# Copyright 2018 United Kingdom Research and Innovation
# Copyright 2018 The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Authors:
# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
import copy
import math
import warnings
from numbers import Number
import numpy
from .labels import AcquisitionDimension, AngleUnit, AcquisitionType, FillType
from .acquisition_data import AcquisitionData
from .image_geometry import ImageGeometry
class ComponentDescription(object):
r'''This class enables the creation of vectors and unit vectors used to describe the components of a tomography system
'''
def __init__ (self, dof):
self._dof = dof
@staticmethod
def create_vector(val):
try:
vec = numpy.array(val, dtype=numpy.float64).reshape(len(val))
except:
raise ValueError("Can't convert to numpy array")
return vec
@staticmethod
def create_unit_vector(val):
vec = ComponentDescription.create_vector(val)
dot_product = vec.dot(vec)
if abs(dot_product)>1e-8:
vec = (vec/numpy.sqrt(dot_product))
else:
raise ValueError("Can't return a unit vector of a zero magnitude vector")
return vec
def length_check(self, val):
try:
val_length = len(val)
except:
raise ValueError("Vectors for {0}D geometries must have length = {0}. Got {1}".format(self._dof,val))
if val_length != self._dof:
raise ValueError("Vectors for {0}D geometries must have length = {0}. Got {1}".format(self._dof,val))
@staticmethod
def test_perpendicular(vector1, vector2):
dor_prod = vector1.dot(vector2)
if abs(dor_prod) <1e-10:
return True
return False
@staticmethod
def test_parallel(vector1, vector2):
'''For unit vectors only. Returns true if directions are opposite'''
dor_prod = vector1.dot(vector2)
if 1- abs(dor_prod) <1e-10:
return True
return False
class PositionVector(ComponentDescription):
r'''This class creates a component of a tomography system with a position attribute
'''
@property
def position(self):
try:
return self._position
except:
raise AttributeError
@position.setter
def position(self, val):
self.length_check(val)
self._position = ComponentDescription.create_vector(val)
class DirectionVector(ComponentDescription):
r'''This class creates a component of a tomography system with a direction attribute
'''
@property
def direction(self):
try:
return self._direction
except:
raise AttributeError
@direction.setter
def direction(self, val):
self.length_check(val)
self._direction = ComponentDescription.create_unit_vector(val)
class PositionDirectionVector(PositionVector, DirectionVector):
r'''This class creates a component of a tomography system with position and direction attributes
'''
pass
class Detector1D(PositionVector):
r'''This class creates a component of a tomography system with position and direction_x attributes used for 1D panels
'''
@property
def direction_x(self):
try:
return self._direction_x
except:
raise AttributeError
@direction_x.setter
def direction_x(self, val):
self.length_check(val)
self._direction_x = ComponentDescription.create_unit_vector(val)
@property
def normal(self):
try:
return ComponentDescription.create_unit_vector([self._direction_x[1], -self._direction_x[0]])
except:
raise AttributeError
class Detector2D(PositionVector):
r'''This class creates a component of a tomography system with position, direction_x and direction_y attributes used for 2D panels
'''
@property
def direction_x(self):
try:
return self._direction_x
except:
raise AttributeError
@property
def direction_y(self):
try:
return self._direction_y
except:
raise AttributeError
@property
def normal(self):
try:
return numpy.cross(self._direction_x, self._direction_y)
except:
raise AttributeError
def set_direction(self, x, y):
self.length_check(x)
x = ComponentDescription.create_unit_vector(x)
self.length_check(y)
y = ComponentDescription.create_unit_vector(y)
dot_product = x.dot(y)
if not numpy.isclose(dot_product, 0):
raise ValueError("vectors detector.direction_x and detector.direction_y must be orthogonal")
self._direction_y = y
self._direction_x = x
class SystemConfiguration:
'''This is a generic class to hold the description of a tomography system'''
SYSTEM_SIMPLE = 'simple'
SYSTEM_OFFSET = 'offset'
SYSTEM_ADVANCED = 'advanced'
@property
def dimension(self):
return self.acquisition_type.dimension
@property
def geometry(self):
return self.acquisition_type.geometry
@property
def acquisition_type(self):
return self._acquisition_type
@acquisition_type.setter
def acquisition_type(self, val):
self._acquisition_type = AcquisitionType(val).validate()
def __init__(self, dof: int, geometry, units='units'):
self.acquisition_type = AcquisitionType(f"{dof}D") | AcquisitionType(geometry)
self.units = units
if AcquisitionType.PARALLEL & self.geometry:
self.ray = DirectionVector(dof)
else:
self.source = PositionVector(dof)
if AcquisitionType.DIM2 & self.dimension:
self.detector = Detector1D(dof)
self.rotation_axis = PositionVector(dof)
else:
self.detector = Detector2D(dof)
self.rotation_axis = PositionDirectionVector(dof)
def __str__(self):
"""Implements the string representation of the system configuration
"""
raise NotImplementedError
def __eq__(self, other):
"""Implements the equality check of the system configuration
"""
raise NotImplementedError
@staticmethod
def rotation_vec_to_y(vec):
''' returns a rotation matrix that will rotate the projection of vec on the x-y plane to the +y direction [0,1, Z]'''
vec = ComponentDescription.create_unit_vector(vec)
axis_rotation = numpy.eye(len(vec))
if numpy.allclose(vec[:2],[0,1]):
pass
elif numpy.allclose(vec[:2],[0,-1]):
axis_rotation[0][0] = -1
axis_rotation[1][1] = -1
else:
theta = math.atan2(vec[0],vec[1])
axis_rotation[0][0] = axis_rotation[1][1] = math.cos(theta)
axis_rotation[0][1] = -math.sin(theta)
axis_rotation[1][0] = math.sin(theta)
return axis_rotation
@staticmethod
def rotation_vec_to_z(vec):
''' returns a rotation matrix that will align vec with the z-direction [0,0,1]'''
vec = ComponentDescription.create_unit_vector(vec)
if len(vec) == 2:
return numpy.array([[1, 0],[0, 1]])
elif len(vec) == 3:
axis_rotation = numpy.eye(3)
if numpy.allclose(vec,[0,0,1]):
pass
elif numpy.allclose(vec,[0,0,-1]):
axis_rotation = numpy.eye(3)
axis_rotation[1][1] = -1
axis_rotation[2][2] = -1
else:
vx = numpy.array([[0, 0, -vec[0]], [0, 0, -vec[1]], [vec[0], vec[1], 0]])
axis_rotation = numpy.eye(3) + vx + vx.dot(vx) * 1 / (1 + vec[2])
else:
raise ValueError("Vec must have length 3, got {}".format(len(vec)))
return axis_rotation
def update_reference_frame(self):
r'''Transforms the system origin to the rotation_axis position
'''
self.set_origin(self.rotation_axis.position)
def set_origin(self, origin):
r'''Transforms the system origin to the input origin
'''
translation = origin.copy()
if hasattr(self,'source'):
self.source.position -= translation
self.detector.position -= translation
self.rotation_axis.position -= translation
def get_centre_slice(self):
"""Returns the 2D system configuration corresponding to the centre slice
"""
raise NotImplementedError
def calculate_magnification(self):
r'''Calculates the magnification of the system using the source to rotate axis,
and source to detector distance along the direction.
