Move ocean and visualization conda-package scripts

conda_package/docs/ocean/moc.rst

@@ -75,14 +75,14 @@ In this example, only the ``mesh.nc`` file is required as an input.  The
 resulting ``xarray.Dataset`` contains both the basin and southern-transect
 masks.
 
-A command-line tool ``moc_southern_boundary_extractor.py`` is also available
+A command-line tool ``moc_southern_boundary_extractor`` is also available
 for this purpose:
 
 .. code-block:: none
 
-    $ moc_southern_boundary_extractor.py --help
+    $ moc_southern_boundary_extractor --help
 
-    usage: moc_southern_boundary_extractor.py [-h] -f IN_FILE -m MESH_FILE -o
+    usage: moc_southern_boundary_extractor [-h] -f IN_FILE -m MESH_FILE -o
                                               OUT_FILE
 
     This script takes a mesh file (-m flag) and a file with MOC regions masks
@@ -92,9 +92,6 @@ for this purpose:
     is applied only to vertices and edges, not cells, because the need for southern
     boundary transect data on cells is not foreseen.
 
-    Author: Xylar Asay-Davis
-    last modified: 5/22/2018
-
     optional arguments:
       -h, --help            show this help message and exit
       -f IN_FILE, --in_file IN_FILE

conda_package/docs/visualization.rst

@@ -39,7 +39,7 @@ ParaVeiw, meaning each cell has the correct polygonal geometry and will be
 visualized with a single, constant value for a given field.  The extractor,
 which is available either through the
 :py:func:`mpas_tools.viz.paraview_extractor.extract_vtk()` function or the
-``paraview_vtk_field_extractor.py`` command-line interface, can also be used to
+``paraview_vtk_field_extractor`` command-line interface, can also be used to
 visualize data on MPAS vertices (visualized on triangles) and edges (visualized
 on quadrilaterals).
 
@@ -128,7 +128,7 @@ The same extraction could be accomplished with the command-line tool as follows:
 
 .. code-block:: none
 
-    $ paraview_vtk_field_extractor.py \
+    $ paraview_vtk_field_extractor \
          -f "analysis_members/mpaso.hist.am.timeSeriesStatsDaily.*.nc" \
          -v timeDaily_avg_activeTracers_temperature -d nVertLevels=0 \
          -m init.nc -o vtk_files --xtime=xtime_startDaily

conda_package/mpas_tools/ocean/coastline_alteration.py

@@ -1,5 +1,4 @@
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+import argparse
 
 import numpy
 import xarray
@@ -35,10 +34,43 @@ def add_critical_land_blockages(dsMask, dsBlockages):
     return dsMask
 
 
+def main_add_critical_land_blockages():
+    """
+    Entry point for add_critical_land_blockages command-line tool
+    """
+    description = """
+Add transects that identify critical regions where narrow strips of land block
+ocean flow.  These are, essentially, the opposite of critical passages, which
+must remain open for ocean flow.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-f", "--input_mask_file", dest="input_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="INPUTMASKFILE", required=True)
+    parser.add_argument("-o", "--output_mask_file",
+                        dest="output_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="OUTPUTMASKFILE", required=True)
+    parser.add_argument("-b", "--blockage_file", dest="blockage_file",
+                        help="Masks for each transect identifying critical "
+                             "land blockage.", metavar="BLOCKFILE",
+                        required=True)
+    args = parser.parse_args()
+
+    dsMask = xarray.open_dataset(args.input_mask_filename)
+
+    dsBlockages = xarray.open_dataset(args.blockage_file)
+
+    dsMask = add_critical_land_blockages(dsMask, dsBlockages)
+    dsMask.to_netcdf(args.output_mask_filename)
+
+
 def widen_transect_edge_masks(dsMask, dsMesh, latitude_threshold=43.0):
     """
-    Alter critical passages at polar latitudes to be at least two cells wide, to
-    avoid sea ice blockage
+    Alter critical passages at polar latitudes to be at least two cells wide,
+    to avoid sea ice blockage
 
     Parameters
     ----------
@@ -78,6 +110,44 @@ def widen_transect_edge_masks(dsMask, dsMesh, latitude_threshold=43.0):
     return dsMask
 
