sofar 1.2.1__py3-none-any.whl

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = sofar
+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)

docs/api_reference.rst

@@ -0,0 +1,20 @@
+.. _api_reference:
+
+API Reference
+=============
+
+This section documents sofar objects and functions. Sofar contains functions
+for reading, writing and comparing SOFA files, functions to handle SOFA
+conventions, and two classes to handle data from SOFA files. The
+:py:class:`~sofar.Sofa` class is used to read and write entire SOFA files. To
+open a SOFA file without reading the entire file into memory,
+:py:class:`~sofar.SofaStream` enables partially reading data.
+
+For examples on how to use sofar refer to the
+:ref:`sofar and SOFA <gallery:/gallery/interactive/sofar_introduction.ipynb>`
+notebook and the documentation below.
+
+.. automodule:: sofar
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -0,0 +1,167 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+import urllib3
+import shutil
+sys.path.insert(0, os.path.abspath('..'))
+
+import sofar
+import resources.conventions
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.intersphinx',
+    'autodocsumm',
+    'sphinx_design',
+    'sphinx_favicon',
+    'sphinx_reredirects',
+    'sphinx_mdinclude',
+]
+
+# show tocs for classes and functions of modules using the autodocsumm
+# package
+autodoc_default_options = {'autosummary': True}
+
+# show the code of plots that follows the command .. plot:: based on the
+# package matplotlib.sphinxext.plot_directive
+plot_include_source = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
+
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'sofar'
+copyright = '2020, The pyfar developers'
+author = 'The pyfar developers'
+
+# The version info for the project you're documenting, acts as replacement
+# for |version| and |release|, also used in various other places throughout
+# the built documents.
+#
+# The short X.Y version.
+version = sofar.__version__
+# The full version, including alpha/beta/rc tags.
+release = sofar.__version__
+
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use (Not defining
+# uses the default style of the html_theme).
+# pygments_style = 'sphinx'
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+add_function_parentheses = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+# default language for highlighting in source code
+highlight_language = "python3"
+
+# intersphinx mapping
+intersphinx_mapping = {
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'gallery': ('https://pyfar-gallery.readthedocs.io/en/latest/', None),
+    }
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'pydata_sphinx_theme'
+html_static_path = ['_static']
+html_css_files = ['css/custom.css']
+html_logo = 'resources/logos/pyfar_logos_fixed_size_sofar.png'
+html_title = "sofar"
+html_favicon = '_static/favicon.ico'
+
+# -- HTML theme options
+# https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/layout.html
+html_sidebars = {
+  "sofar": []
+}
+
+html_theme_options = {
+    "navbar_start": ["navbar-logo"],
+    "navbar_end": ["navbar-icon-links", "theme-switcher"],
+    "navbar_align": "content",
+    "header_links_before_dropdown": 8,
+    "icon_links": [
+        {
+          "name": "GitHub",
+          "url": "https://github.com/pyfar",
+          "icon": "fa-brands fa-square-github",
+          "type": "fontawesome",
+        },
+    ],
+    # Configure secondary (right) side bar
+    "show_toc_level": 3,  # Show all subsections of notebooks
+    "secondary_sidebar_items": ["page-toc"],  # Omit 'show source' link that that shows notebook in json format
+    "navigation_with_keys": True,
+    # Configure navigation depth for section navigation
+    "navigation_depth": 1,
+}
+
+html_context = {
+   "default_mode": "light"
+}
+
+# redirect index to pyfar.html
+redirects = {
+     "index": f"{project}.html"
+}
+
+# -- download navbar and style files from gallery -----------------------------
+branch = 'main'
+link = f'https://github.com/pyfar/gallery/raw/{branch}/docs/'
+folders_in = [
+    '_static/css/custom.css',
+    '_static/favicon.ico',
+    '_static/header.rst',
+    'resources/logos/pyfar_logos_fixed_size_sofar.png',
+    ]
+c = urllib3.PoolManager()
+for file in folders_in:
+    url = link + file
+    filename = file
+    os.makedirs(os.path.dirname(filename), exist_ok=True)
+    with c.request('GET', url, preload_content=False) as res, open(filename, 'wb') as out_file:
+        shutil.copyfileobj(res, out_file)
+
+# replace sofar hard link to internal link
+with open("_static/header.rst", "rt") as fin:
+    with open("header.rst", "wt") as fout:
+        for line in fin:
+            fout.write(line.replace(f'https://{project}.readthedocs.io', project))

docs/contributing.rst

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+.. include:: ../CONTRIBUTING.rst

docs/history.rst

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+.. include:: ../HISTORY.rst

docs/index.rst

@@ -0,0 +1,4 @@
+sofar
+=====
+
+.. include:: header.rst

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=sofar
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.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%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/readme.rst

