unified options to enable automated parsing for documentation

processing/pre/abq_addUserOutput.py

@@ -72,32 +72,28 @@ Or have an existing set of user variables copied over from another *.inp file.
 
 """, version= scriptID)
 
-parser.add_option('-n','--number', dest='number', type='int', \
+parser.add_option('-m', dest='number', type='int', metavar = 'int',
-          help='maximum requested User Defined Variable [%default]')
+                  help='maximum requested User Defined Variable [%default]')
-parser.add_option('--homogenization', dest='homog', \
+parser.add_option('--homogenization', dest='homog', metavar = 'string',
-          help='homogenization identifier (as string or integer [%default])')
+                  help='homogenization name or index [%default]')
-parser.add_option('--crystallite', dest='cryst', \
+parser.add_option('--crystallite', dest='cryst', metavar = 'string',
-          help='crystallite identifier (as string or integer [%default])')
+                  help='crystallite identifier name or index [%default]')
-parser.add_option('--phase', dest='phase', \
+parser.add_option('--phase', dest='phase', metavar = 'string',
-          help='phase identifier (as string or integer [%default])')
+                  help='phase identifier name or index [%default]')
-parser.add_option('--use', dest='useFile', \
+parser.add_option('--use', dest='useFile', metavar = 'string',
-          help='Optionally parse output descriptors from '+
+                  help='optionally parse output descriptors from '+
-               'different <model_job>.outputZZZ file. Saves the effort '+
+                       'outputXXX files of given name')
-               'to start a calculation for each job [%default])')
+parser.add_option('--option', dest='damaskOption', metavar = 'string',
-parser.add_option('--option', dest='damaskOption', \
+                  help='Add DAMASK option to input file, e.g. "periodic x z"')
-          help='Add damask option to input file '+
+ 
-               'for example: "periodic x z" [%default]')
+parser.set_defaults(number = 0,
-parser.set_defaults(number = 0)
+                    homog = '1',
-parser.set_defaults(homog = '1')
+                    cryst = '1',
-parser.set_defaults(cryst = '1')
+                    phase = '1')
-parser.set_defaults(phase = '1')
-parser.set_defaults(useFile = '')
-parser.set_defaults(damaskOption = '')
 
 (options, files) = parser.parse_args()
 
 if not files:
-  parser.print_help()
   parser.error('no file(s) specified...')
 
 me = {  'Homogenization':   options.homog,
@@ -108,7 +104,7 @@ me = {  'Homogenization':   options.homog,
 
 for file in files:
   print '\033[1m'+scriptName+'\033[0m: '+file+'\n'
-  if options.useFile != '':
+  if options.useFile:
     formatFile = os.path.splitext(options.useFile)[0]
   else:
     formatFile = os.path.splitext(file)[0]

processing/pre/geom_canvas.py

@@ -21,11 +21,11 @@ Changes the (three-dimensional) canvas of a spectral geometry description.
 parser.add_option('-g', '--grid',
                   dest = 'grid',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'a,b,c grid of hexahedral box [unchanged]')
+                  help = 'a,b,c grid of hexahedral box [auto]')
 parser.add_option('-o', '--offset',
                   dest = 'offset',
                   type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
-                  help = 'a,b,c offset from old to new origin of grid %default')
+                  help = 'a,b,c offset from old to new origin of grid [%default]')
 parser.add_option('-f', '--fill',
                   dest = 'fill',
                   type = 'int', metavar = 'int',

processing/pre/geom_fromEuclideanDistance.py

@@ -92,11 +92,11 @@ boundaries, triple lines, and quadruple points.
 parser.add_option('-t','--type',
                   dest = 'type',
                   action = 'extend', metavar = '<string LIST>',
-                  help = 'feature type (%s) '%(', '.join(map(lambda x:'|'.join(x['alias']),features))) )
+                  help = 'feature type {%s} '%(', '.join(map(lambda x:'|'.join(x['alias']),features))) )
 parser.add_option('-n','--neighborhood',
                   dest = 'neighborhood',
                   choices = neighborhoods.keys(), metavar = 'string',
-                  help = 'type of neighborhood (%s) [neumann]'%(', '.join(neighborhoods.keys())))
+                  help = 'type of neighborhood {%s} [neumann]'%(', '.join(neighborhoods.keys())))
 parser.add_option('-s', '--scale',
                   dest = 'scale',
                   type = 'float', metavar = 'float',

