def chivecfn(theta):
            """A version of lnprobfn that returns the simple uncertainty 
            normalized residual instead of the log-posterior, for use with 
            least-squares optimization methods like Levenburg-Marquardt.
            """
            lnp_prior = model.prior_product(theta)
            if not np.isfinite(lnp_prior):
                return -np.infty

            # Generate mean model
            t1 = time.time()
            try:
                spec, phot, x = model.mean_model(theta, obs, sps=sps)
            except(ValueError):
                return -np.infty
            d1 = time.time() - t1

            chispec = chi_spec(spec, obs)
            chiphot = chi_phot(phot, obs)
            return np.concatenate([chispec, chiphot])
예제 #2
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def chivecfn(theta):
    """A version of lnprobfn that returns the simple uncertainty 
    normalized residual instead of the log-posterior, for use with 
    least-squares optimization methods like Levenburg-Marquardt.
    
    It's important to note that the returned chi vector does not 
    include the prior probability.
    """
    lnp_prior = model.prior_product(theta)
    if not np.isfinite(lnp_prior):
        return np.zeros(model.ndim) - np.infty

    # Generate mean model
    try:
        spec, phot, x = model.mean_model(theta, obs, sps=sps)
    except (ValueError):
        return np.zeros(model.ndim) - np.infty

    chispec = chi_spec(spec, obs)
    chiphot = chi_phot(phot, obs)
    return np.concatenate([chispec, chiphot])
예제 #3
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def lnprobfn(theta,
             model=None,
             obs=None,
             residuals=False,
             verbose=run_params['verbose']):
    """Given a parameter vector and optionally a dictionary of observational
    ata and a model object, return the ln of the posterior. This requires that
    an sps object (and if using spectra and gaussian processes, a GP object) be
    instantiated.

    :param theta:
        Input parameter vector, ndarray of shape (ndim,)

    :param model:
        bsfh.sedmodel model object, with attributes including ``params``, a
        dictionary of model parameters.  It must also have ``prior_product()``,
        and ``mean_model()`` methods defined.

    :param obs:
        A dictionary of observational data.  The keys should be
          *``wavelength``
          *``spectrum``
          *``unc``
          *``maggies``
          *``maggies_unc``
          *``filters``
          * and optional spectroscopic ``mask`` and ``phot_mask``.

    :returns lnp:
        Ln posterior probability.
    """
    if model is None:
        model = global_model
    if obs is None:
        obs = global_obs

    # Calculate prior probability and exit if not within prior
    lnp_prior = model.prior_product(theta)
    if not np.isfinite(lnp_prior):
        return -np.infty

    # Generate mean model
    t1 = time.time()
    try:
        spec, phot, x = model.mean_model(theta, obs, sps=sps)
    except (ValueError):
        return -np.infty
    d1 = time.time() - t1

    # Return chi vectors for least-squares optimization
    if residuals:
        chispec = chi_spec(spec, obs)
        chiphot = chi_phot(phot, obs)
        return np.concatenate([chispec, chiphot])

    # Noise modeling
    if spec_noise is not None:
        spec_noise.update(**model.params)
    if phot_noise is not None:
        phot_noise.update(**model.params)
    vectors = {
        'spec': spec,
        'unc': obs['unc'],
        'sed': model._spec,
        'cal': model._speccal,
        'phot': phot,
        'maggies_unc': obs['maggies_unc']
    }

    # Calculate likelihoods
    t2 = time.time()
    lnp_spec = lnlike_spec(spec, obs=obs, spec_noise=spec_noise, **vectors)
    lnp_phot = lnlike_phot(phot, obs=obs, phot_noise=phot_noise, **vectors)
    d2 = time.time() - t2
    if verbose:
        write_log(theta, lnp_prior, lnp_spec, lnp_phot, d1, d2)

    return lnp_prior + lnp_phot + lnp_spec
예제 #4
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def lnprobfn(theta,
             model,
             obs,
             sps,
             verbose=False,
             spec_noise=None,
             phot_noise=None,
             residuals=False):
    """Define the likelihood function.
    Given a parameter vector and a dictionary of observational data and a model
    object, return the ln of the posterior. This requires that an sps object
    (and if using spectra and gaussian processes, a GP object) be instantiated.
    """
    from prospect.likelihood import lnlike_spec, lnlike_phot, chi_spec, chi_phot

