From 995fee46f53fbb32b709395cdc87ad27f2864151 Mon Sep 17 00:00:00 2001
From: Carter Francis <csfrancis@wisc.edu>
Date: Wed, 8 May 2024 09:56:04 -0500
Subject: [PATCH 1/3] Documentation: Remove empty examples

---
 doc/user_guide/open_datasets_workflows.rst |  2 +-
 examples/plotting/README.rst               |  3 ---
 examples/plotting/making_a_gif.py          |  8 --------
 examples/processing/calibrating.py         | 22 ----------------------
 4 files changed, 1 insertion(+), 34 deletions(-)
 delete mode 100644 examples/plotting/README.rst
 delete mode 100644 examples/plotting/making_a_gif.py
 delete mode 100644 examples/processing/calibrating.py

diff --git a/doc/user_guide/open_datasets_workflows.rst b/doc/user_guide/open_datasets_workflows.rst
index c14a36e67..15d226c2b 100644
--- a/doc/user_guide/open_datasets_workflows.rst
+++ b/doc/user_guide/open_datasets_workflows.rst
@@ -1,4 +1,4 @@
-===========================
+z===========================
 Open datasets and workflows
 ===========================
 
diff --git a/examples/plotting/README.rst b/examples/plotting/README.rst
deleted file mode 100644
index 65308cd96..000000000
--- a/examples/plotting/README.rst
+++ /dev/null
@@ -1,3 +0,0 @@
-Plotting
-===============
-Below is a gallery of examples on how to make nice plots with Matplotlib from hyperspy/ pyxem signals.
\ No newline at end of file
diff --git a/examples/plotting/making_a_gif.py b/examples/plotting/making_a_gif.py
deleted file mode 100644
index 0835907e7..000000000
--- a/examples/plotting/making_a_gif.py
+++ /dev/null
@@ -1,8 +0,0 @@
-"""
-============
-Making a Gif
-============
-
-This example shows how to create a gif from a series of images.  Here we use the "hyperspy" idea of a
-signal and navigation axes to create a series of images
-"""
diff --git a/examples/processing/calibrating.py b/examples/processing/calibrating.py
deleted file mode 100644
index 1e729b9a9..000000000
--- a/examples/processing/calibrating.py
+++ /dev/null
@@ -1,22 +0,0 @@
-"""
-Calibrating a dataset
-=====================
-
-There are two different ways to calibrate a dataset in pyxem and depending on what
-kind of data you have you may need to use each of these methods.
-
-The first method is to basically ignore the Ewald sphere effects. This is the
-easiest method but not the most correct.  For a 200+ keV microscope the assumption
-that the Ewald sphere is flat is not a bad one.  For lower energy microscopes
-this assumption is not as great but still not terrible.  For x-ray data with longer
-wavelengths this assumption starts to break down.
-"""
-
-# import pyxem as pxm
-
-# al = pxm.data.al_peaks()
-
-# determine the pixel size from one peak
-
-# al.calibrate(scale=0.1, center=None, units="k_nm^-1")
-# al.plot()

From 8adc389d94eb7c4604d8b2d231176a8b6e229e31 Mon Sep 17 00:00:00 2001
From: Carter Francis <csfrancis@wisc.edu>
Date: Wed, 8 May 2024 10:02:00 -0500
Subject: [PATCH 2/3] Refactor: calibrate-->calibration to not interfere with
 hyperspy namespace

---
 examples/processing/azimuthal_integration.py  |  8 +++----
 examples/processing/background_subtraction.py |  2 +-
 examples/standards/pixel_coodinates.py        | 18 +++++++--------
 .../creating_a_segmented_detector.py          |  6 ++---
 .../interactive_virtual_images.py             |  2 +-
 .../virtual_imaging/other_virtual_imaging.py  |  2 +-
 pyxem/generators/calibration_generator.py     |  2 +-
 pyxem/signals/diffraction2d.py                | 22 ++++++++++---------
 pyxem/tests/signals/test_diffraction2d.py     | 18 +++++++--------
 pyxem/tests/utils/test_calibration_utils.py   | 10 ++++-----
 .../tests/utils/test_ransac_ellipse_tools.py  |  4 ++--
 pyxem/utils/calibration.py                    | 10 +++++----
 12 files changed, 54 insertions(+), 50 deletions(-)

diff --git a/examples/processing/azimuthal_integration.py b/examples/processing/azimuthal_integration.py
index 3687a56f3..7877c9abd 100644
--- a/examples/processing/azimuthal_integration.py
+++ b/examples/processing/azimuthal_integration.py
@@ -14,7 +14,7 @@
 import numpy as np
 
 nano_crystals = pxm.data.mgo_nanocrystals(lazy=True)
-nano_crystals.calibrate(
+nano_crystals.calibration(
     center=None
 )  # set the center to None to use center of the diffraction patterns
 nano_crystals1d = nano_crystals.get_azimuthal_integral1d(npt=100, inplace=False)
@@ -49,7 +49,7 @@
 We only show the 1D case here, but the same applies for the 2D case as well!
 """
 
