From 3ba0f065388913526605eb9f47457b7f419b444a Mon Sep 17 00:00:00 2001 From: Azure Pipelines Date: Mon, 7 Aug 2023 10:39:08 +0000 Subject: [PATCH] [skip ci] Update stable --- stable/_modules/mpas_tools/logging.html | 45 ++++++----- .../_modules/mpas_tools/mesh/conversion.html | 80 +++++++------------ .../mpas_tools/mesh/creation/build_mesh.html | 18 ++--- stable/_modules/mpas_tools/mesh/mask.html | 4 +- .../mpas_tools/viz/paraview_extractor.html | 13 +-- stable/api.html | 6 +- .../mpas_tools.logging.check_call.html | 4 +- .../mpas_tools.mesh.conversion.mask.html | 9 +-- ...s.mesh.mask.compute_mpas_region_masks.html | 2 +- ...mesh.mask.compute_mpas_transect_masks.html | 2 +- stable/searchindex.js | 2 +- 11 files changed, 83 insertions(+), 102 deletions(-) diff --git a/stable/_modules/mpas_tools/logging.html b/stable/_modules/mpas_tools/logging.html index bee6e3430..5a8d589a3 100644 --- a/stable/_modules/mpas_tools/logging.html +++ b/stable/_modules/mpas_tools/logging.html @@ -114,7 +114,7 @@

Source code for mpas_tools.logging

 import subprocess
 
 
-
[docs]def check_call(args, logger, log_command=True, timeout=None, **kwargs):
+
[docs]def check_call(args, logger=None, log_command=True, timeout=None, **kwargs):
     """
     Call the given subprocess with logging to the given logger.
 
@@ -124,7 +124,7 @@ 
Source code for mpas_tools.logging
         A list or string of argument to the subprocess.  If ``args`` is a
         string, you must pass ``shell=True`` as one of the ``kwargs``.
 
-    logger : logging.Logger
+    logger : logging.Logger, optional
         The logger to write output to
 
     log_command : bool, optional
@@ -147,25 +147,28 @@ 
Source code for mpas_tools.logging
         print_args = args
     else:
         print_args = ' '.join(args)
-    if log_command:
-        logger.info(f'Running: {print_args}')
-
-    process = subprocess.Popen(args, stdout=subprocess.PIPE,
-                               stderr=subprocess.PIPE, **kwargs)
-    stdout, stderr = process.communicate(timeout=timeout)
-
-    if stdout:
-        stdout = stdout.decode('utf-8')
-        for line in stdout.split('\n'):
-            logger.info(line)
-    if stderr:
-        stderr = stderr.decode('utf-8')
-        for line in stderr.split('\n'):
-            logger.error(line)
-
-    if process.returncode != 0:
-        raise subprocess.CalledProcessError(process.returncode,
-                                            print_args)

+
+    # make a logger if there isn't already one
+    with LoggingContext(print_args, logger=logger) as logger:
+        if log_command:
+            logger.info(f'Running: {print_args}')
+
+        process = subprocess.Popen(args, stdout=subprocess.PIPE,
+                                   stderr=subprocess.PIPE, **kwargs)
+        stdout, stderr = process.communicate(timeout=timeout)
+
+        if stdout:
+            stdout = stdout.decode('utf-8')
+            for line in stdout.split('\n'):
+                logger.info(line)
+        if stderr:
+            stderr = stderr.decode('utf-8')
+            for line in stderr.split('\n'):
+                logger.error(line)
+
+        if process.returncode != 0:
+            raise subprocess.CalledProcessError(process.returncode,
+                                                print_args)

 
 
 
[docs]class LoggingContext(object):
diff --git a/stable/_modules/mpas_tools/mesh/conversion.html b/stable/_modules/mpas_tools/mesh/conversion.html
index a1f55c7c5..9333ebf1c 100644
--- a/stable/_modules/mpas_tools/mesh/conversion.html
+++ b/stable/_modules/mpas_tools/mesh/conversion.html
@@ -111,11 +111,12 @@
   
Source code for mpas_tools.mesh.conversion
 import os
 import xarray
-import subprocess
 from tempfile import TemporaryDirectory
 import shutil
 
+import mpas_tools.io
 from mpas_tools.io import write_netcdf
+from mpas_tools.logging import check_call
 
 
 
[docs]def convert(dsIn, graphInfoFileName=None, logger=None, dir=None):
@@ -159,9 +160,9 @@ 
Source code for mpas_tools.mesh.conversion
 
         outDir = os.path.dirname(outFileName)
 
-        _call_subprocess(['MpasMeshConverter.x', inFileName, outFileName],
+        check_call(['MpasMeshConverter.x', inFileName, outFileName],
                          logger)
-        
+
         dsOut = xarray.open_dataset(outFileName)
         dsOut.load()
 
@@ -255,8 +256,8 @@ 
Source code for mpas_tools.mesh.conversion
 
         outDir = os.path.dirname(outFileName)
 
-        _call_subprocess(args, logger)
-        
+        check_call(args=args, logger=logger)
+
         dsOut = xarray.open_dataset(outFileName)
         dsOut.load()
 
@@ -267,10 +268,10 @@ 
Source code for mpas_tools.mesh.conversion
     return dsOut

 
 
-
[docs]def mask(dsMesh, fcMask=None, fcSeed=None, logger=None, dir=None):
+
[docs]def mask(dsMesh, fcMask=None, logger=None, dir=None, cores=1):
     """
-    Use ``MpasMaskCreator.x`` to create a set of region masks either from
-    mask feature collections or from seed points to be used to flood fill
+    Use ``compute_mpas_region_masks`` to create a set of region masks either
+    from mask feature collections
 
     Parameters
     ----------
@@ -280,10 +281,6 @@ 
Source code for mpas_tools.mesh.conversion
     fcMask : geometric_features.FeatureCollection, optional
         A feature collection containing features to use to create the mask
 
-    fcSeed : geometric_features.FeatureCollection, optional
-        A feature collection with points to use a seeds for a flood fill that
-        will create a mask of all cells connected to the seed points
-
     logger : logging.Logger, optional
         A logger for the output if not stdout
 
@@ -291,6 +288,9 @@ 
Source code for mpas_tools.mesh.conversion
         A directory in which a temporary directory will be added with files
         produced during mask creation and then deleted upon completion.
 
+    cores : int, optional
+        The number of cores to use for python multiprocessing
+
     Returns
     -------
     dsMask : xarray.Dataset
@@ -300,51 +300,29 @@ 
Source code for mpas_tools.mesh.conversion
     if dir is not None:
         dir = os.path.abspath(dir)
     with TemporaryDirectory(dir=dir) as tempdir:
-        inFileName = '{}/mesh_in.nc'.format(tempdir)
+        inFileName = f'{tempdir}/mesh_in.nc'
         write_netcdf(dsMesh, inFileName)
-        outFileName = '{}/mesh_out.nc'.format(tempdir)
-
-        args = ['MpasMaskCreator.x', inFileName, outFileName]
-
-        if fcMask is not None:
-            fileName = '{}/mask.geojson'.format(tempdir)
-            fcMask.to_geojson(fileName)
-            args.extend(['-f', fileName])
-
-        if fcSeed is not None:
-            fileName = '{}/seed.geojson'.format(tempdir)
-            fcSeed.to_geojson(fileName)
-            args.extend(['-s', fileName])
-
-        _call_subprocess(args, logger)
+        outFileName = f'{tempdir}/mask_out.nc'
+
+        geojsonFileName = f'{tempdir}/mask.geojson'
+        fcMask.to_geojson(geojsonFileName)
+        args = ['compute_mpas_region_masks',
+                '-m', inFileName,
+                '-o', outFileName,
+                '-g', geojsonFileName,
+                '-t', 'cell',
+                '--process_count', f'{cores}',
+                '--format', mpas_tools.io.default_format,
+                ]
+        if mpas_tools.io.default_engine is not None:
+            args.extend(['--engine', mpas_tools.io.default_engine])
+
+        check_call(args=args, logger=logger)
 
         dsOut = xarray.open_dataset(outFileName)
         dsOut.load()
 
     return dsOut

-
-
-def _call_subprocess(args, logger):
-    """Call the given subprocess and send the output to the logger"""
-    if logger is None:
-        subprocess.check_call(args)
-    else:
-        process = subprocess.Popen(args, stdout=subprocess.PIPE,
-                                   stderr=subprocess.PIPE)
-        stdout, stderr = process.communicate()
-
-        if stdout:
-            stdout = stdout.decode('utf-8')
-            for line in stdout.split('\n'):
-                logger.info(line)
-        if stderr:
-            stderr = stderr.decode('utf-8')
-            for line in stderr.split('\n'):
-                logger.error(line)
-
-        if process.returncode != 0:
-            raise subprocess.CalledProcessError(process.returncode,
-                                                ' '.join(args))
 

 
            

diff --git a/stable/_modules/mpas_tools/mesh/creation/build_mesh.html b/stable/_modules/mpas_tools/mesh/creation/build_mesh.html
index d73b83807..27e9519e8 100644
--- a/stable/_modules/mpas_tools/mesh/creation/build_mesh.html
+++ b/stable/_modules/mpas_tools/mesh/creation/build_mesh.html
@@ -117,8 +117,7 @@ 
Source code for mpas_tools.mesh.creation.build_mesh
import cartopy.crs as ccrs
 import cartopy
 
-from mpas_tools.mesh.conversion import convert
-from mpas_tools.io import write_netcdf
+from mpas_tools.logging import check_call
 
 from mpas_tools.mesh.creation.jigsaw_driver import jigsaw_driver
 from mpas_tools.mesh.creation.jigsaw_to_netcdf import jigsaw_to_netcdf
@@ -212,9 +211,10 @@ 
Source code for mpas_tools.mesh.creation.build_mesh
sphere_radius=earth_radius)
 
         logger.info('Step 3. Convert from triangles to MPAS mesh')
-        write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc'), dir=dir,
-                             logger=logger),
-                     out_filename)

+        args = ['MpasMeshConverter.x',
+                'mesh_triangles.nc',
+                out_filename]
+        check_call(args=args, logger=logger)

 
 
 
[docs]def build_planar_mesh(cellWidth, x, y, geom_points, geom_edges,
@@ -263,10 +263,10 @@ 
Source code for mpas_tools.mesh.creation.build_mesh
output_name='mesh_triangles.nc', on_sphere=False)
 
         logger.info('Step 3. Convert from triangles to MPAS mesh')
-        write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc'),
-                             logger=logger),
-                     out_filename)

-
+        args = ['MpasMeshConverter.x',
+                'mesh_triangles.nc',
+                out_filename]
+        check_call(args=args, logger=logger)

 

