added verbosity on help messages

processing/pre/geom_canvas.py

@@ -52,11 +52,11 @@ Changes the (three-dimensional) canvas of a spectral geometry description.
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, \
+parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, metavar='int int int ', \
                   help='a,b,c grid of hexahedral box [unchanged]')
-parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
+parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, metavar='int int int', \
                   help='a,b,c offset from old to new origin of grid %default')
-parser.add_option('-f', '--fill', dest='fill', type='int', \
+parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', \
                   help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
 
 parser.set_defaults(grid = ['0','0','0'])
@@ -199,7 +199,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],),
     "size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],),
     "origin\tx %f\ty %f\tz %f"%(newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],),

processing/pre/geom_fromAng.py

@@ -36,19 +36,19 @@ Two phases can be discriminated based on threshold value in a given data column.
 )
 
 
-parser.add_option('--column',              dest='column', type='int', \
+parser.add_option('--column',              dest='column', type='int', metavar = 'int', \
                   help='data column to discriminate phase 1 from 2 [%default]')
-parser.add_option('-t','--threshold',      dest='threshold', type='float', \
+parser.add_option('-t','--threshold',      dest='threshold', type='float', metavar = 'float', \
                   help='threshold value to discriminate phase 1 from 2 [%default]')
-parser.add_option('--homogenization',      dest='homogenization', type='int', \
+parser.add_option('--homogenization',      dest='homogenization', type='int', metavar = 'int', \
                   help='homogenization index to be used [%default]')
-parser.add_option('--phase',               dest='phase', type='int', nargs = 2, \
+parser.add_option('--phase',               dest='phase', type='int', nargs = 2, metavar = 'int int', \
                   help='two phase indices to be used %default')
-parser.add_option('--crystallite',         dest='crystallite', type='int', \
+parser.add_option('--crystallite',         dest='crystallite', type='int', metavar = 'int', \
                   help='crystallite index to be used [%default]')
 parser.add_option('-c', '--configuration', dest='config', action='store_true', \
                   help='output material configuration [%default]')
-parser.add_option('-a', '--axes',         dest='axes', type='string', nargs = 3, \
+parser.add_option('-a', '--axes',         dest='axes', type='string', nargs = 3, metavar = 'string string string', \
                   help='axes assignement of eulerangles x,y,z = %default')
     
                   

processing/pre/geom_fromEuclideanDistance.py

@@ -117,9 +117,9 @@ boundaries, triple lines, and quadruple points.
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-t','--type',        dest='type', action='extend', type='string', \
+parser.add_option('-t','--type',        dest='type', action='extend', type='string', metavar = '<string LIST>', \
-                  help='feature type (%s)'%(', '.join(map(lambda x:', '.join(x['names']),features))))
+                  help='feature type (%s) '%(', '.join(map(lambda x:', '.join(x['names']),features))) )
-parser.add_option('-n','--neighborhood',  dest='neigborhood', choices=neighborhoods.keys(), \
+parser.add_option('-n','--neighborhood',  dest='neigborhood', choices=neighborhoods.keys(), metavar = 'string',  \
                   help='type of neighborhood (%s) [neumann]'%(', '.join(neighborhoods.keys())))
 parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
                   help='output geom file with two-dimensional data arrangement [%default]')
@@ -214,7 +214,7 @@ for file in files:
     file['croak'].write('invalid size x y z.\n')
     sys.exit()
 
-  new_header.append(scriptID,' '+ ' '.join(sys.argv[1:]) + '\n')
+  new_header.append(scriptID + ' ' + ' '.join(sys.argv[1:]) + '\n')
   new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
   new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
   new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))

