def _distribute_thickness_per_interp(glacier_mask,
topo,
cls,
fls,
grid,
smooth=True,
add_slope=True):
"""Where the job is actually done."""
# Thick to interpolate
dx = grid.dx
thick = np.where(glacier_mask, np.NaN, 0)
# Along the lines
vs = []
for cl, fl in zip(cls, fls):
# TODO: here one should see if parabola is always the best choice
vs.extend(cl['volume'])
x, y = utils.tuple2int(fl.line.xy)
thick[y, x] = cl['thick']
vol = np.sum(vs)
# Interpolate
xx, yy = grid.ij_coordinates
pnan = np.nonzero(~np.isfinite(thick))
pok = np.nonzero(np.isfinite(thick))
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
thick[pnan] = griddata(points, np.ravel(thick[pok]), inter, method='cubic')
# Smooth
if smooth:
gsize = np.rint(cfg.PARAMS['smooth_window'] / dx)
thick = gaussian_blur(thick, np.int(gsize))
thick = np.where(glacier_mask, thick, 0.)
# Slope
slope = 1.
if add_slope:
sy, sx = np.gradient(topo, dx, dx)
slope = np.arctan(np.sqrt(sy**2 + sx**2))
slope = np.clip(slope, np.deg2rad(6.), np.pi / 2.)
slope = 1 / slope**(cfg.N / (cfg.N + 2))
# Conserve volume
tmp_vol = np.nansum(thick * slope * dx**2)
final_t = thick * slope * vol / tmp_vol
# Add to grids
final_t = np.where(np.isfinite(final_t), final_t, 0.)
assert np.allclose(np.sum(final_t * dx**2), vol)
return final_t
def _distribute_thickness_per_interp(glacier_mask, topo, cls, fls, grid,
smooth=True, add_slope=True):
"""Where the job is actually done."""
# Thick to interpolate
dx = grid.dx
thick = np.where(glacier_mask, np.NaN, 0)
# Along the lines
vs = []
for cl, fl in zip(cls, fls):
# TODO: here one should see if parabola is always the best choice
vs.extend(cl['volume'])
x, y = utils.tuple2int(fl.line.xy)
thick[y, x] = cl['thick']
vol = np.sum(vs)
# Interpolate
xx, yy = grid.ij_coordinates
pnan = np.nonzero(~ np.isfinite(thick))
pok = np.nonzero(np.isfinite(thick))
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
thick[pnan] = griddata(points, np.ravel(thick[pok]), inter, method='cubic')
# Smooth
if smooth:
gsize = np.rint(cfg.PARAMS['smooth_window'] / dx)
thick = gaussian_blur(thick, np.int(gsize))
thick = np.where(glacier_mask, thick, 0.)
# Slope
slope = 1.
if add_slope:
sy, sx = np.gradient(topo, dx, dx)
slope = np.arctan(np.sqrt(sy**2 + sx**2))
slope = np.clip(slope, np.deg2rad(6.), np.pi/2.)
slope = 1 / slope**(cfg.N / (cfg.N+2))
# Conserve volume
tmp_vol = np.nansum(thick * slope * dx**2)
final_t = thick * slope * vol / tmp_vol
# Add to grids
final_t = np.where(np.isfinite(final_t), final_t, 0.)
assert np.allclose(np.sum(final_t * dx**2), vol)
return final_t
def catchment_area(gdir, div_id=None):
"""Compute the catchment areas of each tributary line.
The idea is to compute the route of lowest cost for any point on the
glacier to rejoin a centerline. These routes are then put together if
they belong to the same centerline, thus creating "catchment areas" for
each centerline.
Parameters
----------
gdir : oggm.GlacierDirectory
"""
# Variables
cls = gdir.read_pickle('centerlines', div_id=div_id)
geoms = gdir.read_pickle('geometries', div_id=div_id)
glacier_pix = geoms['polygon_pix']
fpath = gdir.get_filepath('gridded_data', div_id=div_id)
with netCDF4.Dataset(fpath) as nc:
costgrid = nc.variables['cost_grid'][:]
mask = nc.variables['glacier_mask'][:]
# If we have only one centerline this is going to be easy: take the
# mask and return
if len(cls) == 1:
cl_catchments = [np.array(np.nonzero(mask == 1)).T]
gdir.write_pickle(cl_catchments, 'catchment_indices', div_id=div_id)
return
# Initialise costgrid and the "catching" dict
cost_factor = 0. # Make it cheap
dic_catch = dict()
for i, cl in enumerate(cls):
x, y = tuple2int(cl.line.xy)
costgrid[y, x] = cost_factor
for x, y in [(int(x), int(y)) for x, y in cl.line.coords]:
assert (y, x) not in dic_catch
dic_catch[(y, x)] = set([(y, x)])
# It is much faster to make the array as small as possible (especially
# with divides). We have to trick:
pm = np.nonzero(mask == 1)
ymi, yma = np.min(pm[0])-1, np.max(pm[0])+2
xmi, xma = np.min(pm[1])-1, np.max(pm[1])+2
costgrid = costgrid[ymi:yma, xmi:xma]
mask = mask[ymi:yma, xmi:xma]
# Where did we compute the path already?
computed = np.where(mask == 1, 0, np.nan)
# Coords of Terminus (converted)
endcoords = np.array(cls[0].tail.coords[0])[::-1].astype(np.int64)
endcoords -= [ymi, xmi]
# Start with all the paths at the boundaries, they are more likely
# to cover much of the glacier
for headx, heady in tuple2int(glacier_pix.exterior.coords):
headcoords = np.array([heady-ymi, headx-xmi]) # convert
indices, _ = route_through_array(costgrid, headcoords, endcoords)
inds = np.array(indices).T
computed[inds[0], inds[1]] = 1
set_dump = set([])
for y, x in indices:
y, x = y+ymi, x+xmi # back to original
set_dump.add((y, x))
if (y, x) in dic_catch:
dic_catch[(y, x)] = dic_catch[(y, x)].union(set_dump)
break
# Repeat for the not yet computed pixels
while True:
not_computed = np.where(computed == 0)
if len(not_computed[0]) == 0: # All points computed !!
break
headcoords = np.array([not_computed[0][0], not_computed[1][0]]).astype(np.int64)
indices, _ = route_through_array(costgrid, headcoords, endcoords)
inds = np.array(indices).T
computed[inds[0], inds[1]] = 1
set_dump = set([])
for y, x in indices:
y, x = y+ymi, x+xmi # back to original
set_dump.add((y, x))
if (y, x) in dic_catch:
dic_catch[(y, x)] = dic_catch[(y, x)].union(set_dump)
break
# For each centerline, make a set of all points flowing into it
cl_catchments = []
for cl in cls:
# Union of all
cl_catch = set()
for x, y in [(int(x), int(y)) for x, y in cl.line.coords]:
cl_catch = cl_catch.union(dic_catch[(y, x)])
cl_catchments.append(cl_catch)
# The higher order centerlines will get the points from the upstream
# ones too. The idea is to store the points which are unique to each
# centerline: now, in decreasing line order we remove the indices from
# the tributaries
cl_catchments = cl_catchments[::-1]
for i, cl in enumerate(cl_catchments):
cl_catchments[i] = np.array(list(cl.difference(*cl_catchments[i+1:])))
cl_catchments = cl_catchments[::-1] # put it back in order
# Write the data
gdir.write_pickle(cl_catchments, 'catchment_indices', div_id=div_id)
def merged_glacier_masks(gdir, geometry):
"""Makes a gridded mask of a merged glacier outlines.
