Merge pull request #899 from alicebarthel/add_OSNAP_TSclimtransects

Add osnap T S climtransects

docs/users_guide/analysis_tasks.rst

@@ -34,6 +34,7 @@ Analysis Tasks
    tasks/meridionalHeatTransport
    tasks/streamfunctionMOC
    tasks/indexNino34
+   tasks/osnapTransects
    tasks/woceTransects
    tasks/soseTransects
    tasks/woaTransects

docs/users_guide/tasks/osnapTransects.rst

@@ -0,0 +1,133 @@
+.. _task_osnapTransects:
+
+osnapTransects
+=============
+
+An analysis task for interpolating MPAS fields to
+`Overturning in the Subpolar North Atlantic Program (OSNAP)`_ transects 
+and comparing them with ship-based observations.
+
+Component and Tags::
+
+    component: ocean
+    tags: climatology, transect, osnap
+
+Configuration Options
+---------------------
+
+The following configuration options are available for this task::
+
+    [osnapTransects]
+    ## options related to plotting model vs. OSNAP transects.
+
+    # Times for comparison times (JFM, JAS, ANN)
+    seasons =  ['ANN']
+
+    # The approximate horizontal resolution (in km) of each transect.  Latitude/
+    # longitude between observation points will be subsampled at this interval.
+    # Use 'obs' to indicate no subsampling.
+    horizontalResolution = obs
+
+    # The name of the vertical comparison grid.  Valid values are 'mpas' for the
+    # MPAS vertical grid, 'obs' to use the locations of observations or
+    # any other name if the vertical grid is defined by 'verticalComparisonGrid'
+    # verticalComparisonGridName = obs
+    verticalComparisonGridName = uniform_0_to_4000m_at_10m
+    #verticalComparisonGridName = mpas
+
+    # The vertical comparison grid if 'verticalComparisonGridName' is not 'mpas' or
+    # 'obs'.  This should be numpy array of (typically negative) elevations (in m).
+    verticalComparisonGrid = numpy.linspace(0, -4000, 401)
+
+    # The minimum weight of a destination cell after remapping. Any cell with
+    # weights lower than this threshold will therefore be masked out.
+    renormalizationThreshold = 0.01
+
+
+    [osnapTemperatureTransects]
+    ## options related to plotting OSNAP transects of potential temperature
+
+    # colormap for model/observations
+    colormapNameResult = RdYlBu_r
+    # the type of norm used in the colormap (linear, log, or symLog)
+    normTypeResult = linear
+    # A dictionary with keywords for the norm
+    normArgsResult = {'vmin': 0.0, 'vmax': 18.0}
+    # color indices into colormapName for filled contours
+    #colormapIndicesResult = [0, 40, 80, 110, 140, 170, 200, 230, 255]
+    # colormap levels/values for contour boundaries
+    #colorbarLevelsResult = [0, 1, 2, 3, 4, 6, 8, 10, 14, 18]
+    # place the ticks automatically by default
+    # colorbarTicksResult = numpy.linspace(0.0, 18.0, 9)
+    # contour line levels
+    contourLevelsResult = np.arange(1.0, 18.0, 2.0)
+
+    # colormap for differences
+    colormapNameDifference = RdBu_r
+    # the type of norm used in the colormap (linear, log, or symLog)
+    normTypeDifference = linear
+    # A dictionary with keywords for the norm
+    normArgsDifference = {'vmin': -2.0, 'vmax': 2.0}
+    # color indices into colormapName for filled contours
+    #colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255]
+    # colormap levels/values for contour boundaries
+    #colorbarLevelsDifference = [-2, -1.5, -1.25, -1, -0.2, 0, 0.2, 1, 1.25, 1.5, 2]
+    # place the ticks automatically by default
+    # colorbarTicksDifference = numpy.linspace(-2.0, 2.0, 9)
+    # contour line levels
+    contourLevelsDifference = np.arange(-1.8, 2.0, 0.4)
+
+
+
+    [osnapSalinityTransects]
+    ## options related to plotting OSNAP transects of salinity
+
+    # colormap for model/observations
+    colormapNameResult = BuOr
+    # the type of norm used in the colormap (linear, log, or symLog)
+    normTypeResult = linear
+    # A dictionary with keywords for the norm
+    normArgsResult = {'vmin': 33.0, 'vmax': 36.0}
+    # color indices into colormapName for filled contours
+    #colormapIndicesResult = [0, 40, 80, 110, 140, 170, 200, 230, 255]
+    # colormap levels/values for contour boundaries
+    #colorbarLevelsResult = [33, 34, 34.25, 34.5, 34.6, 34.7, 34.8, 34.9, 35, 36]
+    # place the ticks automatically by default
+    # colorbarTicksResult = numpy.linspace(33.0, 36.0, 9)
+    # contour line levels
+    contourLevelsResult = np.arange(33.3, 36.0, 0.3)
+
+    # colormap for differences
+    colormapNameDifference = RdBu_r
+    # the type of norm used in the colormap (linear, log, or symLog)
+    normTypeDifference = linear
+    # A dictionary with keywords for the norm
+    normArgsDifference = {'vmin': -1.0, 'vmax': 1.0}
+    # color indices into colormapName for filled contours
+    #colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255]
+    # colormap levels/values for contour boundaries
+    #colorbarLevelsDifference = [-1, -0.5, -0.2, -0.05, -0.02, 0,  0.02, 0.05, 0.2, 0.5, 1]
+    # place the ticks automatically by default
+    # colorbarTicksDifference = numpy.linspace(-1.0, 1.0, 9)
+    # contour line levels
+    contourLevelsDifference = np.arange(-0.9, 1.0, 0.4)
+
+For details on these configuration options, see:
+ * :ref:`config_transects`
+ * :ref:`config_remapping`
+ * :ref:`config_colormaps`
+ * :ref:`config_seasons`
+
+Observations
+------------
+
+:ref:`osnap`
+
+Example Result
+--------------
+
+.. image:: examples/osnap_transect.png
+   :width: 500 px
+   :align: center
+
+.. _`Overturning in the Subpolar North Atlantic Program (OSNAP)`: http://www.o-snap.org

