small adjustments for autodoc

processing/post/addCalculation.py

@@ -41,10 +41,7 @@ parser.add_option('-f','--formula',
 
 parser.add_option('-c','--condition',
                   dest   = 'condition', metavar='string',
-                  help   = 'condition to alter existing column data')
+                  help   = 'condition to alter existing column data (optional)')
-
-parser.set_defaults(condition = None,
-                   )
 
 (options,filenames) = parser.parse_args()
 
@@ -80,7 +77,7 @@ for name in filenames:
     condition = options.condition                                                                   # copy per file, since might be altered inline
     breaker = False
   
-    for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))):              # find three groups
+    for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))):  # find three groups
       idx = table.label_index(column)
       dim = table.label_dimension(column)
       if idx < 0 and column not in specials:
@@ -89,15 +86,15 @@ for name in filenames:
       else:
         if column in specials:
           replacement = 'specials["{}"]'.format(column)
-        elif dim == 1:                                                                                # scalar input
+        elif dim == 1:                                                                              # scalar input
           replacement = '{}(table.data[{}])'.format({  '':'float',
-                                                        's#':'str'}[marker],idx)                      # take float or string value of data column
+                                                        's#':'str'}[marker],idx)                    # take float or string value of data column
-        elif dim > 1:                                                                                 # multidimensional input (vector, tensor, etc.)
+        elif dim > 1:                                                                               # multidimensional input (vector, tensor, etc.)
-          replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim)                 # use (flat) array representation
+          replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim)               # use (flat) array representation
        
         condition = condition.replace('#'+all+'#',replacement)
     
-    if breaker: continue                                                                              # found mistake in condition evaluation --> next file
+    if breaker: continue                                                                            # found mistake in condition evaluation --> next file
 
 # ------------------------------------------ build formulas ----------------------------------------
 

processing/post/addCumulative.py

@@ -22,12 +22,9 @@ parser.add_option('-l','--label',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'columns to cumulate')
 
-parser.set_defaults(label = [],
-                   )
-                    
 (options,filenames) = parser.parse_args()
 
-if len(options.label) == 0:
+if options.label is None:
   parser.error('no data column(s) specified.')
 
 # --- loop over input files -------------------------------------------------------------------------

processing/post/addDisplacement.py

@@ -111,7 +111,6 @@ parser.add_option('--nodal',
 
 parser.set_defaults(defgrad = 'f',
                     pos     = 'pos',
-                    nodal   = False,
                    )
 
 (options,filenames) = parser.parse_args()

processing/post/addGaussian.py

@@ -34,12 +34,12 @@ parser.add_option('-o','--order',
                   dest = 'order',
                   type = int,
                   metavar = 'int',
-                  help = 'order of the filter')
+                  help = 'order of the filter [%default]')
 parser.add_option('--sigma',
                   dest = 'sigma',
                   type = float,
                   metavar = 'float',
-                  help = 'standard deviation')
+                  help = 'standard deviation [%default]')
 parser.add_option('--periodic',
                   dest = 'periodic',
                   action = 'store_true',
@@ -50,7 +50,6 @@ parser.add_option('--periodic',
 parser.set_defaults(pos = 'pos',
                     order = 0,
                     sigma = 1,
-                    periodic = False,
                    )
 
 (options,filenames) = parser.parse_args()

processing/post/addGrainID.py

@@ -28,9 +28,9 @@ parser.add_option('-d',
                   help = 'disorientation threshold in degrees [%default]')
 parser.add_option('-s',
                   '--symmetry',
-                  dest = 'symmetry',
+                  dest = 'symmetry', type = 'choice', choices = damask.Symmetry.lattices[1:],
                   metavar = 'string',
-                  help = 'crystal symmetry [%default]')
+                  help = 'crystal symmetry [%default] {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
 parser.add_option('-o',
                   '--orientation',
                   dest = 'quaternion',
@@ -49,7 +49,7 @@ parser.add_option('--quiet',
 parser.set_defaults(disorientation = 5,
                     verbose = True,
                     quaternion = 'orientation',
-                    symmetry = 'cubic',
+                    symmetry = damask.Symmetry.lattices[-1],
                     pos      = 'pos',
                    )
 

processing/post/addInfo.py

@@ -23,11 +23,12 @@ parser.add_option('-i',
                   dest = 'info', action = 'extend', metavar = '<string LIST>',
                   help    = 'items to add')
 
