def build_ocean_basins(gf, plot):
'''
Builds features defining the major ocean basins
Parameters
----------
gf : ``GeometricFeatures``
An object that knows how to download and read geometric featuers
plot : bool
Whether to plot each basin
Returns
-------
fc : ``FeatureCollection``
The new feature collection
'''
# Authors
# -------
# Xylar Asay-Davis
fc = FeatureCollection()
fc.set_group_name(groupName='OceanBasinRegionsGroup')
# build ocean basins from regions with the appropriate tags
for oceanName in [
'Atlantic', 'Pacific', 'Indian', 'Arctic', 'Southern_Ocean',
'Mediterranean'
]:
basinName = '{}_Basin'.format(oceanName)
print(oceanName)
print(' * merging features')
fcBasin = gf.read(componentName='ocean',
objectType='region',
tags=[basinName])
print(' * combining features')
fcBasin = fcBasin.combine(featureName=basinName)
fc.merge(fcBasin)
if plot:
fcBasin.plot(projection='cyl')
plt.title(oceanName)
# add the global ocean, global ocean between 65S and 65S, and
# equatorial region
fc.merge(
gf.read(componentName='ocean',
objectType='region',
featureNames=[
'Global Ocean', 'Global Ocean 65N to 65S',
'Global Ocean 15S to 15N'
]))
return fc
def make_ice_shelf_masks(gf): # {{{
iceShelfNames = [
'Abbot', 'Amery', 'Atka', 'Aviator', 'Bach', 'Baudouin',
'Borchgrevink', 'Brahms', 'Brunt_Stancomb', 'Campbell', 'Cheetham',
'Conger_Glenzer', 'Cook', 'Cosgrove', 'Crosson', 'Dennistoun',
'Dibble', 'Dotson', 'Drygalski', 'Edward_VIII', 'Ekstrom', 'Ferrigno',
'Filchner', 'Fimbul', 'Fitzgerald', 'Frost', 'GeikieInlet',
'George_VI', 'Getz', 'Gillet', 'Hamilton', 'Hannan', 'HarbordGlacier',
'Helen', 'Holmes', 'HolmesWest', 'Hull', 'Jelbart', 'Land', 'Larsen_B',
'Larsen_C', 'Larsen_D', 'Larsen_E', 'Larsen_F', 'Larsen_G', 'Lazarev',
'Lillie', 'Mariner', 'Matusevitch', 'Mendelssohn', 'Mertz',
'Moscow_University', 'Moubray', 'Mulebreen', 'Myers', 'Nansen',
'Nickerson', 'Ninnis', 'Nivl', 'Noll', 'Nordenskjold', 'Pine_Island',
'PourquoiPas', 'Prince_Harald', 'Publications', 'Quar', 'Rayner_Thyer',
'Rennick', 'Richter', 'Riiser-Larsen', 'Ronne', 'Ross_East',
'Ross_West', 'Shackleton', 'Shirase', 'Slava', 'SmithInlet', 'Stange',
'Sulzberger', 'Suvorov', 'Swinburne', 'Thwaites', 'Tinker', 'Totten',
'Tracy_Tremenchus', 'Tucker', 'Underwood', 'Utsikkar', 'Venable',
'Verdi', 'Vigrid', 'Vincennes', 'Voyeykov', 'West', 'Wilkins',
'Wilma_Robert_Downer', 'Withrow', 'Wordie', 'Wylde', 'Zubchatyy'
]
combinedIceShelves = {
'Filchner-Ronne': ['Filchner', 'Ronne'],
'Ross': ['Ross_East', 'Ross_West'],
'Antarctica': [
'AntarcticPenninsulaIMBIE', 'WestAntarcticaIMBIE',
'EastAntarcticaIMBIE'
],
'Peninsula': ['AntarcticPenninsulaIMBIE'],
'West Antarctica': ['WestAntarcticaIMBIE'],
'East Antarctica': ['EastAntarcticaIMBIE']
}
nIMBIEBasins = 27
for basinNumber in range(1, nIMBIEBasins + 1):
basinName = 'Antarctica_IMBIE{}'.format(basinNumber)
combinedIceShelves['IMBIE{}'.format(basinNumber)] = [basinName]
# create a FeatureCollection containing all ice shelves and combined ice-shelf
# regions
fc = FeatureCollection()
# build analysis regions from combining ice shelves from regions with the
# appropriate tags
for shelfName in combinedIceShelves:
subNames = combinedIceShelves[shelfName]
print(shelfName)
print(' * merging features')
fcShelf = gf.read(componentName='iceshelves',
objectType='region',
tags=subNames,
allTags=False)
print(' * combining features')
fcShelf = fcShelf.combine(featureName=shelfName)
# merge the feature for the basin into the collection of all basins
fc.merge(fcShelf)
# build ice shelves from regions with the appropriate tags
for shelfName in iceShelfNames:
print(shelfName)
print(' * merging features')
fcShelf = gf.read(componentName='iceshelves',
objectType='region',
tags=[shelfName])
print(' * combining features')
fcShelf = fcShelf.combine(featureName=shelfName)
# merge the feature for the basin into the collection of all basins
fc.merge(fcShelf)
return fc # }}}
fcSeed = gf.read(componentName='ocean',
objectType='point',
tags=['seed_point'])
if land_blockages:
if options.with_critical_passages:
# merge transects for critical land blockages into
# critical_land_blockages.geojson
fcCritBlockages = gf.read(componentName='ocean',
objectType='transect',
tags=['Critical_Land_Blockage'])
else:
fcCritBlockages = FeatureCollection()
if options.custom_land_blockages is not None:
fcCritBlockages.merge(
read_feature_collection(options.custom_land_blockages))
# create masks from the transects
dsCritBlockMask = conversion.mask(dsBaseMesh, fcMask=fcCritBlockages)
dsLandMask = add_critical_land_blockages(dsLandMask, dsCritBlockMask)
fcCritPassages = FeatureCollection()
dsPreserve = []
if critical_passages:
if options.with_critical_passages:
# merge transects for critical passages into critical_passages.geojson
fcCritPassages.merge(
gf.read(componentName='ocean',
objectType='transect',
def build_MOC_basins(gf):
'''
Builds features defining the ocean basins used in computing the meridional
overturning circulation (MOC)
Parameters
----------
gf : ``GeometricFeatures``
An object that knows how to download and read geometric featuers
Returns
-------
fc : ``FeatureCollection``
The new feature collection
'''
# Authors
# -------
# Xylar Asay-Davis
MOCSubBasins = {
'Atlantic': ['Atlantic', 'Mediterranean'],
'IndoPacific': ['Pacific', 'Indian'],
'Pacific': ['Pacific'],
'Indian': ['Indian']
}
MOCSouthernBoundary = {
'Atlantic': '34S',
'IndoPacific': '34S',
'Pacific': '6S',
'Indian': '6S'
}
fc = FeatureCollection()
fc.set_group_name(groupName='MOCBasinRegionsGroup')
# build MOC basins from regions with the appropriate tags
for basinName in MOCSubBasins:
print('{} MOC'.format(basinName))
print(' * merging features')
tags = ['{}_Basin'.format(basin) for basin in MOCSubBasins[basinName]]
fcBasin = gf.read(componentName='ocean',
objectType='region',
tags=tags,
allTags=False)
print(' * combining features')
fcBasin = fcBasin.combine(featureName='{}_MOC'.format(basinName))
print(' * masking out features south of MOC region')
maskName = 'MOC mask {}'.format(MOCSouthernBoundary[basinName])
fcMask = gf.read(componentName='ocean',
objectType='region',
featureNames=[maskName])
# mask out the region covered by the mask
fcBasin = fcBasin.difference(fcMask)