processing/pre/geom_fromMinimalSurface.py

@@ -55,10 +55,6 @@ parser.add_option('--m',
                   dest = 'microstructure',
                   type = 'int', nargs = 2, metavar = 'int int',
                   help = 'two microstructure indices to be used [%default]')
-parser.add_option('-1', '--onedimensional',
-                  dest = 'oneD',
-                  action = 'store_true',
-                  help = 'output geom file with two-dimensional data arrangement [%default]')
 parser.set_defaults(type = minimal_surfaces[0],
                     threshold = 0.0,
                     periods = 1,
@@ -66,7 +62,6 @@ parser.set_defaults(type = minimal_surfaces[0],
                     size = (1.0,1.0,1.0),
                     homogenization = 1,
                     microstructure = (1,2),
-                    oneD  = False,
                    )
 
 (options,filenames) = parser.parse_args()
@@ -135,9 +130,6 @@ for name in filenames:
       table.data_clear()
       for x in xrange(options.grid[0]):
         table.data_append(options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])])
-        if options.oneD:
-          table.data_write()
-          table.data_clear()
       table.data_write()
 
   table.close()

processing/pre/geom_fromVPSC.py

@@ -30,7 +30,7 @@ parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'in
 parser.add_option('--compress',            dest='compress', action='store_true',
                   help='lump identical microstructure and texture information [%default]')
 parser.add_option('-p', '--precision',    dest='precision', choices=['0','1','2','3'], metavar = 'int',
-                  help = 'euler angles decimal places for output format and compressing (0,1,2,3) [2]')
+                  help = 'euler angles decimal places for output format and compressing {0,1,2,3} [2]')
 
 parser.set_defaults(column         = 7)
 parser.set_defaults(threshold      = 1.0)

processing/pre/geom_fromVoronoiTessellation.py

@@ -113,11 +113,11 @@ Generate geometry description and material configuration by standard Voronoi tes
 parser.add_option('-g', '--grid',
                   dest = 'grid',
                   type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
-                  help = 'a,b,c grid of hexahedral box [from seeds file]')
+                  help = 'a,b,c grid of hexahedral box [auto]')
 parser.add_option('-s', '--size',
                   dest = 'size',
                   type = 'float', nargs = 3, metavar=' '.join(['float']*3),
-                  help = 'x,y,z size of hexahedral box [from seeds file or 1.0 along largest grid point number]')
+                  help = 'x,y,z size of hexahedral box [auto]')
 parser.add_option('-o', '--origin',
                   dest = 'origin',
                   type = 'float', nargs = 3, metavar=' '.join(['float']*3),
@@ -141,7 +141,7 @@ parser.add_option('-e', '--eulers',
 parser.add_option('--axes',
                   dest = 'axes',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'orientation coordinate frame in terms of position coordinate frame [same]')
+                  help = 'orientation coordinate frame in terms of position coordinate frame')
 parser.add_option('--homogenization',
                   dest = 'homogenization',
                   type = 'int', metavar = 'int',
@@ -165,7 +165,7 @@ parser.add_option('--secondphase',
 parser.add_option('-l', '--laguerre',
                   dest = 'laguerre',
                   action = 'store_true',
-                  help = 'use Laguerre (weighted Voronoi) tessellation [%default]')
+                  help = 'use Laguerre (weighted Voronoi) tessellation')
 parser.add_option('--cpus',
                   dest = 'cpus',
                   type = 'int', metavar = 'int',
@@ -173,12 +173,9 @@ parser.add_option('--cpus',
 parser.add_option('--nonperiodic',
                   dest = 'nonperiodic',
                   action = 'store_true',
-                  help = 'use nonperiodic tessellation [%default]')
+                  help = 'use nonperiodic tessellation')
 
