pymodaq_data 0.0.1__tar.gz

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Files changed (27) hide show
  1. pymodaq_data-0.0.1/.gitignore +129 -0
  2. pymodaq_data-0.0.1/LICENSE +21 -0
  3. pymodaq_data-0.0.1/PKG-INFO +160 -0
  4. pymodaq_data-0.0.1/README.rst +103 -0
  5. pymodaq_data-0.0.1/pyproject.toml +58 -0
  6. pymodaq_data-0.0.1/src/pymodaq_data/__init__.py +53 -0
  7. pymodaq_data-0.0.1/src/pymodaq_data/data.py +2901 -0
  8. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/__init__.py +6 -0
  9. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/backends.py +1031 -0
  10. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/browsing.py +101 -0
  11. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/data_saving.py +1107 -0
  12. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/exporter.py +119 -0
  13. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/exporters/__init__.py +0 -0
  14. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/exporters/base.py +111 -0
  15. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/exporters/flimj.py +63 -0
  16. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/exporters/hyperspy.py +143 -0
  17. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/saving.py +411 -0
  18. pymodaq_data-0.0.1/src/pymodaq_data/h5modules/utils.py +115 -0
  19. pymodaq_data-0.0.1/src/pymodaq_data/icon.ico +0 -0
  20. pymodaq_data-0.0.1/src/pymodaq_data/plotting/__init__.py +0 -0
  21. pymodaq_data-0.0.1/src/pymodaq_data/plotting/plotter/plotter.py +91 -0
  22. pymodaq_data-0.0.1/src/pymodaq_data/plotting/plotter/plotters/__init__.py +0 -0
  23. pymodaq_data-0.0.1/src/pymodaq_data/plotting/plotter/plotters/matplotlib_plotters.py +133 -0
  24. pymodaq_data-0.0.1/src/pymodaq_data/post_treatment/__init__.py +6 -0
  25. pymodaq_data-0.0.1/src/pymodaq_data/post_treatment/process_to_scalar.py +234 -0
  26. pymodaq_data-0.0.1/src/pymodaq_data/slicing.py +48 -0
  27. pymodaq_data-0.0.1/src/pymodaq_data/splash.png +0 -0
pymodaq_data-0.0.1/.gitignore ADDED
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+ # Compiled python modules.
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+ *.pyc
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+
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+ # Byte-compiled / optimized / DLL files
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+ __pycache__/
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+
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+
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+ *.py[cod]
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+ *$py.class
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+
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+ # C extensions
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+ *.so
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+ .idea/*
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+
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+ # Distribution / packaging
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+ .Python
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+ documentation/_*
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+ build/
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+ develop-eggs/
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+ dist/
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+ downloads/
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+ eggs/
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+ .eggs/
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+ lib/
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+ lib64/
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+ parts/
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+ sdist/
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+ var/
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+ wheels/
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+ *.egg-info/
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+ .installed.cfg
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+ *.egg
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+ MANIFEST
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+
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+ # PyInstaller
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+ # Usually these files are written by a python script from a template
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+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
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+ *.manifest
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+ *.spec
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+
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+ # Installer logs
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+ pip-log.txt
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+ pip-delete-this-directory.txt
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+
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+ # Unit test / coverage reports
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+ htmlcov/
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+ .tox/
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+ .coverage
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+ .coverage.*
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+ .cache
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+ nosetests.xml
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+ coverage.xml
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+ *.cover
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+ .hypothesis/
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+ .pytest_cache/
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+
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+ *.idea
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+
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+ # Translations
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+ *.mo
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+ *.pot
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+
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+
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+ # Django stuff:
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+ *.log
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+ local_settings.py
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+ db.sqlite3
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+
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+ # Flask stuff:
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+ instance/
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+ .webassets-cache
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+
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+ # Scrapy stuff:
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+ .scrapy
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+
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+ # Sphinx documentation
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+ docs/_build/
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+
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+ # PyBuilder
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+ target/
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+
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+ # Jupyter Notebook
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+ .ipynb_checkpoints
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+
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+ # pyenv
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+ .python-version
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+
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+ # celery beat schedule file
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+ celerybeat-schedule
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+
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+ # SageMath parsed files
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+ *.sage.py
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+
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+ # Environments
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+ .env
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+ .venv
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+ env/
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+ venv/
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+ ENV/
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+ env.bak/
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+ venv.bak/
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+
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+ # Spyder project settings
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+ .spyderproject
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+ .spyproject
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+
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+ # VS code project settings
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+ .vscode/*
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+
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+ # Rope project settings
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+ .ropeproject
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+
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+ # mkdocs documentation
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+ /site
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+
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+ # mypy
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+ .mypy_cache/
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+ .idea/workspace.xml
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+
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+ *.iml
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+
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+
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+ .tox
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+ *.h5
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+ !data.h5
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+
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+ *yacctab.py
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+ *lextab.py
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+
pymodaq_data-0.0.1/LICENSE ADDED
@@ -0,0 +1,21 @@
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2021 Sebastien Weber <sebastien.weber@cemes.fr>
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in
13
+ all copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
21
+ THE SOFTWARE.
