Update upstream source from tag 'upstream/1.7.1'
Update to upstream version '1.7.1'
with Debian dir ec67325d8b1bc23c13f48f62f79b2c90ef769ec3
Picca Frédéric-Emmanuel
3 years ago
| 0 | v1.7.1, 2021-01-02 | |
| 1 | ||
| 2 | * harmonize dependency versions between README and setup.py | |
| 3 | * remove PDF documentation and other generatable content from the GIT | |
| 4 | repository | |
| 5 | * new azure pipeline for documentation generation | |
| 6 | * new azure pipeline for wheel generation (issue #111) | |
| 7 | ||
| 0 | 8 | v1.7.0, 2020-12-08 |
| 1 | 9 | |
| 2 | 10 | * allow string decoding to fail in tif headers |
| 0 | Contributions and feedback of all kind are welcome! Please see below how to | |
| 1 | best reach us or contribute. | |
| 2 | ||
| 3 | Submitting an issue | |
| 4 | =================== | |
| 5 | ||
| 6 | If you have questions about the use of the package please consider contacting | |
| 7 | us via the [mailing list][1] | |
| 8 | ||
| 9 | If you find a bug or have concrete suggestions for improvements feel free to | |
| 10 | open an issue on the [Github issue tracker][2]. | |
| 11 | ||
| 12 | Submitting an patch/pull request | |
| 13 | ================================ | |
| 14 | ||
| 15 | Patches and pull requests can also be submitted via Github. | |
| 16 | ||
| 17 | Styleguide | |
| 18 | ---------- | |
| 19 | ||
| 20 | In order to keep the code readable we try to follow the [PEP8 Style Guide][3] | |
| 21 | ||
| 22 | Consider checking your contribution with the [PEP8 style checker][4] | |
| 23 | ||
| 24 | Noteable exceptions are docstrings which sometimes would get misformated when | |
| 25 | PEP8 is followed strictly. For docstrings we follow the [numpydoc style][5]. | |
| 26 | ||
| 27 | [1]: https://sourceforge.net/p/xrayutilities/mailman/xrayutilities-users | |
| 28 | [2]: https://github.com/dkriegner/xrayutilities/issues | |
| 29 | [3]: https://www.python.org/dev/peps/pep-0008/ | |
| 30 | [4]: https://pypi.org/project/pycodestyle/ | |
| 31 | [5]: http://numpydoc.readthedocs.io |
| 2 | 2 | |
| 3 | 3 | # documentation files |
| 4 | 4 | include README.md |
| 5 | include xrayutilities.pdf | |
| 6 | 5 | recursive-include doc/source * |
| 7 | 6 | |
| 8 | 7 | # examples |
| 0 | 0 | Metadata-Version: 2.1 |
| 1 | 1 | Name: xrayutilities |
| 2 | Version: 1.7.0 | |
| 2 | Version: 1.7.1 | |
| 3 | 3 | Summary: package for x-ray diffraction data evaluation |
| 4 | Home-page: http://xrayutilities.sourceforge.net | |
| 4 | Home-page: https://xrayutilities.sourceforge.io | |
| 5 | 5 | Author: Eugen Wintersberger, Dominik Kriegner |
| 6 | 6 | Author-email: eugen.wintersberger@desy.de, dominik.kriegner@gmail.com |
| 7 | 7 | Maintainer: Dominik Kriegner |
| 10 | 10 | Description: xrayutilities |
| 11 | 11 | ============= |
| 12 | 12 | |
| 13 | ||
| 13 | 14 | [](https://dev.azure.com/dominikkriegner/xrayutilities/_build/latest?definitionId=1&repoName=dkriegner%2Fxrayutilities&branchName=master) |
| 14 | ||
| 15 | 15 | |
| 16 | 16 | xrayutilities is a collection of scripts used to analyze and simulate x-ray |
| 17 | 17 | diffraction data. It consists of a Python package and several routines coded |
| 22 | 22 | diffraction is included. |
| 23 | 23 | |
| 24 | 24 | |
| 25 | Copyright (C) 2009-2020 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 25 | Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 26 | 26 | |
| 27 | 27 | Copyright (C) 2009-2013 Eugen Wintersberger <eugen.wintersberger@desy.de> |
| 28 | 28 | |
| 45 | 45 | * *lib/xrayutilities*: directory with the sources for the Python package |
| 46 | 46 | * *tests*: directory with the unittest scripts |
| 47 | 47 | * *setup.py*: setuptools install script used for the package installation |
| 48 | * *xrayutilities.pdf*: pdf-file with documentation of the package | |
| 49 | 48 | |
| 50 | 49 | |
| 51 | 50 | Installation (pip) |
| 110 | 109 | - sphinx (optional - only when you want to build the documentation) |
| 111 | 110 | - numpydoc (optional - only when you want to build the documentation) |
| 112 | 111 | - rst2pdf (optional - only when you want to build the documentation) |
| 112 | - sphinx_rtd_theme (optional - only when you want to build the documentation) | |
| 113 | - svglib (optional - only when you want to build the pdf documentation) | |
| 113 | 114 | |
| 114 | 115 | refer to your operating system documentation to find out how to install |
| 115 | 116 | those packages. On Microsoft Windows refer to the Documentation for the |
| 171 | 172 | git pull |
| 172 | 173 | |
| 173 | 174 | or download the new tarball from sourceforge |
| 174 | (http://sf.net/projects/xrayutilities) if any code changed during the update you | |
| 175 | (https://sf.net/projects/xrayutilities) if any code changed during the update you | |
| 175 | 176 | need to reinstall the Python package. Thats easiest achieved by |
| 176 | 177 | |
| 177 | 178 | pip install . |
| 193 | 194 | Documentation |
| 194 | 195 | ============= |
| 195 | 196 | |
| 196 | Documentation for xrayutilities is found in the *xrayutilities.pdf* file or on the | |
| 197 | webpage http://xrayutilities.sourceforge.io | |
| 197 | Documentation for xrayutilities is found on the webpage | |
| 198 | https://xrayutilities.sourceforge.io | |
| 198 | 199 | |
| 199 | 200 | The API-documentation can also be browsed by |
| 200 | 201 | |
| 207 | 208 | Classifier: Programming Language :: Python :: 3.6 |
| 208 | 209 | Classifier: Programming Language :: Python :: 3.7 |
| 209 | 210 | Classifier: Programming Language :: Python :: 3.8 |
| 211 | Classifier: Programming Language :: Python :: 3.9 | |
| 210 | 212 | Classifier: Topic :: Scientific/Engineering :: Physics |
| 211 | 213 | Classifier: Intended Audience :: Science/Research |
| 212 | 214 | Classifier: Development Status :: 5 - Production/Stable |
| 215 | 217 | Description-Content-Type: text/markdown |
| 216 | 218 | Provides-Extra: plot |
| 217 | 219 | Provides-Extra: fit |
| 218 | Provides-Extra: lzma | |
| 0 | 0 | xrayutilities |
| 1 | 1 | ============= |
| 2 | 2 | |
| 3 | ||
| 3 | 4 | [](https://dev.azure.com/dominikkriegner/xrayutilities/_build/latest?definitionId=1&repoName=dkriegner%2Fxrayutilities&branchName=master) |
| 4 | ||
| 5 | 5 | |
| 6 | 6 | xrayutilities is a collection of scripts used to analyze and simulate x-ray |
| 7 | 7 | diffraction data. It consists of a Python package and several routines coded |
| 12 | 12 | diffraction is included. |
| 13 | 13 | |
| 14 | 14 | |
| 15 | Copyright (C) 2009-2020 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 15 | Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 16 | 16 | |
| 17 | 17 | Copyright (C) 2009-2013 Eugen Wintersberger <eugen.wintersberger@desy.de> |
| 18 | 18 | |
| 35 | 35 | * *lib/xrayutilities*: directory with the sources for the Python package |
| 36 | 36 | * *tests*: directory with the unittest scripts |
| 37 | 37 | * *setup.py*: setuptools install script used for the package installation |
| 38 | * *xrayutilities.pdf*: pdf-file with documentation of the package | |
| 39 | 38 | |
| 40 | 39 | |
| 41 | 40 | Installation (pip) |
| 100 | 99 | - sphinx (optional - only when you want to build the documentation) |
| 101 | 100 | - numpydoc (optional - only when you want to build the documentation) |
| 102 | 101 | - rst2pdf (optional - only when you want to build the documentation) |
| 102 | - sphinx_rtd_theme (optional - only when you want to build the documentation) | |
| 103 | - svglib (optional - only when you want to build the pdf documentation) | |
| 103 | 104 | |
| 104 | 105 | refer to your operating system documentation to find out how to install |
| 105 | 106 | those packages. On Microsoft Windows refer to the Documentation for the |
| 161 | 162 | git pull |
| 162 | 163 | |
| 163 | 164 | or download the new tarball from sourceforge |
| 164 | (http://sf.net/projects/xrayutilities) if any code changed during the update you | |
| 165 | (https://sf.net/projects/xrayutilities) if any code changed during the update you | |
| 165 | 166 | need to reinstall the Python package. Thats easiest achieved by |
| 166 | 167 | |
| 167 | 168 | pip install . |
| 183 | 184 | Documentation |
| 184 | 185 | ============= |
| 185 | 186 | |
| 186 | Documentation for xrayutilities is found in the *xrayutilities.pdf* file or on the | |
| 187 | webpage http://xrayutilities.sourceforge.io | |
| 187 | Documentation for xrayutilities is found on the webpage | |
| 188 | https://xrayutilities.sourceforge.io | |
| 188 | 189 | |
| 189 | 190 | The API-documentation can also be browsed by |
| 190 | 191 | |
| 0 | name: $(BuildDefinitionName)_$(Date:yyyyMMdd)$(Rev:.rr) | |
| 1 | ||
| 2 | resources: | |
| 3 | repositories: | |
| 4 | - repository: tox | |
| 5 | type: github | |
| 6 | endpoint: github | |
| 7 | name: tox-dev/azure-pipelines-template | |
| 8 | ref: master | |
| 9 | ||
| 10 | jobs: | |
| 11 | - template: run-tox-env.yml@tox | |
| 12 | parameters: | |
| 13 | tox_version: 'tox tox-wheel' | |
| 14 | jobs: | |
| 15 | py39: | |
| 16 | before: | |
| 17 | - task: Cache@2 | |
| 18 | inputs: | |
| 19 | key: testdata20190812 | |
