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Commit 4366bbfc authored by freba's avatar freba :call_me:
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Added docstrings: cls `Plotter`.

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......@@ -354,7 +354,7 @@ def rename(df0, df1, identifier="id"):
sns.set_palette([sns.color_palette("Blues_r")[1], sns.color_palette("Greens_r")[1]])
filename = plot_sns(
filename = Plotter.plot_sns(
dfs=dict(
ts_id=dict(system=df, model=dfm), ts_oos=dict(system=df_oos, model=dfm_oos)
),
......@@ -636,8 +636,9 @@ filepath = Plotter.plot_density(stan_results,
#+END_SRC
This code block is associated with subfigure (b) in Figure 5.
#+NAME: c1_stan_ppc
#+begin_src python :exports none :results file :tangle ./Scripts/c1_stan_ppc.py :noweb yes :return filepath
#+begin_src python :exports code :results file :tangle ./Scripts/c1_stan_ppc.py :noweb yes :return filepath
import numpy as np
<<paper_plotting_header>>
import arviz as az
......@@ -686,8 +687,9 @@ filepath = Plotter.plot_ppc(
#+end_src
This code block is associated with Figure 6.
#+NAME: stan_cosimulate_ID_c0
#+begin_src python :results file :exports results :return filename :tangle ./Scripts/stan_cosimulate_ID_c0.py :noweb yes
#+begin_src python :results file :exports both :return filename :tangle ./Scripts/stan_cosimulate_ID_c0.py :noweb yes
from collections import OrderedDict
import numpy as np
......@@ -739,7 +741,7 @@ filename = Plotter.plot_sectors(
#+end_src
* TODO Stan submodels
* WAIT Stan submodels
#+NAME: sindyc_stan_code_12
#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_12.stan
......@@ -836,7 +838,7 @@ generated quantities {
#+end_src
#+NAME: sindyc_stan_code_23
#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_23.stan
#+begin_src stan :exports none :results none :tangle ./Scripts/sindyc_stan_code_23.stan
functions {
real[] dy_dt(real t, real[] y, real[] xi, real[] params, int[] ncupoly) {
vector[ncupoly[1]] poly;
......@@ -930,7 +932,7 @@ generated quantities {
#+end_src
#+NAME: sindyc_stan_code_34
#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_34.stan
#+begin_src stan :exports none :results none :tangle ./Scripts/sindyc_stan_code_34.stan
functions {
real[] dy_dt(real t, real[] y, real[] xi, real[] params, int[] ncupoly) {
vector[ncupoly[1]] poly;
......@@ -1024,7 +1026,7 @@ generated quantities {
#+end_src
#+NAME: sindyc_stan_code_345
#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_345.stan
#+begin_src stan :exports none :results none :tangle ./Scripts/sindyc_stan_code_345.stan
functions {
real[] dy_dt(real t, real[] y, real[] xi, real[] params, int[] ncupoly) {
vector[ncupoly[1]] poly;
......@@ -1122,7 +1124,7 @@ generated quantities {
#+end_src
#+NAME: sindyc_stan_code_124
#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_124.stan
#+begin_src stan :exports none :results none :tangle ./Scripts/sindyc_stan_code_124.stan
functions {
real[] dy_dt(real t, real[] y, real[] xi, real[] params, int[] ncupoly) {
vector[ncupoly[1]] poly;
......@@ -1220,7 +1222,7 @@ generated quantities {
#+end_src
#+NAME: sindyc_stan_code_1234
#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_1234.stan
#+begin_src stan :exports none :results none :tangle ./Scripts/sindyc_stan_code_1234.stan
functions {
real[] dy_dt(real t, real[] y, real[] xi, real[] params, int[] ncupoly) {
vector[ncupoly[1]] poly;
......@@ -1376,7 +1378,7 @@ def read_from_disc(filename="save.pkl"):
*** Prosumer dynamics
Common prosumer response dynamics shared for both the SIMO as well as MIMO example.
Common prosumer response dynamics.