 
            

diff --git a/stable/_modules/mpas_tools/mesh/mask.html b/stable/_modules/mpas_tools/mesh/mask.html
index 2c9989d55..8a5097562 100644
--- a/stable/_modules/mpas_tools/mesh/mask.html
+++ b/stable/_modules/mpas_tools/mesh/mask.html
@@ -149,7 +149,7 @@ 
Source code for mpas_tools.mesh.mask
     maskTypes : tuple of {'cell', 'edge', 'vertex'}, optional
         Which type(s) of masks to make.  Masks are created based on whether
         the latitude and longitude associated with each of these locations
-        (e.g. ``dsMesh.latCell`` and ``dsMesh.lonCell`` for ``'cells'``) are
+        (e.g. ``dsMesh.latCell`` and ``dsMesh.lonCell`` for ``'cell'``) are
         inside or outside of the regions in ``fcMask``.
 
     logger : logging.Logger, optional
@@ -324,7 +324,7 @@ 
Source code for mpas_tools.mesh.mask
     maskTypes : tuple of {'cell', 'edge', 'vertex'}, optional
         Which type(s) of masks to make.  Masks are created based on whether
         the latitude and longitude associated with each of these locations
-        (e.g. ``dsMesh.latCell`` and ``dsMesh.lonCell`` for ``'cells'``) are
+        (e.g. ``dsMesh.latCell`` and ``dsMesh.lonCell`` for ``'cell'``) are
         inside or outside of the transects in ``fcMask``.
 
     logger : logging.Logger, optional
diff --git a/stable/_modules/mpas_tools/viz/paraview_extractor.html b/stable/_modules/mpas_tools/viz/paraview_extractor.html
index 82142a2d5..f98a18bb4 100644
--- a/stable/_modules/mpas_tools/viz/paraview_extractor.html
+++ b/stable/_modules/mpas_tools/viz/paraview_extractor.html
@@ -205,6 +205,7 @@ 
Source code for mpas_tools.viz.paraview_extractor
from progressbar import ProgressBar, Percentage, Bar, ETA
 from mpas_tools.conversion import mask, cull
 from mpas_tools.io import write_netcdf
+from mpas_tools.logging import check_call
 
 
 
[docs]def extract_vtk(filename_pattern, variable_list='all', dimension_list=None,
@@ -2257,12 +2258,14 @@ 
Source code for mpas_tools.viz.paraview_extractor
print('Making a region mask file')
         ds_mask = mask(dsMesh=ds_mesh, fcMask=fc_region_mask, logger=logger,
                        dir=temp_dir)
-        write_netcdf(ds_mask, '{}/mask.nc'.format(temp_dir))
+        write_netcdf(ds_mask, f'{temp_dir}/mask.nc')
         print('Cropping mesh to region')
         out_mesh_filename = '{}/mesh.nc'.format(temp_dir)
-        ds_culled = cull(dsIn=ds_mesh, dsInverse=ds_mask, logger=logger,
-                         dir=temp_dir)
-        write_netcdf(ds_culled, out_mesh_filename)
+        args = ['MpasCellCuller.x',
+                mesh_filename,
+                out_mesh_filename,
+                '-i', f'{temp_dir}/mask.nc']
+        check_call(args=args, logger=logger)
 
         region_masks = dict()
         cell_mask = ds_mask.regionCellMasks.sum(dim='nRegions') > 0
@@ -2312,8 +2315,6 @@ 
Source code for mpas_tools.viz.paraview_extractor
handler.close()
 
     return out_mesh_filename, out_time_file_names
-
-# vim: set expandtab:
 

 
            

diff --git a/stable/api.html b/stable/api.html
index 4cd296cda..840df0cf9 100644
--- a/stable/api.html
+++ b/stable/api.html
@@ -351,8 +351,8 @@ 
Mesh conversion
cull(dsIn[, dsMask, dsInverse, dsPreserve, ...])

 
Use MpasCellCuller.x to cull cells from a mesh based on the cullCell field in the input file or DataSet and/or the provided masks.

 
-
mask(dsMesh[, fcMask, fcSeed, logger, dir])

-
Use MpasMaskCreator.x to create a set of region masks either from mask feature collections or from seed points to be used to flood fill

+
mask(dsMesh[, fcMask, logger, dir, cores])

+
Use compute_mpas_region_masks to create a set of region masks either from mask feature collections

 
 
 
@@ -716,7 +716,7 @@ 
Sea-ice Tools

 
-
+
diff --git a/stable/generated/mpas_tools.logging.check_call.html b/stable/generated/mpas_tools.logging.check_call.html
index 389fe8af8..3d2814bc5 100644
--- a/stable/generated/mpas_tools.logging.check_call.html
+++ b/stable/generated/mpas_tools.logging.check_call.html
@@ -132,14 +132,14 @@
 
mpas_tools.logging.check_call

 

-mpas_tools.logging.check_call(args, logger, log_command=True, timeout=None, **kwargs)[source]

+mpas_tools.logging.check_call(args, logger=None, log_command=True, timeout=None, **kwargs)[source]
 
Call the given subprocess with logging to the given logger.

 

 
Parameters:

 
    
 
  • args (list or str) – A list or string of argument to the subprocess.  If args is a
 string, you must pass shell=True as one of the kwargs.
    • 
-
  • logger (logging.Logger) – The logger to write output to
    • 
+
  • logger (logging.Logger, optional) – The logger to write output to
    • 
 
  • log_command (bool, optional) – Whether to write the command that is running ot the logger
    • 
 
  • timeout (int, optional) – A timeout in seconds for the call
    • 
 
  • **kwargs (dict) – Keyword arguments to pass to subprocess.Popen
    • 
diff --git a/stable/generated/mpas_tools.mesh.conversion.mask.html b/stable/generated/mpas_tools.mesh.conversion.mask.html
index 30e90759a..3b67ce3f4 100644
--- a/stable/generated/mpas_tools.mesh.conversion.mask.html
+++ b/stable/generated/mpas_tools.mesh.conversion.mask.html
@@ -149,19 +149,18 @@
 
    mpas_tools.mesh.conversion.mask
    
 
    
 
    
-mpas_tools.mesh.conversion.mask(dsMesh, fcMask=None, fcSeed=None, logger=None, dir=None)[source]
    
-
    Use MpasMaskCreator.x to create a set of region masks either from
-mask feature collections or from seed points to be used to flood fill
    
+mpas_tools.mesh.conversion.mask(dsMesh, fcMask=None, logger=None, dir=None, cores=1)[source]
+
    Use compute_mpas_region_masks to create a set of region masks either
+from mask feature collections
    
 
    
 
    Parameters:
    
 
      
 
    • dsMesh (xarray.Dataset, optional) – An MPAS mesh on which the masks should be created
      • 
 
    • fcMask (geometric_features.FeatureCollection, optional) – A feature collection containing features to use to create the mask
      • 
-
    • fcSeed (geometric_features.FeatureCollection, optional) – A feature collection with points to use a seeds for a flood fill that
-will create a mask of all cells connected to the seed points
      • 
 
    • logger (logging.Logger, optional) – A logger for the output if not stdout
      • 
 
    • dir (str, optional) – A directory in which a temporary directory will be added with files
 produced during mask creation and then deleted upon completion.
      • 
+
    • cores (int, optional) – The number of cores to use for python multiprocessing
      • 
 
    
 
    
 
    Returns:
    
diff --git a/stable/generated/mpas_tools.mesh.mask.compute_mpas_region_masks.html b/stable/generated/mpas_tools.mesh.mask.compute_mpas_region_masks.html
index 5b0b86993..c28257659 100644
--- a/stable/generated/mpas_tools.mesh.mask.compute_mpas_region_masks.html
+++ b/stable/generated/mpas_tools.mesh.mask.compute_mpas_region_masks.html
@@ -159,7 +159,7 @@ 
    mpas_tools.mesh.mask.compute_mpas_region_masksgeometric_features.FeatureCollection) – A feature collection containing features to use to create the mask
    
 
  • maskTypes (tuple of {'cell', 'edge', 'vertex'}, optional) – Which type(s) of masks to make.  Masks are created based on whether
 the latitude and longitude associated with each of these locations
-(e.g. dsMesh.latCell and dsMesh.lonCell for 'cells') are
+(e.g. dsMesh.latCell and dsMesh.lonCell for 'cell') are
 inside or outside of the regions in fcMask.
    • 
 
  • logger (logging.Logger, optional) – A logger for the output if not stdout
    • 
 
  • pool (multiprocessing.Pool, optional) – A pool for performing multiprocessing
    • 
diff --git a/stable/generated/mpas_tools.mesh.mask.compute_mpas_transect_masks.html b/stable/generated/mpas_tools.mesh.mask.compute_mpas_transect_masks.html
index 8827c861e..c213980ff 100644
--- a/stable/generated/mpas_tools.mesh.mask.compute_mpas_transect_masks.html
+++ b/stable/generated/mpas_tools.mesh.mask.compute_mpas_transect_masks.html
@@ -160,7 +160,7 @@ 
    mpas_tools.mesh.mask.compute_mpas_transect_masksfloat) – The radius of the earth in meters
    
 
  • maskTypes (tuple of {'cell', 'edge', 'vertex'}, optional) – Which type(s) of masks to make.  Masks are created based on whether
 the latitude and longitude associated with each of these locations
-(e.g. dsMesh.latCell and dsMesh.lonCell for 'cells') are
+(e.g. dsMesh.latCell and dsMesh.lonCell for 'cell') are
 inside or outside of the transects in fcMask.
    • 
 
  • logger (logging.Logger, optional) – A logger for the output if not stdout
    • 
 