-nano_crystals.calibrate.detector(
+nano_crystals.calibration.detector(
     pixel_size=0.001,
     detector_distance=0.125,
     beam_energy=200,
@@ -57,7 +57,7 @@
     units="k_A^-1",
 )  # set the center= None to use the center of the diffraction patterns
 nano_crystals1d_200 = nano_crystals.get_azimuthal_integral1d(npt=100, inplace=False)
-nano_crystals.calibrate.detector(
+nano_crystals.calibration.detector(
     pixel_size=0.001,
     detector_distance=0.075,
     beam_energy=80,
@@ -84,7 +84,7 @@
 affine = np.array(
     [[0.9, 0.1, 0], [0.1, 0.9, 0], [0, 0, 1]]
 )  # Just a random affine transformation for illustration
-nano_crystals.calibrate(mask=mask, affine=affine)
+nano_crystals.calibration(mask=mask, affine=affine)
 nano_crystals.get_azimuthal_integral2d(
     npt=100, npt_azim=360, inplace=False
 ).sum().plot()
diff --git a/examples/processing/background_subtraction.py b/examples/processing/background_subtraction.py
index 2548bcc14..502a9afeb 100644
--- a/examples/processing/background_subtraction.py
+++ b/examples/processing/background_subtraction.py
@@ -42,7 +42,7 @@
 # Set the center of the diffraction pattern to its default,
 # i.e. the middle of the image
 
-s.calibrate.center = None
+s.calibration.center = None
 
 # %%
 # Transform to polar coordinates
diff --git a/examples/standards/pixel_coodinates.py b/examples/standards/pixel_coodinates.py
index 0abdab543..b665f442b 100644
--- a/examples/standards/pixel_coodinates.py
+++ b/examples/standards/pixel_coodinates.py
@@ -17,8 +17,8 @@
 
 
 s = pxm.signals.Diffraction2D(disk((10)))
-s.calibrate.center = None
-print(s.calibrate.center)
+s.calibration.center = None
+print(s.calibration.center)
 
 # %%
 
@@ -27,13 +27,13 @@
 
 # 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
+# if we change the scale using the calibration function it will automatically adjust the center.  Here it is
 # now (-1, -1)
 
-s.calibrate.scale = 0.1
-s.calibrate.units = "nm$^{-1}$"
+s.calibration.scale = 0.1
+s.calibration.units = "nm$^{-1}$"
 s.plot(axes_ticks=True)
-print(s.calibrate.center)
+print(s.calibration.center)
 
 
 # %%
@@ -54,9 +54,9 @@
 # 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.calibration.beam_energy = 200
+s.calibration.detector(pixel_size=0.1, detector_distance=3)
+print(s.calibration.center)
 s.plot()
 
 az = s.get_azimuthal_integral2d(npt=30)
diff --git a/examples/virtual_imaging/creating_a_segmented_detector.py b/examples/virtual_imaging/creating_a_segmented_detector.py
index 23788ccf9..ab40cf97b 100644
--- a/examples/virtual_imaging/creating_a_segmented_detector.py
+++ b/examples/virtual_imaging/creating_a_segmented_detector.py
@@ -16,8 +16,8 @@
 
 
 dp = pxm.data.tilt_boundary_data()
-dp.calibrate.center = None  # Center the diffraction patterns
-dp.calibrate.scale = 0.1  # Scale the diffraction patterns in reciprocal space
+dp.calibration.center = None  # Center the diffraction patterns
+dp.calibration.scale = 0.1  # Scale the diffraction patterns in reciprocal space
 
 
 # Visualizing the virtual detector
@@ -26,7 +26,7 @@
     npt_azim=8,
     radial_range=(1, 5),
     azimuthal_range=(-np.pi, np.pi),
-    affine=dp.calibrate.affine,
+    affine=dp.calibration.affine,
 )[:, :, ::-1]
 poly = hs.plot.markers.Polygons(verts=cp, edgecolor="w", facecolor="none")
 dp.plot()
diff --git a/examples/virtual_imaging/interactive_virtual_images.py b/examples/virtual_imaging/interactive_virtual_images.py
index ea6f0cc5b..032fef8bf 100644
--- a/examples/virtual_imaging/interactive_virtual_images.py
+++ b/examples/virtual_imaging/interactive_virtual_images.py
@@ -20,7 +20,7 @@
 