pymodaq_data-0.0.1/PKG-INFO ADDED
@@ -0,0 +1,160 @@
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+ Metadata-Version: 2.3
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+ Name: pymodaq_data
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+ Version: 0.0.1
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+ Summary: Modular Data Acquisition with Python
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+ Project-URL: Homepage, http://pymodaq.cnrs.fr
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+ Project-URL: Source, https://github.com/PyMoDAQ/PyMoDAQ
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+ Project-URL: Tracker, https://github.com/PyMoDAQ/PyMoDAQ/issues
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+ Author-email: Sébastien Weber <sebastien.weber@cemes.fr>
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+ License: The MIT License (MIT)
10
+
11
+ Copyright (c) 2021 Sebastien Weber <sebastien.weber@cemes.fr>
12
+
13
+ Permission is hereby granted, free of charge, to any person obtaining a copy
14
+ of this software and associated documentation files (the "Software"), to deal
15
+ in the Software without restriction, including without limitation the rights
16
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
17
+ copies of the Software, and to permit persons to whom the Software is
18
+ furnished to do so, subject to the following conditions:
19
+
20
+ The above copyright notice and this permission notice shall be included in
21
+ all copies or substantial portions of the Software.
22
+
23
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
24
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
25
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
26
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
27
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
28
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
29
+ THE SOFTWARE.
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+ License-File: LICENSE
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+ Classifier: Development Status :: 5 - Production/Stable
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+ Classifier: Environment :: Other Environment
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Natural Language :: English
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Programming Language :: Python :: 3.7
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+ Classifier: Programming Language :: Python :: 3.8
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+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Topic :: Scientific/Engineering :: Human Machine Interfaces
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+ Classifier: Topic :: Scientific/Engineering :: Visualization
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+ Classifier: Topic :: Software Development :: Libraries :: Python Modules
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+ Classifier: Topic :: Software Development :: User Interfaces
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+ Requires-Python: >=3.8
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+ Requires-Dist: multipledispatch
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+ Requires-Dist: numpy<2.0.0
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+ Requires-Dist: packaging
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+ Requires-Dist: pint
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+ Requires-Dist: pymodaq-utils
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+ Requires-Dist: python-dateutil
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+ Requires-Dist: scipy
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+ Requires-Dist: tables<3.9
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+ Requires-Dist: toml
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+ Description-Content-Type: text/x-rst
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+
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+ PyMoDAQ Data
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+ ############
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+
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+ .. image:: https://img.shields.io/pypi/v/pymodaq_data.svg
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+ :target: https://pypi.org/project/pymodaq_data/
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+ :alt: Latest Version
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+
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+ .. image:: https://readthedocs.org/projects/pymodaq/badge/?version=latest
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+ :target: https://pymodaq.readthedocs.io/en/stable/?badge=latest
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+ :alt: Documentation Status
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+
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+ .. image:: https://codecov.io/gh/PyMoDAQ/pymodaq_data/branch/0.0.x/graph/badge.svg?token=IQNJRCQDM2
