Merge pull request #608 from hakonanes/vbse-module

Deprecate generators.VirtualBSEGenerator in favor of imaging.VirtualBSEImager
pyxem · Feb 10, 2023 · 88945e2 · 88945e2
2 parents c296cc2 + 571291a
commit 88945e2
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -62,7 +62,7 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.7
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7.3 matplotlib==3.3 numba==0.52 numpy==1.19 orix==0.9.0 scikit-image==0.16.2
+            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7.3 matplotlib==3.3 numba==0.55 numpy==1.19 orix==0.11.0 scikit-image==0.16.2
             LABEL: -oldest
     steps:
       - uses: actions/checkout@v3

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -18,6 +18,9 @@ Unreleased
 
 Added
 -----
+- ``kikuchipy.imaging.VirtualBSEImager`` replaces the
+  ``kikuchipy.generators.VirtualBSEGenerator`` class.
+  (`#608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
 - Adaptive histogram equalization is available to all signals.
   (`#606 <https://github.com/pyxem/kikuchipy/pull/606>`_)
 - Option to return a new signal (lazy or not) instead of operating inplace is added to
@@ -106,6 +109,8 @@ Added
 
 Changed
 -------
+- Minimal version of orix set to >= 0.11 and of numba set to >= 0.55.
+  (`#608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
 - Added warnings when trying to perform adaptive histogram equalization on a signal with
   data in floating type or when some of the data is NaN.
   (`#606 <https://github.com/pyxem/kikuchipy/pull/606>`_)
@@ -143,6 +148,9 @@ Changed
 
 Deprecated
 ----------
+- ``kikuchipy.generators.VirtualBSEGenerator`` class is deprecated and will be removed
+  in version 0.9. Use ``kikuchipy.imaging.VirtualBSEImager`` instead.
+  (`#608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
 - The data module functions ``silicon_ebsd_moving_screen_x()``, where "x" is "in",
   "out5mm" or "out10mm", are deprecated and will be removed in v0.9. Use
   ``si_ebsd_moving_screen(distance)`` instead, where ``distance`` is ``0`` (in), ``5``

diff --git a/benchmarks/indexing/test_refinement.py b/benchmarks/indexing/test_refinement.py
@@ -82,7 +82,7 @@ def test_refine_orientation(benchmark):
 
     # Relaxed check of results, just to make sure results are not way
     # off
-    assert np.all(xmap_ref.rotations.angle_with(rot) < np.deg2rad(0.8))
+    assert np.all(xmap_ref.rotations.angle_with(rot, degrees=True) < 0.8)
 
 
 def test_refine_pc(benchmark):

diff --git a/doc/reference/index.rst b/doc/reference/index.rst
@@ -50,6 +50,7 @@ this:
     draw
     filters
     generators
+    imaging
     indexing
     io
     pattern

diff --git a/doc/tutorials/esteem2022_diffraction_workshop.ipynb b/doc/tutorials/esteem2022_diffraction_workshop.ipynb
diff --git a/doc/tutorials/hough_indexing.ipynb b/doc/tutorials/hough_indexing.ipynb
@@ -99,8 +99,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_gen = kp.generators.VirtualBSEGenerator(s)\n",
-    "print(vbse_gen.grid_shape)"
+    "vbse_imager = kp.imaging.VirtualBSEImager(s)\n",
+    "print(vbse_imager.grid_shape)"
    ]
   },
   {
@@ -118,7 +118,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "maps_vbse_rgb = vbse_gen.get_rgb_image(r=(2, 1), g=(2, 2), b=(2, 3))\n",
+    "maps_vbse_rgb = vbse_imager.get_rgb_image(r=(2, 1), g=(2, 2), b=(2, 3))\n",
     "maps_vbse_rgb"
    ]
   },

diff --git a/doc/tutorials/hybrid_indexing.ipynb b/doc/tutorials/hybrid_indexing.ipynb
diff --git a/doc/tutorials/load_save_data.ipynb b/doc/tutorials/load_save_data.ipynb
@@ -1152,12 +1152,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Get virtual image from generator\n",
-    "vbse_gen = kp.generators.VirtualBSEGenerator(s)\n",
-    "print(vbse_gen)\n",
+    "# Get virtual image from image generator\n",
+    "vbse_imager = kp.imaging.VirtualBSEImager(s)\n",
+    "print(vbse_imager)\n",
     "\n",
-    "print(vbse_gen.grid_shape)\n",
-    "vbse = vbse_gen.get_images_from_grid()\n",
+    "print(vbse_imager.grid_shape)\n",
+    "vbse = vbse_imager.get_images_from_grid()\n",
     "print(vbse)"
    ]
   },

