switched "Geom.materials" to "Geom.material"
This commit is contained in:
Philip Eisenlohr
parent
b995f34834
commit
8c8db5b99f
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@ -66,13 +66,13 @@ for name in filenames:
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grid_original = geom.grid
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damask.util.croak(geom)
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materials = np.tile(geom.materials,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
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grid = np.array(materials.shape)
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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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materials_original = np.copy(materials)
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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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@ -88,14 +88,14 @@ for name in filenames:
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for smoothIter in range(options.N):
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interfaceEnergy = np.zeros(materials.shape,dtype=np.float32)
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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(materials,np.roll(np.roll(np.roll(
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materials,i,axis=0), j,axis=1), k,axis=2)))
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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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@ -143,33 +143,33 @@ for name in filenames:
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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_materials = np.tile(materials,(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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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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materials = periodic_materials[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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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(materials,options.immutable).reshape(grid),
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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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materials = materials[index[0],
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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(materials.shape, dtype=np.bool)
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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 += materials_original == micro
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immutable += material_original == micro
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# undo any changes involving immutable materials
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materials = np.where(immutable, materials_original,materials)
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material = np.where(immutable, material_original,material)
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damask.Geom(materials = materials[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
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damask.Geom(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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@ -100,7 +100,7 @@ def mesh(r,d):
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#-------------------------------------------------------------------------------------------------
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def material():
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def materials():
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return [\
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"*new_mater standard",
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"*mater_option general:state:solid",
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@ -130,10 +130,10 @@ def geometry():
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#-------------------------------------------------------------------------------------------------
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def initial_conditions(materials):
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def initial_conditions(material):
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elements = []
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element = 0
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for id in materials:
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for id in material:
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element += 1
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if len(elements) < id:
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for i in range(id-len(elements)):
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@ -197,14 +197,14 @@ for name in filenames:
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damask.util.report(scriptName,name)
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geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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materials = geom.materials.flatten(order='F')
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material = geom.material.flatten(order='F')
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cmds = [\
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init(),
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mesh(geom.grid,geom.size),
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material(),
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materials(),
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geometry(),
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initial_conditions(materials),
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initial_conditions(material),
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'*identify_sets',
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'*show_model',
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'*redraw',
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@ -101,8 +101,8 @@ class myThread (threading.Thread):
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#--- evaluate current seeds file ------------------------------------------------------------------
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perturbedGeom = damask.Geom.load_ASCII(perturbedGeomVFile)
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myNmaterials = len(np.unique(perturbedGeom.materials))
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currentData=np.bincount(perturbedGeom.materials.ravel())[1:]/points
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myNmaterials = len(np.unique(perturbedGeom.material))
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currentData = np.bincount(perturbedGeom.material.ravel())[1:]/points
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currentError=[]
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currentHist=[]
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for i in range(nMaterials): # calculate the deviation in all bins per histogram
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@ -217,8 +217,8 @@ points = np.array(options.grid).prod().astype('float')
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# ----------- calculate target distribution and bin edges
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targetGeom = damask.Geom.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
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nMaterials = len(np.unique(targetGeom.materials))
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targetVolFrac = np.bincount(targetGeom.materials.flatten())/targetGeom.grid.prod().astype(np.float)
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nMaterials = len(np.unique(targetGeom.material))
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targetVolFrac = np.bincount(targetGeom.material.flatten())/targetGeom.grid.prod().astype(np.float)
