DefDAP 0.93.6__tar.gz → 1.0.0__tar.gz

defdap-1.0.0/.gitattributes

@@ -0,0 +1,12 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.py text
+
+# Declare files that will always have CRLF line endings on checkout.
+
+
+# Denote all files that are truly binary and should not be modified.
+*.ipynb binary

defdap-1.0.0/.github/workflows/test.yml

@@ -0,0 +1,29 @@
+name: Test DefDAP
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --upgrade pytest
+        python -m pip install .[testing]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Test with pytest
+      run: |
+        pytest

defdap-1.0.0/.gitignore

@@ -0,0 +1,38 @@
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Python generated files
+__pycache__
+*.pyc
+
+# ipython generated files
+.ipynb_checkpoints
+
+# Intellij IDE files
+.idea/
+
+# Python Virtual Environment
+venv/
+
+# Sphinx docs build
+docs/build
+# Sphinx autogenerated API documentation
+docs/source/defdap
+
+# Pip install
+DefDAP.egg-info/
+
+# pytest
+.pytest_cache
+
+# coverage
+.coverage
+
+# vscode
+.vscode

defdap-1.0.0/.pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+testpaths = tests
+addopts = --cov=defdap

defdap-1.0.0/.readthedocs.yml

@@ -0,0 +1,13 @@
+version: 2
+sphinx:
+  configuration: docs/source/conf.py
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

