Merge branch 'remove-grain-growth' into 'development'
grain growth not maintained and has issues See merge request damask/DAMASK!510
This commit is contained in:
Philip Eisenlohr
commit
a6e78c5b66
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@ -1,178 +0,0 @@
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#!/usr/bin/env python3
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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from scipy import ndimage
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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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getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0) # 1.0 if A & B are distinct, 0.0 otherwise
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struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
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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 option(s) [geomfile(s)]', description = """
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Smoothen interface roughness by simulated curvature flow.
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This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
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up to a given distance 'd' voxels.
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The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
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References 10.1073/pnas.1111557108 (10.1006/jcph.1994.1105)
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""", version = scriptID)
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parser.add_option('-d', '--distance',
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dest = 'd',
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type = 'float', metavar = 'float',
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help = 'diffusion distance in voxels [%default]')
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parser.add_option('-N', '--iterations',
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dest = 'N',
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type = 'int', metavar = 'int',
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help = 'curvature flow iterations [%default]')
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parser.add_option('-i', '--immutable',
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action = 'extend', dest = 'immutable', metavar = '<int LIST>',
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help = 'list of immutable material indices')
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parser.add_option('--ndimage',
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dest = 'ndimage', action='store_true',
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help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
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parser.set_defaults(d = 1,
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N = 1,
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immutable = [],
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ndimage = False,
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)
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(options, filenames) = parser.parse_args()
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options.immutable = list(map(int,options.immutable))
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if filenames == []: filenames = [None]
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for name in filenames:
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damask.util.report(scriptName,name)
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geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
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grid_original = geom.cells
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damask.util.croak(geom)
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material = np.tile(geom.material,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
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grid = np.array(material.shape)
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# --- initialize support data ---------------------------------------------------------------------
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# store a copy of the initial material indices to find locations of immutable indices
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material_original = np.copy(material)
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if not options.ndimage:
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X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
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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),dtype=np.float32) \
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/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(grid_original == 1))/2.,dtype=np.float32)
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gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size
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gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
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gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:]
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gauss = np.fft.rfftn(gauss).astype(np.complex64)
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for smoothIter in range(options.N):
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interfaceEnergy = np.zeros(material.shape,dtype=np.float32)
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for i in (-1,0,1):
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for j in (-1,0,1):
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for k in (-1,0,1):
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# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
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interfaceEnergy = np.maximum(interfaceEnergy,
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getInterfaceEnergy(material,np.roll(np.roll(np.roll(
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material,i,axis=0), j,axis=1), k,axis=2)))
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# periodically extend interfacial energy array by half a grid size in positive and negative directions
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periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2]
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# transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
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index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,
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return_distances = False,
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return_indices = True)
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# want array index of nearest voxel on periodically extended boundary
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periodic_bulkEnergy = periodic_interfaceEnergy[index[0],
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index[1],
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index[2]].reshape(2*grid) # fill bulk with energy of nearest interface
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if options.ndimage:
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periodic_diffusedEnergy = ndimage.gaussian_filter(
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np.where(ndimage.morphology.binary_dilation(periodic_interfaceEnergy > 0.,
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structure = struc,
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iterations = int(round(options.d*2.))-1, # fat boundary
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),
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periodic_bulkEnergy, # ...and zero everywhere else
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0.),
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sigma = options.d)
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else:
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diffusedEnergy = np.fft.irfftn(np.fft.rfftn(
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np.where(
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ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
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structure = struc,
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iterations = int(round(options.d*2.))-1),# fat boundary
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periodic_bulkEnergy[grid[0]//2:-grid[0]//2, # retain filled energy on fat boundary...