| 20 | path: $(System.DefaultWorkingDirectory)/tests/data | |
| 21 | cacheHitVar: TESTDATA_RESTORED | |
| 22 | displayName: Cache test data | |
| 23 | - script: | | |
| 24 | curl -s -L https://sourceforge.net/projects/xrayutilities/files/xrayutilities-testdata-20190812.tar.gz -o xu_testdata.tar.gz | |
| 25 | tar xzf xu_testdata.tar.gz -C tests | |
| 26 | condition: ne(variables.TESTDATA_RESTORED, 'true') | |
| 27 | displayName: Download test data | |
| 28 | after: | |
| 29 | - publish: $(System.DefaultWorkingDirectory)/dist/ | |
| 30 | artifact: Python $(Agent.JobName) wheel package | |
| 31 | image: [linux, windows, macOs] | |
| 32 | py38: | |
| 33 | image: [linux, windows, macOs] | |
| 34 | after: | |
| 35 | - publish: $(System.DefaultWorkingDirectory)/dist/ | |
| 36 | artifact: Python $(Agent.JobName) wheel package | |
| 37 | py37: | |
| 38 | image: [linux, windows, macOs] | |
| 39 | after: | |
| 40 | - publish: $(System.DefaultWorkingDirectory)/dist/ | |
| 41 | artifact: Python $(Agent.JobName) wheel package | |
| 42 | py36: | |
| 43 | image: [linux, windows, macOs] | |
| 44 | after: | |
| 45 | - publish: $(System.DefaultWorkingDirectory)/dist/ | |
| 46 | artifact: Python $(Agent.JobName) wheel package | |
| 47 | coverage: | |
| 48 | with_toxenv: 'coverage' | |
| 49 | for_envs: [py36, py37, py38, py39] | |
| 50 | ||
| 51 | schedules: | |
| 52 | - cron: "0 12 * * 0" | |
| 53 | displayName: Weekly build | |
| 54 | branches: | |
| 55 | include: | |
| 56 | - master | |
| 57 | always: true |
| 0 | ||
| 1 | xrayutilities | |
| 2 | ============= | |
| 3 | ||
| 4 | **a package with useful scripts for X-ray diffraction** | |
| 5 | ||
| 6 | ||
| 7 | Copyright (C) 2009-2020 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 8 | ||
| 9 | Copyright (C) 2009-2013 Eugen Wintersberger <eugen.wintersberger@desy.de> | |
| 10 | ||
| 11 | ||
| 12 | Obtaining the source code | |
| 13 | ========================= | |
| 14 | ||
| 15 | The sources are hosted on | |
| 16 | `github.com | |
| 17 | <https://github.com/dkriegner/xrayutilities>`_ in are made available | |
| 18 | as tarballs from time to time on | |
| 19 | `github | |
| 20 | <https://github.com/dkriegner/xrayutilities/releases>`_ and | |
| 21 | `sourceforge.net | |
| 22 | <https://sourceforge.net/projects/xrayutilities/files/>`_ | |
| 23 | ||
| 24 | Download the latest tarball or use: | |
| 25 | ||
| 26 | git clone https://github.com/dkriegner/xrayutilities.git | |
| 27 | ||
| 28 | ||
| 29 | to clone the git repository. If you would like to have commit rights | |
| 30 | contact one of the administrators. | |
| 31 | ||
| 32 | ||
| 33 | Installation | |
| 34 | ============ | |
| 35 | ||
| 36 | Installing xrayutilities is a two step process. A few notes on how to install | |
| 37 | on the various can be found in the README shipped with the package's sources. | |
| 38 | ||
| 39 | 1. installing required third party software | |
| 40 | requirements are: | |
| 41 | ||
| 42 | - C-compiler | |
| 43 | - h5py (for HDF5 file access) | |
| 44 | - scipy | |
| 45 | - numpy | |
| 46 | - matplotlib (optionally) | |
| 47 | ||
| 48 | refer to your operating system documentation to find out how to install | |
| 49 | those packages. On Windows we suggest to use Python(x,y) | |
| 50 | ||
| 51 | 2. install *xrayutilities* using | |
| 52 | ||
| 53 | pip install . | |
| 54 | ||
| 55 | ||
| 56 | For details of how to setup your Python installation to find xrayutilities | |
| 57 | after the installation please refer to the documention. | |
| 58 |
| 32 | 32 | # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. |
| 33 | 33 | extensions = [ |
| 34 | 34 | 'sphinx.ext.autodoc', |
| 35 | 'sphinx.ext.autosummary', | |
| 36 | 35 | 'sphinx.ext.coverage', |
| 37 | 36 | 'sphinx.ext.mathjax', |
| 38 | 37 | 'sphinx.ext.viewcode', |
| 53 | 52 | |
| 54 | 53 | # General information about the project. |
| 55 | 54 | project = 'xrayutilities' |
| 56 | copyright = '2020, Dominik Kriegner, Eugen Wintersberger' | |
| 55 | copyright = '2021, Dominik Kriegner, Eugen Wintersberger' | |
| 57 | 56 | |
| 58 | 57 | # The version info for the project you're documenting, acts as replacement for |
| 59 | 58 | # |version| and |release|, also used in various other places throughout the |
| 61 | 60 | # |
| 62 | 61 | moduleroot = os.path.join('..', '..', 'lib', 'xrayutilities') |
| 63 | 62 | with open(os.path.join(moduleroot, 'VERSION')) as version_file: |
| 64 | fullversion = version_file.read().strip() | |
| 63 | fullversion = version_file.read().strip().replace('\n', '.') | |
| 65 | 64 | # The short X.Y version. |
| 66 | 65 | version = re.match(r'^(\d+\.)?(\d+)?', fullversion).group() |
| 67 | 66 | # The full version, including alpha/beta/rc tags. |
| 366 | 365 | # pdf_fit_background_mode = 'scale' |
| 367 | 366 | |
| 368 | 367 | |
| 369 | # my additions for pre-processing the docstring | |
| 370 | 368 | def process_docstring(app, what, name, obj, options, lines): |
| 369 | """my additions for pre-processing the docstring""" | |
| 371 | 370 | # insert note block |
| 372 | 371 | for i in range(len(lines)): |
| 373 | 372 | lines[i] = re.sub(r'^\s*Note:', r'.. note::', lines[i]) |
| 374 | 373 | |
| 374 | def skip(app, what, name, obj, would_skip, options): | |
| 375 | """always document __init__ and __call__ functions""" | |
| 376 | if name in ["__init__", "__call__"]: | |
| 377 | return False | |
| 378 | return would_skip | |
| 375 | 379 | |
| 376 | 380 | def setup(app): |
| 377 | 381 | app.connect('autodoc-process-docstring', process_docstring) |
| 382 | app.connect("autodoc-skip-member", skip) | |
| 5 | 5 | Examples |
| 6 | 6 | ======== |
| 7 | 7 | |
| 8 | In the following a few code-snippets are shown which should help you getting started with *xrayutilities*. Not all of the codes shown in the following will be run-able as stand-alone script. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory in the download found `here <https://sourceforge.net/projects/xrayutilities>`_. | |
| 8 | In the following a few code-snippets are shown which should help you getting started with *xrayutilities*. Not all of the codes shown in the following will be run-able as stand-alone script. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ or in the `download <https://sourceforge.net/projects/xrayutilities>`_. | |
| 9 | 9 | |
| 10 | 10 | |
| 11 | 11 | Reading data from data files |
| 575 | 575 | # levels can be changed in the config file as well |
| 576 | 576 | verbosity = 1 |
| 577 | 577 | |
| 578 | # default wavelength in Angstrom, | |
| 578 | # default wavelength in angstrom, | |
| 579 | 579 | wavelength = MoKa1 # Molybdenum K alpha1 radiation (17479.374eV) |
| 580 | 580 | |
| 581 | 581 | # default energy in eV |
| 664 | 664 | |
| 665 | 665 | * sample tilt angle in degree |
| 666 | 666 | * sample tilt azimuth in degree |
| 667 | * and the x-ray wavelength in Angstrom | |
| 667 | * and the x-ray wavelength in angstrom | |
| 668 | 668 | |
| 669 | 669 | .. literalinclude:: example_xu_ccd_parameter_hkl.py |
| 670 | 670 | :linenos: |
| 193 | 193 | * **sphinx** the Python documentation generator |
| 194 | 194 | * **numpydoc** sphinx-extension needed to parse the API-documention |
| 195 | 195 | * **rst2pdf** pdf-generation using sphinx |
| 196 | * **sphinx_rtd_theme** sphinx theme used | |
| 197 | * **svglib** library needed by rst2pdf to include svg images into the pdf documentation | |
| 196 | 198 | |
| 197 | 199 | After installing all required packages you can continue with installing and |
| 198 | 200 | building the C library. |
| 5 | 5 | Simulation examples |
| 6 | 6 | =================== |
| 7 | 7 | |
| 8 | In the following a few code-snippets are shown which should help you getting started with reflectivity and diffraction simulations using *xrayutilities*. All simulations in *xrayutilities* are for layers systems and currently there are no plans to extend this to other geometries. Note that not all of the codes shown in the following will be run-able as stand-alone scripts. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory in the download found `here <https://sourceforge.net/projects/xrayutilities>`_. | |
| 8 | In the following a few code-snippets are shown which should help you getting started with reflectivity and diffraction simulations using *xrayutilities*. All simulations in *xrayutilities* are for layers systems and currently there are no plans to extend this to other geometries. Note that not all of the codes shown in the following will be run-able as stand-alone scripts. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory in the `download <https://sourceforge.net/projects/xrayutilities>`_. | |
| 9 | 9 | |
| 10 | 10 | Building Layer stacks for simulations |
| 11 | 11 | ------------------------------------- |
| 357 | 357 | |
