------------------------
@@ -545,7 +548,7 @@ class ASCIItable():
                           grid,
                           type = 'i',
                           strict = False):
-    """Read microstructure data (from .geom format)"""
+    """Read microstructure data (from .geom format)."""
     def datatype(item):
       return int(item) if type.lower() == 'i' else float(item)
       

python/damask/dadf5.py

@@ -369,7 +369,7 @@ class DADF5():
       return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str')          # np.bytes_ to string
 
 
-  def read_dataset(self,path,c):
+  def read_dataset(self,path,c=0,plain=False):
     """
     Dataset for all points/cells.
     
@@ -402,6 +402,9 @@ class DADF5():
             a=a.reshape([a.shape[0],1])
           dataset[p,:] = a[u,:]
     
+    if plain and dataset.dtype.names is not None:
+      return dataset.view(('float64',len(dataset.dtype.names)))
+    else:
       return dataset
 
 
@@ -620,7 +623,7 @@ class DADF5():
         raise ValueError
       
       return {
-              'data':  mechanics.deviator(x['data']),
+              'data':  mechanics.deviatoric_part(x['data']),
               'label': 's_{}'.format(x['label']),
               'meta':  {
                         'Unit':        x['meta']['Unit'],

python/damask/geom.py

@@ -2,6 +2,7 @@ import os
 from io import StringIO
 
 import numpy as np
+from scipy import ndimage
 import vtk
 from vtk.util import numpy_support
 
@@ -30,7 +31,6 @@ class Geom():
             comments lines.
 
         """
-    self.__transforms__ = \
         self.set_microstructure(microstructure)
         self.set_size(size)
         self.set_origin(origin)
@@ -250,7 +250,11 @@ class Geom():
             geometry file to read.
 
         """
-    with (open(fname) if isinstance(fname,str) else fname) as f:
+        try:
+            f = open(fname)
+        except TypeError:
+            f = fname
+
         f.seek(0)
         header_length,keyword = f.readline().split()[:2]
         header_length = int(header_length)
@@ -286,7 +290,6 @@ class Geom():
                                         abs(int(items[2])-int(items[0]))+1,dtype=float)
                 else:                        items = list(map(float,items))
             else:                            items = list(map(float,items))
-      
             microstructure[i:i+len(items)] = items
             i += len(items)
         
@@ -299,7 +302,8 @@ class Geom():
         
         return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
 
-  def to_file(self,fname):
+
+    def to_file(self,fname,pack=None):
         """
         Writes a geom file.
 
@@ -307,16 +311,62 @@ class Geom():
         ----------
         fname : str or file handle
             geometry file to write.
+        pack : bool, optional
+            compress geometry with 'x of y' and 'a to b'.
 
         """
         header = self.get_header()
         grid   = self.get_grid()
-    format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
+        
-               else '%g'
+        if pack is None:
+            plain = grid.prod()/np.unique(self.microstructure).size < 250
+        else:
+            plain = not pack
+
+        if plain:
+            format_string = '%g' if self.microstructure.dtype in np.sctypes['float'] else \
+                            '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
             np.savetxt(fname,
                        self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
                        header='\n'.join(header), fmt=format_string, comments='')
+        else:
+            try:
+                f = open(fname,'w')
+            except TypeError:
+                f = fname
 
+            compressType = None
+            former = start = -1
+            reps = 0
+            for current in self.microstructure.flatten('F'):
+                if abs(current - former) == 1 and (start - current) == reps*(former - current):
+                    compressType = 'to'
+                    reps += 1
+                elif current == former and start == former:
+                    compressType = 'of'
+                    reps += 1
+                else:
+                    if   compressType is None:
+                        f.write('\n'.join(self.get_header())+'\n')
+                    elif compressType == '.':
+                        f.write('{}\n'.format(former))
+                    elif compressType == 'to':
+                        f.write('{} to {}\n'.format(start,former))
+                    elif compressType == 'of':
+                        f.write('{} of {}\n'.format(reps,former))
+
+                    compressType = '.'
+                    start = current
+                    reps = 1
+
+                former = current
+
+            if compressType == '.':
+                f.write('{}\n'.format(former))
+            elif compressType == 'to':
+                f.write('{} to {}\n'.format(start,former))
+            elif compressType == 'of':
+                f.write('{} of {}\n'.format(reps,former))
 