defdap-1.0.0/CHANGELOG.md

@@ -0,0 +1,184 @@
+# Change Log
+
+## Current
+
+### Added
+
+
+### Changed
+
+
+### Fixed
+
+
+## 1.0.0 (05-11-2025)
+This was a overhaul of large sections of the code and many changes/additions have been missed from the chnagelog.
+
+### Added
+- Each grain is assigned a phase and slip systems are automatically loaded 
+  for a given phase based on crystal structure. 
+  - This means that unit cells and slip traces plot correctly for grains
+  in a multi-phase EBSD map
+- Add slip system file for FCC but in same order as DAMASK
+- Use example_notebook to generate a 'How To Use' page in the documentation
+- Add reader for EDAX .ang EBSD files, pyvale .csv files and openPIV-XL .npx files
+- Added a `plot_map` function for grains
+- Added more testing
+
+### Changed
+- All functions and arguments are now in snake_case instead of CamelCase
+- Cropping and masking are now performed upon access to data
+- Changed function names from CamelCase to snake_case
+- Overhaul of data storage in the Map classes
+- RDR calculation `calcRDR` in grain inspector is faster and more robust
+- Improve formatting of grain inspector and RDR plot window
+- Refactor boundary lines calculations
+- Use GitHub actions to run `pytest` on commit push or pull request
+
+### Fixed
+- Fix bug in grain inspector (`None` passed to `corrAngle` inadvertently)
+- Fix EBSD grain linker
+- Remove `IPython` and `jupyter` as requirements
+- Bug in IPF traiangle plotting now fixed with options for `up` triangle (like MTEX) and `down` triangle (like OI)
+
+
+## 0.93.5 (20-11-2023)
+
+### Added
+- Add more options for colouring lines
+
+### Fixed
+- Fix bug with accessing slip systems in grain inspector
+- Replace np.float with python float
+- Remove in_place argument to skimage.morphology.remove_small_objects
+- set_window_title has been moved from figure.canvas to figure.canvas.manager
+
+
+## 0.93.5 (20-11-2023)
+
+### Added
+- Add more options for colouring lines
+
+### Fixed
+- Fix bug with accessing slip systems in grain inspector
+- Replace `np.float` with python `float`
+- Remove `in_place` argument to `skimage.morphology.remove_small_objects`
+- `set_window_title` has been moved from `figure.canvas` to `figure.canvas.manager`
+
+
+## 0.93.5 (17-01-2023)
+
+### Added
+- Add equality check for `Quat`
+
+### Fixed
+- Fix bug in boundary line warping
+
+
+## 0.93.4 (07-03-2022)
+
+### Changed
+- Update BCC slip system file and add a separate FCC file with same ordering as in DAMASK
+- Refactor boundary lines in `ebsd.map` class and add methods for warping lines to a DIC map
+- Refactor `linkEbsdMap` method and pass all arguments to transform estimate method
+- Remove IPython and jupyter as requirements
+- Move slip systems to `Phase` class and load automatically based on crystal stucture
+- Make Oxford bonary loader tolerate of unknown data fields
+
+### Fixed
+- Fix ebsd grain linker so it works again
+
+
+## 0.93.3 (23-08-2021)
+
+### Added
+- Store EDX data as a dictionary called `EDX` accessible from the EBSD `Map` object
+- Add option to change IPF map background colour
+
+### Fixed
+- Fix bug with reading cpr EBSD file without EDX data
+- Fix issue with plotting Schmid factor maps
+- Fix bug with maps `component` not updating after masking
+
+
+## 0.93.2 (16-04-2021)
+
+### Added
+- Reading of Channel5 project files that contain EDX data
+
+### Fixed
+- Plotting unit cells
+- Plotting lines with grain inspector
+
+
+## 0.93.1 (12-04-2021)
+
+### Added
+- Started adding type hinting
+- Add save/load support to grainInspector
+- Add `drawLineProfile` function. Click and drag a line, then plot an intensity profile across the line
+
+### Changed
+- Speed up EBSD map data rotation 
+- Speed up `warp` grain finding
+- Store band slope and MAD arrays from EBSD
+- Update `nCorrToDavis.m` script
+  - Better description of how to use the function
+  - Sub-window size is subset radius * 2, as defined in nCorr
+  - Subset spacing is subset spacing, as defined in nCorr
+- Generate phase boundary points and lines at same time as grain boundaries
+- Improve histogram plotting
+  - Options for scatter (as before), `step` and `bar`
+  - Options for `logx`, `logy`, `loglog` and `linear`
+- Updates to example notebook
+
+### Fixed 
+- Fixed docstring links
+- Fix bug in `warp` grain finding algorithm
+
+
+## 0.93.0 (20-02-2021)
+
+### Added
+- Add EBSD file writing to CTF format.
+- Add cretation of EBSD maps from runtime data.
+- Add method to generate all slip systems in a family from a single system.
+- Add grouping of slip systems by family.
+- Add mechanism to define default parameter values stored in single loaction.
+- Add basic filtering for HRDIC maps.
+  - Filtering based on threshold of effective shear strain and subsequent binary dilation.
+  - All current DefDAP functions work with NaN, but the RDR might not work as expected.
+- New grain finding algorithm for HRDIC map which warps the EBSD grain map.
+- Add `addLegend` command to add a marker size legend to a pole plot.
+- Add misorientation calculation between neighbouring EBSD grains.
+- 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.
+- Add Kuwahara filter for EBSD map noise reduction.
+- Add `shape` property to maps.
+- Read EBSD phases from file.
+- Add classes to represent phases and crystal structures.
+
+### Changed
+- Update progress reporting to print elapsed time.
+- Speed up grain finding algorithm.
+- Update plot IPF and Euler map to consider multiple phasess.
+- Drop support of python 3.5.
+- Update boundary and grain finding to consider phase boundaries. 
+- Assign a phase to each grain in an EBSD map.
+- Change equality and hash of slip systems, slip plane and direction must now be equal (-ve allowed but not different norms).
+- Update slip system plane and direction lables  to have overbars - very fancy.
+- Updates to example notebook.
+- Change docs over to readthedocs.
+- Move version number to own file.
+- Update neighbour network to use grains as nodes.
+- Store `grainID` in grain objects.
+- Split plotGrainDataMap into separate array construction and plotting function.
+- Update neighbour network construction to use new EBSD boundary definition.
+- Update flood fill algorithm for grain finding in a EBSD map.
+- Vertical and horizontal boundary pixels are now considered separately.
+- Load phases from CTF file.
+
+### Fixed 
+- Fix bug with comment and blank lines when reading CPR files.
+- Fixes to quat class:
+  - Construction from axis/angle now in passive sense not just a conversion.
+  - Fix big with transform vector where -ve vector was returned in some cases due to intermediate quat being transformed to northern hemisphere.

