From 2d2eb4e001f1623487822cff35676c20cb38a9c3 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 7 Nov 2014 11:13:14 +0000 Subject: [PATCH] using extendable option, numpy as np, etc. --- processing/pre/geom_addPrimitive.py | 74 +++++++++++------------------ processing/pre/geom_rescale.py | 74 +++++++++++------------------ 2 files changed, 56 insertions(+), 92 deletions(-) diff --git a/processing/pre/geom_addPrimitive.py b/processing/pre/geom_addPrimitive.py index 00838f704..00bc27785 100755 --- a/processing/pre/geom_addPrimitive.py +++ b/processing/pre/geom_addPrimitive.py @@ -1,34 +1,16 @@ #!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- -import os,sys,string,re,math,numpy +import os,re,sys,math,string +import numpy as np +from optparse import OptionParser import damask -from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP -scriptID = '$Id: geom_addPrimitive.py 3412 2014-08-22 16:58:53Z MPIE\m.diehl $' -scriptName = scriptID.split()[1] +scriptID = string.replace('$Id: geom_pack.py 3679 2014-11-05 22:01:11Z p.eisenlohr $','\n','\\n') +scriptName = scriptID.split()[1][:-3] oversampling = 2. -#-------------------------------------------------------------------------------------------------- -class extendedOption(Option): -#-------------------------------------------------------------------------------------------------- -# used for definition of new option parser action 'extend', which enables to take multiple option arguments -# taken from online tutorial http://docs.python.org/library/optparse.html - - ACTIONS = Option.ACTIONS + ("extend",) - STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) - TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) - ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) - - def take_action(self, action, dest, opt, value, values, parser): - if action == "extend": - lvalue = value.split(",") - values.ensure_value(dest, []).extend(lvalue) - else: - Option.take_action(self, action, dest, opt, value, values, parser) - - #-------------------------------------------------------------------------------------------------- # MAIN #-------------------------------------------------------------------------------------------------- @@ -49,11 +31,11 @@ mappings = { 'microstructures': lambda x: int(x), } -parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ +parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description. Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids. -""" + string.replace(scriptID,'\n','\\n') -) + +""", version = scriptID) parser.add_option('-o', '--origin', '-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3), @@ -80,7 +62,7 @@ parser.set_defaults(center = [0,0,0], if options.angleaxis != []: options.angleaxis = map(float,options.angleaxis) - rotation = damask.Quaternion().fromAngleAxis(numpy.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], + rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], options.angleaxis[1:4]).conjugated() elif options.quaternion != []: options.rotation = map(float,options.rotation) @@ -88,7 +70,7 @@ elif options.quaternion != []: else: rotation = damask.Quaternion().conjugated() -options.center = numpy.array(options.center) +options.center = np.array(options.center) invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system #--- setup file handles -------------------------------------------------------------------------- @@ -118,15 +100,15 @@ for file in files: #--- interpret header ---------------------------------------------------------------------------- info = { - 'grid': numpy.zeros(3,'i'), - 'size': numpy.zeros(3,'d'), - 'origin': numpy.zeros(3,'d'), + 'grid': np.zeros(3,'i'), + 'size': np.zeros(3,'d'), + 'origin': np.zeros(3,'d'), 'homogenization': 0, 'microstructures': 0, } newInfo = { - 'grid': numpy.zeros(3,'i'), - 'origin': numpy.zeros(3,'d'), + 'grid': np.zeros(3,'i'), + 'origin': np.zeros(3,'d'), 'microstructures': 0, } extra_header = [] @@ -152,15 +134,15 @@ for file in files: 'homogenization: %i\n'%info['homogenization'] + \ 'microstructures: %i\n'%info['microstructures']) - if numpy.any(info['grid'] < 1): + if np.any(info['grid'] < 1): file['croak'].write('invalid grid a b c.\n') continue - if numpy.any(info['size'] <= 0.0): + if np.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') continue #--- read data ------------------------------------------------------------------------------------ - microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array + microstructure = np.zeros(info['grid'].prod(),'i') # initialize as flat array i = 0 while table.data_read(): @@ -183,17 +165,17 @@ for file in files: microstructure = microstructure.reshape(info['grid'],order='F') if options.dimension != None: - mask = (numpy.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one - dim = abs(numpy.array(options.dimension)) # dimensions of primitive body - pos = numpy.zeros(3,dtype='float') -# hiresPrimitive = numpy.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution - for i,pos[0] in enumerate(numpy.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)): - for j,pos[1] in enumerate(numpy.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)): - for k,pos[2] in enumerate(numpy.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)): - gridpos = numpy.floor(rotation*pos) # rotate and lock into spacial grid + mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one + dim = abs(np.array(options.dimension)) # dimensions of primitive body + pos = np.zeros(3,dtype='float') +# hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution + for i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)): + for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)): + for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)): + gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid primPos = invRotation*gridpos # rotate back to primitive coordinate system - if numpy.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ - numpy.