:return: returns [dist_source_center, dist_center_detector, magnification], [0] distance from the source to the rotate axis, [1] distance from the rotate axis to the detector, [2] magnification of the system
:rtype: list
'''
raise NotImplementedError
def system_description(self):
r'''Returns `simple` if the the geometry matches the default definitions with no offsets or rotations,
\nReturns `offset` if the the geometry matches the default definitions with centre-of-rotation or detector offsets
\nReturns `advanced` if the the geometry has rotated or tilted rotation axis or detector, can also have offsets
'''
raise NotImplementedError
def copy(self):
'''returns a copy of SystemConfiguration'''
return copy.deepcopy(self)
class Parallel2D(SystemConfiguration):
r'''This class creates the SystemConfiguration of a parallel beam 2D tomographic system
:param ray_direction: A 2D vector describing the x-ray direction (x,y)
:type ray_direction: list, tuple, ndarray
:param detector_pos: A 2D vector describing the position of the centre of the detector (x,y)
:type detector_pos: list, tuple, ndarray
:param detector_direction_x: A 2D vector describing the direction of the detector_x (x,y)
:type detector_direction_x: list, tuple, ndarray
:param rotation_axis_pos: A 2D vector describing the position of the axis of rotation (x,y)
:type rotation_axis_pos: list, tuple, ndarray
:param units: Label the units of distance used for the configuration
:type units: string
'''
def __init__ (self, ray_direction, detector_pos, detector_direction_x, rotation_axis_pos, units='units'):
"""Constructor method
"""
super(Parallel2D, self).__init__(dof=2, geometry=AcquisitionType.PARALLEL, units=units)
#source
self.ray.direction = ray_direction
#detector
self.detector.position = detector_pos
self.detector.direction_x = detector_direction_x
#rotate axis
self.rotation_axis.position = rotation_axis_pos
def align_reference_frame(self, definition='cil'):
r'''Transforms and rotates the system to backend definitions
'cil' sets the origin to the rotation axis and aligns the y axis with the ray-direction
'tigre' sets the origin to the rotation axis and aligns the y axis with the ray-direction
'''
#in this instance definitions are the same
if definition not in ['cil','tigre']:
raise ValueError("Geometry can be configured for definition = 'cil' or 'tigre' only. Got {}".format(definition))
self.set_origin(self.rotation_axis.position)
rotation_matrix = SystemConfiguration.rotation_vec_to_y(self.ray.direction)
self.ray.direction = rotation_matrix.dot(self.ray.direction.reshape(2,1))
self.detector.position = rotation_matrix.dot(self.detector.position.reshape(2,1))
self.detector.direction_x = rotation_matrix.dot(self.detector.direction_x.reshape(2,1))
def system_description(self):
r'''Returns `simple` if the the geometry matches the default definitions with no offsets or rotations,
\nReturns `offset` if the the geometry matches the default definitions with centre-of-rotation or detector offsets
\nReturns `advanced` if the the geometry has rotated or tilted rotation axis or detector, can also have offsets
'''
rays_perpendicular_detector = ComponentDescription.test_parallel(self.ray.direction, self.detector.normal)
#rotation axis position + ray direction hits detector position
if numpy.allclose(self.rotation_axis.position, self.detector.position): #points are equal so on ray path
rotation_axis_centred = True
else:
vec_a = ComponentDescription.create_unit_vector(self.detector.position - self.rotation_axis.position)
rotation_axis_centred = ComponentDescription.test_parallel(self.ray.direction, vec_a)
if not rays_perpendicular_detector:
config = SystemConfiguration.SYSTEM_ADVANCED
elif not rotation_axis_centred:
config = SystemConfiguration.SYSTEM_OFFSET
else:
config = SystemConfiguration.SYSTEM_SIMPLE
return config
def rotation_axis_on_detector(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the world coordinate system
Returns
-------
cil.framework.system_configuration.PositionVector
Position in the 3D system
"""
Pv = self.rotation_axis.position
ratio = (self.detector.position - Pv).dot(self.detector.normal) / self.ray.direction.dot(self.detector.normal)
out = PositionVector(2)
out.position = Pv + self.ray.direction * ratio
return out
def calculate_centre_of_rotation(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the detector coordinate system
Note
----
- Origin is in the centre of the detector
- Axes directions are specified by detector.direction_x, detector.direction_y
- Units are the units of distance used to specify the component's positions
Returns
-------
Float
Offset position along the detector x_axis at y=0
Float
Angle between the y_axis and the rotation axis projection, in radians
"""
#convert to the detector coordinate system
dp1 = self.rotation_axis_on_detector().position - self.detector.position
offset = self.detector.direction_x.dot(dp1)
return (offset, 0.0)
def set_centre_of_rotation(self, offset):
""" Configures the geometry to have the requested centre of rotation offset at the detector
"""
offset_current = self.calculate_centre_of_rotation()[0]
offset_new = offset - offset_current
self.rotation_axis.position = self.rotation_axis.position + offset_new * self.detector.direction_x
def __str__(self):
def csv(val):
return numpy.array2string(val, separator=', ')
repres = "2D Parallel-beam tomography\n"
repres += "System configuration:\n"
repres += "\tRay direction: {0}\n".format(csv(self.ray.direction))
repres += "\tRotation axis position: {0}\n".format(csv(self.rotation_axis.position))
repres += "\tDetector position: {0}\n".format(csv(self.detector.position))
repres += "\tDetector direction x: {0}\n".format(csv(self.detector.direction_x))
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if numpy.allclose(self.ray.direction, other.ray.direction) \
and numpy.allclose(self.detector.position, other.detector.position)\
and numpy.allclose(self.detector.direction_x, other.detector.direction_x)\
and numpy.allclose(self.rotation_axis.position, other.rotation_axis.position):
return True
return False
def get_centre_slice(self):
return self
def calculate_magnification(self):
'''Method to calculate magnification and distance from the sample to
the detector using the detector positions and the rotation axis.
For parallel beam geometry magnification = 1
Returns
-------
list
A list containing the [0] distance from the source to the rotate
axis, [1] distance from the rotate axis to the detector,
[2] magnification of the system
'''
ab = (self.rotation_axis.position - self.detector.position)
dist_center_detector = float(numpy.sqrt(ab.dot(ab)))
return [None, dist_center_detector, 1.0]
class Parallel3D(SystemConfiguration):
r'''This class creates the SystemConfiguration of a parallel beam 3D tomographic system
:param ray_direction: A 3D vector describing the x-ray direction (x,y,z)
:type ray_direction: list, tuple, ndarray
:param detector_pos: A 3D vector describing the position of the centre of the detector (x,y,z)
:type detector_pos: list, tuple, ndarray
:param detector_direction_x: A 3D vector describing the direction of the detector_x (x,y,z)
:type detector_direction_x: list, tuple, ndarray
:param detector_direction_y: A 3D vector describing the direction of the detector_y (x,y,z)
:type detector_direction_y: list, tuple, ndarray
:param rotation_axis_pos: A 3D vector describing the position of the axis of rotation (x,y,z)
:type rotation_axis_pos: list, tuple, ndarray
:param rotation_axis_direction: A 3D vector describing the direction of the axis of rotation (x,y,z)
:type rotation_axis_direction: list, tuple, ndarray
:param units: Label the units of distance used for the configuration
:type units: string
'''
def __init__ (self, ray_direction, detector_pos, detector_direction_x, detector_direction_y, rotation_axis_pos, rotation_axis_direction, units='units'):
"""Constructor method
"""
super(Parallel3D, self).__init__(dof=3, geometry=AcquisitionType.PARALLEL, units=units)
#source
self.ray.direction = ray_direction
#detector
self.detector.position = detector_pos
self.detector.set_direction(detector_direction_x, detector_direction_y)
#rotate axis
self.rotation_axis.position = rotation_axis_pos
self.rotation_axis.direction = rotation_axis_direction
def align_z(self):
r'''Transforms the system origin to the rotate axis with z direction aligned to the rotate axis direction
'''
self.set_origin(self.rotation_axis.position)
#calculate rotation matrix to align rotation axis direction with z
rotation_matrix = SystemConfiguration.rotation_vec_to_z(self.rotation_axis.direction)
#apply transform
self.rotation_axis.direction = [0,0,1]
self.ray.direction = rotation_matrix.dot(self.ray.direction.reshape(3,1))
self.detector.position = rotation_matrix.dot(self.detector.position.reshape(3,1))
new_x = rotation_matrix.dot(self.detector.direction_x.reshape(3,1))
new_y = rotation_matrix.dot(self.detector.direction_y.reshape(3,1))
self.detector.set_direction(new_x, new_y)
def align_reference_frame(self, definition='cil'):
r'''Transforms and rotates the system to backend definitions
'''
#in this instance definitions are the same
if definition not in ['cil','tigre']:
raise ValueError("Geometry can be configured for definition = 'cil' or 'tigre' only. Got {}".format(definition))
self.align_z()
rotation_matrix = SystemConfiguration.rotation_vec_to_y(self.ray.direction)
self.ray.direction = rotation_matrix.dot(self.ray.direction.reshape(3,1))
self.detector.position = rotation_matrix.dot(self.detector.position.reshape(3,1))
new_direction_x = rotation_matrix.dot(self.detector.direction_x.reshape(3,1))
new_direction_y = rotation_matrix.dot(self.detector.direction_y.reshape(3,1))
self.detector.set_direction(new_direction_x, new_direction_y)
def system_description(self):
r'''Returns `simple` if the the geometry matches the default definitions with no offsets or rotations,
\nReturns `offset` if the the geometry matches the default definitions with centre-of-rotation or detector offsets
\nReturns `advanced` if the the geometry has rotated or tilted rotation axis or detector, can also have offsets
'''
'''
simple
- rays perpendicular to detector
- rotation axis parallel to detector y
- rotation axis position + ray direction hits detector with no x offset (y offsets allowed)
offset
- rays perpendicular to detector
- rotation axis parallel to detector y
rolled
- rays perpendicular to detector
- rays perpendicular to rotation axis
advanced
- not rays perpendicular to detector (for parallel just equates to an effective pixel size change?)
