masking and dataset list (#343)

* compute masks

* update dataset list, showing ECCO

* add datasets

* move order of datasets

* .

* restore all

* restore all

* compute when first masking

* remove ECCO

* include ECCO on dataset list

* first perssit then compute

* improved description of ECCO and daily ECCO

---------

Co-authored-by: Miguel Jimenez <mjimen17@jhu.edu>

docs/conf.py

@@ -238,7 +238,7 @@
 SCISERVER_DATASETS = yaml.safe_load(f)["datasets"]["sciserver"]
 
 for name in SCISERVER_DATASETS:
-    if name in ["Arctic_Control", "LLC4320", "ECCO", "HYCOM"]:
+    if name in ["Arctic_Control", "LLC4320", "HYCOM"]:
         continue
 
     # Section

docs/datasets.rst

@@ -0,0 +1,360 @@
+.. _datasets:
+
+========
+Datasets
+========
+
+List of datasets available on SciServer.
+
+.. _get_started:
+
+-----------
+get_started
+-----------
+
+Small cutout from EGshelfIIseas2km_ASR_crop_.
+Citation:
+
+* Almansi et al., 2020 - GRL.
+
+See also:
+
+* EGshelfIIseas2km_ASR_full_: Full domain without variables to close budgets.
+* EGshelfIIseas2km_ASR_crop_: Cropped domain with variables to close budgets.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('get_started')
+
+.. _IGPwinter:
+
+---------
+IGPwinter
+---------
+
+High-resolution numerical simulation carried out in parallel to the observational
+component of the Iceland Greenland Seas Project (IGP).
+Citation:
+
+* Renfrew et al., 2019 - BAMS.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('IGPwinter')
+
+.. _EGshelfIIseas2km_ASR_full:
+
+-------------------------
+EGshelfIIseas2km_ASR_full
+-------------------------
+
+High-resolution (~2km) numerical simulation covering the east Greenland shelf (EGshelf),
+and the Iceland and Irminger Seas (IIseas) forced by the Arctic System Reanalysis (ASR).
+Citation:
+
+* Almansi et al., 2020 - GRL.
+
+Characteristics:
+
+* full: Full domain without variables to close budgets.
+
+See also:
+
+* EGshelfIIseas2km_ASR_crop_: Cropped domain with variables to close budgets.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfIIseas2km_ASR_full')
+
+.. _EGshelfIIseas2km_ASR_crop:
+
+-------------------------
+EGshelfIIseas2km_ASR_crop
+-------------------------
+
+High-resolution (~2km) numerical simulation covering the east Greenland shelf (EGshelf),
+and the Iceland and Irminger Seas (IIseas) forced by the Arctic System Reanalysis (ASR).
+Citation:
+
+* Almansi et al., 2020 - GRL.
+
+Characteristics:
+
+* crop: Cropped domain with variables to close budgets.
+
+See also:
+
+* EGshelfIIseas2km_ASR_full_: Full domain without variables to close budgets.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfIIseas2km_ASR_crop')
+
+.. _EGshelfIIseas2km_ERAI_6H:
+
+------------------------
+EGshelfIIseas2km_ERAI_6H
+------------------------
+
+High-resolution (~2km) numerical simulation covering the east Greenland shelf (EGshelf),
+and the Iceland and Irminger Seas (IIseas) forced by ERA-Interim.
+Citation:
+
+* `Almansi et al., 2017 - JPO.`_
+
+Characteristics:
+
+* 6H: 6-hour resolution without sea ice and external forcing variables.
+
+See also:
+
+* EGshelfIIseas2km_ERAI_1D_: 1-day resolution with sea ice and external forcing variables.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfIIseas2km_ERAI_6H')
+
+.. _EGshelfIIseas2km_ERAI_1D:
+
+------------------------
+EGshelfIIseas2km_ERAI_1D
+------------------------
+
+High-resolution (~2km) numerical simulation covering the east Greenland shelf (EGshelf),
+and the Iceland and Irminger Seas (IIseas) forced by ERA-Interim.
+Citation:
+
+* `Almansi et al., 2017 - JPO.`_
+
+Characteristics:
+
+* 1D: 1-day resolution with sea ice and external forcing variables.
+
+See also:
+
+* EGshelfIIseas2km_ERAI_6H_: 6-hour resolution without sea ice and external forcing variables.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfIIseas2km_ERAI_1D')
+
+.. _EGshelfSJsec500m_3H_hydro:
+
+-------------------------
+EGshelfSJsec500m_3H_hydro
+-------------------------
+
+Very high-resolution (500m) numerical simulation covering the east Greenland shelf (EGshelf)
+and the Spill Jet section (SJsec). Hydrostatic solutions.
+
+Citation:
+
+* `Magaldi and Haine, 2015 - DSR.`_
+
+Characteristics:
+
