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Reference for pyronn/ct_reconstruction/geometry/geometry_base.py


pyronn.ct_reconstruction.geometry.geometry_base.GeometryBase 

GeometryBase(volume_shape, volume_spacing, detector_shape, detector_spacing, number_of_projections, angular_range, source_detector_distance, source_isocenter_distance, *args, **kwargs)

The Base Class for the different Geometry classes. Provides commonly used members.

volume_shape:               The volume size in Z, Y, X order.
volume_spacing:             The spacing between voxels in Z, Y, X order.
detector_shape:             Shape of the detector in Y, X order.
detector_spacing:           The spacing between detector voxels in Y, X order.
number_of_projections:      Number of equidistant projections.
angular_range:              The covered angular range.
source_detector_distance:   The source to detector distance (sdd).
source_isocenter_distance:  The source to isocenter distance (sid).
Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def __init__(self,
             volume_shape,
             volume_spacing,
             detector_shape,
             detector_spacing,
             number_of_projections,
             angular_range,
             source_detector_distance,
             source_isocenter_distance,
             *args, **kwargs):
    """
        Constructor of Base Geometry Class, should only get called by sub classes.
    Args:
        volume_shape:               The volume size in Z, Y, X order.
        volume_spacing:             The spacing between voxels in Z, Y, X order.
        detector_shape:             Shape of the detector in Y, X order.
        detector_spacing:           The spacing between detector voxels in Y, X order.
        number_of_projections:      Number of equidistant projections.
        angular_range:              The covered angular range.
        source_detector_distance:   The source to detector distance (sdd).
        source_isocenter_distance:  The source to isocenter distance (sid).
    """
    self.np_dtype = np.float32  # datatype for np.arrays make sure everything will be float32
    # self.gpu_device = True
    # Volume Parameters:
    self.volume_shape = np.array(volume_shape)
    self.volume_spacing = np.array(volume_spacing, dtype=self.np_dtype)
    self.volume_origin = -(self.volume_shape - 1) / 2.0 * self.volume_spacing

    # Detector Parameters:
    self.detector_shape = np.array(detector_shape)
    self.detector_spacing = np.array(detector_spacing, dtype=self.np_dtype)
    self.detector_origin = -(self.detector_shape - 1) / 2.0 * self.detector_spacing

    # Trajectory Parameters:
    self.number_of_projections = number_of_projections
    if isinstance(angular_range, list):
        self.angular_range = angular_range
    else:
        self.angular_range = [0, angular_range]

    self.sinogram_shape = np.array([self.number_of_projections, *self.detector_shape])

    self.source_detector_distance = source_detector_distance
    self.source_isocenter_distance = source_isocenter_distance
    self.fan_angle = None
    self.cone_angle = None
    self.projection_multiplier = None
    self.step_size = None

get_dict 

get_dict()

Get the geometry as a dict.

Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def get_dict(self):
    # TODO: Document this function on your own. Could not be documented by the model.
    # TODO: Document this function on your own. Could not be documented by the model.
    '''
        Get the geometry as a dict.
    '''
    info = {}
    for i in dir(self):
        if i[:2] != '__': info[i] = getattr(self, i)
    return info

set_trajectory 

set_trajectory(trajectory)

Sets the member trajectory.

Args: trajectory: np.array defining the trajectory.

Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def set_trajectory(self, trajectory):
    """
        Sets the member trajectory.
    Args:
        trajectory: np.array defining the trajectory.
    """
    self.trajectory = np.array(trajectory, self.np_dtype)

update 

update(dict)

Change the geometry.

