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Merge pull request #177 from mcflugen/mcflugen/plot-directives-to-doc…
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…tests-strat

Convert docstring plot directives to doctests for strat.py
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@mcflugen
mcflugen authored Dec 9, 2024
2 parents abc5464 + ad2f47e commit 65e3b8f
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204 changes: 111 additions & 93 deletions deltametrics/strat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,32 +80,39 @@ def _determine_deposit_from_background(sediment_volume, background):
a background value encoded into it (like ``-1`` or `9999`).
.. plot::
:include-source:
:context: reset
golfcube = dm.sample_data.golf()
golfstrat = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.05)
# background determined from initial basin topography
background0 = dm.strat._determine_deposit_from_background(
golfcube['sandfrac'],
background=golfstrat.Z < golfcube['eta'][0].data)
# background determined from min of bed elevation timeseries
background1 = dm.strat._determine_deposit_from_background(
golfcube['sandfrac'],
background=(golfstrat.Z < np.min(golfcube['eta'].data, axis=0)))
# background determined from a fixed sandfrac value
background2 = dm.strat._determine_deposit_from_background(
golfcube['sandfrac'],
background=0)
fig, ax = plt.subplots(2, 2, figsize=(6, 4))
ax[0, 0].imshow(background0[59], cmap='Greys_r') # just below initial basin depth
ax[0, 1].imshow(background0[60], cmap='Greys_r') # just above initial basin depth
ax[1, 0].imshow(background1[59], cmap='Greys_r') # just below initial basin depth
ax[1, 1].imshow(background2[59], cmap='Greys_r') # just below initial basin depth
plt.tight_layout()
plt.show()
>>> import matplotlib.pyplot as plt
>>> from deltametrics.cube import StratigraphyCube
>>> from deltametrics.sample_data.sample_data import golf
>>> from deltametrics.strat import _determine_deposit_from_background
>>> golfcube = golf()
>>> golfstrat = StratigraphyCube.from_DataCube(golfcube, dz=0.05)
Background determined from initial basin topography
>>> background0 = _determine_deposit_from_background(
... golfcube['sandfrac'],
... background=golfstrat.Z < golfcube['eta'][0].data)
Background determined from min of bed elevation timeseries
>>> background1 = _determine_deposit_from_background(
... golfcube['sandfrac'],
... background=(golfstrat.Z < np.min(golfcube['eta'].data, axis=0)))
Background determined from a fixed sandfrac value
>>> background2 = _determine_deposit_from_background(
... golfcube['sandfrac'],
... background=0)
>>> fig, ax = plt.subplots(2, 2, figsize=(6, 4))
>>> _ = ax[0, 0].imshow(background0[59], cmap='Greys_r') # just below initial basin depth
>>> _ = ax[0, 1].imshow(background0[60], cmap='Greys_r') # just above initial basin depth
>>> _ = ax[1, 0].imshow(background1[59], cmap='Greys_r') # just below initial basin depth
>>> _ = ax[1, 1].imshow(background2[59], cmap='Greys_r') # just below initial basin depth
>>> plt.tight_layout()
"""
if (background is None):
deposit = np.ones(sediment_volume.shape, dtype=bool)
Expand Down Expand Up @@ -160,30 +167,35 @@ def compute_net_to_gross(
--------
.. plot::
:include-source:
golfcube = dm.sample_data.golf()
golfstrat = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.1)
background = (golfstrat.Z < np.min(golfcube['eta'].data, axis=0))
net_to_gross = dm.strat.compute_net_to_gross(
golfstrat['sandfrac'],
net_threshold=0.5,
background=background)
fig, ax = plt.subplots(1, 2)
im0 = ax[0].imshow(
net_to_gross,
extent=golfstrat.extent)
dm.plot.append_colorbar(im0, ax=ax[0])
im1 = ax[1].imshow(
net_to_gross,
cmap=golfstrat.varset['net_to_gross'].cmap,
norm=golfstrat.varset['net_to_gross'].norm,
extent=golfstrat.extent)
dm.plot.append_colorbar(im1, ax=ax[1])
plt.tight_layout()
plt.show()
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> from deltametrics.cube import StratigraphyCube
>>> from deltametrics.plot import append_colorbar
>>> from deltametrics.sample_data.sample_data import golf
>>> from deltametrics.strat import compute_net_to_gross
>>> golfcube = golf()
