From 9c31daa6d3b0ae0d666d92b53fc3b6aaee4b79e8 Mon Sep 17 00:00:00 2001
From: Carter Francis <csfrancis@wisc.edu>
Date: Thu, 11 Apr 2024 10:36:10 -0500
Subject: [PATCH] Documentation: Add Example describing pixel coordinates.

---
 examples/standards/README.rst          |  3 ++
 examples/standards/pixel_coodinates.py | 65 ++++++++++++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 examples/standards/README.rst
 create mode 100644 examples/standards/pixel_coodinates.py

diff --git a/examples/standards/README.rst b/examples/standards/README.rst
new file mode 100644
index 000000000..b90efb7d8
--- /dev/null
+++ b/examples/standards/README.rst
@@ -0,0 +1,3 @@
+Standards
+=========
+Below is a gallery of examples showing different standards in pyxem
\ No newline at end of file
diff --git a/examples/standards/pixel_coodinates.py b/examples/standards/pixel_coodinates.py
new file mode 100644
index 000000000..0abdab543
--- /dev/null
+++ b/examples/standards/pixel_coodinates.py
@@ -0,0 +1,65 @@
+"""
+====================
+Coordinates in Pyxem
+====================
+
+Pyxem is flexible in how it handles coordinates for a diffraction pattern.
+
+There are three main ways to handle coordinates in Pyxem:
+
+1. Pixel coordinates
+2. Calibrated Coordinates with evenly spaced axes
+3. Calibrated Coordinates with unevenly spaced axes (e.g. corrected for the Ewald sphere)
+"""
+
+import pyxem as pxm
+from skimage.morphology import disk
+
+
+s = pxm.signals.Diffraction2D(disk((10)))
+s.calibrate.center = None
+print(s.calibrate.center)
+
+# %%
+
+s.plot(axes_ticks=True)
+# %%
+
+# From the plot above you can see that hyperspy automatically sets the axes ticks to be centered
+# on each pixel. This means that for a 21x21 pixel image, the center is at (-10, -10) in pixel coordinates.
+# if we change the scale using the calibrate function it will automatically adjust the center.  Here it is
+# now (-1, -1)
+
+s.calibrate.scale = 0.1
+s.calibrate.units = "nm$^{-1}$"
+s.plot(axes_ticks=True)
+print(s.calibrate.center)
+
+
+# %%
+
+# Azimuthal Integration
+# ---------------------
+#
+# Now if we do integrate this dataset it will choose the appropriate center based on the center pixel.
+
+az = s.get_azimuthal_integral2d(npt=30)
+az.plot()
+
+# %%
+
+# Non-Linear Axes
+# ---------------
+#
+# Now consider the case where we have non-linear axes. In this case the center is still (10,10)
+# but things are streatched based on the effects of the Ewald Sphere.
+
+s.calibrate.beam_energy = 200
+s.calibrate.detector(pixel_size=0.1, detector_distance=3)
+print(s.calibrate.center)
+s.plot()
+
+az = s.get_azimuthal_integral2d(npt=30)
+az.plot()
+
+# %%