doc updates

docs/background/path_uri.rst

@@ -2,5 +2,3 @@ File paths and URIs
 ===================
 
 Command line and API file parameters can be specified by local file paths or remote URIs.  Orthority uses `fsspec <https://github.com/fsspec/filesystem_spec>`__ for file IO, which provides built-in support for `a number of remote file systems <https://filesystem-spec.readthedocs.io/en/stable/api.html#implementations>`__.  Support for other remote systems, including cloud storage, is available by installing `the relevant extension package <https://filesystem-spec.readthedocs.io/en/latest/api.html#other-known-implementations>`__.  See the `fsspec documentation <https://filesystem-spec.readthedocs.io/en/stable/features.html#configuration>`__ if your file system requires credentials or other configuration.
-
-On the :doc:`command line <../cli/index>`, ``SOURCE`` images can be specified with local or remote wildcard patterns.  Note that some file systems, like HTTP, are read-only and don't support wildcards.

docs/background/vertical_crs.rst

@@ -1,7 +1,7 @@
 Vertical CRS
 ============
 
-DEM and :ref:`world coordinate <background/coordinates:world coordinates>` heights may have different vertical coordinate systems e.g. heights may be referenced to different datums (ellipsoid or geoid) and have different units.  Accurate orthorectification requires conversion of heights into a common system.  When both the DEM and world / ortho CRS have a defined vertical system (either as a 3D CRS, or a 2D+1D compound CRS), this conversion is performed automatically. Otherwise, DEM and world vertical systems are assumed the same, and no conversion is performed.
+DEM and :ref:`world coordinate <background/coordinates:world coordinates>` heights may have different vertical coordinate systems e.g. heights may be referenced to different datums (ellipsoid or geoid) and have different units.  Accurate orthorectification requires conversion of heights into a common system.  When both the DEM and world / ortho CRS have a defined vertical system (as a 3D CRS or a 2D+1D compound CRS), this conversion is performed automatically. Otherwise, DEM and world vertical systems are assumed the same, and no conversion is performed.
 
 .. note::
 

docs/contributing.rst

@@ -28,7 +28,7 @@ If installing with pip_, you can install dependencies and link the repository in
 
 If installing into a conda_ environment, it is best to install the `dependencies <https://github.com/leftfield-geospatial/orthority/blob/main/pyproject.yaml>`__ with ``conda`` first, before running the command above.
 
-Please work on features in a new branch, and submit your changes as a `GitHub pull request <https://docs.github.com/articles/about-pull-requests>`__ for review.  It is recommended to discuss possible pull requests in an issue beforehand.
+Please work on features in a new branch, and submit your changes as a `GitHub pull request <https://docs.github.com/articles/about-pull-requests>`__ for review.  I recommend discussing possible pull requests in an issue beforehand.
 
 Orthority uses `black <https://black.readthedocs.io>`__ for formatting (with settings in |pyproject.yaml|_), and the RST docstring style.  Please include `pytest <https://docs.pytest.org>`__ unit tests with your code.
 

docs/file_formats/csv.rst

@@ -39,7 +39,7 @@ When there is no file header (and ``fieldnames`` is not provided to :meth:`~orth
 
 .. note::
 
-    Conversion from (*roll*, *pitch*, *yaw*) camera orientation is approximate and relies on the :ref:`world <background/coordinates:world coordinates>` CRS having minimal distortion in the imaged area.
+    Conversion from (roll, pitch, yaw) camera orientation is approximate and relies on the :ref:`world <background/coordinates:world coordinates>` CRS having minimal distortion in the imaged area.
 
 Dialect
 -------

docs/file_formats/exif_xmp.rst

@@ -80,7 +80,7 @@ Camera orientation
 
 .. note::
 
-    Conversion from (*roll*, *pitch*, *yaw*) camera orientation is approximate and relies on the :ref:`world <background/coordinates:world coordinates>` CRS having minimal distortion in the imaged area.
+    Conversion from (roll, pitch, yaw) camera orientation is approximate and relies on the :ref:`world <background/coordinates:world coordinates>` CRS having minimal distortion in the imaged area.
 
