DefDAP 1.0.1__tar.gz → 1.1.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (85) hide show
  1. {defdap-1.0.1 → defdap-1.1.2}/DefDAP.egg-info/PKG-INFO +6 -19
  2. defdap-1.1.2/DefDAP.egg-info/SOURCES.txt +34 -0
  3. defdap-1.1.2/DefDAP.egg-info/top_level.txt +6 -0
  4. {defdap-1.0.1 → defdap-1.1.2}/PKG-INFO +6 -19
  5. defdap-1.1.2/defdap/_version.py +1 -0
  6. {defdap-1.0.1 → defdap-1.1.2}/defdap/base.py +7 -2
  7. {defdap-1.0.1 → defdap-1.1.2}/defdap/ebsd.py +21 -0
  8. {defdap-1.0.1 → defdap-1.1.2}/defdap/file_readers.py +2 -1
  9. {defdap-1.0.1 → defdap-1.1.2}/defdap/inspector.py +2 -2
  10. defdap-1.1.2/pyproject.toml +88 -0
  11. defdap-1.0.1/.gitattributes +0 -12
  12. defdap-1.0.1/.github/workflows/test.yml +0 -29
  13. defdap-1.0.1/.gitignore +0 -38
  14. defdap-1.0.1/.pytest.ini +0 -3
  15. defdap-1.0.1/.readthedocs.yml +0 -13
  16. defdap-1.0.1/CHANGELOG.md +0 -188
  17. defdap-1.0.1/CODEOWNERS +0 -1
  18. defdap-1.0.1/DefDAP.egg-info/SOURCES.txt +0 -79
  19. defdap-1.0.1/DefDAP.egg-info/top_level.txt +0 -1
  20. defdap-1.0.1/defdap/_version.py +0 -1
  21. defdap-1.0.1/docs/Makefile +0 -33
  22. defdap-1.0.1/docs/README.md +0 -24
  23. defdap-1.0.1/docs/make.bat +0 -35
  24. defdap-1.0.1/docs/source/_static/branches.png +0 -0
  25. defdap-1.0.1/docs/source/_static/logo.png +0 -0
  26. defdap-1.0.1/docs/source/_static/sample_ebsd.jpg +0 -0
  27. defdap-1.0.1/docs/source/_templates/layout.html +0 -6
  28. defdap-1.0.1/docs/source/contributing.rst +0 -47
  29. defdap-1.0.1/docs/source/index.rst +0 -35
  30. defdap-1.0.1/docs/source/installation.rst +0 -14
  31. defdap-1.0.1/docs/source/license.rst +0 -5
  32. defdap-1.0.1/docs/source/modules.rst +0 -9
  33. defdap-1.0.1/docs/source/papers.rst +0 -107
  34. defdap-1.0.1/notebooks/example_notebook.ipynb +0 -1516
  35. defdap-1.0.1/notebooks/experiment.ipynb +0 -145
  36. defdap-1.0.1/notebooks/twin_boundaries.ipynb +0 -256
  37. defdap-1.0.1/scripts/GB_update.ipynb +0 -371
  38. defdap-1.0.1/scripts/nCorrToDavis.m +0 -57
  39. defdap-1.0.1/setup.py +0 -74
  40. defdap-1.0.1/tests/__init__.py +0 -0
  41. defdap-1.0.1/tests/data/expected_output/ebsd_grain_boundaries_10deg.npz +0 -0
  42. defdap-1.0.1/tests/data/expected_output/ebsd_grain_boundaries_5deg.npz +0 -0
  43. defdap-1.0.1/tests/data/expected_output/ebsd_grains_5deg_0.npz +0 -0
  44. defdap-1.0.1/tests/data/expected_output/ebsd_grains_5deg_10.npz +0 -0
  45. defdap-1.0.1/tests/data/expected_output/ebsd_grains_5deg_100.npz +0 -0
  46. defdap-1.0.1/tests/data/expected_output/ebsd_grains_warped_5deg_0.npz +0 -0
  47. defdap-1.0.1/tests/data/expected_output/ebsd_proxigram.npz +0 -0
