test_integration_3inversions.py 9.1 KB
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import os
import time
import shutil
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import numpy as np
import matplotlib.pyplot as plt
import xarray as xr
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import pytest

from pycif.utils.classes.setup import Setup
from pycif.utils.datastores.dump import read_datastore
from pycif.utils.yml import ordered_dump
from pycif.utils.path import init_dir


@pytest.mark.dummy
@pytest.mark.article
@pytest.mark.parametrize(
    "settings", [
        {"mode": "4dvar", "minimizer": "M1QN3"},
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        # {"mode": "4dvar", "minimizer": "congrad"},
        # {"mode": "analytical"},
        # {"mode": "ensrf"}]
    ]
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)
def test_integration_inversion(dummy_config_inversion, settings):
    """
    Integration test that runs the dummy_forward model.
    """

    tmpdir, config, tag = dummy_config_inversion
    
    # Changing mode
    nsimmax = 5
    if config["datavect"]["components"]["fluxes"]\
            ["parameters"]["CH4"]["hresol"] == "hpixels":
        nsimmax = 10
    
    elif config["datavect"]["components"]["fluxes"]\
            ["parameters"]["CH4"]["hresol"] == "global" \
            and settings.get("minimizer", "congrad"):
        nsimmax = 1
        
    if settings["mode"] == "4dvar":
        mode = {
            "plugin": {"name": "4dvar", "version": "std"},
            "minimizer": {
                "plugin": {"name": settings["minimizer"], "version": "std"},
                "simulator": {
                    "plugin": {"name": "gausscost", "version": "std"},
                    "reload_from_previous": True
                },
                "maxiter": nsimmax,
                "nsim": nsimmax,
                "epsg": 0.02,
                "df1": 0.01
            },
            "save_out_netcdf": True
        }
        prior_dir = os.path.join(tmpdir, "obsoperator/fwd_-001/obsvect")
        posterior_dir = os.path.join(tmpdir, "obsoperator/fwd_-002/obsvect")
    
    elif settings["mode"] == "analytical":
        mode = {"plugin": {"name": "analytic", "version": "std",
                           "dump_nc_base_control": True}}
        prior_dir = os.path.join(tmpdir, "obsvect_prior")
        posterior_dir = os.path.join(tmpdir, "obsvect_posterior")
        return
    
    elif settings["mode"] == "ensrf":
        nsimmax *= 2
        mode = {"plugin": {"name": "EnSRF", "version": "std"},
                "nsample": nsimmax}
        prior_dir = os.path.join(tmpdir, "obsvect_prior")
        posterior_dir = os.path.join(tmpdir, "obsvect_posterior")
      
    config["mode"] = mode
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    config["platform"] = {"plugin": {"name": "docker", "version": "cif"}}
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    # Removing MCF to make computation quicker
    del config["model"]["chemistry"]["acspecies"]["MCF"]
    del config["datavect"]["components"]["fluxes"]["parameters"]["MCF"]
    del config["datavect"]["components"]["concs"]["parameters"]["MCF"]
    
    # Dump yml config file
    dummy_config_file = os.path.join(tmpdir, "dummy_config.yml")
    with open(dummy_config_file, "w") as outfile:
        ordered_dump(outfile, config)
    
    # Run as job
    setup = Setup.yaml_to_setup(dummy_config_file)
    setup.todo_init = ["platform"]
    setup = Setup.load_config(setup)
    platform = setup.platform

    job_file = os.path.join(tmpdir,
                            "job_pycif_{}".format(tmpdir[-5:]))

    exe = "{} -m pycif {}".format(platform.python, dummy_config_file)

    job_id = platform.submit_job(
        exe,
        job_file
    )

    # Wait for the end of the execution
    while not platform.check_jobs([job_id]):
        time.sleep(platform.sleep_time)

    # Get results and check that posterior closer to prior
    components = os.listdir(prior_dir)
    for comp in components:
        comp_dir_prior = os.path.join(prior_dir, comp)
        comp_dir_post = os.path.join(posterior_dir, comp)
        parameters = os.listdir(comp_dir_prior)
        for param in parameters:
            param_dir = os.path.join(comp_dir_prior, param)
            monitor_prior = \
                read_datastore(os.path.join(param_dir, "monitor.nc"))

            param_dir = os.path.join(comp_dir_post, param)
            monitor_post = \
                read_datastore(os.path.join(param_dir, "monitor.nc"))

            assert (
                    (monitor_prior.loc[:, "obs"]
                     - monitor_prior.loc[:, "sim"]).pow(2).sum()
                    - (monitor_post.loc[:, "obs"]
                       - monitor_post.loc[:, "sim"]).pow(2).sum()
                    > 0
            )

    # Dump configuration into CIF examples
    tag += "_{}_{}".format(settings["mode"],
                           "" if settings["mode"] != "4dvar"
                           else settings["minimizer"])

    current_dir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
    example_dir = \
        os.path.abspath(os.path.join(current_dir, "../../examples/dummy/"))

    dummy_config_file = \
        os.path.join(example_dir, "config_4dvar_{}.yml".format(tag))
    with open(dummy_config_file, "w") as outfile:
        ordered_dump(outfile, config)
    
