DAMASK_EICMD/python/tests/test_Geom.py

import pytest
import numpy as np

from damask import VTK
from damask import Geom
from damask import Table
from damask import Rotation
from damask import util
from damask import seeds
from damask import grid_filters


def geom_equal(a,b):
    return np.all(a.material == b.material) and \
           np.all(a.cells    == b.cells) and \
           np.allclose(a.size, b.size) and \
           str(a.diff(b)) == str(b.diff(a))

@pytest.fixture
def default():
    """Simple geometry."""
    x=np.concatenate((np.ones(40,dtype=int),
                      np.arange(2,42),
                      np.ones(40,dtype=int)*2,
                      np.arange(1,41))).reshape(8,5,4,order='F')
    return Geom(x,[8e-6,5e-6,4e-6])

@pytest.fixture
def ref_path(ref_path_base):
    """Directory containing reference results."""
    return ref_path_base/'Geom'


class TestGeom:

    @pytest.fixture(autouse=True)
    def _patch_execution_stamp(self, patch_execution_stamp):
        print('patched damask.util.execution_stamp')

    @pytest.fixture(autouse=True)
    def _patch_datetime_now(self, patch_datetime_now):
        print('patched datetime.datetime.now')

    def test_diff_equal(self,default):
        assert str(default.diff(default)) == ''


    def test_diff_not_equal(self,default):
        new = Geom(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
        assert str(default.diff(new)) != ''

    def test_repr(self,default):
        print(default)

    def test_read_write_vtr(self,default,tmp_path):
        default.save(tmp_path/'default')
        new = Geom.load(tmp_path/'default.vtr')
        assert geom_equal(new,default)

    def test_invalid_vtr(self,tmp_path):
        v = VTK.from_rectilinear_grid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
        v.save(tmp_path/'no_materialpoint.vtr',parallel=False)
        with pytest.raises(ValueError):
            Geom.load(tmp_path/'no_materialpoint.vtr')

    def test_invalid_material(self):
        with pytest.raises(TypeError):
            Geom(np.zeros((3,3,3),dtype='complex'),np.ones(3))

    def test_cast_to_int(self):
        g = Geom(np.zeros((3,3,3)),np.ones(3))
        assert g.material.dtype in np.sctypes['int']

    def test_invalid_size(self,default):
        with pytest.raises(ValueError):
            Geom(default.material[1:,1:,1:],
                 size=np.ones(2))

    def test_save_load_ASCII(self,default,tmp_path):
        default.save_ASCII(tmp_path/'ASCII')
        default.material -= 1
        assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)

    def test_invalid_origin(self,default):
        with pytest.raises(ValueError):
            Geom(default.material[1:,1:,1:],
                 size=np.ones(3),
                 origin=np.ones(4))


    def test_invalid_materials_shape(self,default):
        material = np.ones((3,3))
        with pytest.raises(ValueError):
            Geom(material,
                 size=np.ones(3))


    def test_invalid_materials_type(self,default):
        material = np.random.randint(1,300,(3,4,5))==1
        with pytest.raises(TypeError):
            Geom(material)


    @pytest.mark.parametrize('directions,reflect',[
                                                   (['x'],        False),
                                                   (['x','y','z'],True),
                                                   (['z','x','y'],False),
                                                   (['y','z'],    False)
                                                  ]
                            )
    def test_mirror(self,default,update,ref_path,directions,reflect):
        modified = default.mirror(directions,reflect)
        tag = f'directions_{"-".join(directions)}+reflect_{reflect}'
        reference = ref_path/f'mirror_{tag}.vtr'
        if update: modified.save(reference)
        assert geom_equal(Geom.load(reference),
                          modified)


    @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
    def test_mirror_invalid(self,default,directions):
        with pytest.raises(ValueError):
            default.mirror(directions)


    @pytest.mark.parametrize('directions',[
                                           ['x'],
                                           ['x','y','z'],
                                           ['z','x','y'],
                                           ['y','z'],
                                          ]
                            )
    def test_flip(self,default,update,ref_path,directions):
        modified = default.flip(directions)
        tag = f'directions_{"-".join(directions)}'
        reference = ref_path/f'flip_{tag}.vtr'
        if update: modified.save(reference)
        assert geom_equal(Geom.load(reference),
                          modified)


    def test_flip_invariant(self,default):
        assert geom_equal(default,default.flip([]))


    @pytest.mark.parametrize('direction',[['x'],['x','y']])
    def test_flip_double(self,default,direction):
        assert geom_equal(default,default.flip(direction).flip(direction))


    @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
    def test_flip_invalid(self,default,directions):
        with pytest.raises(ValueError):
            default.flip(directions)


    @pytest.mark.parametrize('stencil',[1,2,3,4])
    @pytest.mark.parametrize('selection',[None,[1],[1,2,3]])
    @pytest.mark.parametrize('periodic',[True,False])
    def test_clean(self,default,update,ref_path,stencil,selection,periodic):
        current = default.clean(stencil,selection,periodic)
        reference = ref_path/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
        if update and stencil > 1:
            current.save(reference)
        assert geom_equal(Geom.load(reference) if stencil > 1 else default,
                          current
                         )


