Merge pull request #632 from hakonanes/fix-622

Maintain not-indexed points in refined crystal maps
pyxem · Apr 7, 2023 · 49e6814 · 49e6814
2 parents 9ccf7ad + a40ef89
commit 49e6814
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,7 +2,7 @@
 Changelog
 =========
 
-kikuchipy is a library for processing, simulating, and analyzing electron backscatter
+kikuchipy is a library for processing, simulating and indexing of electron backscatter
 diffraction (EBSD) patterns in Python, built on the tools for multi-dimensional data
 analysis provided by the HyperSpy library: https://kikuchipy.org.
 
@@ -13,6 +13,22 @@ 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.
 
+0.8.4 (2023-04-07)
+==================
+
+Fixed
+-----
+- Points considered not-indexed in a crystal map are maintained after EBSD refinement.
+  (`#632 <https://github.com/pyxem/kikuchipy/pull/632>`_)
+
+Changed
+-------
+- EBSD detector returned from combined EBSD and projection center (PC) refinement now
+  has PC values equal to the number of indexed points, accounting for points not being
+  in the data, navigation mask *and* points considered as not-indexed. This means that
+  it might not have a 2D navigation shape, even though the returned crystal map has.
+  (`#632 <https://github.com/pyxem/kikuchipy/pull/632>`_)
+
 0.8.3 (2023-03-23)
 ==================
 

diff --git a/README.md b/README.md
@@ -4,8 +4,8 @@
   </a>
 </div>
 
-kikuchipy [ki-ko-chi-pai] is a library for processing, simulating and analyzing electron
-backscatter diffraction (EBSD) patterns in Python, built on the tools for
+kikuchipy [ki-ko-chi-pai] is a library for processing, simulating and indexing of
+electron backscatter diffraction (EBSD) patterns in Python, built on the tools for
 multi-dimensional data analysis provided by the HyperSpy library.
 
 | Deployment    | [![PyPI version](https://img.shields.io/pypi/v/kikuchipy.svg?logo=python&logoColor=white)](https://pypi.org/project/kikuchipy/) | [![Anaconda version](https://img.shields.io/conda/vn/conda-forge/kikuchipy.svg?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/kikuchipy)|

diff --git a/doc/tutorials/esteem2022_diffraction_workshop.ipynb b/doc/tutorials/esteem2022_diffraction_workshop.ipynb
diff --git a/doc/tutorials/hybrid_indexing.ipynb b/doc/tutorials/hybrid_indexing.ipynb
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
@@ -72,7 +72,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2023-03-22 21:20:14,381 - numexpr.utils - INFO - NumExpr defaulting to 4 threads.\n"
+      "2023-04-07 12:00:40,602 - numexpr.utils - INFO - NumExpr defaulting to 4 threads.\n"
      ]
     },
     {
@@ -289,8 +289,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[########################################] | 100% Completed | 101.23 ms\n",
-      "[########################################] | 100% Completed | 101.28 ms\n"
+      "[########################################] | 100% Completed | 101.73 ms\n",
+      "[########################################] | 100% Completed | 101.63 ms\n"
      ]
     }
    ],
@@ -464,11 +464,11 @@
       "  PyOpenCL: True\n",
       "  Projection center (Bruker): (0.4208, 0.2182, 0.4999)\n",
       "  Indexing 9 pattern(s) in 1 chunk(s)\n",
-      "Radon Time: 0.03598728299994036\n",
-      "Convolution Time: 0.003218756000023859\n",
-      "Peak ID Time: 0.0017357010001433082\n",
-      "Band Label Time: 0.04533897600003911\n",
-      "Total Band Find Time: 0.08630177100030778\n"
+      "Radon Time: 0.03620907699996678\n",
+      "Convolution Time: 0.0030053609998503816\n",
+      "Peak ID Time: 0.001584530999934941\n",
+      "Band Label Time: 0.04056105099994056\n",
+      "Total Band Find Time: 0.08138581000002887\n"
      ]
     },
     {
@@ -485,8 +485,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Band Vote Time:  0.02606440699992163\n",
-      "  Indexing speed: 33.98417 patterns/s\n"
+      "Band Vote Time:  0.021481833000052575\n",
+      "  Indexing speed: 29.15122 patterns/s\n"
      ]
     }
    ],
@@ -519,8 +519,8 @@
       "  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 | 81.08 ss\n",
-      "Refinement speed: 0.11099 patterns/s\n"
+      "[########################################] | 100% Completed | 84.17 ss\n",
+      "Refinement speed: 0.10692 patterns/s\n"
      ]
     }
    ],
@@ -974,8 +974,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 13.81 ss\n",
-      "Refinement speed: 0.65164 patterns/s\n"
+      "[########################################] | 100% Completed | 14.47 ss\n",
+      "Refinement speed: 0.62159 patterns/s\n"
      ]
     }
    ],
@@ -1004,11 +1004,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.74 ms\n",
+      "[########################################] | 100% Completed | 101.85 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.21 ms\n",
+      "[########################################] | 100% Completed | 102.18 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 102.05 ms\n"
+      "[########################################] | 100% Completed | 101.81 ms\n"
      ]
     }
    ],
@@ -1047,8 +1047,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 14.38 ss\n",
-      "Refinement speed: 0.62571 patterns/s\n"
+      "[########################################] | 100% Completed | 15.32 ss\n",
+      "Refinement speed: 0.58728 patterns/s\n"
      ]
     }
    ],
@@ -1077,11 +1077,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.21 ms\n",
+      "[########################################] | 100% Completed | 101.73 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.50 ms\n",
+      "[########################################] | 100% Completed | 104.01 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 102.09 ms\n"
+      "[########################################] | 100% Completed | 101.81 ms\n"
      ]
     }
    ],
@@ -1120,8 +1120,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-07\n",
       "Refining 9 orientation(s):\n",
-      "[########################################] | 100% Completed | 13.67 ss\n",
-      "Refinement speed: 0.65818 patterns/s\n"
+      "[########################################] | 100% Completed | 14.67 ss\n",
+      "Refinement speed: 0.61334 patterns/s\n"
      ]
     }
    ],
@@ -1150,11 +1150,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.74 ms\n",
+      "[########################################] | 100% Completed | 102.02 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.58 ms\n",
+      "[########################################] | 100% Completed | 101.76 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 102.28 ms\n"
+      "[########################################] | 100% Completed | 102.76 ms\n"
      ]
     }
    ],
@@ -1309,7 +1309,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,