mpas_analysis/__main__.py

@@ -226,8 +226,12 @@ def build_analysis_list(config, controlConfig):
     analyses.append(ocean.WoceTransects(config, oceanClimatologyTasks['avg'],
                                         controlConfig))
 
-    analyses.append(ocean.AntshipTransects(config, oceanClimatologyTasks['avg'],
-                                        controlConfig))
+    analyses.append(ocean.AntshipTransects(config,
+                                           oceanClimatologyTasks['avg'],
+                                           controlConfig))
+
+    analyses.append(ocean.OsnapTransects(config, oceanClimatologyTasks['avg'],
+                                         controlConfig))
 
     analyses.append(ocean.SoseTransects(config, oceanClimatologyTasks['avg'],
                                         controlConfig))

mpas_analysis/default.cfg

@@ -529,6 +529,7 @@ woa23Subdirectory = WOA23
 schmidtkoSubdirectory = Schmidtko
 woceSubdirectory = WOCE
 antshipSubdirectory = AntShip
+osnapSubdirectory = OSNAP
 no3Subdirectory = BGC/NO3
 po4Subdirectory = BGC/PO4
 sio3Subdirectory = BGC/SiO3
@@ -3228,6 +3229,130 @@ compareAsContoursOnSinglePlot = True
 contourLevelsResult = [1027.2, 1027.4, 1027.6, 1027.7, 1027.8, 1027.85, 1027.9, 1027.95, 1028.0]
 