 # Also we can do the same with a 1D signal
 s = pxm.data.dummy_data.get_cbed_signal()
-s.calibrate(center=None)
+s.calibration(center=None)
 s1d = s.get_azimuthal_integral1d(npt=100, mean=True)
 span = hs.roi.SpanROI(left=15.5, right=20)
 s1d.plot_integrated_intensity(span)
diff --git a/examples/virtual_imaging/other_virtual_imaging.py b/examples/virtual_imaging/other_virtual_imaging.py
index db742aa83..7aeda5149 100644
--- a/examples/virtual_imaging/other_virtual_imaging.py
+++ b/examples/virtual_imaging/other_virtual_imaging.py
@@ -14,7 +14,7 @@
     radius=4, include_labels=True
 )
 c = pxm.data.dummy_data.get_cbed_signal()
-c.calibrate(center=None)
+c.calibration(center=None)
 c.plot()
 for r in rois:
     r.add_widget(c, axes=(2, 3))
diff --git a/pyxem/generators/calibration_generator.py b/pyxem/generators/calibration_generator.py
index 010ff9db7..3b5129e8a 100644
--- a/pyxem/generators/calibration_generator.py
+++ b/pyxem/generators/calibration_generator.py
@@ -49,7 +49,7 @@ class CalibrationGenerator:
     @deprecated(
         since="0.18.0",
         removal="1.0.0",
-        alternative="pyxem.signals.Diffraction2D.calibrate",
+        alternative="pyxem.signals.Diffraction2D.calibration",
     )
     def __init__(
         self, diffraction_pattern=None, grating_image=None, calibration_standard=None
diff --git a/pyxem/signals/diffraction2d.py b/pyxem/signals/diffraction2d.py
index d70cba91e..54e793bad 100644
--- a/pyxem/signals/diffraction2d.py
+++ b/pyxem/signals/diffraction2d.py
@@ -116,7 +116,7 @@ def __init__(self, *args, **kwargs):
             Passed to the __init__ of Signal2D
         """
         super().__init__(*args, **kwargs)
-        self.calibrate = Calibration(self)
+        self.calibration = Calibration(self)
 
     def apply_affine_transformation(
         self, D, order=1, keep_dtype=False, inplace=True, *args, **kwargs
@@ -1781,7 +1781,7 @@ def ai(self):
     @deprecated(
         since="0.18",
         removal="1.0.0",
-        alternative="pyxem.signals.diffraction2d.calibrate",
+        alternative="pyxem.signals.diffraction2d.calibration",
     )
     def set_ai(
         self, center=None, wavelength=None, affine=None, radial_range=None, **kwargs
@@ -1916,11 +1916,11 @@ def get_azimuthal_integral1d(
         if not usepyfai:
             # get_slices1d should be sped up in the future by
             # getting rid of shapely and using numba on the for loop
-            indexes, facts, factor_slices, radial_range = self.calibrate.get_slices1d(
+            indexes, facts, factor_slices, radial_range = self.calibration.get_slices1d(
                 npt, radial_range=radial_range
             )
             if mask is None:
-                mask = self.calibrate.mask
+                mask = self.calibration.mask
             integration = self.map(
                 _slice_radial_integrate1d,
                 indexes=indexes,
@@ -2064,11 +2064,13 @@ def get_azimuthal_integral2d(
         if not usepyfai:
             # get_slices2d should be sped up in the future by
             # getting rid of shapely and using numba on the for loop
-            slices, factors, factors_slice, radial_range = self.calibrate.get_slices2d(
-                npt,
-                npt_azim,
-                radial_range=radial_range,
-                azimuthal_range=azimuth_range,
+            slices, factors, factors_slice, radial_range = (
+                self.calibration.get_slices2d(
+                    npt,
+                    npt_azim,
+                    radial_range=radial_range,
+                    azimuthal_range=azimuth_range,
+                )
             )
             if self._gpu and CUPY_INSTALLED:  # pragma: no cover
                 from pyxem.utils._azimuthal_integrations import (
@@ -2093,7 +2095,7 @@ def get_azimuthal_integral2d(
                 )
             else:
                 if mask is None:
-                    mask = self.calibrate.mask
+                    mask = self.calibration.mask
                 integration = self.map(
                     _slice_radial_integrate,
                     slices=slices,
diff --git a/pyxem/tests/signals/test_diffraction2d.py b/pyxem/tests/signals/test_diffraction2d.py
index 893ee9f8b..ed5d5dd60 100644
--- a/pyxem/tests/signals/test_diffraction2d.py
+++ b/pyxem/tests/signals/test_diffraction2d.py
@@ -124,8 +124,8 @@ def test_1d_azimuthal_integral_2th_units(self, ones, unit):
         np.testing.assert_array_equal(az.data[0:8], np.ones(8))
 
