Martin Diehl
parent
669ca82ce1
commit
2eb964b1ea
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@ -19,7 +19,7 @@ scriptID = ' '.join([scriptName,damask.version])
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Inserts a primitive geometric object at a given position.
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Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
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These objects can be boxes, cylinders, or ellipsoids.
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""", version = scriptID)
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@ -88,11 +88,6 @@ elif options.quaternion is not None:
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else:
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rotation = damask.Rotation()
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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
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options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
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if filenames == []: filenames = [None]
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@ -102,85 +97,38 @@ for name in filenames:
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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grid = geom.get_grid()
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size = geom.get_size()
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origin = geom.get_origin()
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microstructure = geom.get_microstructure()
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# coordinates given in real space, not (default) voxel space
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# scale to box of size [1.0,1.0,1.0]
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if options.realspace:
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options.center -= origin
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options.center *= grid / size
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options.dimension *= grid / size
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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if options.periodic: # use padding to achieve periodicity
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(X, Y, Z) = np.meshgrid(np.arange(-grid[0]/2, (3*grid[0])/2, dtype=np.float32), # 50% padding on each side
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np.arange(-grid[1]/2, (3*grid[1])/2, dtype=np.float32),
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np.arange(-grid[2]/2, (3*grid[2])/2, dtype=np.float32),
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indexing='ij')
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# Padding handling
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X = np.roll(np.roll(np.roll(X,
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-grid[0]//2, axis=0),
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-grid[1]//2, axis=1),
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-grid[2]//2, axis=2)
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Y = np.roll(np.roll(np.roll(Y,
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-grid[0]//2, axis=0),
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-grid[1]//2, axis=1),
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-grid[2]//2, axis=2)
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Z = np.roll(np.roll(np.roll(Z,
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-grid[0]//2, axis=0),
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-grid[1]//2, axis=1),
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-grid[2]//2, axis=2)
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else: # nonperiodic, much lighter on resources
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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(X, Y, Z) = np.meshgrid(np.arange(0, grid[0], dtype=np.float32),
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np.arange(0, grid[1], dtype=np.float32),
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np.arange(0, grid[2], dtype=np.float32),
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indexing='ij')
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center = (np.array(options.center) - geom.get_origin())/size
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r = np.array(options.dimension)/size/2.0
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else:
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center = (np.array(options.center) + 0.5)/grid
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r = np.array(options.dimension)/grid/2.0
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# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
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X -= options.center[0] - 0.5
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Y -= options.center[1] - 0.5
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Z -= options.center[2] - 0.5
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# and then by applying the rotation
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(X, Y, Z) = rotation * (X, Y, Z)
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# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
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X /= options.dimension[0] * 0.5
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Y /= options.dimension[1] * 0.5
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Z /= options.dimension[2] * 0.5
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fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
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if np.any(center<0.0) or np.any(center>=1.0): print('error')
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# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
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old_settings = np.seterr()
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offset = np.ones(3)*0.5 if options.periodic else center
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mask = np.full(grid,False)
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# High exponents can cause underflow & overflow - okay here, just compare to 1, so +infinity and 0 are fine
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np.seterr(over='ignore', under='ignore')
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if options.periodic: # use padding to achieve periodicity
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inside = np.zeros(grid, dtype=bool)
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for i in range(2):
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for j in range(2):
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for k in range(2):
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inside = inside | ( # Most of this is handling the padding
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np.abs(X[grid[0] * i : grid[0] * (i+1),
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grid[1] * j : grid[1] * (j+1),
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grid[2] * k : grid[2] * (k+1)])**options.exponent[0] +
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np.abs(Y[grid[0] * i : grid[0] * (i+1),
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grid[1] * j : grid[1] * (j+1),
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grid[2] * k : grid[2] * (k+1)])**options.exponent[1] +
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np.abs(Z[grid[0] * i : grid[0] * (i+1),
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grid[1] * j : grid[1] * (j+1),
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grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0)
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microstructure = np.where(inside,
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fill if options.inside else microstructure,
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microstructure if options.inside else fill)
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else: # nonperiodic, much lighter on resources
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microstructure = np.where(np.abs(X)**options.exponent[0] +
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np.abs(Y)**options.exponent[1] +
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np.abs(Z)**options.exponent[2] <= 1.0,
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fill if options.inside else microstructure,
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microstructure if options.inside else fill)
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e = np.array(options.exponent)
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for x in range(grid[0]):
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for y in range(grid[1]):
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for z in range(grid[2]):
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coords = np.array([x+0.5,y+0.5,z+0.5])/grid
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mask[x,y,z] = np.sum(np.abs((rotation*(coords-offset))/r)**e) < 1
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if options.periodic:
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shift = ((offset-center)*grid).astype(int)
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mask = np.roll(mask,shift,(0,1,2))
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if options.inside: mask = np.logical_not(mask)
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fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
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microstructure = np.where(mask,microstructure,fill)
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damask.util.croak(geom.update(microstructure))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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