  48. defdap-1.0.1/tests/data/expected_output/hrdic_grain_boundaries_5deg.npz +0 -0
  49. defdap-1.0.1/tests/data/expected_output/hrdic_grains_floodfill_0.npz +0 -0
  50. defdap-1.0.1/tests/data/expected_output/hrdic_grains_floodfill_10.npz +0 -0
  51. defdap-1.0.1/tests/data/expected_output/hrdic_grains_floodfill_100.npz +0 -0
  52. defdap-1.0.1/tests/data/expected_output/hrdic_grains_warp.npz +0 -0
  53. defdap-1.0.1/tests/data/expected_output/hrdic_grains_warped-old.npz +0 -0
  54. defdap-1.0.1/tests/data/expected_output/hrdic_grains_warped.npz +0 -0
  55. defdap-1.0.1/tests/data/testDataDIC.txt +0 -60001
  56. defdap-1.0.1/tests/data/testDataEBSD.cpr +0 -69
  57. defdap-1.0.1/tests/data/testDataEBSD.crc +0 -0
  58. defdap-1.0.1/tests/data/testDataEBSD.ctf +0 -87252
  59. defdap-1.0.1/tests/data/testDataPat.bmp +0 -0
  60. {defdap-1.0.1 → defdap-1.1.2}/DefDAP.egg-info/dependency_links.txt +0 -0
  61. {defdap-1.0.1 → defdap-1.1.2}/DefDAP.egg-info/requires.txt +0 -0
  62. {defdap-1.0.1 → defdap-1.1.2}/LICENSE +0 -0
  63. {defdap-1.0.1 → defdap-1.1.2}/README.md +0 -0
  64. {defdap-1.0.1 → defdap-1.1.2}/defdap/__init__.py +0 -0
  65. {defdap-1.0.1 → defdap-1.1.2}/defdap/_accelerated.py +0 -0
  66. {defdap-1.0.1 → defdap-1.1.2}/defdap/crystal.py +0 -0
  67. {defdap-1.0.1 → defdap-1.1.2}/defdap/crystal_utils.py +0 -0
  68. {defdap-1.0.1 → defdap-1.1.2}/defdap/experiment.py +0 -0
  69. {defdap-1.0.1 → defdap-1.1.2}/defdap/file_writers.py +0 -0
  70. {defdap-1.0.1 → defdap-1.1.2}/defdap/hrdic.py +0 -0
  71. {defdap-1.0.1 → defdap-1.1.2}/defdap/plotting.py +0 -0
  72. {defdap-1.0.1 → defdap-1.1.2}/defdap/quat.py +0 -0
  73. {defdap-1.0.1 → defdap-1.1.2}/defdap/slip_systems/cubic_bcc.txt +0 -0
  74. {defdap-1.0.1 → defdap-1.1.2}/defdap/slip_systems/cubic_bcc_110only.txt +0 -0
  75. {defdap-1.0.1 → defdap-1.1.2}/defdap/slip_systems/cubic_fcc.txt +0 -0
  76. {defdap-1.0.1 → defdap-1.1.2}/defdap/slip_systems/cubic_fcc_damask.txt +0 -0
  77. {defdap-1.0.1 → defdap-1.1.2}/defdap/slip_systems/hexagonal_noca.txt +0 -0
  78. {defdap-1.0.1 → defdap-1.1.2}/defdap/slip_systems/hexagonal_withca.txt +0 -0
  79. {defdap-1.0.1 → defdap-1.1.2}/defdap/utils.py +0 -0
  80. {defdap-1.0.1 → defdap-1.1.2}/docs/source/conf.py +0 -0
  81. {defdap-1.0.1 → defdap-1.1.2}/setup.cfg +0 -0
  82. {defdap-1.0.1 → defdap-1.1.2}/tests/test_ebsd.py +0 -0
  83. {defdap-1.0.1 → defdap-1.1.2}/tests/test_hrdic.py +0 -0
  84. {defdap-1.0.1 → defdap-1.1.2}/tests/test_io.py +0 -0
  85. {defdap-1.0.1 → defdap-1.1.2}/tests/test_quat.py +0 -0
@@ -1,18 +1,17 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: DefDAP
3
- Version: 1.0.1
3
+ Version: 1.1.2
4
4
  Summary: A python library for correlating EBSD and HRDIC data.
