Update documentation

latest/_sources/developers_guide/landice/api.rst.txt

@@ -492,8 +492,7 @@ Landice Framework
    mesh.add_bedmachine_thk_to_ais_gridded_data
    mesh.clean_up_after_interp
    mesh.gridded_flood_fill
-   mesh.interp_ais_bedmachine
-   mesh.interp_ais_measures
+   mesh.interp_gridded2mali
    mesh.mpas_flood_fill
    mesh.preprocess_ais_data
    mesh.set_rectangular_geom_points_and_edges

latest/_sources/developers_guide/landice/framework.rst.txt

@@ -56,13 +56,10 @@ clean up steps after interpolation for the AIS mesh case.
 :py:func:`compass.landice.mesh.gridded_flood_fill()` applies a flood-fill algorithm
 to the gridded dataset in order to separate the ice sheet from peripheral ice.
 
-:py:func:`compass.landice.mesh.interp_ais_bedmachine()` interpolates BedMachine
-thickness and bedTopography dataset to a MALI mesh, accounting for masking of
-the ice extent to avoid interpolation ramps.
-
-:py:func:`compass.landice.mesh.interp_ais_interp_ais_measures()` interpolates
-MEASURES ice velocity dataset to a MALI mesh, accounting for masking at the ice
-edge and extrapolation.
+:py:func:`compass.landice.mesh.interp_gridded2mali()` interpolates gridded data
+(e.g. BedMachine thickness or MEaSUREs ice velocity) to a MALI mesh, accounting
+for masking of the ice extent to avoid interpolation ramps. This functions works
+for both Antarctica and Greenland. 
 
 :py:func:`compass.landice.mesh.preprocess_ais_data()` performs adjustments to
 gridded AIS datasets needed for rest of compass workflow to utilize them.

latest/_sources/developers_guide/landice/generated/compass.landice.mesh.interp_gridded2mali.rst.txt

@@ -0,0 +1,6 @@
+compass.landice.mesh.interp\_gridded2mali
+=========================================
+
+.. currentmodule:: compass.landice.mesh
+
+.. autofunction:: interp_gridded2mali

latest/_sources/users_guide/landice/test_groups/antarctica.rst.txt

@@ -73,7 +73,19 @@ the mesh generation options are adjusted through the config file.
     # path to directory containing BedMachine and Measures datasets
     # (default value is for Perlmutter)
     data_path = /global/cfs/cdirs/fanssie/standard_datasets/AIS_datasets
-
+    
+    # filename of the BedMachine thickness and bedTopography dataset
+    # (default value is for Perlmutter)
+    bedmachine_filename = BedMachineAntarctica_2020-07-15_v02_edits_floodFill_extrap_fillVostok.nc
+    
+    # filename of the MEASURES ice velocity dataset
+    # (default value is for Perlmutter)
+    measures_filename = antarctica_ice_velocity_450m_v2_edits_extrap.nc
+    
+    # projection of the source datasets, according to the dictionary keys
+    # create_SCRIP_file_from_planar_rectangular_grid.py from MPAS_Tools
+    src_proj = ais-bedmap2
+    
     # number of processors to use for ESMF_RegridWeightGen
     nProcs = 128
 

latest/_sources/users_guide/landice/test_groups/greenland.rst.txt

@@ -86,6 +86,26 @@ The other test cases do not use config options.
    use_dist_to_edge = True
    use_bed = True
 
+   [greenland]
+   # path to directory containing BedMachine and Measures datasets
+   # (default value is for Perlmutter)
+   data_path = /global/cfs/cdirs/fanssie/standard_datasets/GIS_datasets/
+   
+   # filename of the BedMachine thickness and bedTopography dataset
+   # (default value is for Perlmutter)
+   bedmachine_filename = BedMachineGreenland-v5_edits_floodFill_extrap.nc
+   
+   # filename of the MEASURES ice velocity dataset
+   # (default value is for Perlmutter)
+   measures_filename = greenland_vel_mosaic500_extrap.nc
+   
+   # projection of the source datasets, according to the dictionary keys
+   # create_SCRIP_file_from_planar_rectangular_grid.py from MPAS_Tools
+   src_proj = gis-gimp
+   
+   # number of processors to use for ESMF_RegridWeightGen
+   nProcs = 128
+
 smoke_test
 ----------
 