diff --git a/doc/tutorials/pc_fit_plane.ipynb b/doc/tutorials/pc_fit_plane.ipynb
@@ -69,8 +69,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2023-03-23 10:28:51,094 - hyperspy.extensions - INFO - Enabling extension kikuchipy\n",
-      "2023-03-23 10:28:51,176 - numexpr.utils - INFO - NumExpr defaulting to 4 threads.\n"
+      "2023-04-07 12:04:36,676 - hyperspy.extensions - INFO - Enabling extension kikuchipy\n",
+      "2023-04-07 12:04:36,746 - numexpr.utils - INFO - NumExpr defaulting to 4 threads.\n"
      ]
     },
     {
@@ -245,7 +245,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[########################################] | 100% Completed | 202.16 ms\n"
+      "[########################################] | 100% Completed | 202.26 ms\n"
      ]
     }
    ],
@@ -439,7 +439,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[########################################] | 100% Completed | 102.25 ms\n"
+      "[########################################] | 100% Completed | 102.28 ms\n"
      ]
     },
     {
@@ -593,8 +593,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[########################################] | 100% Completed | 101.58 ms\n",
-      "[########################################] | 100% Completed | 304.17 ms\n"
+      "[########################################] | 100% Completed | 101.33 ms\n",
+      "[########################################] | 100% Completed | 202.86 ms\n"
      ]
     }
    ],
@@ -797,11 +797,11 @@
       "  PyOpenCL: True\n",
       "  Projection center (Bruker, mean): (0.5197, 0.1587, 0.4918)\n",
       "  Indexing 25 pattern(s) in 1 chunk(s)\n",
-      "Radon Time: 0.0479949600000964\n",
-      "Convolution Time: 0.004770301999997173\n",
-      "Peak ID Time: 0.002234627999996519\n",
-      "Band Label Time: 0.0700682639999286\n",
-      "Total Band Find Time: 0.12508721100016373\n"
+      "Radon Time: 0.04400652200001787\n",
+      "Convolution Time: 0.0037544520000665216\n",
+      "Peak ID Time: 0.001710380999611516\n",
+      "Band Label Time: 0.0670934159998069\n",
+      "Total Band Find Time: 0.11659346299984463\n"
      ]
     },
     {
@@ -818,8 +818,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Band Vote Time:  0.03322376099981739\n",
-      "  Indexing speed: 71.56758 patterns/s\n"
+      "Band Vote Time:  0.03200899400007984\n",
+      "  Indexing speed: 74.46543 patterns/s\n"
      ]
     }
    ],
@@ -925,8 +925,8 @@
       "  Trust region (+/-): [5.  5.  5.  0.1 0.1 0.1]\n",
       "  Relative tolerance: 1e-05\n",
       "Refining 25 orientation(s) and projection center(s):\n",
-      "[########################################] | 100% Completed | 103.80 s\n",
-      "Refinement speed: 0.24082 patterns/s\n"
+      "[########################################] | 100% Completed | 102.16 s\n",
+      "Refinement speed: 0.24470 patterns/s\n"
      ]
     }
    ],
@@ -1233,8 +1233,8 @@
       "  Trust region (+/-): [5 5 5]\n",
       "  Relative tolerance: 1e-05\n",
       "Refining 25 orientation(s):\n",
-      "[########################################] | 100% Completed | 21.51 ss\n",
-      "Refinement speed: 1.16178 patterns/s\n",
+      "[########################################] | 100% Completed | 19.35 ss\n",
+      "Refinement speed: 1.29130 patterns/s\n",
       "0.3339714002609253\n"
      ]
     }
@@ -1318,11 +1318,11 @@
      "output_type": "stream",
      "text": [
       "Finding bands that are in some pattern:\n",
-      "[########################################] | 100% Completed | 101.31 ms\n",
+      "[########################################] | 100% Completed | 104.19 ms\n",
       "Finding zone axes that are in some pattern:\n",
-      "[########################################] | 100% Completed | 102.16 ms\n",
+      "[########################################] | 100% Completed | 104.42 ms\n",
       "Calculating detector coordinates for bands and zone axes:\n",
-      "[########################################] | 100% Completed | 102.27 ms\n"
+      "[########################################] | 100% Completed | 101.90 ms\n"
      ]
     }
    ],
@@ -1395,7 +1395,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,