diff --git a/doc/tutorials/mandm2021_sunday_short_course.ipynb b/doc/tutorials/mandm2021_sunday_short_course.ipynb
diff --git a/doc/tutorials/pattern_matching.ipynb b/doc/tutorials/pattern_matching.ipynb
diff --git a/doc/tutorials/pc_extrapolate_plane.ipynb b/doc/tutorials/pc_extrapolate_plane.ipynb
@@ -282,8 +282,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[########################################] | 100% Completed | 101.45 ms\n",
-      "[########################################] | 100% Completed | 202.57 ms\n"
+      "[########################################] | 100% Completed | 101.33 ms\n",
+      "[########################################] | 100% Completed | 101.19 ms\n"
      ]
     }
    ],
@@ -456,11 +456,11 @@
       "  GPU: True\n",
       "  Projection center: (0.4208, 0.2182, 0.4999)\n",
       "  Indexing 9 pattern(s) in 1 chunk(s)\n",
-      "Radon Time: 0.05065198699958273\n",
-      "Convolution Time: 0.004807140001503285\n",
-      "Peak ID Time: 0.001738914997986285\n",
-      "Band Label Time: 0.05457071899945731\n",
-      "Total Band Find Time: 0.11179470299975947\n"
+      "Radon Time: 0.03806788400106598\n",
+      "Convolution Time: 0.0031347900003311224\n",
+      "Peak ID Time: 0.0016060470006777905\n",
+      "Band Label Time: 0.040003152997087454\n",
+      "Total Band Find Time: 0.0828367710018938\n"
      ]
     },
     {
@@ -477,8 +477,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Band Vote Time:  0.025686940000014147\n",
-      "  Indexing speed: 30.92640 patterns/s\n"
+      "Band Vote Time:  0.01957559899892658\n",
+      "  Indexing speed: 31.14729 patterns/s\n"
      ]
     }
    ],
@@ -511,8 +511,8 @@
       "  Trust region (+/-): [5.   5.   5.   0.05 0.05 0.05]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s) and projection center(s):\n",
-      "[########################################] | 100% Completed | 85.72 ss\n",
-      "Refinement speed: 0.10499 patterns/s\n"
+      "[########################################] | 100% Completed | 78.42 ss\n",
+      "Refinement speed: 0.11476 patterns/s\n"
      ]
     }
    ],
@@ -562,8 +562,10 @@
     "print(\"PC std:      \", det_ref.pc.std(0))\n",
     "print(\"PC max. diff:\", abs(det_cal.pc - det_ref.pc).max(0))\n",
     "\n",
-    "ori_diff = xmap_hi.orientations.angle_with(xmap_ref.orientations).max()\n",
-    "print(\"Ori. max. diff [deg]:\", np.rad2deg(ori_diff))"
+    "ori_diff = xmap_hi.orientations.angle_with(\n",
+    "    xmap_ref.orientations, degrees=True\n",
+    ").max()\n",
+    "print(\"Ori. max. diff [deg]:\", ori_diff)"
    ]
   },
   {
@@ -964,8 +966,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 16.27 ss\n",
-      "Refinement speed: 0.55309 patterns/s\n"
+      "[########################################] | 100% Completed | 14.60 ss\n",
+      "Refinement speed: 0.61588 patterns/s\n"
      ]
     }
    ],
@@ -994,11 +996,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.58 ms\n",
+      "[########################################] | 100% Completed | 101.56 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.69 ms\n",
+      "[########################################] | 100% Completed | 102.22 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 103.87 ms\n"
+      "[########################################] | 100% Completed | 104.01 ms\n"
      ]
     }
    ],
@@ -1037,8 +1039,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 15.86 ss\n",
-      "Refinement speed: 0.56707 patterns/s\n"
+      "[########################################] | 100% Completed | 14.23 ss\n",
+      "Refinement speed: 0.63225 patterns/s\n"
      ]
     }
    ],
@@ -1067,11 +1069,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.37 ms\n",
+      "[########################################] | 100% Completed | 101.42 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.19 ms\n",
+      "[########################################] | 100% Completed | 102.23 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 105.06 ms\n"
+      "[########################################] | 100% Completed | 101.58 ms\n"
      ]
     }
    ],
@@ -1110,8 +1112,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 14.95 ss\n",
-      "Refinement speed: 0.60200 patterns/s\n"
+      "[########################################] | 100% Completed | 13.71 ss\n",
+      "Refinement speed: 0.65594 patterns/s\n"
      ]
     }
    ],
@@ -1140,11 +1142,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.23 ms\n",
+      "[########################################] | 100% Completed | 101.96 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.86 ms\n",
+      "[########################################] | 100% Completed | 102.18 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 101.72 ms\n"
+      "[########################################] | 100% Completed | 103.92 ms\n"
      ]
     }
    ],
@@ -1271,7 +1273,7 @@
     }
    ],
    "source": [
-    "np.rad2deg(xmap_proj.orientations.angle_with(xmap_ext.orientations))"
+    "xmap_proj.orientations.angle_with(xmap_ext.orientations, degrees=True)"
    ]
   },
   {