latest/developers_guide/landice/api.html

@@ -941,34 +941,31 @@ <h2>Landice Framework<a class="headerlink" href="#landice-framework" title="Link
 <tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.gridded_flood_fill.html#compass.landice.mesh.gridded_flood_fill" title="compass.landice.mesh.gridded_flood_fill"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.gridded_flood_fill</span></code></a>(field[, iStart, jStart])</p></td>
 <td><p>Generic flood-fill routine to create mask of connected elements in the desired input array (field) from a gridded dataset.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.interp_ais_bedmachine.html#compass.landice.mesh.interp_ais_bedmachine" title="compass.landice.mesh.interp_ais_bedmachine"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.interp_ais_bedmachine</span></code></a>(self, data_path, ...)</p></td>
-<td><p>Interpolates BedMachine thickness and bedTopography dataset to a MALI mesh</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.interp_gridded2mali.html#compass.landice.mesh.interp_gridded2mali" title="compass.landice.mesh.interp_gridded2mali"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.interp_gridded2mali</span></code></a>(self, source_file, ...)</p></td>
+<td><p>Interpolate gridded dataset (e.g. MEASURES, BedMachine) onto a MALI mesh.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.interp_ais_measures.html#compass.landice.mesh.interp_ais_measures" title="compass.landice.mesh.interp_ais_measures"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.interp_ais_measures</span></code></a>(self, data_path, ...)</p></td>
-<td><p>Interpolates MEASURES ice velocity dataset to a MALI mesh</p></td>
-</tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.mpas_flood_fill.html#compass.landice.mesh.mpas_flood_fill" title="compass.landice.mesh.mpas_flood_fill"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.mpas_flood_fill</span></code></a>(seed_mask, grow_mask, ...)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.mpas_flood_fill.html#compass.landice.mesh.mpas_flood_fill" title="compass.landice.mesh.mpas_flood_fill"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.mpas_flood_fill</span></code></a>(seed_mask, grow_mask, ...)</p></td>
 <td><p>Flood-fill for mpas meshes using mpas cells.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.preprocess_ais_data.html#compass.landice.mesh.preprocess_ais_data" title="compass.landice.mesh.preprocess_ais_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.preprocess_ais_data</span></code></a>(self, ...)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.preprocess_ais_data.html#compass.landice.mesh.preprocess_ais_data" title="compass.landice.mesh.preprocess_ais_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.preprocess_ais_data</span></code></a>(self, ...)</p></td>
 <td><p>Perform adjustments to gridded AIS datasets needed for rest of compass workflow to utilize them</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.set_rectangular_geom_points_and_edges.html#compass.landice.mesh.set_rectangular_geom_points_and_edges" title="compass.landice.mesh.set_rectangular_geom_points_and_edges"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.set_rectangular_geom_points_and_edges</span></code></a>(...)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.set_rectangular_geom_points_and_edges.html#compass.landice.mesh.set_rectangular_geom_points_and_edges" title="compass.landice.mesh.set_rectangular_geom_points_and_edges"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.set_rectangular_geom_points_and_edges</span></code></a>(...)</p></td>
 <td><p>Set node and edge coordinates to pass to <a class="reference external" href="http://mpas-dev.github.io/MPAS-Tools/stable/generated/mpas_tools.mesh.creation.build_mesh.build_planar_mesh.html#mpas_tools.mesh.creation.build_mesh.build_planar_mesh" title="(in mpas_tools vstable)"><code class="xref py py-func docutils literal notranslate"><span class="pre">mpas_tools.mesh.creation.build_mesh.build_planar_mesh()</span></code></a>.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.set_cell_width.html#compass.landice.mesh.set_cell_width" title="compass.landice.mesh.set_cell_width"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.set_cell_width</span></code></a>(self, section_name, thk)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.set_cell_width.html#compass.landice.mesh.set_cell_width" title="compass.landice.mesh.set_cell_width"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.set_cell_width</span></code></a>(self, section_name, thk)</p></td>
 <td><p>Set cell widths based on settings in config file to pass to <a class="reference external" href="http://mpas-dev.github.io/MPAS-Tools/stable/generated/mpas_tools.mesh.creation.build_mesh.build_planar_mesh.html#mpas_tools.mesh.creation.build_mesh.build_planar_mesh" title="(in mpas_tools vstable)"><code class="xref py py-func docutils literal notranslate"><span class="pre">mpas_tools.mesh.creation.build_mesh.build_planar_mesh()</span></code></a>.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.get_dist_to_edge_and_gl.html#compass.landice.mesh.get_dist_to_edge_and_gl" title="compass.landice.mesh.get_dist_to_edge_and_gl"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.get_dist_to_edge_and_gl</span></code></a>(self, thk, ...)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.get_dist_to_edge_and_gl.html#compass.landice.mesh.get_dist_to_edge_and_gl" title="compass.landice.mesh.get_dist_to_edge_and_gl"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.get_dist_to_edge_and_gl</span></code></a>(self, thk, ...)</p></td>
 <td><p>Calculate distance from each point to ice edge and grounding line, to be used in mesh density functions in <a class="reference internal" href="generated/compass.landice.mesh.set_cell_width.html#compass.landice.mesh.set_cell_width" title="compass.landice.mesh.set_cell_width"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.set_cell_width()</span></code></a>.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.build_cell_width.html#compass.landice.mesh.build_cell_width" title="compass.landice.mesh.build_cell_width"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.build_cell_width</span></code></a>(self, section_name, ...)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.build_cell_width.html#compass.landice.mesh.build_cell_width" title="compass.landice.mesh.build_cell_width"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.build_cell_width</span></code></a>(self, section_name, ...)</p></td>
 <td><p>Determine MPAS mesh cell size based on user-defined density function.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.build_mali_mesh.html#compass.landice.mesh.build_mali_mesh" title="compass.landice.mesh.build_mali_mesh"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.build_mali_mesh</span></code></a>(self, cell_width, x1, ...)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.build_mali_mesh.html#compass.landice.mesh.build_mali_mesh" title="compass.landice.mesh.build_mali_mesh"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.build_mali_mesh</span></code></a>(self, cell_width, x1, ...)</p></td>
 <td><p>Create the MALI mesh based on final cell widths determined by <a class="reference internal" href="generated/compass.landice.mesh.build_cell_width.html#compass.landice.mesh.build_cell_width" title="compass.landice.mesh.build_cell_width"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.build_cell_width()</span></code></a>, using Jigsaw and MPAS-Tools functions.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.landice.mesh.make_region_masks.html#compass.landice.mesh.make_region_masks" title="compass.landice.mesh.make_region_masks"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.make_region_masks</span></code></a>(self, mesh_filename, ...)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.landice.mesh.make_region_masks.html#compass.landice.mesh.make_region_masks" title="compass.landice.mesh.make_region_masks"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mesh.make_region_masks</span></code></a>(self, mesh_filename, ...)</p></td>
 <td><p>Create masks for ice-sheet subregions based on data in <code class="docutils literal notranslate"><span class="pre">MPAS-Dev/geometric_fatures</span></code>.</p></td>
 </tr>
 </tbody>