# remove various small polygons that are not part of the main MOC
# basin shapes. Most are tiny but one below Australia is about 20
# deg^2, so make the threshold 100 deg^2 to be on the safe side.
fcBasin = remove_small_polygons(fcBasin, minArea=100.)
# add this basin to the full feature collection
fc.merge(fcBasin)
return fc
def main():
author = 'Milena Veneziani'
# make a geometric features object that knows about the geometric data
# cache up a couple of directories
gf = GeometricFeatures(cacheLocation='../../geometric_data')
fc = FeatureCollection()
# ********* OSNAP array West *********
# Read in OSNAP West lon,lat
OSNAPwestLonLat = csv.reader(open('./OSNAParrayWest20210322.csv', 'r'))
# Skip 4 header lines
next(OSNAPwestLonLat, None)
next(OSNAPwestLonLat, None)
next(OSNAPwestLonLat, None)
next(OSNAPwestLonLat, None)
coords = []
for line in OSNAPwestLonLat:
coords.append([float(line[0]), float(line[1])])
feature = {}
feature['type'] = 'Feature'
feature['properties'] = {}
feature['properties']['name'] = 'OSNAP section West'
feature['properties']['tags'] = 'arctic_sections'
feature['properties']['object'] = 'transect'
feature['properties']['component'] = 'ocean'
feature['properties']['author'] = author
feature['geometry'] = {}
feature['geometry']['type'] = 'LineString'
feature['geometry']['coordinates'] = coords
fcOW = FeatureCollection([feature])
fcOW.plot(projection='northpole')
fc.merge(fcOW)
# ********* OSNAP array East *********
# Read in OSNAP East lon,lat
OSNAPeastLonLat = csv.reader(open('./OSNAParrayEast20210322.csv', 'r'))
# Skip 4 header lines
next(OSNAPeastLonLat, None)
next(OSNAPeastLonLat, None)
next(OSNAPeastLonLat, None)
next(OSNAPeastLonLat, None)
coords = []
for line in OSNAPeastLonLat:
coords.append([float(line[0]), float(line[1])])
feature = {}
feature['type'] = 'Feature'
feature['properties'] = {}
feature['properties']['name'] = 'OSNAP section East'
feature['properties']['tags'] = 'arctic_sections'
feature['properties']['object'] = 'transect'
feature['properties']['component'] = 'ocean'
feature['properties']['author'] = author
feature['geometry'] = {}
feature['geometry']['type'] = 'LineString'
feature['geometry']['coordinates'] = coords
fcOE = FeatureCollection([feature])
fcOE.plot(projection='northpole')
fc.merge(fcOE)
# "split" these features into individual files in the geometric data cache
gf.split(fc)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
plt.show()
def main():
author = 'Xylar Asay-Davis, Alice Barthel, Nicolas Jourdain'
tags = 'Antarctic;ISMIP6'
# make a geometric features object that knows about the geometric data
# cache up a couple of directories
gf = GeometricFeatures('../../geometric_data')
bedmap2_bin_to_netcdf('bedmap2.nc')
fcContour1500 = get_longest_contour(contourValue=-1500., author=author)
fc = FeatureCollection()
lons = [-65., -25., -25., -65.]
lats = [-80., -80., -77., -71.]
fc.merge(
shelf_polygon(lons,
lats,
name='ISMIP6 Weddell Sea',
author=author,
tags=tags,
fcContour=fcContour1500))
lons = [-128., -128., -90., -90.]
lats = [-76., -69., -69., -76.]
fc.merge(
shelf_polygon(lons,
lats,
name='ISMIP6 Amundsen Sea',
author=author,
tags=tags,
fcContour=fcContour1500))
lons = [45., 45., 90., 90.]
lats = [-70., -60., -60., -70.]
fc.merge(
shelf_polygon(lons,
lats,
name='ISMIP6 Amery Sector',
author=author,
tags=tags,
fcContour=fcContour1500))
lons = [-22.5, -22.5, 22.5, 22.5]
lats = [-75., -65., -65., -75.]
fc.merge(
shelf_polygon(lons,
lats,
name='ISMIP6 Dronning Maud Land',
author=author,
tags=tags,
fcContour=fcContour1500))
lons = [110., 110., 130., 130.]
lats = [-70., -60., -60., -70.]
fc.merge(
shelf_polygon(lons,
lats,
name='ISMIP6 Totten Region',
author=author,
tags=tags,
fcContour=fcContour1500))
lons = [165., 165., 180., 180.]
lats = [-80., -71., -73., -80.]
fc_ross = shelf_polygon(lons,
lats,
name='ISMIP6 Western Ross Sea',
author=author,
tags=tags,
fcContour=fcContour1500)
lons = [-180., -180., -150., -150.]
lats = [-80., -73., -77., -80.]