  • pool (multiprocessing.Pool, optional) – A pool for performing multiprocessing
    • 
diff --git a/stable/searchindex.js b/stable/searchindex.js
index 2b49e55a3..d7875e370 100644
--- a/stable/searchindex.js
+++ b/stable/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api", "authors", "building_docs", "cime", "config", "generated/mpas_tools.cime.constants", "generated/mpas_tools.config.MpasConfigParser", "generated/mpas_tools.config.MpasConfigParser.__getitem__", "generated/mpas_tools.config.MpasConfigParser.add_from_file", "generated/mpas_tools.config.MpasConfigParser.add_from_package", "generated/mpas_tools.config.MpasConfigParser.add_user_config", "generated/mpas_tools.config.MpasConfigParser.copy", "generated/mpas_tools.config.MpasConfigParser.get", "generated/mpas_tools.config.MpasConfigParser.getboolean", "generated/mpas_tools.config.MpasConfigParser.getexpression", "generated/mpas_tools.config.MpasConfigParser.getfloat", "generated/mpas_tools.config.MpasConfigParser.getint", "generated/mpas_tools.config.MpasConfigParser.getlist", "generated/mpas_tools.config.MpasConfigParser.has_option", "generated/mpas_tools.config.MpasConfigParser.has_section", "generated/mpas_tools.config.MpasConfigParser.set", "generated/mpas_tools.config.MpasConfigParser.write", "generated/mpas_tools.io.write_netcdf", "generated/mpas_tools.logging.LoggingContext", "generated/mpas_tools.logging.check_call", "generated/mpas_tools.merge_grids.merge_grids", "generated/mpas_tools.mesh.conversion.convert", "generated/mpas_tools.mesh.conversion.cull", "generated/mpas_tools.mesh.conversion.mask", "generated/mpas_tools.mesh.creation.build_mesh", "generated/mpas_tools.mesh.creation.build_mesh.build_planar_mesh", "generated/mpas_tools.mesh.creation.build_mesh.build_spherical_mesh", "generated/mpas_tools.mesh.creation.jigsaw_driver.jigsaw_driver", "generated/mpas_tools.mesh.creation.jigsaw_to_netcdf.jigsaw_to_netcdf", "generated/mpas_tools.mesh.creation.mesh_definition_tools", "generated/mpas_tools.mesh.creation.mesh_definition_tools.AtlanticPacificGrid", "generated/mpas_tools.mesh.creation.mesh_definition_tools.EC_CellWidthVsLat", "generated/mpas_tools.mesh.creation.mesh_definition_tools.RRS_CellWidthVsLat", "generated/mpas_tools.mesh.creation.mesh_definition_tools.mergeCellWidthVsLat", "generated/mpas_tools.mesh.creation.mpas_to_triangle.mpas_to_triangle", "generated/mpas_tools.mesh.creation.signed_distance", "generated/mpas_tools.mesh.creation.signed_distance.distance_from_geojson", "generated/mpas_tools.mesh.creation.signed_distance.mask_from_geojson", "generated/mpas_tools.mesh.creation.signed_distance.signed_distance_from_geojson", "generated/mpas_tools.mesh.creation.triangle_to_netcdf.triangle_to_netcdf", "generated/mpas_tools.mesh.interpolation.interp_bilin", "generated/mpas_tools.mesh.mask.compute_lon_lat_region_masks", "generated/mpas_tools.mesh.mask.compute_mpas_flood_fill_mask", "generated/mpas_tools.mesh.mask.compute_mpas_region_masks", "generated/mpas_tools.mesh.mask.compute_mpas_transect_masks", "generated/mpas_tools.ocean.build_mesh", "generated/mpas_tools.ocean.build_mesh.build_planar_mesh", "generated/mpas_tools.ocean.build_mesh.build_spherical_mesh", "generated/mpas_tools.ocean.coastal_tools", "generated/mpas_tools.ocean.coastal_tools.CPP_projection", "generated/mpas_tools.ocean.coastal_tools.coastal_refined_mesh", "generated/mpas_tools.ocean.coastal_tools.compute_cell_width", "generated/mpas_tools.ocean.coastal_tools.create_background_mesh", "generated/mpas_tools.ocean.coastal_tools.distance_to_coast", "generated/mpas_tools.ocean.coastal_tools.extract_coastlines", "generated/mpas_tools.ocean.coastal_tools.get_convex_hull_coordinates", "generated/mpas_tools.ocean.coastal_tools.get_data_inside_box", "generated/mpas_tools.ocean.coastal_tools.get_indices_inside_quad", "generated/mpas_tools.ocean.coastal_tools.plot_coarse_coast", "generated/mpas_tools.ocean.coastal_tools.plot_region_box", "generated/mpas_tools.ocean.coastal_tools.save_matfile", "generated/mpas_tools.ocean.coastal_tools.smooth_coastline", "generated/mpas_tools.ocean.coastline_alteration", "generated/mpas_tools.ocean.coastline_alteration.add_critical_land_blockages", 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26, 27, 28, 31, 51, 52, 68, 69, 70, 71, 72, 83, 94, 122, 125, 126, 131, 139, 142], "user": [4, 6, 10, 20, 100, 115, 125, 126, 127, 128, 129, 131, 142], "add_user_config": 4, "add_from_fil": 4, "copi": [4, 69, 117, 132, 133, 142], "deep": [4, 11], "parser": [4, 6, 8, 9, 10, 11, 125], "where": [4, 9, 21, 23, 26, 27, 51, 52, 56, 57, 58, 59, 84, 98, 102, 107, 111, 112, 118, 119, 120, 123, 124, 126, 127, 128, 129, 130, 134, 136, 142], "modifi": [4, 22, 53, 126, 128, 129, 132], "without": [4, 118, 125, 128, 132, 136], "affect": [4, 128], "origin": [4, 21, 54, 84, 88, 113, 114, 119, 120, 126, 128, 142], "object": [4, 83, 106, 124, 126, 127, 129, 133, 142], "featur": [4, 28, 46, 47, 48, 49, 83, 118, 126, 127, 129, 131, 132, 133, 142], "analysi": [4, 122, 125, 126, 130, 132], "refer": [4, 122, 130], "year": [4, 136], "start": [4, 47, 56, 126, 128, 142], "ha": [4, 18, 46, 48, 49, 56, 57, 58, 59, 119, 120, 125, 126, 127, 128, 130, 131, 136, 142], "present": [4, 102, 134, 136], "configpars": [4, 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"mpas_tools.ocean.build_mesh": [[50, "module-mpas_tools.ocean.build_mesh"]], "mpas_tools.ocean.build_mesh.build_planar_mesh": [[51, "mpas-tools-ocean-build-mesh-build-planar-mesh"]], "mpas_tools.ocean.build_mesh.build_spherical_mesh": [[52, "mpas-tools-ocean-build-mesh-build-spherical-mesh"]], "mpas_tools.ocean.coastal_tools": [[53, "module-mpas_tools.ocean.coastal_tools"]], "mpas_tools.ocean.coastal_tools.CPP_projection": [[54, "mpas-tools-ocean-coastal-tools-cpp-projection"]], "mpas_tools.ocean.coastal_tools.coastal_refined_mesh": [[55, "mpas-tools-ocean-coastal-tools-coastal-refined-mesh"]], "mpas_tools.ocean.coastal_tools.compute_cell_width": [[56, "mpas-tools-ocean-coastal-tools-compute-cell-width"]], "mpas_tools.ocean.coastal_tools.create_background_mesh": [[57, "mpas-tools-ocean-coastal-tools-create-background-mesh"]], "mpas_tools.ocean.coastal_tools.distance_to_coast": [[58, "mpas-tools-ocean-coastal-tools-distance-to-coast"]], "mpas_tools.ocean.coastal_tools.extract_coastlines": [[59, "mpas-tools-ocean-coastal-tools-extract-coastlines"]], "mpas_tools.ocean.coastal_tools.get_convex_hull_coordinates": [[60, "mpas-tools-ocean-coastal-tools-get-convex-hull-coordinates"]], "mpas_tools.ocean.coastal_tools.get_data_inside_box": [[61, "mpas-tools-ocean-coastal-tools-get-data-inside-box"]], "mpas_tools.ocean.coastal_tools.get_indices_inside_quad": [[62, "mpas-tools-ocean-coastal-tools-get-indices-inside-quad"]], "mpas_tools.ocean.coastal_tools.plot_coarse_coast": [[63, "mpas-tools-ocean-coastal-tools-plot-coarse-coast"]], "mpas_tools.ocean.coastal_tools.plot_region_box": [[64, "mpas-tools-ocean-coastal-tools-plot-region-box"]], "mpas_tools.ocean.coastal_tools.save_matfile": [[65, "mpas-tools-ocean-coastal-tools-save-matfile"]], "mpas_tools.ocean.coastal_tools.smooth_coastline": [[66, "mpas-tools-ocean-coastal-tools-smooth-coastline"]], "mpas_tools.ocean.coastline_alteration": [[67, "module-mpas_tools.ocean.coastline_alteration"]], "mpas_tools.ocean.coastline_alteration.add_critical_land_blockages": [[68, "mpas-tools-ocean-coastline-alteration-add-critical-land-blockages"]], "mpas_tools.ocean.coastline_alteration.add_land_locked_cells_to_mask": [[69, "mpas-tools-ocean-coastline-alteration-add-land-locked-cells-to-mask"]], "mpas_tools.ocean.coastline_alteration.widen_transect_edge_masks": [[70, "mpas-tools-ocean-coastline-alteration-widen-transect-edge-masks"]], "mpas_tools.ocean.depth.add_depth": [[71, "mpas-tools-ocean-depth-add-depth"]], "mpas_tools.ocean.depth.add_zmid": [[72, "mpas-tools-ocean-depth-add-zmid"]], "mpas_tools.ocean.depth.compute_depth": [[73, "mpas-tools-ocean-depth-compute-depth"]], "mpas_tools.ocean.depth.compute_zmid": [[74, "mpas-tools-ocean-depth-compute-zmid"]], "mpas_tools.ocean.depth.write_time_varying_zmid": [[75, "mpas-tools-ocean-depth-write-time-varying-zmid"]], "mpas_tools.ocean.inject_bathymetry.inject_bathymetry": [[76, "mpas-tools-ocean-inject-bathymetry-inject-bathymetry"]], "mpas_tools.ocean.inject_meshDensity.inject_meshDensity_from_file": [[77, "mpas-tools-ocean-inject-meshdensity-inject-meshdensity-from-file"]], "mpas_tools.ocean.inject_meshDensity.inject_planar_meshDensity": [[78, "mpas-tools-ocean-inject-meshdensity-inject-planar-meshdensity"]], "mpas_tools.ocean.inject_meshDensity.inject_spherical_meshDensity": [[79, "mpas-tools-ocean-inject-meshdensity-inject-spherical-meshdensity"]], "mpas_tools.ocean.inject_preserve_floodplain.inject_preserve_floodplain": [[80, "mpas-tools-ocean-inject-preserve-floodplain-inject-preserve-floodplain"]], "mpas_tools.ocean.moc": [[81, "module-mpas_tools.ocean.moc"]], "mpas_tools.ocean.moc.add_moc_southern_boundary_transects": [[82, "mpas-tools-ocean-moc-add-moc-southern-boundary-transects"]], "mpas_tools.ocean.moc.make_moc_basins_and_transects": [[83, "mpas-tools-ocean-moc-make-moc-basins-and-transects"]], "mpas_tools.ocean.transects.find_transect_levels_and_weights": [[84, "mpas-tools-ocean-transects