latest/developers_guide/landice/framework.html

@@ -171,12 +171,10 @@ <h2>mesh<a class="headerlink" href="#mesh" title="Link to this heading">¶</a></
 clean up steps after interpolation for the AIS mesh case.</p>
 <p><a class="reference internal" href="generated/compass.landice.mesh.gridded_flood_fill.html#compass.landice.mesh.gridded_flood_fill" title="compass.landice.mesh.gridded_flood_fill"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.gridded_flood_fill()</span></code></a> applies a flood-fill algorithm
 to the gridded dataset in order to separate the ice sheet from peripheral ice.</p>
-<p><a class="reference internal" href="generated/compass.landice.mesh.interp_ais_bedmachine.html#compass.landice.mesh.interp_ais_bedmachine" title="compass.landice.mesh.interp_ais_bedmachine"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.interp_ais_bedmachine()</span></code></a> interpolates BedMachine
-thickness and bedTopography dataset to a MALI mesh, accounting for masking of
-the ice extent to avoid interpolation ramps.</p>
-<p><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.interp_ais_interp_ais_measures()</span></code> interpolates
-MEASURES ice velocity dataset to a MALI mesh, accounting for masking at the ice
-edge and extrapolation.</p>
+<p><a class="reference internal" href="generated/compass.landice.mesh.interp_gridded2mali.html#compass.landice.mesh.interp_gridded2mali" title="compass.landice.mesh.interp_gridded2mali"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.interp_gridded2mali()</span></code></a> interpolates gridded data
+(e.g. BedMachine thickness or MEaSUREs ice velocity) to a MALI mesh, accounting
+for masking of the ice extent to avoid interpolation ramps. This functions works
+for both Antarctica and Greenland.</p>
 <p><a class="reference internal" href="generated/compass.landice.mesh.preprocess_ais_data.html#compass.landice.mesh.preprocess_ais_data" title="compass.landice.mesh.preprocess_ais_data"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.preprocess_ais_data()</span></code></a> performs adjustments to
 gridded AIS datasets needed for rest of compass workflow to utilize them.</p>
 <p><a class="reference internal" href="generated/compass.landice.mesh.set_rectangular_geom_points_and_edges.html#compass.landice.mesh.set_rectangular_geom_points_and_edges" title="compass.landice.mesh.set_rectangular_geom_points_and_edges"><code class="xref py py-func docutils literal notranslate"><span class="pre">compass.landice.mesh.set_rectangular_geom_points_and_edges()</span></code></a> sets node

latest/developers_guide/landice/generated/compass.landice.mesh.gridded_flood_fill.html

@@ -19,7 +19,7 @@
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
-    <link rel="next" title="compass.landice.mesh.interp_ais_bedmachine" href="compass.landice.mesh.interp_ais_bedmachine.html" />
+    <link rel="next" title="compass.landice.mesh.interp_gridded2mali" href="compass.landice.mesh.interp_gridded2mali.html" />
     <link rel="prev" title="compass.landice.mesh.clean_up_after_interp" href="compass.landice.mesh.clean_up_after_interp.html" /> 
 </head>
 
@@ -163,7 +163,7 @@ <h1>compass.landice.mesh.gridded_flood_fill<a class="headerlink" href="#compass-
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="compass.landice.mesh.clean_up_after_interp.html" class="btn btn-neutral float-left" title="compass.landice.mesh.clean_up_after_interp" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="compass.landice.mesh.interp_ais_bedmachine.html" class="btn btn-neutral float-right" title="compass.landice.mesh.interp_ais_bedmachine" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="compass.landice.mesh.interp_gridded2mali.html" class="btn btn-neutral float-right" title="compass.landice.mesh.interp_gridded2mali" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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