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+ :target: https://codecov.io/gh/PyMoDAQ/pymodaq_data
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+
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+ ====== ======= ======
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+ Python OS Passed
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+ ====== ======= ======
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+ 3.8 Linux |38|
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+ 3.9 Linux |39|
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+ 3.10 Linux |310|
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+ 3.11 Linux |311|
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+ 3.12 Linux |312|
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+ 3.11 Windows |311win|
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+ ====== ======= ======
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+
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+
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+ .. |38| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp38.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp385.yml
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+
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+ .. |39| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp39.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp39.yml
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+
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+ .. |310| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp310.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp310.yml
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+
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+ .. |311| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311.yml
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+
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+ .. |312| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp312.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp312.yml
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+
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+ .. |311win| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311_win.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311_win.yml
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+
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+
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+
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+
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+ .. figure:: http://pymodaq.cnrs.fr/en/latest/_static/splash.png
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+ :alt: shortcut
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+
108
+
109
+ PyMoDAQ__, Modular Data Acquisition with Python, is a set of **python** modules used to interface any kind of
110
+ experiments. It simplifies the interaction with detector and actuator hardware to go straight to the data acquisition
111
+ of interest.
112
+
113
+ __ https://pymodaq.readthedocs.io/en/stable/?badge=latest
114
+
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+ `PyMoDAQ data`__ is a set of utilities (constants, methods and classes) that are used
116
+ for Data Management. It is heavily used with the PyMoDAQ framework but can also be used as a standalone
117
+ package for data management in another context.
118
+
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+ __ https://pymodaq.cnrs.fr/en/latest/developer_folder/data_management.html
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+
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+ What are Data?
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+ --------------
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+
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+ Data are objects with many characteristics able to properly describe real data taken on an experiment
125
+ or calculated from theory:
126
+
127
+
128
+ * a type: float, int, ...
129
+ * a dimensionality: Data0D, Data1D, Data2D and higher
130
+ * units (dealt with the pint python package)
131
+ * axes
132
+ * actual data as numpy arrays
133
+ * uncertainty/error bars
134
+ * ...
135
+
136
+
137
+ .. figure:: https://pymodaq.cnrs.fr/en/latest/_images/data.png
138
+ :alt: What is data?
139
+
140
+ What is PyMoDAQ's data?.
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+
142
+ The `PyMoDAQ Data` package
143
+ --------------------------
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+
145
+ Because of this variety, `PyMoDAQ Data` introduce a set of objects including metadata (for instance the time of
146
+ acquisition) and various methods and properties to manipulate
147
+ them during analysis for instance (getting name, slicing, concatenating...),
148
+ save them and plot them (given you installed one of the available backend: *matplotlib* or *Qt* (
149
+ through the `pymodaq_gui` package)
150
+
151
+ To learn more, check the documentation__.
