Begin reworking the Usage page in the docs (#213)

milancurcic · web-flow · commit f9eff5a9c63b · 2023-07-13T16:47:41.000-04:00
* Begin reworking the Usage page in the docs

* Check for count or rowsize in subset

* Subset to a smaller dataset in Usage

* Fix ordered list in docstring

* Switch to sphinx-book-theme

* Update copyright year

* Complete the mini-tutorial
diff --git a/clouddrift/analysis.py b/clouddrift/analysis.py
@@ -696,12 +696,9 @@ def velocity_from_position(
 
     Difference scheme can take one of three values:
 
-        1. "forward" (default): finite difference is evaluated as
-           dx[i] = dx[i+1] - dx[i];
-        2. "backward": finite difference is evaluated as
-           dx[i] = dx[i] - dx[i-1];
-        3. "centered": finite difference is evaluated as
-           dx[i] = (dx[i+1] - dx[i-1]) / 2.
+    #. "forward" (default): finite difference is evaluated as ``dx[i] = dx[i+1] - dx[i]``;
+    #. "backward": finite difference is evaluated as ``dx[i] = dx[i] - dx[i-1]``;
+    #. "centered": finite difference is evaluated as ``dx[i] = (dx[i+1] - dx[i-1]) / 2``.
 
     Forward and backward schemes are effectively the same except that the
     position at which the velocity is evaluated is shifted one element down in
@@ -977,6 +974,18 @@ def subset(ds: xr.Dataset, criteria: dict) -> xr.Dataset:
     ValueError
         If one of the variable in a criterion is not found in the Dataset
     """
+    # Normally we expect the ragged-array dataset to have a "count" variable.
+    # However, some datasets may have a "rowsize" variable instead, e.g. if they
+    # have not gotten up to speed with our new convention. We check for both.
+    if "count" in ds.variables:
+        count_var = "count"
+    elif "rowsize" in ds.variables:
+        count_var = "rowsize"
+    else:
+        raise ValueError(
+            "Ragged-array Dataset ds must have a 'count' or 'rowsize' variable."
+        )
+
     mask_traj = xr.DataArray(data=np.ones(ds.dims["traj"], dtype="bool"), dims=["traj"])
     mask_obs = xr.DataArray(data=np.ones(ds.dims["obs"], dtype="bool"), dims=["obs"])
 
@@ -990,7 +999,7 @@ def subset(ds: xr.Dataset, criteria: dict) -> xr.Dataset:
             raise ValueError(f"Unknown variable '{key}'.")
 
     # remove data when trajectories are filtered
-    traj_idx = np.insert(np.cumsum(ds["count"].values), 0, 0)
+    traj_idx = np.insert(np.cumsum(ds[count_var].values), 0, 0)
     for i in np.where(~mask_traj)[0]:
         mask_obs[slice(traj_idx[i], traj_idx[i + 1])] = False
 
@@ -1006,7 +1015,7 @@ def subset(ds: xr.Dataset, criteria: dict) -> xr.Dataset:
         # apply the filtering for both dimensions
         ds_sub = ds.isel({"traj": mask_traj, "obs": mask_obs})
         # update the count
-        ds_sub["count"].values = segment(
+        ds_sub[count_var].values = segment(
             ds_sub.ids, 0.5, count=segment(ds_sub.ids, -0.5)
         )
         return ds_sub
diff --git a/docs/conf.py b/docs/conf.py
@@ -19,7 +19,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "CloudDrift"
-copyright = "2022, CloudDrift"
+copyright = "2022-2023, CloudDrift"
 author = "Philippe Miron"
 
 # -- General configuration ---------------------------------------------------
@@ -49,9 +49,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = "pydata_sphinx_theme"  # alabaster, sphinx_rtd_theme
-# html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_book_theme"  # alabaster, sphinx_rtd_theme
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,2 @@
 sphinx
-pydata_sphinx_theme
+sphinx-book-theme
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -3,7 +3,240 @@
 Usage
 =====
 