| 358 | 358 | Powder diffraction patterns can be calculated using :class:`~xrayutilities.simpack.powdermodel.PowderModel`. A specialized class for the definition of powdered materials named :class:`~xrayutilities.simpack.smaterials.Powder` exists. The class constructor takes the materials volume and several material parameters specific for the powder material. Among them are `crystallite_size_gauss` and `strain_gauss` which can be used to include the effect of finite crystallite size and microstrain. Texture modelled by the March-Dollase pole density offers the `preferred_orientation` direction parameter as well as a `preferred_orientation_factor` variable. |
| 359 | 359 | |
| 360 | The :class:`~xrayutilities.simpack.powdermodel.PowderModel` internally uses :class:`~xrayutilities.simpack.powder.PowderDiffraction` for its calculations which is based on the fundamental parameters approach as implemented and documented `here <http://dx.doi.org/10.6028/jres.120.014.c>`_ and `here <http://dx.doi.org/10.6028/jres.120.014>`_. | |
| 360 | The :class:`~xrayutilities.simpack.powdermodel.PowderModel` internally uses :class:`~xrayutilities.simpack.powder.PowderDiffraction` for its calculations which is based on the fundamental parameters approach. The fundamental parameters approach code used here can was originally implemented and documented here: `http://dx.doi.org/10.6028/jres. 120.014.c <http://dx.doi.org/10.6028/jres.120.014.c>`_ and `http://dx.doi.org/10.6028/jres.120.014 <http://dx.doi.org/10.6028/jres.120.014>`_. | |
| 361 | 361 | |
| 362 | 362 | Several setup specific parameters should be adjusted by a user-specific configuration file or by supplying the appropriate parameters using the `fpsettings` argument of :class:`~xrayutilities.simpack.powdermodel.PowderModel`. |
| 363 | 363 | |
| 0 | xrayutilities.analysis package | |
| 1 | ============================== | |
| 2 | ||
| 3 | Submodules | |
| 4 | ---------- | |
| 5 | ||
| 6 | xrayutilities.analysis.line\_cuts module | |
| 7 | ---------------------------------------- | |
| 8 | ||
| 9 | .. automodule:: xrayutilities.analysis.line_cuts | |
| 10 | :members: | |
| 11 | :undoc-members: | |
| 12 | :show-inheritance: | |
| 13 | ||
| 14 | xrayutilities.analysis.misc module | |
| 15 | ---------------------------------- | |
| 16 | ||
| 17 | .. automodule:: xrayutilities.analysis.misc | |
| 18 | :members: | |
| 19 | :undoc-members: | |
| 20 | :show-inheritance: | |
| 21 | ||
| 22 | xrayutilities.analysis.sample\_align module | |
| 23 | ------------------------------------------- | |
| 24 | ||
| 25 | .. automodule:: xrayutilities.analysis.sample_align | |
| 26 | :members: | |
| 27 | :undoc-members: | |
| 28 | :show-inheritance: | |
| 29 | ||
| 30 | Module contents | |
| 31 | --------------- | |
| 32 | ||
| 33 | .. automodule:: xrayutilities.analysis | |
| 34 | :members: | |
| 35 | :undoc-members: | |
| 36 | :show-inheritance: |
| 0 | xrayutilities.io package | |
| 1 | ======================== | |
| 2 | ||
| 3 | Submodules | |
| 4 | ---------- | |
| 5 | ||
| 6 | xrayutilities.io.cbf module | |
| 7 | --------------------------- | |
| 8 | ||
| 9 | .. automodule:: xrayutilities.io.cbf | |
| 10 | :members: | |
| 11 | :undoc-members: | |
| 12 | :show-inheritance: | |
| 13 | ||
| 14 | xrayutilities.io.desy\_tty08 module | |
| 15 | ----------------------------------- | |
| 16 | ||
| 17 | .. automodule:: xrayutilities.io.desy_tty08 | |
| 18 | :members: | |
| 19 | :undoc-members: | |
| 20 | :show-inheritance: | |
| 21 | ||
| 22 | xrayutilities.io.edf module | |
| 23 | --------------------------- | |
| 24 | ||
| 25 | .. automodule:: xrayutilities.io.edf | |
| 26 | :members: | |
| 27 | :undoc-members: | |
| 28 | :show-inheritance: | |
| 29 | ||
| 30 | xrayutilities.io.fastscan module | |
| 31 | -------------------------------- | |
| 32 | ||
| 33 | .. automodule:: xrayutilities.io.fastscan | |
| 34 | :members: | |
| 35 | :undoc-members: | |
| 36 | :show-inheritance: | |
| 37 | ||
| 38 | xrayutilities.io.filedir module | |
| 39 | ------------------------------- | |
| 40 | ||
| 41 | .. automodule:: xrayutilities.io.filedir | |
| 42 | :members: | |
| 43 | :undoc-members: | |
| 44 | :show-inheritance: | |
| 45 | ||
| 46 | xrayutilities.io.helper module | |
| 47 | ------------------------------ | |
| 48 | ||
| 49 | .. automodule:: xrayutilities.io.helper | |
| 50 | :members: | |
| 51 | :undoc-members: | |
| 52 | :show-inheritance: | |
| 53 | ||
| 54 | xrayutilities.io.ill\_numor module | |
| 55 | ---------------------------------- | |
| 56 | ||
| 57 | .. automodule:: xrayutilities.io.ill_numor | |
| 58 | :members: | |
| 59 | :undoc-members: | |
| 60 | :show-inheritance: | |
| 61 | ||
| 62 | xrayutilities.io.imagereader module | |
| 63 | ----------------------------------- | |
| 64 | ||
| 65 | .. automodule:: xrayutilities.io.imagereader | |
| 66 | :members: | |
| 67 | :undoc-members: | |
| 68 | :show-inheritance: | |
| 69 | ||
| 70 | xrayutilities.io.panalytical\_xml module | |
| 71 | ---------------------------------------- | |
| 72 | ||
| 73 | .. automodule:: xrayutilities.io.panalytical_xml | |
| 74 | :members: | |
| 75 | :undoc-members: | |
| 76 | :show-inheritance: | |
| 77 | ||
| 78 | xrayutilities.io.pdcif module | |
| 79 | ----------------------------- | |
| 80 | ||
| 81 | .. automodule:: xrayutilities.io.pdcif | |
| 82 | :members: | |
| 83 | :undoc-members: | |
| 84 | :show-inheritance: | |
| 85 | ||
| 86 | xrayutilities.io.rigaku\_ras module | |
| 87 | ----------------------------------- | |
| 88 | ||
| 89 | .. automodule:: xrayutilities.io.rigaku_ras | |
| 90 | :members: | |
| 91 | :undoc-members: | |
| 92 | :show-inheritance: | |
| 93 | ||
| 94 | xrayutilities.io.rotanode\_alignment module | |
| 95 | ------------------------------------------- | |
| 96 | ||
| 97 | .. automodule:: xrayutilities.io.rotanode_alignment | |
| 98 | :members: | |
| 99 | :undoc-members: | |
| 100 | :show-inheritance: | |
| 101 | ||
| 102 | xrayutilities.io.seifert module | |
| 103 | ------------------------------- | |
| 104 | ||
| 105 | .. automodule:: xrayutilities.io.seifert | |
| 106 | :members: | |
| 107 | :undoc-members: | |
| 108 | :show-inheritance: | |
| 109 | ||
| 110 | xrayutilities.io.spec module | |
| 111 | ---------------------------- | |
| 112 | ||
| 113 | .. automodule:: xrayutilities.io.spec | |
| 114 | :members: | |
| 115 | :undoc-members: | |
| 116 | :show-inheritance: | |
| 117 | ||
| 118 | xrayutilities.io.spectra module | |
| 119 | ------------------------------- | |
| 120 | ||
| 121 | .. automodule:: xrayutilities.io.spectra | |
| 122 | :members: | |
| 123 | :undoc-members: | |
| 124 | :show-inheritance: | |
| 125 | ||
| 126 | Module contents | |
| 127 | --------------- | |
| 128 | ||
| 129 | .. automodule:: xrayutilities.io | |
| 130 | :members: | |
| 131 | :undoc-members: | |
| 132 | :show-inheritance: |
| 0 | xrayutilities.materials package | |
| 1 | =============================== | |
| 2 | ||
| 3 | Submodules | |
| 4 | ---------- | |
| 5 | ||
| 6 | xrayutilities.materials.atom module | |
| 7 | ----------------------------------- | |
| 8 | ||
| 9 | .. automodule:: xrayutilities.materials.atom | |
| 10 | :members: | |
| 11 | :undoc-members: | |
| 12 | :show-inheritance: | |
| 13 | ||
| 14 | xrayutilities.materials.cif module | |
| 15 | ---------------------------------- | |
| 16 | ||
| 17 | .. automodule:: xrayutilities.materials.cif | |
| 18 | :members: | |
| 19 | :undoc-members: | |
| 20 | :show-inheritance: | |
| 21 | ||
| 22 | xrayutilities.materials.database module | |
| 23 | --------------------------------------- | |
| 24 | ||
| 25 | .. automodule:: xrayutilities.materials.database | |
| 26 | :members: | |
| 27 | :undoc-members: | |
| 28 | :show-inheritance: | |
| 29 | ||
| 30 | xrayutilities.materials.elements module | |
| 31 | --------------------------------------- | |
| 32 | ||
| 33 | .. automodule:: xrayutilities.materials.elements | |
| 34 | :members: | |
| 35 | :undoc-members: | |
| 36 | :show-inheritance: | |
| 37 | ||
| 38 | xrayutilities.materials.heuslerlib module | |
| 39 | ----------------------------------------- | |
| 40 | ||
| 41 | .. automodule:: xrayutilities.materials.heuslerlib | |
| 42 | :members: | |
| 43 | :undoc-members: | |
| 44 | :show-inheritance: | |
| 45 | ||
| 46 | xrayutilities.materials.material module | |
| 47 | --------------------------------------- | |
| 48 | ||
| 49 | .. automodule:: xrayutilities.materials.material | |
| 50 | :members: | |
| 51 | :undoc-members: | |
| 52 | :show-inheritance: | |
| 53 | ||
| 54 | xrayutilities.materials.plot module | |
| 55 | ----------------------------------- | |
| 56 | ||
| 57 | .. automodule:: xrayutilities.materials.plot | |
| 58 | :members: | |
| 59 | :undoc-members: | |
| 60 | :show-inheritance: | |
| 61 | ||
| 62 | xrayutilities.materials.predefined\_materials module | |
| 63 | ---------------------------------------------------- | |
| 64 | ||
| 65 | .. automodule:: xrayutilities.materials.predefined_materials | |
| 66 | :members: | |
| 67 | :undoc-members: | |
| 68 | :show-inheritance: | |
| 69 | ||
| 70 | xrayutilities.materials.spacegrouplattice module | |
| 71 | ------------------------------------------------ | |
| 72 | ||
| 73 | .. automodule:: xrayutilities.materials.spacegrouplattice | |
| 74 | :members: | |
| 75 | :undoc-members: | |