defdap-1.0.0/CODEOWNERS

@@ -0,0 +1 @@
+*       @mikesmic @rhysgt

{DefDAP-0.93.6 → defdap-1.0.0}/DefDAP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: DefDAP
-Version: 0.93.6
+Version: 1.0.0
 Summary: A python library for correlating EBSD and HRDIC data.
 Author: Michael D. Atkinson, Rhys Thomas, João Quinta da Fonseca
 Author-email: michael.atkinson@manchester.ac.uk
@@ -16,18 +16,51 @@ Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Framework :: IPython
 Classifier: Framework :: Jupyter
 Classifier: Framework :: Matplotlib
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy>=1.9
+Requires-Dist: numpy
+Requires-Dist: matplotlib>=3.0.0
+Requires-Dist: scikit-image>=0.19
+Requires-Dist: pandas
+Requires-Dist: peakutils
+Requires-Dist: matplotlib_scalebar
+Requires-Dist: networkx
+Requires-Dist: numba
 Provides-Extra: testing
+Requires-Dist: pytest<8; extra == "testing"
+Requires-Dist: coverage; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest_cases; extra == "testing"
 Provides-Extra: docs
-License-File: LICENSE
+Requires-Dist: sphinx==5.0.2; extra == "docs"
+Requires-Dist: sphinx_rtd_theme==0.5.0; extra == "docs"
+Requires-Dist: sphinx_autodoc_typehints==1.11.1; extra == "docs"
+Requires-Dist: nbsphinx==0.9.3; extra == "docs"
+Requires-Dist: ipykernel; extra == "docs"
+Requires-Dist: pandoc; extra == "docs"
+Requires-Dist: ipympl; extra == "docs"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 ![DefDAP](https://defdap.readthedocs.io/en/latest/_images/logo.png)
 #### A python library for correlating EBSD and HRDIC data.
@@ -48,7 +81,7 @@ License-File: LICENSE
 
 ## How to install
 - DefDAP can be installed from PyPI using the command `pip install defdap`
-- If you use conda as your package manager (https://www.anaconda.com/), the prerequisite packages that are available from anaconda can be installed using the command `conda install scipy numpy matplotlib scikit-image pandas networkx jupyter ipython` (Anaconda3-2020.02 has been tested)
+- If you use conda as your package manager (https://www.anaconda.com/), the prerequisite packages that are available from anaconda can be installed using the command `conda install scipy numpy matplotlib scikit-image pandas networkx` (Anaconda3-2020.02 has been tested)
 - For more information, see the [documentation](https://defdap.readthedocs.io/en/latest/installation.html)
 
 ## How to use
@@ -74,8 +107,6 @@ The software uses the following open source packages:
 - [pandas](http://pandas.pydata.org)
 - [peakutils](https://peakutils.readthedocs.io/en/latest/)
 - [matplotlib_scalebar](https://pypi.org/project/matplotlib-scalebar/)
-- [IPython](https://ipython.org/)
-- [jupyter](https://jupyter.org/)
 