This is a simplified version of glacier_masks. We don't need fancy
corrections or smoothing here: The flowlines for the actual model run are
based on a proper call of glacier_masks.
This task is only to get outlines etc. for visualization!
Parameters
----------
gdir : :py:class:`oggm.GlacierDirectory`
where to write the data
geometry: shapely.geometry.multipolygon.MultiPolygon
united outlines of the merged glaciers
"""
# open srtm tif-file:
dem_dr = rasterio.open(gdir.get_filepath('dem'), 'r', driver='GTiff')
dem = dem_dr.read(1).astype(rasterio.float32)
# Grid
nx = dem_dr.width
ny = dem_dr.height
assert nx == gdir.grid.nx
assert ny == gdir.grid.ny
if np.min(dem) == np.max(dem):
raise RuntimeError('({}) min equal max in the DEM.'
.format(gdir.rgi_id))
# Projection
if LooseVersion(rasterio.__version__) >= LooseVersion('1.0'):
transf = dem_dr.transform
else:
transf = dem_dr.affine
x0 = transf[2] # UL corner
y0 = transf[5] # UL corner
dx = transf[0]
dy = transf[4] # Negative
if not (np.allclose(dx, -dy) or np.allclose(dx, gdir.grid.dx) or
np.allclose(y0, gdir.grid.corner_grid.y0, atol=1e-2) or
np.allclose(x0, gdir.grid.corner_grid.x0, atol=1e-2)):
raise RuntimeError('DEM file and Salem Grid do not match!')
dem_dr.close()
# Clip topography to 0 m a.s.l.
dem = dem.clip(0)
# Interpolate shape to a regular path
glacier_poly_hr = list(geometry)
for nr, poly in enumerate(glacier_poly_hr):
# transform geometry to map
_geometry = salem.transform_geometry(poly, to_crs=gdir.grid.proj)
glacier_poly_hr[nr] = _interp_polygon(_geometry, gdir.grid.dx)
glacier_poly_hr = shpg.MultiPolygon(glacier_poly_hr)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise RuntimeError('This glacier geometry is not valid.')
# Rounded geometry to nearest nearest pix
# I can not use _polyg
# glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
def project(x, y):
return np.rint(x).astype(np.int64), np.rint(y).astype(np.int64)
glacier_poly_pix = shapely.ops.transform(project, glacier_poly_hr)
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
for poly in glacier_poly_pix:
(x, y) = poly.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in poly.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(poly.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Last sanity check based on the masked dem
tmp_max = np.max(dem[np.where(glacier_mask == 1)])
tmp_min = np.min(dem[np.where(glacier_mask == 1)])
if tmp_max < (tmp_min + 1):
raise RuntimeError('({}) min equal max in the masked DEM.'
.format(gdir.rgi_id))
# write out the grids in the netcdf file
nc = gdir.create_gridded_ncdf_file('gridded_data')
v = nc.createVariable('topo', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography'
v[:] = dem
v = nc.createVariable('glacier_mask', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
v[:] = glacier_mask
v = nc.createVariable('glacier_ext', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
v[:] = glacier_ext
# add some meta stats and close
nc.max_h_dem = np.max(dem)
nc.min_h_dem = np.min(dem)
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
nc.close()
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries')
def glacier_masks(gdir):
"""Makes a gridded mask of the glacier outlines and topography.
This function fills holes in the source DEM and produces smoothed gridded
topography and glacier outline arrays. These are the ones which will later
be used to determine bed and surface height.
Parameters
----------
gdir : :py:class:`oggm.GlacierDirectory`
where to write the data
"""
# open srtm tif-file:
dem_dr = rasterio.open(gdir.get_filepath('dem'), 'r', driver='GTiff')
dem = dem_dr.read(1).astype(rasterio.float32)
# Grid
nx = dem_dr.width
ny = dem_dr.height
assert nx == gdir.grid.nx
assert ny == gdir.grid.ny
# Correct the DEM
# Currently we just do a linear interp -- filling is totally shit anyway
min_z = -999.
dem[dem <= min_z] = np.NaN
isfinite = np.isfinite(dem)
if np.all(~isfinite):
raise InvalidDEMError('Not a single valid grid point in DEM')
if np.any(~isfinite):
xx, yy = gdir.grid.ij_coordinates
pnan = np.nonzero(~isfinite)
pok = np.nonzero(isfinite)
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
try:
dem[pnan] = griddata(points, np.ravel(dem[pok]), inter,
method='linear')
except ValueError:
raise InvalidDEMError('DEM interpolation not possible.')
log.warning(gdir.rgi_id + ': DEM needed interpolation.')
gdir.add_to_diagnostics('dem_needed_interpolation', True)
gdir.add_to_diagnostics('dem_invalid_perc', len(pnan[0]) / (nx*ny))
isfinite = np.isfinite(dem)
if np.any(~isfinite):
# this happens when extrapolation is needed
# see how many percent of the dem
if np.sum(~isfinite) > (0.5 * nx * ny):
log.warning('({}) many NaNs in DEM'.format(gdir.rgi_id))
xx, yy = gdir.grid.ij_coordinates
pnan = np.nonzero(~isfinite)
pok = np.nonzero(isfinite)
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
try:
dem[pnan] = griddata(points, np.ravel(dem[pok]), inter,
method='nearest')
except ValueError:
raise InvalidDEMError('DEM extrapolation not possible.')
log.warning(gdir.rgi_id + ': DEM needed extrapolation.')
gdir.add_to_diagnostics('dem_needed_extrapolation', True)
gdir.add_to_diagnostics('dem_extrapol_perc', len(pnan[0]) / (nx*ny))
if np.min(dem) == np.max(dem):
raise InvalidDEMError('({}) min equal max in the DEM.'
.format(gdir.rgi_id))
# Projection
if LooseVersion(rasterio.__version__) >= LooseVersion('1.0'):
transf = dem_dr.transform
else:
transf = dem_dr.affine
x0 = transf[2] # UL corner
y0 = transf[5] # UL corner
dx = transf[0]
dy = transf[4] # Negative
if not (np.allclose(dx, -dy) or np.allclose(dx, gdir.grid.dx) or
np.allclose(y0, gdir.grid.corner_grid.y0, atol=1e-2) or
np.allclose(x0, gdir.grid.corner_grid.x0, atol=1e-2)):
raise InvalidDEMError('DEM file and Salem Grid do not match!')
dem_dr.close()
# Clip topography to 0 m a.s.l.
dem = dem.clip(0)
# Smooth DEM?
if cfg.PARAMS['smooth_window'] > 0.:
gsize = np.rint(cfg.PARAMS['smooth_window'] / dx)
smoothed_dem = gaussian_blur(dem, np.int(gsize))
else:
smoothed_dem = dem.copy()
if not np.all(np.isfinite(smoothed_dem)):
raise InvalidDEMError('({}) NaN in smoothed DEM'.format(gdir.rgi_id))
# Geometries
geometry = gdir.read_shapefile('outlines').geometry[0]
# Interpolate shape to a regular path
glacier_poly_hr = _interp_polygon(geometry, gdir.grid.dx)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise InvalidGeometryError('This glacier geometry is not valid.')
# Rounded nearest pix
glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
if glacier_poly_pix.exterior is None:
raise InvalidGeometryError('Problem in converting glacier geometry '
'to grid resolution.')