    @pytest.mark.parametrize('cells',[
                                     (10,11,10),
                                     [10,13,10],
                                     np.array((10,10,10)),
                                     np.array((8, 10,12)),
                                     np.array((5, 4, 20)),
                                     np.array((10,20,2))
                                    ]
                            )
    def test_scale(self,default,update,ref_path,cells):
        modified = default.scale(cells)
        tag = f'grid_{util.srepr(cells,"-")}'
        reference = ref_path/f'scale_{tag}.vtr'
        if update: modified.save(reference)
        assert geom_equal(Geom.load(reference),
                          modified)


    def test_renumber(self,default):
        material = default.material.copy()
        for m in np.unique(material):
            material[material==m] = material.max() + np.random.randint(1,30)
        default.material -= 1
        modified = Geom(material,
                        default.size,
                        default.origin)
        assert not geom_equal(modified,default)
        assert geom_equal(default,
                          modified.renumber())


    def test_substitute(self,default):
        offset = np.random.randint(1,500)
        modified = Geom(default.material + offset,
                        default.size,
                        default.origin)
        assert not geom_equal(modified,default)
        assert geom_equal(default,
                          modified.substitute(np.arange(default.material.max())+1+offset,
                                              np.arange(default.material.max())+1))

    def test_substitute_invariant(self,default):
        f = np.unique(default.material.flatten())[:np.random.randint(1,default.material.max())]
        t = np.random.permutation(f)
        modified = default.substitute(f,t)
        assert np.array_equiv(t,f) or (not geom_equal(modified,default))
        assert geom_equal(default, modified.substitute(t,f))

    def test_sort(self):
        cells = np.random.randint(5,20,3)
        m = Geom(np.random.randint(1,20,cells)*3,np.ones(3)).sort().material.flatten(order='F')
        for i,v in enumerate(m):
            assert i==0 or v > m[:i].max() or v in m[:i]

    @pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
                                           np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
    def test_rotate360(self,default,axis_angle):
        modified = default.copy()
        for i in range(np.rint(360/axis_angle[3]).astype(int)):
            modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
        assert geom_equal(default,modified)


    @pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
                                       [0.0,32.0,240.0]])
    def test_rotate(self,default,update,ref_path,Eulers):
        modified = default.rotate(Rotation.from_Euler_angles(Eulers,degrees=True))
        tag = f'Eulers_{util.srepr(Eulers,"-")}'
        reference = ref_path/f'rotate_{tag}.vtr'
        if update: modified.save(reference)
        assert geom_equal(Geom.load(reference),
                          modified)


    def test_canvas(self,default):
        cells = default.cells
        grid_add = np.random.randint(0,30,(3))
        modified = default.canvas(cells + grid_add)
        assert np.all(modified.material[:cells[0],:cells[1],:cells[2]] == default.material)


    @pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
                                                (np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
    @pytest.mark.parametrize('diameter',[np.random.random(3)*.5,
                                         np.random.randint(4,10,(3)),
                                         np.random.rand(),
                                         np.random.randint(30)])
    @pytest.mark.parametrize('exponent',[np.random.random(3)*.5,
                                         np.random.randint(4,10,(3)),
                                         np.random.rand()*4,
                                         np.random.randint(20)])
    def test_add_primitive_shift(self,center1,center2,diameter,exponent):
        """Same volume fraction for periodic geometries and different center."""
        o = np.random.random(3)-.5
        g = np.random.randint(8,32,(3))
        s = np.random.random(3)+.5
        G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
        G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
        assert np.count_nonzero(G_1.material!=2) == np.count_nonzero(G_2.material!=2)


    @pytest.mark.parametrize('center',[np.random.randint(4,10,(3)),
                                       np.random.randint(2,10),
                                       np.random.rand()*4,
                                       np.random.rand(3)*10])
    @pytest.mark.parametrize('inverse',[True,False])
    @pytest.mark.parametrize('periodic',[True,False])
    def test_add_primitive_rotation(self,center,inverse,periodic):
        """Rotation should not change result for sphere."""
        g = np.random.randint(8,32,(3))
        s = np.random.random(3)+.5
        fill = np.random.randint(10)+2
        G_1 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
        G_2 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,Rotation.from_random(),inverse,periodic=periodic)
        assert geom_equal(G_1,G_2)


    @pytest.mark.parametrize('trigger',[[1],[]])
    def test_vicinity_offset(self,trigger):
        offset = np.random.randint(2,4)
        vicinity = np.random.randint(2,4)

        g = np.random.randint(28,40,(3))
        m = np.ones(g,'i')
        x = (g*np.random.permutation(np.array([.5,1,1]))).astype('i')
        m[slice(0,x[0]),slice(0,x[1]),slice(0,x[2])] = 2
        m2 = m.copy()
        for i in [0,1,2]:
            m2[(np.roll(m,+vicinity,i)-m)!=0] += offset
            m2[(np.roll(m,-vicinity,i)-m)!=0] += offset
        if len(trigger) > 0:
            m2[m==1] = 1

        geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)

        assert np.all(m2==geom.material)