5
- Author: Michael D. Atkinson, Rhys Thomas, João Quinta da Fonseca
6
- Author-email: michael.atkinson@manchester.ac.uk
7
- License: Apache 2.0 License
5
+ Author: Rhys Thomas, João Quinta da Fonseca
6
+ Author-email: "Michael D. Atkinson" <michael.atkinson@ukaea.uk>
7
+ License: Apache-2.0
8
8
  Project-URL: GitHub, https://github.com/MechMicroMan/DefDAP
9
9
  Project-URL: Documentation, https://defdap.readthedocs.io/en/latest
10
- Keywords: defdap,EBSD,HRDIC,deformation,crystal,correlative analysis
10
+ Keywords: EBSD,HRDIC,deformation,crystal,correlative analysis
11
11
  Classifier: Intended Audience :: Science/Research
12
12
  Classifier: Topic :: Scientific/Engineering
13
13
  Classifier: Topic :: Scientific/Engineering :: Information Analysis
14
- Classifier: Development Status :: 4 - Beta
15
- Classifier: License :: OSI Approved :: Apache Software License
14
+ Classifier: Development Status :: 5 - Production/Stable
16
15
  Classifier: Natural Language :: English
17
16
  Classifier: Operating System :: OS Independent
18
17
  Classifier: Programming Language :: Python :: 3
@@ -48,19 +47,7 @@ Requires-Dist: nbsphinx==0.9.3; extra == "docs"
48
47
  Requires-Dist: ipykernel; extra == "docs"
49
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  Requires-Dist: pandoc; extra == "docs"
50
49
  Requires-Dist: ipympl; extra == "docs"
51
- Dynamic: author
52
- Dynamic: author-email
53
- Dynamic: classifier
54
- Dynamic: description
55
- Dynamic: description-content-type
56
- Dynamic: keywords
57
- Dynamic: license
58
50
  Dynamic: license-file
59
- Dynamic: project-url
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- Dynamic: provides-extra
61
- Dynamic: requires-dist
62
- Dynamic: requires-python
63
- Dynamic: summary
64
51
 
65
52
  ![DefDAP](https://defdap.readthedocs.io/en/latest/_images/logo.png)
66
53
  #### A python library for correlating EBSD and HRDIC data.
@@ -0,0 +1,34 @@
1
+ LICENSE
2
+ README.md
3
+ pyproject.toml
4
+ DefDAP.egg-info/PKG-INFO
5
+ DefDAP.egg-info/SOURCES.txt
6
+ DefDAP.egg-info/dependency_links.txt
7
+ DefDAP.egg-info/requires.txt
8
+ DefDAP.egg-info/top_level.txt
9
+ defdap/__init__.py
10
+ defdap/_accelerated.py
11
+ defdap/_version.py
12
+ defdap/base.py
13
+ defdap/crystal.py
14
+ defdap/crystal_utils.py
15
+ defdap/ebsd.py
16
+ defdap/experiment.py
17
+ defdap/file_readers.py
18
+ defdap/file_writers.py
19
+ defdap/hrdic.py
20
+ defdap/inspector.py
21
+ defdap/plotting.py
22
+ defdap/quat.py
23
+ defdap/utils.py
24
+ defdap/slip_systems/cubic_bcc.txt
25
+ defdap/slip_systems/cubic_bcc_110only.txt
26
+ defdap/slip_systems/cubic_fcc.txt
27
+ defdap/slip_systems/cubic_fcc_damask.txt
28
+ defdap/slip_systems/hexagonal_noca.txt
29
+ defdap/slip_systems/hexagonal_withca.txt
30
+ docs/source/conf.py
31
+ tests/test_ebsd.py
32
+ tests/test_hrdic.py
33
+ tests/test_io.py
34
+ tests/test_quat.py
@@ -0,0 +1,6 @@
1
+ defdap
2
+ dist
3
+ docs
4
+ notebooks
5
+ scripts
6
+ tests
@@ -1,18 +1,17 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: DefDAP
3
- Version: 1.0.1
3
+ Version: 1.1.2
4
4
  Summary: A python library for correlating EBSD and HRDIC data.
5
- Author: Michael D. Atkinson, Rhys Thomas, João Quinta da Fonseca
6
- Author-email: michael.atkinson@manchester.ac.uk
7
- License: Apache 2.0 License
5
+ Author: Rhys Thomas, João Quinta da Fonseca
6
+ Author-email: "Michael D. Atkinson" <michael.atkinson@ukaea.uk>
7
+ License: Apache-2.0
8
8
  Project-URL: GitHub, https://github.com/MechMicroMan/DefDAP
9
9
  Project-URL: Documentation, https://defdap.readthedocs.io/en/latest
10
- Keywords: defdap,EBSD,HRDIC,deformation,crystal,correlative analysis
10
+ Keywords: EBSD,HRDIC,deformation,crystal,correlative analysis
11
11
  Classifier: Intended Audience :: Science/Research
12
12
  Classifier: Topic :: Scientific/Engineering
13
13
  Classifier: Topic :: Scientific/Engineering :: Information Analysis
14
- Classifier: Development Status :: 4 - Beta
15
- Classifier: License :: OSI Approved :: Apache Software License
14
+ Classifier: Development Status :: 5 - Production/Stable
16
15
  Classifier: Natural Language :: English
17
16
  Classifier: Operating System :: OS Independent
18
17
  Classifier: Programming Language :: Python :: 3
@@ -48,19 +47,7 @@ Requires-Dist: nbsphinx==0.9.3; extra == "docs"
48
47
  Requires-Dist: ipykernel; extra == "docs"
49
48
  Requires-Dist: pandoc; extra == "docs"
50
49
  Requires-Dist: ipympl; extra == "docs"
51
- Dynamic: author
52
- Dynamic: author-email
53
- Dynamic: classifier
54
- Dynamic: description
55
- Dynamic: description-content-type
56
- Dynamic: keywords
57
- Dynamic: license
58
50
  Dynamic: license-file
59
- Dynamic: project-url
60
- Dynamic: provides-extra
61
- Dynamic: requires-dist
62
- Dynamic: requires-python
63
- Dynamic: summary
64
51
 
65
52
  ![DefDAP](https://defdap.readthedocs.io/en/latest/_images/logo.png)