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
(x, y) = glacier_poly_pix.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in glacier_poly_pix.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(glacier_poly_pix.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Because of the 0 values at nunataks boundaries, some "Ice Islands"
# can happen within nunataks (e.g.: RGI40-11.00062)
# See if we can filter them out easily
regions, nregions = label(glacier_mask, structure=label_struct)
if nregions > 1:
log.debug('(%s) we had to cut an island in the mask', gdir.rgi_id)
# Check the size of those
region_sizes = [np.sum(regions == r) for r in np.arange(1, nregions+1)]
am = np.argmax(region_sizes)
# Check not a strange glacier
sr = region_sizes.pop(am)
for ss in region_sizes:
assert (ss / sr) < 0.1
glacier_mask[:] = 0
glacier_mask[np.where(regions == (am+1))] = 1
# Last sanity check based on the masked dem
tmp_max = np.max(dem[np.where(glacier_mask == 1)])
tmp_min = np.min(dem[np.where(glacier_mask == 1)])
if tmp_max < (tmp_min + 1):
raise InvalidDEMError('({}) min equal max in the masked DEM.'
.format(gdir.rgi_id))
# write out the grids in the netcdf file
nc = gdir.create_gridded_ncdf_file('gridded_data')
v = nc.createVariable('topo', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography'
v[:] = dem
v = nc.createVariable('topo_smoothed', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = ('DEM topography smoothed '
'with radius: {:.1} m'.format(cfg.PARAMS['smooth_window']))
v[:] = smoothed_dem
v = nc.createVariable('glacier_mask', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
v[:] = glacier_mask
v = nc.createVariable('glacier_ext', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
v[:] = glacier_ext
# add some meta stats and close
nc.max_h_dem = np.max(dem)
nc.min_h_dem = np.min(dem)
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
nc.close()
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries')
def distribute_thickness_interp(gdir,
add_slope=True,
smooth_radius=None,
varname_suffix=''):
"""Compute a thickness map by interpolating between centerlines and border.
This is a rather cosmetic task, not relevant for OGGM but for ITMIX.
Parameters
----------
gdir : oggm.GlacierDirectory
the glacier directory to process
add_slope : bool
whether a corrective slope factor should be used or not
smooth_radius : int
pixel size of the gaussian smoothing. Default is to use
cfg.PARAMS['smooth_window'] (i.e. a size in meters). Set to zero to
suppress smoothing.
varname_suffix : str
add a suffix to the variable written in the file (for experiments)
"""
# Variables
grids_file = gdir.get_filepath('gridded_data')
# See if we have the masks, else compute them
with utils.ncDataset(grids_file) as nc:
has_masks = 'glacier_ext_erosion' in nc.variables
if not has_masks:
from oggm.core.gis import interpolation_masks
interpolation_masks(gdir)
with utils.ncDataset(grids_file) as nc:
glacier_mask = nc.variables['glacier_mask'][:]
glacier_ext = nc.variables['glacier_ext_erosion'][:]
ice_divides = nc.variables['ice_divides'][:]
if add_slope:
slope_factor = nc.variables['slope_factor'][:]
else:
slope_factor = 1.
# Thickness to interpolate
thick = glacier_ext * np.NaN
thick[(glacier_ext - ice_divides) == 1] = 0.
# TODO: domain border too, for convenience for a start
thick[0, :] = 0.
thick[-1, :] = 0.
thick[:, 0] = 0.
thick[:, -1] = 0.
# Along the lines
cls = gdir.read_pickle('inversion_output')
fls = gdir.read_pickle('inversion_flowlines')
vs = []
for cl, fl in zip(cls, fls):
vs.extend(cl['volume'])
x, y = utils.tuple2int(fl.line.xy)
thick[y, x] = cl['thick']
init_vol = np.sum(vs)
# Interpolate
xx, yy = gdir.grid.ij_coordinates
pnan = np.nonzero(~np.isfinite(thick))
pok = np.nonzero(np.isfinite(thick))
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
thick[pnan] = griddata(points, np.ravel(thick[pok]), inter, method='cubic')
thick = thick.clip(0)
# Slope
thick *= slope_factor
# Smooth
dx = gdir.grid.dx
if smooth_radius != 0:
if smooth_radius is None:
smooth_radius = np.rint(cfg.PARAMS['smooth_window'] / dx)
thick = gaussian_blur(thick, np.int(smooth_radius))
thick = np.where(glacier_mask, thick, 0.)
# Re-mask
thick[glacier_mask == 0] = np.NaN
assert np.all(np.isfinite(thick[glacier_mask == 1]))
# Conserve volume
tmp_vol = np.nansum(thick * dx**2)
thick *= init_vol / tmp_vol
# write
grids_file = gdir.get_filepath('gridded_data')
with utils.ncDataset(grids_file, 'a') as nc:
vn = 'distributed_thickness' + varname_suffix
if vn in nc.variables:
v = nc.variables[vn]
else:
v = nc.createVariable(vn, 'f4', (
'y',
'x',
), zlib=True)
v.units = '-'
v.long_name = 'Distributed ice thickness'
v[:] = thick
return thick
def test_baltoro_centerlines(self):
cfg.PARAMS['border'] = 2
cfg.PATHS['dem_file'] = get_demo_file('baltoro_srtm_clip.tif')
b_file = get_demo_file('baltoro_wgs84.shp')
rgidf = gpd.GeoDataFrame.from_file(b_file)
kienholz_file = get_demo_file('centerlines_baltoro_wgs84.shp')
kdf = gpd.read_file(kienholz_file)
# loop because for some reason indexing wont work
for index, entity in rgidf.iterrows():
# add fake attribs
entity.O1REGION = 0
entity.BGNDATE = 0
entity.NAME = 'Baltoro'
gdir = oggm.GlacierDirectory(entity, base_dir=self.testdir)
gis.define_glacier_region(gdir, entity=entity)
gis.glacier_masks(gdir)
centerlines.compute_centerlines(gdir)
my_mask = np.zeros((gdir.grid.ny, gdir.grid.nx), dtype=np.uint8)
cls = gdir.read_pickle('centerlines', div_id=1)
for cl in cls:
x, y = tuple2int(cl.line.xy)
my_mask[y, x] = 1
# Transform
kien_mask = np.zeros((gdir.grid.ny, gdir.grid.nx), dtype=np.uint8)
from shapely.ops import transform
for index, entity in kdf.iterrows():
def proj(lon, lat):
return salem.transform_proj(salem.wgs84, gdir.grid.proj, lon,
lat)
kgm = transform(proj, entity.geometry)
# Interpolate shape to a regular path
e_line = []
for distance in np.arange(0.0, kgm.length, gdir.grid.dx):
e_line.append(*kgm.interpolate(distance).coords)
kgm = shpg.LineString(e_line)
# Transform geometry into grid coordinates
def proj(x, y):
return gdir.grid.transform(x, y, crs=gdir.grid.proj)
kgm = transform(proj, kgm)
# Rounded nearest pix
project = lambda x, y: (np.rint(x).astype(np.int64), np.rint(y).
astype(np.int64))
kgm = transform(project, kgm)
x, y = tuple2int(kgm.xy)
kien_mask[y, x] = 1
# We test the Heidke Skill score of our predictions
rest = kien_mask + 2 * my_mask
# gr.plot_array(rest)
na = len(np.where(rest == 3)[0])
nb = len(np.where(rest == 2)[0])
nc = len(np.where(rest == 1)[0])
nd = len(np.where(rest == 0)[0])
denom = np.float64((na + nc) * (nd + nc) + (na + nb) * (nd + nb))
hss = np.float64(2.) * ((na * nd) - (nb * nc)) / denom
self.assertTrue(hss > 0.53)
def glacier_masks(gdir):
"""Makes a gridded mask of the glacier outlines.
