Simularium Metrics Calculator

Calculate plot metrics from spatial agent data

Installation

Stable Release: pip install simularium-metrics-calculator
Development Head: pip install git+https://github.com/simularium/metrics-calculator.git

To install in editable mode with all dev dependencies: just install

Quickstart

from simulariumio import FileConverter, InputFileData
from simularium_metrics_calculator import (
    PLOT_TYPE,
    SCATTER_PLOT_MODE,
    MetricsService,
    PlotInfo,
)

# create main class
metrics_service = MetricsService()

# check the metrics that are available to plot
metrics = metrics_service.available_metrics()

# load simularium trajectory data using simulariumio
traj_data = FileConverter(
    input_file=InputFileData(
        file_path=(
            "simularium_metrics_calculator/tests/data/"
            "aster_pull3D_couples_actin_solid_3_frames_small.json"
        )
    )
)._data

# configure some plots
plot1 = PlotInfo(  # Number of agents vs time scatterplot
    plot_type=PLOT_TYPE.SCATTER,
    metric_info_x=metrics[0]["uid"],
    metric_info_y=metrics[2]["uid"],
    scatter_plot_mode=SCATTER_PLOT_MODE.LINES,
)
plot2 = PlotInfo(  # Nearest neighbor distance histogram
    plot_type=PLOT_TYPE.HISTOGRAM,
    metric_info_x=metrics[3]["uid"],
)

# calculate the plot data
result = manager.plot_data(
    traj_data,
    plots=[
        plot1,
        plot2,
    ],
)

Documentation

For full package documentation please visit simularium.github.io/metrics-calculator.

Development

See CONTRIBUTING.md for information related to developing the code.

Apache Software License 2.0