"""
Calibration of the flooding model
=================================

In this example we are interested in the calibration of the :ref:`flooding model <use-case-flood-model>`.
We calibrate the parameters of a flooding model where only the difference between the
downstream and upstream riverbed levels can be calibrated.
This example shows how to manage the lack of identifiability in a calibration problem.

This example use least squares to calibrate the parametric
model.
Please read :ref:`code_calibration` for more details on code calibration and least squares.
This study is relatively complicated: please read the :doc:`calibration of the Chaboche mechanical model
</auto_calibration/least_squares_and_gaussian_calibration/plot_calibration_chaboche>` first if this is not already done.
The observations that we use in this study are simulated with the script
:doc:`Generate flooding model observations
</auto_calibration/least_squares_and_gaussian_calibration/plot_generate_flooding>`.
"""

# %%
# Parameters to calibrate and observations
# ----------------------------------------
#
# The variables of the model are:
#
# - :math:`Q` : Input. Observed.
# - :math:`K_s`, :math:`Z_v`, :math:`Z_m` : Input. Calibrated.
# - :math:`H`: Output. Observed.
#
# The vector of parameters to calibrate is:
#
# .. math::
#    \theta = (K_s,Z_v,Z_m).
#
# In the description of the :ref:`flooding model<use-case-flood-model>`,
# we see that only one parameter can be identified.
# Hence, calibrating this model requires some regularization.
# We return to this topic when analyzing the singular values of
# the Jacobian matrix.
#
# We consider a sample size equal to:
#
# .. math::
#    n = 10.
#
#
# The observations are the couples :math:`\{(Q_i,H_i)\}_{i=1,...,n}`, i.e. each observation is a
# couple made of the flowrate and the corresponding river height.

from openturns.usecases import flood_model
from matplotlib import pyplot as plt
import openturns.viewer as otv
import numpy as np
import openturns as ot

ot.ResourceMap.SetAsUnsignedInteger("Normal-SmallDimension", 1)

# %%
# Define the observations
# -----------------------
# In practice, we generally use a data set which has been obtained from
# measurements.
# This data set can be loaded using e.g. :meth:`~openturns.Sample.ImportFromCSVFile`.
# Here we import the data from the
# :class:`~openturns.usecases.flood_model.FloodModel`
# class.
fm = flood_model.FloodModel()
Qobs = fm.data[:, 0]
Hobs = fm.data[:, 1]
nbobs = fm.data.getSize()
fm.data

# %%
# Create the physical model
# -------------------------
# We define the model :math:`g` which has 4 inputs and one output H.
#
# The nonlinear least squares algorithm does not take into account for bounds
# in the parameters.
# Therefore, we ensure that the output is computed whatever the inputs.
# The model fails into two situations:
#
# * if :math:`K_s<0`,
# * if :math:`Z_v-Z_m<0`.
#
# In these cases, we return an infinite number, so that the optimization
# algorithm does not get trapped.

# %%


def functionFlooding(X):
    L = 5.0e3
    B = 300.0
    Q, K_s, Z_v, Z_m = X
    alpha = (Z_m - Z_v) / L
    if alpha < 0.0 or K_s <= 0.0:
        H = np.inf
    else:
        H = (Q / (K_s * B * np.sqrt(alpha))) ** (3.0 / 5.0)
    return [H]


g = ot.PythonFunction(4, 1, functionFlooding)
g = ot.MemoizeFunction(g)
g.setInputDescription(["Q ($m^3/s$)", "Ks ($m^{1/3}/s$)", "Zv (m)", "Zm (m)"])
g.setOutputDescription(["H (m)"])

# %%
# Setting the calibration parameters
# ----------------------------------
# Define the value of the reference values of the :math:`\theta` parameter.
# In the Bayesian framework, this is called the mean of the *prior* normal
# distribution.
# In the data assimilation framework, this is called the *background*.
KsInitial = 20.0
ZvInitial = 49.0
ZmInitial = 51.0
thetaPrior = [KsInitial, ZvInitial, ZmInitial]