Parameters
----------
gdir : :py:class:`oggm.GlacierDirectory`
where to write the data
"""
# open srtm tif-file:
dem_dr = rasterio.open(gdir.get_filepath('dem'), 'r', driver='GTiff')
dem = dem_dr.read(1).astype(rasterio.float32)
# Grid
nx = dem_dr.width
ny = dem_dr.height
assert nx == gdir.grid.nx
assert ny == gdir.grid.ny
# Correct the DEM (ASTER...)
# Currently we just do a linear interp -- ASTER is totally shit anyway
min_z = -999.
isfinite = np.isfinite(dem)
if (np.min(dem) <= min_z) or np.any(~isfinite):
xx, yy = gdir.grid.ij_coordinates
pnan = np.nonzero((dem <= min_z) | (~isfinite))
pok = np.nonzero((dem > min_z) | isfinite)
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
dem[pnan] = griddata(points, np.ravel(dem[pok]), inter)
log.warning(gdir.rgi_id + ': DEM needed interpolation.')
isfinite = np.isfinite(dem)
if not np.all(isfinite):
# see how many percent of the dem
if np.sum(~isfinite) > (0.2 * nx * ny):
raise RuntimeError('({}) too many NaNs in DEM'.format(gdir.rgi_id))
log.warning('({}) DEM needed zeros somewhere.'.format(gdir.rgi_id))
dem[isfinite] = 0
if np.min(dem) == np.max(dem):
raise RuntimeError('({}) min equal max in the DEM.'
.format(gdir.rgi_id))
# Proj
if LooseVersion(rasterio.__version__) >= LooseVersion('1.0'):
transf = dem_dr.transform
else:
transf = dem_dr.affine
x0 = transf[2] # UL corner
y0 = transf[5] # UL corner
dx = transf[0]
dy = transf[4] # Negative
assert dx == -dy
assert dx == gdir.grid.dx
assert y0 == gdir.grid.corner_grid.y0
assert x0 == gdir.grid.corner_grid.x0
dem_dr.close()
# Clip topography to 0 m a.s.l.
dem = dem.clip(0)
# Smooth DEM?
if cfg.PARAMS['smooth_window'] > 0.:
gsize = np.rint(cfg.PARAMS['smooth_window'] / dx)
smoothed_dem = gaussian_blur(dem, np.int(gsize))
else:
smoothed_dem = dem.copy()
if not np.all(np.isfinite(smoothed_dem)):
raise RuntimeError('({}) NaN in smoothed DEM'.format(gdir.rgi_id))
# Geometries
outlines_file = gdir.get_filepath('outlines')
geometry = gpd.GeoDataFrame.from_file(outlines_file).geometry[0]
# Interpolate shape to a regular path
glacier_poly_hr = _interp_polygon(geometry, gdir.grid.dx)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise RuntimeError('This glacier geometry is crazy.')
# Rounded nearest pix
glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
(x, y) = glacier_poly_pix.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in glacier_poly_pix.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(glacier_poly_pix.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Because of the 0 values at nunataks boundaries, some "Ice Islands"
# can happen within nunataks (e.g.: RGI40-11.00062)
# See if we can filter them out easily
regions, nregions = label(glacier_mask, structure=label_struct)
if nregions > 1:
log.debug('(%s) we had to cut an island in the mask', gdir.rgi_id)
# Check the size of those
region_sizes = [np.sum(regions == r) for r in np.arange(1, nregions+1)]
am = np.argmax(region_sizes)
# Check not a strange glacier
sr = region_sizes.pop(am)
for ss in region_sizes:
assert (ss / sr) < 0.1
glacier_mask[:] = 0
glacier_mask[np.where(regions == (am+1))] = 1
# Last sanity check based on the masked dem
tmp_max = np.max(dem[np.where(glacier_mask == 1)])
tmp_min = np.min(dem[np.where(glacier_mask == 1)])
if tmp_max < (tmp_min + 1):
raise RuntimeError('({}) min equal max in the masked DEM.'
.format(gdir.rgi_id))
# write out the grids in the netcdf file
nc = gdir.create_gridded_ncdf_file('gridded_data')
v = nc.createVariable('topo', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography'
v[:] = dem
v = nc.createVariable('topo_smoothed', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = ('DEM topography smoothed'
' with radius: {:.1} m'.format(cfg.PARAMS['smooth_window']))
v[:] = smoothed_dem
v = nc.createVariable('glacier_mask', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
v[:] = glacier_mask
v = nc.createVariable('glacier_ext', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
v[:] = glacier_ext
# add some meta stats and close
nc.max_h_dem = np.max(dem)
nc.min_h_dem = np.min(dem)
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
nc.close()
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries')
def merged_glacier_masks(gdir, geometry):
"""Makes a gridded mask of a merged glacier outlines.
This is a simplified version of glacier_masks. We don't need fancy
corrections or smoothing here: The flowlines for the actual model run are
based on a proper call of glacier_masks.
This task is only to get outlines etc. for visualization!
Parameters
----------
gdir : :py:class:`oggm.GlacierDirectory`
where to write the data
geometry: shapely.geometry.multipolygon.MultiPolygon
united outlines of the merged glaciers
"""
# open srtm tif-file:
dem_dr = rasterio.open(gdir.get_filepath('dem'), 'r', driver='GTiff')
dem = dem_dr.read(1).astype(rasterio.float32)
# Grid
nx = dem_dr.width
ny = dem_dr.height
assert nx == gdir.grid.nx
assert ny == gdir.grid.ny
if np.min(dem) == np.max(dem):
raise RuntimeError('({}) min equal max in the DEM.'.format(
gdir.rgi_id))
# Projection
if LooseVersion(rasterio.__version__) >= LooseVersion('1.0'):
transf = dem_dr.transform
else:
transf = dem_dr.affine
x0 = transf[2] # UL corner
y0 = transf[5] # UL corner
dx = transf[0]
dy = transf[4] # Negative
if not (np.allclose(dx, -dy) or np.allclose(dx, gdir.grid.dx)
or np.allclose(y0, gdir.grid.corner_grid.y0, atol=1e-2)
or np.allclose(x0, gdir.grid.corner_grid.x0, atol=1e-2)):
raise RuntimeError('DEM file and Salem Grid do not match!')
dem_dr.close()
# Clip topography to 0 m a.s.l.
dem = dem.clip(0)
# Interpolate shape to a regular path
glacier_poly_hr = list(geometry)
for nr, poly in enumerate(glacier_poly_hr):
# transform geometry to map
_geometry = salem.transform_geometry(poly, to_crs=gdir.grid.proj)
glacier_poly_hr[nr] = _interp_polygon(_geometry, gdir.grid.dx)
glacier_poly_hr = shpg.MultiPolygon(glacier_poly_hr)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise RuntimeError('This glacier geometry is not valid.')
