def load_paleogeography(pg_dir,
env_list=None,
single_file=False,
env_field='ENV'):
# default environment_list is the format used for Cao++ 2017
if env_list is None:
env_list = ['lm', 'm', 'sm', 'i']
if single_file:
print pg_dir
features = pygplates.FeatureCollection(pg_dir)
pg_features = []
for feature in features:
if feature.get_shapefile_attribute(env_field) in env_list:
feature.set_shapefile_attribute(
'Layer', feature.get_shapefile_attribute(env_field))
pg_features.append(feature)
else:
pg_features = []
for env in env_list:
try:
filename = glob.glob('%s/%s_*.shp' % (pg_dir, env))
print filename
features = pygplates.FeatureCollection(filename[0])
for feature in features:
feature.set_shapefile_attribute('Layer', env)
pg_features.append(feature)
except:
print 'no features of type %s' % env
return pg_features
def get_change_mask_multipoints(pg_features,t1,t2,psl_t1,psl_t2,
points,spatial_tree_of_uniform_recon_points,
rotation_model,plot=False):
print 'Working on interpolation from %0.2f Ma to %0.2f Ma .....' % (t1,t2)
plate_partitioner = pygplates.PlatePartitioner(pg_features, rotation_model, reconstruction_time=t1)
(distance_to_land_t1,
distance_to_psl_t1,
distance_to_land_t2,
distance_to_psl_t2,
regression_msk,
transgression_msk,
always_land_msk) = get_change_masks(t1,points,spatial_tree_of_uniform_recon_points,
psl_t1,psl_t2,rotation_model)
coords = zip(*[point.to_lat_lon() for point in points])
pg_points_regression = get_masked_multipoint(coords,regression_msk,plate_partitioner,
valid_time=[t2,t1+0.01])
pg_points_transgression = get_masked_multipoint(coords,transgression_msk,plate_partitioner,
valid_time=[t2,t1+0.01])
pg_points_always_land = get_masked_multipoint(coords,always_land_msk,plate_partitioner,
valid_time=[t2,t1])
pygplates.FeatureCollection(pg_points_regression).write('./tween_feature_collections/mountain_regression_%0.2fMa_%0.2fMa.gpmlz' % (t1,t2))
pygplates.FeatureCollection(pg_points_transgression).write('./tween_feature_collections/mountain_transgression_%0.2fMa_%0.2fMa.gpmlz' % (t1,t2))
pygplates.FeatureCollection(pg_points_always_land).write('./tween_feature_collections/mountain_stable_%0.2fMa_%0.2fMa.gpmlz' % (t1,t2))
def merge_features(young_time, old_time, time_step, outdir, cleanup=False):
# merge the seed points from the 'initial condition' and generated through
# the reconstructed mid-ocean ridges through time into a single file
# TODO
# - why not use gpmlz NO DON'T USE GPML, SERIOUSLY
# - filenames should not be hard-coded
merge_features = []
for time in np.arange(old_time, young_time - time_step, -time_step):
filename = './{:s}/MOR_plus_one_points_{:0.2f}.gmt'.format(
outdir, time)
print('merging seeds from file {:s}'.format(filename))
features = pygplates.FeatureCollection(filename)
for feature in features:
merge_features.append(feature)
merge_filename = './{:s}/MOR_plus_one_merge_{:0.2f}_{:0.2f}.gmt'.format(
outdir, young_time, old_time)
print('Attempting to write merged file {:s}'.format(merge_filename))
pygplates.FeatureCollection(merge_features).write(merge_filename)
if cleanup:
# remove old files that are no longer needed
for f in glob.glob("{:s}/MOR_plus_one_points_*.gmt".format(outdir)):
os.remove(f)
for f in glob.glob(
"{:s}/MOR_plus_one_points_*.gmt.gplates.xml".format(outdir)):
os.remove(f)
def generate_rotation_feature(rotation_filenames):
rotation_features = pygplates.FeatureCollection()
for rotation_filename in rotation_filenames:
rotation_features.add(pygplates.FeatureCollection(rotation_filename))
return rotation_features
def test_post_files(request):
if not request.method == "POST":
return HttpResponseBadRequest('expecting post requests!')