fc_ross.merge(
shelf_polygon(lons,
lats,
name='ISMIP6 Eastern Ross Sea',
author=author,
tags=tags,
fcContour=fcContour1500))
old_props = fc_ross.features[0]['properties']
fc_ross = fc_ross.combine('ISMIP6 Ross Sea')
props = fc_ross.features[0]['properties']
for prop in ['tags', 'zmin', 'zmax']:
props[prop] = old_props[prop]
fc.merge(fc_ross)
fc.plot(projection='southpole')
fc.to_geojson('ismip6_antarctic_ocean_regions.geojson')
# "split" these features into individual files in the geometric data cache
gf.split(fc)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
plt.show()
# create a GeometricFeatures object that points to a local cache of geometric
# data and knows which branch of geometric_feature to use to download
# missing data
gf = GeometricFeatures('./geometric_data')
# create a FeatureCollection containing all iceshelf regions wtih one of the
# 27 IMBIE basin tags tags
fc = FeatureCollection()
for basin in range(1, 28):
print('Adding feature from IMBIE basin {:d}'.format(basin))
basinName = 'Antarctica_IMBIE{:d}'.format(basin)
tags = [basinName]
# load the iceshelf regions for one IMBIE basin
fcBasin = gf.read(componentName='iceshelves',
objectType='region',
tags=tags)
# combine all regions in the basin into a single feature
fcBasin = fcBasin.combine(featureName=basinName)
# merge the feature for the basin into the collection of all basins
fc.merge(fcBasin)
# save the feature collection to a geojson file
fc.to_geojson('Extended_Antarctic_Basins.geojson')
if plot:
fc.plot(projection='southpole')
plt.show()
def main():
author = 'Xylar Asay-Davis'
timTags = 'Antarctic;Timmermann'
orsiTags = 'Antarctic;Orsi'
# make a geometric fieatures object that knows about the geometric data
# cache up a couple of directories
gf = GeometricFeatures('../../geometric_data')
bedmap2_bin_to_netcdf('bedmap2.nc')
fcContour700 = get_longest_contour(contourValue=-700., author=author)
fcContour800 = get_longest_contour(contourValue=-800., author=author)
fc = FeatureCollection()
fcWeddell = split_rectangle(lon0=-63.,
lon1=0.,
lat0=-80.,
lat1=-65.,
name='Weddell Sea',
author=author,
tags=timTags,
fcContour=fcContour800)
# get rid of the Weddell Sea because we're not that happy with this
# definition, but keep the deep/shelf ones
fcWeddell.features = fcWeddell.features[1:]
fc.merge(fcWeddell)
fcEW = split_rectangle(lon0=-20.,
lon1=25.,
lat0=-80.,
lat1=-55.,
name='Eastern Weddell Sea',
author=author,
tags=orsiTags,
fcContour=fcContour800)
fc.merge(fcEW)
fcWW = split_rectangle(lon0=-63.,
lon1=-20.,
lat0=-80.,
lat1=-60.,
name='Western Weddell Sea',
author=author,
tags=orsiTags,
fcContour=fcContour800)
fc.merge(fcWW)
# The Weddell feature is the sum of the Eastern and Western features before
# splitting into shelf/deep
fcWeddell = FeatureCollection()
fcWeddell.features.append(fcEW.features[0])
fcWeddell.features.append(fcWW.features[0])
# now combine these into a single feature
fcWeddell = fcWeddell.combine('Weddell Sea')
props = fcWeddell.features[0]['properties']
props['tags'] = orsiTags
props['zmin'] = -1000.
props['zmax'] = -400.
fc.merge(fcWeddell)
# add the Weddell Sea back as the sum of Eastern and Western
fc.merge(
make_rectangle(lon0=-63.,
lon1=45.,
lat0=-80.,
lat1=-58.,
name='Weddell Sea',
author=author,
tags=orsiTags))
fc.merge(
split_rectangle(lon0=-100.,
lon1=-63.,
lat0=-80.,
lat1=-67.,
name='Bellingshausen Sea',
author=author,
tags=timTags,
fcContour=fcContour700))
fc.merge(
split_rectangle(lon0=-140.,
lon1=-100.,
lat0=-80.,
lat1=-67.,
name='Amundsen Sea',
author=author,
tags=timTags,
fcContour=fcContour800))
fc.merge(
split_rectangle(lon0=-180.,
lon1=-140.,
lat0=-80.,
lat1=-67.,
name='Eastern Ross Sea',
author=author,
tags=timTags,
fcContour=fcContour700))
fc.merge(
split_rectangle(lon0=160.,
lon1=180.,
lat0=-80.,
lat1=-67.,
name='Western Ross Sea',
author=author,
tags=timTags,
fcContour=fcContour700))
fc.merge(
split_rectangle(lon0=25.,
lon1=160.,
lat0=-80.,
lat1=-62.,
name='East Antarctic Seas',
author=author,
tags=orsiTags,
fcContour=fcContour800))
fc.merge(
make_rectangle(lon0=-180.,
lon1=180.,
lat0=-80.,
lat1=-60.,
name='Southern Ocean 60S',
author=author,
tags=timTags))
fcSO = gf.read('ocean', 'region', ['Southern Ocean'])
props = fcSO.features[0]['properties']
props['zmin'] = -1000.
props['zmax'] = -400.
fc.merge(fcSO)
fc.plot(projection='southpole')
fc.to_geojson('antarctic_ocean_regions.geojson')
# "split" these features into individual files in the geometric data cache
gf.split(fc)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
plt.show()
# appropriate tags
for shelfName in combinedIceShelves:
subNames = combinedIceShelves[shelfName]
print(shelfName)
print(' * merging features')
fcShelf = gf.read(componentName='iceshelves',
objectType='region',
tags=subNames,
allTags=False)
print(' * combining features')
fcShelf = fcShelf.combine(featureName=shelfName)
# merge the feature for the basin into the collection of all basins
fc.merge(fcShelf)
# build ice shelves from regions with the appropriate tags
for shelfName in iceShelfNames:
print(shelfName)
print(' * merging features')
fcShelf = gf.read(componentName='iceshelves',
objectType='region',
tags=[shelfName])
print(' * combining features')
fcShelf = fcShelf.combine(featureName=shelfName)
# merge the feature for the basin into the collection of all basins
fc.merge(fcShelf)
def main():
author = 'Milena Veneziani'
# make a geometric features object that knows about the geometric data
# cache up a couple of directories
gf = GeometricFeatures(cacheLocation='../../geometric_data')
fc = FeatureCollection()
