better readable
This commit is contained in:
Martin Diehl
parent
fc1f65c34e
commit
94f85b7f33
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@ -1,10 +1,12 @@
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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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import damask
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from io import StringIO
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from optparse import OptionParser
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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@ -12,18 +14,6 @@ scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [geomfile(s)]', description = """
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Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
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@ -63,9 +53,6 @@ parser.add_option( '--realspace', dest='realspace',
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parser.add_option( '--invert', dest='inside',
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action='store_false',
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help = 'invert the volume filled by the primitive (inside/outside)')
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parser.add_option('--float', dest = 'float',
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action = 'store_true',
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help = 'use float input')
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parser.set_defaults(center = (.0,.0,.0),
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fill = 0.0,
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degrees = False,
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@ -73,7 +60,6 @@ parser.set_defaults(center = (.0,.0,.0),
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periodic = True,
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realspace = False,
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inside = True,
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float = False,
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)
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(options, filenames) = parser.parse_args()
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@ -87,8 +73,6 @@ elif options.quaternion is not None:
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else:
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rotation = damask.Rotation()
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datatype = 'f' if options.float else 'i'
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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
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@ -104,39 +88,32 @@ for name in filenames:
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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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# --- loop over input files -------------------------------------------------------------------------
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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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if filenames == []: filenames = [None]
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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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'microstructures': 0,
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}
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for name in filenames:
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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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options.fill = np.nanmax(microstructure)+1 if options.fill == 0 else options.fill
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microstructure = microstructure.reshape(info['grid'],order='F')
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origin = np.zeros(3)
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for i,line in enumerate(geom.comments):
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if line.lower().strip().startswith('origin'):
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origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z)
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# coordinates given in real space (default) vs voxel space
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if options.realspace:
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options.center -= info['origin']
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options.center *= np.array(info['grid']) / np.array(info['size'])
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options.dimension *= np.array(info['grid']) / np.array(info['size'])
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options.center -= origin
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options.center *= geom.get_grid() / geom.get_size()
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options.dimension *= geom.get_grid() / geom.get_size()
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grid = microstructure.shape
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@ -209,35 +186,11 @@ for name in filenames:
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options.fill if options.inside else microstructure,
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microstructure if options.inside else options.fill)
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np.seterr(**old_settings) # Reset warnings to old state
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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: {}'.format(newInfo['microstructures']))
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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 {}\tb {}\tc {}".format(*info['grid']),
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"size\tx {}\ty {}\tz {}".format(*info['size']),
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"origin\tx {}\ty {}\tz {}".format(*info['origin']),
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"homogenization\t{}".format(info['homogenization']),
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"microstructures\t{}".format(newInfo['microstructures']),
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])
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table.labels_clear()
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table.head_write()
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table.output_flush()
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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((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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table.data_writeArray(format,delimiter = ' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()
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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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