-find-transect-levels-and-weights"]], "mpas_tools.ocean.transects.get_outline_segments": [[85, "mpas-tools-ocean-transects-get-outline-segments"]], "mpas_tools.ocean.transects.interp_mpas_to_transect_triangle_nodes": [[86, "mpas-tools-ocean-transects-interp-mpas-to-transect-triangle-nodes"]], "mpas_tools.ocean.transects.interp_mpas_to_transect_triangles": [[87, "mpas-tools-ocean-transects-interp-mpas-to-transect-triangles"]], "mpas_tools.ocean.transects.interp_transect_grid_to_transect_triangle_nodes": [[88, "mpas-tools-ocean-transects-interp-transect-grid-to-transect-triangle-nodes"]], "mpas_tools.ocean.viz.add_inset": [[89, "mpas-tools-ocean-viz-add-inset"]], "mpas_tools.ocean.viz.plot_ocean_transects": [[90, "mpas-tools-ocean-viz-plot-ocean-transects"]], "mpas_tools.parallel.create_pool": [[91, "mpas-tools-parallel-create-pool"]], "mpas_tools.planar_hex.make_planar_hex_mesh": [[92, "mpas-tools-planar-hex-make-planar-hex-mesh"]], "mpas_tools.scrip.from_mpas.scrip_from_mpas": [[93, "mpas-tools-scrip-from-mpas-scrip-from-mpas"]], "mpas_tools.seaice.mask.extend_seaice_mask": [[94, "mpas-tools-seaice-mask-extend-seaice-mask"]], "mpas_tools.seaice.mesh.make_mpas_scripfile_on_cells": [[95, "mpas-tools-seaice-mesh-make-mpas-scripfile-on-cells"]], "mpas_tools.seaice.mesh.make_mpas_scripfile_on_vertices": [[96, "mpas-tools-seaice-mesh-make-mpas-scripfile-on-vertices"]], "mpas_tools.seaice.mesh.write_2D_scripfile": [[97, "mpas-tools-seaice-mesh-write-2d-scripfile"]], "mpas_tools.seaice.mesh.write_scrip_file": [[98, "mpas-tools-seaice-mesh-write-scrip-file"]], "mpas_tools.seaice.partition.create_partitions": [[99, "mpas-tools-seaice-partition-create-partitions"]], "mpas_tools.seaice.partition.gen_seaice_mesh_partition": [[100, "mpas-tools-seaice-partition-gen-seaice-mesh-partition"]], "mpas_tools.seaice.partition.prepare_partitions": [[101, "mpas-tools-seaice-partition-prepare-partitions"]], "mpas_tools.seaice.regions.make_regions_file": [[102, "mpas-tools-seaice-regions-make-regions-file"]], "mpas_tools.seaice.regrid.regrid_to_other_mesh": [[103, "mpas-tools-seaice-regrid-regrid-to-other-mesh"]], "mpas_tools.split_grids.split_grids": [[104, "mpas-tools-split-grids-split-grids"]], "mpas_tools.tests.test_cime_constants.test_cime_constants": [[105, "mpas-tools-tests-test-cime-constants-test-cime-constants"]], "mpas_tools.transects.Vector": [[106, "mpas-tools-transects-vector"]], "mpas_tools.transects.angular_distance": [[107, "mpas-tools-transects-angular-distance"]], "mpas_tools.transects.cartesian_to_great_circle_distance": [[108, "mpas-tools-transects-cartesian-to-great-circle-distance"]], "mpas_tools.transects.cartesian_to_lon_lat": [[109, "mpas-tools-transects-cartesian-to-lon-lat"]], "mpas_tools.transects.lon_lat_to_cartesian": [[110, "mpas-tools-transects-lon-lat-to-cartesian"]], "mpas_tools.transects.subdivide_great_circle": [[111, "mpas-tools-transects-subdivide-great-circle"]], "mpas_tools.transects.subdivide_planar": [[112, "mpas-tools-transects-subdivide-planar"]], "mpas_tools.translate.center": [[113, "mpas-tools-translate-center"]], "mpas_tools.translate.center_on_mesh": [[114, "mpas-tools-translate-center-on-mesh"]], "mpas_tools.translate.translate": [[115, "mpas-tools-translate-translate"]], "mpas_tools.viz.colormaps.register_sci_viz_colormaps": [[116, "mpas-tools-viz-colormaps-register-sci-viz-colormaps"]], "mpas_tools.viz.mesh_to_triangles.mesh_to_triangles": [[117, "mpas-tools-viz-mesh-to-triangles-mesh-to-triangles"]], "mpas_tools.viz.paraview_extractor.extract_vtk": [[118, "mpas-tools-viz-paraview-extractor-extract-vtk"]], "mpas_tools.viz.transects.find_planar_transect_cells_and_weights": [[119, "mpas-tools-viz-transects-find-planar-transect-cells-and-weights"]], "mpas_tools.viz.transects.find_transect_cells_and_weights": [[120, "mpas-tools-viz-transects-find-transect-cells-and-weights"]], "mpas_tools.viz.transects.make_triangle_tree": [[121, "mpas-tools-viz-transects-make-triangle-tree"]], "MPAS-Tools": [[122, "mpas-tools"]], "User's Guide": [[122, null]], "Developer's Guide": [[122, null]], "Indices and tables": [[122, "indices-and-tables"]], "Authors": [[122, null]], "Versions": [[122, null], [141, "versions"]], "Using logging": [[124, "using-logging"]], "Logging subprocess calls": [[124, "logging-subprocess-calls"]], "Making Changes to mpas_tools": [[125, "making-changes-to-mpas-tools"]], "Entry Points": [[125, "entry-points"]], "Dependencies": [[125, "dependencies"]], "Updating the Version": [[125, "updating-the-version"]], "Mesh Conversion": [[126, "mesh-conversion"]], "Mesh Converter": [[126, "mesh-converter"]], "Cell Culler": [[126, "cell-culler"]], "Mask Creator": [[126, "mask-creator"]], "Mask Creation with Python Multiprocessing": [[126, "mask-creation-with-python-multiprocessing"]], "Computing MPAS Region Masks": [[126, "computing-mpas-region-masks"]], "Computing Transect Masks": [[126, "computing-transect-masks"]], "Computing a Flood-fill Mask": [[126, "computing-a-flood-fill-mask"]], "Computing Lon/Lat Region Masks": [[126, "computing-lon-lat-region-masks"]], "Merging and Splitting": [[126, "merging-and-splitting"]], "Translation": [[126, "translation"]], "Converting Between Mesh Formats": [[126, "converting-between-mesh-formats"]], "MSH to MPAS NetCDF": [[126, "msh-to-mpas-netcdf"]], "Triangle to MPAS NetCDF": [[126, "triangle-to-mpas-netcdf"]], "MPAS NetCDF to Triangle": [[126, "mpas-netcdf-to-triangle"]], "MPAS NetCDF to SCRIP": [[126, "mpas-netcdf-to-scrip"]], "Mesh Creation": [[127, "id1"]], "Uniform, Planar Meshes": [[127, "uniform-planar-meshes"]], "Building a JIGSAW Mesh": [[127, "building-a-jigsaw-mesh"]], "Spherical Meshes": [[127, "spherical-meshes"]], "Planar Meshes": [[127, "planar-meshes"]], "JIGSAW Driver": [[127, "jigsaw-driver"]], "Mesh Definition Tools": [[127, "mesh-definition-tools"]], "Merging Cell Widths": [[127, "merging-cell-widths"]], "Defining an Eddy-closure Mesh": [[127, "defining-an-eddy-closure-mesh"]], "Defining a Rossby-radius Mesh": [[127, "defining-a-rossby-radius-mesh"]], "Defining an Atlantic/Pacific Mesh": [[127, "defining-an-atlantic-pacific-mesh"]], "Signed Distance Functions": [[127, "signed-distance-functions"]], "Coastal Tools": [[128, "coastal-tools"]], "Refining a Mesh": [[128, "refining-a-mesh"]], "Creating a Background Mesh": [[128, "creating-a-background-mesh"]], "Extracting Coastlines": [[128, "extracting-coastlines"]], "Computing Distance to Coast": [[128, "computing-distance-to-coast"]], "Blending Cell Widths": [[128, "blending-cell-widths"]], "Regions": [[128, "regions"]], "Coastline Alteration": [[129, "coastline-alteration"]], "Adding Land Blockages": [[129, "adding-land-blockages"]], "Masking Land-locked Cells": [[129, "masking-land-locked-cells"]], "Widening Transects": [[129, "widening-transects"]], "Adding a Depth Coordinate": [[130, "adding-a-depth-coordinate"]], "Adding a 1D depth coordinate": [[130, "adding-a-1d-depth-coordinate"]], "Adding a 3D zMid coordinate": [[130, "adding-a-3d-zmid-coordinate"]], "Writing a time-dependent, 3D zMid variable": [[130, "writing-a-time-dependent-3d-zmid-variable"]], "Ocean Mesh Creation": [[131, "ocean-mesh-creation"]], "Meridional Overturning Circulation": [[132, "meridional-overturning-circulation"]], "Building MOC Basins": [[132, "building-moc-basins"]], "Adding Southern Transects": [[132, "adding-southern-transects"]], "Building MOC Basins and Transects Together": [[132, "building-moc-basins-and-transects-together"]], "Plotting Ocean Transects": [[133, "plotting-ocean-transects"]], "Mask": [[134, "mask"]], "Extending a Mask": [[134, "extending-a-mask"]], "Mesh": [[135, "mesh"]], "MPAS-Seaice SCRIP files": [[135, "mpas-seaice-scrip-files"]], "SCRIP files for 2D grids": [[135, "scrip-files-for-2d-grids"]], "Graph partitioning": [[136, "graph-partitioning"]], "Running from compass": [[136, "running-from-compass"]], "Conda environment": [[136, "conda-environment"]], "Graph partition tools": [[136, "graph-partition-tools"]], "Graph partition function": [[136, "graph-partition-function"]], "Region masks": [[137, "region-masks"]], "Make a region mask for partitioning": [[137, "make-a-region-mask-for-partitioning"]], "Regrid": [[138, "regrid"]], "Regridding between MPAS-Seaice meshes": [[138, "regridding-between-mpas-seaice-meshes"]], "Testing Changes to mpas_tools": [[139, "testing-changes-to-mpas-tools"]], "Removing the test environment": [[139, "removing-the-test-environment"]], "Subdividing transects": [[140, "subdividing-transects"]], "Low-level functions": [[140, "low-level-functions"]], "ParaView VTK Extractor": [[142, "paraview-vtk-extractor"]], "Extracting a Temperature Time-series": [[142, "extracting-a-temperature-time-series"]], "Extracting Multiple Fields": [[142, "extracting-multiple-fields"]], "Extracting \u201cAll\u201d Fields": [[142, "extracting-all-fields"]], "Indexing Dimensions": [[142, "indexing-dimensions"]], "Indexing Time": [[142, "indexing-time"]], "Ignoring Time": [[142, "ignoring-time"]], "Lon/Lat Coordinates": [[142, "lon-lat-coordinates"]], "Topographic Data": [[142, "topographic-data"]], "Extracting a Region": [[142, "extracting-a-region"]], "ParaView Macros": [[142, "paraview-macros"]], "MPAS Mesh to Triangles": [[142, "mpas-mesh-to-triangles"]], "Colormaps": [[142, "colormaps"]]}, "indexentries": {"module": [[5, "module-mpas_tools.cime.constants"], [29, "module-mpas_tools.mesh.creation.build_mesh"], [34, "module-mpas_tools.mesh.creation.mesh_definition_tools"], [40, "module-mpas_tools.mesh.creation.signed_distance"], [50, "module-mpas_tools.ocean.build_mesh"], [53, "module-mpas_tools.ocean.coastal_tools"], [67, "module-mpas_tools.ocean.coastline_alteration"], [81, "module-mpas_tools.ocean.moc"]], "mpas_tools.cime.constants": [[5, "module-mpas_tools.cime.constants"]], "mpasconfigparser (class in mpas_tools.config)": [[6, "mpas_tools.config.MpasConfigParser"]], "__init__() (mpas_tools.config.mpasconfigparser method)": [[6, "mpas_tools.config.MpasConfigParser.