+* 3H:    3-hour resolution without external forcing variables.
+* hydro: Hydrostatic solutions.
+
+See also:
+
+* EGshelfSJsec500m_6H_hydro_:    6-hour resolution with external forcing variables. Hydrostatic.
+* EGshelfSJsec500m_6H_NONhydro_: 6-hour resolution with external forcing variables. Non-Hydrostatic.
+* EGshelfSJsec500m_3H_NONhydro_: 3-hour resolution without external forcing variables. Non-Hydrostatic.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfSJsec500m_3H_hydro')
+
+.. _EGshelfSJsec500m_6H_hydro:
+
+-------------------------
+EGshelfSJsec500m_6H_hydro
+-------------------------
+
+Very high-resolution (500m) numerical simulation covering the east Greenland shelf (EGshelf)
+and the Spill Jet section (SJsec). Hydrostatic solutions.
+
+Citation:
+
+* `Magaldi and Haine, 2015 - DSR.`_
+
+Characteristics:
+
+* 6H:    6-hour resolution with external forcing variables.
+* hydro: Hydrostatic solutions.
+
+See also:
+
+* EGshelfSJsec500m_3H_hydro_:    3-hour resolution without external forcing variables. Hydrostatic.
+* EGshelfSJsec500m_6H_NONhydro_: 6-hour resolution with external forcing variables. Non-Hydrostatic.
+* EGshelfSJsec500m_3H_NONhydro_: 3-hour resolution without external forcing variables. Non-Hydrostatic.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfSJsec500m_6H_hydro')
+
+.. _EGshelfSJsec500m_3H_NONhydro:
+
+----------------------------
+EGshelfSJsec500m_3H_NONhydro
+----------------------------
+
+Very high-resolution (500m) numerical simulation covering the east Greenland shelf (EGshelf)
+and the Spill Jet section (SJsec). Non-Hydrostatic solutions.
+
+Citation:
+
+* `Magaldi and Haine, 2015 - DSR.`_
+
+Characteristics:
+
+* 3H:       3-hour resolution without external forcing variables.
+* NONhydro: Non-Hydrostatic solutions.
+
+See also:
+
+* EGshelfSJsec500m_6H_NONhydro_: 6-hour resolution with external forcing variables. Non-Hydrostatic.
+* EGshelfSJsec500m_6H_hydro_:    6-hour resolution with external forcing variables. Hydrostatic.
+* EGshelfSJsec500m_3H_hydro_:    3-hour resolution without external forcing variables. Hydrostatic.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfSJsec500m_3H_NONhydro')
+
+.. _EGshelfSJsec500m_6H_NONhydro:
+
+----------------------------
+EGshelfSJsec500m_6H_NONhydro
+----------------------------
+
+Very high-resolution (500m) numerical simulation covering the east Greenland shelf (EGshelf)
+and the Spill Jet section (SJsec). Non-Hydrostatic solutions.
+
+Citation:
+
+* `Magaldi and Haine, 2015 - DSR.`_
+
+Characteristics:
+
+* 6H:       6-hour resolution with external forcing variables.
+* NONhydro: NONHydrostatic solutions.
+
+See also:
+
+* EGshelfSJsec500m_3H_NONhydro_: 3-hour resolution without external forcing variables. Non-Hydrostatic.
+* EGshelfSJsec500m_6H_hydro_:    6-hour resolution with external forcing variables. Hydrostatic.
+* EGshelfSJsec500m_3H_hydro_:    3-hour resolution without external forcing variables. Hydrostatic.
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('EGshelfSJsec500m_6H_NONhydro')
+
+.. _KangerFjord:
+
+-----------
+KangerFjord
+-----------
+
+A realistic numerical model constructed to simulate the oceanic conditions
+and circulation in a large southeast Greenland fjord (Kangerdlugssuaq) and
+the adjacent shelf sea region during winter 2007–2008.
+
+Citation:
+
+* `Fraser et al., 2018 - JGR.`_
+
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('KangerFjord')
+
+.. _ECCO:
+
+----
+ECCO
+----
+
+ECCO_ v4r4 3D dataset, ocean simulations on LLC90 grid
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('ECCO')
+
+.. _daily_ecco:
+
+----------
+daily_ecco
+----------
+
+ECCO_ v4r4 3D dataset, ocean simulations on LLC90 grid
+
+Run the following code to open the dataset:
+
+.. code-block:: ipython
+    :class: no-execute
+
+    import oceanspy as ospy
+    od = ospy.open_oceandataset.from_catalog('daily_ecco')
+
+.. _`Almansi et al., 2017 - JPO.`: https://journals.ametsoc.org/doi/full/10.1175/JPO-D-17-0129.1
+.. _`Magaldi and Haine, 2015 - DSR.`: https://www.sciencedirect.com/science/article/pii/S0967063714001915
+.. _`Fraser et al., 2018 - JGR.`: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018JC014435