processing/pre/geom_fromMinimalSurface.py

@@ -43,19 +43,19 @@ Generate a geometry file of a bicontinuous structure of given type.
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-t','--type', dest='type', choices=minimal_surfaces, \
+parser.add_option('-t','--type', dest='type', choices=minimal_surfaces, metavar='string', \
                   help='type of minimal surface (%s) [primitive]' %(','.join(minimal_surfaces)))
-parser.add_option('-f','--threshold', dest='threshold', type='float', \
+parser.add_option('-f','--threshold', dest='threshold', type='float', metavar='float', \
                   help='threshold value defining minimal surface [%default]')
-parser.add_option('-g', '--grid', dest='grid', type='int', nargs=3, \
+parser.add_option('-g', '--grid', dest='grid', type='int', nargs=3, metavar='int int int', \
                   help='a,b,c grid of hexahedral box %default')
-parser.add_option('-s', '--size', dest='size', type='float', nargs=3, \
+parser.add_option('-s', '--size', dest='size', type='float', nargs=3, metavar='float float float', \
                   help='x,y,z size of hexahedral box %default')
-parser.add_option('-p', '--periods', dest='periods', type='int', \
+parser.add_option('-p', '--periods', dest='periods', type='int', metavar= 'int', \
                   help='number of repetitions of unit cell [%default]')
-parser.add_option('--homogenization', dest='homogenization', type='int', \
+parser.add_option('--homogenization', dest='homogenization', type='int', metavar= 'int', \
                   help='homogenization index to be used [%default]')
-parser.add_option('--m', dest='microstructure', type='int', nargs = 2, \
+parser.add_option('--m', dest='microstructure', type='int', nargs = 2, metavar= 'int int', \
                   help='two microstructure indices to be used %default')
 parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
                   help='output geom file with two-dimensional data arrangement [%default]')
@@ -101,7 +101,7 @@ if numpy.any(info['size'] <= 0.0):
   sys.exit()
 
 #--- write header ---------------------------------------------------------------------------------
-header = [scriptID,' ' + ' '.join(sys.argv[1:])+'\n']
+header = [scriptID + ' ' + ' '.join(sys.argv[1:])+'\n']
 header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
 header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
 header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))

processing/pre/geom_fromOsteonGeometry.py

@@ -36,25 +36,25 @@ Its fiber orientation is oscillating by +/- amplitude within one period.
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, \
+parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, metavar = 'int int', \
                   help='a,b grid of hexahedral box %default')
-parser.add_option('-s', '--size', dest='size', type='float', nargs=2, \
+parser.add_option('-s', '--size', dest='size', type='float', nargs=2, metavar = 'float float', \
                   help='x,y size of hexahedral box %default')
-parser.add_option('-c', '--canal',  dest='canal', type='float', \
+parser.add_option('-c', '--canal',  dest='canal', type='float', metavar = 'float', \
                   help='Haversian canal radius [%default]')
-parser.add_option('-o', '--osteon', dest='osteon', type='float', \
+parser.add_option('-o', '--osteon', dest='osteon', type='float', metavar = 'float', \
                   help='osteon radius (horizontal) [%default]')
-parser.add_option('-l', '--lamella', dest='period', type='float', \
+parser.add_option('-l', '--lamella', dest='period', type='float', metavar = 'float', \
                   help='lamella width [%default]')
-parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \
+parser.add_option('-a', '--amplitude', dest='amplitude', type='float', metavar = 'float', \
                   help='amplitude of twisted plywood wiggle in deg [%default]')
-parser.add_option(      '--aspect', dest='aspect', type='float', \
+parser.add_option(      '--aspect', dest='aspect', type='float', metavar = 'float', \
                   help='osteon aspect ratio (vert/horiz) [%default]')
-parser.add_option('-w', '--omega',  dest='omega', type='float', \
+parser.add_option('-w', '--omega',  dest='omega', type='float', metavar = 'float', \
                   help='rotation angle (around normal) of osteon [%default]')
-parser.add_option('--homogenization', dest='homogenization', type='int', \
+parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \
                   help='homogenization index to be used [%default]')
-parser.add_option('--crystallite',  dest='crystallite', type='int', \
+parser.add_option('--crystallite',  dest='crystallite', type='int', metavar = 'int', \
                   help='crystallite index to be used [%default]')
 parser.add_option('--configuration', dest='config', action='store_true', \
                   help='output material configuration [%default]')
@@ -175,7 +175,7 @@ if options.config:
                                   betaOfGrain[i]))
   
 else:
-  header = [scriptID,' ' + ' '.join(sys.argv[1:])+'\n']
+  header = [scriptID + ' ' + ' '.join(sys.argv[1:])+'\n']
   header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
   header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
   header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))

processing/pre/geom_fromVPSC.py

@@ -36,15 +36,15 @@ Generate geometry description and material configuration from input files used b
 )
 