# %%
# Create the parametric function
# ------------------------------
# In the physical model, the inputs and parameters are ordered as
# presented in the next table.
# Notice that there are no parameters in the physical model.
#
# +-------+----------------+
# | Index | Input variable |
# +=======+================+
# | 0     | Q              |
# +-------+----------------+
# | 1     | Ks             |
# +-------+----------------+
# | 2     | Zv             |
# +-------+----------------+
# | 3     | Zm             |
# +-------+----------------+
#
# +-------+-----------+
# | Index | Parameter |
# +=======+===========+
# | ∅     | ∅         |
# +-------+-----------+
#
# **Table 1.** Indices and names of the inputs and parameters of the physical model.
#
print("Physical Model Inputs:", g.getInputDescription())
print("Physical Model Parameters:", g.getParameterDescription())

# %%
# In order to perform calibration, we have to define a parametric model,
# with observed inputs and parameters to calibrate.
# In order to do this, we create a :class:`~openturns.ParametricFunction`
# where the parameters are `Ks`, `Zv` and `Zm` which have the indices 1, 2
# and 3 in the physical model.
#
# +-------+----------------+
# | Index | Input variable |
# +=======+================+
# | 0     | Q              |
# +-------+----------------+
#
# +-------+-----------+
# | Index | Parameter |
# +=======+===========+
# | 0     | Ks        |
# +-------+-----------+
# | 1     | Zv        |
# +-------+-----------+
# | 2     | Zm        |
# +-------+-----------+
#
# **Table 2.** Indices and names of the inputs and parameters of the parametric model.
#


# %%
# The following statement creates the calibrated function from the model.
# The calibrated parameters :math:`K_s`, :math:`Z_v`, :math:`Z_m` are at
# indices 1, 2, 3 in the inputs arguments of the model.
calibratedIndices = [1, 2, 3]
mycf = ot.ParametricFunction(g, calibratedIndices, thetaPrior)

# %%
# Plot the Y observations versus the X observations.
graph = ot.Graph("Observations", "Q ($m^3/s$)", "H (m)", True)
# Plot the model before calibration
curve = mycf.draw(100.0, 4000.0).getDrawable(0)
curve.setLegend("Model, before calibration")
curve.setLineStyle(ot.ResourceMap.GetAsString("CalibrationResult-ObservationLineStyle"))
graph.add(curve)
# Plot the noisy observations
cloud = ot.Cloud(Qobs, Hobs)
cloud.setLegend("Observations")
cloud.setPointStyle(
    ot.ResourceMap.GetAsString("CalibrationResult-ObservationPointStyle")
)
graph.add(cloud)
#
graph.setLegendPosition("upper left")
view = otv.View(graph)

# %%
# We see that the model does not fit to the data.
# The goal of calibration is to find which parameter best fit to the
# observations.

# %%
# Calibration with linear least squares
# -------------------------------------
# The :class:`~openturns.LinearLeastSquaresCalibration` class performs the linear
# least squares calibration by linearizing the model in the neighbourhood of
# the reference point.
algo = ot.LinearLeastSquaresCalibration(mycf, Qobs, Hobs, thetaPrior, "SVD")

# %%
# The :meth:`~openturns.LinearLeastSquaresCalibration.run` method computes the
# solution of the problem.
algo.run()
calibrationResult = algo.getResult()

# %%
# The :meth:`~openturns.CalibrationResult.getParameterMAP` method returns the
# maximum of the posterior distribution of :math:`\theta`.
thetaMAP = calibrationResult.getParameterMAP()
print("theta After = ", thetaMAP)
print("theta Before = ", thetaPrior)
# %%
# Print the true values of the parameters.
print("True theta")
print("  Ks = ", fm.trueKs)
print("  Zv = ", fm.trueZv)
print("  Zm = ", fm.trueZm)

# %%
# In this case, we see that there seems to be a great distance from the
# reference value of :math:`\theta` to the optimum: the values seem too large in magnitude.
# As we are going to see, there is an identification problem because the
# Jacobian matrix is rank-degenerate.