#+NAME: paper_prosumerDynamics
#+begin_src python :results none :exports code
......@@ -1478,7 +1480,9 @@ class Prosumer:
#+end_src
*** SINDyc identification
*** TODO SINDyc identification
#+NAME: code_identification
#+begin_src python
......@@ -1557,7 +1561,7 @@ class Identification:
#+end_src
*** Stan identification
*** TODO Stan identification
#+NAME: code_stan_fitModel
#+begin_src python :results none :exports code
......@@ -1950,7 +1954,11 @@ y_init_rep[1] = normal_rng(z_init[1], sigma[1]);
#+end_src
*** Signal generator
*** TODO Signal generator
Signal generation:
- ...
#+NAME: code_signal_generator
#+begin_src python
......@@ -2063,6 +2071,10 @@ class SignalGenerator:
*** Evaluation
Model performance evaluation routines:
- ...
#+NAME: code_evaluate_fit
#+begin_src python :exports code :results none
def evaluate(systraj, modeltraj, method='nrmse', n=None, t=5):
......@@ -2159,8 +2171,10 @@ def evaluate(systraj, modeltraj, method='nrmse', n=None, t=5):
** Simulation
A common simulation header:
#+NAME: paper_simulation
#+begin_src python :noweb strip-export :exports none
#+begin_src python :noweb strip-export :exports code
<<paper_simulation_header>>
<<code_signal_generator>>
<<code_identification>>
......@@ -2172,7 +2186,11 @@ simulator = Simulator(simspec, mp) # Initialize simulation
#+end_src
*** System simulation
*** TODO System simulation
General system simulation routines:
- ...
#+NAME: code_system_simulator
#+begin_src python
......@@ -2522,7 +2540,11 @@ class SystemSimulator:
#+end_src
*** Simulator class
*** TODO Simulator class
SINDyc system simulation routines:
- ...
#+NAME: paper_simulation_class
#+begin_src python :noweb strip-export :exports none
......@@ -3507,7 +3529,22 @@ class Simulator(SystemSimulator):
#+end_src
** Plotting
** WAIT Plotting
Common plotting routines:
- =annotate= :: Annotate axis instance `ax` with `annotation`.
- =postprocess= :: Plotting postprocessing routines.
- =generate_filepath= :: Wrapper around `os.path.join`, concatenates the default `PLOTPATH` and provided `filename`.
- =savefig= :: Save current figure to absolute filepath via `generate_filepath`.
- =plot_y= :: Plot series `y` in list of pandas DataFrames `dfs` to `filename`.
- =plot_yu= :: Plot series `y` and `u` in list of pandas DataFrames `dfs` with defaults.
- =plot3D= :: Plot in three dimensions.
- =plot_density= :: Plot the posterior density of the variables specified in `var_names`.
- =plot_ppc= :: TODO
- =plot_draws :: TODO
- =plot_sectors= :: TODO
- =plot_sns= :: TODO
#+NAME: paper_plotting_header
#+begin_src python
......@@ -3531,8 +3568,12 @@ class Plotter:
large = (10, 8)
@classmethod
def annotate(self, ax, annotation):
"""
def annotate(self, ax, annotation) -> None:
"""Annotate axis instance `ax` with `annotation`.
Args:
ax (obj): Instance of `matplotlib.pyplot.Axes`.
annotation (str): Text to be added as annotation.
"""
def set_text(ax, text):
......@@ -3567,7 +3608,12 @@ class Plotter:
print("Failed to annotate axis.")
@classmethod
def postprocess(self, axs, **kwargs):
def postprocess(self, axs, **kwargs) -> None:
"""Plotting postprocessing routines.
Args:
axs (list): List of `matplotlib.pyplot.Axes` instances.
"""
ax_labels = kwargs.get("labels")
if ax_labels is not None:
if isinstance(ax_labels, list):
......@@ -3608,17 +3654,43 @@ class Plotter:
sns.despine()
@classmethod
def generate_filepath(self, filename):
def generate_filepath(self, filename) -> str:
"""Wrapper around `os.path.join`, concatenates the default `PLOTPATH`
and provided `filename`.
Args:
filename (str): Filename.
Returns:
absolute_path (str): Absolute filepath.