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target = []
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for i in range(1,nMaterials+1):
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targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
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@ -244,10 +244,10 @@ initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
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initialGeomVFile.seek(0)
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initialGeom = damask.Geom.load_ASCII(initialGeomVFile)
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if len(np.unique(targetGeom.materials)) != nMaterials:
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if len(np.unique(targetGeom.material)) != nMaterials:
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damask.util.croak('error. Material count mismatch')
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initialData = np.bincount(initialGeom.materials.flatten())/points
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initialData = np.bincount(initialGeom.material.flatten())/points
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for i in range(nMaterials):
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initialHist = np.histogram(initialData,bins=target[i]['bins'])[0]
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target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum())
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@ -263,7 +263,7 @@ for i in range(nMaterials):
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if options.maxseeds < 1:
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maxSeeds = len(np.unique(initialGeom.materials))
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maxSeeds = len(np.unique(initialGeom.material))
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else:
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maxSeeds = options.maxseeds
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@ -47,11 +47,11 @@ for name in filenames:
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damask.util.report(scriptName,name)
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geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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materials = geom.materials.reshape((-1,1),order='F')
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material = geom.material.reshape((-1,1),order='F')
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mask = np.logical_and(np.in1d(materials,options.whitelist,invert=False) if options.whitelist else \
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mask = np.logical_and(np.in1d(material,options.whitelist,invert=False) if options.whitelist else \
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np.full(geom.grid.prod(),True,dtype=bool),
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np.in1d(materials,options.blacklist,invert=True) if options.blacklist else \
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np.in1d(material,options.blacklist,invert=True) if options.blacklist else \
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np.full(geom.grid.prod(),True,dtype=bool))
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seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3,order='F')
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@ -64,5 +64,5 @@ for name in filenames:
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]
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damask.Table(seeds[mask],{'pos':(3,)},comments)\
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.add('material',materials[mask].astype(int))\
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.add('material',material[mask].astype(int))\
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.save(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds',legacy=True)
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@ -76,7 +76,7 @@ for name in filenames:
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g[2] = k + offset[2]
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g %= geom.grid
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seeds[n,0:3] = (g+0.5)/geom.grid # normalize coordinates to box
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seeds[n, 3] = geom.materials[g[0],g[1],g[2]]
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seeds[n, 3] = geom.material[g[0],g[1],g[2]]
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if options.x: g[0] += 1
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if options.y: g[1] += 1
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n += 1
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@ -15,13 +15,13 @@ from . import grid_filters
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class Geom:
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"""Geometry definition for grid solvers."""
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def __init__(self,materials,size,origin=[0.0,0.0,0.0],comments=[]):
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def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
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"""
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New geometry definition from array of materials, size, and origin.
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New geometry definition from array of material, size, and origin.
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Parameters
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----------
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materials : numpy.ndarray
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material : numpy.ndarray
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Material index array (3D).
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size : list or numpy.ndarray
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Physical size of the geometry in meter.
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@ -31,16 +31,16 @@ class Geom:
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Comment lines.
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"""
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if len(materials.shape) != 3:
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raise ValueError(f'Invalid materials shape {materials.shape}.')
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elif materials.dtype not in np.sctypes['float'] + np.sctypes['int']:
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raise TypeError(f'Invalid materials data type {materials.dtype}.')
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if len(material.shape) != 3:
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raise ValueError(f'Invalid material shape {material.shape}.')
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elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
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raise TypeError(f'Invalid material data type {material.dtype}.')
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else:
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self.materials = np.copy(materials)
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self.material = np.copy(material)
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if self.materials.dtype in np.sctypes['float'] and \
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np.all(self.materials == self.materials.astype(int).astype(float)):
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self.materials = self.materials.astype(int)
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if self.material.dtype in np.sctypes['float'] and \
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np.all(self.material == self.material.astype(int).astype(float)):
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self.material = self.material.astype(int)
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if len(size) != 3 or any(np.array(size) <= 0):
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raise ValueError(f'Invalid size {size}.')