 ## License
 [Apache 2.0 license](https://www.apache.org/licenses/LICENSE-2.0)

defdap-1.0.0/DefDAP.egg-info/SOURCES.txt

@@ -0,0 +1,79 @@
+.gitattributes
+.gitignore
+.pytest.ini
+.readthedocs.yml
+CHANGELOG.md
+CODEOWNERS
+LICENSE
+README.md
+setup.py
+.github/workflows/test.yml
+DefDAP.egg-info/PKG-INFO
+DefDAP.egg-info/SOURCES.txt
+DefDAP.egg-info/dependency_links.txt
+DefDAP.egg-info/requires.txt
+DefDAP.egg-info/top_level.txt
+defdap/__init__.py
+defdap/_accelerated.py
+defdap/_version.py
+defdap/base.py
+defdap/crystal.py
+defdap/crystal_utils.py
+defdap/ebsd.py
+defdap/experiment.py
+defdap/file_readers.py
+defdap/file_writers.py
+defdap/hrdic.py
+defdap/inspector.py
+defdap/plotting.py
+defdap/quat.py
+defdap/utils.py
+defdap/slip_systems/cubic_bcc.txt
+defdap/slip_systems/cubic_bcc_110only.txt
+defdap/slip_systems/cubic_fcc.txt
+defdap/slip_systems/cubic_fcc_damask.txt
+defdap/slip_systems/hexagonal_noca.txt
+defdap/slip_systems/hexagonal_withca.txt
+docs/Makefile
+docs/README.md
+docs/make.bat
+docs/source/conf.py
+docs/source/contributing.rst
+docs/source/index.rst
+docs/source/installation.rst
+docs/source/license.rst
+docs/source/modules.rst
+docs/source/papers.rst
+docs/source/_static/branches.png
+docs/source/_static/logo.png
+docs/source/_static/sample_ebsd.jpg
+docs/source/_templates/layout.html
+notebooks/example_notebook.ipynb
+notebooks/experiment.ipynb
+notebooks/twin_boundaries.ipynb
+scripts/GB_update.ipynb
+scripts/nCorrToDavis.m
+tests/__init__.py
+tests/test_ebsd.py
+tests/test_hrdic.py
+tests/test_io.py
+tests/test_quat.py
+tests/data/testDataDIC.txt
+tests/data/testDataEBSD.cpr
+tests/data/testDataEBSD.crc
+tests/data/testDataEBSD.ctf
+tests/data/testDataPat.bmp
+tests/data/expected_output/ebsd_grain_boundaries_10deg.npz
+tests/data/expected_output/ebsd_grain_boundaries_5deg.npz
+tests/data/expected_output/ebsd_grains_5deg_0.npz
+tests/data/expected_output/ebsd_grains_5deg_10.npz
+tests/data/expected_output/ebsd_grains_5deg_100.npz
+tests/data/expected_output/ebsd_grains_warped_5deg_0.npz
+tests/data/expected_output/ebsd_proxigram.npz
+tests/data/expected_output/hrdic_grain_boundaries_5deg.npz
+tests/data/expected_output/hrdic_grains_floodfill_0.npz
+tests/data/expected_output/hrdic_grains_floodfill_10.npz
+tests/data/expected_output/hrdic_grains_floodfill_100.npz
+tests/data/expected_output/hrdic_grains_warp.npz
+tests/data/expected_output/hrdic_grains_warped-old.npz
+tests/data/expected_output/hrdic_grains_warped.npz

{DefDAP-0.93.6 → defdap-1.0.0}/DefDAP.egg-info/requires.txt

@@ -1,11 +1,12 @@
-scipy
+scipy>=1.9
 numpy
 matplotlib>=3.0.0
-scikit-image
+scikit-image>=0.19
 pandas
 peakutils
 matplotlib_scalebar
 networkx
+numba
 
 [docs]
 sphinx==5.0.2
@@ -17,7 +18,7 @@ pandoc
 ipympl
 
 [testing]
-pytest
+pytest<8
 coverage
 pytest-cov
 pytest_cases

{DefDAP-0.93.6 → defdap-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: DefDAP
-Version: 0.93.6
+Version: 1.0.0
 Summary: A python library for correlating EBSD and HRDIC data.
 Author: Michael D. Atkinson, Rhys Thomas, João Quinta da Fonseca
 Author-email: michael.atkinson@manchester.ac.uk
@@ -16,18 +16,51 @@ Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Framework :: IPython
 Classifier: Framework :: Jupyter
 Classifier: Framework :: Matplotlib
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy>=1.9
+Requires-Dist: numpy
+Requires-Dist: matplotlib>=3.0.0
+Requires-Dist: scikit-image>=0.19
+Requires-Dist: pandas
+Requires-Dist: peakutils
+Requires-Dist: matplotlib_scalebar
+Requires-Dist: networkx
+Requires-Dist: numba
 Provides-Extra: testing
+Requires-Dist: pytest<8; extra == "testing"
+Requires-Dist: coverage; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest_cases; extra == "testing"
 Provides-Extra: docs
-License-File: LICENSE
+Requires-Dist: sphinx==5.0.2; extra == "docs"
+Requires-Dist: sphinx_rtd_theme==0.5.0; extra == "docs"
+Requires-Dist: sphinx_autodoc_typehints==1.11.1; extra == "docs"
+Requires-Dist: nbsphinx==0.9.3; extra == "docs"
+Requires-Dist: ipykernel; extra == "docs"
+Requires-Dist: pandoc; extra == "docs"
+Requires-Dist: ipympl; extra == "docs"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 ![DefDAP](https://defdap.readthedocs.io/en/latest/_images/logo.png)
 #### A python library for correlating EBSD and HRDIC data.
@@ -48,7 +81,7 @@ License-File: LICENSE
 