    # Calculate the prior probability and exit if not within the prior
    lnp_prior = model.prior_product(theta)
    if not np.isfinite(lnp_prior):
        return -np.infty

    # Generate the mean model--
    t1 = time()
    try:
        model_spec, model_phot, model_extras = model.mean_model(theta,
                                                                obs,
                                                                sps=sps)
    except (ValueError):
        return -np.infty
    d1 = time() - t1

    # Return chi vectors for least-squares optimization--
    if residuals:
        chispec = chi_spec(model_spec, obs)
        chiphot = chi_phot(model_phot, obs)
        return np.concatenate([chispec, chiphot])

    # Noise modeling--
    if spec_noise:
        spec_noise.update(**model.params)
    if phot_noise:
        phot_noise.update(**model.params)

    vectors = {
        'spec': model_spec,  # model spectrum
        'phot': model_phot,  # model photometry
        'sed': model._spec,  # object spectrum
        'cal': model._speccal,  # object calibration spectrum
    }

    # Calculate likelihoods--
    t2 = time()
    lnp_spec = lnlike_spec(model_spec,
                           obs=obs,
                           spec_noise=spec_noise,
                           **vectors)
    lnp_phot = lnlike_phot(model_phot,
                           obs=obs,
                           phot_noise=phot_noise,
                           **vectors)
    d2 = time() - t2
    if False:
        from prospect.likelihood import write_log
        write_log(theta, lnp_prior, lnp_spec, lnp_phot, d1, d2)

    #if (lnp_prior + lnp_phot + lnp_spec) > 0:
    #    print('Total probability is positive!!', lnp_prior, lnp_phot)
    #    pdb.set_trace()

    return lnp_prior + lnp_phot + lnp_spec
예제 #5
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def lnprobfn(theta, model=None, obs=None, residuals=False,
             verbose=run_params['verbose']):
    """Given a parameter vector and optionally a dictionary of observational
    ata and a model object, return the ln of the posterior. This requires that
    an sps object (and if using spectra and gaussian processes, a GP object) be
    instantiated.

    :param theta:
        Input parameter vector, ndarray of shape (ndim,)

    :param model:
        bsfh.sedmodel model object, with attributes including ``params``, a
        dictionary of model parameters.  It must also have ``prior_product()``,
        and ``mean_model()`` methods defined.

    :param obs:
        A dictionary of observational data.  The keys should be
          *``wavelength``
          *``spectrum``
          *``unc``
          *``maggies``
          *``maggies_unc``
          *``filters``
          * and optional spectroscopic ``mask`` and ``phot_mask``.

    :returns lnp:
        Ln posterior probability.
    """
    if model is None:
        model = global_model
    if obs is None:
        obs = global_obs

    # Calculate prior probability and exit if not within prior
    lnp_prior = model.prior_product(theta)
    if not np.isfinite(lnp_prior):
        return -np.infty

    # Generate mean model
    t1 = time.time()
    try:
        spec, phot, x = model.mean_model(theta, obs, sps=sps)
    except(ValueError):
        return -np.infty
    d1 = time.time() - t1

    # Return chi vectors for least-squares optimization
    if residuals:
        chispec = chi_spec(spec, obs)
        chiphot = chi_phot(phot, obs)
        return np.concatenate([chispec, chiphot])
    
    # Noise modeling
    if spec_noise is not None:
        spec_noise.update(**model.params)
    if phot_noise is not None:
        phot_noise.update(**model.params)
    vectors = {'spec': spec, 'unc': obs['unc'],
               'sed': model._spec, 'cal': model._speccal,
               'phot': phot, 'maggies_unc': obs['maggies_unc']}

    # Calculate likelihoods
    t2 = time.time()
    lnp_spec = lnlike_spec(spec, obs=obs, spec_noise=spec_noise, **vectors)
    lnp_phot = lnlike_phot(phot, obs=obs, phot_noise=phot_noise, **vectors)
    d2 = time.time() - t2
    if verbose:
        write_log(theta, lnp_prior, lnp_spec, lnp_phot, d1, d2)

    return lnp_prior + lnp_phot + lnp_spec