From 420abfa162306ee7108c8c5230a2cb10a047f6b9 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 24 May 2019 22:31:34 +0200 Subject: [PATCH] use new class --- processing/pre/geom_fromMinimalSurface.py | 63 +++---------- processing/pre/geom_rotate.py | 110 ++++++---------------- python/damask/geom.py | 4 +- 3 files changed, 48 insertions(+), 129 deletions(-) diff --git a/processing/pre/geom_fromMinimalSurface.py b/processing/pre/geom_fromMinimalSurface.py index e0023e7ec..66e26c8e2 100755 --- a/processing/pre/geom_fromMinimalSurface.py +++ b/processing/pre/geom_fromMinimalSurface.py @@ -1,7 +1,9 @@ #!/usr/bin/env python3 # -*- coding: UTF-8 no BOM -*- -import os,sys,math +import os +import sys +import math import numpy as np from optparse import OptionParser import damask @@ -71,60 +73,25 @@ parser.set_defaults(type = minimal_surfaces[0], if filenames == []: filenames = [None] for name in filenames: - try: - table = damask.ASCIItable(outname = name, - buffered = False, labeled = False) - except: continue + damask.util.report(scriptName,name) - -# ------------------------------------------ make grid ------------------------------------- - - info = { - 'grid': np.array(options.grid), - 'size': np.array(options.size), - 'origin': np.zeros(3,'d'), - 'microstructures': max(options.microstructure), - 'homogenization': options.homogenization - } - -#--- report --------------------------------------------------------------------------------------- - - damask.util.report_geom(info) - - errors = [] - if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') - if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.') - if errors != []: - damask.util.croak(errors) - table.close(dismiss = True) - continue - -#--- write header --------------------------------------------------------------------------------- - - table.labels_clear() - table.info_clear() - table.info_append([ - scriptID + ' ' + ' '.join(sys.argv[1:]), - "grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']), - "size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']), - "origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']), - "homogenization\t{homog}".format(homog=info['homogenization']), - "microstructures\t{microstructures}".format(microstructures=info['microstructures']), - ]) - table.head_write() - -#--- write data ----------------------------------------------------------------------------------- - X = options.periods*2.0*math.pi*(np.arange(options.grid[0])+0.5)/options.grid[0] Y = options.periods*2.0*math.pi*(np.arange(options.grid[1])+0.5)/options.grid[1] Z = options.periods*2.0*math.pi*(np.arange(options.grid[2])+0.5)/options.grid[2] + microstructure = np.empty(options.grid,dtype='int') for z in range(options.grid[2]): for y in range(options.grid[1]): - table.data_clear() for x in range(options.grid[0]): - table.data_append(options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])]) - table.data_write() + microstructure[x,y,z]=options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])] + + geom=damask.Geom(options.size,microstructure,options.homogenization, + comments=[scriptID + ' ' + ' '.join(sys.argv[1:])]) - table.close() + damask.util.croak('\n'.join(geom.info())) + + if name is None: + sys.stdout.write(str(geom)) + else: + geom.to_file(name) diff --git a/processing/pre/geom_rotate.py b/processing/pre/geom_rotate.py index 7cce5800d..57f4eacbf 100755 --- a/processing/pre/geom_rotate.py +++ b/processing/pre/geom_rotate.py @@ -1,9 +1,11 @@ #!/usr/bin/env python3 # -*- coding: UTF-8 no BOM -*- -import os,sys,math +import os +import sys import numpy as np import damask +from io import StringIO from scipy import ndimage from optparse import OptionParser @@ -42,15 +44,9 @@ parser.add_option('-q', '--quaternion', parser.add_option('-f', '--fill', dest = 'fill', type = 'int', metavar = 'int', - help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]') -parser.add_option('--float', - dest = 'float', - action = 'store_true', - help = 'use float input') + help = 'background grain index, defaults to max + 1') parser.set_defaults(degrees = False, - fill = 0, - float = False, ) (options, filenames) = parser.parse_args() @@ -67,82 +63,38 @@ if options.matrix is not None: if options.eulers is not None: eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True) -datatype = 'f' if options.float else 'i' - # --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: - try: - table = damask.ASCIItable(name = name, - buffered = False, - labeled = False) - except: continue + if name is None: + virt_file = StringIO(''.join(sys.stdin.read())) + geom = damask.Geom.from_file(virt_file) + else: + try: # really needed? Why not simply fail if file does not exists etc. + geom = damask.Geom.from_file(name) + except: continue damask.util.report(scriptName,name) -# --- interpret header ---------------------------------------------------------------------------- + microstructure = geom.microstructure + spacing = geom.get_size()/geom.get_grid() - table.head_read() - info,extra_header = table.head_getGeom() - damask.util.report_geom(info) - - errors = [] - if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') - if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.') - if errors != []: - damask.util.croak(errors) - table.close(dismiss = True) - continue - -# --- read data ------------------------------------------------------------------------------------ - - microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F') # read microstructure - - newGrainID = options.fill if options.fill != 0 else np.nanmax(microstructure)+1 - microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z - microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around X - microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z - -# --- do work ------------------------------------------------------------------------------------ - - newInfo = { - 'size': microstructure.shape*info['size']/info['grid'], - 'grid': microstructure.shape, - 'microstructures': len(np.unique(microstructure)), - } - -# --- report --------------------------------------------------------------------------------------- - - remarks = [] - if (any(newInfo['grid'] != info['grid'])): - remarks.append('--> grid a b c: {}'.format(' x '.join(map(str,newInfo['grid'])))) - if (any(newInfo['size'] != info['size'])): - remarks.append('--> size x y z: {}'.format(' x '.join(map(str,newInfo['size'])))) - if ( newInfo['microstructures'] != info['microstructures']): - remarks.append('--> microstructures: {}'.format(newInfo['microstructures'])) - if remarks != []: damask.util.croak(remarks) - -# --- write header --------------------------------------------------------------------------------- - - table.labels_clear() - table.info_clear() - table.info_append(extra_header+[ - scriptID + ' ' + ' '.join(sys.argv[1:]), - "grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=newInfo['grid']), - "size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=newInfo['size']), - "origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']), - "homogenization\t{homog}".format(homog=info['homogenization']), - "microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']), - ]) - table.head_write() - -# --- write microstructure information ------------------------------------------------------------ - - format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1))) - table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose() - table.data_writeArray(format,delimiter=' ') - -# --- output finalization -------------------------------------------------------------------------- - - table.close() # close ASCII table + newGrainID = options.fill if options.fill is not None else np.nanmax(microstructure)+1 + microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0, + prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z + microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0, + prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around X + microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0, + prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z + + geom.microstructure = microstructure + geom.set_size(microstructure.shape*spacing) + geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + + damask.util.croak('\n'.join(geom.info())) + + if name is None: + sys.stdout.write(str(geom)) + else: + geom.to_file(name) diff --git a/python/damask/geom.py b/python/damask/geom.py index c1a119ca0..0f411458f 100644 --- a/python/damask/geom.py +++ b/python/damask/geom.py @@ -4,10 +4,9 @@ from io import StringIO import io class Geom(): + """Geometry definition for grid solvers""" def __init__(self,size,microstructure,homogenization=1,comments=[]): - """Geometry definition for grid solvers""" - if len(size) != 3 or any(np.array(size)<=0): raise ValueError('invalid size') else: @@ -29,6 +28,7 @@ class Geom(): self.comments = [str(comment) for comment in comments] def __repr__(self): + """Readable string""" f=StringIO() self.to_file(f) f.seek(0)