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| v00.00.00, 2012-04-16 -- pre-init dev beta | ||
| v00.00.01, 2016-06-27 -- AFRL commmit |
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| include *.txt | ||
| recursive-include docs *.txt |
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| # Cryspy: Computational Crystallography in Python: *A Python Toolbox for (some, specialized) EBSD Data Analyses* | ||
|
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||
| Cryspy is a toolbox for computational crystallography in Python. | ||
| It intends to provide a set of open source tools for | ||
| visualization, analysis, and postprocessing of EBSD data. | ||
|
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||
| ## COMPONENTS | ||
|
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| * io : modules for import and export of EBSD data | ||
| * rot : modules for rotation representation, manipulation, and conversion | ||
| * vis : modules for data visualization | ||
| * ebsd : modules for EBSD data analysis and manipulation | ||
| * xtal : modules for crystallography and symmetry calculations | ||
| * util : utilities | ||
|
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||
| ## CONTENT HIGHLIGHTS | ||
|
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| io | ||
| ------------------------------------------------------------------------------ | ||
| * loadang:: support for loading TSL *.ang files | ||
|
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| rot | ||
| ------------------------------------------------------------------------------ | ||
| * angax : class for the angle/axis convention | ||
| * bunge : class for Bunge Euler angles | ||
| * quat : class for quaternion representations | ||
| * rodri : class for Rodrigues vector representations | ||
| * tvec : class for transformation vectors (reshaped rotation matrices) | ||
|
|
||
| xtal | ||
| ------------------------------------------------------------------------------ | ||
| * lattvec : class for representing lattice vectors | ||
| * miller : class for representing lattice plane normals | ||
| * unitcell: class for representing unit cells | ||
| * rotsymm : class for rotational symmetry objects | ||
|
|
||
| vis | ||
| ------------------------------------------------------------------------------ | ||
| * stereoproj : class for plotting stereographic projections | ||
| * eaproj : class for plotting equal area projections | ||
|
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| util | ||
| ------------------------------------------------------------------------------ | ||
| * rationalize : function for turning fractional vectors into rational indices | ||
| * sigdec : function for rounding to n significant digits |
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| # -*- coding: utf-8 -*- | ||
| """ | ||
| Created on Tue Jan 15 16:59:33 2013 | ||
|
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| @author: epayton | ||
| """ | ||
|
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| import ovlib as ov | ||
| from numpy import pi | ||
|
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| # 4.3.1 | ||
| uc = ov.unitcell(a=3., b=4., c=6., beta=120.) | ||
| bodydiag = ov.lattvec(1,1,1) | ||
| print bodydiag.length(uc) # result should be 6.557 | ||
|
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| # 4.3.2 | ||
| uc = ov.unitcell(a=2., b=2., c=3.) | ||
| atom1 = ov.lattsite(1./2., 1./3., 1./4.) | ||
| atom2 = ov.lattsite(1./3., 1./2., 3./4.) | ||
| print atom1.distance(atom2, uc) # result should be 1.572 | ||
|
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| # 4.3.3 | ||
| uc = ov.unitcell() | ||
| atom1 = ov.lattsite(1./2., 1./2., 0.) | ||
| atom2 = ov.lattsite(1./2., 0., 1./2.) | ||
| origin = ov.lattsite(0., 0., 0.) | ||
| print atom1.angle(atom2, uc, origin)*180./pi # result should be 1.572 | ||
|
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||
| # 4.3.4 | ||
| uc = ov.unitcell(a=4., b=6., c=5., beta=120.) | ||
| vec1 = ov.lattvec(1., 0., 1.) | ||
| vec2 = ov.lattvec(-2., 0., 1.) | ||
| print vec1.angle(vec2, uc)*180./pi | ||
|
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| # 6.5(i) | ||
| uc = ov.unitcell(a=2., b=2., c=2.) | ||
| plane = ov.miller(1., 1., 0.) | ||
| print plane.dspacing(uc) | ||
|
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| # 6.5(ii) | ||
| uc = ov.unitcell(a=3., b=4., c=6., gamma=120.) | ||
| plane = ov.miller(1., 1., 1.) | ||
| print plane.dspacing(uc) | ||
|
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| # 6.5(iii) | ||
| uc = ov.unitcell(a=4., b=6., c=5., beta=120.) | ||
| plane1 = ov.miller( 1., 0., 1.) | ||
| plane2 = ov.miller(-2., 0., 1.) | ||
| print plane1.angle(plane2, uc)*180./pi | ||
|
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| # Table 7.2 | ||
| uc = ov.unitcell(beta=45.) | ||
| u = [1., 0., 0., 1., 1., 0., 1.] | ||
