Prepared by Dr. Mohamed Sobh, LIAG (Leibniz Institute for Applied Geophysics)

Reproducible processing of the January 2026 Wadi Ghadir (Eastern Desert, Egypt) survey:

• Gravity: two Scintrex CG-6 meters (#0640 and #0313), GNSS station coordinates, Copernicus GLO-30 DEM and EGM2008 geoid. Products: free-air, simple and complete (terrain-corrected) Bouguer anomalies relative to base 100 for ρ = 2.0–3.0 g/cm³, and Nettleton density analysis.
• Magnetics: diurnally corrected total field. Products: QC and despiking, IGRF-14 anomaly, grids and reduction to the pole.

The technical report is report/REPORT.md. An HTML version with embedded figures is in report/REPORT.html.

With conda or mamba (recommended: rasterio and pyproj come with their binary libraries):

conda env create -f environment.yml
conda activate wghadir
python -m pytest -q              # 18 tests, about 10 s

With pip, using an existing Python ≥ 3.10:

python -m pip install -r requirements.txt
python -m pip install -e .       # optional: makes `import wghadir` work from anywhere

Step by step in Jupyter (recommended for checking every intermediate result):

jupyter lab notebooks/

• notebooks/01_Gravity_Processing.ipynb: gravity, steps 1–14, from loading the CG-6 files to the maps.
• notebooks/02_Magnetic_Processing.ipynb: magnetics, steps 1–8, from loading the workbook to the RTP map.
• notebooks/03_Gravity_OpenSource_Workflow.ipynb: gravity from readings to maps with the open-source stack: pygtide/ETERNA (tide), Boule (normal gravity, gravity disturbance), Harmonica and Choclo (Bouguer and terrain prisms, equivalent sources, filters), Verde (gridding), SGTool (derivatives, tilt angle) and PyGMT (maps). Results go to outputs/open_source/.
• notebooks/04_Section_Modelling_pyGIMLi_SimPEG.ipynb: a cross-section A–B through the residual Bouguer anomaly of notebook 03, 2-D forward modelling with polygons and a depth-weighted 2-D inversion with pyGIMLi (with L-curve), and a 3-D inversion of the gridded residual with SimPEG. Results go to outputs/modelling/.
• notebooks/05_Magnetic_Modelling_pyGIMLi_SimPEG.ipynb: the strongest magnetic anomaly (south-west) in 3-D: a best-fitting block and a depth-weighted inversion with pyGIMLi (MagneticsModelling, Holstein kernels) and a susceptibility inversion with χ ≥ 0 with SimPEG, cut along a north–south section. Results go to outputs/modelling_magnetic/.
• notebooks/06_SimPEG_Gravity_Inversion.ipynb, 07_SimPEG_Magnetic_Inversion.ipynb and 08_SimPEG_Joint_Inversion.ipynb: 3-D inversions of the whole survey with SimPEG on one common mesh below the Copernicus topography: density contrast from the residual complete Bouguer stations (06), susceptibility with χ ≥ 0 from the magnetic readings (07), and both together coupled by a cross-gradient term (08), with data fits, slices, sections, structural similarity and a joint classification. All three are compact inversions: sparse norms (p = 0 on the model, p = 1 on its gradients) solved by iteratively re-weighted least squares (IRLS) within realistic bounds (Δρ ±0.3 g/cm³, χ 0–0.3 SI); the smooth L2 models are run first and kept for comparison. Shared code: wghadir/inversion.py; results in outputs/inversion/ (NumPy, UBC-GIF, CSV). The executed notebooks are also in notebooks/html/ as stand-alone web pages.

Each step has a ✏️ PARAMETERS cell (thresholds, densities, grid spacing and so on, all editable), a ▶ PROCESSING cell that calls the wghadir functions directly, and a 📊 RESULT cell with tables and plots made in the notebook. After a change, re-run that step and the steps below it. The default parameters reproduce the delivered results.

Interactive lab in the browser: open web/Wadi_Ghadir_Gravity_Lab.html in any browser (no installation). It runs the gravity chain in JavaScript on the raw CG-6 files, with every parameter adjustable, and accepts your own CG-6 exports and station table (chapter 2.1). After gridding (5.1) it offers 16 filters and the power spectrum (5.2), cross-sections drawn on the map (6.1), 2-D forward modelling with draggable polygons (6.2), a depth-weighted 2-D inversion with L-curve (6.3), the pyGIMLi and SimPEG results of notebook 04 (6.4), and exports (7.2).