or
- not rays perpendicular to rotation axis (tilted, i.e. laminography)
'''
rays_perpendicular_detector = ComponentDescription.test_parallel(self.ray.direction, self.detector.normal)
rays_perpendicular_rotation = ComponentDescription.test_perpendicular(self.ray.direction, self.rotation_axis.direction)
rotation_parallel_detector_y = ComponentDescription.test_parallel(self.rotation_axis.direction, self.detector.direction_y)
#rotation axis to detector is parallel with ray
if numpy.allclose(self.rotation_axis.position, self.detector.position): #points are equal so on ray path
rotation_axis_centred = True
else:
vec_a = ComponentDescription.create_unit_vector(self.detector.position - self.rotation_axis.position)
rotation_axis_centred = ComponentDescription.test_parallel(self.ray.direction, vec_a)
if not rays_perpendicular_detector or\
not rays_perpendicular_rotation or\
not rotation_parallel_detector_y:
config = SystemConfiguration.SYSTEM_ADVANCED
elif not rotation_axis_centred:
config = SystemConfiguration.SYSTEM_OFFSET
else:
config = SystemConfiguration.SYSTEM_SIMPLE
return config
def __str__(self):
def csv(val):
return numpy.array2string(val, separator=', ')
repres = "3D Parallel-beam tomography\n"
repres += "System configuration:\n"
repres += "\tRay direction: {0}\n".format(csv(self.ray.direction))
repres += "\tRotation axis position: {0}\n".format(csv(self.rotation_axis.position))
repres += "\tRotation axis direction: {0}\n".format(csv(self.rotation_axis.direction))
repres += "\tDetector position: {0}\n".format(csv(self.detector.position))
repres += "\tDetector direction x: {0}\n".format(csv(self.detector.direction_x))
repres += "\tDetector direction y: {0}\n".format(csv(self.detector.direction_y))
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if numpy.allclose(self.ray.direction, other.ray.direction) \
and numpy.allclose(self.detector.position, other.detector.position)\
and numpy.allclose(self.detector.direction_x, other.detector.direction_x)\
and numpy.allclose(self.detector.direction_y, other.detector.direction_y)\
and numpy.allclose(self.rotation_axis.position, other.rotation_axis.position)\
and numpy.allclose(self.rotation_axis.direction, other.rotation_axis.direction):
return True
return False
def calculate_magnification(self):
'''Method to calculate magnification and distance from the sample to
the detector using the detector positions and the rotation axis.
For parallel beam geometry magnification = 1
Returns
-------
list
A list containing the [0] distance from the source to the rotate
axis, [1] distance from the rotate axis to the detector,
[2] magnification of the system
'''
ab = (self.rotation_axis.position - self.detector.position)
dist_center_detector = float(numpy.sqrt(ab.dot(ab)))
return [None, dist_center_detector, 1.0]
def get_centre_slice(self):
"""Returns the 2D system configuration corresponding to the centre slice
"""
dp1 = self.rotation_axis.direction.dot(self.ray.direction)
dp2 = self.rotation_axis.direction.dot(self.detector.direction_x)
if numpy.isclose(dp1, 0) and numpy.isclose(dp2, 0):
temp = self.copy()
#convert to rotation axis reference frame
temp.align_reference_frame()
ray_direction = temp.ray.direction[0:2]
detector_position = temp.detector.position[0:2]
detector_direction_x = temp.detector.direction_x[0:2]
rotation_axis_position = temp.rotation_axis.position[0:2]
return Parallel2D(ray_direction, detector_position, detector_direction_x, rotation_axis_position)
else:
raise ValueError('Cannot convert geometry to 2D. Requires axis of rotation to be perpendicular to ray direction and the detector direction x.')
def rotation_axis_on_detector(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the world coordinate system
Returns
-------
cil.framework.system_configuration.PositionDirectionVector
Position and direction in the 3D system
"""
#calculate the rotation axis line with the detector
vec_a = self.ray.direction
#calculate the intersection with the detector
Pv = self.rotation_axis.position
ratio = (self.detector.position - Pv).dot(self.detector.normal) / vec_a.dot(self.detector.normal)
point1 = Pv + vec_a * ratio
Pv = self.rotation_axis.position + self.rotation_axis.direction
ratio = (self.detector.position - Pv).dot(self.detector.normal) / vec_a.dot(self.detector.normal)
point2 = Pv + vec_a * ratio
out = PositionDirectionVector(3)
out.position = point1
out.direction = point2 - point1
return out
def calculate_centre_of_rotation(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the detector coordinate system
Note
----
- Origin is in the centre of the detector
- Axes directions are specified by detector.direction_x, detector.direction_y
- Units are the units of distance used to specify the component's positions
Returns
-------
Float
Offset position along the detector x_axis at y=0
Float
Angle between the y_axis and the rotation axis projection, in radians
"""
rotate_axis_projection = self.rotation_axis_on_detector()
p1 = rotate_axis_projection.position
p2 = p1 + rotate_axis_projection.direction
#point1 and point2 are on the detector plane. need to return them in the detector coordinate system
dp1 = p1 - self.detector.position
x1 = self.detector.direction_x.dot(dp1)
y1 = self.detector.direction_y.dot(dp1)
dp2 = p2 - self.detector.position
x2 = self.detector.direction_x.dot(dp2)
y2 = self.detector.direction_y.dot(dp2)
#y = m * x + c
#c = y1 - m * x1
#when y is 0
#x=-c/m
#x_y0 = -y1/m + x1
offset_x_y0 = x1 -y1 * (x2 - x1)/(y2-y1)
angle = math.atan2(x2 - x1, y2 - y1)
offset = offset_x_y0
return (offset, angle)
def set_centre_of_rotation(self, offset, angle):
""" Configures the geometry to have the requested centre of rotation offset at the detector
"""
#two points on the detector
x1 = offset
y1 = 0
x2 = offset + math.tan(angle)
y2 = 1
#convert to 3d coordinates in system frame
p1 = self.detector.position + x1 * self.detector.direction_x + y1 * self.detector.direction_y
p2 = self.detector.position + x2 * self.detector.direction_x + y2 * self.detector.direction_y
# find where vec p1 + t * ray dirn intersects plane defined by rotate axis (pos and dir) and det_x direction
vector_pos=p1
vec_dirn=self.ray.direction
plane_pos=self.rotation_axis.position
plane_normal = numpy.cross(self.detector.direction_x, self.rotation_axis.direction)
ratio = (plane_pos - vector_pos).dot(plane_normal) / vec_dirn.dot(plane_normal)
p1_on_plane = vector_pos + vec_dirn * ratio
vector_pos=p2
ratio = (plane_pos - vector_pos).dot(plane_normal) / vec_dirn.dot(plane_normal)
p2_on_plane = vector_pos + vec_dirn * ratio
self.rotation_axis.position = p1_on_plane
self.rotation_axis.direction = p2_on_plane - p1_on_plane
class Cone2D(SystemConfiguration):
r'''This class creates the SystemConfiguration of a cone beam 2D tomographic system
:param source_pos: A 2D vector describing the position of the source (x,y)
:type source_pos: list, tuple, ndarray
:param detector_pos: A 2D vector describing the position of the centre of the detector (x,y)
:type detector_pos: list, tuple, ndarray
:param detector_direction_x: A 2D vector describing the direction of the detector_x (x,y)
:type detector_direction_x: list, tuple, ndarray
:param rotation_axis_pos: A 2D vector describing the position of the axis of rotation (x,y)
:type rotation_axis_pos: list, tuple, ndarray
:param units: Label the units of distance used for the configuration
:type units: string
'''
def __init__ (self, source_pos, detector_pos, detector_direction_x, rotation_axis_pos, units='units'):
"""Constructor method
"""
super(Cone2D, self).__init__(dof=2, geometry=AcquisitionType.CONE, units=units)
#source
self.source.position = source_pos
#detector
self.detector.position = detector_pos
self.detector.direction_x = detector_direction_x
#rotate axis
self.rotation_axis.position = rotation_axis_pos
def align_reference_frame(self, definition='cil'):
r'''Transforms and rotates the system to backend definitions
'''
self.set_origin(self.rotation_axis.position)
if definition=='cil':
rotation_matrix = SystemConfiguration.rotation_vec_to_y(self.detector.position - self.source.position)
elif definition=='tigre':
rotation_matrix = SystemConfiguration.rotation_vec_to_y(self.rotation_axis.position - self.source.position)
else:
raise ValueError("Geometry can be configured for definition = 'cil' or 'tigre' only. Got {}".format(definition))
self.source.position = rotation_matrix.dot(self.source.position.reshape(2,1))
self.detector.position = rotation_matrix.dot(self.detector.position.reshape(2,1))
self.detector.direction_x = rotation_matrix.dot(self.detector.direction_x.reshape(2,1))
def system_description(self):
r'''Returns `simple` if the the geometry matches the default definitions with no offsets or rotations,
\nReturns `offset` if the the geometry matches the default definitions with centre-of-rotation or detector offsets
\nReturns `advanced` if the the geometry has rotated or tilted rotation axis or detector, can also have offsets
'''
vec_src2det = ComponentDescription.create_unit_vector(self.detector.position - self.source.position)