__init__"]], "__getitem__() (mpas_tools.config.mpasconfigparser method)": [[7, "mpas_tools.config.MpasConfigParser.__getitem__"]], "add_from_file() (mpas_tools.config.mpasconfigparser method)": [[8, "mpas_tools.config.MpasConfigParser.add_from_file"]], "add_from_package() (mpas_tools.config.mpasconfigparser method)": [[9, "mpas_tools.config.MpasConfigParser.add_from_package"]], "add_user_config() (mpas_tools.config.mpasconfigparser method)": [[10, "mpas_tools.config.MpasConfigParser.add_user_config"]], "copy() (mpas_tools.config.mpasconfigparser method)": [[11, "mpas_tools.config.MpasConfigParser.copy"]], "get() (mpas_tools.config.mpasconfigparser method)": [[12, "mpas_tools.config.MpasConfigParser.get"]], "getboolean() 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"mpas_tools.config.MpasConfigParser.write"]], "write_netcdf() (in module mpas_tools.io)": [[22, "mpas_tools.io.write_netcdf"]], "loggingcontext (class in mpas_tools.logging)": [[23, "mpas_tools.logging.LoggingContext"]], "__init__() (mpas_tools.logging.loggingcontext method)": [[23, "mpas_tools.logging.LoggingContext.__init__"]], "check_call() (in module mpas_tools.logging)": [[24, "mpas_tools.logging.check_call"]], "merge_grids() (in module mpas_tools.merge_grids)": [[25, "mpas_tools.merge_grids.merge_grids"]], "convert() (in module mpas_tools.mesh.conversion)": [[26, "mpas_tools.mesh.conversion.convert"]], "cull() (in module mpas_tools.mesh.conversion)": [[27, "mpas_tools.mesh.conversion.cull"]], "mask() (in module mpas_tools.mesh.conversion)": [[28, "mpas_tools.mesh.conversion.mask"]], "mpas_tools.mesh.creation.build_mesh": [[29, "module-mpas_tools.mesh.creation.build_mesh"]], "build_planar_mesh() (in module mpas_tools.mesh.creation.build_mesh)": [[30, "mpas_tools.mesh.creation.build_mesh.build_planar_mesh"]], "build_spherical_mesh() (in module mpas_tools.mesh.creation.build_mesh)": [[31, "mpas_tools.mesh.creation.build_mesh.build_spherical_mesh"]], "jigsaw_driver() (in module mpas_tools.mesh.creation.jigsaw_driver)": [[32, "mpas_tools.mesh.creation.jigsaw_driver.jigsaw_driver"]], "jigsaw_to_netcdf() (in module mpas_tools.mesh.creation.jigsaw_to_netcdf)": [[33, "mpas_tools.mesh.creation.jigsaw_to_netcdf.jigsaw_to_netcdf"]], "mpas_tools.mesh.creation.mesh_definition_tools": [[34, "module-mpas_tools.mesh.creation.mesh_definition_tools"]], "atlanticpacificgrid() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[35, "mpas_tools.mesh.creation.mesh_definition_tools.AtlanticPacificGrid"]], "ec_cellwidthvslat() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[36, "mpas_tools.mesh.creation.mesh_definition_tools.EC_CellWidthVsLat"]], "rrs_cellwidthvslat() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[37, "mpas_tools.mesh.creation.mesh_definition_tools.RRS_CellWidthVsLat"]], "mergecellwidthvslat() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[38, "mpas_tools.mesh.creation.mesh_definition_tools.mergeCellWidthVsLat"]], "mpas_to_triangle() (in module mpas_tools.mesh.creation.mpas_to_triangle)": [[39, "mpas_tools.mesh.creation.mpas_to_triangle.mpas_to_triangle"]], "mpas_tools.mesh.creation.signed_distance": [[40, "module-mpas_tools.mesh.creation.signed_distance"]], "distance_from_geojson() (in module mpas_tools.mesh.creation.signed_distance)": [[41, "mpas_tools.mesh.creation.signed_distance.distance_from_geojson"]], "mask_from_geojson() (in module mpas_tools.mesh.creation.signed_distance)": [[42, "mpas_tools.mesh.creation.signed_distance.mask_from_geojson"]], "signed_distance_from_geojson() (in module mpas_tools.mesh.creation.signed_distance)": [[43, "mpas_tools.mesh.creation.signed_distance.signed_distance_from_geojson"]], "triangle_to_netcdf() (in module mpas_tools.mesh.creation.triangle_to_netcdf)": [[44, "mpas_tools.mesh.creation.triangle_to_netcdf.triangle_to_netcdf"]], "interp_bilin() (in module mpas_tools.mesh.interpolation)": [[45, "mpas_tools.mesh.interpolation.interp_bilin"]], "compute_lon_lat_region_masks() (in module mpas_tools.mesh.mask)": [[46, "mpas_tools.mesh.mask.compute_lon_lat_region_masks"]], "compute_mpas_flood_fill_mask() (in module mpas_tools.mesh.mask)": [[47, "mpas_tools.mesh.mask.compute_mpas_flood_fill_mask"]], "compute_mpas_region_masks() (in module mpas_tools.mesh.mask)": [[48, "mpas_tools.mesh.mask.compute_mpas_region_masks"]], "compute_mpas_transect_masks() (in module mpas_tools.mesh.mask)": [[49, "mpas_tools.mesh.mask.compute_mpas_transect_masks"]], "mpas_tools.ocean.build_mesh": [[50, "module-mpas_tools.ocean.build_mesh"]], "build_planar_mesh() (in module mpas_tools.ocean.build_mesh)": [[51, "mpas_tools.ocean.build_mesh.build_planar_mesh"]], "build_spherical_mesh() (in module mpas_tools.ocean.build_mesh)": [[52, "mpas_tools.ocean.build_mesh.build_spherical_mesh"]], "mpas_tools.ocean.coastal_tools": [[53, "module-mpas_tools.ocean.coastal_tools"]], "cpp_projection() (in module mpas_tools.ocean.coastal_tools)": [[54, "mpas_tools.ocean.coastal_tools.CPP_projection"]], "coastal_refined_mesh() (in module mpas_tools.ocean.coastal_tools)": [[55, "mpas_tools.ocean.coastal_tools.coastal_refined_mesh"]], "compute_cell_width() (in module mpas_tools.ocean.coastal_tools)": [[56, "mpas_tools.ocean.coastal_tools.compute_cell_width"]], "create_background_mesh() (in module mpas_tools.ocean.coastal_tools)": [[57, "mpas_tools.ocean.coastal_tools.create_background_mesh"]], "distance_to_coast() (in module mpas_tools.ocean.coastal_tools)": [[58, "mpas_tools.ocean.coastal_tools.distance_to_coast"]], "extract_coastlines() (in module mpas_tools.ocean.coastal_tools)": [[59, "mpas_tools.ocean.coastal_tools.extract_coastlines"]], "get_convex_hull_coordinates() (in module mpas_tools.ocean.coastal_tools)": [[60, "mpas_tools.ocean.coastal_tools.get_convex_hull_coordinates"]], "get_data_inside_box() (in module mpas_tools.ocean.coastal_tools)": [[61, "mpas_tools.ocean.coastal_tools.get_data_inside_box"]], "get_indices_inside_quad() (in module mpas_tools.ocean.coastal_tools)": [[62, "mpas_tools.ocean.coastal_tools.get_indices_inside_quad"]], "plot_coarse_coast() (in module mpas_tools.ocean.coastal_tools)": [[63, "mpas_tools.ocean.coastal_tools.plot_coarse_coast"]], "plot_region_box() (in module mpas_tools.ocean.coastal_tools)": [[64, "mpas_tools.ocean.coastal_tools.plot_region_box"]], "save_matfile() (in module mpas_tools.ocean.coastal_tools)": [[65, "mpas_tools.ocean.coastal_tools.save_matfile"]], "smooth_coastline() (in module mpas_tools.ocean.coastal_tools)": [[66, "mpas_tools.ocean.coastal_tools.smooth_coastline"]], "mpas_tools.ocean.coastline_alteration": [[67, "module-mpas_tools.ocean.coastline_alteration"]], "add_critical_land_blockages() (in module mpas_tools.ocean.coastline_alteration)": [[68, "mpas_tools.ocean.coastline_alteration.add_critical_land_blockages"]], "add_land_locked_cells_to_mask() (in module mpas_tools.ocean.coastline_alteration)": [[69, "mpas_tools.ocean.coastline_alteration.add_land_locked_cells_to_mask"]], "widen_transect_edge_masks() (in module mpas_tools.ocean.coastline_alteration)": [[70, "mpas_tools.ocean.coastline_alteration.widen_transect_edge_masks"]], "add_depth() (in module mpas_tools.ocean.depth)": [[71, "mpas_tools.ocean.depth.add_depth"]], "add_zmid() (in module mpas_tools.ocean.depth)": [[72, "mpas_tools.ocean.depth.add_zmid"]], "compute_depth() (in module mpas_tools.ocean.depth)": [[73, "mpas_tools.ocean.depth.compute_depth"]], "compute_zmid() (in module mpas_tools.ocean.depth)": [[74, "mpas_tools.ocean.depth.compute_zmid"]], "write_time_varying_zmid() (in module mpas_tools.ocean.depth)": [[75, "mpas_tools.ocean.depth.write_time_varying_zmid"]], "inject_bathymetry() (in module mpas_tools.ocean.inject_bathymetry)": [[76, "mpas_tools.ocean.inject_bathymetry.inject_bathymetry"]], "inject_meshdensity_from_file() (in module mpas_tools.ocean.inject_meshdensity)": [[77, "mpas_tools.ocean.inject_meshDensity.inject_meshDensity_from_file"]], "inject_planar_meshdensity() (in module mpas_tools.ocean.inject_meshdensity)": [[78, "mpas_tools.ocean.inject_meshDensity.inject_planar_meshDensity"]], "inject_spherical_meshdensity() (in module mpas_tools.ocean.inject_meshdensity)": [[79, "mpas_tools.ocean.inject_meshDensity.inject_spherical_meshDensity"]], "inject_preserve_floodplain() (in module mpas_tools.ocean.inject_preserve_floodplain)": [[80, "mpas_tools.ocean.inject_preserve_floodplain.inject_preserve_floodplain"]], "mpas_tools.ocean.moc": [[81, "module-mpas_tools.ocean.moc"]], "add_moc_southern_boundary_transects() (in module