Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
This commit is contained in:
Martin Diehl
commit
e20623845a
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@ -995,11 +995,17 @@ class Orientation:
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relationModel,
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direction,
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targetSymmetry = None):
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"""
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orientation relationship
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positive number: fcc --> bcc
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negative number: bcc --> fcc
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"""
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if relationModel not in ['KS','GT','GTdash','NW','Pitsch','Bain']: return None
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if int(direction) == 0: return None
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# KS from S. Morito et al./Journal of Alloys and Compounds 5775 (2013) S587-S592 DOES THIS PAPER EXISTS?
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# KS from S. Morito et al./Journal of Alloys and Compounds 5775 (2013) S587-S592
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# for KS rotation matrices also check K. Kitahara et al./Acta Materialia 54 (2006) 1279-1288
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# GT from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81
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# GT' from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81
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# NW from H. Kitahara et al./Materials Characterization 54 (2005) 378-386
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@ -1226,14 +1232,14 @@ class Orientation:
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myPlane /= np.linalg.norm(myPlane)
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myNormal = [float(i) for i in normals[relationModel][variant,me]] # map(float, planes[...]) does not work in python 3
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myNormal /= np.linalg.norm(myNormal)
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myMatrix = np.array([myPlane,myNormal,np.cross(myPlane,myNormal)])
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myMatrix = np.array([myNormal,np.cross(myPlane,myNormal),myPlane]).T
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otherPlane = [float(i) for i in planes[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3
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otherPlane /= np.linalg.norm(otherPlane)
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otherNormal = [float(i) for i in normals[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3
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otherNormal /= np.linalg.norm(otherNormal)
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otherMatrix = np.array([otherPlane,otherNormal,np.cross(otherPlane,otherNormal)])
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otherMatrix = np.array([otherNormal,np.cross(otherPlane,otherNormal),otherPlane]).T
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rot=np.dot(otherMatrix.T,myMatrix)
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rot=np.dot(otherMatrix,myMatrix.T)
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return Orientation(matrix=np.dot(rot,self.asMatrix())) # no symmetry information ??
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@ -0,0 +1,74 @@
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,h5py
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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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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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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 [geomfile[s]]', description = """
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Convert DREAM3D file to ASCIItable
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""", version = scriptID)
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(options, filenames) = parser.parse_args()
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rootDir ='DataContainers/ImageDataContainer'
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: parser.error('no input file specified.')
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for name in filenames:
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try:
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table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt',
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buffered = False
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)
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except: continue
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damask.util.report(scriptName,name)
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inFile = h5py.File(name, 'r')
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grid = inFile[rootDir+'/_SIMPL_GEOMETRY/DIMENSIONS'][...]
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# --- read comments --------------------------------------------------------------------------------
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coords = (np.mgrid[0:grid[2], 0:grid[1], 0: grid[0]]).reshape(3, -1).T
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coords = (np.fliplr(coords)*inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...] \
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+ inFile[rootDir+'/_SIMPL_GEOMETRY/ORIGIN'][...] \
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+ inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...]*0.5)
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table.data = np.hstack( (coords,
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inFile[rootDir+'/CellData/EulerAngles'][...].reshape(grid.prod(),3),
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inFile[rootDir+'/CellData/Phases'][...].reshape(grid.prod(),1),
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inFile[rootDir+'/CellData/Confidence Index'][...].reshape(grid.prod(),1),
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inFile[rootDir+'/CellData/Fit'][...].reshape(grid.prod(),1),
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inFile[rootDir+'/CellData/Image Quality'][...].reshape(grid.prod(),1)))
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labels = ['1_pos','2_pos','3_pos',
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'1_Euler','2_Euler','3_Euler',
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'PhaseID','CI','Fit','IQ']
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try:
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table.data = np.hstack((table.data, inFile[rootDir+'/CellData/FeatureIds'][...].reshape(grid.prod(),1)))
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labels.append(['FeatureID'])
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except Exception:
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pass
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_clear()
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table.labels_append(labels,reset = True)
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table.head_write()
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# ------------------------------------------ finalize output ---------------------------------------
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table.data_writeArray() #(fmt='%e2.2')
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table.close()
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@ -89,9 +89,9 @@ for name in filenames:
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# Calculates gaussian weights for simulating 3d diffusion
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gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5)
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gauss[:,:,grid[2]/2::] = gauss[:,:,round(grid[2]/2.)-1::-1] # trying to cope with uneven (odd) grid size
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gauss[:,grid[1]/2::,:] = gauss[:,round(grid[1]/2.)-1::-1,:]
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gauss[grid[0]/2::,:,:] = gauss[round(grid[0]/2.)-1::-1,:,:]
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gauss[:,:,grid[2]/2::] = gauss[:,:,int(round(grid[2]/2.))-1::-1] # trying to cope with uneven (odd) grid size
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gauss[:,grid[1]/2::,:] = gauss[:,int(round(grid[1]/2.))-1::-1,:]
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gauss[grid[0]/2::,:,:] = gauss[int(round(grid[0]/2.))-1::-1,:,:]
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gauss = np.fft.rfftn(gauss)
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interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 #1.0 if A & B are distinct & nonzero, 0.0 otherwise
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@ -0,0 +1,117 @@
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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import damask
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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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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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validDirections = ['x','y','z']
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Mirrors spectral geometry description along given directions.
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""", version=scriptID)
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parser.add_option('-d','--direction',
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dest = 'directions',
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action = 'extend', metavar = '<string LIST>',
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help = "directions in which to mirror {'x','y','z'}")
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(options, filenames) = parser.parse_args()
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if options.directions is None:
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parser.error('no direction given.')
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if not set(options.directions).issubset(validDirections):
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invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
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parser.error('invalid directions {}. '.format(*invalidDirections))
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# --- loop over input files -------------------------------------------------------------------------
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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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buffered = False, labeled = False)
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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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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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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']).reshape(info['grid'],order='F') # read microstructure
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if 'z' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
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if 'y' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[:,::-1,:]],1)
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if 'x' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[::-1,:,:]],0)
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'size': microstructure.shape*info['size']/info['grid'],
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'grid': microstructure.shape,
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}
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# --- report ---------------------------------------------------------------------------------------
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remarks = []
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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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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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if remarks != []: damask.util.croak(remarks)
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# --- write header ---------------------------------------------------------------------------------
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table.labels_clear()
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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=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
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extra_header
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])
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
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# --- output finalization --------------------------------------------------------------------------
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table.close() # close ASCII table
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