principal_ray_centred = ComponentDescription.test_parallel(vec_src2det, self.detector.normal)
#rotation axis to detector is parallel with centre ray
if numpy.allclose(self.rotation_axis.position, self.detector.position): #points are equal
rotation_axis_centred = True
else:
vec_b = ComponentDescription.create_unit_vector(self.detector.position - self.rotation_axis.position)
rotation_axis_centred = ComponentDescription.test_parallel(vec_src2det, vec_b)
if not principal_ray_centred:
config = SystemConfiguration.SYSTEM_ADVANCED
elif not rotation_axis_centred:
config = SystemConfiguration.SYSTEM_OFFSET
else:
config = SystemConfiguration.SYSTEM_SIMPLE
return config
def __str__(self):
def csv(val):
return numpy.array2string(val, separator=', ')
repres = "2D Cone-beam tomography\n"
repres += "System configuration:\n"
repres += "\tSource position: {0}\n".format(csv(self.source.position))
repres += "\tRotation axis position: {0}\n".format(csv(self.rotation_axis.position))
repres += "\tDetector position: {0}\n".format(csv(self.detector.position))
repres += "\tDetector direction x: {0}\n".format(csv(self.detector.direction_x))
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if numpy.allclose(self.source.position, other.source.position) \
and numpy.allclose(self.detector.position, other.detector.position)\
and numpy.allclose(self.detector.direction_x, other.detector.direction_x)\
and numpy.allclose(self.rotation_axis.position, other.rotation_axis.position):
return True
return False
def get_centre_slice(self):
return self
def calculate_magnification(self):
ab = (self.rotation_axis.position - self.source.position)
dist_source_center = float(numpy.sqrt(ab.dot(ab)))
ab_unit = ab / numpy.sqrt(ab.dot(ab))
n = self.detector.normal
#perpendicular distance between source and detector centre
sd = float((self.detector.position - self.source.position).dot(n))
ratio = float(ab_unit.dot(n))
source_to_detector = sd / ratio
dist_center_detector = source_to_detector - dist_source_center
magnification = (dist_center_detector + dist_source_center) / dist_source_center
return [dist_source_center, dist_center_detector, magnification]
def rotation_axis_on_detector(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the world coordinate system
Returns
-------
PositionVector
Position in the 3D system
"""
#calculate the point the rotation axis intersects with the detector
vec_a = self.rotation_axis.position - self.source.position
Pv = self.rotation_axis.position
ratio = (self.detector.position - Pv).dot(self.detector.normal) / vec_a.dot(self.detector.normal)
out = PositionVector(2)
out.position = Pv + vec_a * ratio
return out
def calculate_centre_of_rotation(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the detector coordinate system
Note
----
- Origin is in the centre of the detector
- Axes directions are specified by detector.direction_x, detector.direction_y
- Units are the units of distance used to specify the component's positions
Returns
-------
Float
Offset position along the detector x_axis at y=0
Float
Angle between the y_axis and the rotation axis projection, in radians
"""
#convert to the detector coordinate system
dp1 = self.rotation_axis_on_detector().position - self.detector.position
offset = self.detector.direction_x.dot(dp1)
return (offset, 0.0)
def set_centre_of_rotation(self, offset):
""" Configures the geometry to have the requested centre of rotation offset at the detector
"""
offset_current = self.calculate_centre_of_rotation()[0]
offset_new = offset - offset_current
cofr_shift = offset_new * self.detector.direction_x /self.calculate_magnification()[2]
self.rotation_axis.position =self.rotation_axis.position + cofr_shift
class Cone3D(SystemConfiguration):
r'''This class creates the SystemConfiguration of a cone beam 3D tomographic system
:param source_pos: A 3D vector describing the position of the source (x,y,z)
:type source_pos: list, tuple, ndarray
:param detector_pos: A 3D vector describing the position of the centre of the detector (x,y,z)
:type detector_pos: list, tuple, ndarray
:param detector_direction_x: A 3D vector describing the direction of the detector_x (x,y,z)
:type detector_direction_x: list, tuple, ndarray
:param detector_direction_y: A 3D vector describing the direction of the detector_y (x,y,z)
:type detector_direction_y: list, tuple, ndarray
:param rotation_axis_pos: A 3D vector describing the position of the axis of rotation (x,y,z)
:type rotation_axis_pos: list, tuple, ndarray
:param rotation_axis_direction: A 3D vector describing the direction of the axis of rotation (x,y,z)
:type rotation_axis_direction: list, tuple, ndarray
:param units: Label the units of distance used for the configuration
:type units: string
'''
def __init__ (self, source_pos, detector_pos, detector_direction_x, detector_direction_y, rotation_axis_pos, rotation_axis_direction, units='units'):
"""Constructor method
"""
super(Cone3D, self).__init__(dof=3, geometry=AcquisitionType.CONE, units=units)
#source
self.source.position = source_pos
#detector
self.detector.position = detector_pos
self.detector.set_direction(detector_direction_x, detector_direction_y)
#rotate axis
self.rotation_axis.position = rotation_axis_pos
self.rotation_axis.direction = rotation_axis_direction
def align_z(self):
r'''Transforms the system origin to the rotate axis with z direction aligned to the rotate axis direction
'''
self.set_origin(self.rotation_axis.position)
rotation_matrix = SystemConfiguration.rotation_vec_to_z(self.rotation_axis.direction)
#apply transform
self.rotation_axis.direction = [0,0,1]
self.source.position = rotation_matrix.dot(self.source.position.reshape(3,1))
self.detector.position = rotation_matrix.dot(self.detector.position.reshape(3,1))
new_x = rotation_matrix.dot(self.detector.direction_x.reshape(3,1))
new_y = rotation_matrix.dot(self.detector.direction_y.reshape(3,1))
self.detector.set_direction(new_x, new_y)
def align_reference_frame(self, definition='cil'):
r'''Transforms and rotates the system to backend definitions
'''
self.align_z()
if definition=='cil':
rotation_matrix = SystemConfiguration.rotation_vec_to_y(self.detector.position - self.source.position)
elif definition=='tigre':
rotation_matrix = SystemConfiguration.rotation_vec_to_y(self.rotation_axis.position - self.source.position)
else:
raise ValueError("Geometry can be configured for definition = 'cil' or 'tigre' only. Got {}".format(definition))
self.source.position = rotation_matrix.dot(self.source.position.reshape(3,1))
self.detector.position = rotation_matrix.dot(self.detector.position.reshape(3,1))
new_direction_x = rotation_matrix.dot(self.detector.direction_x.reshape(3,1))
new_direction_y = rotation_matrix.dot(self.detector.direction_y.reshape(3,1))
self.detector.set_direction(new_direction_x, new_direction_y)
def system_description(self):
r'''Returns `simple` if the the geometry matches the default definitions with no offsets or rotations,
\nReturns `offset` if the the geometry matches the default definitions with centre-of-rotation or detector offsets
\nReturns `advanced` if the the geometry has rotated or tilted rotation axis or detector, can also have offsets
'''
vec_src2det = ComponentDescription.create_unit_vector(self.detector.position - self.source.position)
principal_ray_centred = ComponentDescription.test_parallel(vec_src2det, self.detector.normal)
centre_ray_perpendicular_rotation = ComponentDescription.test_perpendicular(vec_src2det, self.rotation_axis.direction)
rotation_parallel_detector_y = ComponentDescription.test_parallel(self.rotation_axis.direction, self.detector.direction_y)
#rotation axis to detector is parallel with centre ray
if numpy.allclose(self.rotation_axis.position, self.detector.position): #points are equal
rotation_axis_centred = True
else:
vec_b = ComponentDescription.create_unit_vector(self.detector.position - self.rotation_axis.position)
rotation_axis_centred = ComponentDescription.test_parallel(vec_src2det, vec_b)
if not principal_ray_centred or\
not centre_ray_perpendicular_rotation or\
not rotation_parallel_detector_y:
config = SystemConfiguration.SYSTEM_ADVANCED
elif not rotation_axis_centred:
config = SystemConfiguration.SYSTEM_OFFSET
else:
config = SystemConfiguration.SYSTEM_SIMPLE
return config
def get_centre_slice(self):
"""Returns the 2D system configuration corresponding to the centre slice
"""
#requires the rotate axis to be perpendicular to the normal of the detector, and perpendicular to detector_direction_x
dp1 = self.rotation_axis.direction.dot(self.detector.normal)
dp2 = self.rotation_axis.direction.dot(self.detector.direction_x)
if numpy.isclose(dp1, 0) and numpy.isclose(dp2, 0):
temp = self.copy()
temp.align_reference_frame()
source_position = temp.source.position[0:2]
detector_position = temp.detector.position[0:2]
detector_direction_x = temp.detector.direction_x[0:2]
rotation_axis_position = temp.rotation_axis.position[0:2]
return Cone2D(source_position, detector_position, detector_direction_x, rotation_axis_position)
else:
raise ValueError('Cannot convert geometry to 2D. Requires axis of rotation to be perpendicular to the detector.')