diff --git a/doc/tutorials/reference_frames.ipynb b/doc/tutorials/reference_frames.ipynb
@@ -716,7 +716,7 @@
     "    rot_hi = Rotation(data[-1][\"quat\"]) * post_rot[vendor]\n",
     "    ori_hi = Orientation(rot_hi, mp.phase.point_group)\n",
     "\n",
-    "    print(\"Mori. angle to ground truth:\", np.rad2deg(ori_hi.angle_with(ori)))\n",
+    "    print(\"Mori. angle to ground truth:\", ori_hi.angle_with(ori, degrees=True))\n",
     "    fig = ori.scatter(\n",
     "        \"ipf\",\n",
     "        direction=v_sample,\n",

diff --git a/doc/tutorials/virtual_backscatter_electron_imaging.ipynb b/doc/tutorials/virtual_backscatter_electron_imaging.ipynb
@@ -143,7 +143,7 @@
     "channels to obtain RGB images.\n",
     "\n",
     "First, we initialize a virtual BSE image generator,\n",
-    "[kikuchipy.generators.VirtualBSEGenerator](../reference/generated/kikuchipy.generators.VirtualBSEGenerator.rst),\n",
+    "[kikuchipy.imaging.VirtualBSEImager](../reference/generated/kikuchipy.imaging.VirtualBSEImager.rst),\n",
     "with an [EBSD](../reference/generated/kikuchipy.signals.EBSD.rst) signal, in\n",
     "case the raw EBSD patterns without any background correction or other processing"
    ]
@@ -154,8 +154,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_gen = kp.generators.VirtualBSEGenerator(s)\n",
-    "vbse_gen"
+    "vbse_imager = kp.imaging.VirtualBSEImager(s)\n",
+    "vbse_imager"
    ]
   },
   {
@@ -165,7 +165,7 @@
     "We can set and plot the detector grid on one of the EBSD patterns, also coloring\n",
     "one or more of the grid tiles red, green and blue, as is done in\n",
     "<cite data-cite=\"nolze2017electron\">Nolze et al. (2017)</cite>, by calling\n",
-    "[VirtualBSEGenerator.plot_grid()](../reference/generated/kikuchipy.generators.VirtualBSEGenerator.plot_grid.rst)"
+    "[VirtualBSEImager.plot_grid()](../reference/generated/kikuchipy.imaging.VirtualBSEImager.plot_grid.rst)"
    ]
   },
   {
@@ -174,7 +174,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_gen.grid_shape"
+    "vbse_imager.grid_shape"
    ]
   },
   {
@@ -183,11 +183,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_gen.grid_shape = (10, 10)\n",
+    "vbse_imager.grid_shape = (10, 10)\n",
     "red = [(7, 1), (8, 1), (8, 2), (9, 1), (9, 2)]\n",
     "green = [(8, 4), (8, 5), (9, 4), (9, 5)]\n",
     "blue = [(7, 8), (8, 7), (8, 8), (9, 7), (9, 8)]\n",
-    "p = vbse_gen.plot_grid(\n",
+    "p = vbse_imager.plot_grid(\n",
     "    rgb_channels=[red, green, blue],\n",
     "    visible_indices=True,  # Default\n",
     "    pattern_idx=(10, 20),  # Default is (0, 0)\n",
@@ -209,7 +209,7 @@
    "metadata": {},
    "source": [
     "To obtain an RGB image from the detector grid tiles shown above, we use\n",
-    "[get_rgb_image()](../reference/generated/kikuchipy.generators.VirtualBSEGenerator.get_rgb_image.rst)\n",
+    "[get_rgb_image()](../reference/generated/kikuchipy.imaging.VirtualBSEImager.get_rgb_image.rst)\n",
     "(see the docstring for all available parameters)"