# ********* New Hudson Bay (modified feature) *********
# Extract Foxe Basin from Northwestern Passages, and merge it
# to old Hudson Bay feature. Also combine Hudson Strait with
# Hudson Bay. Note that the created feature needs to be further
# edited by hand to eliminate a seem, due to Foxe Basin not
# completely aligning with one side of the old Hudson Bay feature
# (and this feature is not fixed by the last step in this script
# either).
fcCAA = gf.read('ocean', 'region', ['Northwestern Passages'])
fcbox1 = make_rectangle(lon0=-84.3, lon1=-71.7, lat0=67.1, lat1=70.75,
name='Foxe Basin Box 1', author=author,
tags='Hudson_Bay;Arctic;Atlantic_Basin')
fcbox2 = make_rectangle(lon0=-86., lon1=-71.7, lat0=63.5, lat1=67.1,
name='Foxe Basin Box 2', author=author,
tags='Hudson_Bay;Arctic;Atlantic_Basin')
fcFoxe_tmp = fcbox1.difference(fcCAA)
fcFoxe_tmp = fcbox1.difference(fcFoxe_tmp)
fcFoxe = fcbox2.difference(fcCAA)
fcFoxe = fcbox2.difference(fcFoxe)
fcFoxe.merge(fcFoxe_tmp)
fcFoxe = fcFoxe.combine('Foxe Basin')
fcHudson = gf.read('ocean', 'region', ['Hudson Bay'])
fcHudson.merge(gf.read('ocean', 'region', ['Hudson Strait']))
fcHudson.merge(fcFoxe)
fcHudson = fcHudson.combine('Hudson Bay')
props = fcHudson.features[0]['properties']
props['tags'] = 'Hudson Bay;Arctic;Atlantic_Basin'
props['author'] = author
fc = fcHudson
# ********* New Canadian Archipelago (modified feature) *********
# Remove Foxe Basin from Northwestern Passages and make new
# Canadian Archipelago feature
fcCAA = fcCAA.difference(fcFoxe)
props = fcCAA.features[0]['properties']
props['name'] = 'Canadian Archipelago'
props['tags'] = 'Canadian_Archipelago;Arctic;Atlantic_Basin'
props['author'] = author
fc.merge(fcCAA)
# ********* New Barents Sea (modified feature) *********
# NOTE: this is dependent on existence of *old* features;
# in particular, the Barentsz_Sea feature will
# be removed after this script is applied
# Combine Barentsz_Sea and White_Sea into new Barents Sea feature
fcBS = gf.read('ocean', 'region', ['Barentsz Sea'])
fcBS.merge(gf.read('ocean', 'region', ['White Sea']))
fcBS = fcBS.combine('Barents Sea')
props = fcBS.features[0]['properties']
props['tags'] = 'Barents_Sea;Arctic;Arctic_NSIDC;Arctic_Basin'
props['author'] = author
fc.merge(fcBS)
# ********* Kara Sea (unchanged feature) *********
fcKara = gf.read('ocean', 'region', ['Kara Sea'])
props = fcKara.features[0]['properties']
props['tags'] = 'Kara_Sea;Arctic;Arctic_NSIDC;Arctic_Basin'
fc.merge(fcKara)
# ********* New Arctic Ocean (modified feature) *********
# NOTE: this is dependent on existence of *old* features;
# in particular, the Arctic_Ocean, Chukchi_Sea,
# East_Siberian_Sea, and Laptev_Sea features will
# be superseded after this script is applied
# Define triangle between Greenland Sea and Arctic_Ocean
# (north of Fram Strait) that is not part of any of the
# currently defined Arctic features
fc_tmp = gf.read('ocean', 'region', ['Arctic Ocean'])
fc_tmp.merge(gf.read('ocean', 'region', ['Lincoln Sea']))
fc_tmp.merge(fcBS)
fcArctic = make_rectangle(lon0=-36., lon1=20., lat0=86., lat1=79.,
name='North of Fram Strait', author=author, tags='Arctic_Basin')
fcArctic = fcArctic.difference(fc_tmp)
# Define full Arctic *but* Barents and Kara Seas
fcArctic.merge(gf.read('ocean', 'region', ['Arctic Ocean']))
fcArctic.merge(gf.read('ocean', 'region', ['Laptev Sea']))
fcArctic.merge(gf.read('ocean', 'region', ['East Siberian Sea']))
fcArctic.merge(gf.read('ocean', 'region', ['Chukchi Sea']))
fcArctic.merge(gf.read('ocean', 'region', ['Beaufort Sea']))
fcArctic.merge(gf.read('ocean', 'region', ['Lincoln Sea']))
fcArctic = fcArctic.combine('Arctic Ocean')
props = fcArctic.features[0]['properties']
props['tags'] = 'Arctic_Ocean;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcArctic)
# ********* Beaufort Gyre (entirely new feature) *********
fcContour300 = get_longest_contour(contourValue=-300., author=author)
fcBG_firstTry = make_rectangle(lon0=-170., lon1=-130., lat0=70.5, lat1=80.5,
name='Beaufort Gyre', author=author,
tags='Beaufort_Gyre;Arctic_Proshutinsky')
fcBG = fcBG_firstTry.difference(fcContour300)
fcBG = fcBG_firstTry.difference(fcBG)
fc.merge(fcBG)
# ********* New NSIDC Chukchi Sea (new feature) *********
# Define Chukchi Sea as MASIE region #2 minus intersection with
# Beaufort Gyre, and with Bering Strait transect as southern boundary
fcChukchi = FeatureCollection()
fcChukchi.add_feature(
{"type": "Feature",
"properties": {"name": 'Chukchi Sea NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Chukchi_Sea_NSIDC;Arctic_NSIDC'},
"geometry": {
"type": "Polygon",
"coordinates": [[[-167.15, 65.74],
[-168.01, 65.84],
[-168.62, 65.91],
[-169.43, 66.01],
[-170.24, 66.1],
[-180., 66.6],
[-180., 80.0],
[-156.48, 80.0],
[-156.65, 65.37],
[-167.15, 65.74]]]}})
fcChukchi = fcChukchi.difference(fcBG)
fc.merge(fcChukchi)
# ********* Beaufort Gyre shelf (entirely new feature) *********
# Define Beaufort Gyre shelf region, minus intersection with Chukchi Sea
fcBGshelf_firstTry = make_rectangle(lon0=-170., lon1=-130.,
lat0=68.0, lat1=80.5,
name='Beaufort Gyre Shelf Box',
author=author,
tags='Beaufort_Gyre_Shelf;Arctic_Proshutinsky')
fcBGshelf = fcBGshelf_firstTry.difference(fcContour300)
fcBGshelf_secondTry = fcBGshelf_firstTry.difference(fcBG)
fcBGshelf_secondTry = fcBGshelf_secondTry.difference(fcBGshelf)
fcBGshelf.merge(fcBGshelf_secondTry)