>>> golfstrat = StratigraphyCube.from_DataCube(golfcube, dz=0.1)
>>> background = (golfstrat.Z < np.min(golfcube['eta'].data, axis=0))
>>> net_to_gross = compute_net_to_gross(
... golfstrat['sandfrac'],
... net_threshold=0.5,
... background=background)
>>> fig, ax = plt.subplots(1, 2)
>>> im0 = ax[0].imshow(
... net_to_gross,
... extent=golfstrat.extent)
>>> _ = append_colorbar(im0, ax=ax[0])
>>> im1 = ax[1].imshow(
... net_to_gross,
... cmap=golfstrat.varset['net_to_gross'].cmap,
... norm=golfstrat.varset['net_to_gross'].norm,
... extent=golfstrat.extent)
>>> _ = append_colorbar(im1, ax=ax[1])
>>> plt.tight_layout()
"""
# process the optional inputs
if (net_threshold is None):
Expand Down Expand Up @@ -235,26 +247,29 @@ def compute_thickness_surfaces(top_surface, bottom_surface):
Examples
--------
.. plot::
:include-source:
:context: reset
golfcube = dm.sample_data.golf()
deposit_thickness0 = dm.strat.compute_thickness_surfaces(
golfcube['eta'][-1, :, :],
golfcube['eta'][0, :, :])
deposit_thickness1 = dm.strat.compute_thickness_surfaces(
golfcube['eta'][-1, :, :],
np.min(golfcube['eta'], axis=0))
fig, ax = plt.subplots(1, 2)
im = ax[0].imshow(deposit_thickness0)
dm.plot.append_colorbar(im, ax=ax[0])
ax[0].set_title('thickness above initial basin')
im = ax[1].imshow(deposit_thickness1)
dm.plot.append_colorbar(im, ax=ax[1])
ax[1].set_title('total deposit thickness')
plt.tight_layout()
plt.show()
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> from deltametrics.plot import append_colorbar
>>> from deltametrics.sample_data.sample_data import golf
>>> from deltametrics.strat import compute_thickness_surfaces
>>> golfcube = golf()
>>> deposit_thickness0 = compute_thickness_surfaces(
... golfcube['eta'][-1, :, :],
... golfcube['eta'][0, :, :])
>>> deposit_thickness1 = compute_thickness_surfaces(
... golfcube['eta'][-1, :, :],
... np.min(golfcube['eta'], axis=0))
>>> fig, ax = plt.subplots(1, 2)
>>> im = ax[0].imshow(deposit_thickness0)
>>> _ = append_colorbar(im, ax=ax[0])
>>> _ = ax[0].set_title('thickness above initial basin')
>>> im = ax[1].imshow(deposit_thickness1)
>>> _ = append_colorbar(im, ax=ax[1])
>>> _ = ax[1].set_title('total deposit thickness')
>>> plt.tight_layout()
"""
difference = top_surface - bottom_surface
whr = (difference <= 0)
Expand Down Expand Up @@ -343,29 +358,32 @@ def compute_sedimentograph(
fraction of the deposit for the `golf` `sandfrac` data.
.. plot::
:include-source:
:context: reset
golfcube = dm.sample_data.golf()
golfstrat = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.1)
background = (golfstrat.Z < np.min(golfcube['eta'].data, axis=0))
(sedimentograph, radii, bins) = dm.strat.compute_sedimentograph(
golfstrat['sandfrac'],
num_sections=50,
last_section_radius=2750,
background=background,
origin_idx=[3, 100])
fig, ax = plt.subplots()
ax.plot(
radii,
sedimentograph[:, 1],
marker='o', ls='-')
ax.set_xlabel('section radius (m)')
ax.set_ylabel(f'fraction > {bins[1]}')
plt.show()
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> from deltametrics.cube import StratigraphyCube
>>> from deltametrics.sample_data.sample_data import golf
>>> from deltametrics.strat import compute_sedimentograph
>>> golfcube = golf()
>>> golfstrat = StratigraphyCube.from_DataCube(golfcube, dz=0.1)
>>> background = (golfstrat.Z < np.min(golfcube['eta'].data, axis=0))
>>> (sedimentograph, radii, bins) = compute_sedimentograph(
... golfstrat['sandfrac'],
... num_sections=50,
... last_section_radius=2750,
... background=background,
... origin_idx=[3, 100])
>>> fig, ax = plt.subplots()
>>> _ = ax.plot(
... radii,
... sedimentograph[:, 1],
... marker='o', ls='-')
>>> _ = ax.set_xlabel('section radius (m)')
>>> _ = ax.set_ylabel(f'fraction > {bins[1]}')
.. [1] Liang, M., Van Dyk, C., and Passalacqua, P. (2016), Quantifying
the patterns and dynamics of river deltas under conditions of
Expand Down
1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,7 @@ testpaths = [
"deltametrics/mobility.py",
"deltametrics/plan.py",
"deltametrics/plot.py",
"deltametrics/strat.py",
"deltametrics/utils.py",
"tests",
]
Expand Down

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