Merge pull request #615 from hakonanes/fix-614

Require PyOpenCL context for HI of LazyEBSD
pyxem · Feb 20, 2023 · 1872830 · 1872830
2 parents f8af0fb + c5c6f39
commit 1872830
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -61,9 +61,11 @@ jobs:
         include:
           - 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==0.55 numpy==1.19 orix==0.11.0 scikit-image==0.16.2
             LABEL: -oldest
+          - os: ubuntu-latest
+            python-version: 3.10
+            LABEL: -minimum_requirement
     steps:
       - uses: actions/checkout@v3
 
@@ -79,14 +81,16 @@ jobs:
           pip install -U -e .'[tests]'
 
       - name: Install oldest supported version
-        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        if: contains(matrix.LABEL, 'oldest')
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
       - name: Install optional dependencies
+        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false }}
         shell: bash
         run: |
           pip install -e .'[all]'
+          pip install pyopencl
 
       - name: Display Python, pip and package versions
         run: |
@@ -105,10 +109,6 @@ jobs:
         if: ${{ matrix.os == 'windows-latest' }}
         uses: pyvista/setup-headless-display-action@v1
 
-      - name: Display package versions
-        run: |
-          pip list
-
       - name: Run docstring tests
         if: ${{ matrix.os == 'ubuntu-latest' }}
         continue-on-error: true

diff --git a/.zenodo.json b/.zenodo.json
@@ -17,11 +17,11 @@
       "affiliation": "Norwegian University of Science and Technology"
     },
     {
-      "name": "Zhou Xu",
-      "affiliation": "Monash Centre for Electron Microscopy"
+      "name": "Eric Prestat"
     },
     {
-      "name": "Eric Prestat"
+      "name": "Zhou Xu",
+      "affiliation": "Monash Centre for Electron Microscopy"
     },
     {
       "name": "Magnus Nord",

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -13,6 +13,17 @@ its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>
 List entries are sorted in descending chronological order. Contributors to each release
 were listed in alphabetical order by first name until version 0.7.0.
 
+0.8.1 (2023-02-20)
+==================
+
+Fixed
+-----
+- Hough indexing with PyEBSDIndex of a lazy EBSD signal requires not only PyOpenCL to be
+  installed, but also for PyOpenCL to be able to create a context.
+  (`#615 <https://github.com/pyxem/kikuchipy/pull/615>`_)
+- Missing progressbars for ``EBSD`` methods ``average_neighbour_patterns()`` and
+  ``fft_filter()`` reintroduced. (`#615 <https://github.com/pyxem/kikuchipy/pull/615>`_)
+
 0.8.0 (2023-02-11)
 ==================
 

diff --git a/doc/tutorials/hybrid_indexing.ipynb b/doc/tutorials/hybrid_indexing.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 | 101.33 ms\n",
-      "[########################################] | 100% Completed | 101.19 ms\n"
+      "[########################################] | 100% Completed | 101.17 ms\n",
+      "[########################################] | 100% Completed | 101.52 ms\n"
      ]
     }
    ],
@@ -453,14 +453,14 @@
      "output_type": "stream",
      "text": [
       "Hough indexing with PyEBSDIndex information:\n",
-      "  GPU: True\n",
+      "  PyOpenCL: True\n",
       "  Projection center: (0.4208, 0.2182, 0.4999)\n",
       "  Indexing 9 pattern(s) in 1 chunk(s)\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"
+      "Radon Time: 0.03481806100171525\n",
+      "Convolution Time: 0.004420306999236345\n",
+      "Peak ID Time: 0.0024418800021521747\n",
+      "Band Label Time: 0.04934866500116186\n",
+      "Total Band Find Time: 0.09106226299991249\n"
      ]
     },
     {
@@ -477,8 +477,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Band Vote Time:  0.01957559899892658\n",
-      "  Indexing speed: 31.14729 patterns/s\n"
+      "Band Vote Time:  0.020639727998059243\n",
+      "  Indexing speed: 30.69000 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 | 78.42 ss\n",
-      "Refinement speed: 0.11476 patterns/s\n"
+      "[########################################] | 100% Completed | 79.66 ss\n",
+      "Refinement speed: 0.11297 patterns/s\n"
      ]
     }
    ],
@@ -966,8 +966,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 14.60 ss\n",
-      "Refinement speed: 0.61588 patterns/s\n"
+      "[########################################] | 100% Completed | 13.64 ss\n",
+      "Refinement speed: 0.65973 patterns/s\n"
      ]
     }
    ],
@@ -996,11 +996,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.56 ms\n",
+      "[########################################] | 100% Completed | 101.26 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.22 ms\n",
+      "[########################################] | 100% Completed | 101.34 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 104.01 ms\n"
+      "[########################################] | 100% Completed | 101.74 ms\n"
      ]
     }
    ],
@@ -1039,8 +1039,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 14.23 ss\n",
-      "Refinement speed: 0.63225 patterns/s\n"
+      "[########################################] | 100% Completed | 14.40 ss\n",
+      "Refinement speed: 0.62480 patterns/s\n"
      ]
     }
    ],
@@ -1069,11 +1069,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.42 ms\n",
+      "[########################################] | 100% Completed | 101.55 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.23 ms\n",
+      "[########################################] | 100% Completed | 101.89 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 101.58 ms\n"
+      "[########################################] | 100% Completed | 101.80 ms\n"
      ]
     }
    ],
@@ -1112,8 +1112,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 13.71 ss\n",
-      "Refinement speed: 0.65594 patterns/s\n"
+      "[########################################] | 100% Completed | 13.73 ss\n",
+      "Refinement speed: 0.65522 patterns/s\n"
      ]
     }
    ],
@@ -1142,11 +1142,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.96 ms\n",
+      "[########################################] | 100% Completed | 101.97 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.18 ms\n",
+      "[########################################] | 100% Completed | 101.36 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 103.92 ms\n"
+      "[########################################] | 100% Completed | 102.20 ms\n"
      ]
     }
    ],