 ## How to install
 - DefDAP can be installed from PyPI using the command `pip install defdap`
-- If you use conda as your package manager (https://www.anaconda.com/), the prerequisite packages that are available from anaconda can be installed using the command `conda install scipy numpy matplotlib scikit-image pandas networkx jupyter ipython` (Anaconda3-2020.02 has been tested)
+- If you use conda as your package manager (https://www.anaconda.com/), the prerequisite packages that are available from anaconda can be installed using the command `conda install scipy numpy matplotlib scikit-image pandas networkx` (Anaconda3-2020.02 has been tested)
 - For more information, see the [documentation](https://defdap.readthedocs.io/en/latest/installation.html)
 
 ## How to use
@@ -74,8 +107,6 @@ The software uses the following open source packages:
 - [pandas](http://pandas.pydata.org)
 - [peakutils](https://peakutils.readthedocs.io/en/latest/)
 - [matplotlib_scalebar](https://pypi.org/project/matplotlib-scalebar/)
-- [IPython](https://ipython.org/)
-- [jupyter](https://jupyter.org/)
 
 ## License
 [Apache 2.0 license](https://www.apache.org/licenses/LICENSE-2.0)

{DefDAP-0.93.6 → defdap-1.0.0}/README.md

@@ -17,7 +17,7 @@
 
 ## How to install
 - DefDAP can be installed from PyPI using the command `pip install defdap`
-- If you use conda as your package manager (https://www.anaconda.com/), the prerequisite packages that are available from anaconda can be installed using the command `conda install scipy numpy matplotlib scikit-image pandas networkx jupyter ipython` (Anaconda3-2020.02 has been tested)
+- If you use conda as your package manager (https://www.anaconda.com/), the prerequisite packages that are available from anaconda can be installed using the command `conda install scipy numpy matplotlib scikit-image pandas networkx` (Anaconda3-2020.02 has been tested)
 - For more information, see the [documentation](https://defdap.readthedocs.io/en/latest/installation.html)
 
 ## How to use
@@ -43,8 +43,6 @@ The software uses the following open source packages:
 - [pandas](http://pandas.pydata.org)
 - [peakutils](https://peakutils.readthedocs.io/en/latest/)
 - [matplotlib_scalebar](https://pypi.org/project/matplotlib-scalebar/)
-- [IPython](https://ipython.org/)
-- [jupyter](https://jupyter.org/)
 
 ## License
 [Apache 2.0 license](https://www.apache.org/licenses/LICENSE-2.0)

{DefDAP-0.93.6 → defdap-1.0.0}/defdap/__init__.py

@@ -1,3 +1,5 @@
+from defdap.experiment import Experiment
+
 defaults = {
     # Convention to use when attaching an orthonormal frame to a crystal
     # structure. 'hkl' or 'tsl'
@@ -14,6 +16,10 @@ defaults = {
     'slip_system_file': {
         'FCC': 'cubic_fcc',
         'BCC': 'cubic_bcc',
-        'HCP': 'hexagonal_noca',
+        'HCP': 'hexagonal_withca',
     },
+    # up or down
+    'ipf_triangle_convention': 'up'
 }
+
+anonymous_experiment = Experiment()