Update Gallery (#217)

- Replace LaTeX in figures by unicode symbols
- Replace implicit by explicit pyplot (OO)
- Use by default coordinate system with positive z upwards
- Update for Jupyterlab
  - Replace %matplotlib notebook by %matplotlib widget
  - Document ipympl along with matplotlib

for frequency domain, reproducing, and published. Missing are time domain and educational.

.gitignore

@@ -8,6 +8,7 @@ docs/savefig/
 docs/gallery/*/
 docs/my*.json
 docs/my*.txt
+docs/sg_execution_times.rst
 
 # Pytest and coverage related
 htmlcov

CHANGELOG.rst

@@ -10,6 +10,16 @@ v2.3.x
 """"""
 
 
+latest
+------
+
+- Gallery Update Part I:
+  - Update for Jupyterlab (ipympl/widget) 
+  - Replaced implicit by explicit pyplots
+  - Use by default a positiv z-upwards coordinate system
+  - Part I: frequency domain; reproducing; published
+
+
 v2.3.1: Julia wrapper
 ---------------------
 

docs/conf.py

@@ -1,7 +1,6 @@
 import time
 import warnings
 from empymod import __version__
-from sphinx_gallery.sorting import FileNameSortKey
 
 # ==== 1. Extensions  ====
 
@@ -51,17 +50,17 @@
         'gallery/reproducing',
         'gallery/published',
         ],
-    '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

docs/manual/installation.rst

@@ -18,7 +18,8 @@ Requirements are the modules ``scipy``, ``numba``, and ``libdlf``.
 The modeller empymod comes with add-ons (``empymod.scripts``). These add-ons
 provide some very specific, additional functionalities. Some of these add-ons
 have additional, optional dependencies such as matplotlib. See the
-*Add-ons*-section for their documentation.
+*Add-ons*-section for their documentation. For interactive plots you will need
+ipympl in addition to matplotlib.
 
 If you are new to Python we recommend using a Python distribution, which will
 ensure that all dependencies are met, specifically properly compiled versions

examples/educational/coordinate_system.py

@@ -193,7 +193,7 @@ def repeated(ax, pm):
 ###############################################################################
 
 # Create figure
-fig = plt.figure(figsize=(8, 3.5))
+fig = plt.figure(figsize=(8, 3.5), constrained_layout=True)
 
 # Left-handed system
 ax1 = fig.add_subplot(121, projection=Axes3D.name, facecolor='w')
@@ -211,9 +211,6 @@ def repeated(ax, pm):
 
 repeated(ax2, 1)
 
-plt.tight_layout()
-plt.show()
-
 
 ###############################################################################
 # Dipole
@@ -274,7 +271,7 @@ def repeated(ax, pm):
 # Plotting the two confirms that the results agree, no matter if we use the LHS
 # or the RHS definition.
 
-plt.figure(figsize=(9, 4))
+plt.figure(figsize=(9, 4), constrained_layout=True)
 
 ax1 = plt.subplot(121)
 plt.title('Real')
@@ -300,9 +297,6 @@ def repeated(ax, pm):
 ax2.yaxis.set_label_position("right")
 ax2.yaxis.tick_right()
 
-plt.tight_layout()
-plt.show()
-
 
 ###############################################################################
 # Bipole [x1, x2, y1, y2, z1, z2]
@@ -338,9 +332,6 @@ def repeated(ax, pm):
 plt.ylabel('$E_x$ (V/m)')
 plt.legend()
 
-plt.show()
-
-
 ###############################################################################
 # Bipole [x, y, z, azimuth, dip]
 # ------------------------------
@@ -373,9 +364,6 @@ def repeated(ax, pm):
 plt.ylabel('$E_x$ (V/m)')
 plt.legend()
 
-plt.show()
-
-
 ###############################################################################
 
 empymod.Report()

examples/educational/dipoles_and_loops.py

@@ -122,7 +122,7 @@
 fs = 16  # Fontsize
 
 # Figure
-fig = plt.figure(figsize=(12, 8))
+fig = plt.figure(figsize=(12, 8), constrained_layout=True)
 
 # Frequency Domain
 plt.subplot(231)
@@ -200,8 +200,6 @@
 fig.text(-0.01, 0.5, 'Amplitude; e-rec (V/m); m-rec (A/m)',
          va='center', rotation='vertical', fontsize=fs, color='.4')
 
-plt.tight_layout()
-plt.show()
 
 ###############################################################################
 # The figure shows the main points of Equations (2) and (3):
@@ -300,7 +298,6 @@ def setplot(name):
 
     # Title
     fig.suptitle(title, y=.95, fontsize=20)
-    plt.show()
 
 
 ###############################################################################

examples/educational/dlf_design.py

@@ -114,8 +114,6 @@ def plotresult(depth, res, zsrc, zrec):
     plt.xlim([0, 20e3])
     plt.ylim([1e-14, 1])
 
-    plt.show()
-
 
 ###############################################################################
 # Plot the individual models

examples/educational/dlf_standard_lagged_splined.py

@@ -66,7 +66,6 @@
 import empymod
 import numpy as np
 import matplotlib.pyplot as plt
-from copy import deepcopy as dc
 plt.style.use('ggplot')
 # sphinx_gallery_thumbnail_number = 3
 
@@ -143,7 +142,7 @@
       [f'{i:G}' for i in np.round(relerror*100, 1)]), '%')
 
 # Figure
-plt.figure(figsize=(10, 4))
+plt.figure(figsize=(10, 4), constrained_layout=True)
 plt.suptitle(r'DLF example for $J_0$ Hankel transform using 5 pt filter',
              y=1.05)
 