    @pytest.mark.parametrize('periodic',[True,False])
    def test_vicinity_offset_invariant(self,default,periodic):
        offset = default.vicinity_offset(trigger=[default.material.max()+1,
                                                  default.material.min()-1])
        assert np.all(offset.material==default.material)


    @pytest.mark.parametrize('periodic',[True,False])
    def test_tessellation_approaches(self,periodic):
        cells  = np.random.randint(10,20,3)
        size   = np.random.random(3) + 1.0
        N_seeds= np.random.randint(10,30)
        seeds  = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
        Voronoi  = Geom.from_Voronoi_tessellation( cells,size,seeds,                 np.arange(N_seeds)+5,periodic)
        Laguerre = Geom.from_Laguerre_tessellation(cells,size,seeds,np.ones(N_seeds),np.arange(N_seeds)+5,periodic)
        assert geom_equal(Laguerre,Voronoi)


    def test_Laguerre_weights(self):
        cells  = np.random.randint(10,20,3)
        size   = np.random.random(3) + 1.0
        N_seeds= np.random.randint(10,30)
        seeds  = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
        weights= np.full((N_seeds),-np.inf)
        ms     = np.random.randint(N_seeds)
        weights[ms] = np.random.random()
        Laguerre = Geom.from_Laguerre_tessellation(cells,size,seeds,weights,periodic=np.random.random()>0.5)
        assert np.all(Laguerre.material == ms)


    @pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
    def test_tessellate_bicrystal(self,approach):
        cells = np.random.randint(5,10,3)*2
        size  = cells.astype(np.float)
        seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
        material = np.zeros(cells)
        material[:,cells[1]//2:,:] = 1
        if   approach == 'Laguerre':
            geom = Geom.from_Laguerre_tessellation(cells,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
        elif approach == 'Voronoi':
            geom = Geom.from_Voronoi_tessellation(cells,size,seeds,            periodic=np.random.random()>0.5)
        assert np.all(geom.material == material)


    @pytest.mark.parametrize('surface',['Schwarz P',
                                        'Double Primitive',
                                        'Schwarz D',
                                        'Complementary D',
                                        'Double Diamond',
                                        'Dprime',
                                        'Gyroid',
                                        'Gprime',
                                        'Karcher K',
                                        'Lidinoid',
                                        'Neovius',
                                        'Fisher-Koch S',
                                        ])
    def test_minimal_surface_basic_properties(self,surface):
        cells = np.random.randint(60,100,3)
        size  = np.ones(3)+np.random.rand(3)
        threshold = 2*np.random.rand()-1.
        periods = np.random.randint(2)+1
        materials = np.random.randint(0,40,2)
        geom = Geom.from_minimal_surface(cells,size,surface,threshold,periods,materials)
        assert set(geom.material.flatten()) | set(materials) == set(materials) \
               and (geom.size == size).all() and (geom.cells == cells).all()

    @pytest.mark.parametrize('surface,threshold',[('Schwarz P',0),
                                        ('Double Primitive',-1./6.),
                                        ('Schwarz D',0),
                                        ('Complementary D',0),
                                        ('Double Diamond',-0.133),
                                        ('Dprime',-0.0395),
                                        ('Gyroid',0),
                                        ('Gprime',0.22913),
                                        ('Karcher K',0.17045),
                                        ('Lidinoid',0.14455),
                                        ('Neovius',0),
                                        ('Fisher-Koch S',0),
                                        ])
    def test_minimal_surface_volume(self,surface,threshold):
        cells = np.ones(3,dtype=int)*64
        geom = Geom.from_minimal_surface(cells,np.ones(3),surface,threshold)
        assert np.isclose(np.count_nonzero(geom.material==1)/np.prod(geom.cells),.5,rtol=1e-3)


    def test_from_table(self):
        cells = np.random.randint(60,100,3)
        size = np.ones(3)+np.random.rand(3)
        coords = grid_filters.cell_coord0(cells,size).reshape(-1,3,order='F')
        z=np.ones(cells.prod())
        z[cells[:2].prod()*int(cells[2]/2):]=0
        t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
        g = Geom.from_table(t,'coords',['1_coords','z'])
        assert g.N_materials == g.cells[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == cells[0]).all()


    def test_from_table_recover(self,tmp_path):
        cells = np.random.randint(60,100,3)
        size = np.ones(3)+np.random.rand(3)
        s = seeds.from_random(size,np.random.randint(60,100))
        geom = Geom.from_Voronoi_tessellation(cells,size,s)
        coords = grid_filters.cell_coord0(cells,size)
        t = Table(np.column_stack((coords.reshape(-1,3,order='F'),geom.material.flatten(order='F'))),{'c':3,'m':1})
        assert geom_equal(geom.sort().renumber(),Geom.from_table(t,'c',['m']))

    @pytest.mark.parametrize('periodic',[True,False])
    @pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
    def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
        geom=Geom.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
        current=geom.get_grain_boundaries(periodic,direction)
        if update:
            current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
        reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
        assert current.__repr__() == reference.__repr__()