Merge pull request #322 from hakonanes/pc-calibration

Add moving screen projection center calibration to kikuchipy.detectors module
pyxem · Feb 10, 2021 · bad8891 · bad8891
2 parents 62ec60d + 84eabac
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diff --git a/doc/bibliography.bib b/doc/bibliography.bib
@@ -35,7 +35,7 @@ @article{jackson2019dictionary
 	doi = {10.1007/s40192-019-00137-4},
 }
 @book{gonzalez2017digital,
-	author = {Gonzalez, Rafael C and Woods, Richard E},
+	author = {Gonzalez, Rafael C. and Woods, Richard E.},
 	edition = {4th},
 	isbn = {978-0133356724},
 	keywords = {image processng, computer vision},
@@ -44,7 +44,7 @@ @book{gonzalez2017digital
 	year = {2017}
 }
 @article{callahan2013dynamical,
-	author = {Callahan, Patrick G and {De Graef}, Marc},
+	author = {Callahan, Patrick G. and {De Graef}, Marc},
 	doi = {10.1017/S1431927613001840},
 	isbn = {1431927613001},
 	journal = {Microscopy and Microanalysis},
@@ -55,7 +55,7 @@ @article{callahan2013dynamical
 	year = {2013}
 }
 @article{jackson2014h5ebsd,
-	author = {Jackson, Michael A and Groeber, Michael A and Uchic, Michael D and Rowenhorst, David J and {De Graef}, Marc},
+	author = {Jackson, Michael A. and Groeber, Michael A. and Uchic, Michael D. and Rowenhorst, David J. and {De Graef}, Marc},
 	doi = {10.1186/2193-9772-3-4},
 	journal = {Integrating Materials and Manufacturing Innovation},
 	keywords = {h5ebsd, hdf5, ebsd, emsoft},
@@ -85,13 +85,13 @@ @article{chen2015dictionary
 	year = {2015}
 }
 @book{goshtasby2012image,
-	author = {Goshtasby, A Ardeshir},
+	author = {Goshtasby, Ardeshir A.},
 	publisher = {Springer Science \& Business Media},
 	title = {{Image registration: Principles, tools and methods}},
 	year = {2012}
 }
 @book{aanes2019electron,
-  author = {Ånes, H. W and Hjelen, J. and van Helvoort, A. T. J. and Marthinsen, K.},
+  author = {Ånes, Håkon W. and Hjelen, Jarle and van Helvoort, Antonius T. J. and Marthinsen, Knut},
   title = {{Electron backscatter patterns from Nickel acquired with varying camera gain}},
   year = 2019,
   note = {[Data set].},
@@ -110,7 +110,7 @@ @article{singh2017application
 	year = {2017}
 }
 @article{foden2019indexing,
-	author = {Foden, Alexander and Collins, David M and Wilkinson, Angus J and Britton, T Benjamin},
+	author = {Foden, Alexander and Collins, David M. and Wilkinson, Angus J. and Britton, Thomas B.},
 	journal = {Ultramicroscopy},
 	pages = {112845},
 	publisher = {Elsevier},
@@ -120,7 +120,7 @@ @article{foden2019indexing
 	year = {2019}
 }
 @article{nolze2016pattern,
-	author = {Nolze, Gert and Winkelmann, Aimo and Boyle, Alan P},
+	author = {Nolze, Gert and Winkelmann, Aimo and Boyle, Alan P.},
 	doi = {10.1016/j.ultramic.2015.10.010},
 	journal = {Ultramicroscopy},
 	pages = {146–154},
@@ -136,7 +136,6 @@ @article{nolze2017electron
 	issn = {15214079},
 	journal = {Crystal Research and Technology},
 	keywords = {channeling-in and out, ebsd, element number contrast, image{\_}processing, indexing, lattice parameters, polarity, pseudosymmetry, virtual{\_}imaging},
-	mendeley-tags = {ebsd,image{\_}processing,indexing,virtual{\_}imaging},
 	number = {1},
 	pages = {1–24},
 	title = {{Electron backscatter diffraction beyond the mainstream}},
@@ -150,17 +149,15 @@ @article{wright2015electron
 	issn = {18792723},
 	journal = {Ultramicroscopy},
 	keywords = {EBSD, Electron imaging, PRIAS, Synthetic-BSD, Virtual FSD, ebsd},
-	mendeley-tags = {ebsd},
 	pages = {132–145},
 	pmid = {25461590},
 	publisher = {Elsevier},
 	title = {{Electron imaging with an EBSD detector}},
-	url = {http://dx.doi.org/10.1016/j.ultramic.2014.10.002},
 	volume = {148},
 	year = {2015}
 }
 @article{britton2016tutorial,
-	author = {Britton, T. B. and Jiang, J. and Guo, Y. and Vilalta-Clemente, A. and Wallis, D. and Hansen, L. N. and Winkelmann, A. and Wilkinson, A. J.},
+	author = {Britton, T. B. and Jiang, J. and Guo, Y. and Vilalta-Clemente, A. and Wallis, D. and Hansen, L. N. and Winkelmann, Aimo and Wilkinson, Angus J.},
 	doi = {10.1016/j.matchar.2016.04.008},
 	isbn = {1044-5803},
 	issn = {10445803},
@@ -170,7 +167,6 @@ @article{britton2016tutorial
 	pages = {113–126},
 	publisher = {The Authors},
 	title = {{Tutorial: Crystal orientations and EBSD - Or which way is up?}},
-	url = {http://dx.doi.org/10.1016/j.matchar.2016.04.008},
 	volume = {117},
 	year = {2016}
 }
@@ -186,7 +182,7 @@ @inproceedings{aanes2020processing
 	year = {2020}
 }
 @article{brewick2019nlpar,
-	author = {Brewick, Patrick T and Wright, Stuart and Rowenhorst, David J},
+	author = {Brewick, Patrick T. and Wright, Stuart I. and Rowenhorst, David J.},
 	doi = {10.1016/j.ultramic.2019.02.013},
 	journal = {Ultramicroscopy},
 	pages = {50–61},
@@ -206,4 +202,3 @@ @article{hjelen1991electron
 	volume = {22},
 	year = {1991}
 }
-
diff --git a/doc/changelog.rst b/doc/changelog.rst
@@ -9,7 +9,7 @@ All notable changes to this project will be documented in this file. The format
 is based on `Keep a Changelog <https://keepachangelog.com/en/1.1.0>`_, and this
 project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
-Contributors to each release are listed in alphabetical order by first name. 
+Contributors to each release are listed in alphabetical order by first name.
 List entries are sorted in descending chronological order.
 
