update docs to use new idx instead of y and expand description within…

… the section documentation
sandpiper-toolchain · Nov 17, 2021 · 0a8484f · 0a8484f
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diff --git a/docs/source/guides/10min.rst b/docs/source/guides/10min.rst
@@ -128,7 +128,7 @@ For a data cube, sections are most easily instantiated by the :obj:`~deltametric
 
 .. doctest::
 
-    >>> golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+    >>> golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 which can then be accessed via the :obj:`~deltametrics.cube.Cube.sections` attribute of the Cube.
 

diff --git a/docs/source/guides/userguide.rst b/docs/source/guides/userguide.rst
@@ -153,7 +153,7 @@ For a data cube, sections are most easily instantiated by the :obj:`~deltametric
 
 .. doctest::
 
-    >>> golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+    >>> golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 which creates a section across a constant y-value ``==10``.
 The path of any `Section` in the ``x-y`` plane can always be accessed via the ``.trace`` attribute.
@@ -183,7 +183,7 @@ are sliced themselves, similarly to the cube.
 
 .. doctest::
 
-    >>> golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+    >>> golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
     >>> golfcube.sections['demo']['velocity']
     <xarray.DataArray 'velocity' (z: 101, s: 200)>
     array([[0.2   , 0.2   , 0.2   , ..., 0.2   , 0.2   , 0.2   ],
@@ -220,7 +220,7 @@ You can also create a standalone section, which is not registered to the cube, b
 
 .. doctest::
 
-    >>> sass = dm.section.StrikeSection(golfcube, y=10)
+    >>> sass = dm.section.StrikeSection(golfcube, idx=10)
     >>> np.all(sass['velocity'] == golfcube.sections['demo']['velocity']) #doctest: +SKIP
     True
 
@@ -296,7 +296,7 @@ The following are currently implemented.
 
 .. doctest::
 
-    >>> _strike = dm.section.StrikeSection(golfcube, y=18)
+    >>> _strike = dm.section.StrikeSection(golfcube, idx=18)
     >>> _path = dm.section.PathSection(golfcube, path=np.column_stack((np.linspace(50, 150, num=4000, dtype=int),
     ...                                                                np.linspace(10, 90, num=4000, dtype=int))))
     >>> _circ = dm.section.CircularSection(golfcube, radius=40)
@@ -376,7 +376,7 @@ Let’s add a section at the same location as ``golfcube.sections['demo']``.
 
 .. doctest::
 
-    >>> stratcube.register_section('demo', dm.section.StrikeSection(y=10))
+    >>> stratcube.register_section('demo', dm.section.StrikeSection(idx=10))
     >>> stratcube.sections
     {'demo': <deltametrics.section.StrikeSection object at 0x...>}
 

diff --git a/docs/source/pyplots/examples/preserved_velocities.py b/docs/source/pyplots/examples/preserved_velocities.py
@@ -29,7 +29,7 @@ def pick_velocities(sect):
 
 # loop through all of the sections defined in _ys
 for i, _y in enumerate(_ys):
-    _s = dm.section.StrikeSection(golfcube, y=_y)
+    _s = dm.section.StrikeSection(golfcube, idx=_y)
     _mall[i], _mstrat[i] = pick_velocities(_s)
 
 

diff --git a/docs/source/pyplots/guides/10min_all_sections_strat.py b/docs/source/pyplots/guides/10min_all_sections_strat.py
@@ -3,7 +3,7 @@
 
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta', dz=0.05)
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(5, 1, sharex=True, figsize=(6, 8))
 ax = ax.flatten()

diff --git a/docs/source/pyplots/guides/userguide_all_vars_stratigraphy.py b/docs/source/pyplots/guides/userguide_all_vars_stratigraphy.py
@@ -1,7 +1,7 @@
 golfcube = dm.sample_data.golf()
 
 stratcube = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.05)
-stratcube.register_section('demo', dm.section.StrikeSection(y=10))
+stratcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(5, 1, sharex=True, sharey=True, figsize=(12, 9))
 ax = ax.flatten()

diff --git a/docs/source/pyplots/guides/userguide_compare_slices.py b/docs/source/pyplots/guides/userguide_compare_slices.py
@@ -1,9 +1,9 @@
 import matplotlib.gridspec as gs
 
 golfcube = dm.sample_data.golf()
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 stratcube = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.05)
-stratcube.register_section('demo', dm.section.StrikeSection(y=10))
+stratcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(1, 2, figsize=(8, 2))
 golfcube.sections['demo'].show('velocity', ax=ax[0])

diff --git a/docs/source/pyplots/guides/userguide_frozen_stratigraphy.py b/docs/source/pyplots/guides/userguide_frozen_stratigraphy.py
@@ -2,10 +2,10 @@
 