def __str__(self):
def csv(val):
return numpy.array2string(val, separator=', ')
repres = "3D Cone-beam tomography\n"
repres += "System configuration:\n"
repres += "\tSource position: {0}\n".format(csv(self.source.position))
repres += "\tRotation axis position: {0}\n".format(csv(self.rotation_axis.position))
repres += "\tRotation axis direction: {0}\n".format(csv(self.rotation_axis.direction))
repres += "\tDetector position: {0}\n".format(csv(self.detector.position))
repres += "\tDetector direction x: {0}\n".format(csv(self.detector.direction_x))
repres += "\tDetector direction y: {0}\n".format(csv(self.detector.direction_y))
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if numpy.allclose(self.source.position, other.source.position) \
and numpy.allclose(self.detector.position, other.detector.position)\
and numpy.allclose(self.detector.direction_x, other.detector.direction_x)\
and numpy.allclose(self.detector.direction_y, other.detector.direction_y)\
and numpy.allclose(self.rotation_axis.position, other.rotation_axis.position)\
and numpy.allclose(self.rotation_axis.direction, other.rotation_axis.direction):
return True
return False
def calculate_magnification(self):
ab = (self.rotation_axis.position - self.source.position)
dist_source_center = float(numpy.sqrt(ab.dot(ab)))
ab_unit = ab / numpy.sqrt(ab.dot(ab))
n = self.detector.normal
#perpendicular distance between source and detector centre
sd = float((self.detector.position - self.source.position).dot(n))
ratio = float(ab_unit.dot(n))
source_to_detector = sd / ratio
dist_center_detector = source_to_detector - dist_source_center
magnification = (dist_center_detector + dist_source_center) / dist_source_center
return [dist_source_center, dist_center_detector, magnification]
def rotation_axis_on_detector(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the world coordinate system
Returns
-------
PositionDirectionVector
Position and direction in the 3D system
"""
#calculate the intersection with the detector, of source to pv
Pv = self.rotation_axis.position
vec_a = Pv - self.source.position
ratio = (self.detector.position - Pv).dot(self.detector.normal) / vec_a.dot(self.detector.normal)
point1 = Pv + vec_a * ratio
#calculate the intersection with the detector, of source to pv
Pv = self.rotation_axis.position + self.rotation_axis.direction
vec_a = Pv - self.source.position
ratio = (self.detector.position - Pv).dot(self.detector.normal) / vec_a.dot(self.detector.normal)
point2 = Pv + vec_a * ratio
out = PositionDirectionVector(3)
out.position = point1
out.direction = point2 - point1
return out
def calculate_centre_of_rotation(self):
"""
Calculates the position, on the detector, of the projection of the rotation axis in the detector coordinate system
Note
----
- Origin is in the centre of the detector
- Axes directions are specified by detector.direction_x, detector.direction_y
- Units are the units of distance used to specify the component's positions
Returns
-------
Float
Offset position along the detector x_axis at y=0
Float
Angle between the y_axis and the rotation axis projection, in radians
"""
rotate_axis_projection = self.rotation_axis_on_detector()
p1 = rotate_axis_projection.position
p2 = p1 + rotate_axis_projection.direction
#point1 and point2 are on the detector plane. need to return them in the detector coordinate system
dp1 = p1 - self.detector.position
x1 = self.detector.direction_x.dot(dp1)
y1 = self.detector.direction_y.dot(dp1)
dp2 = p2 - self.detector.position
x2 = self.detector.direction_x.dot(dp2)
y2 = self.detector.direction_y.dot(dp2)
#y = m * x + c
#c = y1 - m * x1
#when y is 0
#x=-c/m
#x_y0 = -y1/m + x1
offset_x_y0 = x1 -y1 * (x2 - x1)/(y2-y1)
angle = math.atan2(x2 - x1, y2 - y1)
offset = offset_x_y0
return (offset, angle)
def set_centre_of_rotation(self, offset, angle):
""" Configures the geometry to have the requested centre of rotation offset at the detector
"""
#two points on the detector
x1 = offset
y1 = 0
x2 = offset + math.tan(angle)
y2 = 1
#convert to 3d coordinates in system frame
p1 = self.detector.position + x1 * self.detector.direction_x + y1 * self.detector.direction_y
p2 = self.detector.position + x2 * self.detector.direction_x + y2 * self.detector.direction_y
# vectors from source define plane
sp1 = p1 - self.source.position
sp2 = p2 - self.source.position
#find vector intersection with a plane defined by rotate axis (pos and dir) and det_x direction
plane_normal = numpy.cross(self.rotation_axis.direction, self.detector.direction_x)
ratio = (self.rotation_axis.position - self.source.position).dot(plane_normal) / sp1.dot(plane_normal)
p1_on_plane = self.source.position + sp1 * ratio
ratio = (self.rotation_axis.position - self.source.position).dot(plane_normal) / sp2.dot(plane_normal)
p2_on_plane = self.source.position + sp2 * ratio
self.rotation_axis.position = p1_on_plane
self.rotation_axis.direction = p2_on_plane - p1_on_plane
class Panel(object):
r'''This is a class describing the panel of the system.
:param num_pixels: num_pixels_h or (num_pixels_h, num_pixels_v) containing the number of pixels of the panel
:type num_pixels: int, list, tuple
:param pixel_size: pixel_size_h or (pixel_size_h, pixel_size_v) containing the size of the pixels of the panel
:type pixel_size: int, lust, tuple
:param origin: the position of pixel 0 (the data origin) of the panel `top-left`, `top-right`, `bottom-left`, `bottom-right`
:type origin: string
'''
@property
def num_pixels(self):
return self._num_pixels
@num_pixels.setter
def num_pixels(self, val):
if isinstance(val,int):
num_pixels_temp = [val, 1]
else:
try:
length_val = len(val)
except:
raise TypeError('num_pixels expected int x or [int x, int y]. Got {}'.format(type(val)))
if length_val == 2:
try:
val0 = int(val[0])
val1 = int(val[1])
except:
raise TypeError('num_pixels expected int x or [int x, int y]. Got {0},{1}'.format(type(val[0]), type(val[1])))
num_pixels_temp = [val0, val1]
else:
raise ValueError('num_pixels expected int x or [int x, int y]. Got {}'.format(val))
if num_pixels_temp[1] > 1 and self._dimension == 2:
raise ValueError('2D acquisitions expects a 1D panel. Expected num_pixels[1] = 1. Got {}'.format(num_pixels_temp[1]))
if num_pixels_temp[0] < 1 or num_pixels_temp[1] < 1:
raise ValueError('num_pixels (x,y) must be >= (1,1). Got {}'.format(num_pixels_temp))
else:
self._num_pixels = numpy.array(num_pixels_temp, dtype=numpy.int16)
@property
def pixel_size(self):
return self._pixel_size
@pixel_size.setter
def pixel_size(self, val):
if val is None:
pixel_size_temp = [1.0,1.0]
else:
try:
length_val = len(val)
except:
try:
temp = float(val)
pixel_size_temp = [temp, temp]
except:
raise TypeError('pixel_size expected float xy or [float x, float y]. Got {}'.format(val))
else:
if length_val == 2:
try:
temp0 = float(val[0])
temp1 = float(val[1])
pixel_size_temp = [temp0, temp1]
except:
raise ValueError('pixel_size expected float xy or [float x, float y]. Got {}'.format(val))
else:
raise ValueError('pixel_size expected float xy or [float x, float y]. Got {}'.format(val))
if pixel_size_temp[0] <= 0 or pixel_size_temp[1] <= 0:
raise ValueError('pixel_size (x,y) at must be > (0.,0.). Got {}'.format(pixel_size_temp))
self._pixel_size = numpy.array(pixel_size_temp)
@property
def origin(self):
return self._origin
@origin.setter
def origin(self, val):
allowed = ['top-left', 'top-right','bottom-left','bottom-right']
if val in allowed:
self._origin=val
else:
raise ValueError('origin expected one of {0}. Got {1}'.format(allowed, val))
def __str__(self):
repres = "Panel configuration:\n"
repres += "\tNumber of pixels: {0}\n".format(self.num_pixels)
repres += "\tPixel size: {0}\n".format(self.pixel_size)
repres += "\tPixel origin: {0}\n".format(self.origin)
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if numpy.array_equal(self.num_pixels, other.num_pixels) \
and numpy.allclose(self.pixel_size, other.pixel_size) \
and self.origin == other.origin:
return True
return False
def __init__ (self, num_pixels, pixel_size, origin, dimension):
"""Constructor method
"""
self._dimension = dimension
self.num_pixels = num_pixels
self.pixel_size = pixel_size
self.origin = origin
class Channels(object):
r'''This is a class describing the channels of the data.
This will be created on initialisation of AcquisitionGeometry.
:param num_channels: The number of channels of data
:type num_channels: int
:param channel_labels: A list of channel labels
:type channel_labels: list, optional
'''
@property
def num_channels(self):
return self._num_channels
@num_channels.setter
def num_channels(self, val):
try:
val = int(val)
except TypeError:
raise ValueError('num_channels expected a positive integer. Got {}'.format(type(val)))
if val > 0:
self._num_channels = val
else:
raise ValueError('num_channels expected a positive integer. Got {}'.format(val))
@property
def channel_labels(self):
return self._channel_labels
@channel_labels.setter
def channel_labels(self, val):
if val is None or len(val) == self._num_channels:
self._channel_labels = val
else:
raise ValueError('labels expected to have length {0}. Got {1}'.format(self._num_channels, len(val)))
def __str__(self):
repres = "Channel configuration:\n"
repres += "\tNumber of channels: {0}\n".format(self.num_channels)
num_print=min(10,self.num_channels)
if hasattr(self, 'channel_labels'):
repres += "\tChannel labels 0-{0}: {1}\n".format(num_print, self.channel_labels[0:num_print])
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if self.num_channels != other.num_channels:
return False
if hasattr(self,'channel_labels'):
if self.channel_labels != other.channel_labels:
return False
return True
def __init__ (self, num_channels, channel_labels):
"""Constructor method
"""
self.num_channels = num_channels
if channel_labels is not None:
self.channel_labels = channel_labels
class Angles(object):
r'''This is a class describing the angles of the data.