# Rounded geometry to nearest nearest pix
# I can not use _polyg
# glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
def project(x, y):
return np.rint(x).astype(np.int64), np.rint(y).astype(np.int64)
glacier_poly_pix = shapely.ops.transform(project, glacier_poly_hr)
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
for poly in glacier_poly_pix:
(x, y) = poly.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in poly.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(poly.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Last sanity check based on the masked dem
tmp_max = np.max(dem[np.where(glacier_mask == 1)])
tmp_min = np.min(dem[np.where(glacier_mask == 1)])
if tmp_max < (tmp_min + 1):
raise RuntimeError('({}) min equal max in the masked DEM.'.format(
gdir.rgi_id))
# write out the grids in the netcdf file
nc = gdir.create_gridded_ncdf_file('gridded_data')
v = nc.createVariable('topo', 'f4', (
'y',
'x',
), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography'
v[:] = dem
v = nc.createVariable('glacier_mask', 'i1', (
'y',
'x',
), zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
v[:] = glacier_mask
v = nc.createVariable('glacier_ext', 'i1', (
'y',
'x',
), zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
v[:] = glacier_ext
# add some meta stats and close
nc.max_h_dem = np.max(dem)
nc.min_h_dem = np.min(dem)
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
nc.close()
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries')
def compute_centerlines(gdir, div_id=None):
"""Compute the centerlines following Kienholz et al., (2014).
They are then sorted according to the modified Strahler number:
http://en.wikipedia.org/wiki/Strahler_number
Parameters
----------
gdir : oggm.GlacierDirectory
"""
# Params
single_fl = not cfg.PARAMS['use_multiple_flowlines']
do_filter_slope = cfg.PARAMS['filter_min_slope']
if 'force_one_flowline' in cfg.PARAMS:
if gdir.rgi_id in cfg.PARAMS['force_one_flowline']:
single_fl = True
# open
geom = gdir.read_pickle('geometries', div_id=div_id)
grids_file = gdir.get_filepath('gridded_data', div_id=div_id)
with netCDF4.Dataset(grids_file) as nc:
# Variables
glacier_mask = nc.variables['glacier_mask'][:]
glacier_ext = nc.variables['glacier_ext'][:]
topo = nc.variables['topo_smoothed'][:]
poly_pix = geom['polygon_pix']
# Find for local maximas on the outline
x, y = tuple2int(poly_pix.exterior.xy)
ext_yx = tuple(reversed(poly_pix.exterior.xy))
zoutline = topo[y[:-1], x[:-1]] # last point is first point
# Size of the half window to use to look for local maximas
maxorder = np.rint(cfg.PARAMS['localmax_window'] / gdir.grid.dx)
maxorder = np.clip(maxorder, 5., np.rint((len(zoutline) / 5.)))
heads_idx = scipy.signal.argrelmax(zoutline,
mode='wrap',
order=maxorder.astype(np.int64))
if single_fl or len(heads_idx[0]) <= 1:
# small glaciers with one or less heads: take the absolute max
heads_idx = (np.atleast_1d(np.argmax(zoutline)), )
# Remove the heads that are too low
zglacier = topo[np.where(glacier_mask)]
head_threshold = np.percentile(zglacier, (1. / 3.) * 100)
heads_idx = heads_idx[0][np.where(zoutline[heads_idx] > head_threshold)]
heads = np.asarray(ext_yx)[:, heads_idx]
heads_z = zoutline[heads_idx]
# careful, the coords are in y, x order!
heads = [shpg.Point(x, y) for y, x in zip(heads[0, :], heads[1, :])]
# get radius of the buffer according to Kienholz eq. (1)
radius = cfg.PARAMS['q1'] * geom['polygon_area'] + cfg.PARAMS['q2']
radius = np.clip(radius, 0, cfg.PARAMS['rmax'])
radius /= gdir.grid.dx # in raster coordinates
# Plus our criteria, quite usefull to remove short lines:
radius += cfg.PARAMS['flowline_junction_pix'] * cfg.PARAMS['flowline_dx']
log.debug('%s: radius in raster coordinates: %.2f', gdir.rgi_id, radius)
# OK. Filter and see.
log.debug('%s: number of heads before radius filter: %d', gdir.rgi_id,
len(heads))
heads, heads_z = _filter_heads(heads, heads_z, radius, poly_pix)
log.debug('%s: number of heads after radius filter: %d', gdir.rgi_id,
len(heads))
# Cost array
costgrid = _make_costgrid(glacier_mask, glacier_ext, topo)
# Terminus
t_coord = _get_terminus_coord(gdir, ext_yx, zoutline)
# Compute the routes
lines = []
for h in heads:
h_coord = np.asarray(h.xy)[::-1].astype(np.int64)
indices, _ = route_through_array(costgrid, h_coord, t_coord)
lines.append(shpg.LineString(np.array(indices)[:, [1, 0]]))
log.debug('%s: computed the routes', gdir.rgi_id)
# Filter the shortest lines out
dx_cls = cfg.PARAMS['flowline_dx']
radius = cfg.PARAMS['flowline_junction_pix'] * dx_cls
radius += 6 * dx_cls
olines, _ = _filter_lines(lines, heads, cfg.PARAMS['kbuffer'], radius)
log.debug('%s: number of heads after lines filter: %d', gdir.rgi_id,
len(olines))
# Filter the lines which are going up instead of down
if do_filter_slope:
olines = _filter_lines_slope(olines, topo, gdir)
log.debug('%s: number of heads after slope filter: %d', gdir.rgi_id,
len(olines))
# And rejoin the cutted tails
olines = _join_lines(olines)
# Adds the line level
for cl in olines:
cl.order = _line_order(cl)
# And sort them per order !!! several downstream tasks rely on this
cls = []
for i in np.argsort([cl.order for cl in olines]):
cls.append(olines[i])
# Final check
if len(cls) == 0:
raise RuntimeError('{} : no centerline found!'.format(gdir.rgi_id))
# Write the data
gdir.write_pickle(cls, 'centerlines', div_id=div_id)
# Netcdf
with netCDF4.Dataset(grids_file, 'a') as nc:
if 'cost_grid' in nc.variables:
# Overwrite
nc.variables['cost_grid'][:] = costgrid
else:
# Create
v = nc.createVariable('cost_grid', 'f4', (
'y',
'x',
), zlib=True)
v.units = '-'
v.long_name = 'Centerlines cost grid'
v[:] = costgrid
def test_baltoro_centerlines(self):
cfg.PARAMS["border"] = 2
cfg.PATHS["dem_file"] = get_demo_file("baltoro_srtm_clip.tif")
b_file = get_demo_file("baltoro_wgs84.shp")
entity = gpd.GeoDataFrame.from_file(b_file).iloc[0]
kienholz_file = get_demo_file("centerlines_baltoro_wgs84.shp")
kdf = gpd.read_file(kienholz_file)
# add fake attribs
entity.O1REGION = 0
entity.BGNDATE = 0
entity.NAME = "Baltoro"
entity.GLACTYPE = "0000"
gdir = oggm.GlacierDirectory(entity, base_dir=self.testdir)
gis.define_glacier_region(gdir, entity=entity)
gis.glacier_masks(gdir)
centerlines.compute_centerlines(gdir)
my_mask = np.zeros((gdir.grid.ny, gdir.grid.nx), dtype=np.uint8)
cls = gdir.read_pickle("centerlines", div_id=1)
for cl in cls:
x, y = tuple2int(cl.line.xy)
my_mask[y, x] = 1
# Transform
kien_mask = np.zeros((gdir.grid.ny, gdir.grid.nx), dtype=np.uint8)
from shapely.ops import transform
for index, entity in kdf.iterrows():
def proj(lon, lat):
return salem.transform_proj(salem.wgs84, gdir.grid.proj, lon, lat)
kgm = transform(proj, entity.geometry)
# Interpolate shape to a regular path
e_line = []
for distance in np.arange(0.0, kgm.length, gdir.grid.dx):
e_line.append(*kgm.interpolate(distance).coords)
kgm = shpg.LineString(e_line)
# Transform geometry into grid coordinates
def proj(x, y):
return gdir.grid.transform(x, y, crs=gdir.grid.proj)
kgm = transform(proj, kgm)
# Rounded nearest pix
project = lambda x, y: (np.rint(x).astype(np.int64), np.rint(y).astype(np.int64))
kgm = transform(project, kgm)
x, y = tuple2int(kgm.xy)
kien_mask[y, x] = 1
# We test the Heidke Skill score of our predictions
rest = kien_mask + 2 * my_mask
# gr.plot_array(rest)
na = len(np.where(rest == 3)[0])
nb = len(np.where(rest == 2)[0])
nc = len(np.where(rest == 1)[0])
nd = len(np.where(rest == 0)[0])
denom = np.float64((na + nc) * (nd + nc) + (na + nb) * (nd + nb))
hss = np.float64(2.0) * ((na * nd) - (nb * nc)) / denom
self.assertTrue(hss > 0.53)
def distribute_thickness_interp(gdir, add_slope=True, smooth_radius=None,
varname_suffix=''):
"""Compute a thickness map by interpolating between centerlines and border.