| 76 | :show-inheritance: | |
| 77 | ||
| 78 | xrayutilities.materials.wyckpos module | |
| 79 | -------------------------------------- | |
| 80 | ||
| 81 | .. automodule:: xrayutilities.materials.wyckpos | |
| 82 | :members: | |
| 83 | :undoc-members: | |
| 84 | :show-inheritance: | |
| 85 | ||
| 86 | Module contents | |
| 87 | --------------- | |
| 88 | ||
| 89 | .. automodule:: xrayutilities.materials | |
| 90 | :members: | |
| 91 | :undoc-members: | |
| 92 | :show-inheritance: |
| 0 | xrayutilities.math package | |
| 1 | ========================== | |
| 2 | ||
| 3 | Submodules | |
| 4 | ---------- | |
| 5 | ||
| 6 | xrayutilities.math.algebra module | |
| 7 | --------------------------------- | |
| 8 | ||
| 9 | .. automodule:: xrayutilities.math.algebra | |
| 10 | :members: | |
| 11 | :undoc-members: | |
| 12 | :show-inheritance: | |
| 13 | ||
| 14 | xrayutilities.math.fit module | |
| 15 | ----------------------------- | |
| 16 | ||
| 17 | .. automodule:: xrayutilities.math.fit | |
| 18 | :members: | |
| 19 | :undoc-members: | |
| 20 | :show-inheritance: | |
| 21 | ||
| 22 | xrayutilities.math.functions module | |
| 23 | ----------------------------------- | |
| 24 | ||
| 25 | .. automodule:: xrayutilities.math.functions | |
| 26 | :members: | |
| 27 | :undoc-members: | |
| 28 | :show-inheritance: | |
| 29 | ||
| 30 | xrayutilities.math.misc module | |
| 31 | ------------------------------ | |
| 32 | ||
| 33 | .. automodule:: xrayutilities.math.misc | |
| 34 | :members: | |
| 35 | :undoc-members: | |
| 36 | :show-inheritance: | |
| 37 | ||
| 38 | xrayutilities.math.transforms module | |
| 39 | ------------------------------------ | |
| 40 | ||
| 41 | .. automodule:: xrayutilities.math.transforms | |
| 42 | :members: | |
| 43 | :undoc-members: | |
| 44 | :show-inheritance: | |
| 45 | ||
| 46 | xrayutilities.math.vector module | |
| 47 | -------------------------------- | |
| 48 | ||
| 49 | .. automodule:: xrayutilities.math.vector | |
| 50 | :members: | |
| 51 | :undoc-members: | |
| 52 | :show-inheritance: | |
| 53 | ||
| 54 | Module contents | |
| 55 | --------------- | |
| 56 | ||
| 57 | .. automodule:: xrayutilities.math | |
| 58 | :members: | |
| 59 | :undoc-members: | |
| 60 | :show-inheritance: |
| 0 | xrayutilities package | |
| 1 | ===================== | |
| 2 | ||
| 3 | Subpackages | |
| 4 | ----------- | |
| 5 | ||
| 6 | .. toctree:: | |
| 7 | :maxdepth: 4 | |
| 8 | ||
| 9 | xrayutilities.analysis | |
| 10 | xrayutilities.io | |
| 11 | xrayutilities.materials | |
| 12 | xrayutilities.math | |
| 13 | xrayutilities.simpack | |
| 14 | ||
| 15 | Submodules | |
| 16 | ---------- | |
| 17 | ||
| 18 | xrayutilities.config module | |
| 19 | --------------------------- | |
| 20 | ||
| 21 | .. automodule:: xrayutilities.config | |
| 22 | :members: | |
| 23 | :undoc-members: | |
| 24 | :show-inheritance: | |
| 25 | ||
| 26 | xrayutilities.exception module | |
| 27 | ------------------------------ | |
| 28 | ||
| 29 | .. automodule:: xrayutilities.exception | |
| 30 | :members: | |
| 31 | :undoc-members: | |
| 32 | :show-inheritance: | |
| 33 | ||
| 34 | xrayutilities.experiment module | |
| 35 | ------------------------------- | |
| 36 | ||
| 37 | .. automodule:: xrayutilities.experiment | |
| 38 | :members: | |
| 39 | :undoc-members: | |
| 40 | :show-inheritance: | |
| 41 | ||
| 42 | xrayutilities.gridder module | |
| 43 | ---------------------------- | |
| 44 | ||
| 45 | .. automodule:: xrayutilities.gridder | |
| 46 | :members: | |
| 47 | :undoc-members: | |
| 48 | :show-inheritance: | |
| 49 | ||
| 50 | xrayutilities.gridder2d module | |
| 51 | ------------------------------ | |
| 52 | ||
| 53 | .. automodule:: xrayutilities.gridder2d | |
| 54 | :members: | |
| 55 | :undoc-members: | |
| 56 | :show-inheritance: | |
| 57 | ||
| 58 | xrayutilities.gridder3d module | |
| 59 | ------------------------------ | |
| 60 | ||
| 61 | .. automodule:: xrayutilities.gridder3d | |
| 62 | :members: | |
| 63 | :undoc-members: | |
| 64 | :show-inheritance: | |
| 65 | ||
| 66 | xrayutilities.mpl\_helper module | |
| 67 | -------------------------------- | |
| 68 | ||
| 69 | .. automodule:: xrayutilities.mpl_helper | |
| 70 | :members: | |
| 71 | :undoc-members: | |
| 72 | :show-inheritance: | |
| 73 | ||
| 74 | xrayutilities.normalize module | |
| 75 | ------------------------------ | |
| 76 | ||
| 77 | .. automodule:: xrayutilities.normalize | |
| 78 | :members: | |
| 79 | :undoc-members: | |
| 80 | :show-inheritance: | |
| 81 | ||
| 82 | xrayutilities.q2ang\_fit module | |
| 83 | ------------------------------- | |
| 84 | ||
| 85 | .. automodule:: xrayutilities.q2ang_fit | |
| 86 | :members: | |
| 87 | :undoc-members: | |
| 88 | :show-inheritance: | |
| 89 | ||
| 90 | xrayutilities.utilities module | |
| 91 | ------------------------------ | |
| 92 | ||
| 93 | .. automodule:: xrayutilities.utilities | |
| 94 | :members: | |
| 95 | :undoc-members: | |
| 96 | :show-inheritance: | |
| 97 | ||
| 98 | xrayutilities.utilities\_noconf module | |
| 99 | -------------------------------------- | |
| 100 | ||
| 101 | .. automodule:: xrayutilities.utilities_noconf | |
| 102 | :members: | |
| 103 | :undoc-members: | |
| 104 | :show-inheritance: | |
| 105 | ||
| 106 | Module contents | |
| 107 | --------------- | |
| 108 | ||
| 109 | .. automodule:: xrayutilities | |
| 110 | :members: | |
| 111 | :undoc-members: | |
| 112 | :show-inheritance: |
| 0 | xrayutilities.simpack package | |
| 1 | ============================= | |
| 2 | ||
| 3 | Submodules | |
| 4 | ---------- | |
| 5 | ||
| 6 | xrayutilities.simpack.darwin\_theory module | |
| 7 | ------------------------------------------- | |
| 8 | ||
| 9 | .. automodule:: xrayutilities.simpack.darwin_theory | |
| 10 | :members: | |
| 11 | :undoc-members: | |
| 12 | :show-inheritance: | |
| 13 | ||
| 14 | xrayutilities.simpack.fit module | |
| 15 | -------------------------------- | |
| 16 | ||
| 17 | .. automodule:: xrayutilities.simpack.fit | |
| 18 | :members: | |
| 19 | :undoc-members: | |
| 20 | :show-inheritance: | |
| 21 | ||
| 22 | xrayutilities.simpack.helpers module | |
| 23 | ------------------------------------ | |
| 24 | ||
| 25 | .. automodule:: xrayutilities.simpack.helpers | |
| 26 | :members: | |
| 27 | :undoc-members: | |
| 28 | :show-inheritance: | |
| 29 | ||
| 30 | xrayutilities.simpack.models module | |
| 31 | ----------------------------------- | |
| 32 | ||
| 33 | .. automodule:: xrayutilities.simpack.models | |
| 34 | :members: | |
| 35 | :undoc-members: | |
| 36 | :show-inheritance: | |
| 37 | ||
| 38 | xrayutilities.simpack.mosaicity module | |
| 39 | -------------------------------------- | |
| 40 | ||
| 41 | .. automodule:: xrayutilities.simpack.mosaicity | |
| 42 | :members: | |
| 43 | :undoc-members: | |
| 44 | :show-inheritance: | |
| 45 | ||
| 46 | xrayutilities.simpack.powder module | |
| 47 | ----------------------------------- | |
| 48 | ||
| 49 | .. automodule:: xrayutilities.simpack.powder | |
| 50 | :members: | |
| 51 | :undoc-members: | |
| 52 | :show-inheritance: | |
| 53 | ||
| 54 | xrayutilities.simpack.powdermodel module | |
| 55 | ---------------------------------------- | |
| 56 | ||
| 57 | .. automodule:: xrayutilities.simpack.powdermodel | |
| 58 | :members: | |
| 59 | :undoc-members: | |
| 60 | :show-inheritance: | |
| 61 | ||
| 62 | xrayutilities.simpack.smaterials module | |
| 63 | --------------------------------------- | |
| 64 | ||
| 65 | .. automodule:: xrayutilities.simpack.smaterials | |
| 66 | :members: | |
| 67 | :undoc-members: | |
| 68 | :show-inheritance: | |
| 69 | ||
| 70 | Module contents | |
| 71 | --------------- | |
| 72 | ||
| 73 | .. automodule:: xrayutilities.simpack | |
| 74 | :members: | |
| 75 | :undoc-members: | |
| 76 | :show-inheritance: |
| 0 | --- build/sphinx/html/index.html.orig 2019-10-09 09:52:01.373904470 +0200 | |
| 1 | +++ build/sphinx/html/index.html 2019-10-09 09:52:53.711409533 +0200 | |
| 2 | @@ -57,7 +57,7 @@ | |
| 3 | ||
| 4 | ||
| 5 | ||
| 6 | - <img src="_static/xray-logo.png" class="logo" alt="Logo"/> | |
| 7 | + <img src="_static/xray-logo.png" class="logo" alt="Logo" style="width: 100%; max-width:265px;"/> | |
| 8 | ||
| 9 | </a> | |
| 10 | ||
| 11 | @@ -165,6 +165,13 @@ | |
| 12 | ||
| 13 | <div class="section" id="welcome-to-xrayutilities-s-documentation"> | |
| 14 | <h1>Welcome to xrayutilities’s documentation!<a class="headerlink" href="#welcome-to-xrayutilities-s-documentation" title="Permalink to this headline">¶</a></h1> | |
| 15 | +<a class="reference external image-reference" href="https://pypi.python.org/pypi/xrayutilities/"><img alt="Latest Version" style="max-height: 25px; max-width:114px;" src="https://img.shields.io/pypi/v/xrayutilities.svg"/></a> | |
| 16 | +<a class="reference external image-reference" href="https://github.com/dkriegner/xrayutilities"><img alt="Git-repo on github" style="max-height: 25px; max-width:144px;" src="https://img.shields.io/badge/development-GIT-green.svg"/></a> | |
