version increase; documentation example updated

hkraemer · Jan 19, 2021 · 7f9704a · 7f9704a
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diff --git a/README.rst b/README.rst
@@ -37,8 +37,9 @@ it is well documented and embedded in the
 `DynamicalSystems.jl <https://juliadynamics.github.io/DynamicalSystems.jl/dev/>`_ ecosystem.
 For instance, the compuations made in the `Univariate example <https://hkraemer.github.io/PECUZAL_python/univariate_example.html>`_ 
 and the `Multivariate example <https://hkraemer.github.io/PECUZAL_python/multivariate_example.html>`_
-in this documentation took approximately `1500s` (approx. 25 mins) and `7500s` (approx. 2 hours!), respectively. In the Julia implementation
-the exact same computation took `3s` and `20s`, respectively! (running on a 2.8GHz Quad-Core i7,  16GB 1600 MHz DDR3)
+in this documentation took approximately `800s` (approx. 13 mins) and `7500s` (approx. 1 hour and 10 mins!), respectively, even when
+using the `econ` option in the function call, for a  In the Julia implementation
+the exact same computation took `4s` and `25s`, respectively! (running on a 2.8GHz Quad-Core i7,  16GB 1600 MHz DDR3)
 
 
 Documentation

diff --git a/docs/compute_documentation_examples.py b/docs/compute_documentation_examples.py
@@ -17,6 +17,7 @@
 from scipy.integrate import odeint
 
 import matplotlib.pyplot as plt
+from mpl_toolkits import mplot3d
 from pecuzal_embedding import pecuzal_embedding, mi
 
 # integrate Roessler system on standard parameters
@@ -49,7 +50,7 @@ def roessler(x,t):
 plt.subplots_adjust(hspace=.3)
 plt.savefig('mi_and_timeseries_y_comp.png')
 
-Y_reconstruct, tau_vals, ts_vals, Ls, eps = pecuzal_embedding(y, taus = range(100), theiler = 7)
+Y_reconstruct, tau_vals, ts_vals, Ls, eps = pecuzal_embedding(y, taus = range(100), theiler = 7, econ = True)
 
 fig = plt.figure(figsize=(14., 8.))
 ax = plt.subplot(121, projection='3d')
@@ -86,6 +87,8 @@ def roessler(x,t):
 plt.savefig('continuity_univariate.png')
 
 print(Ls)
+L_total_uni = np.sum(Ls)
+print(L_total_uni)
 
 
 ## Multivariate example
@@ -119,14 +122,14 @@ def roessler(x,t):
 plt.subplots_adjust(hspace=.3)
 plt.savefig('mi_and_timeseries_multi.png')
 
-Y_reconstruct, tau_vals, ts_vals, Ls, eps = pecuzal_embedding(data, taus = range(100), theiler = 7)
+Y_reconstruct, tau_vals, ts_vals, Ls, eps = pecuzal_embedding(data, taus = range(100), theiler = 7, econ = True)
 
 print(tau_vals)
 print(ts_vals)
 
 print(Ls)
-L_total = np.sum(Ls[:-1])
-print(L_total)
+L_total_multi = np.sum(Ls)
+print(L_total_multi)
 
 ts_labels = ['x','y','z']
 
@@ -173,4 +176,4 @@ def ar_process(u0, alpha, p, N):
 plt.grid()
 plt.savefig('ar_ts.png')
 
-Y_reconstruct, tau_vals, ts_vals, Ls, eps = pecuzal_embedding(data)
+Y_reconstruct, tau_vals, ts_vals, Ls, eps = pecuzal_embedding(data, econ = True)
diff --git a/docs/source/README.md b/docs/source/README.md
diff --git a/docs/source/images/ar_ts.png b/docs/source/images/ar_ts.png
diff --git a/docs/source/images/continuity_univariate.png b/docs/source/images/continuity_univariate.png
diff --git a/docs/source/images/mi_and_timeseries_multi.png b/docs/source/images/mi_and_timeseries_multi.png
diff --git a/docs/source/images/mi_and_timeseries_y_comp.png b/docs/source/images/mi_and_timeseries_y_comp.png
diff --git a/docs/source/images/reconstruction_multi.png b/docs/source/images/reconstruction_multi.png
diff --git a/docs/source/images/reconstruction_y_comp.png b/docs/source/images/reconstruction_y_comp.png
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="pecuzal_embedding", 
-    version="1.2.1",
+    version="1.3.0",
     author="K.H.Kraemer",
     author_email="[email protected]",
     description="PECUZAL automatic embedding of uni- and multivariate time series",

diff --git a/src/__pycache__/pecuzal_embedding.cpython-37.pyc b/src/__pycache__/pecuzal_embedding.cpython-37.pyc