This is a rather cosmetic task, not relevant for OGGM but for ITMIX.
Parameters
----------
gdir : :py:class:`oggm.GlacierDirectory`
the glacier directory to process
add_slope : bool
whether a corrective slope factor should be used or not
smooth_radius : int
pixel size of the gaussian smoothing. Default is to use
cfg.PARAMS['smooth_window'] (i.e. a size in meters). Set to zero to
suppress smoothing.
varname_suffix : str
add a suffix to the variable written in the file (for experiments)
"""
# Variables
grids_file = gdir.get_filepath('gridded_data')
# See if we have the masks, else compute them
with utils.ncDataset(grids_file) as nc:
has_masks = 'glacier_ext_erosion' in nc.variables
if not has_masks:
from oggm.core.gis import interpolation_masks
interpolation_masks(gdir)
with utils.ncDataset(grids_file) as nc:
glacier_mask = nc.variables['glacier_mask'][:]
glacier_ext = nc.variables['glacier_ext_erosion'][:]
ice_divides = nc.variables['ice_divides'][:]
if add_slope:
slope_factor = nc.variables['slope_factor'][:]
else:
slope_factor = 1.
# Thickness to interpolate
thick = glacier_ext * np.NaN
thick[(glacier_ext-ice_divides) == 1] = 0.
# TODO: domain border too, for convenience for a start
thick[0, :] = 0.
thick[-1, :] = 0.
thick[:, 0] = 0.
thick[:, -1] = 0.
# Along the lines
cls = gdir.read_pickle('inversion_output')
fls = gdir.read_pickle('inversion_flowlines')
vs = []
for cl, fl in zip(cls, fls):
vs.extend(cl['volume'])
x, y = utils.tuple2int(fl.line.xy)
thick[y, x] = cl['thick']
init_vol = np.sum(vs)
# Interpolate
xx, yy = gdir.grid.ij_coordinates
pnan = np.nonzero(~ np.isfinite(thick))
pok = np.nonzero(np.isfinite(thick))
points = np.array((np.ravel(yy[pok]), np.ravel(xx[pok]))).T
inter = np.array((np.ravel(yy[pnan]), np.ravel(xx[pnan]))).T
thick[pnan] = griddata(points, np.ravel(thick[pok]), inter, method='cubic')
thick = thick.clip(0)
# Slope
thick *= slope_factor
# Smooth
dx = gdir.grid.dx
if smooth_radius != 0:
if smooth_radius is None:
smooth_radius = np.rint(cfg.PARAMS['smooth_window'] / dx)
thick = gaussian_blur(thick, np.int(smooth_radius))
thick = np.where(glacier_mask, thick, 0.)
# Re-mask
thick[glacier_mask == 0] = np.NaN
assert np.all(np.isfinite(thick[glacier_mask == 1]))
# Conserve volume
tmp_vol = np.nansum(thick * dx**2)
thick *= init_vol / tmp_vol
# write
grids_file = gdir.get_filepath('gridded_data')
with utils.ncDataset(grids_file, 'a') as nc:
vn = 'distributed_thickness' + varname_suffix
if vn in nc.variables:
v = nc.variables[vn]
else:
v = nc.createVariable(vn, 'f4', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Distributed ice thickness'
v[:] = thick
return thick
def compute_centerlines(gdir, div_id=None):
"""Compute the centerlines following Kienholz et al., (2014).
They are then sorted according to the modified Strahler number:
http://en.wikipedia.org/wiki/Strahler_number
Parameters
----------
gdir : oggm.GlacierDirectory
"""
# open
geom = gdir.read_pickle('geometries', div_id=div_id)
grids_file = gdir.get_filepath('gridded_data', div_id=div_id)
with netCDF4.Dataset(grids_file) as nc:
# Variables
glacier_mask = nc.variables['glacier_mask'][:]
glacier_ext = nc.variables['glacier_ext'][:]
topo = nc.variables['topo_smoothed'][:]
poly_pix = geom['polygon_pix']
# Find for local maximas on the outline
x, y = tuple2int(poly_pix.exterior.xy)
ext_yx = tuple(reversed(poly_pix.exterior.xy))
zoutline = topo[y[:-1], x[:-1]] # last point is first point
# Size of the half window to use to look for local maximas
maxorder = np.rint(cfg.PARAMS['localmax_window'] / gdir.grid.dx)
maxorder = np.clip(maxorder, 5., np.rint((len(zoutline) / 5.)))
heads_idx = scipy.signal.argrelmax(zoutline, mode='wrap',
order=maxorder.astype(np.int64))
if (not cfg.PARAMS['use_multiple_flowlines']) or len(heads_idx[0]) <= 1:
# small glaciers with one or less heads: take the absolute max
heads_idx = (np.atleast_1d(np.argmax(zoutline)),)
# Remove the heads that are too low
zglacier = topo[np.where(glacier_mask)]
head_threshold = np.percentile(zglacier, (1./3.)*100)
heads_idx = heads_idx[0][np.where(zoutline[heads_idx] > head_threshold)]
heads = np.asarray(ext_yx)[:, heads_idx]
heads_z = zoutline[heads_idx]
# careful, the coords are in y, x order!
heads = [shpg.Point(x, y) for y, x in zip(heads[0, :],
heads[1, :])]
# get radius of the buffer according to Kienholz eq. (1)
radius = cfg.PARAMS['q1'] * geom['polygon_area'] + cfg.PARAMS['q2']
radius = np.clip(radius, 0, cfg.PARAMS['rmax'])
radius /= gdir.grid.dx # in raster coordinates
# Plus our criteria, quite usefull to remove short lines:
radius += cfg.PARAMS['flowline_junction_pix'] * cfg.PARAMS['flowline_dx']
log.debug('%s: radius in raster coordinates: %.2f',
gdir.rgi_id, radius)