else:
with open('%s/tmp.gpmlz' % settings.MEDIA_ROOT, 'wb+') as destination:
for chunk in request.FILES['file1'].chunks():
destination.write(chunk)
with open('%s/tmp.rot' % settings.MEDIA_ROOT, 'wb+') as destination:
for chunk in request.FILES['file2'].chunks():
destination.write(chunk)
filename = 'reconstruct_to_birth_time.gpmlz'
rotation_model = pygplates.RotationModel('%s/tmp.rot' %
settings.MEDIA_ROOT)
features = pygplates.FeatureCollection('%s/tmp.gpmlz' %
settings.MEDIA_ROOT)
reconstructed_features = reconstruct_to_birth_time(
features, rotation_model)
tmp = pygplates.FeatureCollection(reconstructed_features)
tmp.write('%s/%s' % (settings.MEDIA_ROOT, filename))
f = StringIO(
file('%s/%s' % (settings.MEDIA_ROOT, filename), "rb").read())
response = HttpResponse(f, content_type='application/gpmlz')
response['Content-Disposition'] = 'attachment; filename=%s' % filename
return response
def get_topological_boundaries(request):
"""
http GET request to retrieve reconstructed topological plate polygons
**usage**
<http-address-to-gws>/topology/plate_boundaries/time=\ *reconstruction_time*\&model=\ *reconstruction_model*
**parameters:**
*time* : time for reconstruction [default=0]
*model* : name for reconstruction model [defaults to default model from web service settings]
**returns:**
json containing reconstructed plate boundary features
"""
time = request.GET.get('time', 0)
model = request.GET.get('model', settings.MODEL_DEFAULT)
model_dict = get_reconstruction_model_dict(model)
features = []
rotation_model = pygplates.RotationModel([
str('%s/%s/%s' % (settings.MODEL_STORE_DIR, model, rot_file))
for rot_file in model_dict['RotationFile']
])
# need to handle cases where topologies are in one file, and where they are spread across
# multiple files
topology_features = pygplates.FeatureCollection()
if type(model_dict['PlatePolygons']) is list:
for file in model_dict['PlatePolygons']:
fullfile = str('%s/%s/%s' %
(settings.MODEL_STORE_DIR, model, file))
topology_feature = pygplates.FeatureCollection(fullfile)
topology_features.add(topology_feature)
else:
topology_features = pygplates.FeatureCollection(
str('%s/%s/%s' % (settings.MODEL_STORE_DIR, model,
model_dict['PlatePolygons'])))
resolved_polygons = []
shared_boundary_sections = []
pygplates.resolve_topologies(topology_features, rotation_model,
resolved_polygons, float(time),
shared_boundary_sections)
data = wrap_plate_boundaries(shared_boundary_sections, 0.)
print('here')
ret = json.dumps(pretty_floats(data))
response = HttpResponse(ret, content_type='application/json')
#TODO:
response['Access-Control-Allow-Origin'] = '*'
return response
def write_trees_to_file(input_features, rotation_model, filename,
reconstruction_time_range, time_step=1,
polygon_type='static', root_feature_filename=None):
reconstruction_times = np.arange(reconstruction_time_range[0], reconstruction_time_range[1]+time_step, time_step)
tree_features = None
root_centroid_features = []
for reconstruction_time in reconstruction_times:
print 'working on time %0.2f Ma' % reconstruction_time
reconstructed_polygons = []
if polygon_type is 'topological':
pygplates.resolve_topologies(input_features, rotation_model, reconstructed_polygons, reconstruction_time)
else:
pygplates.reconstruct(input_features, rotation_model, reconstructed_polygons, reconstruction_time)
uniq_plates_from_polygons = get_unique_plate_ids_from_reconstructed_features(reconstructed_polygons)
reconstruction_tree = rotation_model.get_reconstruction_tree(reconstruction_time)
chains = get_plate_chains(uniq_plates_from_polygons, reconstruction_tree)
tree_features = create_hierarchy_features(chains, reconstructed_polygons, tree_features,
valid_time=(reconstruction_time+time_step/2.,
reconstruction_time-time_step/2.))
if root_feature_filename is not None:
polygon_centroids = get_polygon_centroids(reconstructed_polygons)
root_plates = get_root_static_polygon_plate_ids(reconstruction_tree, uniq_plates_from_polygons)
for root_plate in root_plates:
p0 = polygon_centroids[root_plate]
feature = pygplates.Feature()
feature.set_geometry(pygplates.PointOnSphere(p0))
feature.set_name(str(root_plate))
feature.set_valid_time(reconstruction_time+time_step/2.,
reconstruction_time-time_step/2.)
