pygdb
A clean-room Python reader for Geosoft's proprietary .gdb ("Geosoft
Database") binary format and the sibling .grd grid format.
It was built using only publicly available information: vendor-published
open-source code and documentation, independent third-party format
readers, one openly-specified independent successor format (.geoh5,
read via the third-party geoh5py library), and byte-level analysis of
real, publicly downloaded .gdb files. No Geosoft software of any kind
(the geosoft/gxapi/gxpy compiled package, Oasis montaj, Geosoft
Desktop, or the free Geosoft Viewer) was installed, imported, or
executed at any point in producing it.
Reading only — writing or mutating .gdb/.grd files (Geosoft's own
proprietary formats) is out of scope. Exporting what's been read into a
different, openly-specified format is a separate concern and is
supported -- see to_xarray/to_geoh5/to_dataframe below.
Installation
pip install python-gdb
The distribution is named python-gdb on PyPI (pygdb was already
registered there for an unrelated project), but the importable package
is pygdb. On a platform/Python version this project publishes a
prebuilt wheel for, that automatically includes the optional Rust
accelerator (see below) -- nothing extra to install or configure.
Elsewhere, pip falls back to building from source, which needs a Rust
toolchain. numpy is the one required dependency (used to return
correctly-shaped arrays -- see Quick start below); everything else is
optional.
Quick start
from pygdb import GDB
db = GDB("example.gdb")
db.compression # CompressionInfo(code=0, name='DB_COMP_NONE', ...)
db.coordinate_systems # ['NAD83 / UTM zone 11N', 'WGS 84'] (best-effort, may be [])
db.coordinate_channels # {'X': 'Easting', 'Y': 'Northing', 'Z': None} (from the
# file's own internal registry, may be all-None)
db.line_names[:5] # ['L1000', 'L1001', 'L1010', 'L1020', 'L1030']
db.channels_on_line("L1000") # channels that actually have data on this line
db.read("L1000", "Easting") # random access by (line name, channel name)
# -> ndarray, shape (n_rows,) for a scalar
# channel, (n_rows, array_width) for a
# VA/array channel (docs/spec.md section 5)
See the docs for the lower-level, slot-index-based
functions GDB is built on.
db.to_xarray("L1000") exports one line (or db.to_xarray() for the
whole file, every line stacked along a "line" coordinate) to an
xarray.Dataset (pip install python-gdb[xarray], an optional
dependency) — see
the docs for how VA/array channels,
duplicate channel names, and whole-file fill values come through.
db.to_geoh5("survey.geoh5") exports the whole file to a
geoh5py.Workspace (pip install python-gdb[geoh5], an optional
dependency) — see the docs for how
line geometry and VA/array channels come through.
db.to_dataframe() exports the whole file (or db.to_dataframe("L1000")
for just one line) to a pandas.DataFrame (pip install python-gdb[pandas], an optional dependency) — see
the docs for how row-count
mismatches and VA/array channels come through.
Optional Rust-accelerated backend
The pure-Python code in pygdb/ is always the reference implementation
and always fully correct and usable on its own — nothing here depends
on Rust. This package is built with maturin
so that an optional Rust extension (pygdb._native, source under
rust/) rides along and is used automatically when present:
it accelerates the two real CPU-bound hot paths profiling found in this
reader — LZRW1 decompression and fixed-width string decoding — roughly
3-6x on real files, measured against this project's own sample corpus,
and decompresses DB_COMP_SIZE (zlib) data ~11% faster than the stdlib
fallback with one fewer copy, using the flate2 crate on its
zlib-rs backend. pygdb/lzrw1.py/pygdb/gdb_reader.py detect it at
import time and fall back to plain Python transparently if it isn't
there.
Building it yourself (e.g. for local development, or a platform without a published wheel) needs a Rust toolchain:
pip install -e ".[dev]" # compiles pygdb._native as part of the install
or, for a release-optimized build without an editable install:
pip install maturin
maturin build --release --manifest-path rust/Cargo.toml
See rust/src/lib.rs for what's implemented (and,
just as importantly, what was tried and deliberately left out after
being benchmarked as not worth it — a parallel batch decoder and a
memory-mapped-file I/O path, both documented there with real numbers),
and .github/workflows/wheels.yml for
the released wheel matrix: an abi3 wheel per platform covering every
non-free-threaded CPython ≥3.12, an abi3.abi3t wheel per platform
(PEP 803) covering both the GIL-enabled and free-threaded builds of
CPython ≥3.15 with a single wheel, and one version-specific wheel per
platform for 3.14's free-threaded build (3.14t has no stable-ABI
option — abi3t only exists from 3.15 onward).
Documentation
Full documentation — the format specification, usage, contributing
guide, and research provenance — is published at
jcapriot.github.io/pygdb,
built from docs/ with Zensical
(published on every GitHub Release — see
.github/workflows/docs.yml). To view a
work-in-progress version locally instead:
pip install -e ".[docs]"
zensical serve
docs/spec.md— the living reference specification for the.gdb/.grdon-disk format, with a confidence rating (confirmed / likely / guess / unknown) on every field. Updated as more real example files are tested against it.docs/reference.md— API reference forpygdb's public surface, generated from its own numpydoc-style docstrings viamkdocstrings.docs/contributing.md— how to report bugs (reproducible example files welcome) and this project's hard boundary on reverse engineering.docs/provenance/— the original research log and write-up this implementation was derived from.CHANGELOG.md— what changed in each release.
Testing
pip install -e ".[dev]"
pytest
Most of the suite is synthetic-fixture unit tests (tests/test_*.py,
minus test_integration_samples.py) that build minimal .gdb/.grd
byte layouts by hand — no sample data required, safe to run anywhere
including CI. tests/test_integration_samples.py additionally
cross-checks the reader against real files in a local, gitignored
samples/ directory when present, and skips (not fails) when it's
absent.
Sample data
Real .gdb/.grd sample files used during development are not
committed to this repository or otherwise redistributed — we don't
necessarily have redistribution rights for them. See
docs/provenance/notes.md for exact
provenance (source URL/DOI/portal, size) for every sample used, so they
can be re-downloaded independently.
License
MIT — Copyright (c) 2026 Joseph Capriotti.
1 maintainer
Metadata
1 maintainer
Release files for python-gdb 0.4.0
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