# OK. Filter and see.
log.debug('%s: number of heads before radius filter: %d',
gdir.rgi_id, len(heads))
heads, heads_z = _filter_heads(heads, heads_z, radius, poly_pix)
log.debug('%s: number of heads after radius filter: %d',
gdir.rgi_id, len(heads))
# Cost array
costgrid = _make_costgrid(glacier_mask, glacier_ext, topo)
# Terminus
t_coord = np.asarray(ext_yx)[:, np.argmin(zoutline)].astype(np.int64)
# Compute the routes
lines = []
for h in heads:
h_coord = np.asarray(h.xy)[::-1].astype(np.int64)
indices, _ = route_through_array(costgrid, h_coord, t_coord)
lines.append(shpg.LineString(np.array(indices)[:, [1, 0]]))
log.debug('%s: computed the routes', gdir.rgi_id)
# Filter the shortest lines out
radius = cfg.PARAMS['flowline_junction_pix'] * cfg.PARAMS['flowline_dx']
radius += 6 * cfg.PARAMS['flowline_dx']
olines, _ = _filter_lines(lines, heads, cfg.PARAMS['kbuffer'], radius)
log.debug('%s: number of heads after lines filter: %d',
gdir.rgi_id, len(olines))
# And rejoin the cutted tails
olines = _join_lines(olines)
# Adds the line level
for cl in olines:
cl.order = _line_order(cl)
# And sort them per order !!! several downstream tasks rely on this
cls = []
for i in np.argsort([cl.order for cl in olines]):
cls.append(olines[i])
# Final check
if len(cls) == 0:
raise RuntimeError('{} : no centerline found!'.format(gdir.rgi_id))
# Write the data
gdir.write_pickle(cls, 'centerlines', div_id=div_id)
# Netcdf
with netCDF4.Dataset(grids_file, 'a') as nc:
v = nc.createVariable('cost_grid', 'f4', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Centerlines cost grid'
v[:] = costgrid
def _mask_per_divide(gdir, div_id, dem, smoothed_dem):
"""Compute mask and geometries for each glacier divide.
Is called by glacier masks.
Parameters
----------
gdir : oggm.GlacierDirectory
div_id: int
id of the divide to process
dem: 2D array
topography
smoothed_dem: 2D array
smoothed topography
"""
outlines_file = gdir.get_filepath('outlines', div_id=div_id)
geometry = gpd.GeoDataFrame.from_file(outlines_file).geometry[0]
# Interpolate shape to a regular path
glacier_poly_hr = _interp_polygon(geometry, gdir.grid.dx)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise RuntimeError('This glacier geometry is crazy.')
# Rounded nearest pix
glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
(x, y) = glacier_poly_pix.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in glacier_poly_pix.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(glacier_poly_pix.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Because of the 0 values at nunataks boundaries, some "Ice Islands"
# can happen within nunataks (e.g.: RGI40-11.00062)
# See if we can filter them out easily
regions, nregions = label(glacier_mask, structure=label_struct)
if nregions > 1:
log.debug('%s: we had to cut an island in the mask', gdir.rgi_id)
# Check the size of those
region_sizes = [np.sum(regions == r) for r in np.arange(1, nregions+1)]
am = np.argmax(region_sizes)
# Check not a strange glacier
sr = region_sizes.pop(am)
for ss in region_sizes:
assert (ss / sr) < 0.1
glacier_mask[:] = 0
glacier_mask[np.where(regions == (am+1))] = 1
# write out the grids in the netcdf file
nc = gdir.create_gridded_ncdf_file('gridded_data', div_id=div_id)
v = nc.createVariable('topo', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography'
v[:] = dem
v = nc.createVariable('topo_smoothed', 'f4', ('y', 'x', ), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography smoothed' \
' with radius: {:.1} m'.format(cfg.PARAMS['smooth_window'])
v[:] = smoothed_dem
v = nc.createVariable('glacier_mask', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
v[:] = glacier_mask
v = nc.createVariable('glacier_ext', 'i1', ('y', 'x', ), zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
v[:] = glacier_ext
# add some meta stats and close
nc.max_h_dem = np.max(dem)
nc.min_h_dem = np.min(dem)
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
nc.close()
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries', div_id=div_id)
def catchment_area(gdir, div_id=None):
"""Compute the catchment areas of each tributary line.
The idea is to compute the route of lowest cost for any point on the
glacier to rejoin a centerline. These routes are then put together if
they belong to the same centerline, thus creating "catchment areas" for
each centerline.
Parameters
----------
gdir : oggm.GlacierDirectory
"""
# Variables
cls = gdir.read_pickle('centerlines', div_id=div_id)
geoms = gdir.read_pickle('geometries', div_id=div_id)
glacier_pix = geoms['polygon_pix']
fpath = gdir.get_filepath('gridded_data', div_id=div_id)
with netCDF4.Dataset(fpath) as nc:
costgrid = nc.variables['cost_grid'][:]
mask = nc.variables['glacier_mask'][:]
# If we have only one centerline this is going to be easy: take the
# mask and return
if len(cls) == 1:
cl_catchments = [np.array(np.nonzero(mask == 1)).T]
gdir.write_pickle(cl_catchments, 'catchment_indices', div_id=div_id)
return
# Initialise costgrid and the "catching" dict
cost_factor = 0. # Make it cheap
dic_catch = dict()
for i, cl in enumerate(cls):
x, y = tuple2int(cl.line.xy)
costgrid[y, x] = cost_factor
for x, y in [(int(x), int(y)) for x, y in cl.line.coords]:
assert (y, x) not in dic_catch
dic_catch[(y, x)] = set([(y, x)])
# It is much faster to make the array as small as possible (especially
# with divides). We have to trick:
pm = np.nonzero(mask == 1)
ymi, yma = np.min(pm[0])-1, np.max(pm[0])+2
xmi, xma = np.min(pm[1])-1, np.max(pm[1])+2
costgrid = costgrid[ymi:yma, xmi:xma]
mask = mask[ymi:yma, xmi:xma]
# Where did we compute the path already?
computed = np.where(mask == 1, 0, np.nan)
# Coords of Terminus (converted)
endcoords = np.array(cls[0].tail.coords[0])[::-1].astype(np.int64)
endcoords -= [ymi, xmi]
# Start with all the paths at the boundaries, they are more likely
# to cover much of the glacier
for headx, heady in tuple2int(glacier_pix.exterior.coords):
headcoords = np.array([heady-ymi, headx-xmi]) # convert
indices, _ = route_through_array(costgrid, headcoords, endcoords)
inds = np.array(indices).T
computed[inds[0], inds[1]] = 1
set_dump = set([])
for y, x in indices:
y, x = y+ymi, x+xmi # back to original
set_dump.add((y, x))
if (y, x) in dic_catch:
dic_catch[(y, x)] = dic_catch[(y, x)].union(set_dump)
break
# Repeat for the not yet computed pixels
while True:
not_computed = np.where(computed == 0)
if len(not_computed[0]) == 0: # All points computed !!
break
headcoords = np.array([not_computed[0][0], not_computed[1][0]]).astype(np.int64)
indices, _ = route_through_array(costgrid, headcoords, endcoords)
inds = np.array(indices).T
computed[inds[0], inds[1]] = 1
set_dump = set([])
for y, x in indices:
y, x = y+ymi, x+xmi # back to original
set_dump.add((y, x))
if (y, x) in dic_catch:
dic_catch[(y, x)] = dic_catch[(y, x)].union(set_dump)
break
# For each centerline, make a set of all points flowing into it
cl_catchments = []
for cl in cls:
# Union of all
cl_catch = set()
for x, y in [(int(x), int(y)) for x, y in cl.line.coords]:
cl_catch = cl_catch.union(dic_catch[(y, x)])
cl_catchments.append(cl_catch)
# The higher order centerlines will get the points from the upstream
# ones too. The idea is to store the points which are unique to each
# centerline: now, in decreasing line order we remove the indices from
# the tributaries
cl_catchments = cl_catchments[::-1]
for i, cl in enumerate(cl_catchments):
cl_catchments[i] = np.array(list(cl.difference(*cl_catchments[i+1:])))
cl_catchments = cl_catchments[::-1] # put it back in order
# Write the data
gdir.write_pickle(cl_catchments, 'catchment_indices', div_id=div_id)
def _mask_per_divide(gdir, div_id, dem, smoothed_dem):
"""Compute mask and geometries for each glacier divide.
