Calculate plot metrics from spatial agent data
Project description
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
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