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@ -62,7 +62,7 @@ class Geom:
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f'size x y z: {util.srepr(self.size, " x ")}',
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f'origin x y z: {util.srepr(self.origin," ")}',
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f'# materials: {self.N_materials}',
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f'max material: {np.nanmax(self.materials)}',
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f'max material: {np.nanmax(self.material)}',
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])
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@ -103,21 +103,21 @@ class Geom:
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message.append(util.delete(f'# materials: {other.N_materials}'))
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message.append(util.emph( f'# materials: { self.N_materials}'))
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if np.nanmax(other.materials) != np.nanmax(self.materials):
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message.append(util.delete(f'max material: {np.nanmax(other.materials)}'))
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message.append(util.emph( f'max material: {np.nanmax( self.materials)}'))
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if np.nanmax(other.material) != np.nanmax(self.material):
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message.append(util.delete(f'max material: {np.nanmax(other.material)}'))
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message.append(util.emph( f'max material: {np.nanmax( self.material)}'))
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return util.return_message(message)
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@property
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def grid(self):
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return np.asarray(self.materials.shape)
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return np.asarray(self.material.shape)
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@property
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def N_materials(self):
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return np.unique(self.materials).size
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return np.unique(self.material).size
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@staticmethod
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@ -160,7 +160,7 @@ class Geom:
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else:
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comments.append(line.strip())
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materials = np.empty(grid.prod()) # initialize as flat array
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material = np.empty(grid.prod()) # initialize as flat array
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i = 0
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for line in content[header_length:]:
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items = line.split('#')[0].split()
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@ -172,16 +172,16 @@ class Geom:
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abs(int(items[2])-int(items[0]))+1,dtype=float)
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else: items = list(map(float,items))
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else: items = list(map(float,items))
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materials[i:i+len(items)] = items
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material[i:i+len(items)] = items
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i += len(items)
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if i != grid.prod():
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raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
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if not np.any(np.mod(materials,1) != 0.0): # no float present
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materials = materials.astype('int')
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if not np.any(np.mod(material,1) != 0.0): # no float present
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material = material.astype('int')
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return Geom(materials.reshape(grid,order='F'),size,origin,comments)
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return Geom(material.reshape(grid,order='F'),size,origin,comments)
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@staticmethod
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@ -200,9 +200,11 @@ class Geom:
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comments = v.get_comments()
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grid = np.array(v.vtk_data.GetDimensions())-1
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bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
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size = bbox[1] - bbox[0]
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return Geom(v.get('material').reshape(grid,order='F'),size,bbox[0],comments=comments)
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return Geom(material = v.get('material').reshape(grid,order='F'),
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size = bbox[1] - bbox[0],
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origin = bbox[0],
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comments=comments)
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@staticmethod
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@ -243,17 +245,17 @@ class Geom:
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result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
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pool.close()
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pool.join()
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materials = np.array(result.get())
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material = np.array(result.get())
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if periodic:
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materials = materials.reshape(grid*3)
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materials = materials[grid[0]:grid[0]*2,grid[1]:grid[1]*2,grid[2]:grid[2]*2]%seeds.shape[0]
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material = material.reshape(grid*3)
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material = material[grid[0]:grid[0]*2,grid[1]:grid[1]*2,grid[2]:grid[2]*2]%seeds.shape[0]
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else:
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materials = materials.reshape(grid)
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material = material.reshape(grid)
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return Geom(materials = materials+1,
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size = size,
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comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
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return Geom(material = material+1,
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size = size,
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comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
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)
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@ -276,11 +278,11 @@ class Geom:
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"""
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coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
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KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
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devNull,materials = KDTree.query(coords)
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devNull,material = KDTree.query(coords)
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return Geom(materials = materials.reshape(grid)+1,
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size = size,
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comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
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return Geom(material = material.reshape(grid)+1,
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size = size,
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comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
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)
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@ -311,10 +313,10 @@ class Geom:
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plain = not compress
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if plain:
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format_string = '%g' if self.materials.dtype in np.sctypes['float'] else \
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'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.materials)))))
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format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
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'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
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np.savetxt(fname,
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self.materials.reshape([grid[0],np.prod(grid[1:])],order='F').T,
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self.material.reshape([grid[0],np.prod(grid[1:])],order='F').T,
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header='\n'.join(header), fmt=format_string, comments='')
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else:
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try:
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@ -325,7 +327,7 @@ class Geom:
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compressType = None
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former = start = -1
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reps = 0
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for current in self.materials.flatten('F'):
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for current in self.material.flatten('F'):
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if abs(current - former) == 1 and (start - current) == reps*(former - current):
|
||||
compressType = 'to'
|
||||
reps += 1
|
||||
|
|
@ -370,7 +372,7 @@ class Geom:
|
|||
|
||||
"""
|
||||
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
|
||||
v.add(self.materials.flatten(order='F'),'material')
|
||||
v.add(self.material.flatten(order='F'),'material')
|
||||
v.add_comments(self.comments)
|
||||
|
||||
v.save(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr',parallel=False,compress=compress)
|
||||
|
|
@ -402,7 +404,7 @@ class Geom:
|
|||
0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1)
|
||||
1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1)
|
||||
fill : int, optional
|
||||
Fill value for primitive. Defaults to materials.max() + 1.
