works for dtype='float'
This commit is contained in:
Martin Diehl
parent
875643c363
commit
fc1f65c34e
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@ -1,9 +1,11 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import os
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import sys
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import numpy as np
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import damask
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from io import StringIO
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from scipy import ndimage
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from optparse import OptionParser
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@ -11,7 +13,8 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def mostFrequent(arr):
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return np.argmax(np.bincount(arr.astype('int')))
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unique, inverse = np.unique(arr, return_inverse=True)
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return unique[np.argmax(np.bincount(inverse))]
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#--------------------------------------------------------------------------------------------------
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@ -29,8 +32,7 @@ parser.add_option('-s','--stencil',
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type = 'int', metavar = 'int',
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help = 'size of smoothing stencil [%default]')
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parser.set_defaults(stencil = 3,
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)
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parser.set_defaults(stencil = 3)
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(options, filenames) = parser.parse_args()
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@ -40,55 +42,23 @@ parser.set_defaults(stencil = 3,
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if filenames == []: filenames = [None]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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buffered = False,
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labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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if name is None:
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virt_file = StringIO(''.join(sys.stdin.read()))
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geom = damask.Geom.from_file(virt_file)
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else:
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geom = damask.Geom.from_file(name)
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microstructure = geom.microstructure
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# --- interpret header ----------------------------------------------------------------------------
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microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,
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size=(options.stencil,)*3).astype(microstructure.dtype)
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.report_geom(info)
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# --- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_')
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newInfo = {'microstructures': len(np.unique(microstructure))}
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# --- report ---------------------------------------------------------------------------------------
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if ( newInfo['microstructures'] != info['microstructures']):
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damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
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info['microstructures'] == newInfo['microstructures']
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# --- write header ---------------------------------------------------------------------------------
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table.info_clear()
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table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:]),])
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table.head_putGeom(info)
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table.info_append([extra_header])
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table.labels_clear()
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
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table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose()
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table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
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# --- output finalization --------------------------------------------------------------------------
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table.close() # close ASCII table
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geom.microstructure = microstructure
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geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
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damask.util.croak(geom)
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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geom.to_file(name)
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@ -1,9 +1,11 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import os
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import sys
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import numpy as np
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from optparse import OptionParser
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from scipy import ndimage
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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@ -27,137 +29,44 @@ parser.add_option('-s', '--size',
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dest = 'size',
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type = 'string', nargs = 3, metavar = 'string string string',
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help = 'x,y,z size of hexahedral box [unchanged]')
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parser.add_option('-r', '--renumber',
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dest = 'renumber',
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action = 'store_true',
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help = 'renumber microstructure indices from 1..N [%default]')
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parser.add_option('--float',
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dest = 'float',
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action = 'store_true',
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help = 'use float input')
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parser.set_defaults(renumber = False,
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grid = ['0','0','0'],
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size = ['0.0','0.0','0.0'],
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float = False,
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)
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(options, filenames) = parser.parse_args()
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datatype = 'f' if options.float else 'i'
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False,
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labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.report_geom(info)
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# --- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'grid': np.zeros(3,'i'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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}
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newInfo['grid'] = np.array([{True: round(o*float(n.lower().replace('x',''))),
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False: round(float(n.lower().replace('x','')))}[n[-1].lower() == 'x']
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for o,n in zip(info['grid'],options.grid)],'i')
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newInfo['size'] = np.array([{True: o*float(n.lower().replace('x','')),
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False: float(n.lower().replace('x',''))}[n[-1].lower() == 'x']
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for o,n in zip(info['size'],options.size)],'d')
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newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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multiplicity = []
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for j in range(3):
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multiplicity.append([])
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last = 0
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for i in range(info['grid'][j]):
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this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j])
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multiplicity[j].append(this-last)
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last = this
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure = np.repeat(np.repeat(np.repeat(microstructure,
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multiplicity[0], axis=0),multiplicity[1], axis=1),multiplicity[2], axis=2)
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# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
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# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
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if options.renumber:
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newID = 0
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for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))):
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if count != 0:
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newID += 1
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microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape)
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newInfo['microstructures'] = len(np.unique(microstructure))
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# --- report ---------------------------------------------------------------------------------------
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remarks = []
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errors = []
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if (any(newInfo['grid'] != info['grid'])):
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remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
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if (any(newInfo['size'] != info['size'])):
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remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
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if ( newInfo['microstructures'] != info['microstructures']):
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remarks.append('--> microstructures: %i'%newInfo['microstructures'])
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if np.any(newInfo['grid'] < 1): errors.append('invalid new grid a b c.')
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if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.')
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# --- write header ---------------------------------------------------------------------------------
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=newInfo['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=newInfo['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
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])
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table.labels_clear()
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
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table.data = microstructure.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
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table.data_writeArray(format,delimiter=' ')
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# --- output finalization --------------------------------------------------------------------------
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if name is None:
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virt_file = StringIO(''.join(sys.stdin.read()))
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geom = damask.Geom.from_file(virt_file)
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else:
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geom = damask.Geom.from_file(name)
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microstructure = geom.microstructure
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table.close() # close ASCII table
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scale = geom.get_grid().astype('float')
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if options.grid is not None:
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for i,g in enumerate(options.grid):
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scale[i] = scale[i]*float(g.lower().replace('x','')) if g.lower().startswith('x') \
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else float(options.grid[i])/scale[i]
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size = geom.get_size()
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if options.size is not None:
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for i,s in enumerate(options.size):
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size[i] = size[i]*float(s.lower().replace('x','')) if s.lower().startswith('x') \
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else options.size[i]
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microstructure = ndimage.interpolation.zoom(microstructure, scale, output=microstructure.dtype,
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order=0, mode='nearest', prefilter=False)
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geom.microstructure = microstructure
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geom.set_size(size)
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geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
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damask.util.croak(geom)
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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geom.to_file(name)
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