     def test_1d_azimuthal_integral_pyxem(self, ones):
-        ones.calibrate.center = None
-        ones.calibrate.scale = 0.2
+        ones.calibration.center = None
+        ones.calibration.scale = 0.2
         az = ones.get_azimuthal_integral1d(
             npt=10,
             method="splitpixel_pyxem",
@@ -137,8 +137,8 @@ def test_1d_azimuthal_integral_pyxem(self, ones):
         assert az is None
 
     def test_1d_azimuthal_integral_pyxem(self, ones):
-        ones.calibrate.center = None
-        ones.calibrate.scale = 0.2
+        ones.calibration.center = None
+        ones.calibration.scale = 0.2
         az = ones.get_azimuthal_integral1d(
             npt=10,
             method="splitpixel_pyxem",
@@ -335,7 +335,7 @@ class TestVariance:
     @pytest.fixture
     def ones(self):
         ones_diff = Diffraction2D(data=np.ones(shape=(10, 10, 10, 10)))
-        ones_diff.calibrate(scale=0.1, center=None)
+        ones_diff.calibration(scale=0.1, center=None)
         return ones_diff
 
     @pytest.fixture
@@ -343,7 +343,7 @@ def ones_zeros(self):
         data = np.ones(shape=(10, 10, 10, 10))
         data[0:10:2, :, :, :] = 2
         ones_diff = Diffraction2D(data=data)
-        ones_diff.calibrate(scale=0.1, center=None)
+        ones_diff.calibration(scale=0.1, center=None)
         return ones_diff
 
     @pytest.fixture
@@ -355,7 +355,7 @@ def bulls_eye_noisy(self):
         rng = default_rng(seed=1)
         data = rng.poisson(lam=data)
         ones_diff = Diffraction2D(data=data)
-        ones_diff.calibrate(scale=0.1, center=None)
+        ones_diff.calibration(scale=0.1, center=None)
         return ones_diff
 
     def test_FEM_Omega(self, ones, ones_zeros):
@@ -579,7 +579,7 @@ def test_2d_azimuthal_integral_sum(self, ones):
         )
 
     def test_internal_azimuthal_integration(self, ring):
-        ring.calibrate(scale=1)
+        ring.calibration(scale=1)
         az = ring.get_azimuthal_integral2d(npt=40, npt_azim=100, radial_range=(0, 40))
         ring_sum = np.sum(az.data, axis=1)
         assert ring_sum.shape == (40,)
@@ -653,7 +653,7 @@ def test_internal_azimuthal_integration_data_range(self, corner, shape):
     def test_azimuthal_integration_range(
         self, arange, azimuthal_range, expected_output
     ):
-        arange.calibrate.center = None  # set center
+        arange.calibration.center = None  # set center
         quadrant = arange.get_azimuthal_integral2d(
             npt=10, npt_azim=10, azimuth_range=azimuthal_range, mean=True
         )
diff --git a/pyxem/tests/utils/test_calibration_utils.py b/pyxem/tests/utils/test_calibration_utils.py
index 7dacdcc45..ad9f84a03 100644
--- a/pyxem/tests/utils/test_calibration_utils.py
+++ b/pyxem/tests/utils/test_calibration_utils.py
@@ -132,8 +132,8 @@ def test_get_slices2d(self, calibration):
 
     def test_get_slices_and_factors(self):
         s = Diffraction2D(np.zeros((100, 100)))
-        s.calibrate(scale=0.1, center=None)
-        slices, factors, factor_slices = s.calibrate._get_slices_and_factors(
+        s.calibration(scale=0.1, center=None)
+        slices, factors, factor_slices = s.calibration._get_slices_and_factors(
             npt=100, npt_azim=360, radial_range=(0, 4), azimuthal_range=(0, 2 * np.pi)
         )
         # check that the number of pixels for each radial slice is the same
@@ -147,7 +147,7 @@ def test_get_slices_and_factors(self):
         # n = npt_azim
         all_sum = np.sum(sum_factors)
         assert np.allclose(all_sum, 3.1415 * 40**2, atol=1)
-        slices, factors, factor_slices = s.calibrate._get_slices_and_factors(
+        slices, factors, factor_slices = s.calibration._get_slices_and_factors(
             npt=100, npt_azim=360, radial_range=(0, 15), azimuthal_range=(0, 2 * np.pi)
         )
         # check that the number of pixels for each radial slice is the same
@@ -161,8 +161,8 @@ def test_get_slices_and_factors(self):
 
