X-ray polarimetry - release v2.2.0 (#329)

Modeling polarized X-ray signals has been implemented and examples added for simulating polarized pulses (Stokes parameters) using a couple of different atmosphere options. Support for polarized likelihood calculation has also been included. In addition, new integrators (with and without polarimetry) have been implemented to allow atmosphere interpolations with 5 parameters to be performed in 2 steps. --------- Co-authored-by: Bas Dorsman <superbas1996@gmail.com>
xpsi-group · Feb 6, 2024 · 6aeef9a · 6aeef9a
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -34,6 +34,45 @@ and this project adheres to
 .. ^^^^^^^^^^^
 
 
+[v2.2.0] - 2024-02-06
+~~~~~~~~~~~~~~~~~~~~~
+
+Summary
+^^^^^^^
+
+* Modeling polarized X-ray signals has been implemented and examples added for simulating polarized pulses (Stokes parameters) using a couple of different atmosphere options. Support for polarized likelihood calculation has also been included. In addition, new integrators (with and without polarimetry) have been implemented to allow atmosphere interpolations with 5 parameters to be performed in 2 steps.
+
+Added
+^^^^^
+
+* Option to calculate and extract all the Stokes I, Q, and U signals as a function of energy and phase. This can be activated if giving ``stokes=True`` as an input parameter (default is ``stokes=False``) when initializing a photosphere object. The computed (photosphere) stokes signals can then be obtained using the ``signal``, ``signalQ``, and ``signalU`` functions of the Photosphere class. For using Stokes signals in the likelihood calculation, a separate signal object of the Signal class needs to be created for each Stokes signal so that the type of the signal is specified using a ``stokes`` input argument. A list of all the signals can be then given to the likelihood object when initializing it. (T.S.)
+
+* Polarized alternatives for integrators in ``xpsi/cellmesh/integratorIQU_...``, which include the transportation of polarization angle from the star to the observer using the formalism of `Loktev et al. (2020) <https://doi.org/10.1051/0004-6361/202039134>`_. These are used when setting ``stokes=True`` as instructed above. (T.S.)
+
+* A new "split" integrator in ``xpsi/cellmesh/``, which allows atmosphere interpolations with 5 parameters to be performed in 2 steps: first interpolating 3 parameters that do not vary within the hot region (creating a 2D data set) and then interpolating in 2D for each photon energy and emission angle. This can be activated by giving ``split=True`` (default is ``split=False``) input parameter when initializing a hotregion object. Setting ``split=True`` will automatically determine also the atmosphere option. (B.D.)
+
+* New atmosphere options in ``xpsi/cellmesh/surface_radiation_field/``. See the docstring of the HotRegion class for all the options. (B.D., T.S.)
+
+* Polarization tutorial to the documentation pages. (T.S.)
+
+* Example scripts for calculating polarized pulses in ``examples/examples_modeling_tutorial/`` using either an analytical polarized burst atmosphere (``TestRun_Pol.py``) or a numerical 5D atmosphere model (``TestRun_PolNum_split_1spot.py`` or ``TestRun_PolNum_split_inference.py``). (T.S.)
+
+* Example scripts for combining X-PSI to `ixpeobssim <https://github.com/lucabaldini/ixpeobssim>`_ for simulating polarized X-ray observations in ``examples/examples_modeling_tutorial/ixpeobssim/``. See instructions in the documentation. (T.S.)
+
+Changed
+^^^^^^^
+
+* To allow modeling of all Stokes parameters, no error is anymore raised if the data have negative values in ``xpsi/Data.py``. (T.S.)
+
+* No error is anymore raised in ``xpsi/Data.py`` if setting the first and last energy channel to be the same channel. (T.S.)
+
+Attribution
+^^^^^^^^^^^
+
+Tuomo Salmi (T.S.),
+Bas Dorsman (B.D.)
+
+
 [v2.1.2] - 2024-02-05
 ~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/docs/source/Emitting_patterns_2Dprojection.ipynb b/docs/source/Emitting_patterns_2Dprojection.ipynb
diff --git a/docs/source/Example_script_and_modules.rst b/docs/source/Example_script_and_modules.rst
@@ -32,3 +32,21 @@ Fourth script called `examples/examples_modeling_tutorial/TestRun_NumBeam.py`__
 .. _t4: https://github.com/xpsi-group/xpsi/tree/main/examples/examples_modeling_tutorial/TestRun_NumBeam.py
 
 __ t4_
+
+Fifth script called `examples/examples_modeling_tutorial/TestRun_Pol.py`__ is an example script for producing polarized pulses in X-PSI using a simple analytical model for the atmosphere emission.
+
+.. _t5: https://github.com/xpsi-group/xpsi/tree/main/examples/examples_modeling_tutorial/TestRun_Pol.py
+
+__ t5_
+
+Sixth script called `examples/examples_modeling_tutorial/TestRun_PolNum_split_1spot.py`__ is an example script for producing polarized pulses in X-PSI using a numerical atmosphere model with 3+2 dimensional interpolation.
+
+.. _t6: https://github.com/xpsi-group/xpsi/tree/main/examples/examples_modeling_tutorial/TestRun_PolNum_split_1spot.py
+
+__ t6_
+
+Seventh script called `examples/examples_modeling_tutorial/TestRun_PolNum_split_inference.py`__ is a preliminary example script for producing and analyzing polarized pulses in X-PSI using a numerical atmosphere model with 3+2 dimensional interpolation and ST+PDT spot model.
+
+.. _t7: https://github.com/xpsi-group/xpsi/tree/main/examples/examples_modeling_tutorial/TestRun_PolNum_split_inference.py
+
+__ t7_
diff --git a/docs/source/HPC_systems.rst b/docs/source/HPC_systems.rst
@@ -136,7 +136,7 @@ Use the last command to check for the presence of shared objects.
 
     Further details on MKL issues can be found in this `thread <https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/mkl-fails-to-load/m-p/1155538>`_
 
-We also need to the set the environment variable for library path to point at
+We also need to set the environment variable for library path to point at
 MultiNest:
 
 .. code-block:: bash
@@ -200,11 +200,11 @@ If you ever need to reinstall, first clean to recompile C files:
 
 .. note::
 
-    We typically do not used the :mod:`~xpsi.PostProcessing` module, but 
+    We typically do not use the :mod:`~xpsi.PostProcessing` module, but
     instead ``rsync`` output files to a local system to perform plotting. This
     circumvents any potential backend problems and permits straightforward use
     of IPython for interactive plotting. However, if one wishes to use it on an
-    HPC, it would require installation of `GetDist` and `Nestcheck`. See 
+    HPC, it would require the installation of `GetDist` and `Nestcheck`. See
     :ref:`install` page for relevant details.
 
 
@@ -378,7 +378,7 @@ Download and Install the MultiNest package in your ``$HOME`` (e.g. in ``~/Softwa
                 -DCMAKE_Fortran_COMPILER=mpiifort  ..
     make
 
-    ## Check that librairies have been compiled and are present
+    ## Check that libraries have been compiled and are present
     ls ../lib
 
 Install pymultinest in your ``$HOME`` (e.g. in ``~/Softwares``:

diff --git a/docs/source/Hot_region_complexity.ipynb b/docs/source/Hot_region_complexity.ipynb
diff --git a/docs/source/Instrument_synergy.ipynb b/docs/source/Instrument_synergy.ipynb
diff --git a/docs/source/Modeling.ipynb b/docs/source/Modeling.ipynb
diff --git a/docs/source/Modeling_without_statistics.ipynb b/docs/source/Modeling_without_statistics.ipynb