diff --git a/doc/tutorials/pc_fit_plane.ipynb b/doc/tutorials/pc_fit_plane.ipynb
diff --git a/doc/tutorials/pc_orientation_dependence.ipynb b/doc/tutorials/pc_orientation_dependence.ipynb
diff --git a/kikuchipy/__init__.py b/kikuchipy/__init__.py
@@ -20,26 +20,47 @@
 from kikuchipy.release import version as __version__
 
 
-# Attempt import only once
+# Attempt (and fail) import of optional dependencies only once
 try:
     import pyvista
 
     _pyvista_installed = True
 except ImportError:  # pragma: no cover
     _pyvista_installed = False
+
 try:
     import nlopt
 
     _nlopt_installed = True
 except ImportError:  # pragma: no cover
     _nlopt_installed = False
+
 try:
     from pyebsdindex import pcopt, ebsd_index
 
     _pyebsdindex_installed = True
 except ImportError:  # pragma: no cover
     _pyebsdindex_installed = False
 
+# PyOpenCL context available for use with PyEBSDIndex? Required for
+# Hough indexing of Dask arrays.
+# PyOpenCL is an optional dependency of PyEBSDIndex, so it should not be
+# an optional kikuchipy dependency.
+try:  # pragma: no cover
+    import pyopencl as cl
+
+    platform = cl.get_platforms()[0]
+    gpu = platform.get_devices(device_type=cl.device_type.GPU)
+    ctx = cl.Context(devices=gpu)
+    if ctx is None:
+        _pyopencl_context_available = False
+    else:
+        _pyopencl_context_available = True
+except:  # pragma: no cover
+    # Have to use bare except because PyOpenCL might raise its own
+    # LogicError, but we also want to catch import errors here
+    _pyopencl_context_available = False
+
 
 def set_log_level(level: Union[int, str]):  # pragma: no cover
     """Set level of kikuchipy logging messages.

diff --git a/kikuchipy/indexing/_hough_indexing.py b/kikuchipy/indexing/_hough_indexing.py
@@ -376,11 +376,11 @@ def _indexer_is_compatible_with_kikuchipy(
 
 
 def _get_info_message(nav_size: int, chunksize: int, indexer: "EBSDIndexer") -> str:
-    from pyebsdindex import _pyopencl_installed
+    from kikuchipy import _pyopencl_context_available
 
     info = (
         "Hough indexing with PyEBSDIndex information:\n"
-        f"  GPU: {_pyopencl_installed}\n"
+        f"  PyOpenCL: {_pyopencl_context_available}\n"
         "  Projection center"
     )
 