root_centroid_features.append(feature)
tree_feature_collection = pygplates.FeatureCollection(tree_features)
tree_feature_collection.write(filename)
if root_feature_filename is not None:
tree_feature_collection = pygplates.FeatureCollection(root_centroid_features)
tree_feature_collection.write(root_feature_filename)
def get_deposit_candidates():
polygon_points = get_region_of_interest_polygon().values.flatten()
mesh_points = get_mesh_points(polygon_points)
#let's find plate id for the mesh points
static_polygons = pygplates.FeatureCollection(
parameters['static_polygons_file'])
rotation_model = pygplates.RotationModel(
get_files(parameters['rotation_files']))
mesh_plate_ids = get_plate_id(mesh_points.lon.tolist(),
mesh_points.lat.tolist(), static_polygons,
rotation_model)
mesh_points['plate_id'] = mesh_plate_ids
deposit_candidates = []
start_time = parameters["time"]["start"]
end_time = parameters["time"]["end"]
time_step = parameters["time"]["step"]
for t in range(start_time, end_time + 1, time_step):
for index, p in mesh_points.iterrows():
deposit_candidates.append([p['lon'], p['lat'], t, p['plate_id']])
deposit_candidates = pd.DataFrame(
deposit_candidates, columns=['lon', 'lat', 'age', 'plate_id'])
deposit_candidates = deposit_candidates.astype({
"plate_id": int,
"age": int
})
return deposit_candidates
def rotate_to_common_reference(vgps, reconstruction_model, reference_plate_id=701):
'''
Rotate a collection of vgps to a common reference plate
'''
if isinstance(vgps, _gpd.GeoDataFrame):
rotated_vgps = []
for i,row in vgps.iterrows():
vgp_geometry = pygplates.PointOnSphere(row.PoleLatitude,row.PoleLongitude)
feature_rotation = reconstruction_model.rotation_model.get_rotation(row.AverageAge,
row.PlateID,
anchor_plate_id=reference_plate_id)
reconstructed_geometry = feature_rotation * vgp_geometry
rotated_vgps.append(reconstructed_geometry.to_lat_lon())
vgps.PoleLatitude = list(zip(*rotated_vgps))[0]
vgps.PoleLongitude = list(zip(*rotated_vgps))[1]
return vgps
elif isinstance(vgps, pygplates.FeatureCollection):
rotated_vgps = []
for vgp in vgps:
feature_rotation = reconstruction_model.rotation_model.get_rotation(vgp.get(pygplates.PropertyName.gpml_average_age).get_value().get_double(),
vgp.get_reconstruction_plate_id(),
anchor_plate_id=reference_plate_id)
reconstructed_geometry = feature_rotation * vgp.get_geometry()
vgp.set_geometry(reconstructed_geometry)
vgp.set_reconstructed_plate_id(reference_plate_id)
rotated_vgps.append(vgp)
return pygplates.FeatureCollection(rotated_vgps)
def create_gpml_velocity_feature(longitude_array,
latitude_array,
filename=None,
feature_type=None):
# function to make a velocity mesh nodes at an arbitrary set of points defined in Lat
# Long and Lat are assumed to be 1d arrays.
multi_point = pygplates.MultiPointOnSphere(
zip(latitude_array, longitude_array))
# Create a feature containing the multipoint feature.
# optionally, define as 'MeshNode' type, so that GPlates will recognise it as a velocity layer
if feature_type == 'MeshNode':
meshnode_feature = pygplates.Feature(
pygplates.FeatureType.create_from_qualified_string(
'gpml:MeshNode'))
meshnode_feature.set_name('Velocity Mesh Nodes')
else:
meshnode_feature = pygplates.Feature()
meshnode_feature.set_name('Multipoint Feature')
meshnode_feature.set_geometry(multi_point)
output_feature_collection = pygplates.FeatureCollection(meshnode_feature)
if filename is not None:
output_feature_collection.write(filename)
else:
return output_feature_collection
def __make_GPML_velocity_feature(self, coords):
""" function to make a velocity mesh nodes at an arbitrary set of points defined in
coords[# of points, 3] = x, y, z"""
# Add points to a multipoint geometry
multi_point = pygplates.MultiPointOnSphere([
pygplates.PointOnSphere(x=coords[i, 0],
y=coords[i, 1],
z=coords[i, 2],
normalise=True)
for i in range(numpy.shape(coords)[0])
])
# Create a feature containing the multipoint feature, and defined as MeshNode type
meshnode_feature = pygplates.Feature(
pygplates.FeatureType.create_from_qualified_string(
'gpml:MeshNode'))
meshnode_feature.set_geometry(multi_point)
meshnode_feature.set_name('Velocity Mesh Nodes from pygplates')
output_feature_collection = pygplates.FeatureCollection(
meshnode_feature)
# NB: at this point, the feature could be written to a file using
# output_feature_collection.write('myfilename.gpmlz')
# for use within the notebook, the velocity domain feature is returned from the function
return output_feature_collection
def get_velocity_x_y_u_v(time, rotation_model, topology_filenames):
delta_time = 5.
