Format some files using Black 24.2

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
pyxem · May 30, 2024 · 08aab67 · 08aab67
1 parent 03c0870
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,10 +3,16 @@ repos:
     - repo: https://github.com/psf/black-pre-commit-mirror
       rev: 24.4.2
       hooks:
-        - id: black
-          language_version: python3.11
+      - 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]
diff --git a/doc/tutorials/esteem2022_diffraction_workshop.ipynb b/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));"

diff --git a/doc/tutorials/feature_maps.ipynb b/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\");"
    ]

diff --git a/doc/tutorials/hough_indexing.ipynb b/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",
-    "#)"
+    "# )"
    ]
   },
   {

diff --git a/doc/tutorials/hybrid_indexing.ipynb b/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\")"
    ]

diff --git a/doc/tutorials/kinematical_ebsd_simulations.ipynb b/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\")"

diff --git a/doc/tutorials/pattern_matching.ipynb b/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();"
    ]

diff --git a/doc/tutorials/pattern_processing.ipynb b/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)"
    ]
   },

diff --git a/doc/tutorials/pc_calibration_moving_screen_technique.ipynb b/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)"
    ]

diff --git a/doc/tutorials/pc_extrapolate_plane.ipynb b/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",

diff --git a/doc/tutorials/pc_fit_plane.ipynb b/doc/tutorials/pc_fit_plane.ipynb
@@ -1379,7 +1379,9 @@
    "source": [
     "fig, axes = plt.subplots(*grid_shape, figsize=(15, 15))\n",
     "for i in np.ndindex(grid_shape):\n",
-    "    axes[i].imshow((s_grid2.data[i] * ~signal_mask), cmap=\"gray\", vmin=-3, vmax=3)\n",
+    "    axes[i].imshow(\n",
+    "        (s_grid2.data[i] * ~signal_mask), cmap=\"gray\", vmin=-3, vmax=3\n",
+    "    )\n",
     "    axes[i].axis(\"off\")\n",
     "\n",
     "    lines = sim.as_collections(i)[0]\n",
@@ -1434,7 +1436,9 @@
     "    xmap_grid_ref2.orientations, degrees=True\n",
     ")\n",
     "print(angles.max())\n",
-    "xmap_grid_ref2.plot(angles, colorbar=True, colorbar_label=\"Misorientation angle [deg]\")"
+    "xmap_grid_ref2.plot(\n",
+    "    angles, colorbar=True, colorbar_label=\"Misorientation angle [deg]\"\n",
+    ")"
    ]
   },
   {

diff --git a/doc/tutorials/pc_orientation_dependence.ipynb b/doc/tutorials/pc_orientation_dependence.ipynb
@@ -1190,7 +1190,9 @@
     "# Make an array of full map size of zeros (black), and fill colors from\n",
     "# successfully indexed nickel in the correct points\n",
     "rgb = np.zeros((xmap.size, 3))\n",
-    "rgb[xmap.is_indexed] = ckey_m3m.orientation2color(xmap[\"indexed\"].orientations)\n",
+    "rgb[xmap.is_indexed] = ckey_m3m.orientation2color(\n",
+    "    xmap[\"indexed\"].orientations\n",
+    ")\n",
     "fig = xmap.plot(rgb, remove_padding=True, return_figure=True)\n",
     "\n",
     "# Place color key next to map\n",

diff --git a/doc/tutorials/reference_frames.ipynb b/doc/tutorials/reference_frames.ipynb
@@ -664,7 +664,9 @@
     "    Gr_hi = Rotation(data[0][\"quat\"]) * Gr_sample[vendor]\n",
     "    G_hi = Orientation(Gr_hi, mp.phase.point_group)\n",
     "\n",
-    "    print(f\"Average misorientation angle to ground truth: {G_hi.angle_with(G, degrees=True).mean():.4f}\")\n",
+    "    print(\n",
+    "        f\"Average misorientation angle to ground truth: {G_hi.angle_with(G, degrees=True).mean():.4f}\"\n",
+    "    )\n",
     "    fig = G.scatter(\n",
     "        \"ipf\",\n",
     "        direction=v_sample,\n",

diff --git a/kikuchipy/indexing/similarity_metrics/_normalized_cross_correlation.py b/kikuchipy/indexing/similarity_metrics/_normalized_cross_correlation.py
@@ -54,6 +54,7 @@ class NormalizedCrossCorrelationMetric(SimilarityMetric):
     description of the initialization parameters and the list of
     attributes.
     """
+
     _allowed_dtypes: List[type] = [np.float32, np.float64]
     _sign: int = 1
 

