Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Martin Diehl
commit
33391fcf5b
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@ -53,6 +53,20 @@ def report(who,what):
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"""reports script and file name"""
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croak( (emph(who) if who else '') + (': '+what if what else '') )
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# -----------------------------
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def report_geom(info,
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what = ['grid','size','origin','homogenization','microstructures']):
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"""reports (selected) geometry information"""
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output = {
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'grid' : 'grid a b c: {}'.format(' x '.join(map(str,info['grid' ]))),
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'size' : 'size x y z: {}'.format(' x '.join(map(str,info['size' ]))),
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'origin' : 'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
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'homogenization' : 'homogenization: {}'.format(info['homogenization']),
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'microstructures' : 'microstructures: {}'.format(info['microstructures']),
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}
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for item in what: croak(output[item.lower()])
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# -----------------------------
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def emph(what):
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"""emphasizes string on screen"""
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@ -15,25 +15,29 @@ scriptID = ' '.join([scriptName,damask.version])
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Changes the (three-dimensional) canvas of a spectral geometry description.
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Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
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""", version = scriptID)
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parser.add_option('-g', '--grid',
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parser.add_option('-g',
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'--grid',
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dest = 'grid',
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type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
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help = 'a,b,c grid of hexahedral box [auto]')
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parser.add_option('-o', '--offset',
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help = 'a,b,c grid of hexahedral box. [auto]')
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parser.add_option('-o',
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'--offset',
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dest = 'offset',
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type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
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help = 'a,b,c offset from old to new origin of grid [%default]')
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parser.add_option('-f', '--fill',
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parser.add_option('-f',
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'--fill',
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dest = 'fill',
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type = 'float', metavar = 'float',
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help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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parser.add_option('--float',
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dest = 'real',
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action = 'store_true',
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help = 'input data is float [%default]')
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help = 'use float input')
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parser.set_defaults(grid = ['0','0','0'],
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offset = (0,0,0),
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@ -61,13 +65,7 @@ for name in filenames:
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
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'size x y z: %s'%(' x '.join(map(str,info['size']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i'%info['microstructures'],
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])
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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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@ -105,7 +103,7 @@ for name in filenames:
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translate_y = [i - options.offset[1] for i in yindex]
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translate_z = [i - options.offset[2] for i in zindex]
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if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]):
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damask.util.croak('Invaldid grid-offset comination')
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damask.util.croak('invaldid grid-offset combination.')
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table.close(dismiss = True)
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continue
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microstructure_cropped[min(translate_x):(max(translate_x)+1),\
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@ -125,13 +123,13 @@ for name in filenames:
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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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remarks.append('--> grid a b c: {}'.format(' 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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remarks.append('--> size x y z: {}'.format(' x '.join(map(str,newInfo['size']))))
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if (any(newInfo['origin'] != info['origin'])):
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remarks.append('--> origin x y z: %s'%(' : '.join(map(str,newInfo['origin']))))
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remarks.append('--> origin x y z: {}'.format(' : '.join(map(str,newInfo['origin']))))
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if ( newInfo['microstructures'] != info['microstructures']):
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remarks.append('--> microstructures: %i'%newInfo['microstructures'])
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remarks.append('--> microstructures: {}'.format(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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@ -147,11 +145,11 @@ for name in filenames:
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table.info_clear()
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table.info_append([
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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=newInfo['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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"grid\ta {}\tb {}\tc {}".format(*newInfo['grid']),
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"size\tx {}\ty {}\tz {}".format(*newInfo['size']),
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"origin\tx {}\ty {}\tz {}".format(*newInfo['origin']),
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"homogenization\t{}".format(info['homogenization']),
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"microstructures\t{}".format(newInfo['microstructures']),
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extra_header
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])
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table.labels_clear()
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@ -296,13 +296,10 @@ for name in filenames:
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if info['homogenization'] == 0: info['homogenization'] = options.homogenization
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damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
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'size x y z: {}'.format(' x '.join(map(str,info['size']))),
