Initial commit

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*.pyxbldc
+
+# C extensions
+*.so
+
+# Version info for PyPI
+km3noroot/version.txt
+
+# Distribution / packaging
+.Python
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+.eggs
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+.coverage.*
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Sphinx documentation
+doc/_build/
+doc/auto_examples/
+doc/modules/
+doc/api
+
+# VI swap files
+*.swp
+*.swo
+
+# PyCharm files
+.idea
+
+# jupyter files
+.ipynb_checkpoints/
+
+# 
+junit*.xml
+reports
+
+# misc
+*~
+*.dqd
+*.dat
+
+.pytest_cache/
+.DS_Store
+
+# venv, pyenv tmp
+.python-version
+venv

.gitlab-ci.yml

+image: docker.km3net.de/base/python:3
+
+# Change pip's cache directory to be inside the project directory since we can
+# only cache local items.
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+cache:
+  paths:
+    - .cache/pip
+    - venv/
+  key: "$CI_COMMIT_REF_SLUG"
+
+stages:
+  - test
+  - coverage
+  - doc
+
+.virtualenv_template: &virtualenv_definition |
+  python -V
+  pip install virtualenv
+  virtualenv venv
+  source venv/bin/activate
+  pip install -r requirements-dev.txt
+  make install
+
+.junit_template: &junit_definition
+    artifacts:
+      reports:
+        junit: "reports/junit*.xml"
+
+test-py3.5:
+    image: docker.km3net.de/base/python:3.5
+    stage: test
+    script:
+        - *virtualenv_definition
+        - make test
+    <<: *junit_definition
+
+test-py3.6:
+    image: docker.km3net.de/base/python:3.6
+    stage: test
+    script:
+        - *virtualenv_definition
+        - make test
+    <<: *junit_definition
+
+test-py3.7:
+    image: docker.km3net.de/base/python:3.7
+    stage: test
+    script:
+        - *virtualenv_definition
+        - make test
+    <<: *junit_definition
+
+code-style:
+    image: docker.km3net.de/base/python:3.7
+    stage: test
+    script:
+        - *virtualenv_definition
+        - yapf -r -d -e "venv" .
+    allow_failure: true
+
+coverage:
+    image: docker.km3net.de/base/python:3.6
+    stage: coverage
+    script:
+        - *virtualenv_definition
+        - "make test-cov|grep TOTAL| awk '{printf \"COVERAGE: %.2f%%\", (1-$3/$2)*100 }'"
+    coverage: '/COVERAGE:\s*([0-9]*\.[0-9]*%)/'
+    #     - make test-cov
+    # coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
+    artifacts:
+        paths:
+            - reports/coverage
+
+pages:
+    image: docker.km3net.de/base/python:3.6
+    stage: doc
+    script:
+        - *virtualenv_definition
+        - cd doc && make clean && make html
+        - mv _build/html ../public/
+        - cd .. && mv reports/coverage public/coverage
+    artifacts:
+        paths:
+            - public
+    cache: {}
+    only:
+        - tags
+        - master

LICENSE

+The MIT License (MIT)
+
+Copyright (c) 2014 Tamas Gal
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

Makefile

+PKGNAME=km3io
+
+default: build
+
+all: install
+
+install: 
+	pip install .
+
+install-dev:
+	pip install -r requirements-dev.txt
+	pip install -e .
+
+clean:
+	python setup.py clean --all
+
+test: 
+	py.test --junitxml=./reports/junit.xml -o junit_suite_name=$(PKGNAME) $(PKGNAME)
+
+test-cov:
+	py.test --cov ./ --cov-report term-missing --cov-report xml:reports/coverage.xml --cov-report html:reports/coverage $(PKGNAME)
+
+test-loop: 
+	py.test $(PKGNAME)
+	ptw --ext=.py,.pyx --ignore=doc $(PKGNAME)
+
+flake8: 
+	py.test --flake8
+
+pep8: flake8
+
+docstyle: 
+	py.test --docstyle
+
+lint: 
+	py.test --pylint
+
+dependencies:
+	pip install -Ur requirements.txt
+
+.PHONY: yapf
+yapf:
+	yapf -i -r $(PKGNAME)
+	yapf -i setup.py
+
+.PHONY: all clean install install-dev test  test-nocov flake8 pep8 dependencies docstyle

