Fluvial example

.gitignore

@@ -2,12 +2,15 @@
 __pycache__/
 *.nc
 *.pdf
+*.zip
 
 # Sphinx
 docs/_build/
 docs/api/resmda*
 docs/savefig/
 docs/gallery/*
+download/
+docs/sg_execution_times.rst
 
 # Pytest and coverage related
 htmlcov

docs/conf.py

@@ -1,7 +1,6 @@
 import time
 import warnings
 from resmda import __version__
-from sphinx_gallery.sorting import FileNameSortKey
 
 # ==== 1. Extensions  ====
 
@@ -39,17 +38,17 @@
 sphinx_gallery_conf = {
     'examples_dirs': ['../examples', ],
     'gallery_dirs': ['gallery', ],
-    'capture_repr': ('_repr_html_', '__repr__'),
+    'capture_repr': ('_repr_html_', ),
     # Patter to search for example files
     "filename_pattern": r"\.py",
     # Sort gallery example by file name instead of number of lines (default)
-    "within_subsection_order": FileNameSortKey,
+    "within_subsection_order": "FileNameSortKey",
     # Remove the settings (e.g., sphinx_gallery_thumbnail_number)
     'remove_config_comments': True,
     # Show memory
     'show_memory': True,
     # Custom first notebook cell
-    'first_notebook_cell': '%matplotlib notebook',
+    'first_notebook_cell': '%matplotlib widget',
 }
 
 # https://github.com/sphinx-gallery/sphinx-gallery/pull/521/files

examples/basicESMDA.py

@@ -19,8 +19,8 @@
 .. math::
     x_{j,i+1} &= x_{j,i} + (C^e_{xy})_i \left((C^e_{yy})_i +
                  \alpha_iC^e_{dd}\right)^{-1} \left(d + \sqrt{\alpha_i}
-                 \varepsilon_j - g(x_{j,i})\right) \\
-    y_{j,i+1} &= g(x_{j,i+1})
+                 \varepsilon_j - g(x_{j,i})\right) \ , \\
+    y_{j,i+1} &= g(x_{j,i+1}) \ .
 
 The model used for this example is
 
@@ -53,7 +53,7 @@ def forward(x, beta):
 px = np.linspace(-5, 5, 301)
 for i, b in enumerate([0.0, 0.2]):
     axs[i].set_title(
-            f"{['Linear model', 'Nonlinear model'][i]}: $\\beta$ = {b}")
+            f"{['Linear model', 'Nonlinear model'][i]}: β = {b}")
     axs[i].plot(px, forward(px, b))
     axs[i].set_xlabel('x')
     axs[i].set_ylabel('y')
@@ -109,7 +109,6 @@ def plot_result(mpost, dpost, dobs, title, ylim):
     ax2.set_xlabel('y')
     ax2.set_xlim([-5, 8])
     ax2.legend()
-    fig.show()
 
 
 ###############################################################################

examples/basicreservoir.py

@@ -21,7 +21,7 @@
 # ----------------
 
 # Grid extension
-nx = 25
+nx = 30
 ny = 25
 nc = nx*ny
 
@@ -32,7 +32,6 @@
 
 # ESMDA parameters
 ne = 100                  # Number of ensembles
-#  dt = np.logspace(-5, -3, 10)
 dt = np.zeros(10)+0.0001  # Time steps (could be irregular, e.g., increasing!)
 time = np.r_[0, np.cumsum(dt)]
 nt = time.size
@@ -61,25 +60,23 @@
 perm_prior = RP(ne, random=rng)
 
