:py:mod:`pytomography.utils.cardiac_spect`
==========================================

.. py:module:: pytomography.utils.cardiac_spect


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   pytomography.utils.cardiac_spect.shift_object
   pytomography.utils.cardiac_spect.rotate_object
   pytomography.utils.cardiac_spect.get_mask
   pytomography.utils.cardiac_spect.get_shift_values
   pytomography.utils.cardiac_spect.get_angle
   pytomography.utils.cardiac_spect.plot_arrow
   pytomography.utils.cardiac_spect.create_circular_mask
   pytomography.utils.cardiac_spect.masking



.. py:function:: shift_object(object, tx, ty, tz)

   Shift the 3D volume based on the given translation parameters.

   :param object: Input 3D volume to be shifted (torch.Tensor[Lx, Ly, Lz]).
   :param tx: Translation in x direction (voxels).
   :type tx: float
   :param ty: Translation in y direction (voxels).
   :type ty: float
   :param tz: Translation in z direction (voxels).
   :type tz: float

   :returns: The shifted object (torch.Tensor[Lx, Ly, Lz]).
   :rtype: Shifted 3D volume


.. py:function:: rotate_object(object, transaxial_angle, transsagittal_angle)

   Rotates the volume around the transaxial and transsagittal slices.

   :param object: The 3D volume to be rotated (torch.Tensor[Lx, Ly, Lz]).
   :param angle_transaxial: The angle to rotate around the transaxial slice (z-axis).
   :type angle_transaxial: float
   :param angle_transsagittal: The angle to rotate around the transsagittal slice (y-axis).
   :type angle_transsagittal: float

   :returns: The reoriented object (torch.Tensor[Lx, Ly, Lz]).


.. py:function:: get_mask(object, lowerThreshold, upperThreshold)

   Segment the object based on the given thresholds.

   :param object: torch.Tensor[Lx, Ly, Lz]
   :param lowerThreshold: Lower threshold for the binary mask
   :param upperThreshold: Upper threshold for the binary mask


.. py:function:: get_shift_values(slice)

   Calculate the shift values for the given object based on the center of mass.

   :param slice: torch.Tensor[Lx, Ly] representing the slice.
   :type slice: torch.Tensor

   :returns: The shifted image.
             shift_values (torch.Tensor): The shift values in x and y directions.
   :rtype: shifted_image (torch.Tensor)


.. py:function:: get_angle(slice, angle_range_degrees)

   Get the angle of the best line passing through the center of the image.

   :param slice: torch.Tensor[Lx, Ly] representing the slice.
   :type slice: torch.Tensor
   :param angle_range_degrees: torch.Tensor[N] with angles in degrees.
   :type angle_range_degrees: torch.Tensor

   :returns: The best angle in degrees.
   :rtype: best_angle_degree


.. py:function:: plot_arrow(image, angle_degrees, fontsize=10)

   Draws an arrow from the center of the image based on the given angle and displays a polar plot around it.
   The angle is also displayed inside the plot.

   Parameters:
   image (np.ndarray): 2D numpy array representing the image.
   angle_degrees (float): Angle of the arrow with respect to the vertical, measured clockwise.


.. py:function:: create_circular_mask(height, width, radius)

   Create a circular mask.


.. py:function:: masking(object, radius)

   Apply a circular mask to the object in all three views.