def mesh_and_interpolate(args):
set_logger_level(args.verbose)
t1 = perf_counter()
logger.info("~> Reading input files")
axe = get_hydraulic_axis(args.infile_axis)
section_seq = CrossSectionSequence.from_file(
args.infile_cross_sections,
"Cross-section",
field_id=args.attr_cross_sections,
project_straight_line=args.project_straight_line)
# if args.infile_epis is not None and args.dist_corr_epi is not None:
# epis = CrossSectionSequence.from_file(args.infile_epis, "Groynes", field_id=args.attr_epis,
# project_straight_line=args.project_straight_line)
# else:
# epis = None
section_seq.compute_dist_proj_axe(axe, args.dist_max)
section_seq.check_intersections()
section_seq.sort_by_dist()
# section_seq.export_sections_shp('profiles_projected.shp') # DEBUG
if args.infile_constraint_lines is None:
constraint_lines = ConstraintLine.get_lines_and_set_limits_from_sections(
section_seq, args.interp_constraint_lines)
else:
constraint_lines = ConstraintLine.get_lines_from_file(
args.infile_constraint_lines, args.interp_constraint_lines)
if args.nb_pts_lat is not None and len(constraint_lines) != 2:
raise TatooineException(
"Argument `--nb_pts_lat` is only compatible with 2 constraint lines!"
)
if args.interp_values.startswith('BI') and len(constraint_lines) != 2:
raise TatooineException(
"A 2D interpolation is only compatible with 2 constraint lines!"
)
section_seq.find_and_add_limits(constraint_lines, args.dist_max)
mesh_constr = MeshConstructor(section_seq=section_seq,
lat_step=args.lat_step,
nb_pts_lat=args.nb_pts_lat,
interp_values=args.interp_values)
mesh_constr.build_interp(constraint_lines, args.long_step,
args.constant_long_disc)
# mesh_constr.export_segments('check_segments.shp') # DEBUG
# if epis is not None:
# mesh_constr.corr_bathy_on_epis(epis, args.dist_corr_epi)
if args.outfile_nodes is not None:
mesh_constr.export_points(args.outfile_nodes)
if args.outfile_mesh is not None:
mesh_constr.build_mesh()
mesh_constr.export_mesh(args.outfile_mesh, lang=args.lang)
t2 = perf_counter()
logger.info("=> Execution time: {}s".format(t2 - t1))
def summary(self):
try:
nnode, nelem = len(self.triangle['vertices']), len(
self.triangle['triangles'])
except KeyError:
raise TatooineException("The generation of the mesh failed!")
return "Mesh with {} nodes and {} elements".format(nnode, nelem)
def project_straight_line(self):
"""
@brief: Planar projection on a straight line joining first and last point of the cross-section
"""
if self.limits:
raise TatooineException(
"Limits have to be set after calling to project_straight_line!"
)
# Build straight line
first_point = (self.coord.array['X'][0], self.coord.array['Y'][0])
last_point = (self.coord.array['X'][-1], self.coord.array['Y'][-1])
line = LineString((first_point, last_point))
# Update X, Y, Xt columns in self.coord.array
for row in self.coord.array:
point = Point((row['X'], row['Y']))
dist = line.project(point)
point_project = line.interpolate(dist)
row['X'] = point_project.x
row['Y'] = point_project.y
self.coord.compute_Xt()
# Update geom
self.geom = self.coord.convert_as_linestring()
def get_lines_from_file(filename, interp_coord='LINEAR'):
"""
Returns a list of ConstraintLine from an input file
TODO 1: Value is ignored in i2s file format
"""
lines = []
if filename is not None:
if filename.endswith('.i2s'):
with bk.Read(filename) as in_i2s:
in_i2s.read_header()
for i, line in enumerate(in_i2s.get_open_polylines()):
lines.append(
ConstraintLine(i, list(line.polyline().coords),
interp_coord))
elif filename.endswith('.shp'):
if shp.get_shape_type(filename) not in (shapefile.POLYLINE,
shapefile.POLYLINEZ,
shapefile.POLYLINEM):
raise TatooineException(
"The type of file %s is not POLYLINEZ[M]" % filename)
for i, line in enumerate(shp.get_open_polylines(filename)):
lines.append(
ConstraintLine(i, list(line.polyline().coords),
interp_coord))
else:
raise NotImplementedError(
"Only shp and i2s formats are supported for constraint lines"
)
return lines
def densify_cross_sections(args):
set_logger_level(args.verbose)
t1 = perf_counter()
logger.info("~> Reading input files")
axe = get_hydraulic_axis(args.infile_axis)
section_seq = CrossSectionSequence.from_file(
args.infile_cross_sections,
"Cross-section",
field_id=args.attr_cross_sections,
project_straight_line=args.project_straight_line)
section_seq.compute_dist_proj_axe(axe, args.dist_max)
section_seq.check_intersections()
section_seq.sort_by_dist()
if args.infile_constraint_lines is None:
constraint_lines = ConstraintLine.get_lines_and_set_limits_from_sections(
section_seq, args.interp_constraint_lines)
else:
constraint_lines = ConstraintLine.get_lines_from_file(
args.infile_constraint_lines, args.interp_constraint_lines)
if args.nb_pts_lat is not None and len(constraint_lines) != 2:
raise TatooineException(
"Argument `--nb_pts_lat` is only compatible with 2 constraint lines!"
