DOC: Update links/refs for psi-io and cross-referenced examples

Author: ryder-davidson

examples/01_getting_started/p01_simple_scene.py

@@ -24,7 +24,7 @@
 # %%
 # Once instantiated, the Plot3d object can be used to add actors/meshes to the scene. Here we
 # add axes (to display the coordinate system) and a sun (a "reference" sphere, centered
-# at the origin, with radius 1 :math:`R_\odot`). By calling the :func:`~pyvisual.core.plot3d.Plot3d.show`
+# at the origin, with radius 1 :math:`R_\odot`). By calling the :meth:`~pyvista.Plotter.show`
 # method, we can display the scene in an interactive window.
 
 plotter = Plot3d(
@@ -40,7 +40,7 @@
 plotter.show()
 
 # %%
-# By capturing the returned result of the :func:`~pyvisual.Plot3d.add_sun` method, we can
+# By capturing the returned result of the :meth:`~pyvisual.core.plot3d.Plot3d.add_sun` method, we can
 # manipulate the sun actor after it has been added to the scene. For example, we can remove it
 # from the scene and then add it back again.
 

examples/01_getting_started/p03_loading_data.py

@@ -8,7 +8,7 @@
 1. **Fetching a dataset** — :func:`~pyvisual.utils.data.fetch_datasets`
    downloads (or retrieves from cache) a version-pinned HDF5 file from the
    PSI asset server and returns its local path.
-2. **Reading the data** — :func:`~psi_io.read_hdf_by_index` loads the array
+2. **Reading the data** — :func:`~psi_io.psi_io.read_hdf_by_index` loads the array
    values and the three coordinate grids :math:`(r, \\theta, \\phi)` from the
    file.  Passing ``None`` for a dimension selects its full extent; passing an
    integer index fixes that dimension to a single grid point.
@@ -28,7 +28,7 @@
 #
 # :func:`~pyvisual.utils.data.fetch_datasets` accepts a *domain* identifier
 # (``'cor'`` for the coronal domain, ``'hel'`` for heliospheric) and a
-# *variable* name.  It returns a :class:`~collections.namedtuple` whose fields
+# *variable* name.  It returns a :func:`~collections.namedtuple` whose fields
 # are named ``"{domain}_{variable}"``.  The first call downloads the file to
 # the local cache; subsequent calls return the cached copy immediately without
 # hitting the network.
@@ -40,7 +40,7 @@
 # Reading a 2-D Radial Slice
 # --------------------------
 #
-# :func:`~psi_io.read_hdf_by_index` reads the HDF5 file and returns
+# :func:`~psi_io.psi_io.read_hdf_by_index` reads the HDF5 file and returns
 # ``(data, r, t, p)`` — the scalar array followed by the three coordinate
 # vectors.  Index arguments control which portion of the grid is loaded:
 #

examples/03_grid_mesh_mixin/p01_1d_slices.py

@@ -12,7 +12,7 @@
 
 Real coronal magnetic field data from a PSI MAS model (CR 2282) is loaded
 via :func:`~pyvisual.utils.data.fetch_datasets` and sliced using
-:func:`~psi_io.read_hdf_by_index`.  Passing a single integer index for a
+:func:`~psi_io.psi_io.read_hdf_by_index`.  Passing a single integer index for a
 dimension fixes it to a single grid point; ``None`` selects the full extent.
 The function returns the data and the three coordinate arrays in
 :math:`(r, \\theta, \\phi)` order, ready for direct use with

examples/03_grid_mesh_mixin/p02_2d_slices.py

@@ -14,7 +14,7 @@
 *radial shell* (fixed :math:`r`), the *theta cut* (fixed :math:`\\theta`), and
 the *phi cut* (fixed :math:`\\phi`).  Each is produced here by passing a single
 integer index for the pinned dimension to
-:func:`~psi_io.read_hdf_by_index`; ``None`` selects the full extent of the
+:func:`~psi_io.psi_io.read_hdf_by_index`; ``None`` selects the full extent of the
 remaining two axes.
 """
 

examples/03_grid_mesh_mixin/p03_contour.py

@@ -67,7 +67,7 @@
 #
 # To demonstrate this contouring method on :math:`B_r` data from a
 # steady-state Thermodynamic MAS coronal model, we can load in the data
-# using :func:`~psi_io.read_hdf_data`.
+# using :func:`~psi_io.psi_io.read_hdf_data`.
 
 from psi_io import read_hdf_data
 from pyvisual.utils.data import fetch_datasets

examples/04_observer_mixin/p03_los_and_fov_views.py

@@ -48,7 +48,7 @@
 # LOS View — Off-Center Pointing
 # --------------------------------
 #
-# Shifting the angular range off-centre moves the focal point away from
+# Shifting the angular range off-center moves the focal point away from
 # Sun-center.  Here the horizontal window is displaced by :math:`+5°`
 # (``x0 = -5``, ``x1 = +15``) so that the camera is biased to the east
 # limb of the Sun.  The vertical extent remains symmetric.

examples/06_spherical_grid_class/p01_spherical_grid_init.py

@@ -6,10 +6,10 @@
 :class:`~pyvisual.core.mesh3d.SphericalMesh`:
 