66
53
  #### A python library for correlating EBSD and HRDIC data.
@@ -0,0 +1 @@
1
+ __version__ = '1.1.2'
@@ -950,8 +950,13 @@ class Grain(ABC):
950
950
  grain_data = self.grain_data(map_data)
951
951
  x0, y0, xmax, ymax = self.extreme_coords
952
952
 
953
- grain_map_data = np.full((ymax - y0 + 1, xmax - x0 + 1), bg,
954
- dtype=type(grain_data[0]))
953
+ # To support 3D array (ie RGB)
954
+ map_shape = (ymax - y0 + 1, xmax - x0 + 1)
955
+ if grain_data.ndim > 1:
956
+ map_shape = map_shape + grain_data.shape[1:]
957
+
958
+ # Create output array with appropriate dtype
959
+ grain_map_data = np.full(map_shape, bg, dtype=grain_data.dtype)
955
960
 
956
961
  for coord, data in zip(self.data.point, grain_data):
957
962
  grain_map_data[coord[1] - y0, coord[0] - x0] = data
@@ -1309,7 +1309,28 @@ class Grain(base.Grain):
1309
1309
  misori_axis = (2 * dq[1:4] * np.arccos(dq[0])) / np.sqrt(1 - dq[0]**2)
1310
1310
 
1311
1311
  return misori, misori_axis
1312
+
1313
+ def calc_ipf_colour(self, grain_data, direction, bg_colour=None):
1312
1314
 
1315
+ grain_colours = Quat.calc_ipf_colours(
1316
+ grain_data, direction, self.phase.crystal_structure.name
1317
+ ).T
1318
+
1319
+ return grain_colours
1320
+
1321
+ def calc_euler_colour(self, grain_data, bg_colour=None):
1322
+
1323
+ if self.phase.crystal_structure.name == 'cubic':
1324
+ norm = np.array([2 * np.pi, np.pi / 2, np.pi / 2])
1325
+ elif self.phase.crystal_structure.name == 'hexagonal':
1326
+ norm = np.array([np.pi, np.pi, np.pi / 3])
1327
+ else:
1328
+ ValueError("Only hexagonal and cubic symGroup supported")
1329
+
1330
+ grain_colours = grain_data.T / norm
1331
+
1332
+ return grain_colours
1333
+
1313
1334
  def plot_ref_ori(self, direction=np.array([0, 0, 1]), **kwargs):
1314
1335
  """Plot the average grain orientation on an IPF.
1315
1336
 
@@ -646,7 +646,8 @@ class DICDataLoader(ABC):
646
646
  'davis': DavisLoader,
647
647
  'openpiv': OpenPivTextLoader, #Backwards compatability
648
648
  'openpivtext': OpenPivTextLoader,
649
- 'openpivbinary': OpenPivBinaryLoader
649
+ 'openpivbinary': OpenPivBinaryLoader,
650
+ 'pyvale': PyValeLoader
650
651
  }[data_type]
651
652
  except KeyError:
652
653
  raise ValueError(f"No loader for DIC data of type {data_type}.")
