84 lines
3.2 KiB
Python
84 lines
3.2 KiB
Python
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#!/usr/bin/env python
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import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Apply filter(s) to Gwyddion data.
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""" + string.replace(scriptID,'\n','\\n')
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)
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for option in ['opening',
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'closing',
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'erosion',
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'dilation',
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'average',
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'median',
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]:
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parser.add_option('-%s'%option[0], '--%s'%option, dest=option, type='int',
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help = 'stencil size for %s filter'%option)
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parser.set_default(option, 0)
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(options, filenames) = parser.parse_args()
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# ------------------------------------------ read Gwyddion data ---------------------------------------
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for file in filenames:
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filters = ''
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header = []
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with open(file,'r') as f:
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for line in f:
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pieces = line.split()
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if pieces[0] != '#': break
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if pieces[1] == 'Width:': width = float(pieces[2])
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if pieces[1] == 'Height:': height = float(pieces[2])
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header.append(line.lstrip('#').strip())
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elevation = numpy.loadtxt(file)#*1e6
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if options.opening > 0:
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elevation = scipy.ndimage.morphology.grey_opening(elevation,options.opening)
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filters += '_opening%i'%options.opening
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if options.closing > 0:
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elevation = scipy.ndimage.morphology.grey_closing(elevation,options.closing)
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filters += '_closing%i'%options.closing
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if options.erosion > 0:
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elevation = scipy.ndimage.morphology.grey_erosion(elevation,options.erosion)
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filters += '_erosion%i'%options.erosion
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if options.dilation > 0:
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elevation = scipy.ndimage.morphology.grey_dilation(elevation,options.dilation)
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filters += '_dilation%i'%options.dilation
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if options.average > 0:
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elevation = scipy.ndimage.filters.uniform_filter(elevation,options.average)
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filters += '_avg%i'%options.average
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if options.median > 0:
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elevation = scipy.ndimage.filters.median_filter(elevation,options.median)
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filters += '_median%i'%options.median
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numpy.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))
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