-CloudDrift provides an easy way to convert Lagrangian datasets into
+The CloudDrift library provides functions for:
+
+* Easy access to cloud-ready Lagrangian ragged-array datasets;
+* Common Lagrangian analysis tasks on ragged arrays;
+* Adapting custom Lagrangian datasets into ragged arrays.
+
+Let's start by importing the library and accessing a ready-to-use ragged-array
+dataset.
+
+Accessing ragged-array Lagrangian datasets
+------------------------------------------
+
+We recommend to import the ``clouddrift`` using the ``cd`` shorthand, for convenience:
+
+>>> import clouddrift as cd
+
+CloudDrift provides a set of Lagrangian datasets that are ready to use.
+They can be accessed via the ``datasets`` submodule.
+In this example, we will load the NOAA's Global Drifter Program (GDP) hourly
+dataset, which is hosted in a public AWS bucket as a cloud-optimized Zarr
+dataset:
+
+>>> ds = cd.datasets.gdp1h()
+>>> ds
+<xarray.Dataset>
+Dimensions:                (traj: 17324, obs: 165754333)
+Coordinates:
+    ids                    (obs) int64 ...
+    lat                    (obs) float32 ...
+    lon                    (obs) float32 ...
+    time                   (obs) datetime64[ns] ...
+Dimensions without coordinates: traj, obs
+Data variables: (12/55)
+    BuoyTypeManufacturer   (traj) |S20 ...
+    BuoyTypeSensorArray    (traj) |S20 ...
+    CurrentProgram         (traj) float64 ...
+    DeployingCountry       (traj) |S20 ...
+    DeployingShip          (traj) |S20 ...
+    DeploymentComments     (traj) |S20 ...
+    ...                     ...
+    sst1                   (obs) float64 ...
+    sst2                   (obs) float64 ...
+    typebuoy               (traj) |S10 ...
+    typedeath              (traj) int8 ...
+    ve                     (obs) float32 ...
+    vn                     (obs) float32 ...
+Attributes: (12/16)
+    Conventions:       CF-1.6
+    acknowledgement:   Elipot, Shane; Sykulski, Adam; Lumpkin, Rick; Centurio...
+    contributor_name:  NOAA Global Drifter Program
+    contributor_role:  Data Acquisition Center
+    date_created:      2022-12-09T06:02:29.684949
+    doi:               10.25921/x46c-3620
+    ...                ...
+    processing_level:  Level 2 QC by GDP drifter DAC
+    publisher_email:   aoml.dftr@noaa.gov
+    publisher_name:    GDP Drifter DAC
+    publisher_url:     https://www.aoml.noaa.gov/phod/gdp
+    summary:           Global Drifter Program hourly data
+    title:             Global Drifter Program hourly drifting buoy collection
+
+The ``gdp1h`` function returns an Xarray ``Dataset`` instance of the ragged-array dataset.
+While the dataset is quite large, around a dozen GB, it is not downloaded to your
+local machine. Instead, the dataset is accessed directly from the cloud, and only
+the data that is needed for the analysis is downloaded. This is possible thanks to
+the cloud-optimized Zarr format, which allows for efficient access to the data
+stored in the cloud.
+
+Let's look at some variables in this dataset:
+
+>>> ds.lon
+<xarray.DataArray 'lon' (obs: 165754333)>
+[165754333 values with dtype=float32]
+Coordinates:
+    ids      (obs) int64 ...
+    lat      (obs) float32 ...
+    lon      (obs) float32 ...
+    time     (obs) datetime64[ns] ...
+Dimensions without coordinates: obs
+Attributes:
+    long_name:  Longitude
+    units:      degrees_east
+
+You see that this array is very long--it has 165754333 elements.
+This is because in a ragged array, many varying-length arrays are laid out as a
+contiguous 1-dimensional array in memory.
+
+Let's look at the dataset dimensions:
+
+>>> ds.dims
+Frozen({'traj': 17324, 'obs': 165754333})
+
+The ``traj`` dimension has 17324 elements, which is the number of individual
+trajectories in the dataset.
+The sum of their lengths equals the length of the ``obs`` dimension.
+Internally, these dimensions, their lengths, and the ``count`` (or ``rowsize``)
