Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Martin Diehl
commit
e1e528d9a8
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@ -9,8 +9,6 @@ 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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oversampling = 2.
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -123,9 +121,9 @@ for name in filenames:
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microstructure = microstructure.reshape(info['grid'],order='F')
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size = microstructure.shape
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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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# change to coordinate space where the primitive is the unit sphere/cube/etc
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(X, Y, Z) = np.meshgrid(np.arange(-size[0]/2, (3*size[0])/2, dtype=np.float32), # 50% padding on each side
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np.arange(-size[1]/2, (3*size[1])/2, dtype=np.float32),
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np.arange(-size[2]/2, (3*size[2])/2, dtype=np.float32),
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@ -143,23 +141,31 @@ for name in filenames:
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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[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, size[0], dtype=np.float32),
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np.arange(0, size[1], dtype=np.float32),
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np.arange(0, size[2], dtype=np.float32),
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indexing='ij')
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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 quaternion
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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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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# 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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np.seterr(over='ignore', under='ignore')
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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 quaternion
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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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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# 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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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(size, dtype=bool)
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for i in range(2):
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for j in range(2):
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@ -175,35 +181,14 @@ for name in filenames:
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size[1] * j : size[1] * (j+1),
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size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1)
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microstructure = np.where(inside, options.fill, microstructure)
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np.seterr(**old_settings) # Reset warnings to old state
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microstructure = np.where(inside, options.fill, microstructure)
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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, size[0], dtype=np.float32),
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np.arange(0, size[1], dtype=np.float32),
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np.arange(0, size[2], dtype=np.float32),
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indexing='ij')
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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 quaternion (the implementation of quat. does q*v*q.conj)
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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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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# 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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np.seterr(over='ignore', under='ignore')
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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, options.fill, microstructure)
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np.seterr(**old_settings) # Reset warnings to old state
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np.seterr(**old_settings) # Reset warnings to old state
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newInfo['microstructures'] = microstructure.max()
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# --- report ---------------------------------------------------------------------------------------
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