 
+def main_widen_transect_edge_masks():
+    """
+    Entry point for widen_transect_edge_masks command-line tool
+    """
+    description = """
+Alter transects to be at least two cells wide.  This is used for critical
+passages, to avoid sea ice blockage.  Specifically, mark cells on both sides
+of each transect edge mask as a water cell.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-f", "--mask_file", dest="mask_filename",
+                        help="Mask file with cell and edge transect masks.",
+                        metavar="MASKFILE",
+                        required=True)
+    parser.add_argument("-m", "--mesh_file", dest="mesh_filename",
+                        help="MPAS Mesh filename.", metavar="MESHFILE",
+                        required=True)
+    parser.add_argument("-o", "--out_file", dest="out_filename",
+                        help="Output mask file,different from input filename.",
+                        metavar="MASKFILE",
+                        required=True)
+    parser.add_argument("-l", "--latitude_threshold",
+                        dest="latitude_threshold",
+                        help="Minimum latitude, degrees, for transect "
+                             "widening.",
+                        required=False, type=float, default=43.0)
+    args = parser.parse_args()
+
+    dsMask = xarray.open_dataset(args.mask_filename)
+
+    dsMesh = xarray.open_dataset(args.mesh_filename)
+
+    dsMask = widen_transect_edge_masks(dsMask, dsMesh, args.latitude_threshold)
+    dsMask.to_netcdf(args.out_filename)
+
+
 def add_land_locked_cells_to_mask(dsMask, dsMesh, latitude_threshold=43.0,
                                   nSweeps=10):
     """
@@ -143,6 +213,48 @@ def add_land_locked_cells_to_mask(dsMask, dsMesh, latitude_threshold=43.0,
     return dsMask
 
 
+def main_add_land_locked_cells_to_mask():
+    """
+    Entry point for add_land_locked_cells_to_mask command-line tool
+    """
+    description = """
+Find ocean cells that are land-locked, and alter the cell
+mask so that they are counted as land cells.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-f", "--input_mask_file", dest="input_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="INPUTMASKFILE", required=True)
+    parser.add_argument("-o", "--output_mask_file",
+                        dest="output_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="OUTPUTMASKFILE", required=True)
+    parser.add_argument("-m", "--mesh_file", dest="mesh_filename",
+                        help="MPAS Mesh filename.", metavar="MESHFILE",
+                        required=True)
+    parser.add_argument("-l", "--latitude_threshold",
+                        dest="latitude_threshold",
+                        help="Minimum latitude, in degrees, for transect "
+                             "widening.",
+                        required=False, type=float, default=43.0)
+    parser.add_argument("-n", "--number_sweeps", dest="nSweeps",
+                        help="Maximum number of sweeps to search for "
+                             "land-locked cells.",
+                        required=False, type=int, default=10)
+    args = parser.parse_args()
+
+    dsMask = xarray.open_dataset(args.input_mask_filename)
+
+    dsMesh = xarray.open_dataset(args.mesh_filename)
+
+    dsMask = add_land_locked_cells_to_mask(dsMask, dsMesh,
+                                           args.latitude_threshold,
+                                           args.nSweeps)
+    dsMask.to_netcdf(args.output_mask_filename)
+
+
 def _remove_cells_with_isolated_edges1(dsMask, dsMesh, landMask,
                                        latitude_threshold):
     print("Step 1: Searching for land-locked cells.  Remove cells that only "
@@ -307,7 +419,7 @@ def _flood_fill(dsMask, dsMesh, landMask, removable):
             filledNeighbors = numpy.logical_and(neighbors >= 0,
                                                 floodFill[neighbors] == 1)
             fillIndices = cellIndices[filledNeighbors.values]
-            if(len(fillIndices) > 0):
+            if len(fillIndices) > 0:
                 floodFill[fillIndices] = 1
                 newFloodCellsThisSweep += len(fillIndices)
 

conda_package/mpas_tools/ocean/moc.py

@@ -1,10 +1,9 @@
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+import argparse
+import logging
+import sys
 
 import xarray
 import numpy
-import logging
-import sys
 from geometric_features.aggregation.ocean import moc
 
 import mpas_tools.mesh.conversion
@@ -88,8 +87,8 @@ def add_moc_southern_boundary_transects(dsMask, dsMesh, logger=None):
     Returns
     -------
     dsMask : ``xarray.Dataset``
-        Region masks defining MOC basins and the corresponding southern-boundary
-        transects
+        Region masks defining MOC basins and the corresponding
+        southern-boundary transects
     """
 
     useStdout = logger is None
@@ -113,6 +112,41 @@ def add_moc_southern_boundary_transects(dsMask, dsMesh, logger=None):
     return dsMask
 
