Merge 632993e into 79daffd

pyxem · Jan 8, 2023 · 5ed2ef2 · 5ed2ef2
2 parents 79daffd + 632993e
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -18,6 +18,12 @@ Unreleased
 
 Added
 -----
+- Two tutorials showing projection center (PC) fitting and extrapolation to obtain a
+  plane of PCs to index a full dataset.
+  (`#588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
+- Tutorial showing sloppy projection center (PC)/orientation optimization landscape of
+  the Ni dataset from Jackson et al. (2019), replicating the results from Pang et al.
+  (2020). (`#588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
 - Method ``EBSDDetector.fit_pc()`` to fit a plane using a projective or affine
   transformation to projection centers following work by Winkelmann and co-workers
   (2020). (`#587 <https://github.com/pyxem/kikuchipy/pull/587>`_)
@@ -64,6 +70,8 @@ Added
 
 Changed
 -------
+- Exclude documentation and tests from source distribution.
+  (`#588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
 - Minimal version of HyperSpy increased to >= 1.7.3.
   (`#585 <https://github.com/pyxem/kikuchipy/pull/585>`_)
 - Minimal version of Numba increased to >= 0.52.

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,21 +1,13 @@
 include CHANGELOG.rst
-include CODE_OF_CONDUCT.rst
 include CONTRIBUTING.rst
+include CODE_OF_CONDUCT.rst
 include environment.yml
 include kikuchipy/hyperspy_extension.yaml
 include LICENSE
-include MANIFEST.in
 include README.md
 include readthedocs.yaml
 include RELEASE.rst
 include setup.cfg
 include setup.py
-include tutorials/README.rst
-
-recursive-include doc Makefile make.bat *.rst *.py *.bib *.ipynb *.txt *.cfg *.sh
-recursive-include doc/_static *.png *.jpg *.svg *.css *.sh
-
-recursive-include kikuchipy/data *
-recursive-include examples *.rst *.py
 
-recursive-include benchmarks *.py
+recursive-include kikuchipy/data *
diff --git a/doc/tutorials/esteem2022_diffraction_workshop.ipynb b/doc/tutorials/esteem2022_diffraction_workshop.ipynb
diff --git a/doc/tutorials/feature_maps.ipynb b/doc/tutorials/feature_maps.ipynb
@@ -140,7 +140,7 @@
     "[zero-mean normalized](pattern_processing.ipynb#Normalize-intensity) before\n",
     "computing $Q$, we must pass `get_image_quality(normalize=False)`.\n",
     "\n",
-    "Let's compute the image quality $Q$ and plot it for the entire data set"
+    "Let's compute the image quality $Q$ and plot it for the entire data set (using the [CrystalMap.plot()](https://orix.readthedocs.io/en/stable/reference/generated/orix.crystal_map.CrystalMap.plot.html#orix.crystal_map.CrystalMap.plot) method of the [EBSD.xmap](../reference/generated/kikuchipy.signals.EBSD.xmap.rst) attribute)"
    ]
   },
   {
@@ -155,13 +155,23 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "nbsphinx-thumbnail": {
+     "tooltip": "Extraction of information from pattern intensities"
+    },
+    "tags": [
+     "nbsphinx-thumbnail"
+    ]
+   },
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(10, 6))\n",
-    "plt.imshow(iq, cmap=\"gray\")\n",
-    "plt.colorbar(label=r\"Image quality, $Q$\", pad=0.01)\n",
-    "_ = plt.axis(\"off\")"
+    "s.xmap.plot(\n",
+    "    iq.ravel(),\n",
+    "    cmap=\"gray\",\n",
+    "    colorbar=True,\n",
+    "    colorbar_label=\"Image quality, $Q$\",\n",
+    "    remove_padding=True,\n",
+    ")"
    ]
   },
   {
@@ -199,20 +209,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "nbsphinx-thumbnail": {
-     "tooltip": "Extraction of information from pattern intensities"
-    },
-    "tags": [
-     "nbsphinx-thumbnail"
-    ]
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(10, 6))\n",
-    "plt.imshow(adp, cmap=\"gray\")\n",
-    "plt.colorbar(label=\"Average dot product\", pad=0.01)\n",
-    "_ = plt.axis(\"off\")"
+    "s.xmap.plot(\n",
+    "    adp.ravel(),\n",
+    "    cmap=\"gray\",\n",
+    "    colorbar=True,\n",
+    "    colorbar_label=\"Average dot product\",\n",
+    "    remove_padding=True,\n",
+    ")"
    ]
   },
   {
@@ -265,10 +271,13 @@
    "source": [
     "adp2 = s.get_average_neighbour_dot_product_map(window=w2)\n",
     "\n",
-    "plt.figure(figsize=(10, 6))\n",
-    "plt.imshow(adp2, cmap=\"gray\")\n",
-    "plt.colorbar(label=\"Average dot product\", pad=0.01)\n",
-    "_ = plt.axis(\"off\")"
+    "s.xmap.plot(\n",
+    "    adp2.ravel(),\n",
+    "    cmap=\"gray\",\n",
+    "    colorbar=True,\n",
+    "    colorbar_label=\"Average dot product\",\n",
+    "    remove_padding=True,\n",
+    ")"
    ]
   },
   {
@@ -331,9 +340,9 @@
     "\n",
     "s2 = s.inav[x - x_n : x + x_n + 1, y - y_n : y + y_n + 1].deepcopy()\n",
     "s2.rescale_intensity(percentiles=(0.5, 99.5))  # Stretch the contrast a bit\n",
-    "s3 = (\n",
-    "    s2 * s_dp_matrices.inav[x, y].T\n",
-    ")  # Signals must have same navigation shape"
+    "\n",
+    "# Signals must have same navigation shape (warning can be ignored)\n",
+    "s3 = s2 * s_dp_matrices.inav[x, y].T"
    ]
   },
   {
@@ -389,11 +398,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(10, 6))\n",
-    "plt.imshow(adp3, cmap=\"gray\")\n",
-    "plt.colorbar(label=\"Average dot product\", pad=0.01)\n",
-    "plt.scatter(x=x, y=y, marker=\"o\", c=\"r\", s=50)\n",
-    "_ = plt.axis(\"off\")"
+    "s.xmap.plot(\n",
+    "    adp3.ravel(),\n",
+    "    cmap=\"gray\",\n",
+    "    colorbar=True,\n",
+    "    colorbar_label=\"Average dot product\",\n",
+    "    remove_padding=True,\n",
+    ")"
    ]
   }
  ],
@@ -413,7 +424,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.10.8"
   }
  },
  "nbformat": 4,

