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Python AlgoMarker API Wrapper

This project provides a Python wrapper for the AlgoMarker C library (libdyn_AlgoMarker.so). The wrapper allows you to interact with AlgoMarker using Python.

Location

You can find the Python library and a tool for querying AlgoMarkers in the MR_Tools at this folder $MR_Tools/AlgoMarker_python_API

Files

  • AlgoMarker.py: Main Python wrapper for the C library. The wrapper will use the new JSON API if available, or fall back to the older API for compatibility.
  • test_algomarker_lib.py: Utility tool that uses AlgoMarker.py to query AlgoMarker.
  • AlgoMarker_minimal.py: Minimal version of the wrapper with fewer functions.
  • simple_app_example.py: Example app demonstrating usage of the minimal wrapper.

Example Usage

Run the utility tool with:

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python $MR_ROOT/Tools/AlgoMarker_python_API/test_algomarker_lib.py \
  --amconfig /nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/lungflag.amconfig \
  --output /tmp/results.txt \
  --add_data_json_path /nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/examples/data.single.json \
  --request_json_path /nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/examples/req.single.json \
  --amlib /nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/lib/libdyn_AlgoMarker.so
  • --amlib (optional): Specify a custom library path.
  • If your request JSON includes "data", you can run:
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python $MR_ROOT/Tools/AlgoMarker_python_API/test_algomarker_lib.py \
  --amconfig /nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/lungflag.amconfig \
  --output /tmp/results.txt \
  --request_json_path /nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/examples/req.full.json

Simple Usage Example

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from AlgoMarker_minimal import AlgoMarker
import json

ALGOMARKER_PATH = '/nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/lungflag.amconfig'
REQUEST_JSON = '/nas1/Products/LungCancer/QA_Versions/LungFlag3.NEW.2023-07-26.With_ButWhy/examples/req.full.json'

def read_text_file(path):
    with open(path, 'r') as fr:
        return fr.read()

with AlgoMarker(ALGOMARKER_PATH) as algomarker:
    discovery_json = algomarker.discovery()
    print('$> discovery - first 100 characters:')
    print(json.dumps(discovery_json, indent=True)[:100])
    print('$> calculate - first 200 characters:')
    resp = algomarker.calculate(read_text_file(REQUEST_JSON))
    print(json.dumps(resp, indent=True)[:200])

print('All Done')

Running as a FastAPI Server

You can also run the wrapper as a FastAPI server. This will wrapper AlgoMarker.py You will need to setup fastapi package with: 

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python -m pip install fastapi

To configure, edit run_server.sh:

  • Set AM_CONFIG to the path of your AlgoMarker .amconfig file.
  • Set AM_LIB to the path of your compiled library (default is /lib/libdyn_AlgoMarker.so in the same directory as the amconfig file).

After editing, you can run the script.