+variables are used internally to make CloudDrift's analysis functions aware of
+the bounds of each contiguous array within the ragged-array data structure.
+
+Doing common analysis tasks on ragged arrays
+--------------------------------------------
+
+Now that we have a ragged-array dataset loaded as an Xarray ``Dataset`` instance,
+let's do some common analysis tasks on it.
+Our dataset is on a remote server and fairly large (a dozen GB or so), so let's
+first subset it to several trajectories so that we can more easily work with it.
+The variable ``ID`` is the unique identifier for each trajectory:
+
+>>> ds.ID[:10].values
+array([2578, 2582, 2583, 2592, 2612, 2613, 2622, 2623, 2931, 2932])
+
+>>> from clouddrift.analysis import subset
+
+``subset`` allows you to subset a ragged array by some criterion.
+In this case, we will subset it by the ``ID`` variable:
+
+>>> ds_sub = subset(ds, {"ID": list(ds.ID[:5])})
+>>> ds_sub
+<xarray.Dataset>
+Dimensions:                (traj: 5, obs: 13612)
+Coordinates:
+    ids                    (obs) int64 2578 2578 2578 2578 ... 2612 2612 2612
+    lat                    (obs) float32 ...
+    lon                    (obs) float32 ...
+    time                   (obs) datetime64[ns] ...
+Dimensions without coordinates: traj, obs
+Data variables: (12/55)
+    BuoyTypeManufacturer   (traj) |S20 ...
+    BuoyTypeSensorArray    (traj) |S20 ...
+    CurrentProgram         (traj) float64 ...
+    DeployingCountry       (traj) |S20 ...
+    DeployingShip          (traj) |S20 ...
+    DeploymentComments     (traj) |S20 ...
+    ...                     ...
+    sst1                   (obs) float64 ...
+    sst2                   (obs) float64 ...
+    typebuoy               (traj) |S10 ...
+    typedeath              (traj) int8 ...
+    ve                     (obs) float32 ...
+    vn                     (obs) float32 ...
+Attributes: (12/16)
+    Conventions:       CF-1.6
+    acknowledgement:   Elipot, Shane; Sykulski, Adam; Lumpkin, Rick; Centurio...
+    contributor_name:  NOAA Global Drifter Program
+    contributor_role:  Data Acquisition Center
+    date_created:      2022-12-09T06:02:29.684949
+    doi:               10.25921/x46c-3620
+    ...                ...
+    processing_level:  Level 2 QC by GDP drifter DAC
+    publisher_email:   aoml.dftr@noaa.gov
+    publisher_name:    GDP Drifter DAC
+    publisher_url:     https://www.aoml.noaa.gov/phod/gdp
+    summary:           Global Drifter Program hourly data
+    title:             Global Drifter Program hourly drifting buoy collection
+
+You see that we now have a subset of the original dataset, with 5 trajectories
+and a total of 13612 observations.
+This subset is small enough to quickly and easily work with for demonstration
+purposes.
+Let's see how we can compute the mean and maximum velocities of each trajectory.
+To start, we'll need to obtain the velocities over all trajectory times.
+Although the GDP dataset already comes with velocity variables, we won't use
+them here so that we can learn how to compute them ourselves from positions.
+``clouddrift`` provides the ``velocity_from_position`` function that allows you
+to do just that.
+
+>>> from clouddrift.analysis import velocity_from_position
+
+At a minimum ``velocity_from_position`` requires three input parameters:
+consecutive x- and y-coordinates and time, so we could do:
+
+>>> u, v = velocity_from_position(ds_sub.lon, ds_sub.lat, ds_sub.time)
+
+``velocity_from_position`` returns two arrays, ``u`` and ``v``, which are the
+zonal and meridional velocities, respectively.
+By default, it assumes that the coordinates are in degrees, and it handles the
+great circle path calculation and longitude wraparound under the hood.
+However, recall that ``ds_sub.lon``, ``ds_sub.lat``, and ``ds_sub.time`` are
+ragged arrays, so we need a different approach to calculate velocities while