mpas_tools.ocean.moc)": [[82, "mpas_tools.ocean.moc.add_moc_southern_boundary_transects"]], "make_moc_basins_and_transects() (in module mpas_tools.ocean.moc)": [[83, "mpas_tools.ocean.moc.make_moc_basins_and_transects"]], "find_transect_levels_and_weights() (in module mpas_tools.ocean.transects)": [[84, "mpas_tools.ocean.transects.find_transect_levels_and_weights"]], "get_outline_segments() (in module mpas_tools.ocean.transects)": [[85, "mpas_tools.ocean.transects.get_outline_segments"]], "interp_mpas_to_transect_triangle_nodes() (in module mpas_tools.ocean.transects)": [[86, "mpas_tools.ocean.transects.interp_mpas_to_transect_triangle_nodes"]], "interp_mpas_to_transect_triangles() (in module mpas_tools.ocean.transects)": [[87, "mpas_tools.ocean.transects.interp_mpas_to_transect_triangles"]], "interp_transect_grid_to_transect_triangle_nodes() (in module mpas_tools.ocean.transects)": [[88, "mpas_tools.ocean.transects.interp_transect_grid_to_transect_triangle_nodes"]], "add_inset() (in module mpas_tools.ocean.viz)": [[89, "mpas_tools.ocean.viz.add_inset"]], "plot_ocean_transects() (in module mpas_tools.ocean.viz)": [[90, 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"mpas_tools.translate.translate"]], "register_sci_viz_colormaps() (in module mpas_tools.viz.colormaps)": [[116, "mpas_tools.viz.colormaps.register_sci_viz_colormaps"]], "mesh_to_triangles() (in module mpas_tools.viz.mesh_to_triangles)": [[117, "mpas_tools.viz.mesh_to_triangles.mesh_to_triangles"]], "extract_vtk() (in module mpas_tools.viz.paraview_extractor)": [[118, "mpas_tools.viz.paraview_extractor.extract_vtk"]], "find_planar_transect_cells_and_weights() (in module mpas_tools.viz.transects)": [[119, "mpas_tools.viz.transects.find_planar_transect_cells_and_weights"]], "find_transect_cells_and_weights() (in module mpas_tools.viz.transects)": [[120, "mpas_tools.viz.transects.find_transect_cells_and_weights"]], "make_triangle_tree() (in module mpas_tools.viz.transects)": [[121, "mpas_tools.viz.transects.make_triangle_tree"]]}})
\ No newline at end of file
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"generated/mpas_tools.seaice.partition.gen_seaice_mesh_partition", "generated/mpas_tools.seaice.partition.prepare_partitions", "generated/mpas_tools.seaice.regions.make_regions_file", "generated/mpas_tools.seaice.regrid.regrid_to_other_mesh", "generated/mpas_tools.split_grids.split_grids", "generated/mpas_tools.tests.test_cime_constants.test_cime_constants", "generated/mpas_tools.transects.Vector", "generated/mpas_tools.transects.angular_distance", "generated/mpas_tools.transects.cartesian_to_great_circle_distance", "generated/mpas_tools.transects.cartesian_to_lon_lat", "generated/mpas_tools.transects.lon_lat_to_cartesian", "generated/mpas_tools.transects.subdivide_great_circle", "generated/mpas_tools.transects.subdivide_planar", "generated/mpas_tools.translate.center", "generated/mpas_tools.translate.center_on_mesh", "generated/mpas_tools.translate.translate", "generated/mpas_tools.viz.colormaps.register_sci_viz_colormaps", "generated/mpas_tools.viz.mesh_to_triangles.mesh_to_triangles", "generated/mpas_tools.viz.paraview_extractor.extract_vtk", "generated/mpas_tools.viz.transects.find_planar_transect_cells_and_weights", "generated/mpas_tools.viz.transects.find_transect_cells_and_weights", "generated/mpas_tools.viz.transects.make_triangle_tree", "index", "interpolation", "logging", "making_changes", "mesh_conversion", "mesh_creation", "ocean/coastal_tools", "ocean/coastline_alteration", "ocean/depth", "ocean/mesh_creation", "ocean/moc", "ocean/visualization", "seaice/mask", "seaice/mesh", "seaice/partition", "seaice/regions", "seaice/regrid", "testing_changes", "transects", "versions", "visualization"], "filenames": ["api.rst", "authors.rst", "building_docs.rst", "cime.rst", "config.rst", "generated/mpas_tools.cime.constants.rst", "generated/mpas_tools.config.MpasConfigParser.rst", "generated/mpas_tools.config.MpasConfigParser.__getitem__.rst", "generated/mpas_tools.config.MpasConfigParser.add_from_file.rst", "generated/mpas_tools.config.MpasConfigParser.add_from_package.rst", "generated/mpas_tools.config.MpasConfigParser.add_user_config.rst", "generated/mpas_tools.config.MpasConfigParser.copy.rst", "generated/mpas_tools.config.MpasConfigParser.get.rst", "generated/mpas_tools.config.MpasConfigParser.getboolean.rst", "generated/mpas_tools.config.MpasConfigParser.getexpression.rst", "generated/mpas_tools.config.MpasConfigParser.getfloat.rst", "generated/mpas_tools.config.MpasConfigParser.getint.rst", "generated/mpas_tools.config.MpasConfigParser.getlist.rst", "generated/mpas_tools.config.MpasConfigParser.has_option.rst", "generated/mpas_tools.config.MpasConfigParser.has_section.rst", "generated/mpas_tools.config.MpasConfigParser.set.rst", "generated/mpas_tools.config.MpasConfigParser.write.rst", "generated/mpas_tools.io.write_netcdf.rst", "generated/mpas_tools.logging.LoggingContext.rst", 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"mpas-tools-planar-hex-make-planar-hex-mesh"]], "mpas_tools.scrip.from_mpas.scrip_from_mpas": [[93, "mpas-tools-scrip-from-mpas-scrip-from-mpas"]], "mpas_tools.seaice.mask.extend_seaice_mask": [[94, "mpas-tools-seaice-mask-extend-seaice-mask"]], "mpas_tools.seaice.mesh.make_mpas_scripfile_on_cells": [[95, "mpas-tools-seaice-mesh-make-mpas-scripfile-on-cells"]], "mpas_tools.seaice.mesh.make_mpas_scripfile_on_vertices": [[96, "mpas-tools-seaice-mesh-make-mpas-scripfile-on-vertices"]], "mpas_tools.seaice.mesh.write_2D_scripfile": [[97, "mpas-tools-seaice-mesh-write-2d-scripfile"]], "mpas_tools.seaice.mesh.write_scrip_file": [[98, "mpas-tools-seaice-mesh-write-scrip-file"]], "mpas_tools.seaice.partition.create_partitions": [[99, "mpas-tools-seaice-partition-create-partitions"]], "mpas_tools.seaice.partition.gen_seaice_mesh_partition": [[100, "mpas-tools-seaice-partition-gen-seaice-mesh-partition"]], "mpas_tools.seaice.partition.prepare_partitions": [[101, "mpas-tools-seaice-partition-prepare-partitions"]], "mpas_tools.seaice.regions.make_regions_file": [[102, "mpas-tools-seaice-regions-make-regions-file"]], "mpas_tools.seaice.regrid.regrid_to_other_mesh": [[103, "mpas-tools-seaice-regrid-regrid-to-other-mesh"]], "mpas_tools.split_grids.split_grids": [[104, "mpas-tools-split-grids-split-grids"]], "mpas_tools.tests.test_cime_constants.test_cime_constants": [[105, "mpas-tools-tests-test-cime-constants-test-cime-constants"]], "mpas_tools.transects.Vector": [[106, "mpas-tools-transects-vector"]], "mpas_tools.transects.angular_distance": [[107, "mpas-tools-transects-angular-distance"]], "mpas_tools.transects.cartesian_to_great_circle_distance": [[108, "mpas-tools-transects-cartesian-to-great-circle-distance"]], "mpas_tools.transects.cartesian_to_lon_lat": [[109, "mpas-tools-transects-cartesian-to-lon-lat"]], "mpas_tools.transects.lon_lat_to_cartesian": [[110, "mpas-tools-transects-lon-lat-to-cartesian"]], "mpas_tools.transects.subdivide_great_circle": [[111, "mpas-tools-transects-subdivide-great-circle"]], "mpas_tools.transects.subdivide_planar": [[112, "mpas-tools-transects-subdivide-planar"]], "mpas_tools.translate.center": [[113, "mpas-tools-translate-center"]], "mpas_tools.translate.center_on_mesh": [[114, "mpas-tools-translate-center-on-mesh"]], "mpas_tools.translate.translate": [[115, "mpas-tools-translate-translate"]], "mpas_tools.viz.colormaps.register_sci_viz_colormaps": [[116, "mpas-tools-viz-colormaps-register-sci-viz-colormaps"]], "mpas_tools.viz.mesh_to_triangles.mesh_to_triangles": [[117, "mpas-tools-viz-mesh-to-triangles-mesh-to-triangles"]], "mpas_tools.viz.paraview_extractor.extract_vtk": [[118, "mpas-tools-viz-paraview-extractor-extract-vtk"]], "mpas_tools.viz.transects.find_planar_transect_cells_and_weights": [[119, "mpas-tools-viz-transects-find-planar-transect-cells-and-weights"]], "mpas_tools.viz.transects.find_transect_cells_and_weights": [[120, "mpas-tools-viz-transects-find-transect-cells-and-weights"]], "mpas_tools.viz.transects.make_triangle_tree": [[121, "mpas-tools-viz-transects-make-triangle-tree"]], "MPAS-Tools": [[122, "mpas-tools"]], "User's Guide": [[122, null]], "Developer's Guide": [[122, null]], "Indices and tables": [[122, "indices-and-tables"]], "Authors": [[122, null]], "Versions": [[122, null], [141, "versions"]], "Using logging": [[124, "using-logging"]], "Logging subprocess calls": [[124, "logging-subprocess-calls"]], "Making Changes to mpas_tools": [[125, "making-changes-to-mpas-tools"]], "Entry Points": [[125, "entry-points"]], "Dependencies": [[125, "dependencies"]], "Updating the Version": [[125, "updating-the-version"]], "Mesh Conversion": [[126, "mesh-conversion"]], "Mesh Converter": [[126, "mesh-converter"]], "Cell Culler": [[126, "cell-culler"]], "Mask Creator": [[126, "mask-creator"]], "Mask Creation with Python Multiprocessing": [[126, "mask-creation-with-python-multiprocessing"]], "Computing MPAS Region Masks": [[126, "computing-mpas-region-masks"]], "Computing Transect Masks": [[126, "computing-transect-masks"]], "Computing a Flood-fill Mask": [[126, "computing-a-flood-fill-mask"]], "Computing Lon/Lat Region Masks": [[126, "computing-lon-lat-region-masks"]], "Merging and Splitting": [[126, "merging-and-splitting"]], "Translation": [[126, "translation"]], "Converting