| 17 | +<a class="reference external image-reference" href="https://pypi.python.org/pypi/xrayutilities/"><img alt="Supported Python versions" style="max-height: 25px; max-width:193px;" src="https://img.shields.io/pypi/pyversions/xrayutilities.svg" /></a> | |
| 18 | +<a class="reference external image-reference" href="https://pypi.python.org/pypi/xrayutilities/"><img alt="Development Status" style="max-height: 25px; max-width:114px;" src="https://img.shields.io/pypi/status/xrayutilities.svg" /></a> | |
| 19 | +<a class="reference external image-reference" href="https://pypi.python.org/pypi/xrayutilities/"><img alt="License" style="max-height: 25px; max-width:119px;" src="https://img.shields.io/pypi/l/xrayutilities.svg" /></a> | |
| 20 | +<a class="reference external image-reference" href="https://dev.azure.com/dominikkriegner/xrayutilities/_build?definitionId=1"><img alt="Test status" style="max-height: 25px" src="https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=master" /></a> | |
| 21 | + | |
| 22 | <p>If you look for downloading the package go to <a class="reference external" href="https://sourceforge.net/projects/xrayutilities">Sourceforge</a> or <a class="reference external" href="https://github.com/dkriegner/xrayutilities">GitHub</a> (source distribution) or the <a class="reference external" href="https://pypi.python.org/pypi/xrayutilities">Python package index</a> (MS Windows binary).</p> | |
| 23 | <p>Read more about <em>xrayutilities</em> below or in <a class="reference external" href="http://dx.doi.org/10.1107/S0021889813017214">Journal of Applied Crystallography 2013, Volume 46, 1162-1170</a></p> | |
| 24 | </div> | |
| 25 | @@ -724,4 +732,4 @@ | |
| 26 | ||
| 27 | ||
| 28 | </body> | |
| 29 | -</html> | |
| 30 | \ No newline at end of file | |
| 31 | +</html> |
| 39 | 39 | m = xu.simpack.SpecularReflectivityModel(ls) |
| 40 | 40 | pos, eldens = m.densityprofile(500) |
| 41 | 41 | |
| 42 | # slice the layerstack into an Amorphous sublayer at every 0.1 Angstrom. | |
| 42 | # slice the layerstack into an Amorphous sublayer at every 0.1 angstrom. | |
| 43 | 43 | # at the top a vacuum layer is added |
| 44 | 44 | sls = xu.simpack.effectiveDensitySlicing(ls, 0.1) |
| 45 | 45 | ms = xu.simpack.SpecularReflectivityModel(sls) |
| 26 | 26 | """dummy main function to enable multiprocessing on windows""" |
| 27 | 27 | cryst_size = 40e-9 # meter |
| 28 | 28 | |
| 29 | # create Fe BCC (space group nr. 229 Im3m) with a=2.87Angstrom although | |
| 29 | # create Fe BCC (space group nr. 229 Im3m) with a = 2.87 angstrom although | |
| 30 | 30 | # this is already predefined as xu.materials.Fe we will repeat here for |
| 31 | 31 | # educational purposes |
| 32 | 32 | FeBCC = xu.materials.Crystal( |
| 38 | 38 | |
| 39 | 39 | for energy in [8041]: # eV |
| 40 | 40 | |
| 41 | lam = xu.en2lam(energy) # e in eV -> lam in Angstroem | |
| 41 | lam = xu.en2lam(energy) # e in eV -> lam in angstrom | |
| 42 | 42 | print(' %d eV = %8.4f A' % (energy, lam)) |
| 43 | 43 | print('------------------------------------------------------------------' |
| 44 | 44 | '-----------------') |
| 0 | # XRAYUTILITIES user configuration | |
| 1 | # default values for some properties of xrayutilities may be set | |
| 2 | # the syntax follows the one of the ConfigParser Python module, | |
| 3 | # which is similar to .ini files | |
| 4 | ||
| 5 | # if you want to use this user-specific config file you need to place it in | |
| 6 | # ~/.xrayutilities.conf | |
| 7 | # or the local directory | |
| 8 | # ./xrayutilities.conf | |
| 9 | ||
| 10 | # The config file with the default parameters is found in the Python installation | |
| 11 | # path of xrayutilities. It is however not recommended to change things there, | |
| 12 | # instead the user-specific config file | |
| 13 | ||
| 14 | # begin of xrayutilities configuration | |
| 15 | [xrayutilities] | |
| 16 | ||
| 17 | # verbosity level of information and debugging outputs | |
| 18 | # 0: no output | |
| 19 | # 1: very import notes for users | |
| 20 | # 2: less import notes for users (e.g. intermediate results) | |
| 21 | # 3: debuging output (e.g. print everything, which could be interesing) | |
| 22 | verbosity=1 | |
| 23 | ||
| 24 | # default wavelength in Angstrom, | |
| 25 | # wavelength=1.5406 | |
| 26 | ||
| 27 | # default energy in eV | |
| 28 | # if energy is given wavelength settings will be ignored | |
| 29 | # energy=8048 |
| 42 | 42 | |
| 43 | 43 | # load package version |
| 44 | 44 | with open(os.path.join(__path__[0], 'VERSION')) as version_file: |
| 45 | __version__ = version_file.read().strip() | |
| 45 | __version__ = version_file.read().strip().replace('\n', '.') |
| 490 | 490 | matplotlib figure used for plotting the error default: None (creates |
| 491 | 491 | own figure) |
| 492 | 492 | wl : float or str |
| 493 | wavelength of the experiment in Angstrom (default: config.WAVELENGTH) | |
| 493 | wavelength of the experiment in angstrom (default: config.WAVELENGTH) | |
| 494 | 494 | value does not really matter here but does affect the scaling of the |
| 495 | 495 | error |
| 496 | 496 | plotlog : bool |
| 873 | 873 | flag to tell if to return fit object with final parameters and detector |
| 874 | 874 | directions |
| 875 | 875 | wl : float or str |
| 876 | wavelength of the experiment in Angstrom (default: 1) | |
| 876 | wavelength of the experiment in angstrom (default: 1) | |
| 877 | 877 | value does not really matter here but does affect the scaling of the |
| 878 | 878 | error |
| 879 | 879 | debug : bool |
| 938 | 938 | delta must be an numpy array or list of len(*dAngles) used angles |
| 939 | 939 | are than *args - delta |
| 940 | 940 | wl : float or str, optional |
| 941 | x-ray wavelength in angstroem (default: 1 (since it does not matter | |
| 941 | x-ray wavelength in angstrom (default: 1 (since it does not matter | |
| 942 | 942 | here)) |
| 943 | 943 | deg : bool, optional |
| 944 | 944 | flag to tell if angles are passed as degree (default: True) |
| 1108 | 1108 | detector circles e.g. ['z+', 'y-'] would mean a detector arm with a |
| 1109 | 1109 | two rotations |
| 1110 | 1110 | wl : float or str |
| 1111 | wavelength of the experiment in Angstroem | |
| 1111 | wavelength of the experiment in angstrom | |
| 1112 | 1112 | |
| 1113 | 1113 | Returns |
| 1114 | 1114 | ------- |
| 1654 | 1654 | UB : array-like, optional |
| 1655 | 1655 | orientation matrix of the sample |
| 1656 | 1656 | wl : float or str, optional |
| 1657 | x-ray wavelength in angstroem | |
| 1657 | x-ray wavelength in angstrom | |
| 1658 | 1658 | deg : bool, optional |
| 1659 | 1659 | flag to tell if angles are passed as degree (default: True) |
| 1660 | 1660 | |
| 100 | 100 | kwargs : dict, optional |
| 101 | 101 | optional keyword arguments |
| 102 | 102 | wl : float or str, optional |
| 103 | wavelength of the x-rays in Angstroem | |
| 103 | wavelength of the x-rays in angstrom | |
| 104 | 104 | en : float or str, optional |
| 105 | 105 | energy of the x-rays in electronvolt |
| 106 | 106 | UB : array-like, optional |
| 474 | 474 | matrix for conversion from (hkl) coordinates to Q of sample used to |
| 475 | 475 | determine not Q but (hkl) (default: self.UB) |
| 476 | 476 | wl : float or str, optional |
| 477 | x-ray wavelength in angstroem (default: self._wl) | |
| 477 | x-ray wavelength in angstrom (default: self._wl) | |
| 478 | 478 | en : float, optional |
| 479 | 479 | x-ray energy in eV (default is converted self._wl). both wavelength |
| 480 | 480 | and energy can also be an array which enables the QConversion for |
| 554 | 554 | matrix for conversion from (hkl) coordinates to Q of sample used to |
| 555 | 555 | determine not Q but (hkl) (default: self.UB) |
| 556 | 556 | wl : float or str, optional |
| 557 | x-ray wavelength in angstroem (default: self._wl) | |
| 557 | x-ray wavelength in angstrom (default: self._wl) | |
| 558 | 558 | en : float, optional |
| 559 | 559 | x-ray energy in eV (default is converted self._wl). both wavelength |
| 560 | 560 | and energy can also be an array which enables the QConversion for |
| 758 | 758 | region of interest for the detector pixels; e.g. [100, 900] |
| 759 | 759 | (default: self._linear_roi) |
| 760 | 760 | wl : float or str, optional |
| 761 | x-ray wavelength in angstroem (default: self._wl) | |
| 761 | x-ray wavelength in angstrom (default: self._wl) | |
| 762 | 762 | en : float, optional |
| 763 | 763 | x-ray energy in eV (default is converted self._wl). both wavelength |
| 764 | 764 | and energy can also be an array which enables the QConversion for |
| 1008 | 1008 | region of interest for the detector pixels; e.g. |
| 1009 | 1009 | [100, 900, 200, 800] (default: self._area_roi) |
| 1010 | 1010 | wl : float or str, optional |
| 1011 | x-ray wavelength in angstroem (default: self._wl) | |
| 1011 | x-ray wavelength in angstrom (default: self._wl) | |
| 1012 | 1012 | en : float, optional |
| 1013 | 1013 | x-ray energy in eV (default is converted self._wl). both wavelength |
| 1014 | 1014 | and energy can also be an array which enables the QConversion for |
| 1334 | 1334 | inplane reference direction (ipdir points into the primary beam |