@@ -171,9 +170,6 @@
 plt.xlabel(r'$x$')
 plt.xlim([x_x.min(), x_x.max()])
 
-plt.tight_layout()
-plt.show()
-
 ###############################################################################
 # 3. Difference between standard, lagged convolution, and splined DLF
 # -------------------------------------------------------------------
@@ -252,8 +248,6 @@
 plt.ylabel('Fourier transform')
 plt.ylim([-0.1, 1.1])
 
-plt.show()
-
 ###############################################################################
 # 3.2 Lagged Convolution DLF
 # --------------------------
@@ -330,8 +324,6 @@
 plt.ylabel('Fourier transform')
 plt.ylim([-0.1, 1.1])
 
-plt.show()
-
 ###############################################################################
 # 3.3 Splined DLF
 # ---------------
@@ -408,8 +400,6 @@
 plt.ylabel('Fourier transform')
 plt.ylim([-0.1, 1.1])
 
-plt.show()
-
 ###############################################################################
 # 4. Example for the Hankel transform
 # -----------------------------------
@@ -499,9 +489,6 @@
 plt.semilogy(x/1000, np.abs((splin100-resp)/resp), label='Splined 100/dec')
 plt.xlabel('Offset (km)')
 
-plt.tight_layout()
-plt.show()
-
 ###############################################################################
 # Runtimes and number of required wavenumbers for each method:
 #
@@ -554,7 +541,7 @@
 t = np.logspace(0, 2, 100)
 xt = 2000
 
-tparam = dc(params)
+tparam = params.copy()
 tparam['rec'] = [xt, 0, 200]
 tparam['freqtime'] = t
 tparam['signal'] = 0  # Impulse response
@@ -610,9 +597,6 @@
 plt.semilogy(t, np.abs((tspline10-tresp)/tresp), label='Splined 10/dec')
 plt.xlabel('Time (s)')
 
-plt.tight_layout()
-plt.show()
-
 ###############################################################################
 # Runtimes and number of required frequencies for each method:
 #

examples/educational/halfspace_vs_dipole.py

@@ -56,7 +56,6 @@ def plot_t(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dhs', ab=ab, signal=0)
     plot_t(EM, HS, 'Impulse HS', i)
 plt.suptitle('Impulse HS')
-plt.show()
 
 ###############################################################################
 # Switch-on HS
@@ -69,7 +68,6 @@ def plot_t(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dhs', ab=ab, signal=1)
     plot_t(EM, HS, 'Switch-on HS', i)
 plt.suptitle('Switch-on HS')
-plt.show()
 
 ###############################################################################
 # Switch-off HS
@@ -82,7 +80,6 @@ def plot_t(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dhs', ab=ab, signal=-1)
     plot_t(EM, HS, 'Switch-off HS', i)
 plt.suptitle('Switch-off HS')
-plt.show()
 
 ###############################################################################
 # Impulse FS
@@ -95,7 +92,6 @@ def plot_t(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dfs', ab=ab, signal=0)
     plot_t(EM, HS, 'Impulse FS', i)
 plt.suptitle('Impulse FS')
-plt.show()
 
 ###############################################################################
 # Switch-on FS
@@ -108,7 +104,6 @@ def plot_t(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dfs', ab=ab, signal=1)
     plot_t(EM, HS, 'Switch-on FS', i)
 plt.suptitle('Switch-on FS')
-plt.show()
 
 ###############################################################################
 # Switch-off FS
@@ -123,7 +118,6 @@ def plot_t(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dfs', ab=ab, signal=-1)
     plot_t(EM, HS, 'Switch-off FS', i)
 plt.suptitle('Switch-off FS')
-plt.show()
 
 ###############################################################################
 # Frequency domain
@@ -153,7 +147,6 @@ def plot_f(EM, HS, title, i):
     plot_f(EM, HS, 'Frequency HS', i)
 plt.figure('Frequency HS')
 plt.suptitle('Frequency HS')
-plt.show()
 
 ###############################################################################
 # Fullspace
@@ -166,7 +159,6 @@ def plot_f(EM, HS, title, i):
     HS = empymod.analytical(**inpEM, **modFS, solution='dfs', ab=ab)
     plot_f(EM, HS, 'Frequency FS', i)
 plt.suptitle('Frequency FS')
-plt.show()
 
 ###############################################################################
 

examples/educational/ht_ft_with_other_modellers.py

@@ -73,8 +73,6 @@
 plt.xlabel('Frequency (Hz)')
 plt.ylabel('$E_x$ (nV/m)')
 
-plt.show()
-
 ###############################################################################
 # Fourier transform
 # -----------------
@@ -106,8 +104,6 @@
 plt.xlabel('Time (s)')
 plt.ylabel('$E_x$ (uV/m)')
 
-plt.show()
-
 ###############################################################################
 
 empymod.Report()

examples/educational/random_noise_f_domain.py

@@ -211,8 +211,6 @@ def stack(n, data, ntype, **kwargs):
     ax.set_xlim([-4, 10])
 ax2.set_xlabel('Real part')
 
-# fig.tight_layout()
-fig.show()
 
 ###############################################################################
 #

examples/educational/tmte_split.py

@@ -93,8 +93,6 @@
 plt.ylim([1e-17, 1e-9])
 plt.xlim([0, 15])
 
-plt.show()
-
 ###############################################################################
 # The result shows that mainly the TM-mode contributions are sensitive to the
 # reservoir. For TM, all modes contribute significantly except $T^{+-}$, which
@@ -124,8 +122,6 @@
 plt.ylim([1e-17, 1e-9])
 plt.xlim([0, 15])
 
-plt.show()
-
 ###############################################################################
 
 empymod.Report()