Between Mesh Formats": [[126, "converting-between-mesh-formats"]], "MSH to MPAS NetCDF": [[126, "msh-to-mpas-netcdf"]], "Triangle to MPAS NetCDF": [[126, "triangle-to-mpas-netcdf"]], "MPAS NetCDF to Triangle": [[126, "mpas-netcdf-to-triangle"]], "MPAS NetCDF to SCRIP": [[126, "mpas-netcdf-to-scrip"]], "Mesh Creation": [[127, "id1"]], "Uniform, Planar Meshes": [[127, "uniform-planar-meshes"]], "Building a JIGSAW Mesh": [[127, "building-a-jigsaw-mesh"]], "Spherical Meshes": [[127, "spherical-meshes"]], "Planar Meshes": [[127, "planar-meshes"]], "JIGSAW Driver": [[127, "jigsaw-driver"]], "Mesh Definition Tools": [[127, "mesh-definition-tools"]], "Merging Cell Widths": [[127, "merging-cell-widths"]], "Defining an Eddy-closure Mesh": [[127, "defining-an-eddy-closure-mesh"]], "Defining a Rossby-radius Mesh": [[127, "defining-a-rossby-radius-mesh"]], "Defining an Atlantic/Pacific Mesh": [[127, "defining-an-atlantic-pacific-mesh"]], "Signed Distance Functions": [[127, "signed-distance-functions"]], "Coastal Tools": [[128, "coastal-tools"]], "Refining a Mesh": [[128, "refining-a-mesh"]], "Creating a Background Mesh": [[128, "creating-a-background-mesh"]], "Extracting Coastlines": [[128, "extracting-coastlines"]], "Computing Distance to Coast": [[128, "computing-distance-to-coast"]], "Blending Cell Widths": [[128, "blending-cell-widths"]], "Regions": [[128, "regions"]], "Coastline Alteration": [[129, "coastline-alteration"]], "Adding Land Blockages": [[129, "adding-land-blockages"]], "Masking Land-locked Cells": [[129, "masking-land-locked-cells"]], "Widening Transects": [[129, "widening-transects"]], "Adding a Depth Coordinate": [[130, "adding-a-depth-coordinate"]], "Adding a 1D depth coordinate": [[130, "adding-a-1d-depth-coordinate"]], "Adding a 3D zMid coordinate": [[130, "adding-a-3d-zmid-coordinate"]], "Writing a time-dependent, 3D zMid variable": [[130, "writing-a-time-dependent-3d-zmid-variable"]], "Ocean Mesh Creation": [[131, "ocean-mesh-creation"]], "Meridional Overturning Circulation": [[132, "meridional-overturning-circulation"]], "Building MOC Basins": [[132, "building-moc-basins"]], "Adding Southern Transects": [[132, "adding-southern-transects"]], "Building MOC Basins and Transects Together": [[132, "building-moc-basins-and-transects-together"]], "Plotting Ocean Transects": [[133, "plotting-ocean-transects"]], "Mask": [[134, "mask"]], "Extending a Mask": [[134, "extending-a-mask"]], "Mesh": [[135, "mesh"]], "MPAS-Seaice SCRIP files": [[135, "mpas-seaice-scrip-files"]], "SCRIP files for 2D grids": [[135, "scrip-files-for-2d-grids"]], "Graph partitioning": [[136, "graph-partitioning"]], "Running from compass": [[136, "running-from-compass"]], "Conda environment": [[136, "conda-environment"]], "Graph partition tools": [[136, "graph-partition-tools"]], "Graph partition function": [[136, "graph-partition-function"]], "Region masks": [[137, "region-masks"]], "Make a region mask for partitioning": [[137, "make-a-region-mask-for-partitioning"]], "Regrid": [[138, "regrid"]], "Regridding between MPAS-Seaice meshes": [[138, "regridding-between-mpas-seaice-meshes"]], "Testing Changes to mpas_tools": [[139, "testing-changes-to-mpas-tools"]], "Removing the test environment": [[139, "removing-the-test-environment"]], "Subdividing transects": [[140, "subdividing-transects"]], "Low-level functions": [[140, "low-level-functions"]], "ParaView VTK Extractor": [[142, "paraview-vtk-extractor"]], "Extracting a Temperature Time-series": [[142, "extracting-a-temperature-time-series"]], "Extracting Multiple Fields": [[142, "extracting-multiple-fields"]], "Extracting \u201cAll\u201d Fields": [[142, "extracting-all-fields"]], "Indexing Dimensions": [[142, "indexing-dimensions"]], "Indexing Time": [[142, "indexing-time"]], "Ignoring Time": [[142, "ignoring-time"]], "Lon/Lat Coordinates": [[142, "lon-lat-coordinates"]], "Topographic Data": [[142, "topographic-data"]], "Extracting a Region": [[142, "extracting-a-region"]], "ParaView Macros": [[142, "paraview-macros"]], "MPAS Mesh to Triangles": [[142, "mpas-mesh-to-triangles"]], "Colormaps": [[142, "colormaps"]]}, "indexentries": {"module": [[5, "module-mpas_tools.cime.constants"], [29, "module-mpas_tools.mesh.creation.build_mesh"], [34, "module-mpas_tools.mesh.creation.mesh_definition_tools"], [40, "module-mpas_tools.mesh.creation.signed_distance"], [50, "module-mpas_tools.ocean.build_mesh"], [53, "module-mpas_tools.ocean.coastal_tools"], [67, "module-mpas_tools.ocean.coastline_alteration"], [81, "module-mpas_tools.ocean.moc"]], "mpas_tools.cime.constants": 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(mpas_tools.config.mpasconfigparser method)": [[13, "mpas_tools.config.MpasConfigParser.getboolean"]], "getexpression() (mpas_tools.config.mpasconfigparser method)": [[14, "mpas_tools.config.MpasConfigParser.getexpression"]], "getfloat() (mpas_tools.config.mpasconfigparser method)": [[15, "mpas_tools.config.MpasConfigParser.getfloat"]], "getint() (mpas_tools.config.mpasconfigparser method)": [[16, "mpas_tools.config.MpasConfigParser.getint"]], "getlist() (mpas_tools.config.mpasconfigparser method)": [[17, "mpas_tools.config.MpasConfigParser.getlist"]], "has_option() (mpas_tools.config.mpasconfigparser method)": [[18, "mpas_tools.config.MpasConfigParser.has_option"]], "has_section() (mpas_tools.config.mpasconfigparser method)": [[19, "mpas_tools.config.MpasConfigParser.has_section"]], "set() (mpas_tools.config.mpasconfigparser method)": [[20, "mpas_tools.config.MpasConfigParser.set"]], "write() (mpas_tools.config.mpasconfigparser method)": [[21, "mpas_tools.config.MpasConfigParser.write"]], "write_netcdf() (in module mpas_tools.io)": [[22, "mpas_tools.io.write_netcdf"]], "loggingcontext (class in mpas_tools.logging)": [[23, "mpas_tools.logging.LoggingContext"]], "__init__() (mpas_tools.logging.loggingcontext method)": [[23, "mpas_tools.logging.LoggingContext.__init__"]], "check_call() (in module mpas_tools.logging)": [[24, "mpas_tools.logging.check_call"]], "merge_grids() (in module mpas_tools.merge_grids)": [[25, "mpas_tools.merge_grids.merge_grids"]], "convert() (in module mpas_tools.mesh.conversion)": [[26, "mpas_tools.mesh.conversion.convert"]], "cull() (in module mpas_tools.mesh.conversion)": [[27, "mpas_tools.mesh.conversion.cull"]], "mask() (in module mpas_tools.mesh.conversion)": [[28, "mpas_tools.mesh.conversion.mask"]], "mpas_tools.mesh.creation.build_mesh": [[29, "module-mpas_tools.mesh.creation.build_mesh"]], "build_planar_mesh() (in module mpas_tools.mesh.creation.build_mesh)": [[30, "mpas_tools.mesh.creation.build_mesh.build_planar_mesh"]], "build_spherical_mesh() (in module mpas_tools.mesh.creation.build_mesh)": [[31, "mpas_tools.mesh.creation.build_mesh.build_spherical_mesh"]], "jigsaw_driver() (in module mpas_tools.mesh.creation.jigsaw_driver)": [[32, "mpas_tools.mesh.creation.jigsaw_driver.jigsaw_driver"]], "jigsaw_to_netcdf() (in module mpas_tools.mesh.creation.jigsaw_to_netcdf)": [[33, "mpas_tools.mesh.creation.jigsaw_to_netcdf.jigsaw_to_netcdf"]], "mpas_tools.mesh.creation.mesh_definition_tools": [[34, "module-mpas_tools.mesh.creation.mesh_definition_tools"]], "atlanticpacificgrid() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[35, "mpas_tools.mesh.creation.mesh_definition_tools.AtlanticPacificGrid"]], "ec_cellwidthvslat() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[36, "mpas_tools.mesh.creation.mesh_definition_tools.EC_CellWidthVsLat"]], "rrs_cellwidthvslat() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[37, "mpas_tools.mesh.creation.mesh_definition_tools.RRS_CellWidthVsLat"]], "mergecellwidthvslat() (in module mpas_tools.mesh.creation.mesh_definition_tools)": [[38, "mpas_tools.mesh.creation.mesh_definition_tools.mergeCellWidthVsLat"]], "mpas_to_triangle() (in module mpas_tools.mesh.creation.mpas_to_triangle)": [[39, "mpas_tools.mesh.creation.mpas_to_triangle.mpas_to_triangle"]], "mpas_tools.mesh.creation.signed_distance": [[40, "module-mpas_tools.mesh.creation.signed_distance"]], "distance_from_geojson() (in module mpas_tools.mesh.creation.signed_distance)": [[41, "mpas_tools.mesh.creation.signed_distance.distance_from_geojson"]], "mask_from_geojson() (in module mpas_tools.mesh.creation.signed_distance)": [[42, "mpas_tools.mesh.creation.signed_distance.mask_from_geojson"]], "signed_distance_from_geojson() (in module mpas_tools.mesh.creation.signed_distance)": [[43, "mpas_tools.mesh.creation.signed_distance.signed_distance_from_geojson"]], "triangle_to_netcdf() (in module mpas_tools.mesh.creation.triangle_to_netcdf)": [[44, "mpas_tools.mesh.creation.triangle_to_netcdf.triangle_to_netcdf"]], "interp_bilin() (in module mpas_tools.mesh.interpolation)": [[45, "mpas_tools.mesh.interpolation.interp_bilin"]], "compute_lon_lat_region_masks() (in module mpas_tools.mesh.mask)": [[46, "mpas_tools.mesh.mask.compute_lon_lat_region_masks"]], "compute_mpas_flood_fill_mask() (in module mpas_tools.mesh.mask)": [[47, "mpas_tools.mesh.mask.compute_mpas_flood_fill_mask"]], "compute_mpas_region_masks() (in module mpas_tools.mesh.mask)": [[48, "mpas_tools.mesh.mask.compute_mpas_region_masks"]], "compute_mpas_transect_masks() (in module