Xnodes = np.arange(-180, 180, 10)
Ynodes = np.arange(-90, 90, 10)
Xg, Yg = np.meshgrid(Xnodes, Ynodes)
Xg = Xg.flatten()
Yg = Yg.flatten()
velocity_domain_features = make_GPML_velocity_feature(Xg, Yg)
# Load the topological plate polygon features.
topology_features = []
for fname in topology_filenames:
for f in pygplates.FeatureCollection(fname):
topology_features.append(f)
# Call the function we created above to get the velocities
all_velocities = Get_Plate_Velocities(velocity_domain_features,
topology_features, rotation_model,
time, delta_time, 'vector_comp')
uu = []
vv = []
for vel in all_velocities:
if not hasattr(vel, 'get_y'):
uu.append(vel[1])
vv.append(vel[0])
else:
uu.append(vel.get_y())
vv.append(vel.get_x())
u = np.asarray([uu]).reshape((Ynodes.shape[0], Xnodes.shape[0]))
v = np.asarray([vv]).reshape((Ynodes.shape[0], Xnodes.shape[0]))
return Xnodes, Ynodes, u, v
def paleolithology(request):
anchor_plate_id = request.GET.get('pid', 0)
time = request.GET.get('time', 0)
model = request.GET.get('model', settings.MODEL_DEFAULT)
model_dict = get_reconstruction_model_dict(model)
rotation_model = pygplates.RotationModel([
str('%s/%s/%s' % (settings.MODEL_STORE_DIR, model, rot_file))
for rot_file in model_dict['RotationFile']
])
paleolithology_datafile = '%s/boucot_paleolithology_combined.shp' % settings.PALEO_STORE_DIR
static_polygons_filename = str(
'%s/%s/%s' %
(settings.MODEL_STORE_DIR, model, model_dict['StaticPolygons']))
#select points based on age before doing plate id assignment - should be quicker??
paleolithology_points = pygplates.FeatureCollection(
paleolithology_datafile)
valid_points = []
for point in paleolithology_points:
if point.get_valid_time()[0] > float(
time) and point.get_valid_time()[1] <= float(time):
valid_points.append(point)
print(valid_points)
assigned_features = pygplates.partition_into_plates(
static_polygons_filename,
rotation_model,
valid_points,
properties_to_copy=[
pygplates.PartitionProperty.reconstruction_plate_id
],
partition_method=pygplates.PartitionMethod.most_overlapping_plate)
reconstructed_paleolithology_points = []
pygplates.reconstruct(assigned_features,
rotation_model,
reconstructed_paleolithology_points,
float(time),
anchor_plate_id=anchor_plate_id)
ret = write_json_reconstructed_point_features(
reconstructed_paleolithology_points,
attributes=[('LithCode', 'string'), ('Period', 'string')])
#add header for CORS
#http://www.html5rocks.com/en/tutorials/cors/
response = HttpResponse(ret, content_type='application/json')
#TODO:
#The "*" makes the service wide open to anyone. We should implement access control when time comes.
response['Access-Control-Allow-Origin'] = '*'
return response
def GenerateReconstructedDeltasXYZ(rotation_model, raster_times,
raster_filenames,
multipoint_feature_collection,
output_file_stem, force_plate_frame):
for reconstruction_time_index in range(0, len(raster_times[:-1])):
reconstruction_time1 = raster_times[reconstruction_time_index]
reconstruction_time2 = raster_times[reconstruction_time_index + 1]
reconstruction_time_mid = 0.5 * (reconstruction_time1 +
reconstruction_time2)
print('time: %f Ma' % reconstruction_time_mid)
# Exclude any multipoint features that do not exist at either reconstruction time.
filtered_multipoint_feature_collection = pygplates.FeatureCollection()
have_filtered_multipoints = False
for multipoint_feature in multipoint_feature_collection:
multipoint_valid_time = multipoint_feature.get_valid_time(None)
if not multipoint_valid_time:
continue
multipoint_begin_time, multipoint_end_time = multipoint_valid_time
if reconstruction_time1 > multipoint_begin_time or reconstruction_time1 < multipoint_end_time:
continue
if reconstruction_time2 > multipoint_begin_time or reconstruction_time2 < multipoint_end_time:
continue
filtered_multipoint_feature_collection.add(multipoint_feature)
have_filtered_multipoints = True
if not have_filtered_multipoints:
print(
'Skipping mid-time %0.2f since multipoint feature does not exist'
% reconstruction_time_mid)
continue
#InputGridFile1 = GridDir+'gld9NLt-%d.topo_0.5d_corr.0.grd' % reconstruction_time1
InputGridFile1 = raster_filenames[reconstruction_time_index]
#InputGridFile2 = GridDir+'gld9NLt-%d.topo_0.5d_corr.0.grd' % reconstruction_time2
InputGridFile2 = raster_filenames[reconstruction_time_index + 1]
GenerateReconstructedDeltaXYZ(rotation_model, reconstruction_time1,
reconstruction_time2,
filtered_multipoint_feature_collection,
InputGridFile1, InputGridFile2,