)
if args.interp_values.startswith('BI') and len(constraint_lines) != 2:
raise TatooineException(
"A 2D interpolation is only compatible with 2 constraint lines!"
)
section_seq.find_and_add_limits(constraint_lines, args.dist_max)
#section_seq.export_sections_shp('export_cross-sections.shp')
mesh_constr = MeshConstructor(section_seq=section_seq,
lat_step=args.lat_step,
nb_pts_lat=args.nb_pts_lat,
interp_values=args.interp_values)
mesh_constr.build_interp(constraint_lines, args.long_step, True)
mesh_constr.export_sections(args.outfile_sections)
t2 = perf_counter()
logger.info("=> Execution time: {}s".format(t2 - t1))
def build_mesh(self, in_floworiented_crs=False, opts='p'):
"""
@brief: Build mesh under constraints
@param in_floworiented_crs <bool>: boolean to which coordinate system is usec
@param opts <str>: options for the triangulation.
`p` - Triangulates a Planar Straight Line Graph.
`q` - Quality mesh generation with no angles smaller than 20 degrees.
An alternate minimum angle may be specified after the `q`.
`a` - Imposes a maximum triangle area constraint. A fixed area constraint (that applies to every triangle)
may be specified after the `a`, or varying areas may be read from the input dictionary.
"""
logger.info("~> Building mesh")
if in_floworiented_crs:
tri = self.export_floworiented_triangulation_dict()
self.triangle = triangle.triangulate(tri, opts=opts)
self.triangle['vertices'] = self.export_triangulation_dict()[
'vertices'] # overwrite by cartesian coordinates
else:
tri = self.export_triangulation_dict()
self.triangle = triangle.triangulate(tri, opts=opts)
if opts == 'p': # Check that vertices correspond to points
if len(self.points) != len(self.triangle['vertices']):
if len(self.points) < len(self.triangle['vertices']):
logger.error("New nodes are:")
ori_points = np.column_stack(
(self.points['X'], self.points['Y']))
ori_combined = ori_points[:, 0] * ori_points[:, 1] / (
ori_points[:, 0] + ori_points[:, 1])
new_points = self.triangle['vertices']
new_combined = new_points[:, 0] * new_points[:, 1] / (
new_points[:, 0] + new_points[:, 1])
diff = np.setxor1d(ori_combined, new_combined)
logger.error(new_points[np.isin(new_combined, diff)])
raise TatooineException(
"Mesh is corrupted... %i vs %i nodes." %
(len(self.points), len(self.triangle['vertices'])))
if 'triangles' not in self.triangle:
raise TatooineException(
"Mesh was not generated, no triangle found!")
logger.info(self.summary())
def extract_bed(self, bed1_id, bed2_id):
"""
@brief: Extract coordinates of a portion of a cross-section between 2 limits
/!\ bed1_id and bed2_id should be "ordered" correctly, otherwise an exception is raised
@return <Bed>: structured array with columns ('X', 'Y', 'Xt', 'xt')
"""
limit1 = self.get_limit_by_id(bed1_id)
limit2 = self.get_limit_by_id(bed2_id)
Xt1 = limit1['Xt_section']
Xt2 = limit2['Xt_section']
# Check that Xt are increasing from bed1_id to bed2_id
if Xt1 > Xt2:
raise TatooineException(
"Order of beds {} and {} leads to decreasing Xt values for {}".