+respecting the trajectory boundaries.
+For this, we can use the ``ragged_apply`` function, which applies a function
+to each trajectory in a ragged array, and returns the concatenated result.
+
+>>> from clouddrift.analysis import apply_ragged
+>>> u, v = apply_ragged(velocity_from_position, [ds_sub.lon, ds_sub.lat, ds_sub.time], ds_sub.rowsize)
+
+``u`` and ``v`` here are still ragged arrays, which means that the five
+contiguous trajectories are concatenated into 1-dimensional arrays.
+
+Now, let's compute the velocity magnitude in meters per second.
+The time in this dataset is loaded in nanoseconds by default:
+
+>>> ds_sub.time.values
+array(['2005-04-15T20:00:00.000000000', '2005-04-15T21:00:00.000000000',
+       '2005-04-15T22:00:00.000000000', ...,
+       '2005-10-02T03:00:00.000000000', '2005-10-02T04:00:00.000000000',
+       '2005-10-02T05:00:00.000000000'], dtype='datetime64[ns]')
+
+So, to obtain the velocity magnitude in meters per second, we'll need to
+multiply our velocities by ``1e9``.
+
+>>> velocity_magnitude = np.sqrt(u**2 + v**2) * 1e9
+>>> velocity_magnitude
+array([0.28053388, 0.6164632 , 0.89032112, ..., 0.2790803 , 0.20095603,
+       0.20095603])
+
+>>> velocity_magnitude.mean(), velocity_magnitude.max()
+(0.22115242718877506, 1.6958275672626286)
+
+However, these aren't the results we are looking for! Recall that we have the
+velocity magnitude of five different trajectories concatenated into one array.
+This means that we need to use ``apply_ragged`` again to compute the mean and
+maximum values:
+
+>>> apply_ragged(np.mean, [velocity_magnitude], ds_sub.rowsize)
+array([0.32865148, 0.17752435, 0.1220523 , 0.13281067, 0.14041268])
+>>> apply_ragged(np.max, [velocity_magnitude], ds_sub.rowsize)
+array([1.69582757, 1.36804354, 0.97343434, 0.60353528, 1.05044213])
+
+And there you go! We used ``clouddrift`` to:
+
+#. Load a real-world Lagrangian dataset from the cloud;
+#. Subset the dataset by trajectory IDs;
+#. Compute the velocity vectors and their magnitudes for each trajectory;
+#. Compute the mean and maximum velocity magnitudes for each trajectory.
+
+``clouddrift`` offers many more functions for common Lagrangian analysis tasks.
+Please explore the `API <https://cloud-drift.github.io/clouddrift/api.html>`_
+to learn about other functions and how to use them.
+
+Adapting custom Lagrangian datasets into ragged arrays
+------------------------------------------------------
+
+CloudDrift provides an easy way to convert custom Lagrangian datasets into
 `contiguous ragged arrays <https://cfconventions.org/cf-conventions/cf-conventions.html#_contiguous_ragged_array_representation>`_.
 
 .. code-block:: python
@@ -26,14 +259,7 @@ CloudDrift provides an easy way to convert Lagrangian datasets into
 
 This snippet is specific to the hourly GDP dataset, however, you can use the
 ``RaggedArray`` class directly to convert other custom datasets into a ragged
-array structure that is analysis ready via Xarray or Awkward Array packages. 
-We provide step-by-step guides to convert the individual trajectories from the
-Global Drifter Program (GDP) hourly and 6-hourly datasets, the drifters from the
-`CARTHE <http://carthe.org/>`_ experiment, and a typical output from a numerical
-Lagrangian experiment in our
-`repository of example Jupyter Notebooks <https://github.com/cloud-drift/clouddrift-examples>`_.
+array structure that is analysis ready via Xarray or Awkward Array packages.
+The functions to do that are defined in the ``clouddrift.adapters`` submodule.
 You can use these examples as a reference to ingest your own or other custom
-Lagrangian datasets into ``RaggedArray``.
-
-In the future, ``clouddrift`` will be including functions to perform typical
-oceanographic Lagrangian analyses.
+Lagrangian datasets into ``RaggedArray``.

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`sphinx`
`2`		`-pydata_sphinx_theme`
	`2`	`+sphinx-book-theme`