fcBGshelf = fcBGshelf.combine('Beaufort Gyre Shelf')
fcBGshelf = fcBGshelf.difference(fcChukchi)
props = fcBGshelf.features[0]['properties']
props['name'] = 'Beaufort Gyre Shelf'
props['author'] = author
props['tags'] = 'Beaufort_Gyre_Shelf;Arctic_Proshutinsky'
fc.merge(fcBGshelf)
# ********* New NSIDC East Siberian Sea (new feature) *********
# Define East Siberian Sea as MASIE region #3
fcESS = FeatureCollection()
fcESS = make_rectangle(lon0=180., lon1=145., lat0=67., lat1=80.,
name='East Siberian Sea NSIDC', author=author,
tags='East_Siberian_Sea_NSIDC;Arctic_NSIDC')
fc.merge(fcESS)
# ********* New NSIDC Laptev Sea (new feature) *********
# Define Laptev Sea as MASIE region #4, minus intersection with
# Kara Sea
fcLap = FeatureCollection()
fcLap.add_feature(
{"type": "Feature",
"properties": {"name": 'Laptev Sea NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Laptev_Sea_NSIDC;Arctic_NSIDC'},
"geometry": {
"type": "Polygon",
"coordinates": [[[145., 68.],
[145., 80.],
[95.4, 81.29],
[99.89, 78.27],
[102., 72.],
[145., 68.]]]}})
fcLap = fcLap.difference(fcKara)
fc.merge(fcLap)
# ********* Central Arctic (entirely new feature) *********
# Define Central Arctic region as New Arctic Ocean minus BG, BGshelf,
# New Chukchi, New ESS, and New Laptev
fcCentralArctic = fcArctic.difference(fcBG)
fcCentralArctic = fcCentralArctic.difference(fcBGshelf)
fcCentralArctic = fcCentralArctic.difference(fcChukchi)
fcCentralArctic = fcCentralArctic.difference(fcESS)
fcCentralArctic = fcCentralArctic.difference(fcLap)
props = fcCentralArctic.features[0]['properties']
props['name'] = 'Central Arctic'
props['tags'] = 'Central_Arctic;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcCentralArctic)
# "split" these features into individual files in the geometric data cache
gf.split(fc)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
# Fix features if necessary
fcArcticTags = gf.read(componentName='ocean', objectType='region',
tags=['Arctic'])
for feature in fcArcticTags.features:
featureName = feature['properties']['name']
shape = shapely.geometry.shape(feature['geometry'])
print('{} is_valid: {}'.format(featureName, shape.is_valid))
if not shape.is_valid:
fixed = shape.buffer(0)
print(' Fixed? {}'.format(fixed.is_valid))
feature['geometry'] = shapely.geometry.mapping(fixed)
fcArcticNSIDCTags = gf.read(componentName='ocean', objectType='region',
tags=['Arctic_NSIDC'])
for feature in fcArcticNSIDCTags.features:
featureName = feature['properties']['name']
shape = shapely.geometry.shape(feature['geometry'])
print('{} is_valid: {}'.format(featureName, shape.is_valid))
if not shape.is_valid:
fixed = shape.buffer(0)
print(' Fixed? {}'.format(fixed.is_valid))
feature['geometry'] = shapely.geometry.mapping(fixed)
fcArctic = fcArcticTags
fcArctic.merge(fcArcticNSIDCTags)
fcArctic.to_geojson('arctic_ocean_regions.geojson')
fcArctic.plot(projection='northpole')
# "split" these features into individual files in the geometric data cache
gf.split(fcArctic)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
plt.show()
def main():
author = 'Milena Veneziani'
# make a geometric features object that knows about the geometric data
# cache up a couple of directories
gf = GeometricFeatures(cacheLocation='../../geometric_data',
remoteBranchOrTag='master')
fc = FeatureCollection()
# *********** First, fix Atlantic_Basin regions in such a way that ********
# ********** they do not overlap each other (so that, we can combine
# ********* them together to form a Atlantic Basin region)
# ********* New Baltic Sea (modified feature) *********
# Combine old Baltic Sea feature with other small features
fcBalticSea = gf.read('ocean', 'region', ['Baltic Sea'])
fcFinland = gf.read('ocean', 'region', ['Gulf of Finland'])
fcBothnia = gf.read('ocean', 'region', ['Gulf of Bothnia'])
fcRiga = gf.read('ocean', 'region', ['Gulf of Riga'])
fcKattegat = gf.read('ocean', 'region', ['Kattegat'])
fcSkaggerak = gf.read('ocean', 'region', ['Skaggerak'])
fcBalticSea.merge(fcFinland)
fcBalticSea.merge(fcBothnia)
fcBalticSea.merge(fcRiga)
fcBalticSea.merge(fcKattegat)
fcBalticSea.merge(fcSkaggerak)
fcBalticSea = fcBalticSea.combine('Baltic Sea')
props = fcBalticSea.features[0]['properties']
props['tags'] = 'Baltic_Sea;Arctic;Atlantic_Basin'
props['author'] = author
fc = fcBalticSea
# ********* New North Atlantic Ocean (modified feature) *********
# Fix North Atlantic so that it does not overlap with new Labdrador
# Sea, Irminger Sea, North Sea, Greenland Sea, and Norwegian Sea
fcNorthAtlantic = gf.read('ocean', 'region', ['North Atlantic Ocean'])
fcLabSea = gf.read('ocean', 'region', ['Labrador Sea'])
fcIrmSea = gf.read('ocean', 'region', ['Irminger Sea'])
fcGS = gf.read('ocean', 'region', ['Greenland Sea'])
fcNS = gf.read('ocean', 'region', ['Norwegian Sea'])
fcNorthSea = gf.read('ocean', 'region', ['North Sea'])
fc_todiscard = fcLabSea
fc_todiscard.merge(fcIrmSea)
fc_todiscard.merge(fcGS)
fc_todiscard.merge(fcNS)
fc_todiscard.merge(fcNorthSea)
fc_todiscard = fc_todiscard.combine('Combined region to discard')
fcNorthAtlantic.merge(fc_todiscard)
fcNorthAtlantic = fcNorthAtlantic.combine('North Atlantic Ocean')
fcNorthAtlantic = fcNorthAtlantic.difference(fc_todiscard)
props = fcNorthAtlantic.features[0]['properties']
props['tags'] = 'North_Atlantic_Ocean;Atlantic_Basin'
props['author'] = author
fc.merge(fcNorthAtlantic)