| 1335 | 1335 | direction at zero angles) |
| 1336 | 1336 | ndir : list or tuple or array-like |
| 1337 | surface normal of your sample (ndir points in a direction | |
| 1338 | perpendicular to the primary beam and the innermost detector | |
| 1339 | rotation axis) | |
| 1337 | surface normal of your sample. ndir points in a direction | |
| 1338 | perpendicular to the primary beam, how it is orientated in real | |
| 1339 | space is determined by the parameter sampleor (see below). | |
| 1340 | 1340 | |
| 1341 | 1341 | keyargs : dict, optional |
| 1342 | 1342 | optional keyword arguments |
| 1343 | 1343 | qconv : QConversion, optional |
| 1344 | 1344 | QConversion object to use for the Ang2Q conversion |
| 1345 | 1345 | sampleor : {'det', 'sam', '[xyz][+-]'}, optional |
| 1346 | sample orientation specifies the orientation of the sample surface | |
| 1347 | with respect to the coordinate system in which the goniometer | |
| 1348 | rotations are given. You can use the [xyz][+-] syntax to specify | |
| 1349 | the nominal surface orientation (when all goniometer angles are | |
| 1350 | zero). In addition two special values 'det' and 'sam' are | |
| 1351 | available, which will let the code determine the orientation from | |
| 1352 | either the inner most detector or sample rotation. Default is | |
| 1353 | 'det'. | |
| 1346 | determines the sample surface orientation with respect to the | |
| 1347 | coordinate system in which the goniometer rotations are given. You | |
| 1348 | can use the [xyz][+-] syntax to specify the nominal surface | |
| 1349 | orientation (when all goniometer angles are zero). In addition two | |
| 1350 | special values 'det' and 'sam' are available, which will let the | |
| 1351 | code determine the orientation from either the inner most detector | |
| 1352 | or sample rotation. 'det' means the surface is in the plane spanned | |
| 1353 | by the inner most detector rotation (rotation around primary beam | |
| 1354 | is ignored) and perpendicular to the primary beam. 'sam' means the | |
| 1355 | surface orientation is along the innermost sample circles rotation | |
| 1356 | direction (in this case this should be the azimuth motor to yield | |
| 1357 | the expected results). Default is 'det'. | |
| 1358 | Restrictions: the given direction can not be along the primary | |
| 1359 | beam. If one needs that case, let the maintainer know. Currently | |
| 1360 | this case is caught and a different axis is automatically used as | |
| 1361 | z-axis. | |
| 1354 | 1362 | wl : float or str |
| 1355 | wavelength of the x-rays in Angstroem (default: 1.5406A) | |
| 1363 | wavelength of the x-rays in angstrom (default: 1.5406A) | |
| 1356 | 1364 | en : float or str |
| 1357 | 1365 | energy of the x-rays in eV (default: 8048eV == 1.5406A ). |
| 1358 | 1366 | the en keyword overrules the wl keyword |
| 1421 | 1429 | self.ndir[1], |
| 1422 | 1430 | self.ndir[2]) |
| 1423 | 1431 | ostr += "energy: %f (eV)\n" % self._en |
| 1424 | ostr += "wavelength: %f (Anstrom)\n" % (self._wl) | |
| 1432 | ostr += "wavelength: %f (angstrom)\n" % (self._wl) | |
| 1425 | 1433 | ostr += self._A2QConversion.__str__() |
| 1426 | 1434 | |
| 1427 | 1435 | return ostr |
| 1562 | 1570 | delta must be an numpy array or list of length 2. used angles are |
| 1563 | 1571 | than ``(om, tt) - delta`` |
| 1564 | 1572 | wl : float or str, optional |
| 1565 | x-ray wavelength in angstroem (default: self._wl) | |
| 1573 | x-ray wavelength in angstrom (default: self._wl) | |
| 1566 | 1574 | en : float or str, optional |
| 1567 | 1575 | x-ray energy in eV (default: converted self._wl) |
| 1568 | 1576 | deg : bool, optional |
| 1752 | 1760 | matrix for conversion from (hkl) coordinates to Q of sample used to |
| 1753 | 1761 | determine not Q but (hkl) (default: identity matrix) |
| 1754 | 1762 | wl : float or str, optional |
| 1755 | x-ray wavelength in angstroem (default: self._wl) | |
| 1763 | x-ray wavelength in angstrom (default: self._wl) | |
| 1756 | 1764 | deg : bool, optional |
| 1757 | 1765 | flag to tell if angles are passed as degree (default: True) |
| 1758 | 1766 | |
| 2104 | 2112 | matrix for conversion from (hkl) coordinates to Q of sample used to |
| 2105 | 2113 | determine not Q but (hkl) (default: identity matrix) |
| 2106 | 2114 | wl : float or str, optional |
| 2107 | x-ray wavelength in angstroem (default: self._wl) | |
| 2115 | x-ray wavelength in angstrom (default: self._wl) | |
| 2108 | 2116 | deg : bool, optional |
| 2109 | 2117 | flag to tell if angles are passed as degree (default: True) |
| 2110 | 2118 | |
| 2348 | 2356 | matrix for conversion from (hkl) coordinates to Q of sample used to |
| 2349 | 2357 | determine not Q but (hkl) (default: identity matrix) |
| 2350 | 2358 | wl : float or str, optional |
| 2351 | x-ray wavelength in angstroem (default: self._wl) | |
| 2359 | x-ray wavelength in angstrom (default: self._wl) | |
| 2352 | 2360 | deg : bool, optional |
| 2353 | 2361 | flag to tell if angles are passed as degree (default: True) |
| 2354 | 2362 | |
| 2421 | 2429 | matrix for conversion from (hkl) coordinates to Q of sample used to |
| 2422 | 2430 | determine not Q but (hkl) (default: identity matrix) |
| 2423 | 2431 | wl : float or str, optional |
| 2424 | x-ray wavelength in angstroem (default: self._wl) | |
| 2432 | x-ray wavelength in angstrom (default: self._wl) | |
| 2425 | 2433 | deg : bool, optional |
| 2426 | 2434 | flag to tell if angles are passed as degree (default: True) |
| 2427 | 2435 | |
| 158 | 158 | Parameters |
| 159 | 159 | ---------- |
| 160 | 160 | radius: float |
| 161 | atomic radius in Angstrom | |
| 161 | atomic radius in angstrom | |
| 162 | 162 | """ |
| 163 | 163 | if not isinstance(radius, (float, int)): |
| 164 | 164 | raise TypeError("radius parameter must be a number!") |
| 48 | 48 | X, Y, Z : str or Element |
| 49 | 49 | elements |
| 50 | 50 | a : float |
| 51 | cubic lattice parameter in Angstroem | |
| 51 | cubic lattice parameter in angstrom | |
| 52 | 52 | biso : list of floats, optional |
| 53 | 53 | Debye Waller factors for X, Y, Z elements |
| 54 | 54 | occ : list of floats, optional |
| 76 | 76 | X, Y, Z : str or Element |
| 77 | 77 | elements |
| 78 | 78 | a : float |
| 79 | cubic lattice parameter in Angstroem | |
| 79 | cubic lattice parameter in angstrom | |
| 80 | 80 | b2dis : float |
| 81 | 81 | amount of B2-type disorder (0: fully ordered, 1: fully disordered) |
| 82 | 82 | biso : list of floats, optional |
| 111 | 111 | X, Y, Z : str or Element |
| 112 | 112 | elements |
| 113 | 113 | a : float |
| 114 | cubic lattice parameter in Angstroem | |
| 114 | cubic lattice parameter in angstrom | |
| 115 | 115 | a2dis : float |
| 116 | 116 | amount of A2-type disorder (0: fully ordered, 1: fully disordered) |
| 117 | 117 | biso : list of floats, optional |
| 151 | 151 | X, Y, Z : str or Element |
| 152 | 152 | elements |
| 153 | 153 | a : float |
| 154 | cubic lattice parameter in Angstroem | |
| 154 | cubic lattice parameter in angstrom | |
| 155 | 155 | do3disxy : float |
| 156 | 156 | amount of DO_3-type disorder between X and Y atoms (0: fully ordered, |
| 157 | 157 | 1: fully disordered) |
| 195 | 195 | X, Y, Z : str or Element |
| 196 | 196 | elements |
| 197 | 197 | a : float |
| 198 | cubic lattice parameter in Angstroem | |
| 198 | cubic lattice parameter in angstrom | |
| 199 | 199 | |
| 200 | 200 | Returns |
| 201 | 201 | ------- |
| 221 | 221 | X, Y, Z : str or Element |
| 222 | 222 | elements |
| 223 | 223 | a, c : float |
| 224 | tetragonal lattice parameters in Angstroem | |
| 224 | tetragonal lattice parameters in angstrom | |
| 225 | 225 | |
| 226 | 226 | Returns |
| 227 | 227 | ------- |
| 246 | 246 | X, Y, Z : str or Element |
| 247 | 247 | elements |
| 248 | 248 | a, c : float |
| 249 | tetragonal lattice parameters in Angstroem | |
| 249 | tetragonal lattice parameters in angstrom | |
| 250 | 250 | |
| 251 | 251 | Returns |
| 252 | 252 | ------- |
| 272 | 272 | X, Y, Z : str or Element |
| 273 | 273 | elements |
| 274 | 274 | a, c : float |
| 275 | hexagonal lattice parameters in Angstroem | |
| 275 | hexagonal lattice parameters in angstrom | |
| 276 | 276 | |
| 277 | 277 | Returns |
| 278 | 278 | ------- |
| 505 | 505 | |
| 506 | 506 | Parameters |
| 507 | 507 | ---------- |
| 508 | D : array-like | |
| 508 | D : array-like | |
| 509 | 509 | transformation matrix (3x3) |
| 510 | t : array-like | |
| 510 | t : array-like | |
| 511 | 511 | translation vector (3) |
| 512 | m : float, optional | |
| 513 | +1 (default) or -1 to indicate time reversal in magnetic groups | |
| 512 | m : int, optional | |
| 513 | indicates time reversal in magnetic groups. +1 (default, no time | |
| 514 | reveral) or -1 | |
| 514 | 515 | """ |
| 515 | 516 | self._W = numpy.zeros((4, 4)) |
| 516 | 517 | self._W[:3, :3] = numpy.asarray(D) |
| 1406 | 1406 | Hurst factor defining the fractal dimension of the roughness (0..1, |
| 1407 | 1407 | very slow for H != 1 or H != 0.5), default: 1 |
| 1408 | 1408 | vert_correl : float, optional |
