opengate.contrib.phantoms.nemaiec
=================================

.. py:module:: opengate.contrib.phantoms.nemaiec


Attributes
----------

.. autoapisummary::

   opengate.contrib.phantoms.nemaiec.iec_plastic
   opengate.contrib.phantoms.nemaiec.water
   opengate.contrib.phantoms.nemaiec.iec_lung
   opengate.contrib.phantoms.nemaiec.red
   opengate.contrib.phantoms.nemaiec.blue
   opengate.contrib.phantoms.nemaiec.gray
   opengate.contrib.phantoms.nemaiec.transparent


Functions
---------

.. autoapisummary::

   opengate.contrib.phantoms.nemaiec.create_material
   opengate.contrib.phantoms.nemaiec.add_iec_phantom
   opengate.contrib.phantoms.nemaiec.add_iec_body
   opengate.contrib.phantoms.nemaiec.add_iec_central_cylinder
   opengate.contrib.phantoms.nemaiec.add_iec_all_spheres
   opengate.contrib.phantoms.nemaiec.add_iec_one_sphere
   opengate.contrib.phantoms.nemaiec.add_spheres_sources
   opengate.contrib.phantoms.nemaiec.compute_sphere_activity
   opengate.contrib.phantoms.nemaiec.compute_total_spheres_activity
   opengate.contrib.phantoms.nemaiec.dump_spheres_activity
   opengate.contrib.phantoms.nemaiec.dump_bg_activity
   opengate.contrib.phantoms.nemaiec.add_one_sphere_source
   opengate.contrib.phantoms.nemaiec.add_central_cylinder_source
   opengate.contrib.phantoms.nemaiec.add_background_source
   opengate.contrib.phantoms.nemaiec.generate_pos_dir_one_sphere
   opengate.contrib.phantoms.nemaiec.generate_pos_one_sphere
   opengate.contrib.phantoms.nemaiec.generate_pos_dir_spheres
   opengate.contrib.phantoms.nemaiec.generate_pos_spheres
   opengate.contrib.phantoms.nemaiec.get_n_samples_from_ratio
   opengate.contrib.phantoms.nemaiec.compute_sphere_centers_and_volumes
   opengate.contrib.phantoms.nemaiec.get_default_sphere_centers_and_volumes_old
   opengate.contrib.phantoms.nemaiec.get_default_sphere_centers_and_volumes


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

.. py:data:: iec_plastic
   :value: 'IEC_PLASTIC'


.. py:data:: water
   :value: 'G4_WATER'


.. py:data:: iec_lung
   :value: 'G4_LUNG_ICRP'


.. py:data:: red
   :value: [1, 0.7, 0.7, 0.8]


.. py:data:: blue
   :value: [0.5, 0.5, 1, 0.8]


.. py:data:: gray
   :value: [0.5, 0.5, 0.5, 1]


.. py:data:: transparent
   :value: [0, 0, 0, 0]


.. py:function:: create_material(simulation)

.. py:function:: add_iec_phantom(simulation, name='iec', check_overlap=False, sphere_starting_angle=False, toggle_sphere_order=False)

.. py:function:: add_iec_body(simulation, name, thickness=0.0, thickness_z=0.0)

.. py:function:: add_iec_central_cylinder(sim, name, top_interior)

.. py:function:: add_iec_all_spheres(simulation, name, thickness_z, starting_angle=False, reverse_order=False)

   Starting angle : in deg. Indicate the (angle) position of the first smallest sphere.
   It is 180 deg by default.


.. py:function:: add_iec_one_sphere(sim, name, vol, diam, sph_thick, cap_thick, position, thickness_z)

.. py:function:: add_spheres_sources(simulation, iec_name, src_name, spheres, activity_Bq_mL, verbose=False, source_type='GenericSource')

.. py:function:: compute_sphere_activity(simulation, iec_name, src_name, diam)

.. py:function:: compute_total_spheres_activity(simulation, iec_name, src_name)

.. py:function:: dump_spheres_activity(simulation, iec_name, src_name)

.. py:function:: dump_bg_activity(simulation, iec_name, src_name)

.. py:function:: add_one_sphere_source(simulation, iec_name, src_name, diameter, activity_Bq_mL, source_type)

.. py:function:: add_central_cylinder_source(simulation, iec_name, src_name, activity_Bq_mL, verbose=False)

.. py:function:: add_background_source(simulation, iec_name, src_name, activity_Bq_mL, verbose=False)

.. py:function:: generate_pos_dir_one_sphere(center, radius, n, rs=np.random)

   This function should be useful to generate conditional data for condGAN.
   It samples the position in a sphere and isotropic direction.
   The center/radius is the center and radius of the sphere
   A numpy array of (n,6) is returned.
   3 first = position
   3 last = direction


.. py:function:: generate_pos_one_sphere(center, radius, n, rs=np.random)

.. py:function:: generate_pos_dir_spheres(centers, radius, n_samples, shuffle, rs=np.random)

   This function generate conditional data for condGAN.
   It samples the position in several spheres, with isotropic direction.
   The center/radius are the center and radius of the spheres.
   n_samples is the number of samples per sphere, with a total of n.
   Samples can be shuffled (by default).
   A numpy array of (n,6) is returned.


.. py:function:: generate_pos_spheres(centers, radius, n_samples, shuffle, rs=np.random)

   Like generate_pos_dir_spheres, but position only


.. py:function:: get_n_samples_from_ratio(n, ratio)

   For a given proportion of activities (in ratio) and total number of particle n,
   compute the list of particle for each index.


.. py:function:: compute_sphere_centers_and_volumes(sim, name)

.. py:function:: get_default_sphere_centers_and_volumes_old()

   Global spheres centers in the phantom, to avoid using the phantom in same cases.
   Were computed with 10/06/2022 version.
   No translation. To be recomputed with compute_sphere_centers_and_volumes


.. py:function:: get_default_sphere_centers_and_volumes()

   Global spheres centers in the phantom, to avoid using the phantom in same cases.
   Were computed with 23/08/2023 version.
   No translation. To be recomputed with compute_sphere_centers_and_volumes