force_plate_frame)
if force_plate_frame:
#cmd = "gmt nearneighbor output -G%sPlateFrameDelta%0.2f.nc -Rd -I0.5d -N1 -S0.75d -V" % (
# output_file_stem, reconstruction_time_mid)
cmd = "gmt xyz2grd output -G%sPlateFrameDelta%0.2f.nc -Rd -I1d -V" % (
output_file_stem, reconstruction_time_mid)
else:
#cmd = "gmt nearneighbor output -G%sReconstructedDelta%0.2f.nc -Rd -I0.5d -N1 -S0.75d -V" % (
# output_file_stem, reconstruction_time_mid)
cmd = "gmt xyz2grd output -G%sReconstructedDelta%0.2f.nc -Rd -I1d -V" % (
output_file_stem, reconstruction_time_mid)
os.system(cmd)
def gpml_to_dataframe(feature_collection, as_geodataframe=True):
'''
function to read in any gplates-compatible feature collection and
place it into a pandas dataframe
# TODO handle polylines and polygons
'''
if os.path.isfile(feature_collection):
feature_collection = pygplates.FeatureCollection(feature_collection)
elif isinstance(feature_collection, pygplates.FeatureCollection):
pass
else:
raise ValueError(
'Unable to load {:s} as vgp input'.format(feature_collection))
DataFrameTemplate = [
'Longitude', 'Latitude', 'Name', 'Description', 'MaximumAge',
'MinimumAge', 'PlateID'
]
# Get attribute (other than coordinate) names from first feature
for feature in feature_collection:
for attribute in feature.get_shapefile_attributes():
DataFrameTemplate.append(attribute)
break
fs = []
for feature in feature_collection:
f = []
f.append(feature.get_geometry().to_lat_lon()[1])
f.append(feature.get_geometry().to_lat_lon()[0])
f.append(str(feature.get_name()))
f.append(str(feature.get_description()))
geom = feature.get_geometry().to_lat_lon()
f.append(float(geom[1]))
f.append(float(geom[0]))
feature_valid_time = feature.get_valid_time()
f.append(float(feature_valid_time[0]))
f.append(float(feature_valid_time[1]))
f.append(int(feature.get_reconstruction_plate_id()))
f.append(str(feature.get_feature_type()))
f.append(str(feature.get_feature_id()))
for attribute in feature.get_shapefile_attributes():
f.append(feature.get_shapefile_attribute(attribute))
fs.append(f)
if as_geodataframe:
df = _pd.DataFrame(fs, columns=DataFrameTemplate)
return _gpd.GeoDataFrame(df,
geometry=_gpd.points_from_xy(
df.AverageSampleSiteLongitude,
df.AverageSampleSiteLatitude),
crs=4326)
else:
return _pd.DataFrame(fs, columns=DataFrameTemplate)
def merge_polygons(polygons,rotation_model,
time=0,sampling=1.,area_threshold=None,filename=None,
return_raster=False):
multipoints = create_gpml_regular_long_lat_mesh(sampling)
grid_dims = (int(180/sampling)+1,int(360/sampling)+1)
for multipoint in multipoints:
for mp in multipoint.get_all_geometries():
points = mp.to_lat_lon_point_list()
bi = run_grid_pip(time,points,polygons,rotation_model,grid_dims)
if return_raster:
return bi
else:
# To handle edge effects, pad grid before making contour polygons
## --- start
pad_hor = np.zeros((1,bi.shape[1]))
pad_ver = np.zeros((bi.shape[0]+2,1))
pad1 = np.vstack((pad_hor,bi,pad_hor)) # add row of zeros to top and bottom
pad2 = np.hstack((pad_ver,pad1,pad_ver)) # add row of zeros to left and right
#pad3 = np.hstack((pad2,pad_ver))
contours = measure.find_contours(pad2, 0.5, fully_connected='low')
## --- end
contour_polygons = []
contour_features = []
for n,cp in enumerate(contours):
# To handle edge effects again - strip off parts of polygon
# due to padding, and adjust from image coordinates to long/lat
# --- start
cp[:,1] = (cp[:,1]*sampling)-sampling
cp[:,0] = (cp[:,0]*sampling)-sampling
cp[np.where(cp[:,0]<0.),0] = 0
cp[np.where(cp[:,0]>180.),0] = 180
cp[np.where(cp[:,1]<0.),1] = 0
cp[np.where(cp[:,1]>360.),1] = 360
## --- end
cpf = pygplates.PolygonOnSphere(zip(cp[:,0]-90,cp[:,1]-180))
contour_polygons.append(cpf)
feature = pygplates.Feature()
feature.set_geometry(cpf)
contour_features.append(feature)
if filename is not None:
pygplates.FeatureCollection(contour_features).write(filename)
else:
return contour_features
def get_merged_cob_terrane_raster(COBterrane_file, rotation_model, reconstruction_time,
sampling):
polygon_features = pygplates.FeatureCollection(COBterrane_file)
cobter = force_polygon_geometries(polygon_features)
mask = merge_polygons(cobter, rotation_model, time=reconstruction_time,
sampling=sampling, return_raster=True)
return mask
def gpml2gdf(features):
"""
Given a gplates feature collection, or a list of features, or a list
of reconstructed features, returns a geopandas geodataframe containing
the same features
"""
if isinstance(features, pygplates.FeatureCollection):
