From a7c8864f6b149fc05ba4ee9f4e2ae4c9c97127f3 Mon Sep 17 00:00:00 2001
From: Carter Francis <csfrancis@wisc.edu>
Date: Fri, 31 May 2024 15:36:04 -0500
Subject: [PATCH] Refactor: References

---
 doc/bibliography.bib                                     | 9 +++++++++
 examples/orientation_mapping/mulit_phase_orientation.py  | 2 ++
 examples/orientation_mapping/on_zone_orientation.py      | 2 ++
 examples/orientation_mapping/single_phase_orientation.py | 2 ++
 pyxem/signals/polar_diffraction2d.py                     | 7 ++++++-
 5 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/doc/bibliography.bib b/doc/bibliography.bib
index 4800f1a58..1b41a0dc7 100644
--- a/doc/bibliography.bib
+++ b/doc/bibliography.bib
@@ -90,4 +90,13 @@ @article{Viladot:13
 volume = {252},
 journal = {Journal of microscopy},
 doi = {10.1111/jmi.12065}
+}
+@article{pyxemorientationmapping2022,
+    title={Free, flexible and fast: Orientation mapping using the multi-core and GPU-accelerated template matching capabilities in the python-based open source 4D-STEM analysis toolbox Pyxem},
+    author={Cautaerts, Niels and Crout, Phillip and {\AA}nes, H{\aa}kon Wiik and Prestat, Eric and Jeong, Jiwon and Dehm, Gerhard and Liebscher, Christian H},
+    journal={Ultramicroscopy},
+    pages={113517},
+    year={2022},
+    publisher={Elsevier},
+    doi={10.1016/j.ultramic.2022.113517}
 }
\ No newline at end of file
diff --git a/examples/orientation_mapping/mulit_phase_orientation.py b/examples/orientation_mapping/mulit_phase_orientation.py
index c40599302..ef3463b3c 100644
--- a/examples/orientation_mapping/mulit_phase_orientation.py
+++ b/examples/orientation_mapping/mulit_phase_orientation.py
@@ -4,6 +4,8 @@
 You can also calculate the orientation of the grains for multiple phases using the
 :meth:`pyxem.signals.PolarSignal2D.get_orientation` method. This requires that you
 simulate the entire S2 space for the phase and then compare to the simulated diffraction.
+
+For more information on the orientation mapping process see :cite:`pyxemorientationmapping2022`
 """
 
 import pyxem as pxm
diff --git a/examples/orientation_mapping/on_zone_orientation.py b/examples/orientation_mapping/on_zone_orientation.py
index e703d7add..383b1a555 100644
--- a/examples/orientation_mapping/on_zone_orientation.py
+++ b/examples/orientation_mapping/on_zone_orientation.py
@@ -4,6 +4,8 @@
 Sometimes you have a tilt boundary and you might want to know the orientation of the
 grains on each side of the boundary. This can be done using the
 :meth:`pyxem.signals.PolarSignal2D.get_orientation` method.
+
+For more information on the orientation mapping process see :cite:`pyxemorientationmapping2022`
 """
 
 from pyxem.data import si_tilt, si_phase
diff --git a/examples/orientation_mapping/single_phase_orientation.py b/examples/orientation_mapping/single_phase_orientation.py
index 6687ac366..f111f265d 100644
--- a/examples/orientation_mapping/single_phase_orientation.py
+++ b/examples/orientation_mapping/single_phase_orientation.py
@@ -4,6 +4,8 @@
 You can also calculate the orientation of the grains in a single phase sample using the
 :meth:`pyxem.signals.PolarSignal2D.get_orientation` method. This requires that you
 simulate the entire S2 space for the phase and then compare to the simulated diffraction.
+
+For more information on the orientation mapping process see :cite:`pyxemorientationmapping2022`
 """
 
 from pyxem.data import si_phase, si_grains
diff --git a/pyxem/signals/polar_diffraction2d.py b/pyxem/signals/polar_diffraction2d.py
index a3c215b82..9d620f498 100644
--- a/pyxem/signals/polar_diffraction2d.py
+++ b/pyxem/signals/polar_diffraction2d.py
@@ -342,13 +342,18 @@ def get_orientation(
             The gamma correction applied to the diffraction patterns. The default
             value is 0.5 which takes the square root of the diffraction patterns to
             increase the intensity of the low intensity reflections and decrease the
-            intensity of the high intensity reflections.
+            intensity of the high intensity reflections. In most cases gamma<1 is a
+            good starting point.  See :cite:`pyxemorientationmapping2022` for more information.
         kwargs : dict
             Any additional options for the :meth:`~hyperspy.signal.BaseSignal.map` function.
         Returns
         -------
         orientation : BaseSignal
             A signal with the orientation at each navigation position.
+
+        References
+        ----------
+            .. bibliography::
         """
         if gamma != 1:
             self.data = self.data**gamma