# *********** Second, complete definition of oceanography-relevant *********
# ********** Arctic regions, started in part I, and identified with
# ********* tag='Arctic'
# ********* New Canadian Archipelago (modified feature) *********
# Modify old CAA by 1) including the shelf in the Arctic Ocean, and
# 2) including Nares Strait. Old CAA feature will be superseded by this.
fcContour500 = get_longest_contour(contourValue=-500., author=author)
fcContour1000 = get_longest_contour(contourValue=-1000., author=author)
fcCAA1 = make_rectangle(lon0=-130.,
lon1=-90.,
lat0=67.0,
lat1=86.0,
name='West Canadian Archipelago',
author=author,
tags='Canadian_Archipelago;Arctic;Atlantic_Basin')
fcCAA1 = fcCAA1.difference(fcContour500)
fcCAA2 = make_rectangle(lon0=-90.,
lon1=-70.,
lat0=67.0,
lat1=86.0,
name='Mid Canadian Archipelago',
author=author,
tags='Canadian_Archipelago;Arctic;Atlantic_Basin')
fcCAA2 = fcCAA2.difference(fcContour1000)
fcCAA3 = make_rectangle(lon0=-70.,
lon1=-50.5,
lat0=76.0,
lat1=86.0,
name='East Canadian Archipelago',
author=author,
tags='Canadian_Archipelago;Arctic;Atlantic_Basin')
fcCAA3 = fcCAA3.difference(fcContour500)
fcCAA = fcCAA1
fcCAA.merge(fcCAA2)
fcCAA.merge(fcCAA3)
fcCAA = fcCAA.combine('Canadian Archipelago')
fcHudson = gf.read('ocean', 'region', ['Hudson Bay'])
fcCAA = fcCAA.difference(fcHudson)
fcBaffin = gf.read('ocean', 'region', ['Baffin Bay'])
fcCAA = fcCAA.difference(fcBaffin)
props = fcCAA.features[0]['properties']
props['tags'] = 'Canadian_Archipelago;Arctic;Atlantic_Basin'
props['author'] = author
fc.merge(fcCAA)
# ********* Canada Basin (new feature) *********
# This is a slightly modified version of the Beaufort Gyre feature
# defined in part I. Differences include 1) a region that expands to
# the west to touch the northern boundary of the new CAA feature, and
# 2) a region that includes the Canada Basin shelf (whereas, for the
# Beuafort Gyre, we have separated the 'Gyre' from the 'Gyre Shelf').
fcContour300 = get_longest_contour(contourValue=-300., author=author)
fcCB1 = make_rectangle(lon0=-170.,
lon1=-156.65,
lat0=67.0,
lat1=80.0,
name='West Canada Basin',
author=author,
tags='Canada_Basin;Arctic;Arctic_Basin')
fcCB = fcCB1.difference(fcContour300)
fcCB = fcCB1.difference(fcCB)
fcCB2 = make_rectangle(lon0=-156.65,
lon1=-100.0,
lat0=67.0,
lat1=80.0,
name='East Canada Basin',
author=author,
tags='Canada_Basin;Arctic;Arctic_Basin')
fcCB2 = fcCB2.difference(fcCAA)
fcCB.merge(fcCB2)
fcCB = fcCB.combine('Canada Basin')
props = fcCB.features[0]['properties']
props['tags'] = 'Canada_Basin;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcCB)
# ********* Chukchi Sea (new feature) *********
# This supersedes the old Chukchi Sea feature
fcChukchi = make_rectangle(lon0=-180.,
lon1=-156.65,
lat0=65.0,
lat1=80.0,
name='Chukchi Sea',
author=author,
tags='Chukchi_Sea;Arctic;Arctic_Basin')
fcChukchi = fcChukchi.difference(fcContour300)
fcChukchi_NSIDC = gf.read('ocean', 'region', ['Chukchi Sea NSIDC'])
fcChukchi_todiscard = fcChukchi.difference(fcChukchi_NSIDC)
fcChukchi = fcChukchi.difference(fcChukchi_todiscard)
props = fcChukchi.features[0]['properties']
props['tags'] = 'Chukchi_Sea;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcChukchi)
# ********* East Siberian Sea (new feature) *********
# This supersedes the old East Siberian Sea feature
fcESS = make_rectangle(lon0=142.,
lon1=180.0,
lat0=68.5,
lat1=80.0,
name='East Siberian Sea',
author=author,
tags='East_Siberian_Sea;Arctic;Arctic_Basin')
fcESS = fcESS.difference(fcContour300)
props = fcESS.features[0]['properties']
props['tags'] = 'East_Siberian_Sea;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcESS)
# ********* Laptev Sea (new feature) *********
# This supersedes the old Laptev Sea feature
fcLap = make_rectangle(lon0=90.,
lon1=142.0,
lat0=70.0,
lat1=81.25,
name='Laptev Sea',
author=author,
tags='Laptev_Sea;Arctic;Arctic_Basin')
fcLap = fcLap.difference(fcContour300)
fcKara = gf.read('ocean', 'region', ['Kara Sea'])
fcLap = fcLap.difference(fcKara)
props = fcLap.features[0]['properties']
props['tags'] = 'Laptev_Sea;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcLap)
# ********* Central Arctic (new feature) *********
# Define Central Arctic region as Arctic Ocean minus Canadian
# Archipelago, Canada Basin, Chukchi Sea, ESS, and Laptev Sea
fcArctic = gf.read('ocean', 'region', ['Arctic Ocean'])
fcCentralArctic = fcArctic.difference(fcCAA)
fcCentralArctic = fcCentralArctic.difference(fcCB)
fcCentralArctic = fcCentralArctic.difference(fcChukchi)
fcCentralArctic = fcCentralArctic.difference(fcESS)
fcCentralArctic = fcCentralArctic.difference(fcLap)
props = fcCentralArctic.features[0]['properties']
props['name'] = 'Central Arctic'
props['tags'] = 'Central_Arctic;Arctic;Arctic_Basin'
props['author'] = author
fc.merge(fcCentralArctic)
# *********** Third, complete definition of seaice-relevant ***********
# ***** Arctic regions, started in part I, according to NSIDC
# ***** (regions map: https://nsidc.org/data/masie/browse_regions)
# **** and identified with tag='Arctic_NSIDC'
# ********* New Chukchi Sea NSIDC (modified feature) *********
# This supersedes the Chukchi Sea NSIDC feature defined in part I
fcChukchi_NSIDC = FeatureCollection()
fcChukchi_NSIDC.add_feature({
"type": "Feature",
"properties": {
"name": 'Chukchi Sea NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Chukchi_Sea_NSIDC;Arctic_NSIDC'
},
"geometry": {
"type":