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2], # ...and zero everywhere else
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0.)).astype(np.complex64) *
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gauss).astype(np.float32)
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periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the smoothed bulk energy
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# transform voxels close to interface region
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index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.95*np.amax(periodic_diffusedEnergy),
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return_distances = False,
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return_indices = True) # want index of closest bulk grain
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periodic_material = np.tile(material,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the geometry
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material = periodic_material[index[0],
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index[1],
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index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # extent grains into interface region
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# replace immutable materials with closest mutable ones
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index = ndimage.morphology.distance_transform_edt(np.in1d(material,options.immutable).reshape(grid),
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return_distances = False,
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return_indices = True)
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material = material[index[0],
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index[1],
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index[2]]
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immutable = np.zeros(material.shape, dtype=np.bool)
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# find locations where immutable materials have been in original structure
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for micro in options.immutable:
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immutable += material_original == micro
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# undo any changes involving immutable materials
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material = np.where(immutable, material_original,material)
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damask.Grid(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
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size = geom.size,
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origin = geom.origin,
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comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
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)\
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.save(sys.stdout if name is None else name)
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@ -287,7 +287,7 @@ class TestOrientation:
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@pytest.mark.parametrize('family',crystal_families)
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@pytest.mark.parametrize('proper',[True,False])
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def test_in_SST(self,family,proper):
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assert Orientation(family=family).in_SST(np.zeros(3),proper)
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assert Orientation(family=family).in_SST(np.zeros(3),proper)
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@pytest.mark.parametrize('function',['in_SST','IPF_color'])
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def test_invalid_argument(self,function):
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@ -367,13 +367,13 @@ class TestResult:
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@pytest.mark.parametrize('mode',['cell','node'])
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def test_coordinates(self,default,mode):
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if mode == 'cell':
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a = grid_filters.coordinates0_point(default.cells,default.size,default.origin)
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b = default.coordinates0_point.reshape(tuple(default.cells)+(3,),order='F')
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elif mode == 'node':
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a = grid_filters.coordinates0_node(default.cells,default.size,default.origin)
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b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
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assert np.allclose(a,b)
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if mode == 'cell':
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a = grid_filters.coordinates0_point(default.cells,default.size,default.origin)
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b = default.coordinates0_point.reshape(tuple(default.cells)+(3,),order='F')
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elif mode == 'node':
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a = grid_filters.coordinates0_node(default.cells,default.size,default.origin)
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b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
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assert np.allclose(a,b)
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@pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
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@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
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@ -421,7 +421,7 @@ class TestResult:
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def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
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for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
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for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
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os.chdir(tmp_path)
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single_phase.export_XDMF()
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@ -1076,19 +1076,19 @@ class TestRotation:
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def test_from_fiber_component(self,N,sigma):
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p = []
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for run in range(5):
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alpha = np.random.random()*2*np.pi,np.arccos(np.random.random())
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beta = np.random.random()*2*np.pi,np.arccos(np.random.random())
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alpha = np.random.random()*2*np.pi,np.arccos(np.random.random())
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beta = np.random.random()*2*np.pi,np.arccos(np.random.random())
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f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
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f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
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ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
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n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True) # rotation to align fiber axis in crystal and sample system
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f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
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f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
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ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
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n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True) # rotation to align fiber axis in crystal and sample system
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o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
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angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
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dist = np.array(angles) * (np.random.randint(0,2,N)*2-1)
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o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
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angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
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dist = np.array(angles) * (np.random.randint(0,2,N)*2-1)
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p.append(stats.normaltest(dist)[1])
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p.append(stats.normaltest(dist)[1])
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sigma_out = np.degrees(np.std(dist))
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p = np.average(p)
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@ -173,11 +173,11 @@ class TestVTK:
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polyData = VTK.from_poly_data(points)
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polyData.add(points,'coordinates')
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if update:
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polyData.save(ref_path/'polyData')
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polyData.save(ref_path/'polyData')
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else:
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reference = VTK.load(ref_path/'polyData.vtp')
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assert polyData.__repr__() == reference.__repr__() and \
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np.allclose(polyData.get('coordinates'),points)
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reference = VTK.load(ref_path/'polyData.vtp')
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assert polyData.__repr__() == reference.__repr__() and \
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np.allclose(polyData.get('coordinates'),points)
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
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def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
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@ -189,8 +189,8 @@ class TestVTK:
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rectilinearGrid.add(np.ascontiguousarray(c),'cell')
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rectilinearGrid.add(np.ascontiguousarray(n),'node')
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if update:
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rectilinearGrid.save(ref_path/'rectilinearGrid')
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rectilinearGrid.save(ref_path/'rectilinearGrid')
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else:
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reference = VTK.load(ref_path/'rectilinearGrid.vtr')
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assert rectilinearGrid.__repr__() == reference.__repr__() and \
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np.allclose(rectilinearGrid.get('cell'),c)
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reference = VTK.load(ref_path/'rectilinearGrid.vtr')
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assert rectilinearGrid.__repr__() == reference.__repr__() and \
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np.allclose(rectilinearGrid.get('cell'),c)
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