-parser.set_defaults(info = [],
-                   )
 
 (options,filenames) = parser.parse_args()
 
+if options.info is None:
+  parser.error('no info specified.')
+
 # --- loop over input files ------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]

processing/post/addMises.py

@@ -38,13 +38,9 @@ parser.add_option('-s','--stress',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'heading(s) of columns containing stress tensors')
 
-parser.set_defaults(strain = [],
-                    stress = [],
-                   )
-
 (options,filenames) = parser.parse_args()
 
-if len(options.stress+options.strain) == 0:
+if options.stress is None and options.strain is None:
   parser.error('no data column specified...')
 
 # --- loop over input files -------------------------------------------------------------------------

processing/post/addNorm.py

@@ -9,6 +9,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 # definition of element-wise p-norms for matrices
+# ToDo: better use numpy.linalg.norm
 
 def norm(which,object):
 
@@ -18,6 +19,8 @@ def norm(which,object):
     return math.sqrt(sum([x*x for x in object]))
   elif which == 'Max':                                                                              # p = inf
     return max(map(abs, object))
+  else:
+    return -1
 
 # --------------------------------------------------------------------
 #                                MAIN
@@ -43,6 +46,8 @@ parser.set_defaults(norm = 'frobenius',
 
 (options,filenames) = parser.parse_args()
 
+if options.norm.lower() not in normChoices:
+  parser.error('invalid norm ({}) specified.'.format(options.norm))
 if options.label is None:
   parser.error('no data column specified.')
 
@@ -74,7 +79,7 @@ for name in filenames:
     else:
       dims.append(dim)
       columns.append(table.label_index(what))
-      table.labels_append('norm{}({})'.format(options.norm.capitalize(),what))                    # extend ASCII header with new labels
+      table.labels_append('norm{}({})'.format(options.norm.capitalize(),what))                      # extend ASCII header with new labels
 
   if remarks != []: damask.util.croak(remarks)
   if errors  != []:

processing/post/addOrientations.py

@@ -68,12 +68,12 @@ parser.add_option('-R',
                   '--labrotation',
                   dest='labrotation',
                   type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
-                  help = 'angle and axis of additional lab frame rotation')
+                  help = 'angle and axis of additional lab frame rotation [%default]')
 parser.add_option('-r',
                   '--crystalrotation',
                   dest='crystalrotation',
                   type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
-                  help = 'angle and axis of additional crystal frame rotation')
+                  help = 'angle and axis of additional crystal frame rotation [%default]')
 parser.add_option('--eulers',
                   dest = 'eulers',
                   metavar = 'string',
@@ -106,7 +106,6 @@ parser.add_option('-z',
 parser.set_defaults(output = [],
                     labrotation     = (0.,1.,1.,1.),                                                # no rotation about 1,1,1
                     crystalrotation = (0.,1.,1.,1.),                                                # no rotation about 1,1,1
-                    degrees = False,
                    )
 
 (options, filenames) = parser.parse_args()

processing/post/addPole.py

@@ -35,7 +35,6 @@ parser.add_option('-o',
 
 parser.set_defaults(pole = (1.0,0.0,0.0),
                     quaternion = 'orientation',
-                    polar   = False,
                    )
 
 (options, filenames) = parser.parse_args()

processing/post/addSchmidfactors.py

@@ -115,7 +115,7 @@ parser.add_option('-l',
                   help = 'type of lattice structure [%default] {}'.format(latticeChoices))
 parser.add_option('--covera',
                   dest = 'CoverA', type = 'float', metavar = 'float',
-                  help = 'C over A ratio for hexagonal systems')
+                  help = 'C over A ratio for hexagonal systems [%default]')
 parser.add_option('-f',
                   '--force',
                   dest = 'force',

processing/post/addStrainTensors.py

@@ -56,16 +56,15 @@ parser.add_option('-f','--defgrad',
                   metavar = '<string LIST>',
                   help = 'heading(s) of columns containing deformation tensor values [%default]')
 