@@ -419,8 +419,8 @@ class GrainInspector:
419
419
  y_list.extend(ymap - self.selected_dic_grain.extreme_coords[1])
420
420
 
421
421
  # Get u and v values at each coordinate
422
- u = self.selected_dic_map.crop(self.selected_dic_map.data.displacement[0])[ymap, xmap]
423
- v = self.selected_dic_map.crop(self.selected_dic_map.data.displacement[1])[ymap, xmap]
422
+ u = self.selected_dic_map.data.displacement[0][ymap, xmap]
423
+ v = self.selected_dic_map.data.displacement[1][ymap, xmap]
424
424
 
425
425
  # Subtract mean u and v value for each row
426
426
  u_list.extend(u - np.mean(u, axis=1)[:, None])
@@ -0,0 +1,88 @@
1
+ [build-system]
2
+ requires = ["setuptools>=61.2"]
3
+ build-backend = "setuptools.build_meta"
4
+
5
+ [project]
6
+ name = "DefDAP"
7
+ version = "1.1.2"
8
+ authors = [
9
+ {name = "Michael D. Atkinson", email = "michael.atkinson@ukaea.uk"},
10
+ {name = "Rhys Thomas"},
11
+ {name = "João Quinta da Fonseca"},
12
+ ]
13
+ license = {text = "Apache-2.0"}
14
+ description = "A python library for correlating EBSD and HRDIC data."
15
+ readme = "README.md"
16
+ keywords = ["EBSD", "HRDIC", "deformation", "crystal", "correlative analysis"]
17
+ classifiers = [
18
+ "Intended Audience :: Science/Research",
19
+ "Topic :: Scientific/Engineering",
20
+ "Topic :: Scientific/Engineering :: Information Analysis",
21
+ "Development Status :: 5 - Production/Stable",
22
+ "Natural Language :: English",
23
+ "Operating System :: OS Independent",
24
+ "Programming Language :: Python :: 3",
25
+ "Programming Language :: Python :: 3.8",
26
+ "Programming Language :: Python :: 3.9",
27
+ "Programming Language :: Python :: 3.10",
28
+ "Programming Language :: Python :: 3.11",
29
+ "Framework :: IPython",
30
+ "Framework :: Jupyter",
31
+ "Framework :: Matplotlib",
32
+ ]
33
+ requires-python = ">=3.8"
34
+ dependencies = [
35
+ "scipy>=1.9",
36
+ "numpy",
37
+ "matplotlib>=3.0.0",
38
+ "scikit-image>=0.19",
39
+ "pandas",
40
+ "peakutils",
41
+ "matplotlib_scalebar",
42
+ "networkx",
43
+ "numba",
44
+ ]
45
+
46
+ [project.urls]
47
+ GitHub = "https://github.com/MechMicroMan/DefDAP"
48
+ Documentation = "https://defdap.readthedocs.io/en/latest"
49
+
50
+ [project.optional-dependencies]
51
+ testing = [
52
+ "pytest<8",
53
+ "coverage",
54
+ "pytest-cov",
55
+ "pytest_cases",
56
+ ]
57
+ docs = [
58
+ "sphinx==5.0.2",
59
+ "sphinx_rtd_theme==0.5.0",
60
+ "sphinx_autodoc_typehints==1.11.1",
61
+ "nbsphinx==0.9.3",
62
+ "ipykernel",
63
+ "pandoc",
64
+ "ipympl",
65
+ ]
66
+
67
+ [tool.setuptools]
68
+ include-package-data = false
69
+
70
+ [tool.setuptools.packages.find]
71
+ exclude = ["tests"]
72
+
73
+ [tool.setuptools.package-data]
74
+ defdap = ["slip_systems/*.txt"]
75
+
76
+ [tool.commitizen]
77
+ name = "cz_conventional_commits"
78
+ version = "1.1.2"
79
+ tag_format = "v$version"
80
+ version_files = [
81
+ "pyproject.toml:version",
82
+ "defdap/_version.py",
83
+ ]
84
+ bump_message = "bump: $current_version → $new_version [skip ci]"
85
+
86
+ [tool.pytest.ini_options]
87
+ testpaths = ["tests"]
88
+ addopts = "--cov=defdap"
@@ -1,12 +0,0 @@
1
- # Set the default behavior, in case people don't have core.autocrlf set.
2
- * text=auto
3
-
4
- # Explicitly declare text files you want to always be normalized and converted
5
- # to native line endings on checkout.
6
- *.py text
7
-
8
- # Declare files that will always have CRLF line endings on checkout.
9
-
10
-
11
- # Denote all files that are truly binary and should not be modified.