 1. **From an HDF file path** — pass the path directly; the constructor calls
-   :func:`~psi_io.read_hdf_by_index` internally.  Additional positional
+   :func:`~psi_io.psi_io.read_hdf_by_index` internally.  Additional positional
    arguments after the path are forwarded as index arguments to the file reader.
 2. **From data arrays** — read the file manually with
-   :func:`~psi_io.read_hdf_by_index`, then pass the coordinate arrays and data
+   :func:`~psi_io.psi_io.read_hdf_by_index`, then pass the coordinate arrays and data
    to the constructor.
 3. **From an existing** :class:`~pyvisual.core.mesh3d.SphericalMesh` — pass
    another mesh instance to produce a shallow copy.
@@ -32,9 +32,9 @@
 # ---------------------
 #
 # Passing a file path as the first argument triggers the file-path dispatch
-# path: the constructor calls :func:`~psi_io.read_hdf_by_index` on the path,
+# path: the constructor calls :func:`~psi_io.psi_io.read_hdf_by_index` on the path,
 # loading both the scalar data and the three coordinate grids.  Positional
-# arguments after the path are forwarded to :func:`~psi_io.read_hdf_by_index`
+# arguments after the path are forwarded to :func:`~psi_io.psi_io.read_hdf_by_index`
 # as index arguments, controlling which portion of the grid is loaded
 # (see the function documentation for details).
 #
@@ -55,7 +55,7 @@
 #
 # When you need to pre-process the arrays before constructing the mesh —
 # for example to apply a coordinate transform or inspect the raw values —
-# call :func:`~psi_io.read_hdf_by_index` yourself and pass the results
+# call :func:`~psi_io.psi_io.read_hdf_by_index` yourself and pass the results
 # directly to the constructor.  The coordinate arrays go in as the first three
 # positional arguments (``r``, ``t``, ``p``); the scalar values are supplied
 # via the ``data`` keyword.

examples/06_spherical_grid_class/p02_arithmetic.py

@@ -24,7 +24,7 @@
 # ------------
 #
 # We initialize a :class:`~pyvisual.core.mesh3d.SphericalMesh` from the HDF file path, which
-# triggers the file-path dispatch path (see :ref:`sphx_glr_06_spherical_grid_class_p01_construction.py`
+# triggers the file-path dispatch path (see :ref:`sphx_glr_gallery_06_spherical_grid_class_p01_spherical_grid_init.py`
 # for details on the three construction paths.
 mesh = SphericalMesh(br_file)
 mesh

examples/06_spherical_grid_class/p03_filters.py

@@ -29,7 +29,7 @@
 #
 # Load the coronal radial magnetic field (:math:`B_r`) HDF file and construct a
 # :class:`~pyvisual.core.mesh3d.SphericalMesh` via the file-path dispatcher (see
-# :ref:`sphx_glr_06_spherical_grid_class_p01_spherical_grid_init.py` for details on the
+# :ref:`sphx_glr_gallery_06_spherical_grid_class_p01_spherical_grid_init.py` for details on the
 # three construction methods).  A sub-region is then sliced out in
 # :math:`(r, \theta, \phi)` index space and rendered as a semi-transparent volume
 # using a diverging colormap.

examples/07_cartesian_grid_class/p03_cart_filters.py

@@ -13,8 +13,8 @@
 :meth:`~pyvisual.core.mesh3d.CartesianMeshFilters.deconstruct`), but because
 they wrap different PyVista grid types
 (:class:`pyvista.StructuredGrid` vs :class:`pyvista.RectilinearGrid`),
-unmodified PyVista filters such as :meth:`pyvista.DataSetFilters.slice_orthogonal`
-and :meth:`pyvista.DataSetFilters.slice_along_axis` behave differently on each:
+unmodified PyVista filters such as :meth:`~pyvista.DataObjectFilters.slice_orthogonal`
+and :meth:`~pyvista.DataObjectFilters.slice_along_axis` behave differently on each:
 
 - On a :class:`~pyvisual.core.mesh3d.CartesianMesh` PyVista operates on the
   true spatial :math:`(x, y, z)` point coordinates, so slices are flat planes
@@ -24,7 +24,7 @@
   so the same filter methods instead cut surfaces of constant radius,
   colatitude, and longitude.
 
-See also :ref:`sphx_glr_06_spherical_grid_class_p03_filters.py` for the
+See also :ref:`sphx_glr_gallery_06_spherical_grid_class_p03_filters.py` for the
 spherical-mesh equivalent of this example.
 """
 
@@ -59,7 +59,7 @@
 # Indexing a :class:`~pyvisual.core.mesh3d.CartesianMesh` with a 3-tuple of
 # slices selects grid points by their index positions in each axis direction,
 # exactly as for :class:`~pyvisual.core.mesh3d.SphericalMesh` (see
-# :ref:`sphx_glr_06_spherical_grid_class_p03_filters.py`).
+# :ref:`sphx_glr_gallery_06_spherical_grid_class_p03_filters.py`).
 # Because both mesh classes share the same underlying grid topology — the
 # Cartesian conversion is applied to the *coordinates*, not the *connectivity*
 # — identical index slices select the same spatial sub-region regardless of
@@ -78,12 +78,12 @@
 # Orthogonal Slices — CartesianMesh
 # ---------------------------------
 #
-# :meth:`pyvista.DataSetFilters.slice_orthogonal` cuts three mutually
+# :meth:`pyvista.DataObjectFilters.slice_orthogonal` cuts three mutually
 # perpendicular cross-sections through the mesh centroid.  On a
 # :class:`~pyvisual.core.mesh3d.CartesianMesh` the underlying grid stores
 # real :math:`(x, y, z)` point coordinates, so the three slices are flat
 # planes aligned with the coordinate axes — one each of the YZ, XZ, and XY
-# planes passing through the centre of the domain.
+# planes passing through the center of the domain.
 
 plotter = Plot3d()
 plotter.show_axes()