 Unreleased
@@ -21,8 +21,11 @@ Contributors
 
 Added
 -----
+- Projection/pattern center calibration via the moving screen technique in a
+  kikuchipy.detectors.calibration module.
+  (`#322 <https://github.com/pyxem/kikuchipy/pull/322>`_)
 - Three single crystal Si EBSD patterns, from the same sample position but with
-  varying sample-screen distances, to the data module (via external repo).
+  varying detector distances, to the data module (via external repo).
   (`#320 <https://github.com/pyxem/kikuchipy/pull/320>`_)
 - Reading of NORDIF calibration patterns specified in a setting file into an
   EBSD signal. (`#317 <https://github.com/pyxem/kikuchipy/pull/317>`_)

diff --git a/doc/geometrical_ebsd_simulations.ipynb b/doc/geometrical_ebsd_simulations.ipynb
@@ -185,7 +185,7 @@
    "metadata": {},
    "source": [
     "We describe the sample-detector model in an\n",
-    "[kikuchipy.detectors.EBSDDetector](reference.rst#kikuchipy.detectors.ebsd_detector.EBSDDetector)\n",
+    "[kikuchipy.detectors.EBSDDetector](reference.rst#kikuchipy.detectors.EBSDDetector)\n",
     "instance. From Hough indexing we know the projection center to be, in the EDAX\n",
     "TSL convention (see the [reference frame](reference_frames.rst) guide for the\n",
     "various conventions and more details on the use of the sample-detector model),\n",

diff --git a/doc/load_save_data.ipynb b/doc/load_save_data.ipynb
@@ -254,7 +254,7 @@
     "In addition to the HyperSpy provided `metadata`, `original_metadata` and\n",
     "`axes_manager` properties, kikuchipy tries to read a [CrystalMap](https://orix.readthedocs.io/en/stable/reference.html#crystalmap) object with indexing results into a\n",
     "`xmap` property and an\n",
-    "[EBSDDetector](reference.rst#kikuchipy.detectors.ebsd_detector.EBSDDetector)\n",
+    "[EBSDDetector](reference.rst#kikuchipy.detectors.EBSDDetector)\n",
     "object into a `detector` property:"
    ]
   },
@@ -509,7 +509,7 @@
     "| EDAX TSL h5ebsd                 | Yes  | No    |\n",
     "| kikuchipy h5ebsd                | Yes  | Yes   |\n",
     "| NORDIF binary                   | Yes  | Yes   |\n",
-    "| NORDIF Calibration patterns     | Yes  | No    |\n",
+    "| NORDIF calibration patterns     | Yes  | No    |\n",
     "| EMsoft simulated EBSD HDF5      | Yes  | No    |\n",
     "| EMsoft EBSD master pattern HDF5 | Yes  | No    |\n",
     "| Bruker Nano h5ebsd              | Yes  | No    |\n",

diff --git a/doc/pattern_matching.ipynb b/doc/pattern_matching.ipynb
@@ -211,7 +211,8 @@
     "volume). This ensures that projecting parts of the master pattern onto our\n",
     "detector yields dynamically simulated patterns resembling our experimental ones.\n",
     "See the [reference frames](reference_frames.rst) user guide and the\n",
-    "[EBSDDetector](reference.rst#ebsddetector) class for further details."
+    "[EBSDDetector](reference.rst#kikuchipy.detectors.EBSDDetector)\n",
+    "class for further details."
    ]
   },
   {
@@ -235,7 +236,7 @@
    "source": [
     "Let's double check the projection/pattern center (PC) position on the detector\n",
     "using\n",
-    "[plot()](reference.rst#kikuchipy.detectors.ebsd_detector.EBSDDetector.plot)"
+    "[plot()](reference.rst#kikuchipy.detectors.EBSDDetector.plot)"
    ]
   },
   {

