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merge "Seafloorgrid contmask" branch #103

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merged 2 commits into from
Jul 31, 2023
Merged

merge "Seafloorgrid contmask" branch #103

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8c74783
Update SeafloorGrid continent masking
lauren-ilano Jun 2, 2023
30c2bce
Automate continent mask res downsizing
lauren-ilano Jun 4, 2023
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240 changes: 174 additions & 66 deletions gplately/oceans.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,7 @@
from . import grids
from . import tools


# -------------------------------------------------------------------------
# Auxiliary functions for SeafloorGrid

Expand Down Expand Up @@ -381,6 +382,11 @@ class SeafloorGrid(object):
zval_names : list of str
A list containing string labels for the z values to attribute to points.
Will be used as column headers for z value point dataframes.
continent_mask_filename : str
An optional parameter pointing to the full path to a continental mask for each timestep.
Assuming the time is in the filename, i.e. "/path/to/continent_mask_0Ma.nc", it should be
passed as "/path/to/continent_mask_{}Ma.nc" with curly brackets. Include decimal formatting
if needed.
"""

def __init__(
Expand All @@ -400,6 +406,7 @@ def __init__(
initial_ocean_mean_spreading_rate = 75.,
resume_from_checkpoints = False,
zval_names = ("SPREADING_RATE",),
continent_mask_filename = None,
):

# Provides a rotation model, topology features and reconstruction time for
Expand Down Expand Up @@ -510,6 +517,41 @@ def __init__(
self.default_column_headers = ['CURRENT_LONGITUDES', 'CURRENT_LATITUDES', 'SEAFLOOR_AGE', 'BIRTH_LAT_SNAPSHOT', 'POINT_ID_SNAPSHOT']
self.total_column_headers = np.concatenate([self.default_column_headers, self.zval_names])

# Filename for continental masks that the user can provide instead of building it here
self.continent_mask_filename = continent_mask_filename

# If the user provides a continental mask filename, we need to downsize the mask
# resolution for when we create the initial ocean mesh. The mesh does not need to be high-res.
if self.continent_mask_filename is not None:

# Determine which percentage to use to scale the continent mask resolution at max time
def _map_res_to_node_percentage(
self,
continent_mask_filename
):
maskY, maskX = grids.read_netcdf_grid(
continent_mask_filename.format(
self._max_time
)
).shape

mask_deg = _pixels2deg(maskX, self.extent[0], self.extent[1])

if mask_deg <= 0.1:
percentage = 0.1
elif mask_deg <= 0.25:
percentage = 0.3
elif mask_deg <= 0.5:
percentage = 0.5
elif mask_deg < 0.75:
percentage = 0.6
elif mask_deg >= 1:
percentage = 0.75
return mask_deg, percentage

_, self.percentage = _map_res_to_node_percentage(self, self.continent_mask_filename)


# Allow SeafloorGrid time to be updated, and to update the internally-used
# PlotTopologies' time attribute too. If PlotTopologies is used outside the
# object, its `time` attribute is not updated.
Expand Down Expand Up @@ -617,43 +659,78 @@ def create_initial_ocean_seed_points(self):
A feature collection of point objects on the ocean basin.
"""

# Ensure COB terranes at max time have reconstruction IDs and valid times
COB_polygons = ensure_polygon_geometry(
self._PlotTopologies_object.continents,
self.rotation_model,
self._max_time)

# zval is a binary array encoding whether a point
# coordinate is within a COB terrane polygon or not.
# Use the icosahedral mesh MultiPointOnSphere attribute
_, ocean_basin_point_mesh, zvals = point_in_polygon_routine(
self.icosahedral_multi_point,
COB_polygons
)

# Plates to partition with
plate_partitioner = pygplates.PlatePartitioner(
COB_polygons,
self.rotation_model,
)
if self.continent_mask_filename is None:
# Ensure COB terranes at max time have reconstruction IDs and valid times
COB_polygons = ensure_polygon_geometry(
self._PlotTopologies_object.continents,
self.rotation_model,
self._max_time)

# zval is a binary array encoding whether a point
# coordinate is within a COB terrane polygon or not.
# Use the icosahedral mesh MultiPointOnSphere attribute
_, ocean_basin_point_mesh, zvals = point_in_polygon_routine(
self.icosahedral_multi_point,
COB_polygons
)