:param angles: The angular positions of the acquisition data
:type angles: list, ndarray
:param initial_angle: The angular offset of the object from the reference frame
:type initial_angle: float, optional
:param angle_unit: The units of the stored angles 'degree' or 'radian'
:type angle_unit: string
'''
@property
def angle_data(self):
return self._angle_data
@angle_data.setter
def angle_data(self, val):
if val is None:
raise ValueError('angle_data expected to be a list of floats')
else:
try:
self.num_positions = len(val)
except TypeError:
self.num_positions = 1
val = [val]
finally:
try:
self._angle_data = numpy.asarray(val, dtype=numpy.float32)
except:
raise ValueError('angle_data expected to be a list of floats')
@property
def initial_angle(self):
return self._initial_angle
@initial_angle.setter
def initial_angle(self, val):
try:
val = float(val)
except:
raise TypeError('initial_angle expected a float. Got {0}'.format(type(val)))
self._initial_angle = val
@property
def angle_unit(self):
return self._angle_unit.value
@angle_unit.setter
def angle_unit(self,val):
self._angle_unit = AngleUnit(val)
def __str__(self):
repres = "Acquisition description:\n"
repres += "\tNumber of positions: {0}\n".format(self.num_positions)
# max_num_print = 30
if self.num_positions < 31:
repres += "\tAngles 0-{0} in {1}s: {2}\n".format(self.num_positions-1, self.angle_unit, numpy.array2string(self.angle_data[0:self.num_positions], separator=', '))
else:
repres += "\tAngles 0-9 in {0}s: {1}\n".format(self.angle_unit, numpy.array2string(self.angle_data[0:10], separator=', '))
repres += "\tAngles {0}-{1} in {2}s: {3}\n".format(self.num_positions-10, self.num_positions-1, self.angle_unit, numpy.array2string(self.angle_data[self.num_positions-10:self.num_positions], separator=', '))
repres += "\tFull angular array can be accessed with acquisition_data.geometry.angles\n"
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if self.angle_unit != other.angle_unit:
return False
if self.initial_angle != other.initial_angle:
return False
if not numpy.allclose(self.angle_data, other.angle_data):
return False
return True
def __init__ (self, angles, initial_angle, angle_unit):
"""Constructor method
"""
self.angle_data = angles
self.initial_angle = initial_angle
self.angle_unit = angle_unit
class Configuration(object):
r'''This class holds the description of the system components.
'''
def __init__(self, units_distance='units distance'):
self.system = None #has distances
self.angles = None #has angles
self.panel = None #has distances
self.channels = Channels(1, None)
self.units = units_distance
@property
def configured(self):
if self.system is None:
print("Please configure AcquisitionGeometry using one of the following methods:\
\n\tAcquisitionGeometry.create_Parallel2D()\
\n\tAcquisitionGeometry.create_Cone3D()\
\n\tAcquisitionGeometry.create_Parallel2D()\
\n\tAcquisitionGeometry.create_Cone3D()")
return False
configured = True
if self.angles is None:
print("Please configure angular data using the set_angles() method")
configured = False
if self.panel is None:
print("Please configure the panel using the set_panel() method")
configured = False
return configured
def shift_detector_in_plane(self,
pixel_offset,
direction='horizontal'):
"""
Adjusts the position of the detector in a specified direction within the imaging plane.
Parameters:
-----------
pixel_offset : float
The number of pixels to adjust the detector's position by.
direction : {'horizontal', 'vertical'}, optional
The direction in which to adjust the detector's position. Defaults to 'horizontal'.
Notes:
------
- If `direction` is 'horizontal':
- If the panel's origin is 'left', positive offsets translate the detector to the right.
- If the panel's origin is 'right', positive offsets translate the detector to the left.
- If `direction` is 'vertical':
- If the panel's origin is 'bottom', positive offsets translate the detector upward.
- If the panel's origin is 'top', positive offsets translate the detector downward.
Returns:
--------
None
"""
if direction == 'horizontal':
pixel_size = self.panel.pixel_size[0]
pixel_direction = self.system.detector.direction_x
elif direction == 'vertical':
pixel_size = self.panel.pixel_size[1]
pixel_direction = self.system.detector.direction_y
if 'bottom' in self.panel.origin or 'left' in self.panel.origin:
self.system.detector.position -= pixel_offset * pixel_direction * pixel_size
else:
self.system.detector.position += pixel_offset * pixel_direction * pixel_size
def __str__(self):
repres = ""
if self.configured:
repres += str(self.system)
repres += str(self.panel)
repres += str(self.channels)
repres += str(self.angles)
repres += "Distances in units: {}".format(self.units)
return repres
def __eq__(self, other):
if not isinstance(other, self.__class__):
return False
if self.system == other.system\
and self.panel == other.panel\
and self.channels == other.channels\
and self.angles == other.angles:
return True
return False
[docs]
class AcquisitionGeometry(object):
"""This class holds the AcquisitionGeometry of the system.
Please initialise the AcquisitionGeometry using the using the static methods:
`AcquisitionGeometry.create_Parallel2D()`
`AcquisitionGeometry.create_Cone2D()`
`AcquisitionGeometry.create_Parallel3D()`
`AcquisitionGeometry.create_Cone3D()`
"""
#for backwards compatibility
@property
def ANGLE(self):
warnings.warn("use AcquisitionDimension.Angle instead", DeprecationWarning, stacklevel=2)
return AcquisitionDimension.ANGLE
@property
def CHANNEL(self):
warnings.warn("use AcquisitionDimension.Channel instead", DeprecationWarning, stacklevel=2)
return AcquisitionDimension.CHANNEL
@property
def DEGREE(self):
warnings.warn("use AngleUnit.DEGREE", DeprecationWarning, stacklevel=2)
return AngleUnit.DEGREE
@property
def HORIZONTAL(self):
warnings.warn("use AcquisitionDimension.HORIZONTAL instead", DeprecationWarning, stacklevel=2)
return AcquisitionDimension.HORIZONTAL
@property
def RADIAN(self):
warnings.warn("use AngleUnit.RADIAN instead", DeprecationWarning, stacklevel=2)
return AngleUnit.RADIAN
@property
def VERTICAL(self):
warnings.warn("use AcquisitionDimension.VERTICAL instead", DeprecationWarning, stacklevel=2)
return AcquisitionDimension.VERTICAL
@property
def geom_type(self):
return self.config.system.geometry
@property
def num_projections(self):
return len(self.angles)
@property
def pixel_num_h(self):
return self.config.panel.num_pixels[0]
@pixel_num_h.setter
def pixel_num_h(self, val):
self.config.panel.num_pixels[0] = val
@property
def pixel_num_v(self):
return self.config.panel.num_pixels[1]
@pixel_num_v.setter
def pixel_num_v(self, val):
self.config.panel.num_pixels[1] = val
@property
def pixel_size_h(self):
return self.config.panel.pixel_size[0]
@pixel_size_h.setter
def pixel_size_h(self, val):
self.config.panel.pixel_size[0] = val
@property
def pixel_size_v(self):
return self.config.panel.pixel_size[1]
@pixel_size_v.setter
def pixel_size_v(self, val):
self.config.panel.pixel_size[1] = val
@property
def channels(self):
return self.config.channels.num_channels
@property
def angles(self):
return self.config.angles.angle_data
@property
def dist_source_center(self):
out = self.config.system.calculate_magnification()
return out[0]
@property
def dist_center_detector(self):
out = self.config.system.calculate_magnification()
return out[1]
@property
def magnification(self):
out = self.config.system.calculate_magnification()
return out[2]
@property
def dimension(self):
return self.config.system.dimension
@property
def shape(self):
shape_dict = {AcquisitionDimension.CHANNEL: self.config.channels.num_channels,
AcquisitionDimension.ANGLE: self.config.angles.num_positions,
AcquisitionDimension.VERTICAL: self.config.panel.num_pixels[1],
AcquisitionDimension.HORIZONTAL: self.config.panel.num_pixels[0]}
return tuple(shape_dict[label] for label in self.dimension_labels)
@property
def dimension_labels(self):
labels_default = AcquisitionDimension.get_order_for_engine("cil")
shape_default = [self.config.channels.num_channels,
self.config.angles.num_positions,
self.config.panel.num_pixels[1],
self.config.panel.num_pixels[0]
]
try:
labels = self._dimension_labels
except AttributeError:
labels = labels_default
labels = list(labels)
#remove from list labels where len == 1
#
for i, x in enumerate(shape_default):
if x == 0 or x==1:
try:
labels.remove(labels_default[i])
except ValueError:
pass #if not in custom list carry on
return tuple(labels)
@dimension_labels.setter
def dimension_labels(self, val):
if val is not None:
self._dimension_labels = tuple(map(AcquisitionDimension, val))
@property
def ndim(self):
return len(self.dimension_labels)
@property
def system_description(self):
return self.config.system.system_description()
@property
def dtype(self):
return self._dtype
@dtype.setter
def dtype(self, val):
self._dtype = val
def __init__(self):
self._dtype = numpy.float32
def get_centre_of_rotation(self, distance_units='default', angle_units='radian'):
"""
Returns the system centre of rotation offset at the detector
Note
----
- Origin is in the centre of the detector
- Axes directions are specified by detector.direction_x, detector.direction_y
Parameters
----------
distance_units : string, default='default'
Units of distance used to calculate the return values.
