Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Convert docstring plot directives to doctests for strat.py #177

Merged
merged 2 commits into from
Dec 9, 2024
Merged

Convert docstring plot directives to doctests for strat.py #177

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3d57b26
remove code, doctest directives from strat module
mcflugen Dec 6, 2024
ad2f47e
run doctests in strat.py
mcflugen Dec 9, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
204 changes: 111 additions & 93 deletions deltametrics/strat.py
View file
Open in desktop
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
View file
Open in desktop
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
Loading