Геологическая практика — Geological Field Practice

Data processing, visualisation, and ML tools for MSU geology field practice (Crimea, 2025).

Structure

geol_prak/
├── data/                          # Input data files
│   ├── rhythms.txt                # Rhythm layer data (letter-number pairs)
│   ├── legend.txt                 # Rock type legend (letter → description)
│   └── table.md                   # Field sample catalogue (150+ entries)
│
├── scripts/                       # Processing & visualisation scripts
│   ├── rhythmogram.py             # ⭐ Rhythmogram plotter (CLI, coloured bars, legend)
│   ├── main.py                    # Early exploratory plot (hardcoded brigade data)
│   ├── diagrams.py                # Pie chart diagrams (size, composition, roundness)
│   └── renumber_table.py          # Markdown table renumbering utility
│
├── outputs/                       # Generated figures
│   ├── rhythms.png
│   └── pie_charts.png
│
├── photos/                        # Field sample photographs (140+ JPGs)
│
├── training/                      # Gemma 4 E4B fine-tuning sub-project
│   ├── train.py                   # JAX/Kauldron training script
│   ├── infer.py                   # Inference on new form images
│   ├── data_pipeline.py           # Grain data pipeline
│   ├── prepare_data.py            # CSV → JSONL conversion
│   └── README.md                  # Full training documentation
│
├── pyproject.toml                 # Python project config (marimo, matplotlib)
├── devenv.nix / devenv.yaml       # Nix devenv configuration
├── uv.lock                        # Python dependency lock
└── .python-version                # Python version pin

Quick start

# Enter the dev environment
devenv shell

# Generate a rhythmogram from data
python scripts/rhythmogram.py --file data/rhythms.txt --legend data/legend.txt

# Generate pie charts
python scripts/diagrams.py

# Renumber a markdown table
python scripts/renumber_table.py data/table.md

Scripts

Script	Purpose
scripts/rhythmogram.py	Labeled horizontal bar plot of rhythm layers with colour-coded rock types and legend. Reads from file or stdin.
scripts/main.py	Older exploratory script with hardcoded brigade data (20, 21, 22). Plots cumulative thickness vs rhythm index.
scripts/diagrams.py	2×3 pie chart grid showing grain size, composition, and roundness distribution for two datasets.
scripts/renumber_table.py	Utility to ensure N п/п column in markdown tables is sequentially numbered. Backs up original to /tmp.
scripts/sort_specimens.py	Sorts the sample table by purpose (stratigraphy → processes → magmatism) then by stratigraphic age (oldest → youngest). Reads from data/table.md, writes to a separate output file.

Training

The training/ directory contains a JAX-based fine-tuning pipeline for Gemma 4 E4B (multimodal) — teaching the model to OCR Russian-language geological sample registration forms. See training/README.md for details.