# %%
# Diagnostic of the identification issue
# --------------------------------------

# %%
# In this section, we show how to diagnose the identification problem.
#
# The :meth:`~openturns.CalibrationResult.getParameterPosterior` method returns
# the posterior normal distribution of :math:`\theta`.

# %%
distributionPosterior = calibrationResult.getParameterPosterior()
print(distributionPosterior)

# %%
# We see that there is a large covariance matrix diagonal.
#
# Let us compute a 95% confidence interval for the solution :math:`\theta^\star`.

# %%
print(
    distributionPosterior.computeBilateralConfidenceIntervalWithMarginalProbability(
        0.95
    )[0]
)

# %%
# The confidence interval is *very* large.
# In order to clarify the situation, we compute the Jacobian matrix of the
# model at the candidate point.

# %%
mycf.setParameter(thetaPrior)
thetaDim = len(thetaPrior)
jacobianMatrix = ot.Matrix(nbobs, thetaDim)
for i in range(nbobs):
    jacobianMatrix[i, :] = mycf.parameterGradient(Qobs[i]).transpose()
print(jacobianMatrix[0:5, :])

# %%
# The rank of the problem can be seen from the singular values of the Jacobian
# matrix.

# %%
print(jacobianMatrix.computeSingularValues())

# %%
# We can see that there are two singular values which are relatively close to zero.
#
# This explains why the Jacobian matrix is close to being rank-degenerate.
#
# Moreover, this allows one to compute the actual dimensionality of the problem.
# The algorithm we use computes the singular values in descending order.
# Moreover, by definition, the singular values are nonnegative.
# We see that the first singular value is close to :math:`10`
# and the others are very close to :math:`0` in comparison.
# This implies that the (numerical) rank of the Jacobian matrix is 1,
# even if there are 3 parameters.
#
# Hence, only one parameter can be identified, be it :math:`K_s`, :math:`Z_v`
# or :math:`Z_m`.
# The choice of the particular parameter to identify is free.
# However, in hydraulic studies, the parameter :math:`K_s` is classically
# calibrated while :math:`Z_v` and :math:`Z_m` are left constant.

# %%
# Conclusion of the linear least squares calibration
# --------------------------------------------------

# %%
# There are several methods to solve the problem.
#
# * Given that the problem is not identifiable, we can use some regularization
#   method. Two methods are provided in the library: the Gaussian linear least
#   squares `GaussianLinearCalibration` and the Gaussian non linear least
#   squares `GaussianNonlinearCalibration`.
# * We can change the problem, replacing it with a problem which is identifiable.
#   In the flooding model, we can view :math:`Z_v` and :math:`Z_m` as
#   constants and calibrate :math:`K_s` only.
#
# In this example, we do not change the problem and see how the different
# methods perform.

# %%
# Calibration with non linear least squares
# -----------------------------------------
# The :class:`~openturns.NonLinearLeastSquaresCalibration` class performs the
# non linear least squares calibration by minimizing the squared Euclidian norm
# between the predictions and the observations.

# %%
algo = ot.NonLinearLeastSquaresCalibration(mycf, Qobs, Hobs, thetaPrior)

# %%
# The :meth:`~openturns.NonLinearLeastSquaresCalibration.run` method computes
# the solution of the problem.
algo.run()
calibrationResult = algo.getResult()

# %%
# Analysis of the results
# -----------------------

# %%
# The :meth:`~openturns.CalibrationResult.getParameterMAP` method returns the
# maximum of the posterior distribution of :math:`\theta`.