12
- *.ipynb binary
@@ -1,29 +0,0 @@
1
- name: Test DefDAP
2
-
3
- on: [push, pull_request]
4
-
5
- jobs:
6
- build:
7
-
8
- runs-on: ubuntu-latest
9
- strategy:
10
- fail-fast: false
11
- matrix:
12
- python-version: ["3.8", "3.9", "3.10", "3.11"]
13
-
14
- steps:
15
- - uses: actions/checkout@v2
16
- - name: Set up Python ${{ matrix.python-version }}
17
- uses: actions/setup-python@v2
18
- with:
19
- python-version: ${{ matrix.python-version }}
20
- - name: Install dependencies
21
- run: |
22
- python -m pip install --upgrade pip
23
- python -m pip install --upgrade pytest
24
- python -m pip install .[testing]
25
- if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
26
-
27
- - name: Test with pytest
28
- run: |
29
- pytest
defdap-1.0.1/.gitignore DELETED
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- # OS generated files
2
- .DS_Store
3
- .DS_Store?
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- ._*
5
- .Spotlight-V100
6
- .Trashes
7
- ehthumbs.db
8
- Thumbs.db
9
-
10
- # Python generated files
11
- __pycache__
12
- *.pyc
13
-
14
- # ipython generated files
15
- .ipynb_checkpoints
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-
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- # Intellij IDE files
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- .idea/
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-
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- # Python Virtual Environment
21
- venv/
22
-
23
- # Sphinx docs build
24
- docs/build
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- # Sphinx autogenerated API documentation
26
- docs/source/defdap
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-
28
- # Pip install
29
- DefDAP.egg-info/
30
-
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- # pytest
32
- .pytest_cache
33
-
34
- # coverage
35
- .coverage
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-
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- # vscode
38
- .vscode
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- [pytest]
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- testpaths = tests
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- addopts = --cov=defdap
@@ -1,13 +0,0 @@
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- version: 2
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- sphinx:
3
- configuration: docs/source/conf.py
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- build:
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- os: ubuntu-22.04
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- tools:
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- python: "3.10"
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- python:
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- install:
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- - method: pip
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- path: .
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- extra_requirements:
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- - docs
defdap-1.0.1/CHANGELOG.md DELETED
@@ -1,188 +0,0 @@
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- # Change Log
2
-
3
- ## Current
4
-
5
- ### Added
6
-
7
- ### Changed
8
-
9
- ### Fixed
10
-
11
-
12
- ## 1.0.1 (03-12-2025)
13
-
14
- ### Fixed
15
- - Plotting slip traces for ebsd grain with colours from phase
16
-
17
-
18
- ## 1.0.0 (05-11-2025)
19
- This was a overhaul of large sections of the code and many changes/additions have been missed from the chnagelog.
20
-
21
- ### Added
22
- - Each grain is assigned a phase and slip systems are automatically loaded
23
- for a given phase based on crystal structure.
24
- - This means that unit cells and slip traces plot correctly for grains
25
- in a multi-phase EBSD map
26
- - Add slip system file for FCC but in same order as DAMASK
27
- - Use example_notebook to generate a 'How To Use' page in the documentation
28
- - Add reader for EDAX .ang EBSD files, pyvale .csv files and openPIV-XL .npx files
29
- - Added a `plot_map` function for grains
30
- - Added more testing
31
-
32
- ### Changed
33
- - All functions and arguments are now in snake_case instead of CamelCase
34
- - Cropping and masking are now performed upon access to data
35
- - Changed function names from CamelCase to snake_case
36
- - Overhaul of data storage in the Map classes
37
- - RDR calculation `calcRDR` in grain inspector is faster and more robust
38
- - Improve formatting of grain inspector and RDR plot window
39
- - Refactor boundary lines calculations
40
- - Use GitHub actions to run `pytest` on commit push or pull request
41
-
42
- ### Fixed
43
- - Fix bug in grain inspector (`None` passed to `corrAngle` inadvertently)
44
- - Fix EBSD grain linker
45
- - Remove `IPython` and `jupyter` as requirements
46
- - Bug in IPF traiangle plotting now fixed with options for `up` triangle (like MTEX) and `down` triangle (like OI)
47
-
48
-
49
- ## 0.93.5 (20-11-2023)
50
-
51
- ### Added
52
- - Add more options for colouring lines
53
-
54
- ### Fixed
55