# Plates to partition with
plate_partitioner = pygplates.PlatePartitioner(
COB_polygons,
self.rotation_model,
)

# Plate partition the ocean basin points
meshnode_feature = pygplates.Feature(
pygplates.FeatureType.create_from_qualified_string('gpml:MeshNode')
)
meshnode_feature.set_geometry(
ocean_basin_point_mesh
#multi_point
)
ocean_basin_meshnode = pygplates.FeatureCollection(meshnode_feature)
# Plate partition the ocean basin points
meshnode_feature = pygplates.Feature(
pygplates.FeatureType.create_from_qualified_string('gpml:MeshNode')
)
meshnode_feature.set_geometry(
ocean_basin_point_mesh
#multi_point
)
ocean_basin_meshnode = pygplates.FeatureCollection(meshnode_feature)

paleogeography = plate_partitioner.partition_features(
ocean_basin_meshnode, partition_return = pygplates.PartitionReturn.separate_partitioned_and_unpartitioned,
properties_to_copy=[pygplates.PropertyName.gpml_shapefile_attributes]
)
ocean_points = paleogeography[1] # Separate those inside polygons
continent_points = paleogeography[0] # Separate those outside polygons
paleogeography = plate_partitioner.partition_features(
ocean_basin_meshnode, partition_return = pygplates.PartitionReturn.separate_partitioned_and_unpartitioned,
properties_to_copy=[pygplates.PropertyName.gpml_shapefile_attributes]
)
ocean_points = paleogeography[1] # Separate those inside polygons
continent_points = paleogeography[0] # Separate those outside polygons

# If a set of continent masks was passed, we can use max_time's continental
# mask to build the initial profile of seafloor age.
else:
max_time_cont_mask = grids.Raster(
self.continent_mask_filename.format(self._max_time)
)
# If the input grid is at 0.5 degree uniform spacing, then the input
# grid is 7x more populated than a 6-level stripy icosahedral mesh and
# using this resolution for the initial ocean mesh will dramatically slow down
# reconstruction by topologies.
# Scale down the resolution based on the input mask resolution
# (percentage was found in __init__.)
max_time_cont_mask.resize(
int(max_time_cont_mask.shape[0]*self.percentage),
int(max_time_cont_mask.shape[1]*self.percentage),
inplace=True
)

lat = np.linspace(-90,90, max_time_cont_mask.shape[0])
lon = np.linspace(-180,180,max_time_cont_mask.shape[1])

llon, llat = np.meshgrid(lon, lat)

mask_inds = np.where(max_time_cont_mask.data.flatten() == 0)
mask_vals = max_time_cont_mask.data.flatten()
mask_lon = llon.flatten()[mask_inds]
mask_lat = llat.flatten()[mask_inds]

ocean_pt_feature = pygplates.Feature()
ocean_pt_feature.set_geometry(pygplates.MultiPointOnSphere(zip(mask_lat,mask_lon)))
ocean_points = [ocean_pt_feature]


# Now that we have ocean points...
# Determine age of ocean basin points using their proximity to MOR features
# and an assumed globally-uniform ocean basin mean spreading rate.
# We need resolved topologies at the `max_time` to pass into the proximity
Expand Down Expand Up @@ -1074,7 +1151,11 @@ def prepare_for_reconstruction_by_topologies(self):
# - seeding was completed but the subsequent gridding input creation was interrupted,
# seeding is assumed completed and skipped. The workflow automatically proceeds to re-gridding.

self.build_all_continental_masks()
if self.continent_mask_filename is None:
self.build_all_continental_masks()
else:
print("Continent masks passed to SeafloorGrid - skipping continental mask generation!")

self.build_all_MOR_seedpoints()

# ALL-TIME POINTS -----------------------------------------------------
Expand Down Expand Up @@ -1174,18 +1255,31 @@ def reconstruct_by_topologies(self):
]
)
# In addition to the default subduction detection, also detect continental collisions
if self.file_collection is not None:
# Use the input continent mask if it is provided.
if self.continent_mask_filename is not None:
collision_spec = reconstruction._ContinentCollision(
self.save_directory+"/"+self.file_collection+"_continent_mask_{}Ma.nc",