 
-parser.add_option('--column',          dest='column', type='int', \
+parser.add_option('--column',          dest='column', type='int', metavar = 'int', \
                   help='data column to discriminate phase 1 from 2 [%default]')
-parser.add_option('-t','--treshold',  dest='threshold', type='float', \
+parser.add_option('-t','--treshold',  dest='threshold', type='float', metavar = 'float', \
                   help='threshold value to discriminate phase 1 from 2 [%default]')
-parser.add_option('--homogenization', dest='homogenization', type='int', \
+parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \
                   help='homogenization index to be used [%default]')
-parser.add_option('--phase', dest='phase', type='int', nargs = 2, \
+parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', \
                   help='two phase indices to be used %default')
-parser.add_option('--crystallite', dest='crystallite', type='int', \
+parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', \
                   help='crystallite index to be used [%default]')
 parser.add_option('-c', '--configuration', dest='config', action='store_true', \
                   help='output material configuration [%default]')
@@ -132,7 +132,7 @@ for file in files:
     file['output'].write('\n'.join(microstructure) + \
                          '\n'.join(texture))
   else:
-    header = [scriptID,' ' + ' '.join(sys.argv[1:])+'\n']
+    header = [scriptID + ' ' + ' '.join(sys.argv[1:])+'\n']
     header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
     header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
     header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))

processing/pre/geom_fromVoronoiTessellation.py

@@ -74,15 +74,15 @@ Generate geometry description and material configuration by standard Voronoi tes
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
+parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar = 'int int int', \
                   help='a,b,c grid of hexahedral box [from seeds file]')
-parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \
+parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar = 'float float float', \
                   help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
-parser.add_option('--homogenization', dest='homogenization', type='int', \
+parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \
                   help='homogenization index to be used [%default]')
-parser.add_option('--phase', dest='phase', type='int', \
+parser.add_option('--phase', dest='phase', type='int', metavar = 'int', \
                   help='phase index to be used [%default]')
-parser.add_option('--crystallite', dest='crystallite', type='int', \
+parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', \
                   help='crystallite index to be used [%default]')
 parser.add_option('-c', '--configuration', dest='config', action='store_true', \
                   help='output material configuration [%default]')
@@ -249,7 +249,7 @@ for file in files:
     theTable.labels_clear()
     theTable.info_clear()
     theTable.info_append(extra_header+[
-      scriptID,
+      scriptID + ' ' + ' '.join(sys.argv[1:]),
       "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
       "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
       "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),

processing/pre/geom_grainGrowth.py

@@ -57,21 +57,16 @@ The final geometry is assembled by selecting at each voxel that grain index for
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-d', '--distance', dest='d', type='int', \
+parser.add_option('-d', '--distance', dest='d', type='int', metavar='int', \
-                  help='diffusion distance in voxels [%default]', metavar='float')
+                  help='diffusion distance in voxels [%default]')
-parser.add_option('-N', '--smooth', dest='N', type='int', \
+parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int', \
                  help='N for curvature flow [%default]')
-parser.add_option('-b', '--black', dest='black', action='extend', type='string', \
-                 help='indices of stationary microstructures', metavar='<LIST>')
 
 parser.set_defaults(d = 1)
 parser.set_defaults(N = 1)
-parser.set_defaults(p = [1,1,1])
-parser.set_defaults(black = [])
-
 (options, filenames) = parser.parse_args()
 
-options.black = map(int,options.black)
+
 
 #--- setup file handles --------------------------------------------------------------------------   
 files = []
@@ -162,8 +157,7 @@ for file in files:
   microstructure = microstructure.reshape([2 if i == 1 else i for i in info['grid']],order='F')
 