'default' uses the same units the system and panel were specified in.
'pixels' uses pixels sizes in the horizontal and vertical directions as appropriate.
angle_units : string
Units to return the angle in. Can take 'radian' or 'degree'.
Returns
-------
Dictionary
{'offset': (offset, distance_units), 'angle': (angle, angle_units)}
where,
'offset' gives the position along the detector x_axis at y=0
'angle' gives the angle between the y_axis and the projection of the rotation axis on the detector
"""
if hasattr(self.config.system, 'calculate_centre_of_rotation'):
offset_distance, angle_rad = self.config.system.calculate_centre_of_rotation()
else:
raise NotImplementedError
if distance_units == 'default':
offset = offset_distance
offset_units = self.config.units
elif distance_units == 'pixels':
offset = offset_distance/ self.config.panel.pixel_size[0]
offset_units = 'pixels'
if AcquisitionType.DIM3 & self.dimension and self.config.panel.pixel_size[0] != self.config.panel.pixel_size[1]:
#if aspect ratio of pixels isn't 1:1 need to convert angle by new ratio
y_pix = 1 /self.config.panel.pixel_size[1]
x_pix = math.tan(angle_rad)/self.config.panel.pixel_size[0]
angle_rad = math.atan2(x_pix,y_pix)
else:
raise ValueError("`distance_units` is not recognised. Must be 'default' or 'pixels'. Got {}".format(distance_units))
angle_units = AngleUnit(angle_units)
angle = angle_rad
if angle_units == AngleUnit.DEGREE:
angle = numpy.degrees(angle_rad)
return {'offset': (offset, offset_units), 'angle': (angle, angle_units.value)}
def set_centre_of_rotation(self, offset=0.0, distance_units='default', angle=0.0, angle_units='radian'):
"""
Configures the system geometry to have the requested centre of rotation offset at the detector.
Note
----
- Origin is in the centre of the detector
- Axes directions are specified by detector.direction_x, detector.direction_y
Parameters
----------
offset: float, default 0.0
The position of the centre of rotation along the detector x_axis at y=0
distance_units : string, default='default'
Units the offset is specified in. Can be 'default'or 'pixels'.
'default' interprets the input as same units the system and panel were specified in.
'pixels' interprets the input in horizontal pixels.
angle: float, default=0.0
The angle between the detector y_axis and the rotation axis direction on the detector
Notes
-----
If aspect ratio of pixels is not 1:1 ensure the angle is calculated from the x and y values in the correct units.
angle_units : string, default='radian'
Units the angle is specified in. Can take 'radian' or 'degree'.
"""
if not hasattr(self.config.system, 'set_centre_of_rotation'):
raise NotImplementedError()
angle_units = AngleUnit(angle_units)
angle_rad = angle
if angle_units == AngleUnit.DEGREE:
angle_rad = numpy.radians(angle)
if distance_units =='default':
offset_distance = offset
elif distance_units =='pixels':
offset_distance = offset * self.config.panel.pixel_size[0]
else:
raise ValueError("`distance_units` is not recognised. Must be 'default' or 'pixels'. Got {}".format(distance_units))
if AcquisitionType.DIM2 & self.dimension:
self.config.system.set_centre_of_rotation(offset_distance)
else:
self.config.system.set_centre_of_rotation(offset_distance, angle_rad)
def set_centre_of_rotation_by_slice(self, offset1, slice_index1=None, offset2=None, slice_index2=None):
"""
Configures the system geometry to have the requested centre of rotation offset at the detector.
If two slices are passed the rotation axis will be rotated to pass through both points.
Note
----
- Offset is specified in pixels
- Offset can be sub-pixels
- Offset direction is specified by detector.direction_x
Parameters
----------
offset1: float
The offset from the centre of the detector to the projected rotation position at slice_index_1
slice_index1: int, optional
The slice number of offset1
offset2: float, optional
The offset from the centre of the detector to the projected rotation position at slice_index_2
slice_index2: int, optional
The slice number of offset2
"""
if not hasattr(self.config.system, 'set_centre_of_rotation'):
raise NotImplementedError()
if AcquisitionType.DIM2 & self.dimension:
if offset2 is not None:
warnings.warn("2D so offset2 is ingored", UserWarning, stacklevel=2)
self.set_centre_of_rotation(offset1)
if offset2 is None or offset1 == offset2:
offset_x_y0 = offset1
angle = 0
else:
if slice_index1 is None or slice_index2 is None or slice_index1 == slice_index2:
raise ValueError("Cannot calculate angle. Please specify `slice_index1` and `slice_index2` to define a rotated axis")
offset_x_y0 = offset1 -slice_index1 * (offset2 - offset1)/(slice_index2-slice_index1)
angle = math.atan2(offset2 - offset1, slice_index2 - slice_index1)
self.set_centre_of_rotation(offset_x_y0, 'pixels', angle, 'radian')
[docs]
def set_angles(self, angles, initial_angle=0, angle_unit='degree'):
r'''This method configures the angular information of an AcquisitionGeometry object.
:param angles: The angular positions of the acquisition data
:type angles: list, ndarray
:param initial_angle: The angular offset of the object from the reference frame
:type initial_angle: float, optional
:param angle_unit: The units of the stored angles 'degree' or 'radian'
:type angle_unit: string
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
self.config.angles = Angles(angles, initial_angle, angle_unit)
return self
[docs]
def set_panel(self, num_pixels, pixel_size=(1,1), origin='bottom-left'):
r'''This method configures the panel information of an AcquisitionGeometry object.
:param num_pixels: num_pixels_h or (num_pixels_h, num_pixels_v) containing the number of pixels of the panel
:type num_pixels: int, list, tuple
:param pixel_size: pixel_size_h or (pixel_size_h, pixel_size_v) containing the size of the pixels of the panel
:type pixel_size: int, list, tuple, optional
:param origin: the position of pixel 0 (the data origin) of the panel 'top-left', 'top-right', 'bottom-left', 'bottom-right'
:type origin: string, default 'bottom-left'
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
dof = {AcquisitionType.DIM2: 2, AcquisitionType.DIM3: 3}[self.config.system.dimension]
self.config.panel = Panel(num_pixels, pixel_size, origin, dof)
return self
[docs]
def set_channels(self, num_channels=1, channel_labels=None):
r'''This method configures the channel information of an AcquisitionGeometry object.
:param num_channels: The number of channels of data
:type num_channels: int, optional
:param channel_labels: A list of channel labels
:type channel_labels: list, optional
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
self.config.channels = Channels(num_channels, channel_labels)
return self
[docs]
def set_labels(self, labels=None):
r'''This method configures the dimension labels of an AcquisitionGeometry object.
