xraydc 0.0.0__tar.gz

xraydc-0.0.0/.gitignore

@@ -0,0 +1,9 @@
+*~
+\#*
+.\#*
+__pycache__
+dist/
+*.egg-info
+_version.py
+.ipynb_checkpoints
+*.orig

xraydc-0.0.0/.gitlab-ci.yml

@@ -0,0 +1,106 @@
+default:
+  image:
+    name: python:latest
+
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+  PYPI_RELEASE_URL: https://test.pypi.org/legacy/
+
+cache:
+  paths:
+    - .cache/pip
+    - venv/
+
+stages:
+  - test
+  - build
+  - release
+
+testing:
+  stage: test
+  script:
+    - python --version
+    - pip install virtualenv
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip install -e ".[test]"
+    - coverage run -m --source nx5d pytest
+    - coverage report
+    - coverage xml
+  coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+
+packaging:
+  stage: build
+  script:
+    - python --version
+    - pip install virtualenv
+    - virtualenv venv
+    - source venv/bin/activate
+    - export PACK_VERSION=`echo $CI_COMMIT_TAG | sed -n /v[0-9].*/p | cut -b 2-`
+    - echo "Packaging Version $PACK_VERSION"
+    - pip install --upgrade build
+    - python3 -m build
+    - pip install --upgrade twine
+    - twine check dist/*
+    - pip install dist/*.whl
+  artifacts:
+    paths:
+      - dist/*
+
+analysis:
+  stage: test
+  allow_failure: true
+  script: 
+    - python --version
+    - pip install virtualenv
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip install --upgrade pylint-gitlab
+    - pip install --upgrade anybadge
+    - mkdir -p public/badges public/lint
+    - echo undefined > public/badges/"$CI_JOB_NAME".score
+    - pylint --exit-zero --output-format=text $(find -type f -name "*.py" ! -path "**/venv/**") | tee /tmp/pylint.txt
+    - sed -n 's/^Your code has been rated at \([-0-9.]*\)\/.*/\1/p' /tmp/pylint.txt > public/badges/"$CI_JOB_NAME".score
+    - pylint --exit-zero --output-format=pylint_gitlab.GitlabCodeClimateReporter $(find -type f -name "*.py" ! -path "**/venv/**") > codeclimate.json
+    - pylint --exit-zero --output-format=pylint_gitlab.GitlabPagesHtmlReporter $(find -type f -name "*.py" ! -path "**/venv/**") > public/lint/index.html
+  after_script:
+    - anybadge --overwrite --label "$CI_JOB_NAME" --value=$(cat public/badges/$CI_JOB_NAME.score) --file=public/badges/$CI_JOB_NAME.svg 4=red 6=orange 8=yellow 10=green
+    - |
+      echo "Your score is: $(cat public/badges/$CI_JOB_NAME.score)"
+  artifacts:
+    paths:
+      - public
+    reports:
+      codequality: codeclimate.json
+    when: always
+
+pypi upload:
+  stage: release
+  rules:
+    - if: $CI_COMMIT_TAG =~ "/^v[0-9].*/"
+  script:
+    - python --version
+    - pip install virtualenv
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip install --upgrade twine
+    - export TWINE_USERNAME=__token__
+    - export TWINE_PASSWORD="$PYPI_RELEASE_TOKEN"
+    - python -m twine upload --repository-url "${PYPI_RELEASE_URL}" dist/*
+
+gitlab release:
+  stage: release
+  image: registry.gitlab.com/gitlab-org/release-cli:latest
+  rules:
+    - if: $CI_COMMIT_TAG =~ "/^v[0-9].*/"
+  script:
+    - echo "Releasing:"
+    - ls dist/*
+  release:
+    tag_name: $CI_COMMIT_TAG
+    description: $CI_COMMIT_TAG