152
+
153
+ __ https://pymodaq.cnrs.fr/en/latest/developer_folder/data_management.html
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+
155
+
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+ Published under the MIT FREE SOFTWARE LICENSE
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+
158
+ GitHub repo: https://github.com/PyMoDAQ
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+
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+ Documentation: http://pymodaq.cnrs.fr/
pymodaq_data-0.0.1/README.rst ADDED
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+ PyMoDAQ Data
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+ ############
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+
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+ .. image:: https://img.shields.io/pypi/v/pymodaq_data.svg
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+ :target: https://pypi.org/project/pymodaq_data/
6
+ :alt: Latest Version
7
+
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+ .. image:: https://readthedocs.org/projects/pymodaq/badge/?version=latest
9
+ :target: https://pymodaq.readthedocs.io/en/stable/?badge=latest
10
+ :alt: Documentation Status
11
+
12
+ .. image:: https://codecov.io/gh/PyMoDAQ/pymodaq_data/branch/0.0.x/graph/badge.svg?token=IQNJRCQDM2
13
+ :target: https://codecov.io/gh/PyMoDAQ/pymodaq_data
14
+
15
+ ====== ======= ======
16
+ Python OS Passed
17
+ ====== ======= ======
18
+ 3.8 Linux |38|
19
+ 3.9 Linux |39|
20
+ 3.10 Linux |310|
21
+ 3.11 Linux |311|
22
+ 3.12 Linux |312|
23
+ 3.11 Windows |311win|
24
+ ====== ======= ======
25
+
26
+
27
+ .. |38| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp38.yml/badge.svg?branch=0.0.x_dev
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+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp385.yml
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+
30
+ .. |39| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp39.yml/badge.svg?branch=0.0.x_dev
31
+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp39.yml
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+
33
+ .. |310| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp310.yml/badge.svg?branch=0.0.x_dev
34
+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp310.yml
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+
36
+ .. |311| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311.yml/badge.svg?branch=0.0.x_dev
37
+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311.yml
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+
39
+ .. |312| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp312.yml/badge.svg?branch=0.0.x_dev
40
+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp312.yml
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+
42
+ .. |311win| image:: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311_win.yml/badge.svg?branch=0.0.x_dev
43
+ :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/Testp311_win.yml
44
+
45
+
46
+
47
+
48
+ .. figure:: http://pymodaq.cnrs.fr/en/latest/_static/splash.png
49
+ :alt: shortcut
50
+
51
+
52
+ PyMoDAQ__, Modular Data Acquisition with Python, is a set of **python** modules used to interface any kind of
53
+ experiments. It simplifies the interaction with detector and actuator hardware to go straight to the data acquisition
54
+ of interest.
55
+
56
+ __ https://pymodaq.readthedocs.io/en/stable/?badge=latest
57
+
58
+ `PyMoDAQ data`__ is a set of utilities (constants, methods and classes) that are used
59
+ for Data Management. It is heavily used with the PyMoDAQ framework but can also be used as a standalone
60
+ package for data management in another context.
61
+
62
+ __ https://pymodaq.cnrs.fr/en/latest/developer_folder/data_management.html
63
+
64
+ What are Data?
65
+ --------------
66
+
67
+ Data are objects with many characteristics able to properly describe real data taken on an experiment
68
+ or calculated from theory:
69
+
70
+
71
+ * a type: float, int, ...
72
+ * a dimensionality: Data0D, Data1D, Data2D and higher
73
+ * units (dealt with the pint python package)
74
+ * axes
75
+ * actual data as numpy arrays
76
+ * uncertainty/error bars
77
+ * ...
78
+
79
+
80
+ .. figure:: https://pymodaq.cnrs.fr/en/latest/_images/data.png
81
+ :alt: What is data?
82
+
83
+ What is PyMoDAQ's data?.
84
+
85
+ The `PyMoDAQ Data` package
86
+ --------------------------
87
+
88
+ Because of this variety, `PyMoDAQ Data` introduce a set of objects including metadata (for instance the time of
89
+ acquisition) and various methods and properties to manipulate
90
+ them during analysis for instance (getting name, slicing, concatenating...),
91
+ save them and plot them (given you installed one of the available backend: *matplotlib* or *Qt* (
92
+ through the `pymodaq_gui` package)
93
+
94
+ To learn more, check the documentation__.
