Correct detector shape of returned EBSD signal from downsample()

.github/workflows/perhaps_make_tagged_release_draft.py

@@ -19,7 +19,6 @@
 
 from outdated import check_outdated
 
-
 with open("../../kikuchipy/release.py") as fid:
     for line in fid:
         if line.startswith("version"):

.github/workflows/tests.yml

@@ -8,17 +8,24 @@ on:
     branches:
       - '*'
   workflow_dispatch:
-    workflow: '*'
 
 jobs:
   code:
     name: code style
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: psf/black@stable
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - uses: isort/isort-action@master
+        with:
+          configuration: --profile black --filter-files --force-sort-within-sections --check-only --diff
+
       - name: Install Black with Jupyter extension
         run: |
           pip install black[jupyter]
@@ -32,9 +39,9 @@ jobs:
     name: check manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -60,17 +67,17 @@ jobs:
         python-version: ['3.10', '3.11']
         include:
           - os: ubuntu-latest
-            python-version: 3.7
-            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.1 hyperspy==1.7.3 matplotlib==3.5 numba==0.55 numpy==1.21.6 orix==0.11.1 pooch==1.3.0 pyebsdindex==0.2 scikit-image==0.16.2
+            python-version: 3.8
+            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.1 hyperspy==1.7.3 matplotlib==3.5 numba==0.57 numpy==1.23.0 orix==0.11.1 pooch==1.3.0 pyebsdindex==0.2 scikit-image==0.21.0
             LABEL: -oldest
           - os: ubuntu-latest
             python-version: 3.11
             LABEL: -minimum_requirement
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -85,13 +92,20 @@ jobs:
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
-      - name: Install optional dependencies
-        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false }}
+      - name: Install optional dependencies on Linux and Windows
+        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false && matrix.os != 'macos-latest' }}
         shell: bash
         run: |
           pip install -e .'[all]'
           pip install pyopencl
 
+      - name: Install optional dependencies on macOS (without nlopt)
+        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false && matrix.os == 'macos-latest' }}
+        shell: bash
+        run: |
+          pip install -e .
+          pip install 'pyebsdindex[gpu]' pyvista
+
       - name: Display Python, pip and package versions
         run: |
           python -V

.pre-commit-config.yaml

@@ -1,5 +1,18 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
+    # https://black.readthedocs.io/en/stable/index.html
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 24.4.2
+      hooks:
       - id: black
+        language_version: python3.11
+      - id: black-jupyter
+        files: \.ipynb
+        args: [--line-length=77]
+    # https://pycqa.github.io/isort/
+    - repo: https://github.com/pycqa/isort
+      rev: 5.13.2
+      hooks:
+        - id: isort
+          name: isort (python)
+          args:
+            [--profile=black, --filter-files, --force-sort-within-sections]

CHANGELOG.rst

@@ -21,6 +21,14 @@ Added
 
 Changed
 -------
+- Minimum Python version is now 3.8.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Minimum NumPy version is now 1.23.0.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Minimum Numba version is now 0.57.0.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Minimum scikit-image version is now 0.22.0.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
 
 Deprecated
 ----------
@@ -30,7 +38,11 @@ Removed
 
 Fixed
 -----
-
+- The order of the new shape of the detector of a downsampled EBSD signal, returned from
+  ``downsample()``, was previously previously incorrect, (n columns, n rows). This is
+  now correct, (n rows, n columns).
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+
 0.9.0 (2023-11-03)
 ==================
 
@@ -531,8 +543,8 @@ Deprecated
   removed in version 0.7. Use the ``kikuchipy.simulations.KikuchiPatternSimulator``
   class instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - The ``kikuchipy.crystallography.matrices`` module is deprecated and will be removed in
-  version 0.7, access the matrices via :class:`diffpy.structure.lattice.Lattice`
-  attributes instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
+  version 0.7, access the matrices via ``diffpy.structure.lattice.Lattice`` attributes
+  instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - The following functions for processing of pattern chunks in the
   ``kikuchipy.pattern.chunk`` module are deprecated and will be removed in version 0.7:
   ``get_image_quality()``, ``remove_dynamic_background()`` and

doc/_static/image/reference_frames/doc_reference_frames.py

@@ -19,9 +19,8 @@
 
 import matplotlib.pyplot as plt
 
-from kikuchipy.detectors import EBSDDetector
 from kikuchipy import load
-
+from kikuchipy.detectors import EBSDDetector
 
 data = "/home/hakon/kode/kikuchipy/kikuchipy/data/kikuchipy_h5ebsd/patterns.h5"
 outdir = "/home/hakon/kode/kikuchipy/doc/_static/image"

doc/conf.py

@@ -5,16 +5,15 @@
 from datetime import datetime
 import inspect
 import os
-from os.path import relpath, dirname
+from os.path import dirname, relpath
 import re
 import sys
 