 
+[osnapTransects]
+## options related to plotting model vs. Overturning in the Subpolar North Atlantic Program
+## (OSNAP) transects.
+
+# Times for comparison times (valid values: JFM, JAS, ANN)
+seasons =  ['ANN']
+
+# The approximate horizontal resolution (in km) of each transect.  Latitude/
+# longitude between observation points will be subsampled at this interval.
+# Use 'obs' to indicate no subsampling. Use 'mpas' to indicate plotting of
+# model data on the native grid, in which case comparison with observations
+# will take place on the observation grid.
+horizontalResolution = mpas
+#horizontalResolution = obs
+#horizontalResolution = 5
+
+# Horizontal bounds of the plot (in km), or an empty list for automatic bounds
+# The bounds are a 2-element list of the minimum and maximum distance along the
+# transect.  Note: only East and West are valid transects
+horizontalBounds = {'OSNAP_East': [],
+                    'OSNAP_West': []}
+
+# The name of the vertical comparison grid.  Valid values are 'mpas' for the
+# MPAS vertical grid, 'obs' to use the locations of observations or
+# any other name if the vertical grid is defined by 'verticalComparisonGrid'.
+# If horizontalResolution is 'mpas', model data (both main and control) will be
+# plotted on the MPAS vertical grid, regardless of the comparison grid.
+verticalComparisonGridName = mpas
+#verticalComparisonGridName = obs
+#verticalComparisonGridName = uniform_0_to_4000m_at_10m
+
+# The vertical comparison grid if 'verticalComparisonGridName' is not 'mpas' or
+# 'obs'.  This should be numpy array of (typically negative) elevations (in m).
+# The first and last entries are used as axis bounds for 'mpas' and 'obs'
+# vertical comparison grids
+verticalComparisonGrid = numpy.linspace(0, -4000, 401)
+
+# A range for the y axis (if any)
+verticalBounds = [-4000., 0.]
+
+# The minimum weight of a destination cell after remapping. Any cell with
+# weights lower than this threshold will therefore be masked out.
+renormalizationThreshold = 0.01
+
+
+[osnapTemperatureTransects]
+## options related to plotting OSNAP transects of potential temperature
+
+# colormap for model/observations
+colormapNameResult = RdYlBu_r
+# whether the colormap is indexed or continuous
+colormapTypeResult = continuous
+# the type of norm used in the colormap (linear, log, or symLog)
+normTypeResult = linear
+# A dictionary with keywords for the norm
+normArgsResult = {'vmin': 0.0, 'vmax': 18.0}
+# color indices into colormapName for filled contours
+#colormapIndicesResult = [0, 40, 80, 110, 140, 170, 200, 230, 255]
+# colormap levels/values for contour boundaries
+#colorbarLevelsResult = [0, 1, 2, 3, 4, 6, 8, 10, 14, 18]
+# place the ticks automatically by default
+# colorbarTicksResult = numpy.linspace(0.0, 18.0, 9)
+# contour line levels (use [] for automatic contour selection, 'none' for no
+# contour lines)
+contourLevelsResult = np.arange(1.0, 18.0, 2.0)
+
+# colormap for differences
+colormapNameDifference = balance
+# whether the colormap is indexed or continuous
+colormapTypeDifference = continuous
+# the type of norm used in the colormap (linear, log, or symLog)
+normTypeDifference = linear
+# A dictionary with keywords for the norm
+normArgsDifference = {'vmin': -3.0, 'vmax': 3.0}
+# color indices into colormapName for filled contours
+#colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255]
+# colormap levels/values for contour boundaries
+#colorbarLevelsDifference = [-2, -1.5, -1.25, -1, -0.2, 0, 0.2, 1, 1.25, 1.5, 2]
+# place the ticks automatically by default
+# colorbarTicksDifference = numpy.linspace(-2.0, 2.0, 9)
+# contour line levels (use [] for automatic contour selection, 'none' for no
+# contour lines)
+contourLevelsDifference = np.arange(-1.8, 2.0, 0.4)
+
+[osnapSalinityTransects]
+## options related to plotting OSNAP transects of salinity
+
+# colormap for model/observations
+colormapNameResult = haline
+# whether the colormap is indexed or continuous
+colormapTypeResult = continuous
+# the type of norm used in the colormap (linear, log, or symLog)
+normTypeResult = linear
+# A dictionary with keywords for the norm
+normArgsResult = {'vmin': 33.0, 'vmax': 36.0}
+# color indices into colormapName for filled contours
+#colormapIndicesResult = [0, 40, 80, 110, 140, 170, 200, 230, 255]
+# colormap levels/values for contour boundaries
+#colorbarLevelsResult = [33, 34, 34.25, 34.5, 34.6, 34.7, 34.8, 34.9, 35, 36]
+# place the ticks automatically by default
+# colorbarTicksResult = numpy.linspace(33.0, 36.0, 9)
+# contour line levels (use [] for automatic contour selection, 'none' for no
+# contour lines)
+contourLevelsResult = np.arange(33.3, 36.0, 0.3)
+
+# colormap for differences
+colormapNameDifference = balance
+# whether the colormap is indexed or continuous
+colormapTypeDifference = continuous
+# the type of norm used in the colormap (linear, log, or symLog)
+normTypeDifference = linear
+# A dictionary with keywords for the norm
+normArgsDifference = {'vmin': -1.0, 'vmax': 1.0}
+# color indices into colormapName for filled contours
+#colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255]
+# colormap levels/values for contour boundaries
+#colorbarLevelsDifference = [-1, -0.5, -0.2, -0.05, -0.02, 0,  0.02, 0.05, 0.2, 0.5, 1]
+# place the ticks automatically by default
+# colorbarTicksDifference = numpy.linspace(-1.0, 1.0, 9)
+# contour line levels (use [] for automatic contour selection, 'none' for no
+# contour lines)
+contourLevelsDifference = np.arange(-0.9, 1.0, 0.4)
+
+
 [geojsonTransects]
 ## options related to plotting model transects at points determined by a
 ## geojson file.  To generate your own geojson file, go to:

mpas_analysis/obs/observational_datasets.xml

@@ -1597,6 +1597,66 @@
     </nameInDocs>
   </observation>
 
+  <observation>
+    <name>
+      OSNAP Temperature Salinity and Velocity Climatology
+    </name>
+    <component>
+      ocean
+    </component>
+    <description>
+      OSNAP is designed to provide a continuous record of the full-water 
+      column, trans-basin fluxes of heat, mass and freshwater in the subpolar 
+      North Atlantic. It consists of two legs: one extending from southern 
+      Labrador to the southwestern tip of Greenland across the mouth of the 
+      Labrador Sea (OSNAP West), and the second from the southeastern tip of 
+      Greenland to Scotland (OSNAP East). The observing system also includes 
+      subsurface floats (OSNAP Floats) in order to trace the pathways of 
+      overflow waters in the basin and to assess the connectivity of currents 
+      crossing the OSNAP line. The location of the OSNAP East and West legs 
+      purposefully melds with a number of long-term observational efforts in 
+      the North Atlantic: the Canadian repeat AR7W program in the Labrador 
+      Sea; the German Labrador Sea western boundary array at 53°N; the 
+      global Ocean Observatories Initiative node to be placed in the 
+      southwestern Irminger Sea; the repeat A1E/AR7E hydrographic sections 
+      across the Irminger and Iceland basins; and the Ellett line in the 
+      Rockall region. Importantly, this observing system, in conjunction with 
+      the RAPID/MOCHA array at 26ºN and the EU THOR/NACLIM program, will 
+      provide a comprehensive measure of the Atlantic Meridional Overturning 
+      Circulation (AMOC) and provide a means to evaluate intergyre 
+      connectivity in the North Atlantic. OSNAP is a collaborative effort, 
+      which includes several countries including US, Canada, China, France, 
+      Germany, Netherlands and the UK.
+    </description>
+    <source>
+      [Overturning in the Subpolar North Atlantic Program (OSNAP) website]
+      (https://www.o-snap.org/data-access/)
+    </source>
+    <releasePolicy>
+      Acknowledgment: OSNAP data were collected and made freely available by the OSNAP (Overturning in the Subpolar North Atlantic Program) project and all the national programs that contribute to it (www.o-snap.org).
+    </releasePolicy>
+    <references>
+    </references>
+    <bibtex>
+    </bibtex>
+    <dataUrls>
+      - https://duke.app.box.com/s/4qbi9ocpvmxdv44wnx2g5rgoyy85jmz6
+    </dataUrls>
+    <preprocessing>
+      - preprocess_observations/preprocessingOSNAP30day.ipynb
+    </preprocessing>
+    <tasks>
+      - climatologyMapOSNAP
+    </tasks>
+    <subdirectory>
+      Ocean/OSNAP
+    </subdirectory>
+    <nameInDocs>
+      osnap_t_s
+    </nameInDocs>
+  </observation>
+
+
 <!--
   <observation>
     <name>

mpas_analysis/ocean/__init__.py

@@ -54,6 +54,7 @@
 
 from mpas_analysis.ocean.woce_transects import WoceTransects
 from mpas_analysis.ocean.antship_transects import AntshipTransects
+from mpas_analysis.ocean.osnap_transects import OsnapTransects
 from mpas_analysis.ocean.sose_transects import SoseTransects
 from mpas_analysis.ocean.woa_transects import WoaTransects
 from mpas_analysis.ocean.geojson_transects import GeojsonTransects