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 stratcube = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.05)
-stratcube.register_section('demo', dm.section.StrikeSection(y=10))
+stratcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fs = stratcube.export_frozen_variable('sandfrac')
 fe = stratcube.Z  # exported volume does not have coordinate information!

diff --git a/docs/source/pyplots/guides/userguide_quick_stratigraphy_all_variables.py b/docs/source/pyplots/guides/userguide_quick_stratigraphy_all_variables.py
@@ -1,6 +1,6 @@
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 
 fig, ax = plt.subplots(5, 1, sharex=True, sharey=True, figsize=(12, 12))

diff --git a/docs/source/pyplots/guides/userguide_quick_stratigraphy_sections.py b/docs/source/pyplots/guides/userguide_quick_stratigraphy_sections.py
@@ -1,6 +1,6 @@
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 
 fig, ax = plt.subplots(3, 1, sharex=True, figsize=(12, 8))

diff --git a/docs/source/pyplots/guides/userguide_section_type_demos.py b/docs/source/pyplots/guides/userguide_section_type_demos.py
@@ -2,11 +2,11 @@
 
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 _strike = dm.section.StrikeSection(golfcube, y=18)
-__path = np.column_stack((np.linspace(50, 150, num=4000, dtype=int),
-                          np.linspace(10, 90, num=4000, dtype=int)))
+__path = np.column_stack((np.linspace(10, 90, num=4000, dtype=int),
+                          np.linspace(50, 150, num=4000, dtype=int)))
 _path = dm.section.PathSection(golfcube, path=__path)
 _circular = dm.section.CircularSection(golfcube, radius=40)
 _rad = dm.section.RadialSection(golfcube, azimuth=70)

diff --git a/docs/source/pyplots/guides/userguide_stratigraphy_planform_slice.py b/docs/source/pyplots/guides/userguide_stratigraphy_planform_slice.py
@@ -1,7 +1,7 @@
 golfcube = dm.sample_data.golf()
 
 stratcube = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.05)
-stratcube.register_section('demo', dm.section.StrikeSection(y=10))
+stratcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 elev_idx = (np.abs(stratcube.z - -2)).argmin()  # find nearest idx to -2 m
 

diff --git a/docs/source/pyplots/guides/userguide_strikesection_location.py b/docs/source/pyplots/guides/userguide_strikesection_location.py
@@ -1,5 +1,5 @@
 golfcube = dm.sample_data.golf()
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(figsize=(5, 3))
 golfcube.show_plan('eta', t=-1, ax=ax, ticks=True)

diff --git a/docs/source/pyplots/guides/userguide_three_spacetime_sections.py b/docs/source/pyplots/guides/userguide_three_spacetime_sections.py
@@ -1,5 +1,5 @@
 golfcube = dm.sample_data.golf()
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(3, 1, sharex=True, figsize=(12, 6))
 golfcube.show_section('demo', 'eta', ax=ax[0])

diff --git a/docs/source/pyplots/guides/userguide_three_stratigraphy.py b/docs/source/pyplots/guides/userguide_three_stratigraphy.py
@@ -2,10 +2,10 @@
 
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 stratcube = dm.cube.StratigraphyCube.from_DataCube(golfcube, dz=0.05)
-stratcube.register_section('demo', dm.section.StrikeSection(y=10))
+stratcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(3, 1, sharex=True, sharey=True, figsize=(12, 6))
 golfcube.sections['demo'].show('time', style='lines',

diff --git a/docs/source/pyplots/guides/visualization_datacube_section_display_style.py b/docs/source/pyplots/guides/visualization_datacube_section_display_style.py
@@ -1,6 +1,6 @@
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
 fig, ax = plt.subplots(3, 2, sharex=True, figsize=(8, 6))
 _v = 'velocity'

diff --git a/docs/source/pyplots/section/section_demo_quick_strat.py b/docs/source/pyplots/section/section_demo_quick_strat.py
@@ -4,7 +4,7 @@
 