diff --git a/doc/pattern_processing.ipynb b/doc/pattern_processing.ipynb
@@ -270,7 +270,7 @@
     "\\end{equation}\n",
     "\n",
     "where $a = (m - 1)/2$ and $b = (n - 1)/2$. The window $w$, a\n",
-    "[Window](reference.rst#kikuchipy.filters.window.Window) object, can be plotted:"
+    "[Window](reference.rst#kikuchipy.filters.Window) object, can be plotted:"
    ]
   },
   {
@@ -290,13 +290,13 @@
     "Any 1D or 2D window with desired coefficients can be used. This custom window\n",
     "can be passed to the `window` parameter in\n",
     "[average_neighbour_patterns()](reference.rst#kikuchipy.signals.EBSD.average_neighbour_patterns)\n",
-    "or [Window](reference.rst#kikuchipy.filters.window.Window) as a `numpy.ndarray`\n",
+    "or [Window](reference.rst#kikuchipy.filters.Window) as a `numpy.ndarray`\n",
     "or a `dask.array.Array`. Additionally, any window in\n",
     "[scipy.signal.windows.get_window()](https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.get_window.html)\n",
     "passed as a string via `window` with the necessary parameters as keyword\n",
     "arguments (like `std=1` for `window=\"gaussian\"`) can be used. To demonstrate the\n",
     "creation and use of an asymmetrical circular window (and the use of\n",
-    "[make_circular()](reference.rst#kikuchipy.filters.window.Window.make_circular),\n",
+    "[make_circular()](reference.rst#kikuchipy.filters.Window.make_circular),\n",
     "although we could create a circular window directly by calling\n",
     "`window=\"circular\"` upon window initialization):"
    ]
@@ -420,7 +420,7 @@
     "[fft_filter()](reference.rst#kikuchipy.signals.EBSD.fft_filter). This method\n",
     "takes a spatial kernel defined in the spatial domain, or a transfer function\n",
     "defined in the frequency domain, in the `transfer_function` argument as a\n",
-    "`numpy.ndarray` or a [Window](reference.rst#kikuchipy.filters.window.Window).\n",
+    "`numpy.ndarray` or a [Window](reference.rst#kikuchipy.filters.Window).\n",
     "Which domain the transfer function is defined in must be passed to the\n",
     "`function_domain` argument. Whether to shift zero-frequency components to the\n",
     "centre of the FFT can also be controlled via `shift`, but note that this is\n",

diff --git a/doc/reference.rst b/doc/reference.rst
@@ -36,7 +36,6 @@ crystallography
 ===============
 
 .. automodule:: kikuchipy.crystallography
-
 .. currentmodule:: kikuchipy.crystallography
 
 .. autosummary::
@@ -73,21 +72,37 @@ detectors
 =========
 
 .. automodule:: kikuchipy.detectors
-
-.. currentmodule:: kikuchipy.detectors.ebsd_detector
+.. currentmodule:: kikuchipy.detectors
 
 .. autosummary::
     EBSDDetector
+    PCCalibrationMovingScreen
 
 EBSDDetector
 ------------
 
-.. currentmodule:: kikuchipy.detectors.ebsd_detector.EBSDDetector
+.. currentmodule:: kikuchipy.detectors.EBSDDetector
+
+.. autosummary::
+    plot
+
+.. autoclass:: kikuchipy.detectors.EBSDDetector
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+    .. automethod:: __init__
+
+PCCalibrationMovingScreen
+-------------------------
+
+.. currentmodule:: kikuchipy.detectors.PCCalibrationMovingScreen
 
 .. autosummary::
+    make_lines
     plot
 
-.. autoclass:: kikuchipy.detectors.ebsd_detector.EBSDDetector
+.. autoclass:: kikuchipy.detectors.PCCalibrationMovingScreen
     :members:
     :undoc-members:
     :show-inheritance:
@@ -100,7 +115,6 @@ draw
 ====
 
 .. automodule:: kikuchipy.draw
-
 .. currentmodule:: kikuchipy.draw
 
 markers
@@ -128,8 +142,7 @@ filters
 =======
 
 .. automodule:: kikuchipy.filters
-
-.. currentmodule:: kikuchipy.filters.window
+.. currentmodule:: kikuchipy.filters
 
 .. autosummary::
     distance_to_origin
@@ -146,15 +159,15 @@ filters
 Window
 ------
 
-.. currentmodule:: kikuchipy.filters.window.Window
+.. currentmodule:: kikuchipy.filters.Window
 
 .. autosummary::
     is_valid
     make_circular
     plot
     shape_compatible
 
-.. autoclass:: kikuchipy.filters.window.Window
+.. autoclass:: kikuchipy.filters.Window
     :members:
     :undoc-members:
     :show-inheritance: