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Add docs (#13)
* Update docstrings and add docs
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‎.github/workflows/doc.yml

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name: documentation
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: write
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jobs:
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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v3
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- name: Install dependencies
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run: |
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pip install sphinx sphinx_rtd_theme myst_parser
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pip install .
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- name: Sphinx build
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run: |
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sphinx-build docs _build
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v3
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if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: _build/
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force_orphan: true

‎docs/Makefile

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

‎docs/api/segfast.loader.rst

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======
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Loader
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======
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.. automethod:: segfast.loader.open

‎docs/api/segfast.memmap_loader.rst

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============
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MemmapLoader
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============
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.. autoclass:: segfast.memmap_loader.MemmapLoader
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:members:
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:undoc-members:
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:member-order: bysource

‎docs/api/segfast.rst

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===
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API
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===
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.. toctree::
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:maxdepth: 5
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segfast.loader
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segfast.memmap_loader
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segfast.segyio_loader
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segfast.trace_header_spec
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segfast.utils

‎docs/api/segfast.segyio_loader.rst

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============
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SegyioLoader
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============
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.. autoclass:: segfast.segyio_loader.SegyioLoader
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:members:
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:undoc-members:
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:member-order: bysource
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.. autoclass:: segfast.segyio_loader.SafeSegyioLoader
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:members:
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:undoc-members:
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:member-order: bysource

‎docs/api/segfast.trace_header_spec.rst

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===============
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TraceHeaderSpec
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===============
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.. autoclass:: segfast.trace_header_spec.TraceHeaderSpec
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:members:
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:undoc-members:
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:member-order: bysource

‎docs/api/segfast.utils.rst

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=====
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Utils
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=====
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.. autoclass:: segfast.utils.ForPoolExecutor

‎docs/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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import sys, os
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sys.path.insert(0, os.path.abspath('..'))
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import segfast
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master_doc = 'index'
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project = 'segfast'
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author = 'Analysis Center'
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copyright = '2024, ' + author
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release = segfast.__version__
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version = '.'.join(release.split('.'))
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.doctest',
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'sphinx.ext.coverage',
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'sphinx.ext.mathjax',
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'sphinx.ext.viewcode',
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'sphinx.ext.githubpages',
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'sphinx.ext.intersphinx',
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'sphinx.ext.napoleon',
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'sphinx_rtd_theme',
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]
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templates_path = ['_templates']
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exclude_patterns = []
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language = 'en'
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_title = "SegFast"
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html_theme = "sphinx_rtd_theme"
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html_static_path = ['_static']
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html_theme_options = {
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'logo_only': False
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}
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {
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'python': ('https://docs.python.org/', None),
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'numpy': ('https://docs.scipy.org/doc/numpy/', None),
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'segyio': ('https://segyio.readthedocs.io/en/latest/', None)
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}

‎docs/index.rst

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.. segfast documentation master file, created by
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sphinx-quickstart on Thu Feb 1 14:09:14 2024.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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segfast documentation
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=====================
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**segfast** is a library for interacting with SEG-Y seismic data. Main features are:
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* Faster access to read data: both traces headers and values
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* Optional bufferization, where the user can provide a preallocated memory to load the data into
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* Convenient API that relies on :class:`numpy.memmap` for most operations, while providing
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`segyio <https://segyio.readthedocs.io/en/latest/>`_ as a fallback engine
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Implementation details
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----------------------
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We rely on **segyio** to infer file-wide parameters.
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For headers and traces, we use custom methods of reading binary data.
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Main differences to **segyio** C++ implementation:
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- we read all of the requested headers in one file-wide sweep, speeding up by an order of magnitude
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compared to the **segyio** sequential read of every requested header.
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Also, we do that in multiple processes across chunks.
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- a memory map over trace data is used for loading values. Avoiding redundant copies and leveraging
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:mod:`numpy` superiority allows to speed up reading, especially in case of trace slicing along the samples axis.
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This is extra relevant in the case of loading horizontal (depth) slices.
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.. toctree::
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:maxdepth: 1
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:titlesonly:
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installation
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start
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segy
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api/segfast

‎docs/installation.rst

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Installation
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============
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* With ``pip``/``pip3``:
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.. code-block:: bash
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pip3 install segfast
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* Developer version (add ``--depth 1`` if needed)
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.. code-block:: bash
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git clone https://github.com/analysiscenter/segfast.git

‎docs/make.bat

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

‎docs/segy.rst

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SEG-Y description
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=================
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The most complete description can be found in `the official SEG-Y specification <https://library.seg.org/pb-assets/technical-standards/seg_y_rev2_0-mar2017-1686080998003.pdf>`_ but here we give
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a brief intro into SEG-Y format.
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The SEG-Y is a binary file divided into several blocks:
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- file-wide information block which in most cases takes the first 3600 bytes:
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- **textual header**: the first 3200 bytes are reserved for textual info about the file. Most of the software uses
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this header to keep acquisition meta, date of creation, author, etc.
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- **binary header**: 3200–3600 bytes contain file-wide headers, which describe the number of traces, the format used
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for storing numbers, the number of samples for each trace, acquisition parameters, etc.
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- (optional) 3600+ bytes can be used to store the **extended textual information**. If there is such a header,
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then this is indicated by the value in one of the 3200–3600 bytes.
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- a sequence of traces, where each trace is a combination of its header and signal data:
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- **trace header** takes the first 240 bytes and describes the meta info about its trace: shot/receiver coordinates,
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the method of acquisition, current trace length, etc. Analogously to binary file header, each trace also
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can have extended headers.
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- **trace data** is usually an array of amplitude values, which can be stored in various numerical types.
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As the original SEG-Y is quite old (1975), one of those numerical formats is IBM float,
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which is very different from standard IEEE floats; therefore, special caution is required to
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correctly decode values from such files.
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For the most part, SEG-Y files are written with a constant size of each trace, although the standard itself allows
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for variable-sized traces. We do not work with such files.

‎docs/start.rst

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Quick start
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===========
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* Open the file:
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.. code-block:: python
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import segfast
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segy_file = segfast.open('/path/to/file.sgy')
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* Load headers:
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.. code-block:: python
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headers = segy_file.load_headers(['CDP_X', 'CDP_Y', 'INLINE_3D', 'CROSSLINE_3D'])
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* Load inline:
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.. code-block:: python
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traces_idx = headers[headers['INLINE_3D'] == INLINE_IDX].index
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inline = segy_file.load_traces(traces_idx)
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* Load certain depths from all traces:
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.. code-block:: python
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segy_file.load_depth_slices(DEPTHS)
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The resulting array will have shape ``(n_traces, len(DEPTHS))`` so it must be processed to be transformed
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to an array of the field shape.

‎pylintrc

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argument-rgx=(.*[a-z][a-z0-9_]{1,30}|[a-z_])$ # snake_case + single letters
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[MESSAGE CONTROL]
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disable=no-value-for-parameter, no-self-use, too-few-public-methods, unsubscriptable-object, no-member, too-many-lines,
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disable=no-value-for-parameter, too-few-public-methods, unsubscriptable-object, no-member, too-many-lines,
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arguments-differ, too-many-locals, import-error, cyclic-import, duplicate-code, relative-beyond-top-level,
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unused-argument, too-many-public-methods, invalid-name, attribute-defined-outside-init, arguments-renamed,
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abstract-method, no-name-in-module, import-self

‎segfast/loader.py

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def Loader(path, engine='memmap', endian='big', strict=False, ignore_geometry=True):
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""" Selector class for loading SEG-Y with either segyio-based loader or memmap-based one. """
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""" Selector class for loading SEG-Y with either segyio-based loader or memmap-based one.
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Parameters
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----------
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path : str
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Path to the SEG-Y file
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engine : 'memmap' or 'segyio'
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Engine to load data from file: ``'memmap'`` is based on :class:`numpy.memmap` created for the whole file and
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``'segyio'`` is for using **segyio** library instruments. in any case, **segyio** is used to load information
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about the entire file (e.g. ``'sample_interval'`` or ``'shape'``).
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endian : 'big' or 'little'
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Byte order in the file.
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strict : bool
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See :func:`segyio.open`
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ignore_geometry : bool
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See :func:`segyio.open`
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Return
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------
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:class:`~.memmap_loader.MemmapLoader` or :class:`~.segyio_loader.SegyioLoader`
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"""
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loader_class = _select_loader_class(engine)
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return loader_class(path=path, endian=endian, strict=strict, ignore_geometry=ignore_geometry)
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open = File = Loader

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