# %%
thetaMAP = calibrationResult.getParameterMAP()
print(thetaMAP)

# %%
# We can compute a 95% confidence interval of the parameter :math:`\theta^\star`.
#
# This confidence interval is based on bootstrap, based on a sample size equal
# to 100 (as long as the value of the :class:`~openturns.ResourceMap` key
# "NonLinearLeastSquaresCalibration-BootstrapSize" is unchanged).
# This confidence interval reflects the sensitivity of the optimum
# to the variability in the observations.
print(
    ot.ResourceMap.GetAsUnsignedInteger(
        "NonLinearLeastSquaresCalibration-BootstrapSize"
    )
)

# %%
thetaPosterior = calibrationResult.getParameterPosterior()
print(thetaPosterior.computeBilateralConfidenceIntervalWithMarginalProbability(0.95)[0])

# %%
# In this case, the values of the parameters are quite accurately
# computed.

# %%
# Increase the default number of points in the plots.
# This produces smoother spiky distributions.
ot.ResourceMap.SetAsUnsignedInteger("Distribution-DefaultPointNumber", 300)

# %%
graph = calibrationResult.drawObservationsVsInputs()
graph.setLegendPosition("upper left")
view = otv.View(graph)

# %%
# We see that there is a good fit after calibration, since the predictions after calibration
# are close to the observations.

# %%
graph = calibrationResult.drawObservationsVsPredictions()
view = otv.View(graph)

# %%
# We see that there is a much better fit after calibration, since the
# predictions are close to the diagonal of the graphics.

# %%
observationError = calibrationResult.getObservationsError()
print(observationError)

# %%
# We can see that the observation error has a sample mean close to zero and a
# sample standard deviation approximately equal to 0.11.

# sphinx_gallery_thumbnail_number = 5
graph = calibrationResult.drawResiduals()
graph.setLegendPosition("upper left")
view = otv.View(graph)

# %%
# The analysis of the residuals shows that the distribution is centered on
# zero and symmetric.
# This indicates that the calibration performed well.
# Moreover, the distribution of the residuals is close to being Gaussian.
# This is an important hypothesis of the least squares method so that
# checking that this hypothesis occurs in the study is an important
# verification.

# %%
graph = calibrationResult.drawParameterDistributions()
view = otv.View(
    graph,
    figure_kw={"figsize": (8.0, 3.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(right=0.8, bottom=0.2)


# %%
def plotDistributionGridPDF(distribution):
    """
    Plot the marginal and bi-dimensional iso-PDF on a grid.

    Parameters
    ----------
    distribution : ot.Distribution
        The distribution.

    Returns
    -------
    grid : ot.GridLayout(dimension, dimension)
        The grid of plots.

    """
    dimension = distribution.getDimension()
    grid = ot.GridLayout(dimension, dimension)
    for i in range(dimension):
        for j in range(dimension):
            if i == j:
                distributionI = distribution.getMarginal([i])
                graph = distributionI.drawPDF()
            else:
                distributionJI = distribution.getMarginal([j, i])
                graph = distributionJI.drawPDF()
            graph.setLegends([""])
            graph.setTitle("")
            if i < dimension - 1:
                graph.setXTitle("")
            if j > 0:
                graph.setYTitle("")
            grid.setGraph(i, j, graph)
    grid.setTitle("Iso-PDF values")
    return grid


# %%
# Plot the PDF values of the distribution of the optimum parameters.
grid = plotDistributionGridPDF(thetaPosterior)
view = otv.View(
    grid,
    figure_kw={"figsize": (9.0, 6.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(wspace=1.0, hspace=0.5)

# %%
# Gaussian linear calibration
# ---------------------------

# %%
# The standard deviation of the observations.
sigmaH = 0.5  # (m^2)

# %%
# Define the covariance matrix of the output Y of the model.
errorCovariance = ot.CovarianceMatrix(1)
errorCovariance[0, 0] = sigmaH**2