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'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
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'homogenization: {}'.format(info['homogenization']),
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'microstructures: {}{}'.format(info['microstructures'],
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damask.util.report_geom(info,['grid','size','origin','homogenization',])
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damask.util.croak(['microstructures: {}{}'.format(info['microstructures'],
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(' out of {}'.format(NgrainIDs) if NgrainIDs != info['microstructures'] else '')),
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])
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])
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config_header = []
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formatwidth = 1+int(math.log10(NgrainIDs))
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@ -23,29 +23,38 @@ Examples:
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""", version = scriptID)
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parser.add_option('-p', '--positions',
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dest = 'pos',
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type = 'string', metavar = 'string',
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help = 'coordinate label [%default]')
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parser.add_option('-p',
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'--pos', '--seedposition',
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dest = 'pos',
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type = 'string', metavar = 'string',
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help = 'label of coordinates [%default]')
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parser.add_option('--boundingbox',
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dest = 'box',
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type = 'float', nargs = 6, metavar = ' '.join(['float']*6),
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help = 'min (x,y,z) and max (x,y,z) coordinates of bounding box [tight]')
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parser.add_option('-i', '--index',
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dest = 'index',
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parser.add_option('-m',
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'--microstructure',
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dest = 'microstructure',
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type = 'string', metavar = 'string',
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help = 'microstructure index label [%default]')
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parser.add_option('-w','--white',
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help = 'label of microstructures [%default]')
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parser.add_option('--weight',
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dest = 'weight',
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type = 'string', metavar = 'string',
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help = 'label of weights [%default]')
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parser.add_option('-w',
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'--white',
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dest = 'whitelist',
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action = 'extend', metavar = '<int LIST>',
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help = 'whitelist of microstructure indices')
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parser.add_option('-b','--black',
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parser.add_option('-b',
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'--black',
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dest = 'blacklist',
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action = 'extend', metavar = '<int LIST>',
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help = 'blacklist of microstructure indices')
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parser.set_defaults(pos = 'pos',
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index ='microstructure',
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parser.set_defaults(pos = 'pos',
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microstructure = 'microstructure',
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weight = None,
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)
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(options,filenames) = parser.parse_args()
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@ -58,10 +67,9 @@ if options.blacklist is not None: options.blacklist = map(int,options.blacklist)
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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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outname = os.path.splitext(name)[0]+'.seeds' if name else name,
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buffered = False)
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try: table = damask.ASCIItable(name = name,
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outname = os.path.splitext(name)[0]+'.seeds' if name else name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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@ -69,14 +77,17 @@ for name in filenames:
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# ------------------------------------------ sanity checks ---------------------------------------
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missing_labels = table.data_readArray([options.pos,options.index])
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missing_labels = table.data_readArray([options.pos,options.microstructure] +
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([options.weight] if options.weight else []))
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errors = []
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if len(missing_labels) > 0:
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errors.append('column{} {} not found'.format('s' if len(missing_labels) > 1 else '',
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', '.join(missing_labels)))
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for label, dim in {options.pos: 3,
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options.index: 1}.iteritems():
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input = {options.pos: 3,
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options.microstructure: 1,}
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if options.weight: input.update({options.weight: 1})
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for label, dim in input.iteritems():
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if table.label_dimension(label) != dim:
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errors.append('column {} has wrong dimension'.format(label))
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@ -113,11 +124,12 @@ for name in filenames:
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table.info = [
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scriptID,
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'size %s'%(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
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'size {}'.format(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
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map(str,boundingBox[1,:]-boundingBox[0,:])))))),
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]
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table.labels_clear()
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table.labels_append(['1_pos','2_pos','3_pos','microstructure']) # implicitly switching label processing/writing on
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table.labels_append(['1_pos','2_pos','3_pos','microstructure'] +
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['weight'] if options.weight else []) # implicitly switching label processing/writing on
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table.head_write()
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# ------------------------------------------ output result ---------------------------------------
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