    ]
   },
@@ -219,7 +219,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_rgb_img = vbse_gen.get_rgb_image(r=red, g=green, b=blue)\n",
+    "vbse_rgb_img = vbse_imager.get_rgb_image(r=red, g=green, b=blue)\n",
     "vbse_rgb_img"
    ]
   },
@@ -252,7 +252,7 @@
    "metadata": {},
    "source": [
     "To obtain one grey scale virtual BSE image from each grid tile, we use\n",
-    "[get_images_from_grid()](../reference/generated/kikuchipy.generators.VirtualBSEGenerator.get_images_from_grid.rst)"
+    "[get_images_from_grid()](../reference/generated/kikuchipy.imaging.VirtualBSEImager.get_images_from_grid.rst)"
    ]
   },
   {
@@ -261,8 +261,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_gen.grid_shape = (3, 3)\n",
-    "vbse_imgs = vbse_gen.get_images_from_grid()\n",
+    "vbse_imager.grid_shape = (3, 3)\n",
+    "vbse_imgs = vbse_imager.get_images_from_grid()\n",
     "vbse_imgs"
    ]
   },
@@ -353,7 +353,7 @@
    "metadata": {},
    "source": [
     "To obtain a rectangular ROI from the grid, we can use\n",
-    "[VirtualBSEGenerator.roi_from_grid()](../reference/generated/kikuchipy.generators.VirtualBSEGenerator.roi_from_grid.rst)"
+    "[VirtualBSEGenerator.roi_from_grid()](../reference/generated/kikuchipy.imaging.VirtualBSEImager.roi_from_grid.rst)"
    ]
   },
   {
@@ -362,7 +362,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "roi2 = vbse_gen.roi_from_grid((3, 3))  # (Row, column)\n",
+    "roi2 = vbse_imager.roi_from_grid((3, 3))  # (Row, column)\n",
     "roi2"
    ]
   },

diff --git a/doc/tutorials/visualizing_patterns.ipynb b/doc/tutorials/visualizing_patterns.ipynb
@@ -96,7 +96,7 @@
     "## Virtual image\n",
     "\n",
     "A virtual backscatter electron (VBSE) image created from any detector region of interest with the [get_virtual_bse_intensity()](../reference/generated/kikuchipy.signals.EBSD.get_virtual_bse_intensity.rst) method or\n",
-    "[get_rgb_image()](../reference/generated/kikuchipy.generators.VirtualBSEGenerator.get_rgb_image.rst) explained in the [virtual backscatter electron imaging](virtual_backscatter_electron_imaging.ipynb) tutorial, can be used as a navigator for a scan `s`"
+    "[get_rgb_image()](../reference/generated/kikuchipy.imaging.VirtualBSEImager.get_rgb_image.rst) explained in the [virtual backscatter electron imaging](virtual_backscatter_electron_imaging.ipynb) tutorial, can be used as a navigator for a scan `s`"
    ]
   },
   {
@@ -105,9 +105,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_gen = kp.generators.VirtualBSEGenerator(s)\n",
-    "print(vbse_gen)\n",
-    "print(vbse_gen.grid_shape)"
+    "vbse_imager = kp.imaging.VirtualBSEImager(s)\n",
+    "print(vbse_imager)\n",
+    "print(vbse_imager.grid_shape)"
    ]
   },
   {
@@ -116,7 +116,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_rgb = vbse_gen.get_rgb_image(r=(3, 1), b=(3, 2), g=(3, 3))\n",
+    "vbse_rgb = vbse_imager.get_rgb_image(r=(3, 1), b=(3, 2), g=(3, 3))\n",
     "vbse_rgb"
    ]
   },