    # Loop with different number of simulations
    for nsim in range(10, nsimmax + 1, 10):
        file_config = "{}/dummy_config.yml".format(tmpdir)
        inv_setup = Setup.from_yaml(file_config)

        obs_root = "obsvect_posterior"
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        control_root = "controlvect"
        title = "Analytical"
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        if settings.get("minimizer", None) == "congrad":
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            title = "CONGRAD"
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            obs_root = "obsoperator/fwd_-002/obsvect"
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            control_root = "obsoperator/fwd_-002/controlvect"
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            inv_setup["mode"]["minimizer"]["maxiter"] = int(nsim / 2)
            if os.path.isdir("{}/obsoperator/fwd_-002".format(tmpdir)):
                shutil.rmtree("{}/obsoperator/fwd_-002".format(tmpdir))
        elif settings.get("minimizer", None) == "M1QN3":
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            title = "M1QN3"
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            obs_root = "obsoperator/fwd_-002/obsvect"
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            control_root = "obsoperator/fwd_-002/controlvect"
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            inv_setup["mode"]["minimizer"]["maxiter"] = int(nsim / 2)
            inv_setup["mode"]["minimizer"]["nsim"] = int(nsim / 2)
            if os.path.isdir("{}/obsoperator/fwd_-002".format(tmpdir)):
                shutil.rmtree("{}/obsoperator/fwd_-002".format(tmpdir))
        elif settings["mode"] == "EnSRF":
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            title = "EnSRF"
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            inv_setup["mode"]["nsample"] = nsim
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        # Execute a partial inversion with less simulations
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        inv_setup = Setup.from_dict(inv_setup, convert_none=True)
        inv_setup = inv_setup.load_config(inv_setup)
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        controlvect, obsvect = inv_setup.mode.execute()
        
        # Compute the cost function
        departures = obsvect.ysim - obsvect.yobs
        j_o = 0.5 * (departures * obsvect.rinvprod(departures)).sum()
        
        dx = controlvect.x - controlvect.xb
        bfull = np.linalg.inv(
            inv_setup.controlvect
                .build_b(inv_setup.controlvect)
        )
        j_b = (bfull.dot(dx[:, np.newaxis]) * dx).sum()
        
        # Dump to text file for later plot
        with open("{}/varying_cost_function.txt".format(tmpdir), "a") as f:
            f.write("{} {} {}\n".format(nsim, j_o, j_b))

    # Domain limits
    xmin = inv_setup.domain.xmin
    xmax = inv_setup.domain.xmax
    ymin = inv_setup.domain.ymin
    ymax = inv_setup.domain.ymax

    # Read observations
    file_obs = "{}/obsvect/concs/CH4/monitor.nc".format(tmpdir)
    monitor_ref = read_datastore(file_obs)
    coords = monitor_ref.loc[:, ["lon", "lat", "alt"]].drop_duplicates()
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    # Compute fluxes from control vector
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    file_flx = "{}/{}/fluxes/" \
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               "controlvect_fluxes_CH4.nc".format(tmpdir, control_root)
    ds = xr.open_dataset(file_flx)
    dflx = ds["x_phys"].mean(axis=(0, 1)) - ds["xb_phys"].mean(axis=(0, 1))
    
    # Fetch resolution for figure name
    resol = ""
    if config["datavect"]["components"][
            "fluxes"]["parameters"]["CH4"]["hresol"] == "hpixels":
        if config["datavect"]["components"][
                "fluxes"]["parameters"]["CH4"]["hcorrelations"]["sigma"] == 500:
            resol = "lowcorr"
        else:
            resol = "highcorr"

    elif config["datavect"]["components"]["fluxes"] \
            ["parameters"]["CH4"]["hresol"] == "bands":
        resol = "bands"

    elif config["datavect"]["components"]["fluxes"] \
            ["parameters"]["CH4"]["hresol"] == "global":
        resol = "global"
    
    # Plot the figure
    plt.figure(figsize=(21, 11))
    
    ax0 = plt.axes([0.05, 0.05, 0.73, 0.87])
    im = plt.imshow(dflx, extent=(xmin, xmax, ymin, ymax), cmap="YlOrRd",
                    vmin=-0.2, vmax=0.5)
    sc = plt.scatter(coords["lon"], coords["lat"], c=coords["alt"],
                     cmap="Blues", linewidths=1, edgecolors="k", s=600)
    plt.yticks(fontsize=25)
    plt.xticks(fontsize=25)
    
    ax1 = plt.axes([0.74, 0.05, 0.05, 0.87])
    cb1 = plt.colorbar(im, cax=ax1)
    plt.yticks(fontsize=25)
    plt.ylabel("Fluxes (a.u.)", fontsize=30)
    
    ax2 = plt.axes([0.86, 0.05, 0.05, 0.87])
    cb2 = plt.colorbar(sc, cax=ax2)
    plt.yticks(fontsize=25)
    plt.ylabel("Station altitude (m a.g.l)", fontsize=30)
    
    ax0.set_title(title, fontsize=45)
    plt.savefig("{}/map_dx_{}_{}.pdf".format(tmpdir, title, resol))
    plt.close()