 
+def moc_southern_boundary_extractor():
+    """
+    Entry point for moc_southern_boundary_extractor command-line tool
+    """
+    description = """
+This script takes a mesh file (-m flag) and a file with MOC regions masks
+(-f flag) produce by the MPAS mask creator.  The script produces a copy of
+the contents of the MOC mask file, adding transects that mark the southern
+boundary of each region in a file indicated with the -o flag.  The transect
+is applied only to vertices and edges, not cells, because the need for southern
+boundary transect data on cells is not foreseen.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument('-f', '--in_file', dest='in_file',
+                        help='Input file with MOC masks', metavar='IN_FILE',
+                        required=True)
+    parser.add_argument('-m', '--mesh_file', dest='mesh_file',
+                        help='Input mesh file', metavar='MESH_FILE',
+                        required=True)
+    parser.add_argument('-o', '--out_file', dest='out_file',
+                        help='Output file for MOC masks and southern-boundary '
+                        'transects', metavar='OUT_FILE',
+                        required=True)
+    args = parser.parse_args()
+
+    dsMasks = xarray.open_dataset(args.in_file)
+    dsMesh = xarray.open_dataset(args.mesh_file)
+
+    dsMasksAndTransects = add_moc_southern_boundary_transects(dsMasks, dsMesh)
+
+    write_netcdf(dsMasksAndTransects, args.out_file)
+
+
 def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
     """
     Extracts the southern boundary of each region mask in mocMask.  Mesh info
@@ -125,7 +159,7 @@ def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
     nEdges = mesh.sizes['nEdges']
 
     nRegions = mocMask.sizes['nRegions']
-    assert(mocMask.sizes['nCells'] == nCells)
+    assert mocMask.sizes['nCells'] == nCells
 
     # convert to python zero-based indices
     cellsOnEdge = mesh.variables['cellsOnEdge'].values-1
@@ -198,7 +232,7 @@ def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
         startIndices = numpy.arange(1, len(edgeSequence))[belowToAbove]
         endIndices = numpy.arange(1, len(edgeSequence))[aboveToBelow]
 
-        assert(len(startIndices) == len(endIndices))
+        assert len(startIndices) == len(endIndices)
 
         if len(startIndices) == 0:
             # the whole sequence is the southern boundary
@@ -232,7 +266,8 @@ def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
 
 
 def _add_transects_to_moc(mesh, mocMask, southernBoundaryEdges,
-                          southernBoiundaryEdgeSigns, southernBoundaryVertices):
+                          southernBoiundaryEdgeSigns,
+                          southernBoundaryVertices):
     """
     Creates transect fields in mocMask from the edges, edge signs and
     vertices defining the southern boundaries.  Mesh info (nEdges and
@@ -354,7 +389,7 @@ def _get_edge_sequence_on_boundary(startEdge, edgeSign, edgesOnVertex,
     edgeSequence = []
     vertexSequence = []
     while True:
-        assert(edgeSign[iEdge] == 1. or edgeSign[iEdge] == -1.)
+        assert edgeSign[iEdge] == 1. or edgeSign[iEdge] == -1.
         if edgeSign[iEdge] == 1.:
             v = 0
         else:
@@ -369,7 +404,7 @@ def _get_edge_sequence_on_boundary(startEdge, edgeSign, edgesOnVertex,
             if edge != -1 and edge != iEdge and edgeSign[edge] != 0:
                 nextEdge = edge
                 break
-        assert(nextEdge != -1)
+        assert nextEdge != -1
 
         edgeSequence.append(iEdge)
         vertexSequence.append(iVertex)

conda_package/recipe/build.sh

@@ -3,13 +3,11 @@
 set -x
 set -e
 
-cp -r ocean landice visualization mesh_tools conda_package
-
 cd conda_package
 ${PYTHON} -m pip install . --no-deps --no-build-isolation -vv
 
 # build and install ocean topography smoothing tool
-cd ${SRC_DIR}/conda_package/ocean/smooth_topo
+cd ${SRC_DIR}/ocean/smooth_topo
 mkdir build
 cd build
 cmake \
@@ -20,7 +18,7 @@ cmake --build .
 cmake --install .
 
 # build and install sea ice partitioning tool
-cd ${SRC_DIR}/conda_package/mesh_tools/seaice_grid_tools
+cd ${SRC_DIR}/mesh_tools/seaice_grid_tools
 mkdir build
 cd build
 cmake \
@@ -31,7 +29,7 @@ cmake --build .
 cmake --install .
 
 # build and install legacy mask creator
-cd ${SRC_DIR}/conda_package/mesh_tools/mesh_conversion_tools
+cd ${SRC_DIR}/mesh_tools/mesh_conversion_tools
 mkdir build
 cd build
 cmake \
@@ -42,7 +40,7 @@ cmake --build .
 cp MpasMaskCreator.x ${PREFIX}/bin
 
 # build and install mesh conversion tools
-cd ${SRC_DIR}/conda_package/mesh_tools/mesh_conversion_tools_netcdf_c
+cd ${SRC_DIR}/mesh_tools/mesh_conversion_tools_netcdf_c
 mkdir build
 cd build
 cmake \