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'km3io'
+copyright = '2019, Zineb Aly, Tamas Gal, Johannes Schumann'
+author = 'Zineb Aly, Tamas Gal, Johannes Schumann'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

doc/index.rst

+.. km3io documentation master file, created by
+   sphinx-quickstart on Fri Nov  1 14:27:13 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to km3io's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

km3io/DataReader.py

+import uproot
+
+class DataReader:
+
+    def __init__(self, file_path):
+        self.file_path = file_path
+        self.data = uproot.open(self.file_path)['E']
+        self.lazy_data = self.data.lazyarrays()
+
+    def event_reader(self, key):
+        """event_reader function reads data stored in a branch of interest in an event tree.
+        
+        Parameters
+        ----------
+        key : str
+            name of the branch of interest in event data.
+        
+        Returns
+        -------
+        lazyarray
+            Lazyarray of all data stored in a branch of interest (in an event tree). A lazyarray is an array-like
+            object that reads data on demand. Here, only the first and last chunks of data are 
+            read in memory, and not all data in the array. The output of event_reader can be used
+            with all `Numpy's universal functions <https://docs.scipy.org/doc/numpy/reference/ufuncs.html>`.
+        
+        Raises
+        ------
+        NameError
+            Some branches in an Aanet file structure are "fake branches" and do not contain data. Therefore,
+            the keys corresponding to these fake branches are not read.
+        """
+        evt_tree = self.data['Evt']
+        evt_keys = self._event_keys(evt_tree)
+        if key in evt_keys:
+            evt_key_lazy = self.lazy_data[key]
+            return evt_key_lazy
+        else:
+            raise NameError("The event key must be one of the following: 'id', 'det_id', 'mc_id', 'run_id', 'mc_run_id', 'frame_index', 'trigger_mask', 'trigger_counter', 'overlays', 'hits', 'trks', 'w', 'w2list', 'w3list', 'mc_t', 'mc_hits', 'mc_trks', 'comment', 'index', 'flags', 't.fSec', 't.fNanoSec' ")
+
+    def _event_keys(self, evt_tree):
+        """_event_keys function returns a list of all the keys of interest
+            for data analysis, and removes the keys of empty "fake branches" 
+            found in Aanet event files. 
+        
+        Parameters
+        ----------
+        evt_tree : aanet event (Evt) tree.
+        
+        Returns
+        -------
+        list of str
+            list of all the event keys.
+        """
+        fake_branches = ['Evt', 'AAObject', 'TObject','t']
+        t_baskets = ['t.fSec', 't.fNanoSec']
+        # 
+        all_keys_evt = [key.decode('utf-8') for key in evt_tree.keys() if key.decode('utf-8') not in fake_branches] + t_baskets
+        return all_keys_evt
+
+    def hits_reader(self, hits_key):
+        """hits_reader function reads data stored in a branch of interest in hits tree from an Aanet
+        event file.
+        
+        Parameters
+        ----------
+        hits_key : str
+            name of the branch of interest in hits tree.
+        
+        Returns
+        -------
+        lazyarray
+            Lazyarray of all data stored in a branch of interest (in hits tree). A lazyarray is an array-like
+            object that reads data on demand. Here, only the first and last chunks of data are 
+            read in memory, and not all data in the array. The output of event_reader can be used
+            with all `Numpy's universal functions <https://docs.scipy.org/doc/numpy/reference/ufuncs.html>`.
+        
+        Raises
+        ------
+        NameError
+            the hits.key stored in an Aanet file must be used to access the branch of interest
+            from hits tree data.
+        """
+        hits_tree = self.data['Evt']['hits']
+        hits_keys = [key.decode('utf8') for key in hits_tree.keys()]
+        if hits_key in hits_keys:
+            hits_key_lazy = self.lazy_data[hits_key]
+            return hits_key_lazy
+        else:
+            raise NameError("The hits key must be one of the following: 'hits.fUniqueID', 'hits.fBits', 'hits.usr', 'hits.usr_names', 'hits.id', 'hits.dom_id', 'hits.channel_id', 'hits.tdc', 'hits.tot', 'hits.trig', 'hits.pmt_id', 'hits.t', 'hits.a', 'hits.pos.x', 'hits.pos.y', 'hits.pos.z', 'hits.dir.x', 'hits.dir.y', 'hits.dir.z', 'hits.pure_t', 'hits.pure_a', 'hits.type', 'hits.origin', 'hits.pattern_flags'")
+
+    def tracks_reader(self, tracks_key ):
+        """tracks_reader function reads data stored in a branch of interest in tracks tree
+        from an Aanet event file.
+        
+        Parameters
+        ----------
+        tracks_key : str
+            name of the branch of interest in tracks tree.
+        
+        Returns
+        -------
+        lazyarray
+            Lazyarray of all data stored in a branch of interest (in tracks tree). A lazyarray is an array-like
+            object that reads data on demand. Here, only the first and last chunks of data are 
+            read in memory, and not all data in the array. The output of event_reader can be used
+            with all `Numpy's universal functions <https://docs.scipy.org/doc/numpy/reference/ufuncs.html>`.
+        
+        Raises
+        ------
+        NameError
+            the trks.key stored in an Aanet file must be used to access the branch of interest
+            from tracks tree data.
+        """
+        tracks_tree = self.data['Evt']['trks']
+        tracks_keys = [key.decode('utf8') for key in tracks_tree.keys()]
+        if tracks_key in tracks_keys:
+            tracks_key_lazy = self.lazy_data[tracks_key]
+            return tracks_key_lazy
+        else:
+            raise NameError("The tracks key must be one the following: 'trks.fUniqueID', 'trks.fBits', 'trks.usr', 'trks.usr_names', 'trks.id', 'trks.pos.x', 'trks.pos.y', 'trks.pos.z', 'trks.dir.x', 'trks.dir.y', 'trks.dir.z', 'trks.t', 'trks.E', 'trks.len', 'trks.lik', 'trks.type', 'trks.rec_type', 'trks.rec_stages', 'trks.fitinf', 'trks.hit_ids', 'trks.error_matrix', 'trks.comment'")
+
+  
+