Interactive magnetic lab: web/Wadi_Ghadir_Magnetic_Lab.html runs the magnetic chain the same way, from the readings (workbook or CSV, chapter 2.1) through day segments, Hampel despike, IGRF-14, crossovers, gridding and reduction to the pole to filters and the power spectrum, cross-sections, 2-D magnetic forward modelling (polygons with susceptibility and remanence), a 2-D susceptibility inversion with χ ≥ 0 and the pyGIMLi and SimPEG results of notebook 05. Rebuild it with python scripts/build_magnetic_lab.py. Rebuild it after changing the Python results with python scripts/build_gravity_lab.py; its sources are in web/src/.

Inversion explorer: web/Wadi_Ghadir_Inversion_Explorer.html shows the SimPEG inversions of notebooks 06–08 interactively: horizontal slices at any elevation, vertical sections along preset or hand-drawn lines, a 3-D view of the anomalous cells under the terrain, side-by-side comparison of any two models (compact, smooth, joint, joint units), the data fit of every model (maps, cross-plot, residual histogram) and the convergence of every run. Rebuild it with python scripts/build_inversion_explorer.py after running the notebooks.

From the command line:

python scripts/run_all.py                # gravity, then magnetics (~5 min incl. 400 dpi maps)
python scripts/run_gravity.py            # gravity only   (--no-figures: ~1 min)
python scripts/run_magnetics.py          # magnetics only (~1 min)
python scripts/build_gravity_lab.py      # rebuild web/Wadi_Ghadir_Gravity_Lab.html
python scripts/build_magnetic_lab.py     # rebuild web/Wadi_Ghadir_Magnetic_Lab.html
python scripts/build_inversion_explorer.py  # rebuild web/Wadi_Ghadir_Inversion_Explorer.html

From Python:

from wghadir.chains import GravityChain, MagneticChain

g = GravityChain(raw_dir="data/raw", external_dir="data/external", out_dir="outputs")
g.step01_inventory()          # ... each step can be run and inspected separately
g.run_all()                   # or all 14 steps

m = MagneticChain(mag_file="data/raw/magnetics/All_Data_Corrected_Total_Intensity.xlsx", out_dir="outputs")
m.run_all()

Gravity step 7 needs the Copernicus GLO-30 DEM window (12 MB) and the EGM2008 geoid window in data/external/. Both are in the repository. In the code-only zip (Wadi_Ghadir_Processing_Chains.zip) the DEM is left out to keep the download small, and step 7 downloads it automatically on the first run (internet needed once; it is then cached).

All tunable values are in wghadir/gravity/settings.py and wghadir/magnetic/settings.py.

environment.yml, requirements.txt, pyproject.toml   installation
notebooks/                 01_Gravity_Processing, 02_Magnetic_Processing, 03_Gravity_OpenSource_Workflow,
                           04_Section_Modelling_pyGIMLi_SimPEG, 05_Magnetic_Modelling_pyGIMLi_SimPEG,
                           06/07/08_SimPEG_{Gravity,Magnetic,Joint}_Inversion (.ipynb); html/ (web versions)
web/                       Wadi_Ghadir_Gravity_Lab.html, Wadi_Ghadir_Magnetic_Lab.html (interactive labs), Wadi_Ghadir_Inversion_Explorer.html, sources in web/src/
third_party/sgtool/        SGTool filter engine (MIT, vendored unchanged; see its README)
scripts/                   run_all.py, run_gravity.py, run_magnetics.py, build_report_html.py, make_package.py
wghadir/
  chains/gravity.py        GravityChain   – the gravity chain, steps 1-14
  chains/magnetic.py       MagneticChain  – the magnetic chain, steps 1-8
  gravity/                 settings, cg6 reader, tide, qc, gnss, inventory, positioning, base_control,
                           instruments, reduce, terrain, reductions, nettleton, density,
                           figures, maps, nettleton_figs, export
  magnetic/                settings, processing (QC, IGRF, gridding, RTP), maps, export
  common/                  geodata (DEM, geoid), mapping (map style), excel, display (notebooks)
tests/                     regression tests (python -m pytest -q)
data/raw/                  supplied files, unchanged (SHA-256 in outputs/tables/01_file_inventory.csv)
data/external/             Copernicus GLO-30 and EGM2008 windows used (with provenance)
outputs/                   results: deliverables/, tables/, maps/, grids/, figures/, nettleton/, magnetics/,
                           open_source/ (notebook 03), modelling/ (notebook 04), modelling_magnetic/ (notebook 05),
                           inversion/ (notebooks 06-08)
report/                    REPORT.md and REPORT.html
reference_results/         (zip only) delivered result sheets and summaries, to compare a local run with