diff --git a/kikuchipy/indexing/similarity_metrics/_normalized_dot_product.py b/kikuchipy/indexing/similarity_metrics/_normalized_dot_product.py
@@ -44,6 +44,7 @@ class NormalizedDotProductMetric(SimilarityMetric):
     description of the initialization parameters and the list of
     attributes.
     """
+
     _allowed_dtypes: List[type] = [np.float32, np.float64]
     _sign: int = 1
 

diff --git a/kikuchipy/io/_io.py b/kikuchipy/io/_io.py
@@ -20,14 +20,14 @@
 from pathlib import Path
 from typing import List, Optional, Union
 
+from h5py import File, Group, is_hdf5
 from hyperspy.io_plugins import hspy
 from hyperspy.misc.io.tools import overwrite as overwrite_method
-from hyperspy.misc.utils import strlist2enumeration, find_subclasses
+from hyperspy.misc.utils import find_subclasses, strlist2enumeration
 from hyperspy.signal import BaseSignal
-from h5py import File, is_hdf5, Group
 import numpy as np
 
-import kikuchipy.signals
+from kikuchipy.io._util import _ensure_directory, _get_input_bool
 from kikuchipy.io.plugins import (
     bruker_h5ebsd,
     ebsd_directory,
@@ -43,8 +43,7 @@
     oxford_binary,
     oxford_h5ebsd,
 )
-from kikuchipy.io._util import _get_input_bool, _ensure_directory
-
+import kikuchipy.signals
 
 plugins = [
     bruker_h5ebsd,
@@ -69,9 +68,7 @@
         default_write_ext.add(plugin.file_extensions[plugin.default_extension])
 
 
-def load(
-    filename: Union[str, Path], lazy: bool = False, **kwargs
-) -> Union[
+def load(filename: Union[str, Path], lazy: bool = False, **kwargs) -> Union[
     "EBSD",
     "EBSDMasterPattern",
     "ECPMasterPattern",

diff --git a/kikuchipy/io/plugins/bruker_h5ebsd.py b/kikuchipy/io/plugins/bruker_h5ebsd.py
@@ -25,8 +25,7 @@
 from orix.crystal_map import CrystalMap
 
 from kikuchipy.detectors import EBSDDetector
-from kikuchipy.io.plugins._h5ebsd import _hdf5group2dict, H5EBSDReader
-
+from kikuchipy.io.plugins._h5ebsd import H5EBSDReader, _hdf5group2dict
 
 __all__ = ["file_reader"]
 
@@ -169,30 +168,27 @@ def scan2dict(self, group: h5py.Group, lazy: bool = False) -> dict:
         )
         scan_dict["data"] = data
 
-        # --- Axes
         scan_dict["axes"] = self.get_axes_list((ny, nx, sy, sx), (dy, dx, px_size))
 
-        # --- Original metadata
         scan_dict["original_metadata"] = {
             "manufacturer": self.manufacturer,
             "version": self.version,
         }
         scan_dict["original_metadata"].update(hd)
 
-        # --- Crystal map
         # TODO: Use reader from orix
         xmap = CrystalMap.empty(shape=(ny, nx), step_sizes=(dy, dx))
         scan_dict["xmap"] = xmap
 
-        # --- Static background
         scan_dict["static_background"] = hd.get("StaticBackground")
 
-        # --- Detector
         pc = np.column_stack(
             (dd.get("PCX", 0.5), dd.get("PCY", 0.5), dd.get("DD", 0.5))
         )
         if pc.size > 3:
             pc = pc.reshape((ny, nx, 3))
+        tilt = hd.get("CameraTilt", 0.0)
+        sample_tilt = hd.get("SampleTilt", 0.0)
         scan_dict["detector"] = EBSDDetector(
             shape=(sy, sx),
             px_size=px_size,

diff --git a/setup.py b/setup.py
@@ -16,8 +16,8 @@
 # along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
 
 from itertools import chain
-from setuptools import setup, find_packages
 
+from setuptools import find_packages, setup
 
 # Get release information without importing anything from the project
 with open("kikuchipy/release.py") as fid:
@@ -84,6 +84,7 @@
 # Create a development project including all extra dependencies
 extra_feature_requirements["dev"] = [
     "black[jupyter]                     >= 23.1",
+    "isort",
     "manifix",
     "outdated",
     "pre-commit                         >= 1.16",