Parameters:

Name Type Description Default
dict

new geometry values. Choose your target properties by setting them as the keys.

 required
Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def update(self, dict):
    # TODO: Document this function on your own. Could not be documented by the model.
    # TODO: Document this function on your own. Could not be documented by the model.
    '''
        Change the geometry.

    args:
        dict: new geometry values. Choose your target properties by setting them as the keys.
    '''
    changed = []
    for key in dict:
        if key in dir(self):
            setattr(self, key, dict[key])
            self.key = dict[key]
            changed.append(key)
        else:
            print(f'{key} is not a property of geometry! Please check it!')
    if changed:
        print(f'The following properties has been changed: {changed}')
        if 'trajectory' not in changed:
            print(f'Please confirm whether you need to modify the trajectory.')




pyronn.ct_reconstruction.geometry.geometry_base.GeometryParallel2D 

GeometryParallel2D(volume_shape, volume_spacing, detector_shape, detector_spacing, number_of_projections, angular_range, *args, **kwargs)

Bases: GeometryBase

2D Parallel specialization of Geometry.

Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def __init__(self,
             volume_shape, volume_spacing,
             detector_shape, detector_spacing,
             number_of_projections, angular_range, *args, **kwargs):
    # init base selfmetry class with 2 dimensional members:
    # TODO: Document this function on your own. Could not be documented by the model.
    # TODO: Document this function on your own. Could not be documented by the model.
    super().__init__(volume_shape, volume_spacing,
                     detector_shape, detector_spacing,
                     number_of_projections, angular_range,
                     None, None, *args, **kwargs)




pyronn.ct_reconstruction.geometry.geometry_base.GeometryFan2D 

GeometryFan2D(volume_shape, volume_spacing, detector_shape, detector_spacing, number_of_projections, angular_range, source_detector_distance, source_isocenter_distance, *args, **kwargs)

Bases: GeometryBase

2D Fan specialization of Geometry.

Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def __init__(self,
             volume_shape, volume_spacing,
             detector_shape, detector_spacing,
             number_of_projections, angular_range,
             source_detector_distance, source_isocenter_distance, *args, **kwargs):
    # init base Geometry class with 2 dimensional members:
    # TODO: Document this function on your own. Could not be documented by the model.
    # TODO: Document this function on your own. Could not be documented by the model.
    super().__init__(volume_shape, volume_spacing,
                     detector_shape, detector_spacing,
                     number_of_projections, angular_range,
                     source_detector_distance, source_isocenter_distance, *args, **kwargs)

    # defined by geometry so calculate for convenience use
    self.fan_angle = np.arctan(((self.detector_shape[0] - 1) / 2.0 * self.detector_spacing[0]) / self.source_detector_distance)




pyronn.ct_reconstruction.geometry.geometry_base.GeometryCone3D 

GeometryCone3D(volume_shape, volume_spacing, detector_shape, detector_spacing, number_of_projections, angular_range, source_detector_distance, source_isocenter_distance, *args, **kwargs)

Bases: GeometryBase

3D Cone specialization of Geometry.

Source code in pyronn/ct_reconstruction/geometry/geometry_base.py 
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def __init__(self,
             volume_shape, volume_spacing,
             detector_shape, detector_spacing,
             number_of_projections, angular_range,
             source_detector_distance, source_isocenter_distance, *args, **kwargs):
    # init base Geometry class with 3 dimensional members:
    # TODO: Document this function on your own. Could not be documented by the model.
    # TODO: Document this function on your own. Could not be documented by the model.
    super().__init__(volume_shape, volume_spacing,
                     detector_shape, detector_spacing,
                     number_of_projections, angular_range,
                     source_detector_distance, source_isocenter_distance, *args, **kwargs)

    # defined by geometry so calculate for convenience use
    self.fan_angle = np.arctan(((self.detector_shape[1] - 1) / 2.0 * self.detector_spacing[1]) / self.source_detector_distance)
    self.cone_angle = np.arctan(((self.detector_shape[0] - 1) / 2.0 * self.detector_spacing[0]) / self.source_detector_distance)

    # Containing the constant part of the distance weight and discretization invariant
    self.projection_multiplier = self.source_isocenter_distance * self.source_detector_distance * detector_spacing[-1] * np.pi / self.number_of_projections
    # TODO: need to be changed or not?
    self.step_size = 0.2