medextract 0.3.0

Extract readings from medical device images using a local LLM (Ollama + MedGemma)

medextract

Extract blood pressure readings from medical device photos using a local AI model — no API key, no internet, no cost.

Built on Ollama + MedGemma, the library processes photos of BP monitors and returns structured data (systolic, diastolic, pulse, brand, AHA classification, and 10 more fields) ready for CSV export or direct use in Python.

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Features

• Fully local — runs on your machine via Ollama, no data sent to any server
• No API key required — free to use with no rate limits
• 14 fields extracted per image — systolic, diastolic, pulse, brand, date, time, IHB, AFib, battery, glare, confidence, and more
• Parallel processing — multiple images processed simultaneously
• Progress bar — live tqdm progress with current reading and ETA
• Resume support — safely restart a crashed 1000-image batch without reprocessing
• AHA BP classification — Normal → Elevated → Stage 1/2 → Hypertensive Crisis
• Validation — flags out-of-range and physiologically impossible readings
• Input validation — clear errors for invalid parameters before processing starts
• 37 tests, CI on every push — GitHub Actions runs tests across Python 3.10, 3.11, 3.12
• Works as a Python library or CLI tool

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Prerequisites

Install Ollama, then pull the model:

ollama serve
ollama pull medgemma1.5:4b

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Install

From GitHub:

pip install git+https://github.com/shaunakmirajgaonkar/Healthnexaa.git

For local development:

git clone https://github.com/shaunakmirajgaonkar/Healthnexaa.git
cd Healthnexaa
pip install -e .

Dependencies installed automatically: ollama>=0.6.1, pillow>=10.2.0, pandas>=2.1.1, tqdm>=4.66.1

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Quickstart

Process a folder

from medextract import extract_folder

rows = extract_folder("/path/to/bp-monitor-photos")

for row in rows:
    print(row["systolic"], "/", row["diastolic"], "—", row["bp_classification"])

Single image

from medextract import analyze_image, classify_bp

result = analyze_image("/path/to/photo.jpg")

if result:
    print("Systolic :", result["systolic"])
    print("Diastolic:", result["diastolic"])
    print("Pulse    :", result["pulse"])
    print("Brand    :", result["brand"])
    print("Category :", classify_bp(result["systolic"], result["diastolic"]))
    print("Confidence:", result["confidence"], "/ 10")

Save to CSV

import pandas as pd
from medextract import extract_folder

rows = extract_folder("/path/to/photos")
pd.DataFrame(rows).to_csv("results.csv", index=False)

Validate readings

from medextract import extract_folder, validate_bp, classify_bp

rows = extract_folder("/path/to/photos")

for row in rows:
    warnings = validate_bp(row)
    category = classify_bp(row["systolic"], row["diastolic"])
    print(f"{row['file_name']:30s}  {row['systolic']}/{row['diastolic']}  {category}")
    if warnings:
        print("  WARNINGS:", warnings)

1000+ images — progress bar and resume

from medextract import extract_folder

# tqdm progress bar shown automatically with live BP readout and ETA
rows = extract_folder("/path/to/1000-photos", workers=5)

If the run crashes midway, resume without reprocessing done images:

rows = extract_folder(
    "/path/to/photos",
    resume_csv="results.csv",   # skips files already in this CSV
    workers=5,
)

All parameters

from medextract import extract_folder

rows = extract_folder(
    folder="/path/to/photos",
    model="medgemma1.5:4b",     # any Ollama vision model
    workers=5,                   # parallel workers (more = faster on M2/M3)
    image_size=768,              # max px before encoding (larger = more accurate)
    max_retries=5,               # retries per image on failure
    resume_csv="results.csv",    # resume a crashed batch
)

CLI

# Basic
python3 -m medextract.cli /path/to/photos --output results.csv

# Full options
python3 -m medextract.cli /path/to/photos \
    --output results.csv \
    --workers 5 \
    --model medgemma1.5:4b \
    --image-size 768 \
    --max-retries 5 \
    --resume

# Help
python3 -m medextract.cli --help

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Output Fields

Field	Type	Description
file_name	string	Source image filename
systolic	int	Top BP number (0 if unreadable)
diastolic	int	Bottom BP number (0 if unreadable)
pulse	int	Pulse / BPM (0 if unreadable)
brand	string	Device brand ("Unknown" if not visible)
date	string	Date shown on device (YYYY-MM-DD or null)
time	string	Time shown on device (HH:MM or null)
memory_slot	string	M1, M2, or null
ihb	bool	Irregular heartbeat indicator shown
afib	bool	AFib indicator shown
battery_low	bool	Battery warning shown
has_glare	bool	Glare affecting readability
confidence	int 1–10	Model confidence (always clamped to 1–10)
bp_classification	string	AHA category
extracted_at	string	Timestamp (YYYY-MM-DD HH:MM:SS)

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BP Classification (AHA Standard)

Classification	Systolic	Diastolic
Normal	< 120	< 80
Elevated	120–129	< 80
Stage 1 Hypertension	130–139	80–89
Stage 2 Hypertension	≥ 140	≥ 90
HYPERTENSIVE CRISIS	> 180	> 120

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Performance (Apple Silicon)

Workers	100 images	500 images	1000 images
3 (default)	~19 min	~97 min	~3.2 hrs
5	~12 min	~58 min	~1.9 hrs
8	~7 min	~36 min	~1.2 hrs

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Supported Image Formats

.png .jpg .jpeg .webp

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Running Tests

pip install -e ".[dev]"
pytest tests/ -v

37 tests covering classify_bp, validate_bp, image loading, Ollama checks, input validation, resume, and analyze_image — all with mocked Ollama responses (no model required to run tests).

Tests run automatically on every push and pull request via GitHub Actions across Python 3.10, 3.11, and 3.12.

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Project Structure

medextract/                  ← installable Python library
├── __init__.py              ← public API (5 exports)
├── extractor.py             ← core logic — no global state
└── cli.py                   ← command-line interface

.github/workflows/
└── tests.yml                ← CI — auto-runs tests on every push

tests/                       ← pytest test suite (37 tests)
└── test_extractor.py

examples/                    ← original standalone scripts (reference only)
├── README.md
└── *.py

plans/                       ← project documentation
├── usage-guide.md
├── library-creation-guide.md
├── project-plan.md
└── medical-device-extraction-guide.md

pyproject.toml               ← package config, pinned deps

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License

MIT — see LICENSE