|
||||
Fill value for primitive. Defaults to material.max() + 1.
|
||||
R : damask.Rotation, optional
|
||||
Rotation of primitive. Defaults to no rotation.
|
||||
inverse : Boolean, optional
|
||||
|
|
@ -428,12 +430,12 @@ class Geom:
|
|||
if periodic: # translate back to center
|
||||
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
|
||||
|
||||
fill_ = np.full_like(self.materials,np.nanmax(self.materials)+1 if fill is None else fill)
|
||||
fill_ = np.full_like(self.material,np.nanmax(self.material)+1 if fill is None else fill)
|
||||
|
||||
return Geom(materials = np.where(np.logical_not(mask) if inverse else mask, self.materials,fill_),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','add_primitive')],
|
||||
return Geom(material = np.where(np.logical_not(mask) if inverse else mask, self.material,fill_),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','add_primitive')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -455,19 +457,19 @@ class Geom:
|
|||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
|
||||
limits = [None,None] if reflect else [-2,0]
|
||||
ms = self.materials.copy()
|
||||
mat = self.material.copy()
|
||||
|
||||
if 'x' in directions:
|
||||
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
|
||||
mat = np.concatenate([mat,mat[limits[0]:limits[1]:-1,:,:]],0)
|
||||
if 'y' in directions:
|
||||
ms = np.concatenate([ms,ms[:,limits[0]:limits[1]:-1,:]],1)
|
||||
mat = np.concatenate([mat,mat[:,limits[0]:limits[1]:-1,:]],1)
|
||||
if 'z' in directions:
|
||||
ms = np.concatenate([ms,ms[:,:,limits[0]:limits[1]:-1]],2)
|
||||
mat = np.concatenate([mat,mat[:,:,limits[0]:limits[1]:-1]],2)
|
||||
|
||||
return Geom(materials = ms,
|
||||
size = self.size/self.grid*np.asarray(ms.shape),
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','mirror')],
|
||||
return Geom(material = mat,
|
||||
size = self.size/self.grid*np.asarray(mat.shape),
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','mirror')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -486,12 +488,12 @@ class Geom:
|
|||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
|
||||
ms = np.flip(self.materials, (valid.index(d) for d in directions if d in valid))
|
||||
mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
|
||||
|
||||
return Geom(materials = ms,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','flip')],
|
||||
return Geom(material = mat,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','flip')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -507,17 +509,17 @@ class Geom:
|
|||
Assume geometry to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
return Geom(materials = ndimage.interpolation.zoom(
|
||||
self.materials,
|
||||
return Geom(material = ndimage.interpolation.zoom(
|
||||
self.material,
|
||||
grid/self.grid,
|
||||
output=self.materials.dtype,
|
||||
output=self.material.dtype,
|
||||
order=0,
|
||||
mode=('wrap' if periodic else 'nearest'),
|
||||
prefilter=False
|
||||
),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','scale')],
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','scale')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -543,29 +545,29 @@ class Geom:
|
|||
else:
|
||||
return me
|
||||
|
||||
return Geom(materials = ndimage.filters.generic_filter(
|
||||
self.materials,
|
||||
return Geom(material = ndimage.filters.generic_filter(
|
||||
self.material,
|
||||
mostFrequent,
|
||||
size=(stencil if selection is None else stencil//2*2+1,)*3,
|
||||
mode=('wrap' if periodic else 'nearest'),
|
||||
extra_keywords=dict(selection=selection),
|
||||
).astype(self.materials.dtype),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','clean')],
|
||||
).astype(self.material.dtype),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','clean')],
|
||||
)
|
||||
|
||||
|
||||
def renumber(self):
|
||||
"""Renumber sorted material indices to 1,...,N."""