 #--- domain decomposition -------------------------------------------------------------------------  
-  numProc = int(options.p[0]*options.p[1]*options.p[2])
+  stride = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
-  stride = numpy.array([2 if i == 1 else i for i in info['grid']],'i')/options.p
   if numpy.any(numpy.floor(stride) != stride): 
     file['croak'].write('invalid domain decomposition.\n')
     continue
@@ -209,7 +203,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID+ ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
     "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
     "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),

processing/pre/geom_pack.py

@@ -122,7 +122,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
     "size\tx %e\ty %e\tz %e"%(info['size'][0],info['size'][1],info['size'][2],),
     "origin\tx %e\ty %e\tz %e"%(info['origin'][0],info['origin'][1],info['origin'][2],),

processing/pre/geom_rescale.py

@@ -53,13 +53,13 @@ Either absolute values or relative factors (like "0.25x") can be used.
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, \
+parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar = 'int int int', \
                   help='a,b,c grid of hexahedral box [unchanged]')
-parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, \
+parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar = 'float float float', \
                   help='x,y,z size of hexahedral box [unchanged]')
 
-parser.set_defaults(grid = ['0','0','0'])
+parser.set_defaults(grid = [0,0,0])
-parser.set_defaults(size  = ['0.0','0.0','0.0'])
+parser.set_defaults(size = [0.0,0.0,0.0])
 
 (options, filenames) = parser.parse_args()
 
@@ -191,7 +191,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],),
     "size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],),
     "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),

processing/pre/geom_translate.py

@@ -52,11 +52,11 @@ translate microstructure indices (shift or substitute) and/or geometry origin.
 )
 
 parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, \
-                  help='offset from old to new origin of grid', metavar='<x y z>')
+                  help='offset from old to new origin of grid', metavar='float float float')
 parser.add_option('-m', '--microstructure', dest='microstructure', type='int', \
-                  help='offset from old to new microstructure indices', metavar='<int>')
+                  help='offset from old to new microstructure indices', metavar='int')
 parser.add_option('-s', '--substitute', action='extend', dest='substitute', type='string', \
-                  help='substitutions of microstructure indices from,to,from,to,...', metavar='<list>')
+                  help='substitutions of microstructure indices from,to,from,to,...', metavar='<string LIST>')
 
 parser.set_defaults(origin = [0.0,0.0,0.0])
 parser.set_defaults(microstructure = 0)
@@ -154,11 +154,8 @@ for file in files:
 
 #--- do work ------------------------------------------------------------------------------------
   substituted = numpy.copy(microstructure)
-  for k, v in sub.iteritems(): substituted[microstructure==k] = v                                   # substitute microstructure indices
+  for k, v in sub.iteritems(): substituted[microstructure==k] = v                                    # substitute microstructure indices
 
-#  for i in xrange(N):
-#    if microstructure[i] in sub: microstructure[i] = sub[microstructure[i]]                         # substitute microstructure indices
-    
   substituted += options.microstructure                                                              # shift microstructure indices
 
   newInfo['origin'] = info['origin'] + options.origin
@@ -174,7 +171,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
     "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
     "origin\tx %f\ty %f\tz %f"%(newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],),

processing/pre/geom_unpack.py

@@ -143,7 +143,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
     "size\tx %e\ty %e\tz %e"%(info['size'][0],info['size'][1],info['size'][2],),
     "origin\tx %e\ty %e\tz %e"%(info['origin'][0],info['origin'][1],info['origin'][2],),

processing/pre/geom_vicinityOffset.py

@@ -54,9 +54,9 @@ i.e. within the region close to a grain/phase boundary.
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
+parser.add_option('-v', '--vicinity', dest='vicinity', type='int', metavar='int', \
                   help='voxel distance checked for presence of other microstructure [%default]')
-parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', \
+parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', metavar='int', \
                   help='offset (positive or negative) for tagged microstructure. '+
                        '"0" selects maximum microstructure index [%default]')
 
@@ -164,7 +164,7 @@ for file in files:
   theTable.labels_clear()
   theTable.info_clear()
   theTable.info_append(extra_header+[
-    scriptID,
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
     "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
     "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
     "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),