xraydc-0.0.0/PKG-INFO

@@ -0,0 +1,30 @@
+Metadata-Version: 2.4
+Name: xraydc
+Version: 0.0.0
+Summary: X-Ray Diffraction Cooking -- nx5d data processing recipes
+Author-email: Matthias Rössle <matthias.roessle@helmholtz-berlin.de>, Florin Boariu <florin.pt@rootshell.ro>
+Project-URL: Source Code, https://gitlab.com/kmc3-xpp/xraydc/
+Project-URL: Bug Tracker, https://gitlab.com/kmc3-xpp/xraydc/
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: nx5d
+Requires-Dist: xarray
+Requires-Dist: scipy
+Requires-Dist: dask
+Requires-Dist: xrayutilities
+Provides-Extra: all
+Requires-Dist: xraydc[doc,test]; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: tqdm; extra == "test"
+Provides-Extra: doc
+Requires-Dist: mkdocs; extra == "doc"
+Requires-Dist: mkdocstrings[python]; extra == "doc"

xraydc-0.0.0/doc/mkdocs.yml

@@ -0,0 +1,29 @@
+docs_dir: mkdocs
+site_name: nx5d
+site_url: https://nx5d.readthedocs.io/
+  
+nav:
+  - Home: index.md
+  - A First Example: spice-example.ipynb
+  - Core Concepts: concepts.md
+  - User Guide: user-guide/index.md
+  - API Reference: api.md
+  - License: license.md
+
+theme:
+  name: readthedocs
+  features:
+    - content.code.copy
+  
+plugins:
+  - mkdocstrings
+  - mkdocs-jupyter
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences

xraydc-0.0.0/pyproject.toml

@@ -0,0 +1,66 @@
+[build-system]
+requires = ["setuptools>=64.0", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "xraydc"
+authors = [
+    { name = "Matthias Rössle", email = "matthias.roessle@helmholtz-berlin.de" },
+    { name = "Florin Boariu", email = "florin.pt@rootshell.ro" },
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Operating System :: POSIX :: Linux",
+    "Development Status :: 2 - Pre-Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering"
+]
+dependencies = [
+    "nx5d",
+    "xarray",
+    "scipy",
+    "dask",
+    "xrayutilities"
+]
+dynamic = ["version"]
+description = "X-Ray Diffraction Cooking -- nx5d data processing recipes"
+readme = "README.md"
+requires-python = ">=3.8"
+keywords = []
+
+[project.urls]
+"Source Code" = "https://gitlab.com/kmc3-xpp/xraydc/"
+"Bug Tracker" = "https://gitlab.com/kmc3-xpp/xraydc/"
+#"Documentation" = "https://xraydc.readthedocs.io/"
+
+[project.optional-dependencies]
+all = [
+    "xraydc[test,doc]"
+]
+
+test = [
+    "pytest",
+    "pytest-cov",
+    "tqdm",
+]
+
+doc = [
+    "mkdocs",
+    "mkdocstrings[python]",
+]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -m 'not xfel'"
+log_cli = true
+testpaths = [
+    "tests",
+]
+markers = [ ]
+
+[tool.setuptools_scm]
+write_to = "src/xraydc/_version.py"
+
+[project.scripts]

xraydc-0.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

xraydc-0.0.0/src/kmc3recipes/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.1.dev0+d20250925'
+__version_tuple__ = version_tuple = (0, 1, 'dev0', 'd20250925')
+
+__commit_id__ = commit_id = None