|
||||
renumbered = np.empty(self.grid,dtype=self.materials.dtype)
|
||||
for i, oldID in enumerate(np.unique(self.materials)):
|
||||
renumbered = np.where(self.materials == oldID, i+1, renumbered)
|
||||
renumbered = np.empty(self.grid,dtype=self.material.dtype)
|
||||
for i, oldID in enumerate(np.unique(self.material)):
|
||||
renumbered = np.where(self.material == oldID, i+1, renumbered)
|
||||
|
||||
return Geom(materials = renumbered,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','renumber')],
|
||||
return Geom(material = renumbered,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','renumber')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -578,32 +580,32 @@ class Geom:
|
|||
R : damask.Rotation
|
||||
Rotation to apply to the geometry.
|
||||
fill : int or float, optional
|
||||
Material index to fill the corners. Defaults to materials.max() + 1.
|
||||
Material index to fill the corners. Defaults to material.max() + 1.
|
||||
|
||||
"""
|
||||
if fill is None: fill = np.nanmax(self.materials) + 1
|
||||
dtype = float if np.isnan(fill) or int(fill) != fill or self.materials.dtype==np.float else int
|
||||
if fill is None: fill = np.nanmax(self.material) + 1
|
||||
dtype = float if np.isnan(fill) or int(fill) != fill or self.material.dtype==np.float else int
|
||||
|
||||
Eulers = R.as_Eulers(degrees=True)
|
||||
materials_in = self.materials.copy()
|
||||
material_in = self.material.copy()
|
||||
|
||||
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
|
||||
# see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
|
||||
for angle,axes in zip(Eulers[::-1], [(0,1),(1,2),(0,1)]):
|
||||
materials_out = ndimage.rotate(materials_in,angle,axes,order=0,
|
||||
material_out = ndimage.rotate(material_in,angle,axes,order=0,
|
||||
prefilter=False,output=dtype,cval=fill)
|
||||
if np.prod(materials_in.shape) == np.prod(materials_out.shape):
|
||||
if np.prod(material_in.shape) == np.prod(material_out.shape):
|
||||
# avoid scipy interpolation errors for rotations close to multiples of 90°
|
||||
materials_in = np.rot90(materials_in,k=np.rint(angle/90.).astype(int),axes=axes)
|
||||
material_in = np.rot90(material_in,k=np.rint(angle/90.).astype(int),axes=axes)
|
||||
else:
|
||||
materials_in = materials_out
|
||||
material_in = material_out
|
||||
|
||||
origin = self.origin-(np.asarray(materials_in.shape)-self.grid)*.5 * self.size/self.grid
|
||||
origin = self.origin-(np.asarray(material_in.shape)-self.grid)*.5 * self.size/self.grid
|
||||
|
||||
return Geom(materials = materials_in,
|
||||
size = self.size/self.grid*np.asarray(materials_in.shape),
|
||||
origin = origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','rotate')],
|
||||
return Geom(material = material_in,
|
||||
size = self.size/self.grid*np.asarray(material_in.shape),
|
||||
origin = origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','rotate')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -618,12 +620,12 @@ class Geom:
|
|||
offset : numpy.ndarray of shape (3)
|
||||
Offset (measured in grid points) from old to new geometry [0,0,0].
|
||||
fill : int or float, optional
|
||||
Material index to fill the background. Defaults to materials.max() + 1.
|
||||
Material index to fill the background. Defaults to material.max() + 1.
|
||||
|
||||
"""
|
||||
if offset is None: offset = 0
|
||||
if fill is None: fill = np.nanmax(self.materials) + 1
|
||||
dtype = float if int(fill) != fill or self.materials.dtype in np.sctypes['float'] else int
|
||||
if fill is None: fill = np.nanmax(self.material) + 1
|
||||
dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
|
||||
|
||||
canvas = np.full(self.grid if grid is None else grid,fill,dtype)
|
||||
|
||||
|
|
@ -632,35 +634,35 @@ class Geom:
|
|||
ll = np.clip(-offset, 0,np.minimum( grid,self.grid-offset))
|
||||
ur = np.clip(-offset+self.grid,0,np.minimum( grid,self.grid-offset))
|
||||
|
||||
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.materials[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
|
||||
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
|
||||
|
||||
return Geom(materials = canvas,
|
||||
size = self.size/self.grid*np.asarray(canvas.shape),
|
||||
origin = self.origin+offset*self.size/self.grid,
|
||||
comments = self.comments+[util.execution_stamp('Geom','canvas')],
|
||||
return Geom(material = canvas,
|
||||
size = self.size/self.grid*np.asarray(canvas.shape),
|
||||
origin = self.origin+offset*self.size/self.grid,
|
||||
comments = self.comments+[util.execution_stamp('Geom','canvas')],
|
||||
)
|
||||
|
||||
|
||||
def substitute(self,from_materials,to_materials):
|
||||
def substitute(self,from_material,to_material):
|
||||
"""
|
||||
Substitute material indices.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
from_materials : iterable of ints
|
||||
from_material : iterable of ints
|
||||
Material indices to be substituted.