-parser.set_defaults(right       = False,
+parser.set_defaults(
-                    left        = False,
-                    logarithmic = False,
-                    biot        = False,
-                    green       = False,
                     defgrad     = ['f'],
                    )
 
 (options,filenames) = parser.parse_args()
 
+if len(options.defgrad) > 1:
+  options.defgrad = options.defgrad[1:]
+
 stretches = []
 strains = []
 

processing/post/addTable.py

@@ -24,6 +24,10 @@ parser.add_option('-a', '--add','--table',
 
 (options,filenames) = parser.parse_args()
 
+if options.table is None:
+  parser.error('no table specified.')
+
+
 # --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]

processing/post/averageDown.py

@@ -34,16 +34,14 @@ parser.add_option('--shift',
 parser.add_option('-g', '--grid',
                   dest = 'grid',
                   type = 'int', nargs = 3, metavar = 'int int int',
-                  help = 'grid in x,y,z [autodetect]')
+                  help = 'grid in x,y,z (optional)')
 parser.add_option('-s', '--size',
                   dest = 'size',
                   type = 'float', nargs = 3, metavar = 'float float float',
-                  help = 'size in x,y,z [autodetect]')
+                  help = 'size in x,y,z (optional)')
 parser.set_defaults(pos     = 'pos',
                     packing = (2,2,2),
                     shift   = (0,0,0),
-                    grid    = (0,0,0),
-                    size    = (0.0,0.0,0.0),
                    )
 
 (options,filenames) = parser.parse_args()
@@ -92,7 +90,7 @@ for name in filenames:
 
   table.data_readArray()
 
-  if (any(options.grid) == 0 or any(options.size) == 0.0):
+  if (options.grid is None or options.size is None):
     grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
   else:
     grid   = np.array(options.grid,'i')

processing/post/binXY.py

@@ -37,15 +37,15 @@ parser.add_option('-t','--type',
 parser.add_option('-x','--xrange',
                   dest = 'xrange',
                   type = 'float', nargs = 2, metavar = 'float float',
-                  help = 'min max value in x direction [autodetect]')
+                  help = 'min max limits in x direction (optional)')
 parser.add_option('-y','--yrange',
                   dest = 'yrange',
                   type = 'float', nargs = 2, metavar = 'float float',
-                  help = 'min max value in y direction [autodetect]')
+                  help = 'min max limits in y direction (optional)')
 parser.add_option('-z','--zrange',
                   dest = 'zrange',
                   type = 'float', nargs = 2, metavar = 'float float',
-                  help = 'min max value in z direction [autodetect]')
+                  help = 'min max limits in z direction (optional)')
 parser.add_option('-i','--invert',
                   dest = 'invert',
                   action = 'store_true',
@@ -64,9 +64,6 @@ parser.set_defaults(bins = (10,10),
                     xrange = (0.0,0.0),
                     yrange = (0.0,0.0),
                     zrange = (0.0,0.0),
-                    invert = False,
-                    normRow = False,
-                    normCol = False,
                    )
 
 (options,filenames) = parser.parse_args()

processing/post/blowUp.py

@@ -27,10 +27,10 @@ parser.add_option('-p','--packing',
                   help = 'dimension of packed group [%default]')
 parser.add_option('-g','--grid',
                   dest = 'resolution', type = 'int', nargs = 3, metavar = 'int int int',
-                  help = 'resolution in x,y,z [autodetect]')
+                  help = 'grid in x,y,z (optional)')
 parser.add_option('-s','--size',
                   dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
-                  help = 'dimension in x,y,z [autodetect]')
+                  help = 'size in x,y,z (optional)')
 parser.set_defaults(pos  = 'pos',
                     packing = (2,2,2),
                     grid    = (0,0,0),

processing/post/rotateData.py

@@ -29,7 +29,7 @@ parser.add_option('-r', '--rotation',
 parser.add_option('--degrees',
                   dest = 'degrees',
                   action = 'store_true',
-                  help = 'angles are given in degrees [%default]')
+                  help = 'angles are given in degrees')
 
 parser.set_defaults(rotation = (0.,1.,1.,1.),                                                       # no rotation about 1,1,1
                     degrees = False,