# %%
# Define the covariance matrix of the parameters :math:`\theta` to calibrate.
sigmaKs = 5.0
sigmaZv = 1.0
sigmaZm = 1.0
#
sigma = ot.CovarianceMatrix(3)
sigma[0, 0] = sigmaKs**2
sigma[1, 1] = sigmaZv**2
sigma[2, 2] = sigmaZm**2
print(sigma)

# %%
# The :class:`~openturns.GaussianLinearCalibration` class performs Gaussian
# linear calibration by linearizing the model in the neighbourhood of the prior.
algo = ot.GaussianLinearCalibration(
    mycf, Qobs, Hobs, thetaPrior, sigma, errorCovariance, "SVD"
)

# %%
# The :meth:`~openturns.GaussianLinearCalibration.run` method computes
# the solution of the problem.
algo.run()
calibrationResult = algo.getResult()

# %%
# Analysis of the results
# -----------------------
# The :meth:`~openturns.CalibrationResult.getParameterMAP` method returns the
# maximum of the posterior distribution of :math:`\theta`.
thetaMAP = calibrationResult.getParameterMAP()
print(thetaMAP)

# %%
graph = calibrationResult.drawObservationsVsInputs()
graph.setLegendPosition("upper left")
view = otv.View(graph)

# %%
# We see that the output of the model after calibration is closer to the
# observations.

# %%
graph = calibrationResult.drawObservationsVsPredictions()
view = otv.View(graph)

# %%
# In this case, the fit is satisfactory after calibration.

# %%
graph = calibrationResult.drawResiduals()
graph.setLegendPosition("upper left")
view = otv.View(graph)

# %%
# We see that the distribution of the residual is centered on zero after
# calibration.

# %%
# The :meth:`~openturns.CalibrationResult.getParameterPosterior` method
# returns the posterior normal distribution of :math:`\theta`.

# %%
distributionPosterior = calibrationResult.getParameterPosterior()
print(distributionPosterior)

# %%
# We can compute a 95% credibility interval of the parameter :math:`\theta^\star`.
print(
    distributionPosterior.computeBilateralConfidenceIntervalWithMarginalProbability(
        0.95
    )[0]
)

# %%
# We see that there is a large uncertainty on the value of the parameter
# :math:`K_s` which can be as small as :math:`14` and as large as :math:`34`.

# %%
# We can compare the prior and posterior distributions of the marginals of :math:`\theta`.

# %%
graph = calibrationResult.drawParameterDistributions()
view = otv.View(
    graph,
    figure_kw={"figsize": (8.0, 3.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(right=0.8, bottom=0.2)

# %%
# The two distributions are different, which shows that the calibration is
# sensitive to the observations (if the observations were not sensitive, the
# two distributions were superimposed).
# Moreover, the two distributions are quite close, which implies that the prior
# distribution has played a role in the calibration (otherwise the two
# distributions would be completely different,
# indicating that only the observations were taken into account).

# %%
# Plot the PDF values of the distribution of the optimum parameters.
grid = plotDistributionGridPDF(thetaPosterior)
view = otv.View(
    grid,
    figure_kw={"figsize": (9.0, 6.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(wspace=1.0, hspace=0.5)

# %%
# Gaussian nonlinear calibration
# ------------------------------
# The :class:`~openturns.GaussianNonLinearCalibration` class performs Gaussian
# nonlinear calibration.
algo = ot.GaussianNonLinearCalibration(
    mycf, Qobs, Hobs, thetaPrior, sigma, errorCovariance
)

# %%
# The :meth:`~openturns.GaussianNonLinearCalibration.run` method computes the
# solution of the problem.
algo.run()
calibrationResult = algo.getResult()

# %%
# Analysis of the results
# -----------------------
# The :meth:`~openturns.CalibrationResult.getParameterMAP` method returns the
# maximum of the posterior distribution of :math:`\theta`.
thetaMAP = calibrationResult.getParameterMAP()
print(thetaMAP)

# %%
graph = calibrationResult.drawObservationsVsInputs()
graph.setLegendPosition("upper left")
view = otv.View(graph)

# %%
# We see that the output of the model after calibration is in the middle of the
# observations: the calibration seems correct.