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box + if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ + np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box microstructure[(gridpos[0]+options.center[0])%info['grid'][0], (gridpos[1]+options.center[1])%info['grid'][1], (gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index 9c7c7bb3e..1af26592d 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.py @@ -1,31 +1,13 @@ #!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- -import os,sys,string,re,math,numpy +import os,sys,string,re,math +import numpy as np +from optparse import OptionParser import damask -from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP - -scriptID = '$Id$' -scriptName = scriptID.split()[1] - -#-------------------------------------------------------------------------------------------------- -class extendedOption(Option): -#-------------------------------------------------------------------------------------------------- -# used for definition of new option parser action 'extend', which enables to take multiple option arguments -# taken from online tutorial http://docs.python.org/library/optparse.html - - ACTIONS = Option.ACTIONS + ("extend",) - STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) - TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) - ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) - - def take_action(self, action, dest, opt, value, values, parser): - if action == "extend": - lvalue = value.split(",") - values.ensure_value(dest, []).extend(lvalue) - else: - Option.take_action(self, action, dest, opt, value, values, parser) +scriptID = string.replace('$Id$','\n','\\n') +scriptName = scriptID.split()[1][:-3] #-------------------------------------------------------------------------------------------------- # MAIN @@ -47,11 +29,11 @@ mappings = { 'microstructures': lambda x: int(x), } -parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ +parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ Scales a geometry description independently in x, y, and z direction in terms of grid and/or size. Either absolute values or relative factors (like "0.25x") can be used. -""" + string.replace(scriptID,'\n','\\n') -) + +""", version = scriptID) parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar = 'string string string', \ help='a,b,c grid of hexahedral box [unchanged]') @@ -93,15 +75,15 @@ for file in files: #--- interpret header ---------------------------------------------------------------------------- info = { - 'grid': numpy.zeros(3,'i'), - 'size': numpy.zeros(3,'d'), - 'origin': numpy.zeros(3,'d'), + 'grid': np.zeros(3,'i'), + 'size': np.zeros(3,'d'), + 'origin': np.zeros(3,'d'), 'homogenization': 0, 'microstructures': 0, } newInfo = { - 'grid': numpy.zeros(3,'i'), - 'size': numpy.zeros(3,'d'), + 'grid': np.zeros(3,'i'), + 'size': np.zeros(3,'d'), 'microstructures': 0, } extra_header = [] @@ -127,15 +109,15 @@ for file in files: 'homogenization: %i\n'%info['homogenization'] + \ 'microstructures: %i\n'%info['microstructures']) - if numpy.any(info['grid'] < 1): + if np.any(info['grid'] < 1): file['croak'].write('invalid grid a b c.\n') continue - if numpy.any(info['size'] <= 0.0): + if np.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') continue #--- read data ------------------------------------------------------------------------------------ - microstructure = numpy.zeros(info['grid'].prod(),'i') + microstructure = np.zeros(info['grid'].prod(),'i') i = 0 table.data_rewind() while table.data_read(): @@ -152,10 +134,10 @@ for file in files: #--- do work ------------------------------------------------------------------------------------ - newInfo['grid'] = numpy.array([{True:round(o*float(n.translate(None,'xX'))), False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i') - newInfo['size'] = numpy.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX')) }[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d') - newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid']) - newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size']) + newInfo['grid'] = np.array([{True:round(o*float(n.translate(None,'xX'))), False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i') + newInfo['size'] = np.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX')) }[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d') + newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid']) + newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size']) multiplicity = [] for j in xrange(3): @@ -167,19 +149,19 @@ for file in files: last = this microstructure = microstructure.reshape(info['grid'],order='F') - microstructure = numpy.repeat( - numpy.repeat( - numpy.repeat(microstructure,multiplicity[0], axis=0), + microstructure = np.repeat( + np.repeat( + np.repeat(microstructure,multiplicity[0], axis=0), multiplicity[1], axis=1), multiplicity[2], axis=2) # --- renumber to sequence 1...Ngrains if requested ------------------------------------------------ -# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array +# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array if options.renumber: newID=0 - for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(newInfo['grid'].prod()))): + for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))): if count != 0: newID+=1 - microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape) + microstructure=np.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape) newInfo['microstructures'] = microstructure.max() @@ -191,10 +173,10 @@ for file in files: if (newInfo['microstructures'] != info['microstructures']): file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) - if numpy.any(newInfo['grid'] < 1): + if np.any(newInfo['grid'] < 1): file['croak'].write('invalid new grid a b c.\n') continue - if numpy.any(newInfo['size'] <= 0.0): + if np.any(newInfo['size'] <= 0.0): file['croak'].write('invalid new size x y z.\n') continue