| 1409 | vertical correlation length in (Angstrom), 0 means full replication | |
| 1409 | vertical correlation length in angstrom, 0 means full replication | |
| 1410 | 1410 | vert_nu : float, optional |
| 1411 | 1411 | exponent in the vertical correlation function |
| 1412 | 1412 | method : int, optional |
| 1532 | 1532 | Parameters |
| 1533 | 1533 | ---------- |
| 1534 | 1534 | lam : float |
| 1535 | x-ray wavelength in Angstrom | |
| 1535 | x-ray wavelength in angstrom | |
| 1536 | 1536 | delta : list or array-like |
| 1537 | 1537 | vector with the 1-n values (N+1 components, 1st component..layer at |
| 1538 | 1538 | the free surface, last component..substrate) |
| 1962 | 1962 | Parameters |
| 1963 | 1963 | ---------- |
| 1964 | 1964 | layerstack : initial LayerStack, can contain only Amorhous layers! |
| 1965 | step : thickness (in Angstrom) of the slices in the returned | |
| 1965 | step : thickness (in angstrom) of the slices in the returned | |
| 1966 | 1966 | LayerStack |
| 1967 | roughness : roughness of the created sublayers (in Angstrom) | |
| 1967 | roughness : roughness of the created sublayers (in angstrom) | |
| 1968 | 1968 | cutoff : layers with relative weights below this value will be ignored |
| 1969 | 1969 | |
| 1970 | 1970 | Returns |
| 31 | 31 | qz : array-like |
| 32 | 32 | vector of the qz values (offset from the Bragg peak) |
| 33 | 33 | RL : float |
| 34 | lateral block radius in Angstrom | |
| 34 | lateral block radius in angstrom | |
| 35 | 35 | RV : float |
| 36 | vertical block radius in Angstrom | |
| 36 | vertical block radius in angstrom | |
| 37 | 37 | Delta : float |
| 38 | 38 | root mean square misorientation of the grains in degree |
| 39 | 39 | hx : float |
| 80 | 80 | # in the axial convolver the parameters slit_length_source can not be equal to |
| 81 | 81 | # slit_length_target! |
| 82 | 82 | |
| 83 | # in this file SI units (m) are used for wavelengths, while by default Angstrom | |
| 83 | # in this file SI units (m) are used for wavelengths, while by default angstrom | |
| 84 | 84 | # are used in the remaining of the package |
| 85 | 85 | |
| 86 | 86 | import atexit |
| 1192 | 1192 | spect = numpy.array(( |
| 1193 | 1193 | xx.emiss_wavelengths, xx.emiss_intensities, |
| 1194 | 1194 | xx.emiss_lor_widths, xx.emiss_gauss_widths)) |
| 1195 | # convert to Angstroms, like Topas | |
| 1195 | # convert to angstroms, like Topas | |
| 1196 | 1196 | spect[0] *= 1e10 * self.length_scale_m |
| 1197 | spect[2] *= 1e13 * self.length_scale_m # milli-Angstroms | |
| 1198 | spect[3] *= 1e13 * self.length_scale_m # milli-Angstroms | |
| 1197 | spect[2] *= 1e13 * self.length_scale_m # milli-angstroms | |
| 1198 | spect[3] *= 1e13 * self.length_scale_m # milli-angstroms | |
| 1199 | 1199 | nm = 1e9 * self.length_scale_m |
| 1200 | 1200 | items = ["emission and broadening:"] |
| 1201 | 1201 | items.append("spectrum=\n" + str(spect.transpose())) |
| 39 | 39 | keyword arguments. |
| 40 | 40 | |
| 41 | 41 | Note: |
| 42 | After the end-of-use it is advisable to call the `close()` method to | |
| 43 | cleanup the multiprocessing calculation! | |
| 42 | After the end-of-use it is advisable to call the `close()` method | |
| 43 | to cleanup the multiprocessing calculation! | |
| 44 | 44 | |
| 45 | 45 | Parameters |
| 46 | 46 | ---------- |
| 56 | 56 | loaded from the config file. |
| 57 | 57 | I0 : float, optional |
| 58 | 58 | scaling factor for the simulation result |
| 59 | ||
| 59 | 60 | |
| 60 | 61 | In particular interesting in fpsettings might be: |
| 61 | 62 | {'displacement': {'specimen_displacement': z-displacement of the sample |
| 244 | 244 | an xrayutilties material describing optical and crystal properties of |
| 245 | 245 | the thin film |
| 246 | 246 | thickness : float |
| 247 | film thickness in Angstrom | |
| 247 | film thickness in angstrom | |
| 248 | 248 | """ |
| 249 | 249 | |
| 250 | 250 | _valid_init_kwargs = {'roughness': 'root mean square roughness', |
| 262 | 262 | an xrayutilties material describing optical and crystal properties |
| 263 | 263 | of the thin film |
| 264 | 264 | thickness : float |
| 265 | film thickness in Angstrom | |
| 265 | film thickness in angstrom | |
| 266 | 266 | kwargs : dict |
| 267 | 267 | optional keyword arguments with further layer properties. |
| 268 | 268 | roughness : float, optional |
| 269 | root mean square roughness of the top interface in Angstrom | |
| 269 | root mean square roughness of the top interface in angstrom | |
| 270 | 270 | density : float, optional |
| 271 | 271 | density of the material in kg/m^3; If not specified the density of |
| 272 | 272 | the material will be used. |
| 77 | 77 | |
| 78 | 78 | def lam2en(inp): |
| 79 | 79 | """ |
| 80 | converts the input wavelength in Angstrom to an energy in eV | |
| 80 | converts the input wavelength in angstrom to an energy in eV | |
| 81 | 81 | |
| 82 | 82 | Parameters |
| 83 | 83 | ---------- |
| 84 | 84 | inp : float or str |
| 85 | wavelength in Angstrom | |
| 85 | wavelength in angstrom | |
| 86 | 86 | |
| 87 | 87 | Returns |
| 88 | 88 | ------- |
| 102 | 102 | |
| 103 | 103 | def en2lam(inp): |
| 104 | 104 | """ |
| 105 | converts the input energy in eV to a wavelength in Angstrom | |
| 105 | converts the input energy in eV to a wavelength in angstrom | |
| 106 | 106 | |
| 107 | 107 | Parameters |
| 108 | 108 | ---------- |
| 112 | 112 | Returns |
| 113 | 113 | ------- |
| 114 | 114 | float |
| 115 | wavlength in Angstrom | |
| 115 | wavlength in angstrom | |
| 116 | 116 | |
| 117 | 117 | Examples |
| 118 | 118 | -------- |
| 162 | 162 | Parameters |
| 163 | 163 | ---------- |
| 164 | 164 | wl : float, array-like or str |
| 165 | wavelength; If scalar or array the wavelength in Angstrom will be | |
| 165 | wavelength; If scalar or array the wavelength in angstrom will be | |
| 166 | 166 | returned unchanged, string with emission name is converted to |
| 167 | 167 | wavelength |
| 168 | 168 | |
| 169 | 169 | Returns |
| 170 | 170 | ------- |
| 171 | 171 | float or array-like |
| 172 | wavelength in Angstrom | |
| 172 | wavelength in angstrom | |
| 173 | 173 | """ |
| 174 | 174 | |
| 175 | 175 | if isinstance(wl, numbers.Number): |
| 18 | 18 | info_all = 2 |
| 19 | 19 | debug = 3 |
| 20 | 20 | |
| 21 | # default wavelength in Angstrom | |
| 21 | # default wavelength in angstrom | |
| 22 | 22 | wavelength = CuKa1 |
| 23 | 23 | |
| 24 | 24 | # default energy in eV |
| 0 | 0 | Metadata-Version: 2.1 |
| 1 | 1 | Name: xrayutilities |
| 2 | Version: 1.7.0 | |
| 2 | Version: 1.7.1 | |
| 3 | 3 | Summary: package for x-ray diffraction data evaluation |
| 4 | Home-page: http://xrayutilities.sourceforge.net | |
| 4 | Home-page: https://xrayutilities.sourceforge.io | |
| 5 | 5 | Author: Eugen Wintersberger, Dominik Kriegner |
| 6 | 6 | Author-email: eugen.wintersberger@desy.de, dominik.kriegner@gmail.com |
| 7 | 7 | Maintainer: Dominik Kriegner |
| 10 | 10 | Description: xrayutilities |
| 11 | 11 | ============= |
| 12 | 12 | |
| 13 | ||
| 13 | 14 | [](https://dev.azure.com/dominikkriegner/xrayutilities/_build/latest?definitionId=1&repoName=dkriegner%2Fxrayutilities&branchName=master) |
| 14 | ||
| 15 | 15 | |
| 16 | 16 | xrayutilities is a collection of scripts used to analyze and simulate x-ray |
| 17 | 17 | diffraction data. It consists of a Python package and several routines coded |
| 22 | 22 | diffraction is included. |
| 23 | 23 | |
| 24 | 24 | |
| 25 | Copyright (C) 2009-2020 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 25 | Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 26 | 26 | |
| 27 | 27 | Copyright (C) 2009-2013 Eugen Wintersberger <eugen.wintersberger@desy.de> |
| 28 | 28 | |
| 45 | 45 | * *lib/xrayutilities*: directory with the sources for the Python package |
| 46 | 46 | * *tests*: directory with the unittest scripts |
| 47 | 47 | * *setup.py*: setuptools install script used for the package installation |
| 48 | * *xrayutilities.pdf*: pdf-file with documentation of the package | |
| 49 | 48 | |
| 50 | 49 | |
| 51 | 50 | Installation (pip) |
| 110 | 109 | - sphinx (optional - only when you want to build the documentation) |
| 111 | 110 | - numpydoc (optional - only when you want to build the documentation) |
| 112 | 111 | - rst2pdf (optional - only when you want to build the documentation) |
| 112 | - sphinx_rtd_theme (optional - only when you want to build the documentation) | |
| 113 | - svglib (optional - only when you want to build the pdf documentation) | |
| 113 | 114 | |
| 114 | 115 | refer to your operating system documentation to find out how to install |
| 115 | 116 | those packages. On Microsoft Windows refer to the Documentation for the |
| 171 | 172 | git pull |
| 172 | 173 | |
| 173 | 174 | or download the new tarball from sourceforge |
| 174 | (http://sf.net/projects/xrayutilities) if any code changed during the update you | |
| 175 | (https://sf.net/projects/xrayutilities) if any code changed during the update you | |
| 175 | 176 | need to reinstall the Python package. Thats easiest achieved by |
| 176 | 177 | |