-parser.set_defaults(grid   = None,
+parser.set_defaults(position       = 'pos',
-                    size   = None,
-                    origin = None,
-                    position       = 'pos',
                     weight         = 'weight',
                     microstructure = 'microstructure',
                     eulers         = 'eulerangles',

processing/pre/geom_unpack.py

@@ -15,16 +15,9 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
 Unpack geometry files containing ranges "a to b" and/or "n of x" multiples (exclusively in one line).
+
 """, version = scriptID)
 
-parser.add_option('-1', '--onedimensional',
-                  dest = 'oneD',
-                  action = 'store_true',
-                  help = 'output geom file with one-dimensional data arrangement [%default]')
-
-parser.set_defaults(oneD = False,
-                   )
-
 (options, filenames) = parser.parse_args()
 
 # --- loop over input files -------------------------------------------------------------------------
@@ -76,8 +69,7 @@ for name in filenames:
 
   microstructure = table.microstructure_read(info['grid'])                                          # read microstructure
   formatwidth = int(math.floor(math.log10(microstructure.max())+1))                                 # efficient number printing format
-  table.data = microstructure if options.oneD else \
+  table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
-               microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
   table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
     
 #--- output finalization --------------------------------------------------------------------------

processing/pre/gmsh_identifySurfaces.py

@@ -23,28 +23,22 @@ def func(seq):
 #--------------------------------------------------------------------------------------------------
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
-        Recognize bounding surfaces and append them as physical sufaces in the geo file. """, version = scriptID)
+Recognize bounding surfaces and append them as physical sufaces in the geo file. 
-parser.add_option('-n','--numvol', dest = 'N', \
+
-                                   type='int',\
+""", version = scriptID)
-                                   metavar='int',\
+
+parser.add_option('-n','--numvol', dest = 'N', type='int', metavar='int',
                                    help='number of physical volumes' )
-parser.add_option('-f','--faces',  dest = 'surfaces', \
+parser.add_option('-f','--faces',  dest = 'surfaces', action = 'extend', type = 'string', metavar = '<string LIST>',
-                                   action = 'extend', \
+                                   help = 'surfaces to tag {x, y, z}')
-                                   type = 'string', \
+parser.add_option('-s','--size',   dest = 'size', type='float', metavar='float',
-                                   metavar = '<string LIST>', \
+                                   help='mesh size [%default]' )
-                                   help = 'surfaces to tag (x, y, and/or z)')
+parser.add_option('-d','--dim',    dest = 'dimension', type='int', metavar='int',
-parser.add_option('-s','--size',   dest = 'size', \
+                                   help='dimension of geometry [%default]' )
-                                   type='float',\
-                                   metavar='float',\
-                                   help='mesh size' )
-parser.add_option('-d','--dim',    dest = 'dimension', \
-                                   type='int',\
-                                   metavar='float',\
-                                   help='dimension of geometry' )
 
 (options, filename) = parser.parse_args()
-parser.set_defaults(size = 0.1)
+parser.set_defaults(size = 0.1,
-parser.set_defaults(dimension = 3)
+                    dimension = 3)
 
 my_geofile   = filename[0]
 numVol       = options.N
@@ -200,5 +194,3 @@ elif (options.dimension == 2):
     f.write('Background Field = 1;\n')     
  
   f.close()
-
-

processing/pre/hybridIA_linODFsampling.py

@@ -201,17 +201,19 @@ def TothVanHoutteSTAT (ODF,nSamples):
 # --------------------------------------------------------------------
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
 Transform linear binned ODF data into given number of orientations.
+IA: integral approximation, STAT: Van Houtte, MC: Monte Carlo
 
 """, version = scriptID)
 