"""
return os.path.join(PLOTPATH, filename)
@classmethod
def savefig(self, filename):
def savefig(self, filename) -> str:
"""Save current figure to absolute filepath via `generate_filepath`.
Args:
filename (str): Filename.
Returns:
filepath (str): Absolute filepath.
"""
filepath = self.generate_filepath(filename)
plt.savefig(filepath, transparent=True)
return filepath
@classmethod
def plot_y(self, dfs, filename, **kwargs):
def plot_y(self, dfs, filename, **kwargs) -> str:
"""Plot series `y` in list of pandas DataFrames `dfs` to `filename`.
Args:
dfs (list): Of pandas DataFrames.
filename (str): Filename to save to.
Returns:
absolute_filepath (str): Of saved plot.
"""
_, ax = plt.subplots(figsize=kwargs.get("figsize", (8, 4)))
for linestyle, df in zip(Plotter.linestyles, dfs):
......@@ -3646,7 +3718,25 @@ class Plotter:
bw=True,
axs=None,
,**kwargs,
):
) -> str:
"""Plot series `y` and `u` in list of pandas DataFrames `dfs` with
defaults.
Args:
dfs (list): Of pandas DataFrames.
filename (str): Filename to save to.
show (bool): Whether or not to show plotted figure.
save (bool): Whether or not to save plotted figure.
df_P (None/pd.DataFrame): DataFrame with uncertainty estimates.
forcesingle_u (bool): When using a single excitation signal, plot
only this one.
bw (bool): Toggle black and white plotting.
axs (list): Of `matplotlib.pyplot.Axes` instances.
Returns:
absolute_filepath (str): Returned conditionally, based on argument
`save`.
"""
gridspec_kw = kwargs.get("gridspec_kw", None)
if axs is None:
_, axs = plt.subplots(
......@@ -3718,6 +3808,29 @@ class Plotter:
filename="plot3D.pdf",
,**kwargs,
):
"""Plot in three dimensions.
Args:
ode_lin (fun): Linear functional, must accept two array arguments
corresponding to the `x` and `u` spaces (input spaces).
ode_nl (fun): Nonlinear functional, must accept two array arguments
corresponding to the `x` and `u` spaces (input spaces).
xmin (float): Lower boundary definition (`x` space).
xmax (float): Upper boundary definition (`x` space).
umin (float): Lower boundary definition (`u` space).
umax (float): Upper boundary definition (`u` space).
zlim (tuple): Boundary definition (`z` space).
step (float): Grid size.
show (bool): Flag indicating whether to show the plot.
save (bool): Flag indicating whether to save the plot.
fig (None/obj): Figure instance.
ax (None/obj): Axes instance.
filename (str): Filename.
Returns:
None/str/obj: Conditionally returns `None`, plot path (`str`) or
an object `obj`, depending on the input arguments.
"""
from matplotlib.ticker import LinearLocator, FormatStrFormatter
......@@ -3799,6 +3912,26 @@ class Plotter:
):
"""Plot the posterior density of the variables specified in
`var_names`.
Args:
stan_results (dict): Dictionary with results keyed
`densities, fit, df`.
var_names (dict): Dictionary with variable name definitions.
filename (str): Filename specification.
resolution (int): Kernel density evaluation space specification.
var_prior (None): Prior values to plot.
mark_max_LL (bool): Specify whether to mark maximum likelihood in
the plot.
ci (list): Of floating point values defining confidence intervals.
original_model_obj (None): Obtain original model densities.
show (bool): Flag indicating whether to show the plot.
save (bool): Flag indicating whether to save the plot.
var_labels (None/list): If provided as list, specifies the variable
labels of the plot.
Returns:
None, str: Conditionally returns the absolute filepath to the plot
based on the input arguments.
"""
var_prior_ = var_prior[var_prior != 0]
from scipy import stats
......@@ -4098,7 +4231,8 @@ class Plotter:
return ax, sm
def plot_sns(dfs, filename, show=False, save=True):
@classmethod
def plot_sns(self, dfs, filename, show=False, save=True):
"""Cosimulation and out of sample plot.
"""
filepath = os.path.join(PLOTPATH, filename)
......
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