def transform_coordinates(self, coordinates, argument=None):
"""
translates coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the translation.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the translation.
#. argument (object): Any python object. Not used in this generator.
"""
# generate translation axis
translationAxis = generate_vectors_in_solid_angle(
direction=self.axis, maxAngle=self.__angle, numberOfVectors=1)[0]
# get translation amplitude
maxAmp = self.amplitude[1] - self.amplitude[0]
if self.direction is None:
amplitude = (1 - 2 * generate_random_float()) * maxAmp
elif self.direction:
amplitude = generate_random_float() * maxAmp
else:
amplitude = -generate_random_float() * maxAmp
# compute baseVector
baseVector = FLOAT_TYPE(
np.sign(amplitude) * translationAxis * self.amplitude[0])
# compute translation vector
vector = baseVector + translationAxis * FLOAT_TYPE(amplitude)
# translate and return
return coordinates + vector
def transform_coordinates(self, coordinates, argument=None):
"""
translate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the translation.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the translation.
#. argument (object): Any python object. Not used in this generator.
"""
# get axis
_,_,_,_,X,Y,Z =get_principal_axis(coordinates)
axis = [X,Y,Z][self.axis]
# generate translation axis
translationAxis = generate_vectors_in_solid_angle(direction=axis,
maxAngle=self.__angle,
numberOfVectors=1)[0]
# get translation amplitude
maxAmp = self.amplitude[1]-self.amplitude[0]
if self.direction is None:
amplitude = (1-2*generate_random_float())*maxAmp
elif self.direction:
amplitude = generate_random_float()*maxAmp
else:
amplitude = -generate_random_float()*maxAmp
# compute baseVector
baseVector = FLOAT_TYPE(np.sign(amplitude)*translationAxis*self.amplitude[0])
# compute translation vector
vector = baseVector + translationAxis*FLOAT_TYPE(amplitude)
# translate and return
return coordinates+vector
def __get_translation_axis(self, direction):
# normalize direction
norm = np.sqrt(np.add.reduce(direction**2))
direction[0] /= norm
direction[1] /= norm
direction[2] /= norm
# get vector
if self.__angle is None:
vector = direction
else:
vector = generate_vectors_in_solid_angle(direction=direction,
maxAngle=self.__angle,
numberOfVectors=1)[0]
# return
return vector
def __get_translation_axis(self, direction):
# normalize direction
norm = np.sqrt(np.add.reduce(direction**2))
direction[0] /= norm
direction[1] /= norm
direction[2] /= norm
# get vector
if self.__angle is None:
vector = direction
else:
vector = generate_vectors_in_solid_angle(direction=direction,
maxAngle=self.__angle,
numberOfVectors=1)[0]
# return
return vector
def transform_coordinates(self, coordinates, argument=None):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply
the rotation.
#. argument (object): Not used here.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying
the rotation.
"""
if coordinates.shape[0] <= 1:
# atoms where removed, fall back to random translation
return coordinates + generate_random_vector(
minAmp=self.__amplitude[0], maxAmp=self.__amplitude[1])
else:
# create flip flag
if self.__flip is None:
flip = FLOAT_TYPE(np.sign(1 - 2 * generate_random_float()))
elif self.__flip:
flip = FLOAT_TYPE(-1)
else:
flip = FLOAT_TYPE(1)
# get group axis
groupAxis = self.__get_group_axis__(coordinates)
# get align axis within offset angle
orientationAxis = flip * self.__get_orientation_axis__()
orientationAxis = generate_vectors_in_solid_angle(
direction=orientationAxis,
maxAngle=self.__maximumOffsetAngle,
numberOfVectors=1)[0]
# get coordinates center
center = np.array(np.sum(coordinates, 0) / coordinates.shape[0],
dtype=FLOAT_TYPE)
# translate to origin
rotatedCoordinates = coordinates - center
# align coordinates
rotatedCoordinates = orient(rotatedCoordinates, groupAxis,
orientationAxis)
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates + center, dtype=FLOAT_TYPE)
def transform_coordinates(self, coordinates, argument=None):
"""
translate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply
the translation.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying
the translation.
#. argument (object): Not used here.
"""
if coordinates.shape[0]<=1:
# atoms where removed, fall back to random translation
return coordinates+generate_random_vector(minAmp=self.__amplitude[0],
maxAmp=self.__amplitude[1])
else:
# get axis
_,_,_,_,X,Y,Z =get_principal_axis(coordinates)
axis = [X,Y,Z][self.axis]
# generate translation axis
translationAxis = generate_vectors_in_solid_angle(direction=axis,
maxAngle=self.__angle,
numberOfVectors=1)[0]
# get translation amplitude
maxAmp = self.amplitude[1]-self.amplitude[0]
if self.direction is None:
amplitude = (1-2*generate_random_float())*maxAmp
elif self.direction:
amplitude = generate_random_float()*maxAmp
else:
amplitude = -generate_random_float()*maxAmp
# compute baseVector
baseVector = FLOAT_TYPE(np.sign(amplitude)*translationAxis*self.amplitude[0])
# compute translation vector
vector = baseVector + translationAxis*FLOAT_TYPE(amplitude)
# translate and return
return coordinates+vector
def transform_coordinates(self, coordinates, argument=None):
"""
Rotate coordinates.
:Parameters:
#. coordinates (np.ndarray): The coordinates on which to apply the rotation
#. argument (object): Any python object. Not used in this generator.
:Returns:
#. coordinates (np.ndarray): The new coordinates after applying the rotation.
"""
# create flip flag
if self.__flip is None:
flip = FLOAT_TYPE( np.sign(1-2*generate_random_float()) )
elif self.__flip:
flip = FLOAT_TYPE(-1)
else:
flip = FLOAT_TYPE(1)
# get group axis
groupAxis = self.__get_group_axis__(coordinates)
# get align axis within offset angle
orientationAxis = flip*self.__get_orientation_axis__()
orientationAxis = generate_vectors_in_solid_angle(direction=orientationAxis,
maxAngle=self.__maximumOffsetAngle,
numberOfVectors=1)[0]
# get coordinates center
center = np.array(np.sum(coordinates, 0)/coordinates.shape[0] , dtype=FLOAT_TYPE)
# translate to origin
rotatedCoordinates = coordinates-center
# align coordinates
rotatedCoordinates = orient(rotatedCoordinates, groupAxis, orientationAxis)
# translate back to center and return rotated coordinates
return np.array(rotatedCoordinates+center, dtype=FLOAT_TYPE)