Is called by glacier masks.
Parameters
----------
gdir : oggm.GlacierDirectory
div_id: int
id of the divide to process
dem: 2D array
topography
smoothed_dem: 2D array
smoothed topography
"""
outlines_file = gdir.get_filepath('outlines', div_id=div_id)
geometry = gpd.GeoDataFrame.from_file(outlines_file).geometry[0]
# Interpolate shape to a regular path
glacier_poly_hr = _interp_polygon(geometry, gdir.grid.dx)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise RuntimeError('This glacier geometry is crazy.')
# Rounded nearest pix
glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
(x, y) = glacier_poly_pix.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in glacier_poly_pix.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(glacier_poly_pix.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Because of the 0 values at nunataks boundaries, some "Ice Islands"
# can happen within nunataks (e.g.: RGI40-11.00062)
# See if we can filter them out easily
regions, nregions = label(glacier_mask, structure=label_struct)
if nregions > 1:
log.debug('%s: we had to cut an island in the mask', gdir.rgi_id)
# Check the size of those
region_sizes = [
np.sum(regions == r) for r in np.arange(1, nregions + 1)
]
am = np.argmax(region_sizes)
# Check not a strange glacier
sr = region_sizes.pop(am)
for ss in region_sizes:
assert (ss / sr) < 0.1
glacier_mask[:] = 0
glacier_mask[np.where(regions == (am + 1))] = 1
# write out the grids in the netcdf file
nc = gdir.create_gridded_ncdf_file('gridded_data', div_id=div_id)
v = nc.createVariable('topo', 'f4', (
'y',
'x',
), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography'
v[:] = dem
v = nc.createVariable('topo_smoothed', 'f4', (
'y',
'x',
), zlib=True)
v.units = 'm'
v.long_name = 'DEM topography smoothed' \
' with radius: {:.1} m'.format(cfg.PARAMS['smooth_window'])
v[:] = smoothed_dem
v = nc.createVariable('glacier_mask', 'i1', (
'y',
'x',
), zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
v[:] = glacier_mask
v = nc.createVariable('glacier_ext', 'i1', (
'y',
'x',
), zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
v[:] = glacier_ext
# add some meta stats and close
nc.max_h_dem = np.max(dem)
nc.min_h_dem = np.min(dem)
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
nc.close()
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries', div_id=div_id)
def glacier_masks(gdir):
"""Makes a gridded mask of the glacier outlines that can be used by OGGM.
For a more robust solution (not OGGM compatible) see simple_glacier_masks.
Parameters
----------
gdir : :py:class:`oggm.GlacierDirectory`
where to write the data
"""
# In case nominal, just raise
if gdir.is_nominal:
raise GeometryError('{} is a nominal glacier.'.format(gdir.rgi_id))
if not os.path.exists(gdir.get_filepath('gridded_data')):
# In a possible future, we might actually want to raise a
# deprecation warning here
process_dem(gdir)
# Geometries
geometry = gdir.read_shapefile('outlines').geometry[0]
# Interpolate shape to a regular path
glacier_poly_hr = _interp_polygon(geometry, gdir.grid.dx)
# Transform geometry into grid coordinates
# It has to be in pix center coordinates because of how skimage works
def proj(x, y):
grid = gdir.grid.center_grid
return grid.transform(x, y, crs=grid.proj)
glacier_poly_hr = shapely.ops.transform(proj, glacier_poly_hr)
# simple trick to correct invalid polys:
# http://stackoverflow.com/questions/20833344/
# fix-invalid-polygon-python-shapely
glacier_poly_hr = glacier_poly_hr.buffer(0)
if not glacier_poly_hr.is_valid:
raise InvalidGeometryError('This glacier geometry is not valid.')
# Rounded nearest pix
glacier_poly_pix = _polygon_to_pix(glacier_poly_hr)
if glacier_poly_pix.exterior is None:
raise InvalidGeometryError('Problem in converting glacier geometry '
'to grid resolution.')
# Compute the glacier mask (currently: center pixels + touched)
nx, ny = gdir.grid.nx, gdir.grid.ny
glacier_mask = np.zeros((ny, nx), dtype=np.uint8)
glacier_ext = np.zeros((ny, nx), dtype=np.uint8)
(x, y) = glacier_poly_pix.exterior.xy
glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
for gint in glacier_poly_pix.interiors:
x, y = tuple2int(gint.xy)
glacier_mask[skdraw.polygon(y, x)] = 0
glacier_mask[y, x] = 0 # on the nunataks, no
x, y = tuple2int(glacier_poly_pix.exterior.xy)
glacier_mask[y, x] = 1
glacier_ext[y, x] = 1
# Because of the 0 values at nunataks boundaries, some "Ice Islands"
# can happen within nunataks (e.g.: RGI40-11.00062)
# See if we can filter them out easily
regions, nregions = label(glacier_mask, structure=label_struct)
if nregions > 1:
log.debug('(%s) we had to cut an island in the mask', gdir.rgi_id)
# Check the size of those
region_sizes = [np.sum(regions == r) for r in np.arange(1, nregions+1)]
am = np.argmax(region_sizes)
# Check not a strange glacier
sr = region_sizes.pop(am)
for ss in region_sizes:
assert (ss / sr) < 0.1
glacier_mask[:] = 0
glacier_mask[np.where(regions == (am+1))] = 1
# Write geometries
geometries = dict()
geometries['polygon_hr'] = glacier_poly_hr
geometries['polygon_pix'] = glacier_poly_pix
geometries['polygon_area'] = geometry.area
gdir.write_pickle(geometries, 'geometries')
# write out the grids in the netcdf file
with GriddedNcdfFile(gdir) as nc:
if 'glacier_mask' not in nc.variables:
v = nc.createVariable('glacier_mask', 'i1', ('y', 'x', ),
zlib=True)
v.units = '-'
v.long_name = 'Glacier mask'
else:
v = nc.variables['glacier_mask']
v[:] = glacier_mask
if 'glacier_ext' not in nc.variables:
v = nc.createVariable('glacier_ext', 'i1', ('y', 'x', ),
zlib=True)
v.units = '-'
v.long_name = 'Glacier external boundaries'
else:
v = nc.variables['glacier_ext']
v[:] = glacier_ext
dem = nc.variables['topo'][:]
valid_mask = nc.variables['topo_valid_mask'][:]
# Last sanity check based on the masked dem
tmp_max = np.max(dem[np.where(glacier_mask == 1)])
tmp_min = np.min(dem[np.where(glacier_mask == 1)])
if tmp_max < (tmp_min + 1):
raise InvalidDEMError('({}) min equal max in the masked DEM.'
.format(gdir.rgi_id))
# Log DEM that needed processing within the glacier mask
if gdir.get_diagnostics().get('dem_needed_interpolation', False):
pnan = (valid_mask == 0) & glacier_mask
gdir.add_to_diagnostics('dem_invalid_perc_in_mask',
np.sum(pnan) / np.sum(glacier_mask))
# add some meta stats and close
dem_on_g = dem[np.where(glacier_mask)]
nc.max_h_glacier = np.max(dem_on_g)
nc.min_h_glacier = np.min(dem_on_g)