diff --git a/kikuchipy/indexing/tests/test_merge_crystal_maps.py b/kikuchipy/indexing/tests/test_merge_crystal_maps.py
@@ -173,10 +173,7 @@ def test_merge_crystal_maps_2d(
         for v1, v2 in zip(
             merged_xmap._coordinates.values(), xmaps[0]._coordinates.values()
         ):
-            if v1 is None:
-                assert v1 is v2
-            else:
-                np.allclose(v1, v2)
+            assert np.allclose(v1, v2)
 
         assert np.allclose(merged_xmap.phase_id, desired_phase_ids)
         assert np.allclose(merged_xmap.prop[scores_prop], desired_scores)

diff --git a/kikuchipy/release.py b/kikuchipy/release.py
@@ -26,8 +26,8 @@
     "Lars Andreas Hastad Lervik",
     "Ole Natlandsmyr",
     "Tina Bergh",
-    "Zhou Xu",
     "Eric Prestat",
+    "Zhou Xu",
     "Magnus Nord",
 ]
 license = "GPLv3+"
@@ -36,4 +36,4 @@
 name = "kikuchipy"
 platforms = ["Linux", "MacOS X", "Windows"]
 status = "Development"
-version = "0.8.0"
+version = "0.8.1"
diff --git a/kikuchipy/signals/ebsd.py b/kikuchipy/signals/ebsd.py
@@ -39,7 +39,7 @@
 from scipy.ndimage import correlate, gaussian_filter
 from skimage.util.dtype import dtype_range
 
-from kikuchipy import _pyebsdindex_installed
+from kikuchipy import _pyebsdindex_installed, _pyopencl_context_available
 from kikuchipy.detectors import EBSDDetector
 from kikuchipy.filters.fft_barnes import _fft_filter, _fft_filter_setup
 from kikuchipy.filters.window import Window
@@ -900,7 +900,7 @@ def fft_filter(
 
         return_lazy = lazy_output or (lazy_output is None and self._lazy)
         register_pbar = show_progressbar or (
-            show_progressbar is not None and hs.preferences.General.show_progressbar
+            show_progressbar is None and hs.preferences.General.show_progressbar
         )
         if not return_lazy and register_pbar:
             pbar = ProgressBar()
@@ -1066,7 +1066,7 @@ def average_neighbour_patterns(
 
         return_lazy = lazy_output or (lazy_output is None and self._lazy)
         register_pbar = show_progressbar or (
-            show_progressbar is not None and hs.preferences.General.show_progressbar
+            show_progressbar is None and hs.preferences.General.show_progressbar
         )
         if not return_lazy and register_pbar:
             pbar = ProgressBar()
@@ -1661,16 +1661,12 @@ def hough_indexing(
                 "pip install pyebsdindex. See "
                 "https://kikuchipy.org/en/stable/user/installation.html for details"
             )
-        if self._lazy:
-            from pyebsdindex import _pyopencl_installed
-
-            if not _pyopencl_installed:  # pragma: no cover
-                raise ValueError(
-                    "Hough indexing of lazy signals must use the GPU, which requires "
-                    "pyopencl to be installed. See "
-                    "https://documen.tician.de/pyopencl/misc.html for installation "
-                    "instructions"
-                )
+        if self._lazy and not _pyopencl_context_available:  # pragma: no cover
+            raise ValueError(
+                "Hough indexing of lazy signals must use PyOpenCL, which must be able "
+                "to create a context. See https://documen.tician.de/pyopencl/misc.html "
+                "for details"
+            )
 
         am = self.axes_manager
         nav_shape = am.navigation_shape[::-1]
@@ -1767,16 +1763,12 @@ def hough_indexing_optimize_pc(
                 "pip install pyebsdindex. See "
                 "https://kikuchipy.org/en/stable/user/installation.html for details"
             )
-        if self._lazy:
-            from pyebsdindex import _pyopencl_installed
-
-            if not _pyopencl_installed:  # pragma: no cover
-                raise ValueError(
-                    "Hough indexing of lazy signals must use the GPU, which requires "
-                    "pyopencl to be installed. See "
-                    "https://documen.tician.de/pyopencl/misc.html for installation "
-                    "instructions"
-                )
+        if self._lazy and not _pyopencl_context_available:  # pragma: no cover
+            raise ValueError(
+                "Hough indexing of lazy signals must use PyOpenCL, which must be able "
+                "to create a context. See https://documen.tician.de/pyopencl/misc.html "
+                "for details"
+            )
 
         pc0 = np.asarray(pc0)
         if pc0.size != 3: