Passing my observed data to distance()

I have a rather simple setup with a list of observed data (plus some other parameters), a custom synthetic data generator function, and a custom and distance estimator between the observed and synthetic data.

I don’t understand how to pass the observed data to the distance() function. Below is a (non-working) minimal example of my setup. Could you point me on how I should modify this to make it work please?

import pyabc
import os
import tempfile
from . import synth_data_generator, custom_dist


# This list contains data required for the synth_data_generator() function
synth_args = [...]
# This list contains my observed data and some other objects required for
# my custom_dist() function
obs_data = [...]

def model(parameter):
    model_p = (parameter['A'], parameter['B'])
    synth_data = synth_data_generator(model_p, *synth_args)
    return synth_data

def distance(synth_data):
    return custom_dist(synth_data, obs_data)


prior = pyabc.Distribution(A=pyabc.RV("uniform", 0, 1), B=pyabc.RV("uniform", 100, 10000))
abc = pyabc.ABCSMC(model, prior, distance, population_size=10)

db_path = ("sqlite:///" + os.path.join(tempfile.gettempdir(), "test.db"))
abc.new(db_path)

history = abc.run(minimum_epsilon=.1, max_nr_populations=10)

[yannikschaelte]

With minimal modifications, the code in your third comment should look like:

import numpy as np
import pyabc
import os
import tempfile


def main(obs_data, synth_args):
    """
    """
    prior = pyabc.Distribution(
        A=pyabc.RV("uniform", 0, 1),
        B=pyabc.RV("uniform", 100, 10000),
    )

    def model(parameter):
        model_p = (parameter['A'], parameter['B'])
        synth_data = synth_data_generator(model_p, synth_args)
        return {"y": synth_data}

    # Y: Two args: Simulation and observation (automatically filled by pyABC)
    def distance(synth, obs): # <-- DUMMY PARAMETER HERE
        return custom_dist(synth['y'], obs["y"])

    abc = pyabc.ABCSMC(model, prior, distance, population_size=10)

    db_path = ("sqlite:///" + os.path.join(tempfile.gettempdir(), "test.db"))
    # Y: Pass observed data (not necessary if distance custom-handles 2nd argument but always better)
    abc.new(db_path, obs_data)

    history = abc.run(minimum_epsilon=-.1, max_nr_populations=10)
    breakpoint()


def synth_data_generator(model_p, synth_args):
    synth_data = np.random.uniform(4.)
    return synth_data


def custom_dist(synth_data, obs_data):
    return np.random.uniform()


if __name__ == '__main__':
    # This list contains data required for the synth_data_generator() function
    synth_args = [0.]
    # This list contains my observed data and some other objects required for
    # my custom_dist() function
    # Y: Observed data must be of same form as model, a dictionary
    obs_data = {"y": synth_data_generator({"A": 0.5, "B": 0.6}, synth_args)}
    main(obs_data, synth_args)

[Gabriel-p]

Thank you Yannik