diff --git a/doc/tutorials/geometrical_ebsd_simulations.ipynb b/doc/tutorials/geometrical_ebsd_simulations.ipynb
@@ -152,10 +152,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ref = ReciprocalLatticeVector(\n",
+    "rlv = ReciprocalLatticeVector(\n",
     "    phase=phase, hkl=[[1, 1, 1], [2, 0, 0], [2, 2, 0], [3, 1, 1]]\n",
     ")\n",
-    "ref"
+    "rlv"
    ]
   },
   {
@@ -171,8 +171,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ref = ref.symmetrise().unique()\n",
-    "ref.size"
+    "rlv = rlv.symmetrise().unique()\n",
+    "rlv.size"
    ]
   },
   {
@@ -181,7 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ref.print_table()"
+    "rlv.print_table()"
    ]
   },
   {
@@ -190,8 +190,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Dictionary with {hkl} as key and indices into `ref` as values\n",
-    "hkl_sets = ref.get_hkl_sets()\n",
+    "# Dictionary with {hkl} as key and indices into ReciprocalLatticeVector as values\n",
+    "hkl_sets = rlv.get_hkl_sets()\n",
     "hkl_sets"
    ]
   },
@@ -201,7 +201,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hkl_colors = np.zeros((ref.size, 3))\n",
+    "hkl_colors = np.zeros((rlv.size, 3))\n",
     "for idx, color in zip(\n",
     "    hkl_sets.values(),\n",
     "    [\n",
@@ -221,7 +221,7 @@
    "outputs": [],
    "source": [
     "hkl_labels = []\n",
-    "for hkl in ref.hkl.round(0).astype(int):\n",
+    "for hkl in rlv.hkl.round(0).astype(int):\n",
     "    hkl_labels.append(str(hkl).replace(\"[\", \"(\").replace(\"]\", \")\"))"
    ]
   },
@@ -231,7 +231,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ref.scatter(c=hkl_colors, grid=True, ec=\"k\", vector_labels=hkl_labels)"
+    "rlv.scatter(c=hkl_colors, grid=True, ec=\"k\", vector_labels=hkl_labels)"
    ]
   },
   {
@@ -247,7 +247,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ref.draw_circle(\n",
+    "rlv.draw_circle(\n",
     "    color=hkl_colors, hemisphere=\"both\", figure_kwargs=dict(figsize=(15, 10))\n",
     ")"
    ]
@@ -270,7 +270,7 @@
    "outputs": [],
    "source": [
     "rot = s.xmap.rotations\n",
-    "rot = rot.reshape(*s.axes_manager.navigation_shape[::-1])\n",
+    "rot = rot.reshape(*s.xmap.shape)\n",
     "rot  # Quaternions"
    ]
   },
@@ -317,7 +317,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulator = kp.simulations.KikuchiPatternSimulator(ref)"
+    "simulator = kp.simulations.KikuchiPatternSimulator(rlv)"
    ]
   },
   {
@@ -479,7 +479,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.10.8"
   }
  },
  "nbformat": 4,