"Polygon",
"coordinates": [[[-156.65, 65.37], [-180.0, 66.0], [-180.0, 80.0],
[-156.48, 80.0], [-156.65, 65.37]]]
}
})
fc.merge(fcChukchi_NSIDC)
# ********* Beaufort Sea NSIDC (new feature) *********
fcBS_NSIDC = FeatureCollection()
fcBS_NSIDC.add_feature({
"type": "Feature",
"properties": {
"name": 'Beaufort Sea NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Beaufort_Sea_NSIDC;Arctic_NSIDC'
},
"geometry": {
"type":
"Polygon",
"coordinates":
[[[-156.65, 65.37], [-156.48, 80.0], [-112.34, 77.69],
[-124.58, 75.67], [-124.0, 65.0], [-156.65, 65.37]]]
}
})
fc.merge(fcBS_NSIDC)
# ********* Canadian Archipelago NSIDC (new feature) *********
fcCAA_NSIDC = FeatureCollection()
fcCAA_NSIDC.add_feature({
"type": "Feature",
"properties": {
"name": 'Canadian Archipelago NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Canadian_Archipelago_NSIDC;Arctic_NSIDC'
},
"geometry": {
"type":
"Polygon",
"coordinates":
[[[-103.41, 60.69], [-124.0, 65.0], [-124.58, 75.67],
[-112.34, 77.69], [-69.33, 82.67], [-81.21, 71.79],
[-83.94, 70.43], [-84.45, 67.27], [-93.04, 65.70],
[-103.41, 60.69]]]
}
})
fc.merge(fcCAA_NSIDC)
# ********* Hudson Bay NSIDC (new feature) *********
fcHudson_NSIDC = FeatureCollection()
fcHudson_NSIDC.add_feature({
"type": "Feature",
"properties": {
"name": 'Hudson Bay NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Hudson_Bay_NSIDC;Arctic_NSIDC'
},
"geometry": {
"type":
"Polygon",
"coordinates": [[[-81.24, 49.19], [-103.41, 60.69],
[-93.04, 65.70], [-84.45, 67.27], [-83.94, 70.43],
[-81.21, 71.79], [-70.70, 66.95], [-70.12, 65.99],
[-63.70, 57.35], [-81.24, 49.19]]]
}
})
fc.merge(fcHudson_NSIDC)
# ********* Baffin Bay NSIDC (new feature) *********
fcBaffin_NSIDC = FeatureCollection()
fcBaffin_NSIDC.add_feature({
"type": "Feature",
"properties": {
"name": 'Baffin Bay NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Baffin_Bay_NSIDC;Arctic_NSIDC'
},
"geometry": {
"type":
"Polygon",
"coordinates": [[[-53.20, 42.0], [-68.07, 38.38], [-76.82, 48.01],
[-60.85, 54.33], [-63.70, 57.35], [-70.12, 65.99],
[-70.70, 66.95], [-81.21, 71.79], [-69.33, 82.67],
[-45.0, 60.0], [-45.0, 42.0], [-53.20, 42.0]]]
}
})
fc.merge(fcBaffin_NSIDC)
# ********* Central Arctic NSIDC (new feature) *********
fcCentralArctic_NSIDC = FeatureCollection()
fcCentralArctic_NSIDC.add_feature({
"type": "Feature",
"properties": {
"name": 'Central Arctic NSIDC',
"author": author,
"object": 'region',
"component": 'ocean',
"tags": 'Central_Arctic_NSIDC;Arctic_NSIDC'
},
"geometry": {
"type":
"Polygon",
"coordinates": [[[180.0, 80.0], [180.0, 90.0], [-69.33, 90.0],
[-180.0, 90.0], [-180.0, 80.0], [-156.48, 80.0],
[-112.34, 77.69], [-69.33, 82.67],
[-51.66, 74.25], [-12.72, 81.41], [18.99, 79.18],
[58.68, 81.08], [94.95, 81.08], [145.0, 80.0],
[180.0, 80.0]]]
}
})
fc.merge(fcCentralArctic_NSIDC)
# "split" these features into individual files in the geometric data cache
gf.split(fc)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
# Fix features if necessary
fcArcticTags = gf.read(componentName='ocean',
objectType='region',
tags=['Arctic'])
for feature in fcArcticTags.features:
featureName = feature['properties']['name']
shape = shapely.geometry.shape(feature['geometry'])
print('{} is_valid: {}'.format(featureName, shape.is_valid))
if not shape.is_valid:
fixed = shape.buffer(0)
print(' Fixed? {}'.format(fixed.is_valid))
feature['geometry'] = shapely.geometry.mapping(fixed)
fcArcticTags.plot(projection='northpole')
fcArcticTags.to_geojson('arctic_ocean_regions.geojson')
fcArcticNSIDCTags = gf.read(componentName='ocean',
objectType='region',
tags=['Arctic_NSIDC'])
for feature in fcArcticNSIDCTags.features:
featureName = feature['properties']['name']
shape = shapely.geometry.shape(feature['geometry'])
print('{} is_valid: {}'.format(featureName, shape.is_valid))
if not shape.is_valid:
fixed = shape.buffer(0)
print(' Fixed? {}'.format(fixed.is_valid))
feature['geometry'] = shapely.geometry.mapping(fixed)
fcArcticNSIDCTags.plot(projection='northpole')
fcArcticNSIDCTags.to_geojson('arcticNSIDC_ocean_regions.geojson')
fcArctic = fcArcticTags
fcArctic.merge(fcArcticNSIDCTags)
# "split" these features into individual files in the geometric data cache
gf.split(fcArctic)
# update the database of feature names and tags
write_feature_names_and_tags(gf.cacheLocation)
# move the resulting file into place
shutil.copyfile('features_and_tags.json',
'../../geometric_features/features_and_tags.json')
plt.show()
def _cull_mesh_with_logging(logger, with_cavities, with_critical_passages,
custom_critical_passages, custom_land_blockages,
preserve_floodplain, use_progress_bar,
process_count):
""" Cull the mesh once the logger is defined for sure """
critical_passages = with_critical_passages or \
(custom_critical_passages is not None)
land_blockages = with_critical_passages or \
(custom_land_blockages is not None)
gf = GeometricFeatures()
# start with the land coverage from Natural Earth
fcLandCoverage = gf.read(componentName='natural_earth',
objectType='region',
featureNames=['Land Coverage'])
# remove the region south of 60S so we can replace it based on ice-sheet
# topography
fcSouthMask = gf.read(componentName='ocean', objectType='region',
featureNames=['Global Ocean 90S to 60S'])
fcLandCoverage = fcLandCoverage.difference(fcSouthMask)
# Add "land" coverage from either the full ice sheet or just the grounded
# part
if with_cavities:
fcAntarcticLand = gf.read(