+algorithms = ['IA', 'STAT','MC']
 parser.add_option('-n', '--nsamples',
                   dest = 'number',
                   type = 'int', metavar = 'int',
                   help = 'number of orientations to be generated [%default]')
 parser.add_option('-a','--algorithm',
                   dest = 'algorithm',
-                  type = 'string', metavar = 'string',
+                  choices = algorithms, metavar = 'string',
-                  help = 'sampling algorithm. IA: integral approximation, STAT: Van Houtte, MC: Monte Carlo. [%default].') #make choice
+                  help = 'sampling algorithm {%s} [IA]'%(', '.join(algorithms)))
 parser.add_option('-p','--phase',
                   dest = 'phase',
                   type = 'int', metavar = 'int',

processing/pre/patchFromReconstructedBoundaries.py

@@ -787,78 +787,63 @@ reconstructed boundary file
 
 """, version = scriptID)
 
-parser.add_option("-o", "--output", action='extend', dest='output', \
+meshes=['dt_planar_trimesh','af_planar_trimesh','af_planar_quadmesh']
-        help="types of output [image, mentat, procedure, spectral]")
+parser.add_option('-o', '--output', action='extend', dest='output', metavar = '<string LIST>',
-parser.add_option("-p", "--port", type="int",\
+        help='types of output {image, mentat, procedure, spectral}')
-        dest="port",\
+parser.add_option('-p', '--port', type='int', metavar = 'int',
-        help="Mentat connection port [%default]")
+        dest='port', help='Mentat connection port [%default]')
-parser.add_option("-2", "--twodimensional", action="store_true",\
+parser.add_option('-2', '--twodimensional', action='store_true',
-        dest="twoD",\
+        dest='twoD',help='use 2D model')
-        help="twodimensional model [%default]")
+parser.add_option('-s','--patchsize', type='float', metavar = 'float',
-parser.add_option("-s","--patchsize", type="float",\
+        dest='size', help='height of patch [%default]')
-        dest="size",\
+parser.add_option('-e', '--strain', type='float', metavar = 'float',
-        help="height of patch [%default]")
+        dest='strain', help='final strain to reach in simulation [%default]')
-parser.add_option("-e", "--strain", type="float",\
+parser.add_option('--rate', type='float', metavar = 'float',
-        dest="strain",\
+        dest='strainrate', help='engineering strain rate to simulate [%default]')
-        help="final strain to reach in simulation [%default]")
+parser.add_option('-N', '--increments', type='int', metavar = 'int',
-parser.add_option("--rate", type="float",\
+        dest='increments', help='number of increments to take [%default]')
-        dest="strainrate",\
+parser.add_option('-t', '--tolerance', type='float', metavar = 'float',
-        help="(engineering) strain rate to simulate [%default]")
+        dest='tolerance', help='relative tolerance of pixel positions to be swept [%default]')
-parser.add_option("-N", "--increments", type="int",\
+parser.add_option('-m', '--mesh', choices = meshes,
-        dest="increments",\
+        metavar = '<string LIST>', dest='mesh', 
-        help="number of increments to take [%default]")
+        help='algorithm and element type for automeshing {%s} [dt_planar_trimesh]'%(', '.join(meshes)))
-parser.add_option("-t", "--tolerance", type="float",\
+parser.add_option('-x', '--xmargin', type='float', metavar = 'float',
-        dest="tolerance",\
+        dest='xmargin',help='margin in x in units of patch size [%default]')
-        help="relative tolerance of pixel positions to be swept [%default]")
+parser.add_option('-y', '--ymargin', type='float', metavar = 'float',
-parser.add_option("-m", "--mesh", choices=['dt_planar_trimesh','af_planar_trimesh','af_planar_quadmesh'],\
+        dest='ymargin', help='margin in y in units of patch size [%default]')
-        dest="mesh",\
+parser.add_option('-r', '--resolution', type='int', metavar = 'int',
-        help="algorithm and element type for automeshing (dt_planar_trimesh, af_planar_trimesh, af_planar_quadmesh) [%default]")
+        dest='resolution',help='number of Fourier points/Finite Elements across patch size + x_margin [%default]')
-parser.add_option("-x", "--xmargin", type="float",\
+parser.add_option('-z', '--extrusion', type='int', metavar = 'int',
-        dest="xmargin",\
+        dest='extrusion', help='number of repetitions in z-direction [%default]')
-        help="margin in x in units of patch size [%default]")
+parser.add_option('-i', '--imagesize', type='int', metavar = 'int',
-parser.add_option("-y", "--ymargin", type="float",\
+        dest='imgsize', help='size of PNG image [%default]')
-        dest="ymargin",\
+parser.add_option('-M', '--coordtransformation', type='float', nargs=4, metavar = ' '.join(['float']*4),
-        help="margin in y in units of patch size [%default]")
+        dest='M', help='2x2 transformation from rcb to Euler coords [%default]')
-parser.add_option("-r", "--resolution", type="int",\
+parser.add_option('--scatter', type='float', metavar = 'float',
-        dest="resolution",\
+        dest='scatter',help='orientation scatter [%default]')
-        help="number of Fourier points/Finite Elements across patch size + x_margin [%default]")
+parser.add_option('--segment', type='int', metavar = 'int', dest='segmentcolumn',
-parser.add_option("-z", "--extrusion", type="int",\
+        help='column holding the first entry for the segment end points in the rcb file [%default]')
-        dest="extrusion",\
+parser.add_option('--id', type='int', dest='idcolumn', metavar = 'int',
-        help="number of repetitions in z-direction [%default]")
+        help='column holding the right hand grain ID in the rcb file [%default]')
-parser.add_option("-i", "--imagesize", type="int",\
-        dest="imgsize",\
-        help="size of PNG image [%default]")
-parser.add_option("-M", "--coordtransformation", type="float", nargs=4, \
-        dest="M",\
-        help="2x2 transformation from rcb to Euler coords [%default]")
-parser.add_option("--scatter", type="float",\
-        dest="scatter",\
-        help="orientation scatter %default")
-parser.add_option("--segment", type="int",\
-        dest="segmentcolumn",\
-        help="column holding the first entry for the segment end points in the rcb file [%default]")
-parser.add_option("--id", type="int",\
-        dest="idcolumn",\
-        help="column holding the right hand grain ID in the rcb file [%default]")
 