                  
     def to_vtk(self,fname=None):
@@ -387,3 +437,91 @@ class Geom():
         self.to_file(f)
         f.seek(0)
         return ''.join(f.readlines())
+
+
+    def mirror(self,directions,reflect=False):
+        """
+        Mirror microstructure along given directions.
+
+        Parameters
+        ----------
+        directions : iterable containing str
+            direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
+        reflect : bool, optional
+            reflect (include) outermost layers.
+
+        """
+        valid = {'x','y','z'}
+        if not all(isinstance(d, str) for d in directions):
+            raise TypeError('Directions are not of type str.')
+        elif not set(directions).issubset(valid):
+            raise ValueError('Invalid direction specified {}'.format(*set(directions).difference(valid)))
+
+        limits = [None,None] if reflect else [-2,0]
+        ms = self.get_microstructure()
+
+        if 'z' in directions:
+            ms = np.concatenate([ms,ms[:,:,limits[0]:limits[1]:-1]],2)
+        if 'y' in directions:
+            ms = np.concatenate([ms,ms[:,limits[0]:limits[1]:-1,:]],1)
+        if 'x' in directions:
+            ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
+     
+        return self.update(ms,rescale=True)
+        #self.add_comments('tbd')
+
+
+    def scale(self,grid):
+        """
+        Scale microstructure to new grid.
+
+        Parameters
+        ----------
+        grid : iterable of int
+            new grid dimension
+
+        """
+        return self.update(
+                           ndimage.interpolation.zoom(
+                                                      self.microstructure,
+                                                      grid/self.get_grid(),
+                                                      output=self.microstructure.dtype,
+                                                      order=0,
+                                                      mode='nearest',
+                                                      prefilter=False
+                                                     )
+                          )
+        #self.add_comments('tbd')
+
+
+    def clean(self,stencil=3):
+        """
+        Smooth microstructure by selecting most frequent index within given stencil at each location.
+
+        Parameters
+        ----------
+        stencil : int, optional
+            size of smoothing stencil.
+
+        """
+        def mostFrequent(arr):
+            unique, inverse = np.unique(arr, return_inverse=True)
+            return unique[np.argmax(np.bincount(inverse))]
+
+        return self.update(ndimage.filters.generic_filter(
+                                                          self.microstructure,
+                                                          mostFrequent,
+                                                          size=(stencil,)*3
+                                                         ).astype(self.microstructure.dtype)
+                          )
+        #self.add_comments('tbd')
+
+
+    def renumber(self):
+        """Renumber sorted microstructure indices to 1,...,N."""
+        renumbered = np.empty(self.get_grid(),dtype=self.microstructure.dtype)
+        for i, oldID in enumerate(np.unique(self.microstructure)):
+          renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
+
+        return self.update(renumbered)
+        #self.add_comments('tbd')

python/damask/mechanics.py

@@ -48,10 +48,10 @@ def strain_tensor(F,t,m):
     
     if   m > 0.0:
         eps = 1.0/(2.0*abs(m)) * (+ np.matmul(n,np.einsum('ij,ikj->ijk',w**m,n)) 
-                                  - np.broadcast_to(np.ones(3),[F_.shape[0],3]))
+                                  - np.broadcast_to(np.eye(3),[F_.shape[0],3,3]))
     elif m < 0.0:
         eps = 1.0/(2.0*abs(m)) * (- np.matmul(n,np.einsum('ij,ikj->ijk',w**m,n))
-                                  + np.broadcast_to(np.ones(3),[F_.shape[0],3]))
+                                  + np.broadcast_to(np.eye(3),[F_.shape[0],3,3]))
     else:
         eps = np.matmul(n,np.einsum('ij,ikj->ijk',0.5*np.log(w),n))
       
@@ -190,7 +190,7 @@ def rotational_part(x):
       Tensor of which the rotational part is computed.
 
     """
-    return __polar_decomposition(x,'R')
+    return __polar_decomposition(x,'R')[0]
 
 
 def left_stretch(x):
@@ -203,7 +203,7 @@ def left_stretch(x):
       Tensor of which the left stretch is computed.
 
     """
-    return __polar_decomposition(x,'V')
+    return __polar_decomposition(x,'V')[0]
   
   
 def right_stretch(x):
@@ -216,7 +216,7 @@ def right_stretch(x):
       Tensor of which the right stretch is computed.
 
