now a library function

PRIVATE

@@ -1 +1 @@
-Subproject commit 3fc9d58a35614fd8ffa1179e634431eb457d0150
+Subproject commit a52584687a93b9f007cf019861fce68eb31451ab

processing/pre/geom_addPrimitive.py

@@ -1,75 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-from optparse import OptionParser
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-#--------------------------------------------------------------------------------------------------
-#                                MAIN
-#--------------------------------------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
-Inserts a primitive geometric object at a given position.
-These objects can be boxes, cylinders, or ellipsoids.
-
-""", version = scriptID)
-
-parser.add_option('-c', '--center',
-                  dest='center',
-                  type='float', nargs = 3, metavar=' '.join(['float']*3),
-                  help='a,b,c origin of primitive %default')
-parser.add_option('-d', '--dimension',
-                  dest='dimension',
-                  type='float', nargs = 3, metavar=' '.join(['float']*3),
-                  help='a,b,c extension of hexahedral box')
-parser.add_option('-e', '--exponent',
-                  dest='exponent',
-                  type='float', nargs = 3, metavar=' '.join(['float']*3),
-                  help='i,j,k exponents for axes: '+
-                  '0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), '+
-                  '1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), '+
-                  'large values produce boxes, negative turn concave.')
-parser.add_option('-f', '--fill',
-                  dest='fill',
-                  type='float', metavar = 'int',
-                  help='microstructure index to fill primitive, defaults to max microstructure index + 1')
-parser.add_option('-q', '--quaternion',
-                  dest='quaternion',
-                  type='float', nargs = 4, metavar=' '.join(['float']*4),
-                  help = 'rotation of primitive as quaternion')
-parser.add_option('-a', '--angleaxis',
-                  dest='angleaxis',
-                  type=float, nargs = 4, metavar=' '.join(['float']*4),
-                  help = 'axis and angle to rotate primitive')
-parser.add_option(     '--degrees',
-                  dest='degrees',
-                  action='store_true',
-                  help = 'angle is given in degrees')
-parser.add_option(     '--nonperiodic',
-                  dest='periodic',
-                  action='store_false',
-                  help = 'wrap around edges')
-parser.add_option(     '--realspace',
-                  dest='realspace',
-                  action='store_true',
-                  help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
-parser.add_option(     '--invert',
-                  dest='inside',
-                  action='store_false',
-                  help = 'invert the volume filled by the primitive (inside/outside)')
-
-parser.set_defaults(center = (.0,.0,.0),
-                    degrees = False,
-                    exponent = (20,20,20), # box shape by default
-                    periodic = True,
-                    realspace = False,
-                    inside = True,
-                   )
-
-print('This script is broken and does nothing')

processing/pre/geom_vicinityOffset.py

@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from io import StringIO
-from optparse import OptionParser
-
-import numpy as np
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-#--------------------------------------------------------------------------------------------------
-#                                MAIN
-#--------------------------------------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
-Offset microstructure index for points which see a microstructure different from themselves
-(or listed as triggers) within a given (cubic) vicinity, i.e. within the region close to a grain/phase boundary.
-
-""", version = scriptID)
-
-parser.add_option('-v', '--vicinity',
-                  dest = 'vicinity',
-                  type = 'int', metavar = 'int',
-                  help = 'voxel distance checked for presence of other microstructure [%default]')
-parser.add_option('-o', '--offset',
-                  dest='offset',
-                  type = 'int', metavar = 'int',
-                  help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index')
-parser.add_option('-t', '--trigger',
-                  dest = 'trigger',
-                  action = 'extend', metavar = '<int LIST>',
-                  help = 'list of microstructure indices triggering a change')
-parser.add_option('-n', '--nonperiodic',
-                  dest = 'mode',
-                  action = 'store_const', const = 'nearest',
-                  help = 'assume geometry to be non-periodic')
-
-parser.set_defaults(vicinity = 1,
-                    trigger  = [],
-                    mode     = 'wrap',
-                   )
-
-(options, filenames) = parser.parse_args()
-
-options.trigger = np.array(options.trigger, dtype=int)
-
-
-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.vicinity_offset(options.vicinity,options.offset,options.trigger,
-                                           True if options.mode is 'wrap' else False))
-    geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
-    geom.to_file(sys.stdout if name is None else name,pack=False)