# %%
graph = calibrationResult.drawObservationsVsPredictions()
view = otv.View(graph)

# %%
# The fit is excellent after calibration. Indeed, the cloud of points after calibration is on the diagonal.

# %%
graph = calibrationResult.drawResiduals()
view = otv.View(
    graph,
    figure_kw={"figsize": (8.0, 4.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(right=0.6)

# %%
# We see that the distribution of the residual is centered on zero.
# This is a proof that the calibration did perform correctly.

# %%
# The :meth:`~openturns.CalibrationResult.getParameterPosterior` method
# returns the posterior normal distribution of :math:`\theta`.
distributionPosterior = calibrationResult.getParameterPosterior()

# %%
# We can compute a 95% credibility interval of the parameter :math:`\theta^\star`.
print(
    distributionPosterior.computeBilateralConfidenceIntervalWithMarginalProbability(
        0.95
    )[0]
)

# %%
# We see that there is a small uncertainty on the value of all parameters.

# %%
# We can compare the prior and posterior distributions of the marginals of :math:`\theta`.
graph = calibrationResult.drawParameterDistributions()
view = otv.View(
    graph,
    figure_kw={"figsize": (8.0, 3.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(right=0.8, bottom=0.2)

# %%
# The two distributions are very different, with a spiky posterior distribution.
# This shows that the calibration is very sensitive to the observations.

# %%
# Plot the PDF values of the distribution of the optimum parameters.
grid = plotDistributionGridPDF(thetaPosterior)
view = otv.View(
    grid,
    figure_kw={"figsize": (9.0, 6.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(wspace=1.0, hspace=0.5)

# %%
# Tuning the posterior distribution estimation
# --------------------------------------------
#
# The "GaussianNonLinearCalibration-BootstrapSize" key of the
# :class:`~openturns.ResourceMap` controls the posterior distribution estimation.
#
# * If "GaussianNonLinearCalibration-BootstrapSize" > 0 (by default it is equal to 100),
#   then a bootstrap resample algorithm is used to see the dispersion of the MAP estimator.
#   This allows one to see the variability of the estimator with respect to
#   the finite noisy observation sample.
# * If "GaussianNonLinearCalibration-BootstrapSize" is zero, then the
#   Gaussian linear calibration estimator is used (i.e. the :class:`~openturns.GaussianLinearCalibration`
#   class) at the optimum. This is called the Laplace approximation.
#

# %%
# The default value of the key is nonzero, meaning that bootstrap is used.
# This can be costly in some cases, because it requires to repeat the
# optimization several times.
print(ot.ResourceMap.GetAsUnsignedInteger("GaussianNonLinearCalibration-BootstrapSize"))

# %%
# We must configure the key before creating the object (otherwise changing
# the parameter does not change the result).
ot.ResourceMap.SetAsUnsignedInteger("GaussianNonLinearCalibration-BootstrapSize", 0)
algo = ot.GaussianNonLinearCalibration(
    mycf, Qobs, Hobs, thetaPrior, sigma, errorCovariance
)
algo.run()
calibrationResult = algo.getResult()
graph = calibrationResult.drawParameterDistributions()
view = otv.View(
    graph,
    figure_kw={"figsize": (8.0, 3.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(right=0.8, bottom=0.2)

# %%
# As we can see, this does not change much the posterior distribution, which remains spiky.

# %%
# Plot the PDF values of the distribution of the optimum parameters.
grid = plotDistributionGridPDF(thetaPosterior)
view = otv.View(
    grid,
    figure_kw={"figsize": (9.0, 6.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
)
plt.subplots_adjust(wspace=1.0, hspace=0.5)

# %%
otv.View.ShowAll()