     """
-    return __polar_decomposition(x,'U')
+    return __polar_decomposition(x,'U')[0]
 
 
 def __polar_decomposition(x,requested):
@@ -227,7 +227,7 @@ def __polar_decomposition(x,requested):
     ----------
     x : numpy.array of shape (:,3,3) or (3,3)
       Tensor of which the singular values are computed.
-    requested : list of str
+    requested : iterable of str
       Requested outputs: ‘R’ for the rotation tensor, 
       ‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
 

python/damask/solver/marc.py

@@ -79,9 +79,9 @@ class Marc(Solver):
     exitnumber = -1
     fid_out = open(outFile,'r')
     for line in fid_out:
-      if (string.find(line,'tress iteration') is not -1):
+      if (string.find(line,'tress iteration') != -1):
         print(line)
-      elif (string.find(line,'Exit number') is not -1):
+      elif (string.find(line,'Exit number')   != -1):
         substr = line[string.find(line,'Exit number'):len(line)]
         exitnumber = int(substr[12:16])
 

python/damask/test.py

@@ -1,10 +1,8 @@
-# -*- coding: UTF-8 no BOM -*-
-
 import os,sys,shutil
 import logging,logging.config
 import damask
 import numpy as np
-from collections import Iterable
+from collections.abc import Iterable
 from optparse import OptionParser
 
 class Test():
@@ -17,7 +15,7 @@ class Test():
   variants = []
   
   def __init__(self, **kwargs):
-
+    """New test."""
     defaults = {'description': '',
                 'keep':          False,
                 'accept':        False,
@@ -120,22 +118,22 @@ class Test():
     """Delete directory tree containing current results."""
     try:
       shutil.rmtree(self.dirCurrent())
-    except:
+    except FileNotFoundError:
       logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
 
     try:
       os.mkdir(self.dirCurrent())
       return True
-    except:
+    except FileExistsError:
       logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
       return False
     
   def prepareAll(self):
-    """Do all necessary preparations for the whole test"""
+    """Do all necessary preparations for the whole test."""
     return True
 
   def prepare(self,variant):
-    """Do all necessary preparations for the run of each test variant"""
+    """Do all necessary preparations for the run of each test variant."""
     return True
 
 
@@ -207,9 +205,9 @@ class Test():
     for source,target in zip(list(map(mapA,A)),list(map(mapB,B))):
       try:
         shutil.copy2(source,target)
-      except:
+      except FileNotFoundError:
         logging.critical('error copying {} to {}'.format(source,target))
-        raise
+        raise FileNotFoundError
 
 
   def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
@@ -218,9 +216,9 @@ class Test():
     for i,f in enumerate(sourcefiles):
       try:
         shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
-      except:
+      except FileNotFoundError:
         logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
-        raise
+        raise FileNotFoundError
 
 
   def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
@@ -230,10 +228,10 @@ class Test():
     for i,f in enumerate(sourcefiles):
       try:
         shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
-      except:
+      except FileNotFoundError:
         logging.error(os.path.join(source,f))
         logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
-        raise
+        raise FileNotFoundError
 
 
   def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
@@ -242,9 +240,9 @@ class Test():
     for i,f in enumerate(sourcefiles):
       try:
         shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
-      except:
+      except FileNotFoundError:
         logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
-        raise
+        raise FileNotFoundError
 
 
   def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
@@ -253,9 +251,9 @@ class Test():
     for i,f in enumerate(sourcefiles):
       try:
         shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
-      except:
+      except FileNotFoundError:
         logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
-        raise
+        raise FileNotFoundError
 
 
   def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
@@ -263,9 +261,10 @@ class Test():
     for i,f in enumerate(sourcefiles):
       try:
         shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
-      except:
+      except FileNotFoundError:
         logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
-        raise
+        raise FileNotFoundError
+
 
   def execute_inCurrentDir(self,cmd,streamIn=None,env=None):
 
@@ -439,7 +438,7 @@ class Test():
                      stdTol = 1.0e-6,
                      preFilter = 1.0e-9):
     """
-    Calculate statistics of tables
+    Calculate statistics of tables.
 
     threshold can be used to ignore small values (a negative number disables this feature)
     """
@@ -492,7 +491,7 @@ class Test():
                      rtol    = 1e-5,
                      atol    = 1e-8,
                      debug   = False):
-    """Compare multiple tables with np.allclose"""
+    """Compare multiple tables with np.allclose."""
     if not (isinstance(files, Iterable) and not isinstance(files, str)):       # check whether list of files is requested
       files = [str(files)]
 

python/damask/test/__init__.py

@@ -1,3 +0,0 @@
-"""Test functionality."""
-
-from .test import Test      # noqa