 
-# TODO: change scale in imshow to represent meters
-
 # QC covariance, reference model, and first two random models
-fig, axs = plt.subplots(2, 2, constrained_layout=True)
-axs[0, 0].set_title('Model')
-im = axs[0, 0].imshow(perm_true.T, vmin=perm_min, vmax=perm_max)
-axs[0, 1].set_title('Lower Covariance Matrix')
-im2 = axs[0, 1].imshow(RP.cov, cmap='plasma')
-axs[1, 0].set_title('Random Model 1')
-axs[1, 0].imshow(perm_prior[0, ...].T, vmin=perm_min, vmax=perm_max)
-axs[1, 1].set_title('Random Model 2')
-axs[1, 1].imshow(perm_prior[1, ...].T, vmin=perm_min, vmax=perm_max)
-fig.colorbar(im, ax=axs[1, :], orientation='horizontal',
-             label='Log of Permeability (mD)')
-for ax in axs[1, :]:
-    ax.set_xlabel('x-direction')
-for ax in axs[:, 0]:
-    ax.set_ylabel('y-direction')
-fig.show()
+pinp1 = {"origin": "lower", "vmin": perm_min, "vmax": perm_max}
+fig, axs = plt.subplots(2, 2, figsize=(6, 6), constrained_layout=True)
+axs[0, 0].set_title("Model")
+im = axs[0, 0].imshow(perm_true.T, **pinp1)
+axs[0, 1].set_title("Lower Covariance Matrix")
+im2 = axs[0, 1].imshow(RP.cov, cmap="plasma")
+axs[1, 0].set_title("Random Model 1")
+axs[1, 0].imshow(perm_prior[0, ...].T, **pinp1)
+axs[1, 1].set_title("Random Model 2")
+axs[1, 1].imshow(perm_prior[1, ...].T, **pinp1)
+fig.colorbar(im, ax=axs[1, :], orientation="horizontal",
+             label="Log of Permeability (mD)")
+for ax in axs[1, :].ravel():
+    ax.set_xlabel("x-direction")
+for ax in axs[:, 0].ravel():
+    ax.set_ylabel("y-direction")
 
 
 ###############################################################################
@@ -101,15 +98,14 @@ def sim(x):
 data_obs = rng.normal(data_true, dstd)
 
 # QC data and priors
-fig, ax = plt.subplots(1, 1)
-ax.set_title('Observed and prior data')
-ax.plot(time, data_prior.T, color='.6', alpha=0.5)
-ax.plot(time, data_true, 'ko', label='True data')
-ax.plot(time, data_obs, 'C3o', label='Obs. data')
+fig, ax = plt.subplots(1, 1, constrained_layout=True)
+ax.set_title("Observed and prior data")
+ax.plot(time*24*60*60, data_prior.T, color=".6", alpha=0.5)
+ax.plot(time*24*60*60, data_true, "ko", label="True data")
+ax.plot(time*24*60*60, data_obs, "C3o", label="Obs. data")
 ax.legend()
-ax.set_xlabel('Time (???)')
-ax.set_ylabel('Pressure (???)')
-fig.show()
+ax.set_xlabel("Time (s)")
+ax.set_ylabel("Pressure (bar)")
 
 
 ###############################################################################
@@ -143,14 +139,14 @@ def restrict_permeability(x):
 # and posterior ensembles to see how the models have been updated.
 
 # Plot posterior
-fig, ax = plt.subplots(1, 3, figsize=(12, 5))
-ax[0].set_title('Prior Mean')
-ax[0].imshow(perm_prior.mean(axis=0).T)
-ax[1].set_title('Post Mean')
-ax[1].imshow(perm_post.mean(axis=0).T)
-ax[2].set_title('"Truth"')
-ax[2].imshow(perm_true.T)
-fig.show()
+fig, ax = plt.subplots(1, 2, figsize=(8, 5), constrained_layout=True)
+pinp2 = {"origin": "lower", "vmin": 2.5, "vmax": 3.5}
+ax[0].set_title("Prior Mean")
+im = ax[0].imshow(perm_prior.mean(axis=0).T, **pinp2)
+ax[1].set_title("Post Mean")
+ax[1].imshow(perm_post.mean(axis=0).T, **pinp2)
+fig.colorbar(im, ax=ax, label="Log of Permeability (mD)",
+             orientation="horizontal")
 
 
 ###############################################################################
@@ -162,15 +158,14 @@ def restrict_permeability(x):
 
 
 # Compare posterior to prior and observed data
-fig, ax = plt.subplots(1, 1)
-ax.set_title('Prior and posterior data')
-ax.plot(time, data_prior.T, color='.6', alpha=0.5)
-ax.plot(time, data_post.T, color='C0', alpha=0.5)
-ax.plot(time, data_true, 'ko')
-ax.plot(time, data_obs, 'C3o')
-ax.set_xlabel('Time (???)')
-ax.set_ylabel('Pressure (???)')
-fig.show()
+fig, ax = plt.subplots(1, 1, constrained_layout=True)
+ax.set_title("Prior and posterior data")
+ax.plot(time*24*60*60, data_prior.T, color=".6", alpha=0.5)
+ax.plot(time*24*60*60, data_post.T, color="C0", alpha=0.5)
+ax.plot(time*24*60*60, data_true, "ko")
+ax.plot(time*24*60*60, data_obs, "C3o")
+ax.set_xlabel("Time (s)")
+ax.set_ylabel("Pressure (bar)")
 
 
 ###############################################################################