improved help for automatic documentation and simplified some scripts

processing/post/addOrientations.py

@@ -21,29 +21,28 @@ Orientation is given by quaternion, Euler angles, rotation matrix, or crystal fr
 
 outputChoices = ['quaternion','eulers']
 parser.add_option('-o', '--output',     dest='output', action='extend', metavar='<string LIST>',
-                                        help = 'output orientation formats (%s)'%(','.join(outputChoices)))
+                  help = 'output orientation formats {%s}'%(','.join(outputChoices)))
 parser.add_option('-s', '--symmetry',   dest='symmetry', type='choice', 
-                                        choices=damask.Symmetry.lattices[1:], metavar='string',
+                  choices=damask.Symmetry.lattices[1:], metavar='string',
-                                        help = 'crystal symmetry (%s) [cubic]'%(', '.join(damask.Symmetry.lattices[1:])))
+                  help = 'crystal symmetry [cubic] {%s}'%(', '.join(damask.Symmetry.lattices[1:])))
 parser.add_option('-r', '--rotation',   dest='rotation', type='float', nargs=4, metavar='float float float float',
-                                        help = 'angle and axis to (pre)rotate orientation')
+                  help = 'angle and axis to (pre)rotate orientation')
 parser.add_option('-e', '--eulers',     dest='eulers', metavar='string',
-                                        help = 'Euler angles label')
+                  help = 'Euler angles label')
 parser.add_option('-d', '--degrees',    dest='degrees', action='store_true',
-                                        help = 'Euler angles are given in degrees [%default]')
+                  help = 'Euler angles are given in degrees [%default]')
 parser.add_option('-m', '--matrix',     dest='matrix', metavar='string',
-                                        help = 'orientation matrix label')
+                  help = 'orientation matrix label')
 parser.add_option('-a',                 dest='a', metavar='string',
-                                        help = 'crystal frame a vector label')
+                  help = 'crystal frame a vector label')
 parser.add_option('-b',                 dest='b', metavar='string',
-                                        help = 'crystal frame b vector label')
+                  help = 'crystal frame b vector label')
 parser.add_option('-c',                 dest='c', metavar='string',
-                                        help = 'crystal frame c vector label')
+                  help = 'crystal frame c vector label')
 parser.add_option('-q', '--quaternion', dest='quaternion', metavar='string',
-                                        help = 'quaternion label')
+                  help = 'quaternion label')
-parser.set_defaults(output = [])
 parser.set_defaults(symmetry = 'cubic')
-parser.set_defaults(rotation = [0.,1.,1.,1.])       # no rotation about 1,1,1
+parser.set_defaults(rotation = (0.,1.,1.,1.))       # no rotation about 1,1,1
 parser.set_defaults(degrees = False)
 
 (options, filenames) = parser.parse_args()
@@ -75,10 +74,8 @@ if options.quaternion != None:
   datainfo['quaternion']['label'] += [options.quaternion]
   input = 'quaternion'
 
-inputGiven = 0
+if len(input) != 1: parser.error('needs exactly one input format...')
-for datatype,info in datainfo.items():
+input = input[0]
-  inputGiven += len(info['label'])
-if inputGiven != 1: parser.error('select exactly one input format...')
 
 toRadians = math.pi/180.0 if options.degrees else 1.0                                               # rescale degrees to radians
 options.output = map(lambda x: x.lower(), options.output)

processing/post/addPK2.py

@@ -20,24 +20,14 @@ Add column(s) containing Second Piola--Kirchhoff stress based on given column(s)
 """, version = scriptID)
 
 parser.add_option('-f','--defgrad',     dest='defgrad', metavar='string',
-                                        help='heading of columns containing deformation gradient [%default]')
+                  help='heading of columns containing deformation gradient [%default]')
 parser.add_option('-p','--stress',      dest='stress', metavar='string',
-                                        help='heading of columns containing first Piola--Kirchhoff stress [%default]')
+                  help='heading of columns containing first Piola--Kirchhoff stress [%default]')
 parser.set_defaults(defgrad = 'f')
 parser.set_defaults(stress = 'p')
 
 (options,filenames) = parser.parse_args()
 
-datainfo = {                                                                                        # list of requested labels per datatype
-             'defgrad':    {'len':9,
-                            'label':[]},
-             'stress':     {'len':9,
-                            'label':[]},
-           }
-
-datainfo['defgrad']['label'].append(options.defgrad)
-datainfo['stress']['label'].append(options.stress)
-
 # ------------------------------------------ setup file handles ------------------------------------
 files = []
 if filenames == []:
@@ -56,37 +46,28 @@ for file in files:
   table.head_read()                                                                                 # read ASCII header info
   table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
 
