diff --git a/processing/pre/geom_clean.py b/processing/pre/geom_clean.py index 1d0769ab3..a4027efa0 100755 --- a/processing/pre/geom_clean.py +++ b/processing/pre/geom_clean.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 @@ -11,7 +13,8 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) def mostFrequent(arr): - return np.argmax(np.bincount(arr.astype('int'))) + unique, inverse = np.unique(arr, return_inverse=True) + return unique[np.argmax(np.bincount(inverse))] #-------------------------------------------------------------------------------------------------- @@ -29,8 +32,7 @@ parser.add_option('-s','--stencil', type = 'int', metavar = 'int', help = 'size of smoothing stencil [%default]') -parser.set_defaults(stencil = 3, - ) +parser.set_defaults(stencil = 3) (options, filenames) = parser.parse_args() @@ -40,55 +42,23 @@ parser.set_defaults(stencil = 3, if filenames == []: filenames = [None] for name in filenames: - try: table = damask.ASCIItable(name = name, - buffered = False, - labeled = False) - except: continue damask.util.report(scriptName,name) + + if name is None: + virt_file = StringIO(''.join(sys.stdin.read())) + geom = damask.Geom.from_file(virt_file) + else: + geom = damask.Geom.from_file(name) + microstructure = geom.microstructure -# --- interpret header ---------------------------------------------------------------------------- + microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent, + size=(options.stencil,)*3).astype(microstructure.dtype) - 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']).reshape(info['grid'],order='F') # read microstructure - -# --- do work ------------------------------------------------------------------------------------ - - microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_') - newInfo = {'microstructures': len(np.unique(microstructure))} - -# --- report --------------------------------------------------------------------------------------- - if ( newInfo['microstructures'] != info['microstructures']): - damask.util.croak('--> microstructures: %i'%newInfo['microstructures']) - info['microstructures'] == newInfo['microstructures'] - -# --- write header --------------------------------------------------------------------------------- - - table.info_clear() - table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:]),]) - table.head_putGeom(info) - table.info_append([extra_header]) - table.labels_clear() - table.head_write() - -# --- write microstructure information ------------------------------------------------------------ - - formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1)) - table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose() - table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ') - -# --- output finalization -------------------------------------------------------------------------- - - table.close() # close ASCII table + geom.microstructure = microstructure + geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + + damask.util.croak(geom) + if name is None: + sys.stdout.write(str(geom.show())) + else: + geom.to_file(name) diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index 4a14c0050..48d26e8f5 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.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 from optparse import OptionParser +from scipy import ndimage import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] @@ -27,137 +29,44 @@ parser.add_option('-s', '--size', dest = 'size', type = 'string', nargs = 3, metavar = 'string string string', help = 'x,y,z size of hexahedral box [unchanged]') -parser.add_option('-r', '--renumber', - dest = 'renumber', - action = 'store_true', - help = 'renumber microstructure indices from 1..N [%default]') -parser.add_option('--float', - dest = 'float', - action = 'store_true', - help = 'use float input') - -parser.set_defaults(renumber = False, - grid = ['0','0','0'], - size = ['0.0','0.0','0.0'], - float = False, - ) (options, filenames) = parser.parse_args() -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 damask.util.report(scriptName,name) - -# --- interpret header ---------------------------------------------------------------------------- - - 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) # read microstructure - -# --- do work ------------------------------------------------------------------------------------ - - newInfo = { - 'grid': np.zeros(3,'i'), - 'origin': np.zeros(3,'d'), - 'microstructures': 0, - } - - newInfo['grid'] = np.array([{True: round(o*float(n.lower().replace('x',''))), - False: round(float(n.lower().replace('x','')))}[n[-1].lower() == 'x'] - for o,n in zip(info['grid'],options.grid)],'i') - newInfo['size'] = np.array([{True: o*float(n.lower().replace('x','')), - False: float(n.lower().replace('x',''))}[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 range(3): - multiplicity.append([]) - last = 0 - for i in range(info['grid'][j]): - this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j]) - multiplicity[j].append(this-last) - last = this - - microstructure = microstructure.reshape(info['grid'],order='F') - 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/np-frequency-counts-for-unique-values-in-an-array - - if options.renumber: - newID = 0 - for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))): - if count != 0: - newID += 1 - microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape) - - newInfo['microstructures'] = len(np.unique(microstructure)) - -# --- report --------------------------------------------------------------------------------------- - - remarks = [] - errors = [] - - if (any(newInfo['grid'] != info['grid'])): - remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid'])))) - if (any(newInfo['size'] != info['size'])): - remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size'])))) - if ( newInfo['microstructures'] != info['microstructures']): - remarks.append('--> microstructures: %i'%newInfo['microstructures']) - - if np.any(newInfo['grid'] < 1): errors.append('invalid new grid a b c.') - if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.') - - if remarks != []: damask.util.croak(remarks) - if errors != []: - damask.util.croak(errors) - table.close(dismiss = True) - continue - -# --- write header --------------------------------------------------------------------------------- - - 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.labels_clear() - 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],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose() - table.data_writeArray(format,delimiter=' ') -# --- output finalization -------------------------------------------------------------------------- + if name is None: + virt_file = StringIO(''.join(sys.stdin.read())) + geom = damask.Geom.from_file(virt_file) + else: + geom = damask.Geom.from_file(name) + microstructure = geom.microstructure - table.close() # close ASCII table + scale = geom.get_grid().astype('float') + if options.grid is not None: + for i,g in enumerate(options.grid): + scale[i] = scale[i]*float(g.lower().replace('x','')) if g.lower().startswith('x') \ + else float(options.grid[i])/scale[i] + + size = geom.get_size() + if options.size is not None: + for i,s in enumerate(options.size): + size[i] = size[i]*float(s.lower().replace('x','')) if s.lower().startswith('x') \ + else options.size[i] + + microstructure = ndimage.interpolation.zoom(microstructure, scale, output=microstructure.dtype, + order=0, mode='nearest', prefilter=False) + + geom.microstructure = microstructure + geom.set_size(size) + geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + + damask.util.croak(geom) + if name is None: + sys.stdout.write(str(geom.show())) + else: + geom.to_file(name)