format(bed1_id, bed2_id, self))
Xt_section = self.coord.array['Xt']
sub_coord = self.coord.array[np.logical_and(Xt_section >= Xt1,
Xt_section <= Xt2)]
# Add starting point if necessary
if Xt1 not in Xt_section:
row = np.array([
tuple(limit1[var] if var not in ('Xt', 'xt') else Xt1
for var in sub_coord.dtype.names)
],
dtype=sub_coord.dtype)
row['xt'] = 0.0
sub_coord = np.insert(sub_coord, 0, row)
# Add last point if necessary
if Xt2 not in Xt_section:
row = np.array([
tuple(limit2[var] if var not in ('Xt', 'xt') else Xt2
for var in sub_coord.dtype.names)
],
dtype=sub_coord.dtype)
row['xt'] = 1.0
sub_coord = np.append(sub_coord, row)
# Check order of points
if not strictly_increasing(sub_coord['Xt']):
logger.debug("/!\ Xt values are not strictly increasing"
) # FIXME: It should not happen!
logger.debug(sub_coord['Xt'])
logger.debug("Please check the following limits below:")
logger.debug(limit1)
logger.debug(limit2)
points_to_keep = np.ediff1d(sub_coord['Xt'], to_begin=1.) != 0.
sub_coord = sub_coord[points_to_keep]
return Bed(sub_coord, ['xt'])
def export_segments(self, path):
if path.endswith('.shp'):
logger.info("~> Export segments in a shp file")
with shapefile.Writer(path, shapeType=shapefile.POLYLINE) as w:
w.field('id_seg', 'N', decimal=6)
for i, (node1, node2) in enumerate(self.segments):
point1 = self.points[node1]
point2 = self.points[node2]
w.line([[[point1['X'], point1['Y']],
[point2['X'], point2['Y']]]])
w.record(id_seg=i)
else:
raise TatooineException(
"Only the shp format is supported for segments")
def corr_bathy_on_epis(self, epis, dist_corr_epi):
raise NotImplementedError #TODO
logger.info("~> Correction bathymetry around 'épis'")
if self.var_names() != ['Z']:
raise TatooineException(
"Impossible to correct elevation of 'épis' for the sediment layers"
)
for epi in epis:
epi_geom = epi.coord.convert_as_linestring()
for i, coord in enumerate(self.points):
pt_node = Point((coord['X'], coord['Y']))
if epi_geom.distance(pt_node) < dist_corr_epi:
Xt_proj = epi_geom.project(pt_node)
pt_proj = epi_geom.interpolate(Xt_proj)
epi.coord.values['Z'][i] = pt_proj.z
def compute_xp(self):
"""
Compute dimensionless from starting to ending point distance projetée adimensionnée sur droite début->fin
"""
trace = LineString([self.array[['X', 'Y']][0], self.array[['X', 'Y']][-1]])
Xp = np.empty(len(self.array), dtype=np.float)
for i, row in enumerate(self.array):
point = Point(list(row)[:2])
Xp[i] = trace.project(point)
if not strictly_increasing(Xp):
raise TatooineException("L'abscisse projetée n'est pas strictement croissante le long du profil. "
"Le profil n'est pas suffisamment droit...")
xp = Xp/Xp[-1]
self.array = append_fields(self.array, 'xp', xp, usemask=False)
def find_and_add_limit(self, constraint_line, dist_max=None):
"""
@param constraint_line <shapely.geometry.LineString>: 2D constraint line
@param dist_max <float>: maximum search distance to rescue intersections for limits
"""
if self.geom.intersects(constraint_line.geom):
intersection = self.geom.intersection(constraint_line.geom)
if isinstance(intersection, MultiPoint):
logger.warn(
"Intersection between '{}' and '{}' contains multiple points, "
"only the first is kept.".format(self, constraint_line))
intersection = intersection[0]
if isinstance(intersection, Point):
# Compute projections
Xt_section = self.geom.project(intersection)
Xt_line = constraint_line.geom.project(intersection)
self.add_limit(constraint_line.id, Xt_section, Xt_line,
intersection)
else:
raise TatooineException(
"Intersection between '{}' and '{}' is empty or not supported: {}"
.format(self, constraint_line, type(intersection)))
else:
if dist_max is not None:
distance = self.geom.distance(constraint_line.geom)
if distance < dist_max:
for i, coord in enumerate(constraint_line.coord):
# Try to find a point of the constraint line which is in the vicinity of the current section
point = Point(coord)
dist = self.geom.distance(point)
if dist < dist_max:
# A point is found and is considered
Xt_line = constraint_line.geom.project(point)
Xt_section = self.geom.project(point)
intersection = self.geom.interpolate(Xt_section)
self.add_limit(constraint_line.id, Xt_section,
Xt_line, intersection)
logger.debug(
"Add a limit with the line {} after {} iterations (distance = {})"
.format(constraint_line.id, i, dist))
break
def add_points(self, coord, zone_index, xl, bed_index):
"""!