| v = [0., 1., 0., 1., 0., 1., 1.] | ||
| w = [0., 0., 1., 0., 1., 1., 1.] | ||
| vec1 = ov.lattvec(u, v, w) | ||
| cart1 = vec1.to_cartesian(uc) | ||
| xproj1, yproj1, hemi1 = ov.stereotrans(cart1) | ||
|
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| # Table 7.2 | ||
| vec2 = ov.miller(u, v, w) | ||
| cart2 = vec2.to_cartesian(uc) | ||
| xproj2, yproj2, hemi2 = ov.stereotrans(cart2) | ||
|
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| # Fig 7.11(a) | ||
| sg = ov.stereoproj() # initialize the stereographic projection | ||
| sg.add_lattvec(vec1,uc) # add our lattice vectors to the projection | ||
| sg.add_lattveclabels(vec1,uc) | ||
| sg.grid_greatcircles() | ||
| sg.grid_smallcircles() | ||
| sg.grid_spokes(degreestep=45) | ||
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| from matplotlib.font_manager import FontProperties | ||
| font=FontProperties() | ||
| font.set_size('large') | ||
| font.set_style('italic') | ||
| sg.add_eastlabel(fontproperties=font) | ||
| sg.add_southlabel(fontproperties=font) | ||
| sg.add_centerlabel(fontproperties=font) | ||
| sg.add_coordinatereadout(uc) | ||
|
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| # Fig 7.11(b) | ||
| sg = ov.stereoproj() # initialize the stereographic projection | ||
| sg.add_miller(vec2,uc) # add our lattice vectors to the projection | ||
| sg.add_millerlabels(vec2,uc) | ||
| sg.grid_wulffnet() | ||
|
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| from matplotlib.font_manager import FontProperties | ||
| font=FontProperties() | ||
| font.set_size('large') | ||
| font.set_style('italic') | ||
| sg.add_eastlabel(fontproperties=font) | ||
| sg.add_southlabel(fontproperties=font) | ||
| sg.add_centerlabel(fontproperties=font) | ||
| sg.add_coordinatereadout(uc) | ||
| # NOTE THAT (111) and (110) are in the wrong places in the figure in the text! | ||
|
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| ## Fig 7.11(b) as equal area proj | ||
| sg = ov.eaproj() # initialize the stereographic projection | ||
| sg.add_miller(vec2,uc) # add our lattice vectors to the projection | ||
| sg.add_millerlabels(vec2,uc) | ||
| sg.grid_spokes() | ||
| # | ||
| from matplotlib.font_manager import FontProperties | ||
| font=FontProperties() | ||
| font.set_size('large') | ||
| font.set_style('italic') | ||
| sg.add_eastlabel(fontproperties=font) | ||
| sg.add_southlabel(fontproperties=font) | ||
| sg.add_centerlabel(fontproperties=font) | ||
| sg.add_coordinatereadout(uc) |
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| # -*- coding: utf-8 -*- | ||
| """ | ||
| Created on Wed Apr 11 11:18:08 2012 | ||
|
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| @author: epayton | ||
| """ | ||
|
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| from ovlib import * | ||
| from numpy import array, pi | ||
|
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| ################################################################################ | ||
|
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| print "\n check that we can initialize" | ||
| print quat() | ||
| print tvec() | ||
| print bunge() | ||
| print rodri() | ||
|
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|
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| ################################################################################ | ||
| print '-----------------' | ||
| print "\n check that we can construct individual quaternions" | ||
|
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| # check that we can construct with a single rotation given as a tuple | ||
| q1a=quat(0.6070,-0.7043,0.0634,-0.3627) | ||
| print q1a | ||
|
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| # check that we can construct with a tuple of lists | ||
| q2a=quat([0.6070],[-0.7043],[0.0634],[-0.3627]) | ||
| print q2a | ||
|
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| # check that we can construct with an array | ||
| q3a=quat(array([0.6070]),array([-0.7043]),array([0.0634]),array([-0.3627])) | ||
| print q3a | ||
|
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| ################################################################################ | ||
| print '-----------------' | ||
| print "\n check that we can construct multiple quaternions" | ||
|
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| # check that we can construct with multiple rotations given as tuples | ||
| a=0.6070,0.9688 | ||
| b=-0.7043,0.1176 | ||
| c=0.0634,0.0263 | ||
| d=-0.3627,0.2166 | ||
| q1b=quat(a,b,c,d) | ||
| print q1b | ||
|
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| # check that we can construct with multiple values in a tuple of lists | ||
| a=[0.6070,0.9688] | ||
| b=[-0.7043,0.1176] | ||
| c=[0.0634,0.0263] | ||
| d=[-0.3627,0.2166] | ||
| q2b=quat(a,b,c,d) | ||
| print q2b | ||
|
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| # check that we can construct with a tuple of arrays | ||