+# --------------- figure out columns to process  ---------------------------------------------------
+  missingColumns = False
+  column={ 'defgrad': table.labels.index('1_'+options.defgrad), 
+           'stress':  table.labels.index('1_'+options.stress)}
+  for key in column:
+    if column[key]<1:
+      file['croak'].write('column %s not found...\n'%key)
+      missingColumns=True
+  if missingColumns: continue
   active = defaultdict(list)
   column = defaultdict(dict)
   missingColumns = False
-  
-  for datatype,info in datainfo.items():
-    for label in info['label']:
-      key = '1_%s'%label
-      if key not in table.labels:
-        file['croak'].write('column %s not found...\n'%key)
-        missingColumns = True                                                                       # break if label not found
-      else:
-        active[datatype].append(label)
-        column[datatype][label] = table.labels.index(key)                                           # remember columns of requested data
 
-  if missingColumns:
+# ------------------------------------------ assemble header --------------------------------------
-    continue
-
- # ------------------------------------------ assemble header --------------------------------------
   table.labels_append(['%i_S'%(i+1) for i in xrange(datainfo['stress']['len'])])                    # extend ASCII header with new labels
   table.head_write()
 
 # ------------------------------------------ process data ------------------------------------------
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    F = np.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
+    F = np.array(map(float,table.data[column['defgrad']:column['defgrad']+9]),'d').reshape(3,3)
-                                      column['defgrad'][active['defgrad'][0]]+
+    P = np.array(map(float,table.data[column['stress'] :column['stress']+9]),'d').reshape(3,3)
-                                             datainfo['defgrad']['len']]),'d').reshape(3,3)
-    P = np.array(map(float,table.data[column['stress'][active['stress'][0]]:
-                                      column['stress'][active['stress'][0]]+
-                                             datainfo['stress']['len']]),'d').reshape(3,3)
-
     table.data_append(list(np.dot(np.linalg.inv(F),P).reshape(9)))                                  # [S] =[P].[F-1]
     outputAlive = table.data_write()                                                                # output processed line
 

processing/post/addPole.py

@@ -19,24 +19,24 @@ Add x,y coordinates of stereographic projection of given direction (pole) in cry
 """, version = scriptID)
 
 parser.add_option('-p', '--pole',       dest='pole', type='float', nargs=3, metavar='float float float',
-                                        help = 'crystal frame direction for pole figure %default')
+                  help = 'crystal frame direction for pole figure [%default]')
 parser.add_option('--polar',            dest='polar', action='store_true',
-                                        help = 'output polar coordinates r,phi [%default]')
+                  help = 'output polar coordinates r,phi [%default]')
 parser.add_option('-e', '--eulers',     dest='eulers', metavar='string',
-                                        help = 'Euler angles label')
+                  help = 'Euler angles label')
 parser.add_option('-d', '--degrees',    dest='degrees', action='store_true',
-                                        help = 'Euler angles are given in degrees [%default]')
+                  help = 'Euler angles are given in degrees [%default]')
 parser.add_option('-m', '--matrix',     dest='matrix', metavar='string',
-                                        help = 'orientation matrix label')
+                  help = 'orientation matrix label')
 parser.add_option('-a',                 dest='a', metavar='string',
-                                        help = 'crystal frame a vector label')
+                  help = 'crystal frame a vector label')
 parser.add_option('-b',                 dest='b', metavar='string',
-                                        help = 'crystal frame b vector label')
+                  help = 'crystal frame b vector label')
 parser.add_option('-c',                 dest='c', metavar='string',
-                                        help = 'crystal frame c vector label')
+                  help = 'crystal frame c vector label')
 parser.add_option('-q', '--quaternion', dest='quaternion', metavar='string',
-                                        help = 'quaternion label')
+                  help = 'quaternion label')
-parser.set_defaults(pole = [1.0,0.0,0.0])
+parser.set_defaults(pole = (1.0,0.0,0.0))
 parser.set_defaults(degrees = False)
 parser.set_defaults(polar   = False)
 

processing/post/addSchmidfactors.py

@@ -247,33 +247,34 @@ Add columns listing Schmid factors (and optional trace vector of selected system
 
 """, version = scriptID)
 