-parser.set_defaults(output = [])
+parser.set_defaults(output = [],
-parser.set_defaults(size = 1.0)
+                    size = 1.0,
-parser.set_defaults(port = 40007)
+                    port = 40007,
-parser.set_defaults(xmargin = 0.0)
+                    xmargin = 0.0,
-parser.set_defaults(ymargin = 0.0)
+                    ymargin = 0.0,
-parser.set_defaults(resolution = 64)
+                    resolution = 64,
-parser.set_defaults(extrusion = 2)
+                    extrusion = 2,
-parser.set_defaults(imgsize = 512)
+                    imgsize = 512,
-parser.set_defaults(M = [0.0,1.0,1.0,0.0])  # M_11, M_12, M_21, M_22.  x,y in RCB is y,x of Eulers!!
+                    M = (0.0,1.0,1.0,0.0),  # M_11, M_12, M_21, M_22.  x,y in RCB is y,x of Eulers!!
-parser.set_defaults(tolerance = 1.0e-3)
+                    tolerance = 1.0e-3,
-parser.set_defaults(scatter = 0.0)
+                    scatter = 0.0,
-parser.set_defaults(strain = 0.2)
+                    strain = 0.2,
-parser.set_defaults(strainrate = 1.0e-3)
+                    strainrate = 1.0e-3,
-parser.set_defaults(increments = 200)
+                    increments = 200,
-parser.set_defaults(mesh = 'dt_planar_trimesh')
+                    mesh = 'dt_planar_trimesh',
-parser.set_defaults(twoD = False)
+                    twoD = False,
-parser.set_defaults(segmentcolumn = 9)
+                    segmentcolumn = 9,
-parser.set_defaults(idcolumn = 13)
+                    idcolumn = 13)
 
 (options, args) = parser.parse_args()