Generate PNG image from scalar data on grid deformed by (periodic) deformation gradient.
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Philip Eisenlohr
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string
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import numpy as np
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from optparse import OptionParser
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from PIL import Image, ImageDraw
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import damask
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scriptID = string.replace('$Id: imageDataDeformed.py 4188 2015-05-20 23:21:35Z p.eisenlohr $','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Generate PNG image from scalar data on grid deformed by (periodic) deformation gradient.
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""", version = scriptID)
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parser.add_option('-l','--label', dest='label', type='string', metavar='string',
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help='column containing data)')
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parser.add_option('-r','--range', dest='range', type='float', nargs=2, metavar='float float',
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help='data range (min max) [auto]')
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parser.add_option('--color', dest='color', type='string', metavar='string',
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help='color scheme')
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parser.add_option('--invert', dest='invert', action='store_true',
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help='invert color scheme')
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parser.add_option('--abs', dest='abs', action='store_true',
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help='magnitude of values')
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parser.add_option('--log', dest='log', action='store_true',
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help='log10 of values')
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parser.add_option('-d','--dimension', dest='dimension', type='int', nargs=3, metavar=' '.join(['int']*3),
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help='data dimension (x/y/z)')
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parser.add_option('-s','--size', dest='size', type='float', nargs=3, metavar=' '.join(['float']*3),
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help='box size (x/y/z)')
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parser.add_option('-f','--defgrad', dest='defgrad', metavar='string',
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help='column label of deformation gradient [%default]')
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parser.add_option('--scaling', dest='scaling', type='float', nargs=3, metavar = ' '.join(['float']*3),
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help='x/y/z scaling of displacment fluctuation [%default]')
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parser.add_option('-z','--layer', dest='z', type='int', metavar='int',
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help='index of z plane to plot [%default]')
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parser.add_option('--fliplr', dest='flipLR', action='store_true',
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help='flip around vertical axis')
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parser.add_option('--flipud', dest='flipUD', action='store_true',
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help='flip around horizontal axis')
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parser.add_option('--crop', dest='crop', type='int', nargs=4, metavar=' '.join(['int']*3),
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help='pixels cropped on left, right, top, bottom')
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parser.add_option('--show', dest='show', action='store_true',
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help='show resulting image')
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parser.add_option('-N','--pixelsize', dest='pixelsize', type='int', metavar='int',
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help='pixels per cell edge')
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parser.set_defaults(label = None,
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range = [0.0,0.0],
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dimension = [],
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size = [],
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z = 1,
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abs = False,
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log = False,
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defgrad = 'f',
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scaling = [1.,1.,1.],
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flipLR = False,
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flipUD = False,
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color = "gray",
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invert = False,
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crop = [0,0,0,0],
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pixelsize = 1,
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show = False,
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)
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(options,filenames) = parser.parse_args()
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options.size = np.array(options.size)
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options.dimension = np.array(options.dimension)
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options.range = np.array(options.range)
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if options.z > 0: options.z -= 1 # adjust to 0-based indexing
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# --- color palette ---------------------------------------------------------------------------------
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theMap = damask.Colormap(predefined=options.color)
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if options.invert: theMap = theMap.invert()
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theColors = np.uint8(np.array(theMap.export(format='list',steps=256))*255)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []:
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filenames = ['STDIN']
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for name in filenames:
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if name == 'STDIN':
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file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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else:
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if not os.path.exists(name): continue
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file = {'name':name,
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'input':open(name),
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'output':open(os.path.splitext(name)[0]+ \
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('' if options.label == None else '_'+options.label)+ \
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'.png','w'),
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'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],
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buffered = False, # make unbuffered ASCII_table
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labels = options.label != None) # no labels when taking 2D dataset
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table.head_read() # read ASCII header info
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# --------------- figure out columns to process ---------------------------------------------------
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errors = []
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if table.label_dimension(options.label) != 1:
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errors.append('no scalar data (%s) found...'%options.label)
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if table.label_dimension(options.defgrad) != 9:
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errors.append('no deformation gradient tensor (1..9_%s) found...'%options.defgrad)
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if errors != []:
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file['croak'].write('\n'.join(errors)+'\n')
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table.close(dismiss = True)
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continue
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table.data_readArray([options.label,options.defgrad])
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F = table.data[:,1:10].transpose().reshape([3,3]+list(options.dimension),order='F')
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data = table.data[:,0 ].transpose().reshape( list(options.dimension),order='F')
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if options.abs: data = np.abs(data)
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if options.log: data = np.log10(data)
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if np.all(options.range == 0.0): options.range = np.array([data.min(),data.max()])
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elif options.log: options.range = np.log10(options.range)
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data = ( data - options.range.min()) / \
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(options.range.max() - options.range.min()) # data scaled to fraction of range
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data = np.clip(data,0.0,1.0) # cut off outliers (should be none)
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# ---------------- calculate coordinates -----------------------------------------------------------
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Favg = damask.core.math.tensorAvg(F)
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centroids = damask.core.mesh.deformedCoordsFFT(options.size,F,Favg,options.scaling)
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nodes = damask.core.mesh.nodesAroundCentres(options.size,Favg,centroids)
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boundingBox = np.array([ \
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[np.amin(nodes[0,:,:,options.z]),np.amin(nodes[1,:,:,options.z]),np.amin(nodes[2,:,:,options.z])],
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[np.amax(nodes[0,:,:,options.z]),np.amax(nodes[1,:,:,options.z]),np.amax(nodes[2,:,:,options.z])],
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]) # find x-y bounding box for given z layer
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nodes -= boundingBox[0].repeat(np.prod(options.dimension+1)).reshape([3]+list(options.dimension+1))
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nodes *= (options.pixelsize*options.dimension/options.size).repeat(np.prod(options.dimension+1)).reshape([3]+list(options.dimension+1))
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imagesize = (options.pixelsize*(boundingBox[1]-boundingBox[0])*options.dimension\
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/options.size)[:2].astype('i') # determine image size from number of cells in overall bounding box
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im = Image.new('RGBA',imagesize)
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draw = ImageDraw.Draw(im)
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for y in xrange(options.dimension[1]):
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for x in xrange(options.dimension[0]):
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draw.polygon([nodes[0,x ,y ,options.z],
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nodes[1,x ,y ,options.z],
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nodes[0,x+1,y ,options.z],
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nodes[1,x+1,y ,options.z],
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nodes[0,x+1,y+1,options.z],
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nodes[1,x+1,y+1,options.z],
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nodes[0,x ,y+1,options.z],
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nodes[1,x ,y+1,options.z],
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],
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fill = tuple(theColors[int(255*data[x,y,options.z])]),
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outline = None)
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# if options.flipLR: table.data = np.fliplr(table.data)
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# if options.flipUD: table.data = np.flipud(table.data)
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# (height,width,bands) = table.data.shape
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# im = Image.fromarray(table.data.astype('uint8'), 'RGB').\
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# crop(( options.crop[0],
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# options.crop[2],
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# width -options.crop[1],
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# height-options.crop[3]))
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# ------------------------------------------ output result -----------------------------------------
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im.save(file['output'],format = "PNG")
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if options.show: im.show()
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table.close() # close ASCII table file handles
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