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=5))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=5))
 
 fig, ax = plt.subplots(4, 1, sharex=True, figsize=(8, 6))
 golfcube.sections['demo'].show('depth', data='spacetime',

diff --git a/docs/source/pyplots/section/section_demo_spacetime.py b/docs/source/pyplots/section/section_demo_spacetime.py
@@ -6,5 +6,5 @@
 
 
 fig, ax = plt.subplots(figsize=(8, 2))
-golfcube.register_section('demo', dm.section.StrikeSection(y=5))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=5))
 golfcube.sections['demo'].show('velocity')
diff --git a/docs/source/pyplots/section/section_lexicon.py b/docs/source/pyplots/section/section_lexicon.py
@@ -4,17 +4,17 @@
 
 golfcube = dm.sample_data.golf()
 golfcube.stratigraphy_from('eta')
-golfcube.register_section('demo', dm.section.StrikeSection(y=10))
+golfcube.register_section('demo', dm.section.StrikeSection(idx=10))
 
-fig, ax = plt.subplots(2, 1, sharex=True, figsize=(6, 3.5))
+fig, ax = plt.subplots(2, 1, sharex=True, figsize=(6, 4))
 
-ax[0].imshow(golfcube.sections['demo']['velocity'],
-             origin='lower', cmap=golfcube.varset['velocity'].cmap)
+golfcube.sections['demo'].show('velocity', ax=ax[0])
 ax[0].set_ylabel('$t$ coordinate')
 
-ax[1].imshow(golfcube.sections['demo']['velocity'].strat.as_preserved(),
-             origin='lower', cmap=golfcube.varset['velocity'].cmap)
+golfcube.sections['demo'].show('velocity', data='preserved', ax=ax[1])
 ax[1].set_ylabel('$t$ coordinate')
 
 ax[1].set_xlabel('$s$ coordinate')
+
+plt.tight_layout()
 plt.show()
diff --git a/docs/source/reference/plan/index.rst b/docs/source/reference/plan/index.rst
@@ -18,18 +18,18 @@ Planform types
     :toctree: ../../_autosummary
 
     OpeningAnglePlanform
-		MorphologicalPlanform
+    MorphologicalPlanform
 
 Functions
 =========
 
 .. autosummary::
-	:toctree: ../../_autosummary
-
-	compute_shoreline_roughness
-	compute_shoreline_length
-  compute_shoreline_distance
-  compute_channel_width
-	compute_channel_depth
-	shaw_opening_angle_method
-	morphological_closing_method
+    :toctree: ../../_autosummary
+
+    compute_shoreline_roughness
+    compute_shoreline_length
+    compute_shoreline_distance
+    compute_channel_width
+    compute_channel_depth
+    shaw_opening_angle_method
+    morphological_closing_method
diff --git a/docs/source/reference/section/lexicon.rst b/docs/source/reference/section/lexicon.rst
@@ -3,7 +3,7 @@
 
 The `Section` module defines some terms that are used throughout the code and rest of the documentation. 
 
-Most importantly, a Section is defined by a set of coordinates in the x-y plane of a `Cube`.
+Most importantly, a Section is defined by a set of coordinates in the `dim1`-`dim2` plane of a `Cube`.
 
 Therefore, we transform variable definitions when extracting the `Section`, and the coordinate system of the section is defined by the along-section direction :math:`s` and a vertical section coordinate, which is :math:`z` when viewing stratigraphy, and :math:`t` when viewing a spacetime section.
 
@@ -12,7 +12,7 @@ The data that make up the section can view the section as a `spacetime` section
 .. doctest::
 
     >>> rcm8cube = dm.sample_data.rcm8()
-    >>> strike = dm.section.StrikeSection(rcm8cube, y=10)
+    >>> strike = dm.section.StrikeSection(rcm8cube, idx=10)
     >>> strike['velocity']
     <xarray.DataArray 'velocity' (z: 51, s: 240)>
     array([[0., 0., 0., ..., 0., 0., 0.],
@@ -63,12 +63,13 @@ We can display the arrays using `matplotlib` to examine the spatiotemporal chang
 .. code::
 
     >>> fig, ax = plt.subplots(2, 1, sharex=True, figsize=(6, 3.5))
-    >>> ax[0].imshow(rcm8cube.sections['demo']['velocity'],
-    ...              origin='lower', cmap=rcm8cube.varset['velocity'].cmap)
+    >>> golfcube.sections['demo'].show('velocity', ax=ax[0])
     >>> ax[0].set_ylabel('$t$ coordinate')
-    >>> ax[1].imshow(rcm8cube.sections['demo']['velocity'].as_preserved(),
-    ...              origin='lower', cmap=rcm8cube.varset['velocity'].cmap)
+
+    >>> golfcube.sections['demo'].show('velocity', data='preserved', ax=ax[1])
     >>> ax[1].set_ylabel('$t$ coordinate')
+    
+    >>> ax[1].set_xlabel('$s$ coordinate')
 
 .. plot:: section/section_lexicon.py