-parser.add_option('-l','--lattice',   dest='lattice', type='choice',
+parser.add_option('-l','--lattice',   dest='lattice', type='choice', choices=('fcc','bcc','hex'), metavar='string',
-                                      choices=('fcc','bcc','hex'), metavar='string',
+                  help="type of lattice structure [%default] {fcc,bcc',hex}")
-                                      help="type of lattice structure {'fcc','bcc','hex'} [%default]")
 parser.add_option('--direction',      dest='forcedirection', type='int', nargs=3, metavar='int int int',
-                                      help='force direction in lab coordinates %default')
+                  help='force direction in lab coordinates %default')
 parser.add_option('-n','--normal',    dest='stressnormal', type='int', nargs=3, metavar='int int int',
-                                      help='stress plane normal in lab coordinates ')
+                  help='stress plane normal in lab coordinates ')
 parser.add_option('--trace',          dest='traceplane', type='int', nargs=3, metavar='int int int',
-                                      help='normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported')
+                  help='normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported')
 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')
 parser.add_option('-r','--rank',      dest='rank', type='int', nargs=3, metavar='int int int',
-                                      help="report trace of r'th highest Schmid factor [%default]")
+                  help="report trace of r'th highest Schmid factor [%default]")
 parser.add_option('-e', '--eulers',   dest='eulers', metavar='string',
-                                      help='Euler angles label')
+                  help='Euler angles label')
 parser.add_option('-d', '--degrees',  dest='degrees', action='store_true',
-                                      help='Euler angles are given in degrees [%default]')
+                  help='Euler angles are given in degrees [%default]')
 parser.set_defaults(lattice = 'fcc')
-parser.set_defaults(forcedirection = [0, 0, 1])
+parser.set_defaults(forcedirection = (0, 0, 1))
 parser.set_defaults(stressnormal = None)
 parser.set_defaults(traceplane = None)
 parser.set_defaults(rank = 0)
-parser.set_defaults(CoverA = 1.587)
 parser.set_defaults(eulers = 'eulerangles')
 
 (options,filenames) = parser.parse_args()
 
+if options.lattice=='hex' and options.CoverA == None:
+  parser.error('hex lattice needs c over a ration...')
+
 options.forcedirection = normalize(options.forcedirection)
 if options.stressnormal:
   if abs(sum([options.forcedirection[i] * options.stressnormal[i] for i in range(3)])) < 1e-3:

processing/post/addSpectralDecomposition.py

@@ -20,12 +20,11 @@ Add column(s) containing eigenvalues and eigenvectors of requested tensor column
 """, version = scriptID)
 
 parser.add_option('-t','--tensor',      dest='tensor', action='extend', metavar='<string LIST>',
-                                        help='heading of columns containing tensor field values')
+                  help='heading of columns containing tensor field values')
-parser.set_defaults(tensor = [])
 
 (options,filenames) = parser.parse_args()
 
-if len(options.tensor) == 0:
+if options.tensor == None:
   parser.error('no data column specified...')
 
 datainfo = {                                                                                        # list of requested labels per datatype

processing/post/addStrainTensors.py

@@ -31,17 +31,17 @@ Add column(s) containing given strains based on given stretches of requested def
 """, version = scriptID)
 
 parser.add_option('-u','--right',       dest='right', action='store_true',
-                                        help='material strains based on right Cauchy--Green deformation, i.e., C and U [%default]')
+                  help='material strains based on right Cauchy--Green deformation, i.e., C and U [%default]')
 parser.add_option('-v','--left',        dest='left', action='store_true',
-                                        help='spatial strains based on left Cauchy--Green deformation, i.e., B and V [%default]')
+                  help='spatial strains based on left Cauchy--Green deformation, i.e., B and V [%default]')
 parser.add_option('-l','-0','--logarithmic', dest='logarithmic', action='store_true',
-                                        help='calculate logarithmic strain tensor [%default]')
+                  help='calculate logarithmic strain tensor [%default]')
 parser.add_option('-b','-1','--biot',   dest='biot', action='store_true',
-                                        help='calculate biot strain tensor [%default]')
+                  help='calculate biot strain tensor [%default]')
 parser.add_option('-g','-2','--green',  dest='green', action='store_true',
-                                        help='calculate green strain tensor [%default]')
+                  help='calculate green strain tensor [%default]')
 parser.add_option('-f','--defgrad',     dest='defgrad', action='extend', metavar = '<string LIST>',
-                                        help='heading(s) of columns containing deformation tensor values %default')
+                  help='heading(s) of columns containing deformation tensor values %default')
 parser.set_defaults(right       = False)
 parser.set_defaults(left        = False)
 parser.set_defaults(logarithmic = False)