- - Fix bug with accessing slip systems in grain inspector
56
- - Replace np.float with python float
57
- - Remove in_place argument to skimage.morphology.remove_small_objects
58
- - set_window_title has been moved from figure.canvas to figure.canvas.manager
59
-
60
-
61
- ## 0.93.5 (20-11-2023)
62
-
63
- ### Added
64
- - Add more options for colouring lines
65
-
66
- ### Fixed
67
- - Fix bug with accessing slip systems in grain inspector
68
- - Replace `np.float` with python `float`
69
- - Remove `in_place` argument to `skimage.morphology.remove_small_objects`
70
- - `set_window_title` has been moved from `figure.canvas` to `figure.canvas.manager`
71
-
72
-
73
- ## 0.93.5 (17-01-2023)
74
-
75
- ### Added
76
- - Add equality check for `Quat`
77
-
78
- ### Fixed
79
- - Fix bug in boundary line warping
80
-
81
-
82
- ## 0.93.4 (07-03-2022)
83
-
84
- ### Changed
85
- - Update BCC slip system file and add a separate FCC file with same ordering as in DAMASK
86
- - Refactor boundary lines in `ebsd.map` class and add methods for warping lines to a DIC map
87
- - Refactor `linkEbsdMap` method and pass all arguments to transform estimate method
88
- - Remove IPython and jupyter as requirements
89
- - Move slip systems to `Phase` class and load automatically based on crystal stucture
90
- - Make Oxford bonary loader tolerate of unknown data fields
91
-
92
- ### Fixed
93
- - Fix ebsd grain linker so it works again
94
-
95
-
96
- ## 0.93.3 (23-08-2021)
97
-
98
- ### Added
99
- - Store EDX data as a dictionary called `EDX` accessible from the EBSD `Map` object
100
- - Add option to change IPF map background colour
101
-
102
- ### Fixed
103
- - Fix bug with reading cpr EBSD file without EDX data
104
- - Fix issue with plotting Schmid factor maps
105
- - Fix bug with maps `component` not updating after masking
106
-
107
-
108
- ## 0.93.2 (16-04-2021)
109
-
110
- ### Added
111
- - Reading of Channel5 project files that contain EDX data
112
-
113
- ### Fixed
114
- - Plotting unit cells
115
- - Plotting lines with grain inspector
116
-
117
-
118
- ## 0.93.1 (12-04-2021)
119
-
120
- ### Added
121
- - Started adding type hinting
122
- - Add save/load support to grainInspector
123
- - Add `drawLineProfile` function. Click and drag a line, then plot an intensity profile across the line
124
-
125
- ### Changed
126
- - Speed up EBSD map data rotation
127
- - Speed up `warp` grain finding
128
- - Store band slope and MAD arrays from EBSD
129
- - Update `nCorrToDavis.m` script
130
- - Better description of how to use the function
131
- - Sub-window size is subset radius * 2, as defined in nCorr
132
- - Subset spacing is subset spacing, as defined in nCorr
133
- - Generate phase boundary points and lines at same time as grain boundaries
134
- - Improve histogram plotting
135
- - Options for scatter (as before), `step` and `bar`
136
- - Options for `logx`, `logy`, `loglog` and `linear`
137
- - Updates to example notebook
138
-
139
- ### Fixed
140
- - Fixed docstring links
141
- - Fix bug in `warp` grain finding algorithm
142
-
143
-
144
- ## 0.93.0 (20-02-2021)
145
-
146
- ### Added
147
- - Add EBSD file writing to CTF format.
148
- - Add cretation of EBSD maps from runtime data.
149
- - Add method to generate all slip systems in a family from a single system.
150
- - Add grouping of slip systems by family.
151
- - Add mechanism to define default parameter values stored in single loaction.
152
- - Add basic filtering for HRDIC maps.
153
- - Filtering based on threshold of effective shear strain and subsequent binary dilation.
154
- - All current DefDAP functions work with NaN, but the RDR might not work as expected.
155
- - New grain finding algorithm for HRDIC map which warps the EBSD grain map.
156
- - Add `addLegend` command to add a marker size legend to a pole plot.
157
- - Add misorientation calculation between neighbouring EBSD grains.
158
- - Add a `BoundarySegment` class to represent a section of grain boundary between 2 grain in an EBSD map. Objects of this class are assigned to edges of the neighbour network and contain all the boundary points between the grains.
159
- - Add Kuwahara filter for EBSD map noise reduction.
160
- - Add `shape` property to maps.
161
- - Read EBSD phases from file.
162
- - Add classes to represent phases and crystal structures.
163
-
164
- ### Changed
165
- - Update progress reporting to print elapsed time.
166
- - Speed up grain finding algorithm.
167
- - Update plot IPF and Euler map to consider multiple phasess.
168
- - Drop support of python 3.5.
169
- - Update boundary and grain finding to consider phase boundaries.
170
- - Assign a phase to each grain in an EBSD map.
171
- - Change equality and hash of slip systems, slip plane and direction must now be equal (-ve allowed but not different norms).
172
- - Update slip system plane and direction lables to have overbars - very fancy.
173
- - Updates to example notebook.
174
- - Change docs over to readthedocs.
175
- - Move version number to own file.
176
- - Update neighbour network to use grains as nodes.