     def test_get_slices_and_factors1d(self):
         s = Diffraction2D(np.zeros((100, 100)))
-        s.calibrate(scale=0.1, center=None)
-        slices, factors, factor_slices, _ = s.calibrate.get_slices1d(
+        s.calibration(scale=0.1, center=None)
+        slices, factors, factor_slices, _ = s.calibration.get_slices1d(
             100, radial_range=(0, 4)
         )
         # check that the number of pixels for each radial slice is the same
diff --git a/pyxem/tests/utils/test_ransac_ellipse_tools.py b/pyxem/tests/utils/test_ransac_ellipse_tools.py
index 2d0c6780f..e230d8bb4 100644
--- a/pyxem/tests/utils/test_ransac_ellipse_tools.py
+++ b/pyxem/tests/utils/test_ransac_ellipse_tools.py
@@ -931,7 +931,7 @@ def test_determine_ellipse_rotated(self, execution_number):
         center, affine = ret.determine_ellipse(
             s, mask=mask, use_ransac=False, num_points=2000
         )
-        s.calibrate(
+        s.calibration(
             center=center, affine=affine, scale=0.1, units="k_nm^-1", beam_energy=200
         )
         s_az = s.get_azimuthal_integral2d(npt=100)
@@ -949,7 +949,7 @@ def test_determine_ellipse_ring(self, rot):
         mask = np.zeros_like(s.data, dtype=bool)
         mask[100 - 20 : 100 + 20, 100 - 20 : 100 + 20] = True
         center, affine = ret.determine_ellipse(s, mask=mask, use_ransac=False)
-        s.calibrate(
+        s.calibration(
             center=center, affine=affine, scale=0.1, units="k_nm^-1", beam_energy=200
         )
         s_az = s.get_azimuthal_integral2d(npt=100)
diff --git a/pyxem/utils/calibration.py b/pyxem/utils/calibration.py
index 0f9fc57f8..11350b72f 100644
--- a/pyxem/utils/calibration.py
+++ b/pyxem/utils/calibration.py
@@ -182,7 +182,7 @@ def detector(
 
         This sets the signal axes to be a `~hyperspy.axes.DataAxis` instead of a UniformAxis to
         account for the Ewald sphere curvature. This is the most accurate method of calibration
-        but requires a known beam energy/wavelength and detector distance or to calibrate the
+        but requires a known beam energy/wavelength and detector distance or to calibration the
         experimental configuration with a known standard.
 
         Parameters
@@ -493,7 +493,7 @@ def center(self, center=None):
         if not self.flat_ewald:
             raise ValueError(
                 "To set the center of a curved ewald sphere "
-                "use the s.calibrate.detector method"
+                "use the s.calibration.detector method"
             )
         if center is None:
             for ax in self.signal.axes_manager.signal_axes:
@@ -533,7 +533,7 @@ def to_pyfai(self):
             )
             if pixel_size is None or dist is None:
                 raise ValueError(
-                    "The dector must be first initialized with the s.calibrate.detector method"
+                    "The dector must be first initialized with the s.calibration.detector method"
                 )
             detector = Detector(
                 pixel1=pixel_size,
@@ -552,7 +552,9 @@ def to_pyfai(self):
 
 
 @deprecated(
-    since="0.18.0", removal="1.0.0", alternative="pyxem.signals.Diffraction2D.calibrate"
+    since="0.18.0",
+    removal="1.0.0",
+    alternative="pyxem.signals.Diffraction2D.calibration",
 )
 def find_diffraction_calibration(
     patterns,

From 7a7c7997998d749f0500289ddc17be57abadb300 Mon Sep 17 00:00:00 2001
From: Carter Francis <csfrancis@wisc.edu>
Date: Wed, 8 May 2024 10:36:35 -0500
Subject: [PATCH 3/3] Documentation: Fix broken link

---
 doc/bibliography.bib | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/bibliography.bib b/doc/bibliography.bib
index 79b06c93d..3e247826b 100644
--- a/doc/bibliography.bib
+++ b/doc/bibliography.bib
@@ -57,7 +57,7 @@ @article{Kottler:07
 pages = {1175--1181},
 publisher = {OSA},
 title = {{A two-directional approach for grating based differential phase contrast imaging using hard x-rays}},
-url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-15-3-1175},
+url = {https://doi.org/10.1364/OE.15.001175},
 volume = {15},
 year = {2007}
 }