@brief: Add vertices/nodes
@param coord <2D-array float>: table with columns 'X', 'Y', 'Xt_upstream' and 'Xt_downstream'
"""
if self.casiers_nodes_idx:
raise TatooineException(
"Impossible to add points in river bed after having considered the floodplain"
)
new_coord = np.empty(len(coord), dtype=self.points.dtype)
# FIXME: avoid copying in using np.lib.recfunctions.append_fields?
for var in ['X', 'Y', 'xt', 'Xt_upstream',
'Xt_downstream']: # copy existing columns
new_coord[var] = coord[var]
new_coord['zone'] = zone_index
new_coord['bed'] = bed_index
new_coord['Xl'] = self.section_seq[zone_index].dist_proj_axe * (1 - xl) + \
self.section_seq[zone_index + 1].dist_proj_axe * xl
new_coord['xl'] = xl
self.i_pt += len(new_coord)
self.points = np.hstack((self.points, new_coord))
def __init__(self, id, coord, label='Cross-section'):
"""
Create a cross-section from coordinates X and Y
Limits are not set at the object instantiation
@param id <integer|str>: unique identifier
@label <str>: type of section (`Cross-section` or `Transverse constraint line`)
@param coords <[tuple]>: sequence of X and Y coordinates
"""
self.id = id
self.label = label
self.coord = Coord(np.array(coord, dtype=float_vars(['X', 'Y'])),
['Xt', 'xt'])
self.nb_points = len(self.coord.array)
if len(coord) < 2:
raise TatooineException("%s %s does not have at least 2 points!" %
(label, id))
self.geom = LineString(
coord) # FIXME: might contains duplicated points
self.limits = OrderedDict()
self.dist_proj_axe = -1
def export_points(self, path):
if path.endswith('.xyz'):
logger.info("~> Exports points in xyz")
with open(path, 'wb') as fileout:
z_array = self.interp_values_from_geom()[0, :]
np.savetxt(fileout,
np.vstack((self.points['X'], self.points['Y'],
z_array)).T,
delimiter=' ',
fmt='%.{}f'.format(DIGITS))
elif path.endswith('.shp'):
logger.info("~> Exports points in shp")
z_array = self.interp_values_from_geom()[0, :]
with shapefile.Writer(path, shapeType=shapefile.POINT) as w:
w.field('zone', 'N', decimal=6)
w.field('bed', 'N', decimal=6)
w.field('Xt_upstream', 'N', decimal=6)
w.field('Xt_downstream', 'N', decimal=6)
w.field('xt', 'N', decimal=6)
w.field('xl', 'N', decimal=6)
w.field('Z', 'N', decimal=6)
for row, z in zip(self.points, z_array):
w.point(row['X'], row['Y'])
w.record(
**{
'zone': float(row['zone']),
'bed': float(row['bed']),
'Xt_upstream': row['Xt_upstream'],
'Xt_downstream': row['Xt_downstream'],
'xt': row['xt'],
'xl': row['xl'],
'Z': z
})
else:
raise TatooineException(
"Only shp and xyz are supported for points set")
def compute_dist_proj_axe(self, axe_geom, dist_max):
"""
@brief: Compute distance along hydraulic axis
@param axe_geom <shapely.geometry.LineString>: hydraulic axis (/!\ Beware of its orientation)
@param dist_max <float>: maximum search distance to rescue intersections for limits
"""
logger.info(
"~> Compute distances along hydraulic axis to order cross-sections"
)
to_keep_list = []
for section in self:
section_geom = section.geom
if section_geom.intersects(axe_geom):
intersection = section_geom.intersection(axe_geom)
if isinstance(intersection, Point):
section.dist_proj_axe = axe_geom.project(intersection)
else:
raise TatooineException(
"Intersection between '{}' and the hydraulic axis "
"is not a unique point".format(section))
else:
if dist_max is not None:
for pos in (0, -1):
dist = section_geom.distance(
Point(axe_geom.coords[pos]))
if dist < dist_max:
section.dist_proj_axe = 0.0 if pos == 0 else axe_geom.length
if section.dist_proj_axe == -1:
logger.warn(
"{} do not intersect the hydraulic axis (distance = {}m) and is ignored"