pass
elif isinstance(features, list):
if isinstance(features[0], pygplates.Feature):
features = pygplates.FeatureCollection(features)
elif isinstance(features[0], pygplates.ReconstructedFeatureGeometry):
features = _reconstructed_features_to_features(features)
features = pygplates.FeatureCollection(features)
elif isinstance(features[0], pygplates.ResolvedTopologicalBoundary):
features = [
resolved_topology.get_resolved_feature()
for resolved_topology in features
]
features = pygplates.FeatureCollection(features)
else:
raise TypeError(
'Unexpected list item of type {:s} for gpml2gdf input'.format(
type(features[0])))
else:
raise TypeError('Unexpected type {:s} for gpml2gdf input'.format(
type(features)))
temporary_file = tempfile.NamedTemporaryFile(delete=True,
suffix='.geojson')
temporary_file.close()
features.write(temporary_file.name)
gdf = gpd.read_file(temporary_file.name)
gdf['NAME'] = gdf['NAME'].astype(str)
os.unlink(temporary_file.name)
return gdf
def calculate_velocities_over_time(output_filename_prefix,
output_filename_extension,
rotation_filenames,
reconstructable_filenames,
threshold_sampling_distance_radians,
time_young,
time_old,
time_increment,
velocity_delta_time=1.0,
anchor_plate_id=0):
if time_increment <= 0:
print('The time increment "{0}" is not positive and non-zero.'.format(
time_increment),
file=sys.stderr)
return
if time_young > time_old:
print('The young time {0} is older (larger) than the old time {1}.'.
format(time_young, time_old),
file=sys.stderr)
return
rotation_model = pygplates.RotationModel(rotation_filenames)
# Read/parse the reconstructable features once so we're not doing at each time iteration.
reconstructable_features = [
pygplates.FeatureCollection(reconstructable_filename)
for reconstructable_filename in reconstructable_filenames
]
# Iterate over the time range.
time = time_young
while time <= pygplates.GeoTimeInstant(time_old):
print('Time {0}'.format(time))
# Returns a list of tesselated subduction zone points and associated convergence parameters
# to write to the output file for the current 'time'.
output_data = calculate_velocities(
rotation_model, reconstructable_features,
threshold_sampling_distance_radians, time, velocity_delta_time,
anchor_plate_id)
if output_data:
output_filename = '{0}_{1:0.2f}.{2}'.format(
output_filename_prefix, time, output_filename_extension)
write_output_file(output_filename, output_data)
# Increment the time further into the past.
time += time_increment
return 0 # Success
def test_post(request):
if not request.method == "POST":
return HttpResponseBadRequest('expecting post requests!')
else:
#print request.POST
json_feature_collection = json.loads(request.body)
model = request.GET.get('model', settings.MODEL_DEFAULT)
features = []
for json_feature in json_feature_collection['features']:
feature = pygplates.Feature()
point = json_feature['geometry']['coordinates']
feature.set_geometry(pygplates.PointOnSphere(point[1], point[0]))
feature.set_valid_time(json_feature['properties']['age'], 0)
features.append(feature)
model_dict = get_reconstruction_model_dict(model)
rotation_model = pygplates.RotationModel([
str('%s/%s/%s' % (settings.MODEL_STORE_DIR, model, rot_file))
for rot_file in model_dict['RotationFile']
])
static_polygons_filename = str(
'%s/%s/%s' %
(settings.MODEL_STORE_DIR, model, model_dict['StaticPolygons']))
# assign plate-ids to points using static polygons
assigned_point_features = pygplates.partition_into_plates(
static_polygons_filename,
rotation_model,
features,
properties_to_copy=[
pygplates.PartitionProperty.reconstruction_plate_id
])
feature_collection = pygplates.FeatureCollection(
assigned_point_features)
reconstructed_features = reconstruct_to_birth_time(
feature_collection, rotation_model)
# prepare the response to be returned
ret = '{"coordinates":['
for g in reconstructed_features:
ret += '[{0:5.2f},{1:5.2f}],'.format(
g.get_geometry().to_lat_lon()[1],
g.get_geometry().to_lat_lon()[0])
ret = ret[0:-1]
ret += ']}'
return HttpResponse(ret, content_type='application/json')
def __init__(self,
rotation_filenames,
topology_filenames,
geologic_zero,
nseeds=1000,
nneighbours=3,
delta_time=1.):
"""
A class for importing surface velocities from pygplates.
Each time surface velocity points are generated for [nseeds] of equidistantial points at the surface.
With these points a cKDTree obect is generated each time, which will be used to interpolate onto required grid points.