mpas_tools.mesh.mask)": [[49, "mpas_tools.mesh.mask.compute_mpas_transect_masks"]], "mpas_tools.ocean.build_mesh": [[50, "module-mpas_tools.ocean.build_mesh"]], "build_planar_mesh() (in module mpas_tools.ocean.build_mesh)": [[51, "mpas_tools.ocean.build_mesh.build_planar_mesh"]], "build_spherical_mesh() (in module mpas_tools.ocean.build_mesh)": [[52, "mpas_tools.ocean.build_mesh.build_spherical_mesh"]], "mpas_tools.ocean.coastal_tools": [[53, "module-mpas_tools.ocean.coastal_tools"]], "cpp_projection() (in module mpas_tools.ocean.coastal_tools)": [[54, "mpas_tools.ocean.coastal_tools.CPP_projection"]], "coastal_refined_mesh() (in module mpas_tools.ocean.coastal_tools)": [[55, "mpas_tools.ocean.coastal_tools.coastal_refined_mesh"]], "compute_cell_width() (in module mpas_tools.ocean.coastal_tools)": [[56, "mpas_tools.ocean.coastal_tools.compute_cell_width"]], "create_background_mesh() (in module mpas_tools.ocean.coastal_tools)": [[57, "mpas_tools.ocean.coastal_tools.create_background_mesh"]], "distance_to_coast() (in module mpas_tools.ocean.coastal_tools)": [[58, "mpas_tools.ocean.coastal_tools.distance_to_coast"]], "extract_coastlines() (in module mpas_tools.ocean.coastal_tools)": [[59, "mpas_tools.ocean.coastal_tools.extract_coastlines"]], "get_convex_hull_coordinates() (in module mpas_tools.ocean.coastal_tools)": [[60, "mpas_tools.ocean.coastal_tools.get_convex_hull_coordinates"]], "get_data_inside_box() (in module mpas_tools.ocean.coastal_tools)": [[61, "mpas_tools.ocean.coastal_tools.get_data_inside_box"]], "get_indices_inside_quad() (in module mpas_tools.ocean.coastal_tools)": [[62, "mpas_tools.ocean.coastal_tools.get_indices_inside_quad"]], "plot_coarse_coast() (in module mpas_tools.ocean.coastal_tools)": [[63, "mpas_tools.ocean.coastal_tools.plot_coarse_coast"]], "plot_region_box() (in module mpas_tools.ocean.coastal_tools)": [[64, "mpas_tools.ocean.coastal_tools.plot_region_box"]], "save_matfile() (in module mpas_tools.ocean.coastal_tools)": [[65, "mpas_tools.ocean.coastal_tools.save_matfile"]], "smooth_coastline() (in module mpas_tools.ocean.coastal_tools)": [[66, "mpas_tools.ocean.coastal_tools.smooth_coastline"]], "mpas_tools.ocean.coastline_alteration": [[67, "module-mpas_tools.ocean.coastline_alteration"]], "add_critical_land_blockages() (in module mpas_tools.ocean.coastline_alteration)": [[68, "mpas_tools.ocean.coastline_alteration.add_critical_land_blockages"]], "add_land_locked_cells_to_mask() (in module mpas_tools.ocean.coastline_alteration)": [[69, "mpas_tools.ocean.coastline_alteration.add_land_locked_cells_to_mask"]], "widen_transect_edge_masks() (in module mpas_tools.ocean.coastline_alteration)": [[70, "mpas_tools.ocean.coastline_alteration.widen_transect_edge_masks"]], "add_depth() (in module mpas_tools.ocean.depth)": [[71, "mpas_tools.ocean.depth.add_depth"]], "add_zmid() (in module mpas_tools.ocean.depth)": [[72, "mpas_tools.ocean.depth.add_zmid"]], "compute_depth() (in module mpas_tools.ocean.depth)": [[73, "mpas_tools.ocean.depth.compute_depth"]], "compute_zmid() (in module mpas_tools.ocean.depth)": [[74, "mpas_tools.ocean.depth.compute_zmid"]], "write_time_varying_zmid() (in module mpas_tools.ocean.depth)": [[75, "mpas_tools.ocean.depth.write_time_varying_zmid"]], "inject_bathymetry() (in module mpas_tools.ocean.inject_bathymetry)": [[76, "mpas_tools.ocean.inject_bathymetry.inject_bathymetry"]], "inject_meshdensity_from_file() (in module mpas_tools.ocean.inject_meshdensity)": [[77, "mpas_tools.ocean.inject_meshDensity.inject_meshDensity_from_file"]], "inject_planar_meshdensity() (in module mpas_tools.ocean.inject_meshdensity)": [[78, "mpas_tools.ocean.inject_meshDensity.inject_planar_meshDensity"]], "inject_spherical_meshdensity() (in module mpas_tools.ocean.inject_meshdensity)": [[79, "mpas_tools.ocean.inject_meshDensity.inject_spherical_meshDensity"]], "inject_preserve_floodplain() (in module mpas_tools.ocean.inject_preserve_floodplain)": [[80, "mpas_tools.ocean.inject_preserve_floodplain.inject_preserve_floodplain"]], "mpas_tools.ocean.moc": [[81, "module-mpas_tools.ocean.moc"]], "add_moc_southern_boundary_transects() (in module mpas_tools.ocean.moc)": [[82, "mpas_tools.ocean.moc.add_moc_southern_boundary_transects"]], "make_moc_basins_and_transects() (in module mpas_tools.ocean.moc)": [[83, "mpas_tools.ocean.moc.make_moc_basins_and_transects"]], "find_transect_levels_and_weights() (in module mpas_tools.ocean.transects)": [[84, "mpas_tools.ocean.transects.find_transect_levels_and_weights"]], "get_outline_segments() (in module mpas_tools.ocean.transects)": [[85, "mpas_tools.ocean.transects.get_outline_segments"]], "interp_mpas_to_transect_triangle_nodes() (in module mpas_tools.ocean.transects)": [[86, "mpas_tools.ocean.transects.interp_mpas_to_transect_triangle_nodes"]], "interp_mpas_to_transect_triangles() (in module mpas_tools.ocean.transects)": [[87, "mpas_tools.ocean.transects.interp_mpas_to_transect_triangles"]], "interp_transect_grid_to_transect_triangle_nodes() (in module mpas_tools.ocean.transects)": [[88, "mpas_tools.ocean.transects.interp_transect_grid_to_transect_triangle_nodes"]], "add_inset() (in module mpas_tools.ocean.viz)": [[89, "mpas_tools.ocean.viz.add_inset"]], "plot_ocean_transects() (in module mpas_tools.ocean.viz)": [[90, "mpas_tools.ocean.viz.plot_ocean_transects"]], "create_pool() (in module mpas_tools.parallel)": [[91, "mpas_tools.parallel.create_pool"]], "make_planar_hex_mesh() (in module mpas_tools.planar_hex)": [[92, "mpas_tools.planar_hex.make_planar_hex_mesh"]], "scrip_from_mpas() (in module mpas_tools.scrip.from_mpas)": [[93, "mpas_tools.scrip.from_mpas.scrip_from_mpas"]], "extend_seaice_mask() (in module mpas_tools.seaice.mask)": [[94, "mpas_tools.seaice.mask.extend_seaice_mask"]], "make_mpas_scripfile_on_cells() (in module mpas_tools.seaice.mesh)": [[95, "mpas_tools.seaice.mesh.make_mpas_scripfile_on_cells"]], "make_mpas_scripfile_on_vertices() (in module mpas_tools.seaice.mesh)": [[96, "mpas_tools.seaice.mesh.make_mpas_scripfile_on_vertices"]], "write_2d_scripfile() (in module mpas_tools.seaice.mesh)": [[97, "mpas_tools.seaice.mesh.write_2D_scripfile"]], "write_scrip_file() (in module mpas_tools.seaice.mesh)": [[98, "mpas_tools.seaice.mesh.write_scrip_file"]], "create_partitions() (in module mpas_tools.seaice.partition)": [[99, "mpas_tools.seaice.partition.create_partitions"]], "gen_seaice_mesh_partition() (in module mpas_tools.seaice.partition)": [[100, "mpas_tools.seaice.partition.gen_seaice_mesh_partition"]], "prepare_partitions() (in module mpas_tools.seaice.partition)": [[101, "mpas_tools.seaice.partition.prepare_partitions"]], "make_regions_file() (in module mpas_tools.seaice.regions)": [[102, "mpas_tools.seaice.regions.make_regions_file"]], "regrid_to_other_mesh() (in module mpas_tools.seaice.regrid)": [[103, "mpas_tools.seaice.regrid.regrid_to_other_mesh"]], "split_grids() (in module mpas_tools.split_grids)": [[104, "mpas_tools.split_grids.split_grids"]], "test_cime_constants() (in module mpas_tools.tests.test_cime_constants)": [[105, "mpas_tools.tests.test_cime_constants.test_cime_constants"]], "vector (class in mpas_tools.transects)": [[106, "mpas_tools.transects.Vector"]], "__init__() (mpas_tools.transects.vector method)": [[106, "mpas_tools.transects.Vector.__init__"]], "angular_distance() (in module mpas_tools.transects)": [[107, "mpas_tools.transects.angular_distance"]], "cartesian_to_great_circle_distance() (in module mpas_tools.transects)": [[108, "mpas_tools.transects.cartesian_to_great_circle_distance"]], "cartesian_to_lon_lat() (in module mpas_tools.transects)": [[109, "mpas_tools.transects.cartesian_to_lon_lat"]], "lon_lat_to_cartesian() (in module mpas_tools.transects)": [[110, "mpas_tools.transects.lon_lat_to_cartesian"]], "subdivide_great_circle() (in module mpas_tools.transects)": [[111, "mpas_tools.transects.subdivide_great_circle"]], "subdivide_planar() (in module mpas_tools.transects)": [[112, "mpas_tools.transects.subdivide_planar"]], "center() (in module mpas_tools.translate)": [[113, "mpas_tools.translate.center"]], "center_on_mesh() (in module mpas_tools.translate)": [[114, "mpas_tools.translate.center_on_mesh"]], "translate() (in module mpas_tools.translate)": [[115, "mpas_tools.translate.translate"]], "register_sci_viz_colormaps() (in module mpas_tools.viz.colormaps)": [[116, "mpas_tools.viz.colormaps.register_sci_viz_colormaps"]], "mesh_to_triangles() (in module mpas_tools.viz.mesh_to_triangles)": [[117, "mpas_tools.viz.mesh_to_triangles.mesh_to_triangles"]], "extract_vtk() (in module mpas_tools.viz.paraview_extractor)": [[118, "mpas_tools.viz.paraview_extractor.extract_vtk"]], "find_planar_transect_cells_and_weights() (in module mpas_tools.viz.transects)": [[119, "mpas_tools.viz.transects.find_planar_transect_cells_and_weights"]], "find_transect_cells_and_weights() (in module mpas_tools.viz.transects)": [[120, "mpas_tools.viz.transects.find_transect_cells_and_weights"]], "make_triangle_tree() (in module mpas_tools.viz.transects)": [[121, "mpas_tools.viz.transects.make_triangle_tree"]]}})
\ No newline at end of file


 
check_call(args, logger[, log_command, timeout])
check_call(args[, logger, log_command, timeout])

 
Call the given subprocess with logging to the given logger.

 

 
LoggingContext(name[, logger, log_filename])