 .. note::
 

docs/file_formats/oty_ext.rst

@@ -14,7 +14,7 @@ This is the native Orthority format for frame camera :ref:`exterior parameters <
         ]
     }
 
-Each ``Feature`` corresponds to a source image file, where the Feature geometry is the camera position in geographic coordinates.  The ``Feature`` properties are as follows:
+Each ``Feature`` corresponds to a source image file, where the ``Feature`` geometry is the camera position in geographic coordinates.  The ``Feature`` properties are as follows:
 
 .. list-table::
     :widths: auto

docs/getting_started/cli/basic_orthorectification.rst

@@ -35,7 +35,7 @@ In the next example, exterior parameters are in CSV format with ``x``, ``y`` & `
 
 .. note::
 
-    See the :doc:`file format documentation <../../file_formats/index>` for supported parameter formats.
+    See the :doc:`file format documentation <../../file_formats/index>` for supported frame camera parameter formats.
 
 ``oty exif``
 ------------
@@ -89,8 +89,14 @@ The world / ortho CRS defaults to the WGS84 geographic 3D CRS.  This can be chan
     oty rpc --dem ngi/dem.tif --crs EPSG:32735 rpc/qb2_basic1b.tif
 
 
-Output files
-------------
+File IO
+-------
+
+Files can be read from or written to local or remote :doc:`file paths / URIs <../../background/path_uri>`.  ``SOURCE`` images can be specified with local or remote wildcard patterns.
+
+.. note::
+
+    Some file systems, like HTTP, are read-only and don't support wildcards.
 
 Ortho images are named automatically based on the source image names.  The output directory for ortho images and :doc:`exported files <model_export>` can be changed from its default with the ``--out-dir`` option.  Passing ``--overwrite`` overwrites existing files.  These options are common to all |oty|_ orthorectification sub-commands.  E.g., this repeats the :ref:`getting_started/cli/basic_orthorectification:``oty odm``` example, creating and using :file:`ortho` as the output directory, and overwriting existing files:
 

docs/getting_started/cli/camera_config.rst

@@ -7,11 +7,11 @@ Required camera model parameters are read from file.  Additional command line op
 
 The ``--full-remap`` option configures a camera to remap the source to ortho image in one step.  This uses the full model including distortion, and is the default behaviour.  With ``--no-full-remap``, the source is first remapped to an undistorted image, then remapped to the ortho image using a pinhole model excluding distortion.  ``--no-full-remap`` is faster, but can use more memory and reduce ortho quality, as it remaps and interpolates twice.
 
-The ``--alpha`` option can be supplied with ``--no-full-remap`` to specify the scaling of the undistorted image.  An ``--alpha`` value of 0 scales the undistorted image so that all its pixels are valid.  An ``--alpha`` value of 1 (the default) scales the undistorted image so that it includes all source pixels.  The plot below illustrates this for ``--alpha`` values of 0 and 1:
+The ``--alpha`` option can be supplied with ``--no-full-remap`` to specify the scaling of the undistorted image.  An ``--alpha`` value of ``0`` scales the undistorted image so that all its pixels are valid.  An ``--alpha`` value of ``1`` (the default) scales the undistorted image so that it includes all source pixels.  The plot below illustrates this for ``--alpha`` values of ``0`` and ``1``:
 
 .. image:: alpha_plot.webp
 
-To show the use of these options, we orthorectify the OpenDroneMap dataset using the ``--no-full-remap`` option with an ``--alpha`` value of 0:
+To show the use of these options, we orthorectify the OpenDroneMap dataset using the ``--no-full-remap`` option with an ``--alpha`` value of ``0``:
 
 .. code-block:: bash