# This filename string should not have a time formatted into it - this is
# taken care of later.
self.continent_mask_filename,
default_collision,
verbose=False,
)
else:
collision_spec = reconstruction._ContinentCollision(
self.save_directory+"/continent_mask_{}Ma.nc",
default_collision,
verbose=False,
)
# If a continent mask is not provided, use the ones made.
if self.file_collection is not None:

collision_spec = reconstruction._ContinentCollision(
self.save_directory+"/"+self.file_collection+"_continent_mask_{}Ma.nc",
default_collision,
verbose=False,
)
else:
collision_spec = reconstruction._ContinentCollision(
self.save_directory+"/continent_mask_{}Ma.nc",
default_collision,
verbose=False,
)

# Call the reconstruct by topologies object
topology_reconstruction = reconstruction._ReconstructByTopologies(
Expand Down Expand Up @@ -1361,6 +1455,7 @@ def lat_lon_z_to_netCDF(
resX=self.spacingX,
resY=self.spacingY,
unmasked=unmasked,
continent_mask_filename=self.continent_mask_filename
)
else:
from joblib import delayed
Expand All @@ -1376,6 +1471,7 @@ def lat_lon_z_to_netCDF(
resX=self.spacingX,
resY=self.spacingY,
unmasked=unmasked,
continent_mask_filename=self.continent_mask_filename
)
for time in time_arr
)
Expand All @@ -1391,6 +1487,7 @@ def _lat_lon_z_to_netCDF_time(
resX,
resY,
unmasked=False,
continent_mask_filename=None
):
# Read the gridding input made by ReconstructByTopologies:
if file_collection is not None:
Expand Down Expand Up @@ -1429,41 +1526,46 @@ def _lat_lon_z_to_netCDF_time(
Z = griddata((lons, lats), zdata, (X, Y), method='nearest')

# Access continental grids from the save directory
if save_directory is not None:
if file_collection is not None:
if file_collection is not None:
if continent_mask_filename is not None:
full_directory=continent_mask_filename.format(time)
else:
full_directory = "{}/{}_continent_mask_{}Ma.nc".format(
save_directory,
file_collection,
time
)
grid_output_unmasked = "{}/{}_{}_grid_unmasked_{}Ma.nc".format(
save_directory,
file_collection,
str(zval_name),
time
)
grid_output_dir = "{}/{}_{}_grid_{}Ma.nc".format(
save_directory,
file_collection,
str(zval_name),
time
)
grid_output_unmasked = "{}/{}_{}_grid_unmasked_{}Ma.nc".format(
save_directory,
file_collection,
str(zval_name),
time
)
grid_output_dir = "{}/{}_{}_grid_{}Ma.nc".format(
save_directory,
file_collection,
str(zval_name),
time
)
else:
if continent_mask_filename is not None:
full_directory=continent_mask_filename.format(time)
else:
full_directory = "{}/{}_continent_mask_{}Ma.nc".format(
save_directory,
zval_name,
time
)
grid_output_unmasked = "{}/{}_grid_unmasked_{}Ma.nc".format(
save_directory,
zval_name,
time
)
grid_output_dir = "{}/{}_grid_{}Ma.nc".format(
save_directory,
zval_name,
time
)
grid_output_unmasked = "{}/{}_grid_unmasked_{}Ma.nc".format(
save_directory,
zval_name,
time
)
grid_output_dir = "{}/{}_grid_{}Ma.nc".format(
save_directory,
zval_name,
time
)

if unmasked:
grids.write_netcdf_grid(
Expand All @@ -1475,6 +1577,12 @@ def _lat_lon_z_to_netCDF_time(
# Identify regions in the grid in the continental mask
cont_mask = grids.Raster(data=str(full_directory))

# We need the continental mask to match the number of nodes
# in the uniform grid defined above. This is important if we
# pass our own continental mask to SeafloorGrid
if cont_mask.shape[1] != resX:
cont_mask.resize(resX, resY, inplace=True)

# Use the continental mask
Z = np.ma.array(
grids.Raster(data=Z).data.data,
Expand Down
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