| a=array([0.6070,0.9688]) | ||
| b=array([-0.7043,0.1176]) | ||
| c=array([0.0634,0.0263]) | ||
| d=array([-0.3627,0.2166]) | ||
| q3b=quat(a,b,c,d) | ||
| print q3b | ||
|
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| ################################################################################ | ||
| print '-----------------' | ||
| print "\n check that we can convert quaternions to tvecs" | ||
|
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||
| tq1=tvec.from_quat(q1a) | ||
| print tq1 | ||
|
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||
| tq2=tvec.from_quat(q1b) | ||
| print tq2 | ||
|
|
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| ################################################################################ | ||
| print '-----------------' | ||
| print "\n check that we can convert tvecs to quats" | ||
|
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| qt1=quat.from_tvec(tq1) | ||
| print qt1 | ||
|
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| qt2=quat.from_tvec(tq2) | ||
| print qt2 | ||
|
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| ################################################################################ | ||
| print '-----------------' | ||
| print "\n check that we can convert Bunge Euler to quats" | ||
|
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| be1=quat.from_bunge(bunge(phi1=pi,PHI=pi/7.,phi2=0.0)) | ||
|
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| ################################################################################ | ||
| print '-----------------' | ||
| print "\n check that we can get symmetries" | ||
|
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| r1 = rotationelements('m-3m') # rotation symmetry elements | ||
| r2 = pointgroupelements('6/mmm') # point group elements | ||
| cs = rotsymm('m3') # rotational symmetry class | ||
| print cs | ||
|
|
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| # -*- coding: utf-8 -*- | ||
| """ | ||
| Created on Thu Jul 04 17:05:51 2013 | ||
|
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||
| @author: epayton | ||
| """ | ||
|
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| import ovlib as ov | ||
|
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| uc = ov.unitcell() | ||
|
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| # From Lecture notes for CMU 27-750, Fall 2009, "Analysis of EBSD Data (L17)" | ||
| # by B. El-Dasher, A.D. Rollett, G.S. Rohrer, P.N. Kalu, p. 35: | ||
| # "A simple test of the frames used for Euler angles is to have the softwares | ||
| # [sic] plot pole figures for a single orientation..." | ||
|
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| ''' | ||
| Check if Euler angles are working properly in passive convention | ||
| ''' | ||
| pf = ov.stereoproj() | ||
| m = ov.miller(1,0,0) | ||
| pf.add_miller(m.rotate(ov.rmat.from_bunge(ov.bunge(0.2,0,0))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
|
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| # the red marker should appear counterclockwise from the blue | ||
| m = ov.miller(0,0,1) | ||
| pf.add_miller(m.rotate(ov.rmat.from_bunge(ov.bunge(0.0,0.2,0))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
|
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||
| ''' | ||
| Check if ang/ax is working properly in passive convention | ||
| ''' | ||
| pf = ov.stereoproj() | ||
| # the red marker should appear in same directions as above: | ||
| m = ov.miller(1,0,0) | ||
| pf.add_miller(m.rotate(ov.rmat.from_angax(ov.angax(0.2,0,0,1))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
| m = ov.miller(0,0,1) | ||
| pf.add_miller(m.rotate(ov.rmat.from_angax(ov.angax(0.2,1,0,0))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
|
|
||
| ''' | ||
| Check if quat is working properly in passive convention | ||
| ''' | ||
| # the red marker should appear in same directions as above: | ||
| pf = ov.stereoproj() | ||
| m = ov.miller(1,0,0) | ||
| pf.add_miller(m.rotate(ov.quat.from_angax(ov.angax(0.2,0,0,1))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
| m = ov.miller(0,0,1) | ||
| pf.add_miller(m.rotate(ov.quat.from_angax(ov.angax(0.2,1,0,0))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
|
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| pf = ov.stereoproj() | ||
| m = ov.miller(1,0,0) | ||
| pf.add_miller(m.rotate(ov.quat.from_bunge(ov.bunge(0.2,0,0))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
| m = ov.miller(0,0,1) | ||
| pf.add_miller(m.rotate(ov.quat.from_bunge(ov.bunge(0,0.2,0))), uc, uppermarkerfacecolor='r', lowermarkerfacecolor='r') | ||
| pf.add_miller(m, uc) | ||
|
|
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@paytonej, would an MIT license make more sense here? That would be more in line with the "free in both the 'beer' and 'speech' senses" ideology (docs/faq.rst, line 20)