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+.. mdinclude:: ../README.md

docs/resources/conventions.py

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+import os
+import sys
+import json
+sys.path.insert(0, os.path.abspath(os.path.join('..', '..')))
+
+import sofar as sf
+
+base_dir = os.path.dirname(__file__)
+
+# get conventions (paths, names, version) and upgrade rules -------------------
+paths = sf.utils._get_conventions('path')
+names_versions = sf.utils._get_conventions('name_version')
+
+# using Sofa()._verification_rules() does not work on readthedocs
+upgrade_rules = os.path.join(
+    os.path.dirname(paths[0]), '..', 'rules', 'upgrade.json')
+with open(upgrade_rules) as file:
+    upgrade_rules = json.load(file)
+
+deprecation_rules = os.path.join(
+    os.path.dirname(paths[0]), '..', 'rules', 'deprecations.json')
+with open(deprecation_rules) as file:
+    deprecation_rules = json.load(file)
+
+# write general information ---------------------------------------------------
+docs = (
+    '.. _conventions_introduction:\n\n'
+    'SOFA Conventions\n'
+    '================\n\n'
+    'SOFA conventions specify what data and metadata must be stored in a SOFA '
+    'file. Different conventions can be used to store different types of data,'
+    'e.g., head-related impulse responses or musical instrument directivities.'
+    'It is advised to always use the conventions that is most specific for the'
+    'data.\n\n'
+    'In the following, SOFA conventions are described in tables with the '
+    'information\n\n'
+    '* **Name:** The Name of the data. The prefix *GLOBAL* denotes global '
+    'attribute, i.e., attributes that pertain the entire data set. Underscores'
+    ' denote attributes that are data specific. E.g., *SourcePosition_Units* '
+    'denotes the *Units* of the data *SourcePosition*.\n'
+    '* **Type:** The Type of the data.\n\n'
+    '  * **Attribute:** A verbose description given by a string\n'
+    '  * **Double:** A numeric array of data\n'
+    '  * **String:** A string array of data\n\n'
+    '* **Default:** The default value\n'
+    '* **Dimensions:** The dimensions of the data. Lower case letters denote '
+    'the data that sets the dimension.\n\n'
+    '  * **E:** Number of emitters\n'
+    '  * **R:** Number of receivers\n'
+    '  * **M:** Number of measurements\n'
+    '  * **N:** Number of samples or frequency bins of the data\n'
+    '  * **C:** Number of coordinates (always 3)\n'
+    '  * **I:** Unity dimensions (always 1)\n'
+    '  * **S:** Lengths of the longest string contained in the data '
+    '(detected automatically)\n\n'
+    '* **Flags:**\n\n'
+    '  * **r:** read only data. Data can be written if flag is missing.\n'
+    '  * **m:** mandatory data. Data is optional if flag is missing\n\n')
+
+# write table of content ------------------------------------------------------
+docs += '.. _conventions:\n\nConventions\n-----------\n\n'
+for path, name_version in zip(paths, names_versions):
+    name, version = name_version
+
+    label = f'{name} v{version}'
+    if 'deprecated' in path:
+        label += ' (deprecated)'
+    reference = f'{name}_{version}'
+
+    docs += f'* :ref:`{label} <{reference}>`\n'
+
+# write conventions -----------------------------------------------------------
+docs += '\nCurrent\n-------\n\n'
+
+# loop conventions
+deprecated = False
+for path, name_version in zip(paths, names_versions):
+    name, version = name_version
+
+    # read convention from json file
+    with open(path, 'r') as file:
+        convention = json.load(file)
+
+    # write section title
+    if 'deprecated' in path and not deprecated:
+        docs += 'Deprecated\n----------\n\n'
+        deprecated = True
+
+    # write convention name, version
+    docs += f'.. _{name}_{version}:\n\n'
+    docs += f'**{name} v{version}**\n\n'
+
+    # name new convention if current convention is deprecated
+    if deprecated:
+        # upgrade rules give best feedback
+        if name in upgrade_rules:
+            for upgrade in upgrade_rules[name]['from_to']:
+                if version in upgrade[0]:
+                    upgrade_to = upgrade[1]
+                    references = [f':ref:`{u} <{u}>`' for u in upgrade_to]
+                    ':ref:`{label} <{reference}>`'
+                    docs += ('This convention is deprecated. '
+                             f'Use {", ".join(references)} instead.\n\n')
+        # deprecations are used if no upgrade rules are available
+        elif name in deprecation_rules['GLOBAL:SOFAConventions']:
+            docs += ("This convention is deprecated. Use "
+                     f"{deprecation_rules['GLOBAL:SOFAConventions'][name]} "
+                     "instead.\n\n")
+
+    # name purpose of the convention
+    docs += f'{convention["GLOBAL:SOFAConventions"]["comment"]}\n\n'
+
+    # write header
+    docs += (
+        '.. list-table::\n'
+        '   :widths: 20 50 25 30 100\n'
+        '   :header-rows: 1\n\n'
+        '   * - Name (Type)\n'
+        '     - Default\n'
+        '     - Dim.\n'
+        '     - Flags\n'
+        '     - Comment\n')
+
+    # loop entries
+    for key, value in convention.items():
+
+        if value["dimensions"] is None:
+            dimensions = ""
+        else:
+            dimensions = value["dimensions"]
+
+        if value["flags"] is None:
+            flags = ""
+        elif len(value["flags"]) > 1:
+            flags = f'{value["flags"][0]}, {value["flags"][1]}'
+        else:
+            flags = value["flags"]
+
+        if key == "GLOBAL:SOFAConventions":
+            value["comment"] = ""
+
+        if value["type"] == 'attribute':
+            type_str = 'attr.'
+        elif value["type"] == 'double':
+            type_str = 'doub.'
+        else:
+            type_str = 'str.'
+
+        docs += (
+            f'   * - {key.replace(":", "_").replace(".", "_")} '
+            f'(*{value["type"]}*)\n'
+            f'     - {value["default"]}\n'
+            f'     - {dimensions}\n'
+            f'     - {flags}\n'
+            f'     - {value["comment"]}\n')
+
+    docs += '\n:ref:`back to top <conventions>`\n\n'
+
+# write docs to rst file ------------------------------------------------------
+docs_file = os.path.join(base_dir, 'conventions.rst')
+with open(docs_file, 'w') as file:
+    file.writelines(docs)