-import pyvista as pv
 from numpydoc.docscrape_sphinx import SphinxDocString
+import pyvista as pv
 
 import kikuchipy as kp
 
-
 # If extensions (or modules to document with autodoc) are in another
 # directory, add these directories to sys.path here. If the directory
 # is relative to the documentation root, use os.path.abspath to make it

doc/tutorials/esteem2022_diffraction_workshop.ipynb

@@ -2178,7 +2178,9 @@
     }
    ],
    "source": [
-    "fig = simulator.plot(hemisphere=\"upper\", mode=\"lines\", return_figure=True, color=\"w\")\n",
+    "fig = simulator.plot(\n",
+    "    hemisphere=\"upper\", mode=\"lines\", return_figure=True, color=\"w\"\n",
+    ")\n",
     "fig.axes[0].scatter(ref, c=hkl_rgb, s=50)\n",
     "\n",
     "fig.axes[0].imshow(mp_sp.data, cmap=\"gray\", extent=(-1, 1, -1, 1));"

doc/tutorials/feature_maps.ipynb

@@ -404,7 +404,7 @@
     "    colorbar=True,\n",
     "    colorbar_label=\"Average dot product\",\n",
     "    remove_padding=True,\n",
-    "    return_figure=True\n",
+    "    return_figure=True,\n",
     ")\n",
     "fig.axes[0].scatter(x, y, c=\"r\");"
    ]

doc/tutorials/hough_indexing.ipynb

@@ -339,7 +339,7 @@
     "    [[1, 1, 1], [2, 0, 0], [2, 2, 0], [3, 1, 1]],\n",
     "    nBands=10,\n",
     "    tSigma=2,\n",
-    "    rSigma=2\n",
+    "    rSigma=2,\n",
     ")\n",
     "\n",
     "print(indexer.vendor)\n",
@@ -475,7 +475,7 @@
     "    [[1, 1, 1], [2, 0, 0], [2, 2, 0], [3, 1, 1]],\n",
     "    nBands=10,\n",
     "    tSigma=2,\n",
-    "    rSigma=2\n",
+    "    rSigma=2,\n",
     ")\n",
     "indexer.PC"
    ]
@@ -527,14 +527,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#io.save(\"xmap_ni.h5\", xmap)\n",
-    "#io.save(\n",
+    "# io.save(\"xmap_ni.h5\", xmap)\n",
+    "# io.save(\n",
     "#    \"xmap_ni.ang\",\n",
     "#    xmap,\n",
     "#    image_quality_prop=\"pq\",\n",
     "#    confidence_index_prop=\"cm\",\n",
     "#    extra_prop=\"nmatch\",\n",
-    "#)"
+    "# )"
    ]
   },
   {

doc/tutorials/hybrid_indexing.ipynb

@@ -68,11 +68,13 @@
     "from orix.vector import Vector3d\n",
     "\n",
     "\n",
-    "plt.rcParams.update({\n",
-    "    \"figure.facecolor\": \"w\",\n",
-    "    \"font.size\": 15,\n",
-    "    \"figure.dpi\": 75,\n",
-    "})"
+    "plt.rcParams.update(\n",
+    "    {\n",
+    "        \"figure.facecolor\": \"w\",\n",
+    "        \"font.size\": 15,\n",
+    "        \"figure.dpi\": 75,\n",
+    "    }\n",
+    ")"
    ]
   },
   {
@@ -1335,9 +1337,7 @@
     "\n",
     "# Place color key in bottom right corner, coordinates are\n",
     "# [left, bottom, width, height]\n",
-    "ax_ckey = fig.add_axes(\n",
-    "    [0.76, 0.08, 0.2, 0.2], projection=\"ipf\", symmetry=pg\n",
-    ")\n",
+    "ax_ckey = fig.add_axes([0.76, 0.08, 0.2, 0.2], projection=\"ipf\", symmetry=pg)\n",
     "ax_ckey.plot_ipf_color_key(show_title=False)\n",
     "ax_ckey.patch.set_facecolor(\"None\")"
    ]

doc/tutorials/kinematical_ebsd_simulations.ipynb

@@ -425,7 +425,9 @@
     "ni_kin_data[mask] = np.nan\n",
     "\n",
     "fig, axes = plt.subplots(ncols=2, layout=\"tight\")\n",
-    "for ax, data, title in zip(axes, [ni_kin_data, ni_dyn_data], [\"kinematical\", \"dynamical\"]):\n",
+    "for ax, data, title in zip(\n",
+    "    axes, [ni_kin_data, ni_dyn_data], [\"kinematical\", \"dynamical\"]\n",
+    "):\n",
     "    ax.imshow(data, cmap=\"gray\")\n",
     "    ax.axis(\"off\")\n",
     "    ax.set(title=f\"Ni {title} 20 kV\")"