xraydc-0.0.0/src/kmc3recipes/cooking_BACKUP_116041.py

@@ -0,0 +1,89 @@
+from kmc3recipe.signal import QMapper
+
+all = [
+    "sRSM",
+    "TRSM",
+    "rocking",
+    
+    #"xRSS",
+    #"tRSS",
+]
+
+# Recipe map to use for easy seeding of all herein supported types.
+RecipeMap = {
+    # static RSM    
+    sRSM="pymod:///kmc3recipes.cooking#sRSM",
+
+    # temperature-dependent RSM
+    tRSM="pymod:///kmc3recipes.cooking#TRSM",
+
+    # omega-2theta-scan (treat like RSM?)
+    rocking="pymod:///kmc3recipes.cooking#sRSM",
+
+    # some kind (?) of RSS
+    xRSS=None,
+
+    # time-dependent (?) RSS
+    tRSS=None,
+}
+
+def _kmc3_recipe_helper_datamangle(data, **spice):
+    # Helper for KMC3 recipes: changes data (mostly by applying offsets)
+    # returns new dataset
+    
+    data2 = data.copy()
+    
+    if 'offsets' in spice:
+        for k, v in spice['offsets'].items():
+            data2[k] = data[k] + spice['offsets'][k]
+
+    return data2
+
+
+def _kmc3_recipe_helper_expimangle(expi, **spice):
+    # Helper for KMC3 recipes: changes experimental info
+    # using spice info from 'image', 'energy', and possibly others.
+    # Returns new experimental info, and a qmap parameters dict.
+    expi2 = expi.copy()
+
+    #if 'energy' in spice:
+    #    expi2['beamEnergy'] = spice['energy']['energy']    
+
+    if 'image' in spice:
+        expi2['imageCenter'] = spice['image']['imageCenter']
+        expi2['imageDistance'] = spice['image']['imageDistance']
+
+    return expi2, {}
+
+
+def sRSM(data, **spice):
+    '''
+    Generating static reciprocal space maps (RSMs).
+
+    Requires `exp_info` spice. Also performs basic data mangling
+    if appropriate spice types (`offsets`) available, and
+    modifies exp_info if exp_info modifiers (`image`) also available.
+
+    "Static" RSMs don't depend on any external parameters.
+    '''
+    data2 = _kmc3_recipe_helper_datamangle(data, **spice)
+    expi2, qpar = _kmc3_recipe_helper_expimangle(spice['exp_info'], **spice)
+    return QMapper(**expi2).qmap(data2, **qpar)
+
+
+def TRSM(data, **spice):
+    '''
+    Generating temperature (T) dependent RSMs, uses 'temp' dataset
+    '''
+    from nx5d.xrd.signal import QMapper
+    data2 = _kmc3_recipe_helper_datamangle(data, **spice)
+    expi2, qpar = _kmc3_recipe_helper_expimangle(spice['exp_info'], **spice)
+
+    data2['temp'] = data2.temp.round()
+        
+    return data2.groupby('temp').map(QMapper(**expi2).qmap, **qpar)
+
+
+def rocking(data, **spice):
+    raise RuntimeError('recipe for rocking data not implemented')
+

xraydc-0.0.0/src/kmc3recipes/cooking_BASE_116041.py

@@ -0,0 +1,66 @@
+from kmc3recipe.signal import QMapper
+
+all = [
+    "sRSM",
+    "TRSM",
+    "rocking"
+]
+
+def _kmc3_recipe_helper_datamangle(data, **spice):
+    # Helper for KMC3 recipes: changes data (mostly by applying offsets)
+    # returns new dataset
+    
+    data2 = data.copy()
+    
+    if 'offsets' in spice:
+        for k, v in spice['offsets'].items():
+            data2[k] = data[k] + spice['offsets'][k]
+
+    return data2
+
+
+def _kmc3_recipe_helper_expimangle(expi, **spice):
+    # Helper for KMC3 recipes: changes experimental info
+    # using spice info from 'image', 'energy', and possibly others.
+    # Returns new experimental info, and a qmap parameters dict.
+    expi2 = expi.copy()
+
+    #if 'energy' in spice:
+    #    expi2['beamEnergy'] = spice['energy']['energy']    
+
+    if 'image' in spice:
+        expi2['imageCenter'] = spice['image']['imageCenter']
+        expi2['imageDistance'] = spice['image']['imageDistance']
+
+    return expi2, {}
+
+
+def sRSM(data, **spice):
+    '''
+    Generating static RSMs.
+
+    Requires `exp_info` spice. Also performs basic data mangling
+    if appropriate spice types (`offsets`) available, and
+    modifies exp_info if exp_info modifiers (`image`) also available.
+    '''
+    data2 = _kmc3_recipe_helper_datamangle(data, **spice)
+    expi2, qpar = _kmc3_recipe_helper_expimangle(spice['exp_info'], **spice)
+    return QMapper(**expi2).qmap(data2, **qpar)
+
+
+def TRSM(data, **spice):
+    '''
+    Generating temperature (T) dependent RSMs, uses 'temp' dataset
+    '''
+    from nx5d.xrd.signal import QMapper
+    data2 = _kmc3_recipe_helper_datamangle(data, **spice)
+    expi2, qpar = _kmc3_recipe_helper_expimangle(spice['exp_info'], **spice)
+
+    data2['temp'] = data2.temp.round()
+        
+    return data2.groupby('temp').map(QMapper(**expi2).qmap, **qpar)
+
+
+def rocking(data, **spice):
+    raise RuntimeError('recipe for rocking data not implemented')
+