.format(section, section.geom.distance(axe_geom)))
to_keep_list.append(False)
else:
to_keep_list.append(True)
self.section_list = [
p for p, to_keep in zip(self.section_list, to_keep_list) if to_keep
]
def __init__(self, array, vars2add, remove_duplicates=False):
"""
@param array: structured array. `X`, `Y` are compulsory but other variables (such as Z) and distances are optional
@param var2add <[str]>: list including eventually `Xt` and/or `xt` top compute them if they are not already present
@param remove_duplicates <bool>: remove consecutive duplicated points
"""
self.array = array
self.coord_labels = list(self.array.dtype.fields.keys())
self.values = None
if 'X' not in self.coord_labels and 'Y' not in self.coord_labels:
raise TatooineException("Columns X and Y are compulsory.")
if 'Xt' in vars2add:
self.compute_Xt()
if 'xt' in vars2add:
self.compute_xt()
if remove_duplicates:
if not strictly_increasing(self.array['Xt']):
logger.warn("Duplicated points are removed")
# Suppression des doublons (points superposés dans la polyligne)
points2keep = np.ediff1d(self.array['Xt'], to_begin=1.) != 0.
self.array = self.array[points2keep]
def mesh_crue10_run(args):
set_logger_level(args.verbose)
t1 = perf_counter()
# Read the model and its submodels from xml/shp files
etude = Etude(args.infile_etu)
modele = etude.get_modele(args.model_name)
modele.read_all()
logger.info(modele)
for sous_modele in modele.liste_sous_modeles:
sous_modele.remove_sectioninterpolee()
sous_modele.normalize_geometry()
logger.info(sous_modele.summary())
# sous_modele.write_shp_limites_lits_numerotes('limites_lits.shp') # DEBUG
logger.info(modele)
global_mesh_constr = MeshConstructor()
# Handle branches in minor bed
for i, branche in enumerate(modele.get_liste_branches()):
# Ignore branch if branch_patterns is set and do not match with current branch name
if args.branch_patterns is not None:
ignore = True
for pattern in args.branch_patterns:
if pattern in branche.id:
ignore = False
break
else:
ignore = False
if branche.type not in args.branch_types_filter or not branche.is_active:
ignore = True
if not ignore:
logger.info("===== TRAITEMENT DE LA BRANCHE %s =====" % branche.id)
axe = branche.geom
try:
section_seq = CrossSectionSequence()
for crue_section in branche.liste_sections_dans_branche:
if isinstance(crue_section, SectionProfil):
coords = list(crue_section.get_coord(add_z=True))
section = CrossSection(crue_section.id,
[(coord[0], coord[1])
for coord in coords],
'Section')
# Determine some variables (constant over the simulation) from the geometry
z = np.array([coord[2] for coord in coords])
is_bed_active = crue_section.get_is_bed_active_array()
mean_strickler = crue_section.get_friction_coeff_array(
)
section.coord.values = np.core.records.fromarrays(
np.column_stack(
(z, is_bed_active, mean_strickler)).T,
names=VARIABLES_FROM_GEOMETRY)
section_seq.add_section(section)
section_seq.compute_dist_proj_axe(axe, args.dist_max)
if len(section_seq) >= 2:
section_seq.check_intersections()
# section_seq.sort_by_dist() is useless because profiles are already sorted
constraint_lines = ConstraintLine.get_lines_and_set_limits_from_sections(
section_seq, args.interp_constraint_lines)
mesh_constr = MeshConstructor(
section_seq=section_seq,
lat_step=args.lat_step,
nb_pts_lat=args.nb_pts_lat,
interp_values=args.interp_values)
mesh_constr.build_interp(constraint_lines, args.long_step,
args.constant_long_disc)
mesh_constr.build_mesh(in_floworiented_crs=True)
global_mesh_constr.append_mesh_constr(mesh_constr)
else:
logger.warning("Branche ignorée par manque de sections")
except TatooineException as e:
logger.error(
"/!\\ Branche ignorée à cause d'une erreur bloquante :")
logger.error(e.message)
logger.info("\n")
# Handle casiers in floodplain
nb_casiers = len(modele.get_liste_casiers())
if args.infile_dem and nb_casiers > 0:
logger.info("===== TRAITEMENT DES CASIERS =====")
if not os.path.exists(args.infile_dem):
raise TatooineException("File not found: %s" % args.infile_dem)
from gdal import Open
raster = Open(args.infile_dem)
dem_interp = interp_raster(raster)
floodplain_step = args.floodplain_step if not None else args.long_step
max_elem_area = floodplain_step * floodplain_step / 2.0
simplify_dist = floodplain_step / 2.0
for i, casier in enumerate(modele.get_liste_casiers()):
if casier.is_active:
if casier.geom is None:
raise TatooineException(
"Geometry of %s could not be found" % casier)
line = casier.geom.simplify(simplify_dist)
if not line.is_closed:
raise RuntimeError
coords = resample_2d_line(
line.coords,
floodplain_step)[1:] # Ignore last duplicated node
hard_nodes_xy = np.array(coords, dtype=np.float)
hard_nodes_idx = np.arange(0, len(hard_nodes_xy), dtype=np.int)
hard_segments = np.column_stack(
(hard_nodes_idx, np.roll(hard_nodes_idx, 1)))
tri = {
'vertices':
np.array(
np.column_stack(
(hard_nodes_xy[:, 0], hard_nodes_xy[:, 1]))),
'segments':
hard_segments,
}
triangulation = triangle.triangulate(tri,
opts='qpa%f' %
max_elem_area)
nodes_xy = np.array(triangulation['vertices'], dtype=np.float)
bottom = dem_interp(nodes_xy)
points = unstructured_to_structured(np.column_stack(
(nodes_xy, bottom)),
names=['X', 'Y', 'Z'])
global_mesh_constr.add_floodplain_mesh(triangulation, points)
if len(global_mesh_constr.points) == 0:
raise ExceptionCrue10(
"Aucun point à traiter, adaptez l'option `--branch_patterns` et/ou `--branch_types_filter`"
)
logger.info(global_mesh_constr.summary()
) # General information about the merged mesh
if args.infile_rcal:
# Read rcal result file
results = RunResults(args.infile_rcal)
logger.info(results.summary())
# Check result consistency
missing_sections = modele.get_missing_active_sections(
results.emh['Section'])
if missing_sections:
raise ExceptionCrue10("Sections manquantes :\n%s" %
missing_sections)
# Subset results to get requested variables at active sections
varnames_1d = results.variables['Section']
logger.info("Variables 1D disponibles aux sections: %s" % varnames_1d)
try:
pos_z = varnames_1d.index('Z')
except ValueError:
raise TatooineException(
"La variable Z doit être présente dans les résultats aux sections"
)
if global_mesh_constr.has_floodplain:
try:
pos_z_fp = results.variables['Casier'].index('Z')
except ValueError:
raise TatooineException(
"La variable Z doit être présente dans les résultats aux casiers"
)
else:
pos_z_fp = None
pos_variables = [
results.variables['Section'].index(var) for var in varnames_1d
]
pos_sections_list = [
results.emh['Section'].index(profil.id)
for profil in global_mesh_constr.section_seq
]
if global_mesh_constr.has_floodplain:
pos_casiers_list = [
results.emh['Casier'].index(casier.id)
for casier in modele.get_liste_casiers() if casier.is_active
]
else:
pos_casiers_list = []
additional_variables_id = ['H']
if 'Vact' in varnames_1d:
additional_variables_id.append('M')
values_geom = global_mesh_constr.interp_values_from_geom()
z_bottom = values_geom[0, :]
with Serafin.Write(args.outfile_mesh, args.lang,
overwrite=True) as resout:
title = '%s (written by TatooineMesher)' % os.path.basename(
args.outfile_mesh)
output_header = Serafin.SerafinHeader(title=title, lang=args.lang)