177
- - Store `grainID` in grain objects.
178
- - Split plotGrainDataMap into separate array construction and plotting function.
179
- - Update neighbour network construction to use new EBSD boundary definition.
180
- - Update flood fill algorithm for grain finding in a EBSD map.
181
- - Vertical and horizontal boundary pixels are now considered separately.
182
- - Load phases from CTF file.
183
-
184
- ### Fixed
185
- - Fix bug with comment and blank lines when reading CPR files.
186
- - Fixes to quat class:
187
- - Construction from axis/angle now in passive sense not just a conversion.
188
- - Fix big with transform vector where -ve vector was returned in some cases due to intermediate quat being transformed to northern hemisphere.
defdap-1.0.1/CODEOWNERS DELETED
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- * @mikesmic @rhysgt
@@ -1,79 +0,0 @@
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- .gitattributes
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- .gitignore
3
- .pytest.ini
4
- .readthedocs.yml
5
- CHANGELOG.md
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- CODEOWNERS
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- LICENSE
8
- README.md
9
- setup.py
10
- .github/workflows/test.yml
11
- DefDAP.egg-info/PKG-INFO
12
- DefDAP.egg-info/SOURCES.txt
13
- DefDAP.egg-info/dependency_links.txt
14
- DefDAP.egg-info/requires.txt
15
- DefDAP.egg-info/top_level.txt
16
- defdap/__init__.py
17
- defdap/_accelerated.py
18
- defdap/_version.py
19
- defdap/base.py
20
- defdap/crystal.py
21
- defdap/crystal_utils.py
22
- defdap/ebsd.py
23
- defdap/experiment.py
24
- defdap/file_readers.py
25
- defdap/file_writers.py
26
- defdap/hrdic.py
27
- defdap/inspector.py
28
- defdap/plotting.py
29
- defdap/quat.py
30
- defdap/utils.py
31
- defdap/slip_systems/cubic_bcc.txt
32
- defdap/slip_systems/cubic_bcc_110only.txt
33
- defdap/slip_systems/cubic_fcc.txt
34
- defdap/slip_systems/cubic_fcc_damask.txt
35
- defdap/slip_systems/hexagonal_noca.txt
36
- defdap/slip_systems/hexagonal_withca.txt
37
- docs/Makefile
38
- docs/README.md
39
- docs/make.bat
40
- docs/source/conf.py
41
- docs/source/contributing.rst
42
- docs/source/index.rst
43
- docs/source/installation.rst
44
- docs/source/license.rst
45
- docs/source/modules.rst
46
- docs/source/papers.rst
47
- docs/source/_static/branches.png
48
- docs/source/_static/logo.png
49
- docs/source/_static/sample_ebsd.jpg
50
- docs/source/_templates/layout.html
51
- notebooks/example_notebook.ipynb
52
- notebooks/experiment.ipynb
53
- notebooks/twin_boundaries.ipynb
54
- scripts/GB_update.ipynb
55
- scripts/nCorrToDavis.m
56
- tests/__init__.py
57
- tests/test_ebsd.py
58
- tests/test_hrdic.py
59
- tests/test_io.py
60
- tests/test_quat.py
61
- tests/data/testDataDIC.txt
62
- tests/data/testDataEBSD.cpr
63
- tests/data/testDataEBSD.crc
64
- tests/data/testDataEBSD.ctf
65
- tests/data/testDataPat.bmp
66
- tests/data/expected_output/ebsd_grain_boundaries_10deg.npz
67
- tests/data/expected_output/ebsd_grain_boundaries_5deg.npz
68
- tests/data/expected_output/ebsd_grains_5deg_0.npz
69
- tests/data/expected_output/ebsd_grains_5deg_10.npz
70
- tests/data/expected_output/ebsd_grains_5deg_100.npz
71
- tests/data/expected_output/ebsd_grains_warped_5deg_0.npz
72
- tests/data/expected_output/ebsd_proxigram.npz
73
- tests/data/expected_output/hrdic_grain_boundaries_5deg.npz
74
- tests/data/expected_output/hrdic_grains_floodfill_0.npz
75
- tests/data/expected_output/hrdic_grains_floodfill_10.npz
76
- tests/data/expected_output/hrdic_grains_floodfill_100.npz
77
- tests/data/expected_output/hrdic_grains_warp.npz
78
- tests/data/expected_output/hrdic_grains_warped-old.npz
79
- tests/data/expected_output/hrdic_grains_warped.npz
@@ -1 +0,0 @@
1
- defdap
@@ -1 +0,0 @@
1
- __version__ = '1.0.1'