xraydc-0.0.0/src/kmc3recipes/cooking_REMOTE_116041.py

@@ -0,0 +1,89 @@
+from kmc3recipe.signal import QMapper
+
+all = [
+    "sRSM",
+    "TRSM",
+    "rocking",
+    
+    #"xRSS",
+    #"tRSS",
+]
+
+# Recipe map to use for easy seeding of all herein supported types.
+RecipeMap = {
+    # static RSM    
+    sRSM="pymod:///kmc3recipes.cooking#sRSM",
+
+    # temperature-dependent RSM
+    tRSM="pymod:///kmc3recipes.cooking#TRSM",
+
+    # omega-2theta-scan (treat like RSM?)
+    rocking="pymod:///kmc3recipes.cooking#sRSM",
+
+    # some kind (?) of RSS
+    xRSS=None,
+
+    # time-dependent (?) RSS
+    tRSS=None,
+}
+
+def _kmc3_recipe_helper_datamangle(data, **spice):
+    # Helper for KMC3 recipes: changes data (mostly by applying offsets)
+    # returns new dataset
+    
+    data2 = data.copy()
+    
+    if 'offsets' in spice:
+        for k, v in spice['offsets'].items():
+            data2[k] = data[k] + spice['offsets'][k]
+
+    return data2
+
+
+def _kmc3_recipe_helper_expimangle(expi, **spice):
+    # Helper for KMC3 recipes: changes experimental info
+    # using spice info from 'image', 'energy', and possibly others.
+    # Returns new experimental info, and a qmap parameters dict.
+    expi2 = expi.copy()
+
+    #if 'energy' in spice:
+    #    expi2['beamEnergy'] = spice['energy']['energy']    
+
+    if 'image' in spice:
+        expi2['imageCenter'] = spice['image']['imageCenter']
+        expi2['imageDistance'] = spice['image']['imageDistance']
+
+    return expi2, {}
+
+
+def sRSM(data, **spice):
+    '''
+    Generating static reciprocal space maps (RSMs).
+
+    Requires `exp_info` spice. Also performs basic data mangling
+    if appropriate spice types (`offsets`) available, and
+    modifies exp_info if exp_info modifiers (`image`) also available.
+
+    "Static" RSMs don't depend on any external parameters.
+    '''
+    data2 = _kmc3_recipe_helper_datamangle(data, **spice)
+    expi2, qpar = _kmc3_recipe_helper_expimangle(spice['exp_info'], **spice)
+    return QMapper(**expi2).qmap(data2, **qpar)
+
+
+def TRSM(data, **spice):
+    '''
+    Generating temperature (T) dependent RSMs, uses 'temp' dataset
+    '''
+    from nx5d.xrd.signal import QMapper
+    data2 = _kmc3_recipe_helper_datamangle(data, **spice)
+    expi2, qpar = _kmc3_recipe_helper_expimangle(spice['exp_info'], **spice)
+
+    data2['temp'] = data2.temp.round()
+        
+    return data2.groupby('temp').map(QMapper(**expi2).qmap, **qpar)
+
+
+def rocking(data, **spice):
+    raise RuntimeError('recipe for rocking data not implemented')
+

xraydc-0.0.0/src/xraydc/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.0.0'
+__version_tuple__ = version_tuple = (0, 0, 0)
+
+__commit_id__ = commit_id = 'gf46a0458e'