Interpolation is a weighted average of [nneighbours] closest points, unless the closest points is closer than ~numerical zero.
input:
rotation_filenames: list of rotation files
topology_filenames: list of dynamic polygon files
geologic_zero: what is the oldest geologic time available in this model
nseeds: number of seed points to generate
nneighbours: when interpolating between the seed points and mesh points, how many neighboring points should be used
delta_time: how many million years should it take before we read in plate velocities again (is passed on to pygplates for
time averaging too)
"""
# Rotation model(s)
self.rotation_model = pygplates.RotationModel(rotation_filenames)
if nneighbours < 2:
raise ValueError('nneighbours should be at least 2')
else:
self.nneighbours = nneighbours
# Topological plate polygon feature(s).
self.topology_features = []
for fname in topology_filenames:
for f in pygplates.FeatureCollection(fname):
self.topology_features.append(f)
# geologic_zero is the same as model_time=0
self.geologic_zero = geologic_zero
# time window for velocity interpolations
self.delta_time = delta_time
# NB: Not sure if we really need to keep seeds at this stage
self.seeds = self.__fibonacci_sphere(samples=int(nseeds))
#
self.velocity_domain_features = self.__make_GPML_velocity_feature(
self.seeds)
# last reconstruction time
self.reconstruction_time = None
# Flag to know when to recalculate surface velocities.
self.recalculation_flg = False
def plot_velocities(self, m):
delta_time = 5.
Xnodes = np.arange(-180, 180, 5)
Ynodes = np.arange(-90, 90, 5)
Xg, Yg = np.meshgrid(Xnodes, Ynodes)
Xg = Xg.flatten()
Yg = Yg.flatten()
velocity_domain_features = velocity_utils.make_GPML_velocity_feature(
Xg, Yg)
# Load one or more rotation files into a rotation model.
rotation_model = pygplates.RotationModel(rotation_filenames)
# Load the topological plate polygon features.
topology_features = []
for fname in topology_filenames:
for f in pygplates.FeatureCollection(fname):
topology_features.append(f)
# Call the function we created above to get the velocities
all_velocities = velocity_utils.Get_Plate_Velocities(
velocity_domain_features, topology_features, rotation_model,
self.reconstruction_time, delta_time, 'vector_comp')
uu = []
vv = []
for vel in all_velocities:
if not hasattr(vel, 'get_y'):
uu.append(vel[1])
vv.append(vel[0])
else:
uu.append(vel.get_y())
vv.append(vel.get_x())
u = np.asarray([uu]).reshape((Ynodes.shape[0], Xnodes.shape[0]))
v = np.asarray([vv]).reshape((Ynodes.shape[0], Xnodes.shape[0]))
# compute native x,y coordinates of grid.
x, y = m(Xg, Yg)
uproj, vproj, xx, yy = m.transform_vector(u,
v,
Xnodes,
Ynodes,
15,
15,
returnxy=True,
masked=True)
# now plot.
Q = m.quiver(xx, yy, uproj, vproj, scale=1000, color='grey')
# make quiver key.
qk = plt.quiverkey(Q, 0.95, 1.05, 50, '50 mm/yr', labelpos='W')
def gdf2gpml(gdf):
"""
Given a geopandas geodataframe, returns a gplates feature collection
"""
temporary_file = tempfile.NamedTemporaryFile(delete=True,
suffix='.geojson')
temporary_file.close()
gdf.to_file(temporary_file.name, driver='GeoJSON')
feature_collection = pygplates.FeatureCollection(temporary_file.name)
os.unlink(temporary_file.name)
return feature_collection
def assign_plate_ids(vgps, reconstruction_model):
'''
assign plate ids to Virtual Geomagnetic Poles (vgps), which is a special case
of plate partitioning where we must use the 'AverageSampleSitePosition' rather than
the feature geometry
The input type can be a geodataframe or a pygplates FeatureCollection. The output type
will match the input
'''
plate_partitioner = pygplates.PlatePartitioner(reconstruction_model.static_polygons,
reconstruction_model.rotation_model)
if isinstance(vgps, _gpd.GeoDataFrame):
partition_plate_ids = []
for i,row in vgps.iterrows():
partition_polygon = plate_partitioner.partition_point(pygplates.PointOnSphere(row.geometry.y,
row.geometry.x))
partition_plate_ids.append(partition_polygon.get_feature().get_reconstruction_plate_id())
vgps['PlateID'] = partition_plate_ids
return vgps
elif isinstance(vgps, (pygplates.FeatureCollection, list)):
if isinstance(vgps, list):
vgps = pygplates.FeatureCollection(vgps)
partitioned_vgps = []
for vgp in vgps:
partition_polygon = plate_partitioner.partition_point(vgp.get(pygplates.PropertyName.gpml_average_sample_site_position).get_value().get_geometry())
vgp.set_reconstruction_plate_id(partition_polygon.get_feature().get_reconstruction_plate_id())
partitioned_vgps.append(vgp)
return pygplates.FeatureCollection(partitioned_vgps)
else:
raise TypeError('Unexpected type {:} for vgp input'.format(type(vgps)))
def get_merged_cob_terrane_polygons(COBterrane_file, rotation_model, reconstruction_time,
sampling, area_threshold=None, return_raster=False):
polygon_features = pygplates.FeatureCollection(COBterrane_file)
cobter = force_polygon_geometries(polygon_features)
cf = merge_polygons(cobter, rotation_model, time=reconstruction_time, sampling=sampling)
if area_threshold is not None:
sieve_polygons = polygon_area_threshold(cf, area_threshold)
return sieve_polygons
else:
return cf
def make_GPML_velocity_feature(Long,Lat):
# Add points to a multipoint geometry
multi_point = pygplates.MultiPointOnSphere([(float(lat),float(lon)) for lat, lon in zip(Lat,Long)])
# Create a feature containing the multipoint feature, and defined as MeshNode type
meshnode_feature = pygplates.Feature(pygplates.FeatureType.create_from_qualified_string('gpml:MeshNode'))
meshnode_feature.set_geometry(multi_point)
meshnode_feature.set_name('Velocity Mesh Nodes from pygplates')
output_feature_collection = pygplates.FeatureCollection(meshnode_feature)
# NB: at this point, the feature could be written to a file using
# output_feature_collection.write('myfilename.gpmlz')
# for use within the notebook, the velocity domain feature is returned from the function
return output_feature_collection
def subduction(request):
if not request.method == "POST":
return HttpResponseBadRequest('expecting post requests!')
else:
#print request.POST
json_feature_collection = json.loads(request.body)
model = request.GET.get('model', settings.MODEL_DEFAULT)
features = []
for json_feature in json_feature_collection['features']:
feature = pygplates.Feature()
point = json_feature['geometry']['coordinates']
feature.set_geometry(pygplates.PointOnSphere(point[1], point[0]))
feature.set_valid_time(json_feature['properties']['age'], 0)
features.append(feature)
model_dict = get_reconstruction_model_dict(model)
rotation_model = pygplates.RotationModel([
str('%s/%s/%s' % (settings.MODEL_STORE_DIR, model, rot_file))
for rot_file in model_dict['RotationFile']
])
static_polygons_filename = str(
'%s/%s/%s' %
(settings.MODEL_STORE_DIR, model, model_dict['StaticPolygons']))
# assign plate-ids to points using static polygons
assigned_point_features = pygplates.partition_into_plates(
static_polygons_filename,
rotation_model,
features,
properties_to_copy=[
pygplates.PartitionProperty.reconstruction_plate_id
])
seed_point_features = pygplates.FeatureCollection(
assigned_point_features)
df_OreDepositBirthTimeStats = subduction_parameters(
seed_point_features, rotation_model)
html_table = df_OreDepositBirthTimeStats.to_html(index=False)
return render(request, 'list_template.html',
{'html_table': html_table})
def random_points_feature(N,filename=None):
# function to call Marsaglia's method and return
# feature collection or save to file
points = marsaglias_method(N)
#multipoint = pygplates.MultiPointOnSphere((points.T))
multipoint_feature = pygplates.Feature()
multipoint_feature.set_geometry(pygplates.MultiPointOnSphere((points.T)))
multipoint_feature.set_name('Random Points from Marsaglia''s method')
multipoint_feature_collection = pygplates.FeatureCollection(multipoint_feature)
if filename is not None:
multipoint_feature_collection.write(filename)
else:
return multipoint_feature_collection
def create_gpml_crustal_thickness(longitude_array,latitude_array,thickness,filename=None):
multi_point = pygplates.MultiPointOnSphere(zip(latitude_array,longitude_array))
scalar_coverages = {
pygplates.ScalarType.create_gpml('CrustalThickness'): thickness}
ct_feature = pygplates.Feature()
ct_feature.set_geometry((multi_point,scalar_coverages))
ct_feature.set_name('Crustal Thickness')
output_feature_collection = pygplates.FeatureCollection(ct_feature)
if filename is not None:
output_feature_collection.write(filename)
else:
return output_feature_collection
def create_gpml_velocity_feature(longitude_array, latitude_array):
# function to make a velocity mesh nodes at an arbitrary set of points defined in Lat
# Long and Lat are assumed to be 1d arrays.
multi_point = pygplates.MultiPointOnSphere(
zip(latitude_array, longitude_array))
# Create a feature containing the multipoint feature.
# optionally, define as 'MeshNode' type, so that GPlates will recognise it as a velocity layer
meshnode_feature = pygplates.Feature()
meshnode_feature.set_name('Multipoint Feature')
meshnode_feature.set_geometry(multi_point)
output_feature_collection = pygplates.FeatureCollection(meshnode_feature)
return output_feature_collection