|
||||
to_materials : iterable of ints
|
||||
to_material : iterable of ints
|
||||
New material indices.
|
||||
|
||||
"""
|
||||
substituted = self.materials.copy()
|
||||
for from_ms,to_ms in zip(from_materials,to_materials):
|
||||
substituted[self.materials==from_ms] = to_ms
|
||||
substituted = self.material.copy()
|
||||
for from_ms,to_ms in zip(from_material,to_material):
|
||||
substituted[self.material==from_ms] = to_ms
|
||||
|
||||
return Geom(materials = substituted,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','substitute')],
|
||||
return Geom(material = substituted,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','substitute')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -679,7 +681,7 @@ class Geom:
|
|||
Defaults to 1.
|
||||
offset : int, optional
|
||||
Offset (positive or negative) to tag material indices,
|
||||
defaults to materials.max() + 1.
|
||||
defaults to material.max() + 1.
|
||||
trigger : list of ints, optional
|
||||
List of material indices that trigger a change.
|
||||
Defaults to [], meaning that any different neighbor triggers a change.
|
||||
|
|
@ -698,15 +700,15 @@ class Geom:
|
|||
trigger = list(trigger)
|
||||
return np.any(np.in1d(stencil,np.array(trigger)))
|
||||
|
||||
offset_ = np.nanmax(self.materials) if offset is None else offset
|
||||
mask = ndimage.filters.generic_filter(self.materials,
|
||||
offset_ = np.nanmax(self.material) if offset is None else offset
|
||||
mask = ndimage.filters.generic_filter(self.material,
|
||||
tainted_neighborhood,
|
||||
size=1+2*vicinity,
|
||||
mode='wrap' if periodic else 'nearest',
|
||||
extra_keywords={'trigger':trigger})
|
||||
|
||||
return Geom(materials = np.where(mask, self.materials + offset_,self.materials),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','vicinity_offset')],
|
||||
return Geom(material = np.where(mask, self.material + offset_,self.material),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','vicinity_offset')],
|
||||
)
|
||||
|
|
|
|||
|
|
@ -11,8 +11,8 @@ from damask import util
|
|||
|
||||
|
||||
def geom_equal(a,b):
|
||||
return np.all(a.materials == b.materials) and \
|
||||
np.all(a.grid == b.grid) and \
|
||||
return np.all(a.material == b.material) and \
|
||||
np.all(a.grid == b.grid) and \
|
||||
np.allclose(a.size, b.size) and \
|
||||
str(a.diff(b)) == str(b.diff(a))
|
||||
|
||||
|
|
@ -38,7 +38,7 @@ class TestGeom:
|
|||
|
||||
|
||||
def test_diff_not_equal(self,default):
|
||||
new = Geom(default.materials[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
|
||||
new = Geom(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
|
||||
assert str(default.diff(new)) != ''
|
||||
|
||||
|
||||
|
|
@ -93,28 +93,28 @@ class TestGeom:
|
|||
|
||||
def test_invalid_size(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
Geom(default.materials[1:,1:,1:],
|
||||
Geom(default.material[1:,1:,1:],
|
||||
size=np.ones(2))
|
||||
|
||||
|
||||
def test_invalid_origin(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
Geom(default.materials[1:,1:,1:],
|
||||
Geom(default.material[1:,1:,1:],
|
||||
size=np.ones(3),
|
||||
origin=np.ones(4))
|
||||
|
||||
|
||||
def test_invalid_materials_shape(self,default):
|
||||
materials = np.ones((3,3))
|
||||
material = np.ones((3,3))
|
||||
with pytest.raises(ValueError):
|
||||
Geom(materials,
|
||||
Geom(material,
|
||||
size=np.ones(3))
|
||||
|
||||
|
||||
def test_invalid_materials_type(self,default):
|
||||
materials = np.random.randint(1,300,(3,4,5))==1
|
||||
material = np.random.randint(1,300,(3,4,5))==1
|
||||
with pytest.raises(TypeError):
|
||||
Geom(materials)
|
||||
Geom(material)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('directions,reflect',[