componentName='bedmachine', objectType='region',
featureNames=['AntarcticGroundedIceCoverage'])
else:
fcAntarcticLand = gf.read(
componentName='bedmachine', objectType='region',
featureNames=['AntarcticIceCoverage'])
fcLandCoverage.merge(fcAntarcticLand)
# save the feature collection to a geojson file
fcLandCoverage.to_geojson('land_coverage.geojson')
# these defaults may have been updated from config options -- pass them
# along to the subprocess
netcdf_format = mpas_tools.io.default_format
netcdf_engine = mpas_tools.io.default_engine
# Create the land mask based on the land coverage, i.e. coastline data
args = ['compute_mpas_region_masks',
'-m', 'base_mesh.nc',
'-g', 'land_coverage.geojson',
'-o', 'land_mask.nc',
'-t', 'cell',
'--process_count', '{}'.format(process_count),
'--format', netcdf_format,
'--engine', netcdf_engine]
check_call(args, logger=logger)
dsBaseMesh = xarray.open_dataset('base_mesh.nc')
dsLandMask = xarray.open_dataset('land_mask.nc')
dsLandMask = add_land_locked_cells_to_mask(dsLandMask, dsBaseMesh,
latitude_threshold=43.0,
nSweeps=20)
# create seed points for a flood fill of the ocean
# use all points in the ocean directory, on the assumption that they are,
# in fact, in the ocean
fcSeed = gf.read(componentName='ocean', objectType='point',
tags=['seed_point'])
if land_blockages:
if with_critical_passages:
# merge transects for critical land blockages into
# critical_land_blockages.geojson
fcCritBlockages = gf.read(
componentName='ocean', objectType='transect',
tags=['Critical_Land_Blockage'])
else:
fcCritBlockages = FeatureCollection()
if custom_land_blockages is not None:
fcCritBlockages.merge(read_feature_collection(
custom_land_blockages))
# create masks from the transects
fcCritBlockages.to_geojson('critical_blockages.geojson')
args = ['compute_mpas_transect_masks',
'-m', 'base_mesh.nc',
'-g', 'critical_blockages.geojson',
'-o', 'critical_blockages.nc',
'-t', 'cell',
'-s', '10e3',
'--process_count', '{}'.format(process_count),
'--format', netcdf_format,
'--engine', netcdf_engine]
check_call(args, logger=logger)
dsCritBlockMask = xarray.open_dataset('critical_blockages.nc')
dsLandMask = add_critical_land_blockages(dsLandMask, dsCritBlockMask)
fcCritPassages = FeatureCollection()
dsPreserve = []
if critical_passages:
if with_critical_passages:
# merge transects for critical passages into fcCritPassages
fcCritPassages.merge(gf.read(componentName='ocean',
objectType='transect',
tags=['Critical_Passage']))
if custom_critical_passages is not None:
fcCritPassages.merge(read_feature_collection(
custom_critical_passages))
# create masks from the transects
fcCritPassages.to_geojson('critical_passages.geojson')
args = ['compute_mpas_transect_masks',
'-m', 'base_mesh.nc',
'-g', 'critical_passages.geojson',
'-o', 'critical_passages.nc',
'-t', 'cell', 'edge',
'-s', '10e3',
'--process_count', '{}'.format(process_count),
'--format', netcdf_format,
'--engine', netcdf_engine]
check_call(args, logger=logger)
dsCritPassMask = xarray.open_dataset('critical_passages.nc')
# Alter critical passages to be at least two cells wide, to avoid sea
# ice blockage
dsCritPassMask = widen_transect_edge_masks(dsCritPassMask, dsBaseMesh,
latitude_threshold=43.0)
dsPreserve.append(dsCritPassMask)
if preserve_floodplain:
dsPreserve.append(dsBaseMesh)
# cull the mesh based on the land mask
dsCulledMesh = cull(dsBaseMesh, dsMask=dsLandMask,
dsPreserve=dsPreserve, logger=logger)
# create a mask for the flood fill seed points
dsSeedMask = compute_mpas_flood_fill_mask(dsMesh=dsCulledMesh,
fcSeed=fcSeed,
logger=logger)
# cull the mesh a second time using a flood fill from the seed points
dsCulledMesh = cull(dsCulledMesh, dsInverse=dsSeedMask,
graphInfoFileName='culled_graph.info', logger=logger)
write_netcdf(dsCulledMesh, 'culled_mesh.nc')
if critical_passages:
# make a new version of the critical passages mask on the culled mesh
fcCritPassages.to_geojson('critical_passages.geojson')
args = ['compute_mpas_transect_masks',
'-m', 'culled_mesh.nc',
'-g', 'critical_passages.geojson',
'-o', 'critical_passages_mask_final.nc',
'-t', 'cell',
'-s', '10e3',
'--process_count', '{}'.format(process_count),
'--format', netcdf_format,
'--engine', netcdf_engine]
check_call(args, logger=logger)
if with_cavities:
fcAntarcticIce = gf.read(
componentName='bedmachine', objectType='region',
featureNames=['AntarcticIceCoverage'])
fcAntarcticIce.to_geojson('ice_coverage.geojson')
args = ['compute_mpas_region_masks',
'-m', 'culled_mesh.nc',
'-g', 'ice_coverage.geojson',
'-o', 'ice_coverage.nc',
'-t', 'cell',
'--process_count', '{}'.format(process_count),
'--format', netcdf_format,
'--engine', netcdf_engine]
check_call(args, logger=logger)
dsMask = xarray.open_dataset('ice_coverage.nc')
landIceMask = dsMask.regionCellMasks.isel(nRegions=0)
dsLandIceMask = xarray.Dataset()
dsLandIceMask['landIceMask'] = landIceMask
write_netcdf(dsLandIceMask, 'land_ice_mask.nc')
dsLandIceCulledMesh = cull(dsCulledMesh, dsMask=dsMask, logger=logger)
write_netcdf(dsLandIceCulledMesh, 'no_ISC_culled_mesh.nc')
extract_vtk(ignore_time=True, dimension_list=['maxEdges='],
variable_list=['allOnCells'],
filename_pattern='culled_mesh.nc',
out_dir='culled_mesh_vtk',
use_progress_bar=use_progress_bar)
if with_cavities:
extract_vtk(ignore_time=True, dimension_list=['maxEdges='],
variable_list=['allOnCells'],
filename_pattern='no_ISC_culled_mesh.nc',
out_dir='no_ISC_culled_mesh_vtk',
use_progress_bar=use_progress_bar)