docs/sofar.rst

@@ -0,0 +1,82 @@
+sofar
+=====
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   readme
+   api_reference
+   resources/conventions
+   contributing
+   history
+
+
+Python package for handling SOFA files.
+
+SOFA files store spatially distributed acoustic data such as head-related
+transfer functions. Sofar can read, create, write, manipulate, and verify SOFA
+files.
+
+.. grid:: 1 2 2 3
+    :gutter: 4
+
+    .. grid-item-card::
+        :link: readme.html
+        :text-align: center
+
+        **Getting Started**
+        ^^^^
+
+        .. raw:: html
+
+            <i class="fa-solid fa-rocket icon-style"></i>
+
+
+    .. grid-item-card::
+        :link: api_reference
+        :link-type: ref
+        :text-align: center
+
+        **API Reference**
+        ^^^^
+
+        .. raw:: html
+
+            <i class="fa-solid fa-file-lines icon-style"></i>
+
+    .. grid-item-card::
+        :link: conventions_introduction
+        :link-type: ref
+        :text-align: center
+
+        **SOFA Conventions**
+        ^^^^
+
+        .. raw:: html
+
+            <i class="fa-solid fa-book-open icon-style"></i>
+
+
+    .. grid-item-card::
+        :link: contributing.html
+        :text-align: center
+
+        **Contributing**
+        ^^^^
+
+        .. raw:: html
+
+            <i class="fa-solid fa-pen icon-style"></i>
+
+    .. grid-item-card::
+        :link: history.html
+        :text-align: center
+
+        **History**
+        ^^^^
+
+        .. raw:: html
+
+            <i class="fa-solid fa-clock-rotate-left icon-style">
+            </i>

sofar/__init__.py

@@ -0,0 +1,28 @@
+"""Main init that determines how the sofar package is structured."""
+# -*- coding: utf-8 -*-
+__author__ = """The pyfar developers"""
+__email__ = 'info@pyfar.org'
+__version__ = '1.2.1'
+
+from .sofa import Sofa
+
+from .sofastream import SofaStream
+
+from .io import read_sofa, read_sofa_as_netcdf, write_sofa
+
+from .utils import (list_conventions,
+                    equals,
+                    version)
+
+from .update_conventions import update_conventions
+
+
+__all__ = ['Sofa',
+           'SofaStream',
+           'update_conventions',
+           'list_conventions',
+           'read_sofa',
+           'read_sofa_as_netcdf',
+           'write_sofa',
+           'equals',
+           'version']