| 177 | 178 | pip install . |
| 193 | 194 | Documentation |
| 194 | 195 | ============= |
| 195 | 196 | |
| 196 | Documentation for xrayutilities is found in the *xrayutilities.pdf* file or on the | |
| 197 | webpage http://xrayutilities.sourceforge.io | |
| 197 | Documentation for xrayutilities is found on the webpage | |
| 198 | https://xrayutilities.sourceforge.io | |
| 198 | 199 | |
| 199 | 200 | The API-documentation can also be browsed by |
| 200 | 201 | |
| 207 | 208 | Classifier: Programming Language :: Python :: 3.6 |
| 208 | 209 | Classifier: Programming Language :: Python :: 3.7 |
| 209 | 210 | Classifier: Programming Language :: Python :: 3.8 |
| 211 | Classifier: Programming Language :: Python :: 3.9 | |
| 210 | 212 | Classifier: Topic :: Scientific/Engineering :: Physics |
| 211 | 213 | Classifier: Intended Audience :: Science/Research |
| 212 | 214 | Classifier: Development Status :: 5 - Production/Stable |
| 215 | 217 | Description-Content-Type: text/markdown |
| 216 | 218 | Provides-Extra: plot |
| 217 | 219 | Provides-Extra: fit |
| 218 | Provides-Extra: lzma | |
| 0 | 0 | CHANGES.txt |
| 1 | CONTRIBUTING.md | |
| 2 | 1 | LICENSE.txt |
| 3 | 2 | MANIFEST.in |
| 4 | 3 | README.md |
| 5 | azure-pipelines.yml | |
| 6 | 4 | setup.py |
| 7 | xrayutilities.pdf | |
| 8 | doc/README_sf.rst | |
| 9 | doc/webpage.patch | |
| 10 | 5 | doc/source/conf.py |
| 11 | 6 | doc/source/example_xu_ccd_parameter.py |
| 12 | 7 | doc/source/example_xu_ccd_parameter_hkl.py |
| 15 | 10 | doc/source/examples.rst |
| 16 | 11 | doc/source/favicon.ico |
| 17 | 12 | doc/source/index.rst |
| 18 | doc/source/modules.rst | |
| 19 | 13 | doc/source/simulations.rst |
| 20 | doc/source/xrayutilities.analysis.rst | |
| 21 | doc/source/xrayutilities.io.rst | |
| 22 | doc/source/xrayutilities.materials.rst | |
| 23 | doc/source/xrayutilities.math.rst | |
| 24 | doc/source/xrayutilities.rst | |
| 25 | doc/source/xrayutilities.simpack.rst | |
| 26 | 14 | doc/source/pics/fit_xrd.svg |
| 27 | 15 | doc/source/pics/line_cut_intdir.png |
| 28 | 16 | doc/source/pics/line_cut_radial.png |
| 80 | 68 | examples/xrayutilities_read_spec.py |
| 81 | 69 | examples/xrayutilities_reflection_strength.py |
| 82 | 70 | examples/xrayutilities_show_reciprocal_space_plane.py |
| 83 | examples/xrayutilities_user.conf | |
| 84 | 71 | examples/data/BaF2.cif |
| 85 | 72 | examples/data/Calcite.cif |
| 86 | 73 | examples/data/LaB6_d500_si_psd.xye.bz2 |
| 184 | 171 | src/qconversion.c |
| 185 | 172 | src/qconversion.h |
| 186 | 173 | src/xrayutilities.h |
| 187 | tests/README.txt | |
| 188 | 174 | tests/__init__.py |
| 189 | 175 | tests/test_HXRD.py |
| 190 | 176 | tests/test_NonCOP.py |
| 0 | 0 | numpy>=1.9.2 |
| 1 | scipy>=0.11.0 | |
| 1 | scipy>=0.13.0 | |
| 2 | 2 | h5py |
| 3 | 3 | |
| 4 | 4 | [fit] |
| 5 | 5 | lmfit>=1.0.1 |
| 6 | 6 | |
| 7 | [lzma] | |
| 8 | lzma | |
| 9 | ||
| 10 | 7 | [plot] |
| 11 | 8 | matplotlib>=3.1.0 |
| 13 | 13 | # along with this program; if not, see <http://www.gnu.org/licenses/>. |
| 14 | 14 | # |
| 15 | 15 | # Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger@desy.de> |
| 16 | # Copyright (C) 2010-2020 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 16 | # Copyright (C) 2010-2021 Dominik Kriegner <dominik.kriegner@gmail.com> | |
| 17 | 17 | |
| 18 | 18 | import glob |
| 19 | 19 | import os.path |
| 140 | 140 | sources=glob.glob(os.path.join('src', '*.c'))) |
| 141 | 141 | |
| 142 | 142 | with open('lib/xrayutilities/VERSION') as version_file: |
| 143 | version = version_file.read().strip() | |
| 143 | version = version_file.read().strip().replace('\n', '.') | |
| 144 | 144 | |
| 145 | 145 | try: |
| 146 | 146 | import sphinx |
| 178 | 178 | "Programming Language :: Python :: 3.6", |
| 179 | 179 | "Programming Language :: Python :: 3.7", |
| 180 | 180 | "Programming Language :: Python :: 3.8", |
| 181 | "Programming Language :: Python :: 3.9", | |
| 181 | 182 | "Topic :: Scientific/Engineering :: Physics", |
| 182 | 183 | "Intended Audience :: Science/Research", |
| 183 | 184 | "Development Status :: 5 - Production/Stable", |
| 197 | 198 | }, |
| 198 | 199 | python_requires='~=3.6', |
| 199 | 200 | setup_requires=['numpy', 'scipy', 'h5py'], |
| 200 | install_requires=['numpy>=1.9.2', 'scipy>=0.11.0', 'h5py'], | |
| 201 | install_requires=['numpy>=1.9.2', 'scipy>=0.13.0', 'h5py'], | |
| 201 | 202 | extras_require={ |
| 202 | 203 | 'plot': ["matplotlib>=3.1.0"], |
| 203 | 204 | 'fit': ["lmfit>=1.0.1"], |
| 204 | 'lzma': ["lzma"], | |
| 205 | 205 | }, |
| 206 | 206 | include_dirs=[numpy.get_include()], |
| 207 | 207 | ext_modules=[extmodul], |
| 208 | 208 | cmdclass=cmdclass, |
| 209 | url="http://xrayutilities.sourceforge.net", | |
| 209 | url="https://xrayutilities.sourceforge.io", | |
| 210 | 210 | license="GPLv2", |
| 211 | 211 | script_args=args |
| 212 | 212 | ) |
| 275 | 275 | " of investigated crystal (9)\n" |
| 276 | 276 | " sampledis ....... sample displacement vector in same unit as the\n" |
| 277 | 277 | " detector distance\n" |
| 278 | " lambda .......... wavelength of the used x-rays in Angstroem\n" | |
| 278 | " lambda .......... wavelength of the used x-rays in angstrom\n" | |
| 279 | 279 | " nthreads ........ number of threads to use in parallel section of the\n" |
| 280 | 280 | " code\n" |
| 281 | 281 | " flags ........... integer flags to select sub-function\n" |
| 1201 | 1201 | * of investigated crystal (3, 3) |
| 1202 | 1202 | * sampledis ....... sample displacement vector, same units as the |
| 1203 | 1203 | * detector distance |
| 1204 | * lambda .......... wavelength of the used x-rays in Angstroem (Npoints,) | |
| 1204 | * lambda .......... wavelength of the used x-rays in angstrom (Npoints,) | |
| 1205 | 1205 | * nthreads ........ number of threads to use in parallel section of |
| 1206 | 1206 | * the code |
| 1207 | 1207 | * flags ........... integer with flags: (1: has_translations; |
| 1399 | 1399 | * tilt ............ tilt of the detector direction from dir |
| 1400 | 1400 | * UB .............. orientation matrix and reciprocal space conversion |
| 1401 | 1401 | * of investigated crystal (3, 3) |
| 1402 | * lambda .......... wavelength of the used x-rays in Angstroem (Npoints,) | |
| 1402 | * lambda .......... wavelength of the used x-rays in angstrom (Npoints,) | |
| 1403 | 1403 | * Npoints ......... number of points to calculate |
| 1404 | 1404 | * Ns .............. number of sample axes |
| 1405 | 1405 | * Nd .............. number of detector axes |
| 1516 | 1516 | * of investigated crystal (3, 3) |
| 1517 | 1517 | * sampledis ....... sample displacement vector, same units as the |
| 1518 | 1518 | * detector distance |
| 1519 | * lambda .......... wavelength of the used x-rays in Angstroem (Npoints,) | |
| 1519 | * lambda .......... wavelength of the used x-rays in angstrom (Npoints,) | |
| 1520 | 1520 | * Npoints ......... number of points to calculate |
| 1521 | 1521 | * Ns .............. number of sample axes |
| 1522 | 1522 | * Nd .............. number of detector axes |
| 1633 | 1633 | * tilt ............ tilt of the detector direction from dir |
| 1634 | 1634 | * UB .............. orientation matrix and reciprocal space conversion |
| 1635 | 1635 | * of investigated crystal (3, 3) |
| 1636 | * lambda .......... wavelength of the used x-rays in Angstroem (Npoints,) | |
| 1636 | * lambda .......... wavelength of the used x-rays in angstrom (Npoints,) | |
| 1637 | 1637 | * Npoints ......... number of points to calculate |
| 1638 | 1638 | * Ns .............. number of sample axes |
| 1639 | 1639 | * Nd .............. number of detector axes |
| 1746 | 1746 | * of investigated crystal (3, 3) |
| 1747 | 1747 | * sampledis ....... sample displacement vector, same units as the |
| 1748 | 1748 | * detector distance |
| 1749 | * lambda .......... wavelength of the used x-rays in Angstroem (Npoints,) | |
| 1749 | * lambda .......... wavelength of the used x-rays in angstrom (Npoints,) | |
| 1750 | 1750 | * Npoints ......... number of points to calculate |
| 1751 | 1751 | * Ns .............. number of sample axes |
| 1752 | 1752 | * Nd .............. number of detector axes |
| 0 | xrayutilities unittests | |
| 1 | ======================= | |
| 2 | ||
| 3 | To run ALL the unittests execute in the package root | |
| 4 | ||
| 5 | python setup.py test | |
| 6 | ||
| 7 | or | |
| 8 | ||
| 9 | python -m unittest discover | |
| 10 | ||
| 11 | ||
| 12 | Individual tests can be run by | |
| 13 | ||
| 14 | python -m unitest <testfile> | |
| 15 | ||
| 16 | ||
| 17 | Additional test data | |
| 18 | -------------------- | |
| 19 | ||
| 20 | To run specific tests (file parsers) additional test data files are needed. | |
| 21 | If those files are not present the tests are skipped. Because of their size | |
| 22 | they are shipped seperately and can be downloaded at | |
| 23 | https://sourceforge.net/projects/xrayutilities/files/ | |
| 24 | ||
| 25 | The latest 'testdata' tarball has to be unpacked and placed in the | |
| 26 | 'tests' directory, which will place all data under 'tests/data'. |