95
+
96
+ __ https://pymodaq.cnrs.fr/en/latest/developer_folder/data_management.html
97
+
98
+
99
+ Published under the MIT FREE SOFTWARE LICENSE
100
+
101
+ GitHub repo: https://github.com/PyMoDAQ
102
+
103
+ Documentation: http://pymodaq.cnrs.fr/
pymodaq_data-0.0.1/pyproject.toml ADDED
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+ [build-system]
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+ requires = ["hatchling>=1.9.0", "hatch-vcs"]
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+ build-backend = "hatchling.build"
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+
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+ [project]
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+ name = "pymodaq_data"
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+ dynamic = [
8
+ "version",
9
+ ]
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+ description = "Modular Data Acquisition with Python"
11
+ readme = "README.rst"
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+ license = { file="LICENSE" }
13
+ requires-python = ">=3.8"
14
+ authors = [
15
+ { name = "Sébastien Weber", email = "sebastien.weber@cemes.fr" },
16
+ ]
17
+ classifiers = [
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+ "Development Status :: 5 - Production/Stable",
19
+ "Environment :: Other Environment",
20
+ "Intended Audience :: Science/Research",
21
+ "License :: OSI Approved :: MIT License",
22
+ "Natural Language :: English",
23
+ "Operating System :: OS Independent",
24
+ "Programming Language :: Python :: 3.7",
25
+ "Programming Language :: Python :: 3.8",
26
+ "Programming Language :: Python :: 3.9",
27
+ "Programming Language :: Python :: 3.10",
28
+ "Programming Language :: Python :: 3.11",
29
+ "Topic :: Scientific/Engineering :: Human Machine Interfaces",
30
+ "Topic :: Scientific/Engineering :: Visualization",
31
+ "Topic :: Software Development :: Libraries :: Python Modules",
32
+ "Topic :: Software Development :: User Interfaces",
33
+ ]
34
+ dependencies = [
35
+ "pymodaq_utils",
36
+ "multipledispatch",
37
+ "numpy < 2.0.0",
38
+ "packaging",
39
+ "pint",
40
+ "python-dateutil",
41
+ "scipy",
42
+ "toml",
43
+ "tables<3.9", # issue with some version of required package blosc2>=2.2.8
44
+ ]
45
+
46
+
47
+ [project.urls]
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+ Homepage = "http://pymodaq.cnrs.fr"
49
+ Source = "https://github.com/PyMoDAQ/PyMoDAQ"
50
+ Tracker = "https://github.com/PyMoDAQ/PyMoDAQ/issues"
51
+
52
+ [tool.hatch.version]
53
+ source = "vcs"
54
+
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+ [tool.hatch.build.targets.sdist]
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+ include = [
57
+ "/src",
58
+ ]
pymodaq_data-0.0.1/src/pymodaq_data/__init__.py ADDED
@@ -0,0 +1,53 @@
1
+ import importlib.util
2
+ import os
3
+ import sys
4
+ from pint import UnitRegistry
5
+
6
+ try:
7
+ from pymodaq_utils.logger import set_logger
8
+ from pymodaq_utils.utils import get_version, PackageNotFoundError
9
+ try:
10
+ __version__ = get_version('pymodaq_data')
11
+ except PackageNotFoundError:
12
+ __version__ = '0.0.0dev'
13
+ try:
14
+ logger = set_logger('pymodaq_data', add_handler=True, base_logger=True)
15
+ except Exception:
16
+ print("Couldn't create the local folder to store logs , presets...")
17
+
18
+ logger.info('************************')
19
+ logger.info('Initializing the pint unit register')
20
+ logger.info('************************')
21
+ ureg = UnitRegistry()
22
+ ureg.default_format = '~'
23
+ Q_ = ureg.Quantity
24
+ Unit = ureg.Unit
25
+ logger.info('')
26
+ logger.info('')
27
+
28
+ from pymodaq_data.h5modules.utils import register_exporters
29
+ logger.info('')
30
+ logger.info('')
31
+ logger.info('************************')
32
+ logger.info(f"Registering exporters...")
33
+ register_exporters()
34
+ logger.info(f"Done")
35
+ logger.info('************************')
36
+
37
+ from pymodaq_data.plotting.plotter.plotter import register_plotter, PlotterFactory
38
+ logger.info('')
39
+ logger.info('')
40
+ logger.info('************************')
41
+ logger.info(f"Registering plotters...")
42
+ register_plotter()
43
+ logger.info(f"Done")
44
+ logger.info('************************')
45
+
46
+ from pymodaq_data.data import (DataRaw, DataFromPlugins, DataWithAxes, DataToExport, Axis,
47
+ DataCalculated, DataDim, DataDistribution, DataSource, DataBase)
48
+
49
+ except Exception as e:
50
+ try:
51
+ logger.exception(str(e))
52
+ except Exception as e:
53
+ print(str(e))