km3io/tests/test_km3io.py

+import unittest
+
+
+class TestImport(unittest.TestCase):
+    def test_import(self):
+        import km3io

requirements-dev.txt

+pytest
+pytest-cov
+pytest-flake8
+pytest-pylint
+pytest-watch
+sphinx
+yapf

requirements.txt

+uproot

setup.py

+#!/usr/bin/env python
+# Filename: setup.py
+"""
+The km3io setup script.
+
+"""
+from setuptools import setup
+import sys
+
+with open('requirements.txt') as fobj:
+    requirements = [l.strip() for l in fobj.readlines()]
+
+try:
+    with open("README.rst") as fh:
+        long_description = fh.read()
+except UnicodeDecodeError:
+    long_description = "km3io, a library to read KM3NeT files without ROOT"
+
+setup(
+    name='km3io',
+    url='http://git.km3net.de/km3py/km3io',
+    description='KM3NeT I/O without ROOT',
+    long_description=long_description,
+    author='Zineb Aly, Tamas Gal, Johannes Schumann',
+    author_email='zaly@km3net.de, jschumann@km3net.de, tgal@km3net.de',
+    packages=['km3io'],
+    include_package_data=True,
+    platforms='any',
+    setup_requires=['setuptools_scm'],
+    use_scm_version={
+        'write_to': 'km3io/version.txt',
+        'tag_regex': r'^(?P<prefix>v)?(?P<version>[^\+]+)(?P<suffix>.*)?$',
+    },
+    install_requires=requirements,
+    python_requires='>=3.5',
+    classifiers=[
+        'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
+        'Programming Language :: Python',
+    ],
+)
+
+__author__ = 'Zineb Aly, Tamas Gal and Johannes Schumann'