|
||||
|
|
@ -205,10 +205,10 @@ class TestGeom:
|
|||
|
||||
|
||||
def test_renumber(self,default):
|
||||
materials = default.materials.copy()
|
||||
for m in np.unique(materials):
|
||||
materials[materials==m] = materials.max() + np.random.randint(1,30)
|
||||
modified = Geom(materials,
|
||||
material = default.material.copy()
|
||||
for m in np.unique(material):
|
||||
material[material==m] = material.max() + np.random.randint(1,30)
|
||||
modified = Geom(material,
|
||||
default.size,
|
||||
default.origin)
|
||||
assert not geom_equal(modified,default)
|
||||
|
|
@ -218,13 +218,13 @@ class TestGeom:
|
|||
|
||||
def test_substitute(self,default):
|
||||
offset = np.random.randint(1,500)
|
||||
modified = Geom(default.materials + offset,
|
||||
modified = Geom(default.material + offset,
|
||||
default.size,
|
||||
default.origin)
|
||||
assert not geom_equal(modified,default)
|
||||
assert geom_equal(default,
|
||||
modified.substitute(np.arange(default.materials.max())+1+offset,
|
||||
np.arange(default.materials.max())+1))
|
||||
modified.substitute(np.arange(default.material.max())+1+offset,
|
||||
np.arange(default.material.max())+1))
|
||||
|
||||
|
||||
@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]),
|
||||
|
|
@ -251,7 +251,7 @@ class TestGeom:
|
|||
grid = default.grid
|
||||
grid_add = np.random.randint(0,30,(3))
|
||||
modified = default.canvas(grid + grid_add)
|
||||
assert np.all(modified.materials[:grid[0],:grid[1],:grid[2]] == default.materials)
|
||||
assert np.all(modified.material[:grid[0],:grid[1],:grid[2]] == default.material)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
|
||||
|
|
@ -271,7 +271,7 @@ class TestGeom:
|
|||
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.materials!=2) == np.count_nonzero(G_2.materials!=2)
|
||||
assert np.count_nonzero(G_1.material!=2) == np.count_nonzero(G_2.material!=2)
|
||||
|
||||
|
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@pytest.mark.parametrize('center',[np.random.randint(4,10,(3)),
|
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|
@ -308,14 +308,14 @@ class TestGeom:
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geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
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|
||||
assert np.all(m2==geom.materials)
|
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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.materials.max()+1,
|
||||
default.materials.min()-1])
|
||||
assert np.all(offset.materials==default.materials)
|
||||
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])
|
||||
|
|
@ -338,7 +338,7 @@ class TestGeom:
|
|||
ms = np.random.randint(1, N_seeds+1)
|
||||
weights[ms-1] = np.random.random()
|
||||
Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,weights,np.random.random()>0.5)
|
||||
assert np.all(Laguerre.materials == ms)
|
||||
assert np.all(Laguerre.material == ms)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
|
||||
|
|
@ -346,10 +346,10 @@ class TestGeom:
|
|||
grid = np.random.randint(5,10,3)*2
|
||||
size = grid.astype(np.float)
|
||||
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
|
||||
materials = np.ones(grid)
|
||||
materials[:,grid[1]//2:,:] = 2
|
||||
material = np.ones(grid)
|
||||
material[:,grid[1]//2:,:] = 2
|
||||
if approach == 'Laguerre':
|
||||
geom = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(2),np.random.random()>0.5)
|
||||
elif approach == 'Voronoi':
|
||||
geom = Geom.from_Voronoi_tessellation(grid,size,seeds, np.random.random()>0.5)
|
||||
assert np.all(geom.materials == materials)
|
||||
assert np.all(geom.material == material)
|
||||
|
|
|
|||
Loading…
Reference in New Issue