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Merged
mark-petersen merged 1 commit into from
Mar 6, 2019
Merged

Add critical land blockages to global_ocean tests #169

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1 change: 1 addition & 0 deletions testing_and_setup/compass/ocean/global_ocean/config_files/config_culled_mesh.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
<add_link source_path="script_configuration_dir" source="cull_mesh.py" dest="cull_mesh.py"/>
<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_critical_land_blockages_to_mask.py" dest="add_critical_land_blockages_to_mask.py"/>

<run_script name="run.py">
<step executable="./cull_mesh.py">
Expand Down
82 changes: 66 additions & 16 deletions testing_and_setup/compass/ocean/global_ocean/cull_mesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,10 @@
The optional --with_critical_passages flag indicates that critical
passages are to be opened. Otherwise, steps 2, 5 and 9 are skipped
"""

from __future__ import absolute_import, division, print_function, \
unicode_literals

import os
import os.path
import subprocess
Expand Down Expand Up @@ -58,7 +62,8 @@ def removeFile(fileName):
'-f', landCoverage,
'-m', landCoverageMask,
'-o', 'land_coverage.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# Add the appropriate land coverage below 60S (either all ice or grounded ice).
Expand All @@ -71,29 +76,37 @@ def removeFile(fileName):

args = ['{}/merge_features.py'.format(path), '-f', antarcticLandCoverage,
'-o', 'land_coverage.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())


# Create the land mask based on the land coverage, i.e. coastline data.
# Run command is:
# ./MpasMaskCreator.x base_mesh.nc land_mask.nc -f land_coverage.geojson
args = [
'./MpasMaskCreator.x',
'base_mesh.nc',
'land_mask_1_from_land_coverage.nc',
'-f',
'land_coverage.geojson']
print "running", ' '.join(args)
'-f', 'land_coverage.geojson']
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

if options.with_critical_passages:
outMaskFile = 'land_mask_2_from_land_locked_cells.nc'
else:
outMaskFile = 'land_mask_final.nc'

# Add land-locked cells to land coverage mask.
args = ['./add_land_locked_cells_to_mask.py',
'-f', 'land_mask_1_from_land_coverage.nc',
'-o', 'land_mask_final.nc',
'-o', outMaskFile,
'-m', 'base_mesh.nc',
'-l', '43.0',
'-n', '20']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# create seed points for a flood fill of the ocean
Expand All @@ -104,7 +117,8 @@ def removeFile(fileName):
'-d', '{}/ocean/point'.format(path),
'-t', 'seed_point',
'-o', 'seed_points.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

if options.with_critical_passages:
Expand All @@ -114,7 +128,8 @@ def removeFile(fileName):
'-d', '{}/ocean/transect'.format(path),
'-t', 'Critical_Passage',
'-o', 'critical_passages.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# create masks from the transects
Expand All @@ -123,7 +138,8 @@ def removeFile(fileName):
# -f critical_passages.geojson
args = ['./MpasMaskCreator.x', 'base_mesh.nc', 'critical_passages_mask.nc',
'-f', 'critical_passages.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# Alter critical passages to be at least two cells wide, to avoid sea ice
Expand All @@ -132,7 +148,36 @@ def removeFile(fileName):
'-f', 'critical_passages_mask.nc',
'-m', 'base_mesh.nc',
'-l', '43.0']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# merge transects for critical land blockages into
# critical_land_blockages.geojson
removeFile('critical_land_blockages.geojson')
args = ['{}/merge_features.py'.format(path),
'-d', '{}/ocean/transect'.format(path),
'-t', 'Critical_Land_Blockage',
'-o', 'critical_land_blockages.geojson']
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# create masks from the transects for critical land blockages
args = ['./MpasMaskCreator.x', 'base_mesh.nc',
'critical_land_blockages_mask.nc',
'-f', 'critical_land_blockages.geojson']
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# add critical land blockages to land_mask_final.nc
args = ['./add_critical_land_blockages_to_mask.py',
'-f', 'land_mask_2_from_land_locked_cells.nc',
'-o', 'land_mask_final.nc',
'-b', 'critical_land_blockages_mask.nc']
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# Cull the mesh based on the land mask while keeping critical passages open
Expand All @@ -141,7 +186,8 @@ def removeFile(fileName):
# -p critical_passages_mask.nc
args = ['./MpasCellCuller.x', 'base_mesh.nc', 'culled_mesh_preliminary.nc',
'-m', 'land_mask_final.nc', '-p', 'critical_passages_mask.nc']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())
else:

Expand All @@ -150,15 +196,17 @@ def removeFile(fileName):
# ./MpasCellCuller.x base_mesh.nc culled_mesh_preliminary.nc -m land_mask_final.nc
args = ['./MpasCellCuller.x', 'base_mesh.nc', 'culled_mesh_preliminary.nc',
'-m', 'land_mask_final.nc']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

# create a mask for the flood fill seed points
# Run command is:
# ./MpasMaskCreator.x culled_mesh_preliminary.nc seed_mask.nc -s seed_points.geojson
args = ['./MpasMaskCreator.x', 'culled_mesh_preliminary.nc', 'seed_mask.nc',
'-s', 'seed_points.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())


Expand All @@ -168,7 +216,8 @@ def removeFile(fileName):
args = ['./MpasCellCuller.x', 'culled_mesh_preliminary.nc', 'culled_mesh.nc',
'-i', 'seed_mask.nc']

print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())

if options.with_critical_passages:
Expand All @@ -179,5 +228,6 @@ def removeFile(fileName):
args = ['./MpasMaskCreator.x', 'culled_mesh.nc',
'critical_passages_mask_final.nc',
'-f', 'critical_passages.geojson']
print "running", ' '.join(args)
print("running {}".format(' '.join(args)))

subprocess.check_call(args, env=os.environ.copy())