:param labels: The order of the dimensions describing the data.\
Expects a list containing at least one of the unique labels: 'channel' 'angle' 'vertical' 'horizontal'
default = ['channel','angle','vertical','horizontal']
:type labels: list, optional
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
self.dimension_labels = labels
return self
[docs]
@staticmethod
def create_Parallel2D(ray_direction=[0, 1], detector_position=[0, 0], detector_direction_x=[1, 0], rotation_axis_position=[0, 0], units='units distance'):
r'''This creates the AcquisitionGeometry for a parallel beam 2D tomographic system
:param ray_direction: A 2D vector describing the x-ray direction (x,y)
:type ray_direction: list, tuple, ndarray, optional
:param detector_position: A 2D vector describing the position of the centre of the detector (x,y)
:type detector_position: list, tuple, ndarray, optional
:param detector_direction_x: A 2D vector describing the direction of the detector_x (x,y)
:type detector_direction_x: list, tuple, ndarray
:param rotation_axis_position: A 2D vector describing the position of the axis of rotation (x,y)
:type rotation_axis_position: list, tuple, ndarray, optional
:param units: Label the units of distance used for the configuration, these should be consistent for the geometry and panel
:type units: string
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
AG = AcquisitionGeometry()
AG.config = Configuration(units)
AG.config.system = Parallel2D(ray_direction, detector_position, detector_direction_x, rotation_axis_position, units)
return AG
[docs]
@staticmethod
def create_Cone2D(source_position, detector_position, detector_direction_x=[1,0], rotation_axis_position=[0,0], units='units distance'):
r'''This creates the AcquisitionGeometry for a cone beam 2D tomographic system
:param source_position: A 2D vector describing the position of the source (x,y)
:type source_position: list, tuple, ndarray
:param detector_position: A 2D vector describing the position of the centre of the detector (x,y)
:type detector_position: list, tuple, ndarray
:param detector_direction_x: A 2D vector describing the direction of the detector_x (x,y)
:type detector_direction_x: list, tuple, ndarray
:param rotation_axis_position: A 2D vector describing the position of the axis of rotation (x,y)
:type rotation_axis_position: list, tuple, ndarray, optional
:param units: Label the units of distance used for the configuration, these should be consistent for the geometry and panel
:type units: string
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
AG = AcquisitionGeometry()
AG.config = Configuration(units)
AG.config.system = Cone2D(source_position, detector_position, detector_direction_x, rotation_axis_position, units)
return AG
[docs]
@staticmethod
def create_Parallel3D(ray_direction=[0,1,0], detector_position=[0,0,0], detector_direction_x=[1,0,0], detector_direction_y=[0,0,1], rotation_axis_position=[0,0,0], rotation_axis_direction=[0,0,1], units='units distance'):
r'''This creates the AcquisitionGeometry for a parallel beam 3D tomographic system
:param ray_direction: A 3D vector describing the x-ray direction (x,y,z)
:type ray_direction: list, tuple, ndarray, optional
:param detector_position: A 3D vector describing the position of the centre of the detector (x,y,z)
:type detector_position: list, tuple, ndarray, optional
:param detector_direction_x: A 3D vector describing the direction of the detector_x (x,y,z)
:type detector_direction_x: list, tuple, ndarray
:param detector_direction_y: A 3D vector describing the direction of the detector_y (x,y,z)
:type detector_direction_y: list, tuple, ndarray
:param rotation_axis_position: A 3D vector describing the position of the axis of rotation (x,y,z)
:type rotation_axis_position: list, tuple, ndarray, optional
:param rotation_axis_direction: A 3D vector describing the direction of the axis of rotation (x,y,z)
:type rotation_axis_direction: list, tuple, ndarray, optional
:param units: Label the units of distance used for the configuration, these should be consistent for the geometry and panel
:type units: string
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
AG = AcquisitionGeometry()
AG.config = Configuration(units)
AG.config.system = Parallel3D(ray_direction, detector_position, detector_direction_x, detector_direction_y, rotation_axis_position, rotation_axis_direction, units)
return AG
[docs]
@staticmethod
def create_Cone3D(source_position, detector_position, detector_direction_x=[1,0,0], detector_direction_y=[0,0,1], rotation_axis_position=[0,0,0], rotation_axis_direction=[0,0,1], units='units distance'):
r'''This creates the AcquisitionGeometry for a cone beam 3D tomographic system
:param source_position: A 3D vector describing the position of the source (x,y,z)
:type source_position: list, tuple, ndarray, optional
:param detector_position: A 3D vector describing the position of the centre of the detector (x,y,z)
:type detector_position: list, tuple, ndarray, optional
:param detector_direction_x: A 3D vector describing the direction of the detector_x (x,y,z)
:type detector_direction_x: list, tuple, ndarray
:param detector_direction_y: A 3D vector describing the direction of the detector_y (x,y,z)
:type detector_direction_y: list, tuple, ndarray
:param rotation_axis_position: A 3D vector describing the position of the axis of rotation (x,y,z)
:type rotation_axis_position: list, tuple, ndarray, optional
:param rotation_axis_direction: A 3D vector describing the direction of the axis of rotation (x,y,z)
:type rotation_axis_direction: list, tuple, ndarray, optional
:param units: Label the units of distance used for the configuration, these should be consistent for the geometry and panel
:type units: string
:return: returns a configured AcquisitionGeometry object
:rtype: AcquisitionGeometry
'''
AG = AcquisitionGeometry()
AG.config = Configuration(units)
AG.config.system = Cone3D(source_position, detector_position, detector_direction_x, detector_direction_y, rotation_axis_position, rotation_axis_direction, units)
return AG
def get_order_by_label(self, dimension_labels, default_dimension_labels):
order = []
for i, el in enumerate(default_dimension_labels):
for j, ek in enumerate(dimension_labels):
if el == ek:
order.append(j)
break
return order
def __eq__(self, other):
if isinstance(other, self.__class__) \
and self.config == other.config \
and self.dtype == other.dtype:
return True
return False
def clone(self):
'''returns a copy of the AcquisitionGeometry'''
return copy.deepcopy(self)
def copy(self):
'''alias of clone'''
return self.clone()
def get_centre_slice(self):
'''returns a 2D AcquisitionGeometry that corresponds to the centre slice of the input'''
if AcquisitionType.DIM2 & self.dimension:
return self
AG_2D = copy.deepcopy(self)
AG_2D.config.system = self.config.system.get_centre_slice()
AG_2D.config.panel.num_pixels[1] = 1
AG_2D.config.panel.pixel_size[1] = abs(self.config.system.detector.direction_y[2]) * self.config.panel.pixel_size[1]
return AG_2D
[docs]
def get_ImageGeometry(self, resolution=1.0):
'''returns a default configured ImageGeometry object based on the AcquisitionGeomerty'''
num_voxel_xy = int(numpy.ceil(self.config.panel.num_pixels[0] * resolution))
voxel_size_xy = self.config.panel.pixel_size[0] / (resolution * self.magnification)
if AcquisitionType.DIM3 & self.dimension:
num_voxel_z = int(numpy.ceil(self.config.panel.num_pixels[1] * resolution))
voxel_size_z = self.config.panel.pixel_size[1] / (resolution * self.magnification)
else:
num_voxel_z = 0
voxel_size_z = 1
return ImageGeometry(num_voxel_xy, num_voxel_xy, num_voxel_z, voxel_size_xy, voxel_size_xy, voxel_size_z, channels=self.channels)
def __str__ (self):
return str(self.config)
[docs]
def get_slice(self, channel=None, angle=None, vertical=None, horizontal=None):
'''
Returns a new AcquisitionGeometry of a single slice of in the requested direction. Will only return reconstructable geometries.
'''
geometry_new = self.copy()
if channel is not None:
geometry_new.config.channels.num_channels = 1
if hasattr(geometry_new.config.channels,'channel_labels'):
geometry_new.config.panel.channel_labels = geometry_new.config.panel.channel_labels[channel]
if angle is not None:
geometry_new.config.angles.angle_data = geometry_new.config.angles.angle_data[angle]
if vertical is not None:
if AcquisitionType.PARALLEL & geometry_new.geom_type or vertical == 'centre' or abs(geometry_new.pixel_num_v/2 - vertical) < 1e-6:
geometry_new = geometry_new.get_centre_slice()
else:
raise ValueError("Can only subset centre slice geometry on cone-beam data. Expected vertical = 'centre'. Got vertical = {0}".format(vertical))
if horizontal is not None:
raise ValueError("Cannot calculate system geometry for a horizontal slice")
return geometry_new
[docs]
def allocate(self, value=0, **kwargs):
'''allocates an AcquisitionData according to the size expressed in the instance
:param value: accepts numbers to allocate an uniform array, or a string as 'random' or 'random_int' to create a random array or None.
:type value: number or string, default None allocates empty memory block
:param dtype: numerical type to allocate
:type dtype: numpy type, default numpy.float32
'''
dtype = kwargs.get('dtype', self.dtype)
if kwargs.get('dimension_labels', None) is not None:
raise ValueError("Deprecated: 'dimension_labels' cannot be set with 'allocate()'. Use 'geometry.set_labels()' to modify the geometry before using allocate.")
out = AcquisitionData(geometry=self.copy(),
dtype=dtype,
suppress_warning=True)
if isinstance(value, Number):
# it's created empty, so we make it 0
out.array.fill(value)
elif value in FillType:
if value == FillType.RANDOM:
seed = kwargs.get('seed', None)
if seed is not None:
numpy.random.seed(seed)
if numpy.iscomplexobj(out.array):
r = numpy.random.random_sample(self.shape) + 1j * numpy.random.random_sample(self.shape)
out.fill(r)
else:
out.fill(numpy.random.random_sample(self.shape))
elif value == FillType.RANDOM_INT:
seed = kwargs.get('seed', None)
if seed is not None:
numpy.random.seed(seed)
max_value = kwargs.get('max_value', 100)
if numpy.iscomplexobj(out.array):
r = numpy.random.randint(max_value,size=self.shape, dtype=numpy.int32) + 1j*numpy.random.randint(max_value,size=self.shape, dtype=numpy.int32)
else:
r = numpy.random.randint(max_value,size=self.shape, dtype=numpy.int32)
out.fill(numpy.asarray(r, dtype=dtype))
elif value is None:
pass
else:
raise ValueError(f'Value {value} unknown')
return out