doc/tutorials/pattern_matching.ipynb

@@ -1107,7 +1107,9 @@
     "    alpha=0.5,\n",
     "    label=ncc_after_ori_ref_label,\n",
     ")\n",
-    "ax.set(xlabel=\"Normalized cross correlation (NCC) scores\", ylabel=\"Frequency\")\n",
+    "ax.set(\n",
+    "    xlabel=\"Normalized cross correlation (NCC) scores\", ylabel=\"Frequency\"\n",
+    ")\n",
     "ax.legend()\n",
     "fig.tight_layout();"
    ]
@@ -1200,9 +1202,7 @@
     "\n",
     "# Place color key in bottom right corner,\n",
     "# coordinates are [left, bottom, width, height]\n",
-    "ax_ckey = fig.add_axes(\n",
-    "    [0.75, 0.08, 0.2, 0.2], projection=\"ipf\", symmetry=pg\n",
-    ")\n",
+    "ax_ckey = fig.add_axes([0.75, 0.08, 0.2, 0.2], projection=\"ipf\", symmetry=pg)\n",
     "ax_ckey.plot_ipf_color_key(show_title=False)\n",
     "ax_ckey.patch.set_facecolor(\"None\")\n",
     "_ = [text.set_color(\"w\") for text in ax_ckey.texts]  # White [uvw]"
@@ -1418,7 +1418,9 @@
     "    alpha=0.5,\n",
     "    label=ncc_after_pc_ref_label,\n",
     ")\n",
-    "ax.set(xlabel=\"Normalized cross correlation (NCC) scores\", ylabel=\"Frequency\")\n",
+    "ax.set(\n",
+    "    xlabel=\"Normalized cross correlation (NCC) scores\", ylabel=\"Frequency\"\n",
+    ")\n",
     "ax.legend()\n",
     "fig.tight_layout();"
    ]
@@ -1643,7 +1645,9 @@
     "    alpha=0.5,\n",
     "    label=ncc_after_ori_pc_ref_label,\n",
     ")\n",
-    "ax.set(xlabel=\"Normalized cross correlation (NCC) scores\", ylabel=\"Frequency\")\n",
+    "ax.set(\n",
+    "    xlabel=\"Normalized cross correlation (NCC) scores\", ylabel=\"Frequency\"\n",
+    ")\n",
     "ax.legend()\n",
     "fig.tight_layout();"
    ]

doc/tutorials/pattern_processing.ipynb

@@ -650,7 +650,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s11 = s3.inav[0, 0].normalize_intensity(num_std=1, dtype_out=np.float32, inplace=False)\n",
+    "s11 = s3.inav[0, 0].normalize_intensity(\n",
+    "    num_std=1, dtype_out=np.float32, inplace=False\n",
+    ")\n",
     "np.mean(s11.data)"
    ]
   },

doc/tutorials/pc_calibration_moving_screen_technique.ipynb

@@ -107,7 +107,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, axes = plt.subplots(ncols=2, sharex=True, sharey=True, figsize=(14, 7), layout=\"tight\")\n",
+    "fig, axes = plt.subplots(\n",
+    "    ncols=2, sharex=True, sharey=True, figsize=(14, 7), layout=\"tight\"\n",
+    ")\n",
     "for ax, data in zip(axes, [s_in.data, s_out5mm.data]):\n",
     "    ax.imshow(data, cmap=\"gray\")"
    ]
@@ -276,7 +278,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "det_ref = s_in.hough_indexing_optimize_pc(pc0=det.pc, indexer=indexer, method=\"PSO\")\n",
+    "det_ref = s_in.hough_indexing_optimize_pc(\n",
+    "    pc0=det.pc, indexer=indexer, method=\"PSO\"\n",
+    ")\n",
     "\n",
     "print(det.pc - det_ref.pc)"
    ]

doc/tutorials/pc_extrapolate_plane.ipynb

@@ -179,7 +179,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "r_pattern = kp.filters.distance_to_origin(s_cal.axes_manager.signal_shape[::-1], origin=(230, 220))\n",
+    "r_pattern = kp.filters.distance_to_origin(\n",
+    "    s_cal.axes_manager.signal_shape[::-1], origin=(230, 220)\n",
+    ")\n",
     "signal_mask = r_pattern > 310  # Exclude pixels set to True"
    ]
   },
@@ -1272,7 +1274,9 @@
    "source": [
     "fig, axes = plt.subplots(ncols=3, nrows=3, figsize=(12, 12))\n",
     "for i, ax in enumerate(axes.ravel()):\n",
-    "    ax.imshow(s_cal2.inav[i].data * ~signal_mask, cmap=\"gray\", vmin=-3, vmax=3)\n",
+    "    ax.imshow(\n",
+    "        s_cal2.inav[i].data * ~signal_mask, cmap=\"gray\", vmin=-3, vmax=3\n",
+    "    )\n",
     "    ax.axis(\"off\")\n",
     "\n",
     "    # Affine\n",