output_header.from_triangulation(
global_mesh_constr.triangle['vertices'],
global_mesh_constr.triangle['triangles'] + 1)
for var_name in VARIABLES_FROM_GEOMETRY:
if var_name in ['B', 'W']:
output_header.add_variable_from_ID(var_name)
else:
output_header.add_variable_str(var_name, var_name, '')
for var_id in additional_variables_id:
output_header.add_variable_from_ID(var_id)
for var_name in varnames_1d:
output_header.add_variable_str(var_name, var_name, '')
resout.write_header(output_header)
if args.calc_unsteady is None:
for i, calc_name in enumerate(results.calc_steady_dict.keys()):
logger.info("~> Calcul permanent %s" % calc_name)
# Read a single *steady* calculation
res_steady = results.get_res_steady(calc_name)
variables_at_profiles = res_steady['Section'][
pos_sections_list, :][:, pos_variables]
if global_mesh_constr.has_floodplain:
z_at_casiers = res_steady['Casier'][pos_casiers_list,
pos_z_fp]
else:
z_at_casiers = None
# Interpolate between sections and set in casiers
values_res = global_mesh_constr.interp_values_from_res(
variables_at_profiles, z_at_casiers, pos_z)
# Compute water depth: H = Z - Zf and clip below 0m (avoid negative values)
depth = np.clip(values_res[pos_z, :] - z_bottom,
a_min=0.0,
a_max=None)
# Merge and write values
if 'Vact' in varnames_1d:
# Compute velocity magnitude from Vact and apply mask "is active bed"
velocity = values_res[
varnames_1d.index('Vact'), :] * values_geom[1, :]
values = np.vstack(
(values_geom, depth, velocity, values_res))
else:
values = np.vstack((values_geom, depth, values_res))
resout.write_entire_frame(output_header, 3600.0 * i,
values)
else:
calc_unsteady = results.get_calc_unsteady(args.calc_unsteady)
logger.info("Calcul transitoire %s" % args.calc_unsteady)
res_unsteady = results.get_res_unsteady(args.calc_unsteady)
for i, (time, _) in enumerate(calc_unsteady.frame_list):
logger.info("~> %fs" % time)
res_at_sections = res_unsteady['Section'][i, :, :]
variables_at_profiles = res_at_sections[
pos_sections_list, :][:, pos_variables]
if global_mesh_constr.has_floodplain:
z_at_casiers = res_unsteady['Casier'][i,
pos_casiers_list,
pos_z_fp]
else:
z_at_casiers = None
# Interpolate between sections
values_res = global_mesh_constr.interp_values_from_res(
variables_at_profiles, z_at_casiers, pos_z)
# Compute water depth: H = Z - Zf and clip below 0m (avoid negative values)
depth = np.clip(values_res[pos_z, :] - z_bottom,
a_min=0.0,
a_max=None)
# Merge and write values
if 'Vact' in varnames_1d:
# Compute velocity magnitude from Vact and apply mask "is active bed"
velocity = values_res[
varnames_1d.index('Vact'), :] * values_geom[1, :]
values = np.vstack(
(values_geom, depth, velocity, values_res))
else:
values = np.vstack((values_geom, depth, values_res))
resout.write_entire_frame(output_header, time, values)
else:
# Write a single frame with only variables from geometry
global_mesh_constr.export_mesh(args.outfile_mesh, lang=args.lang)
t2 = perf_counter()
logger.info("=> Execution time: {}s".format(t2 - t1))
def mesh_mascaret_run(args):
set_logger_level(args.verbose)
t1 = perf_counter()
masc_geo = MascaretGeoFile(args.infile_geo)
logger.info("Read %s " % masc_geo)
# masc_geo.export_shp_lines(args.infile_geo.replace('.georef', '.shp'))
if not masc_geo.has_ref:
raise TatooineException(
"The file `%s` does not contain any georeferenced data" %
masc_geo.file_name)
global_mesh_constr = MeshConstructor()
for reach_id, reach in masc_geo.reaches.items():
logger.info(reach)
section_seq = CrossSectionSequence()
dist_proj_axe = 0.0
prev_x, prev_y = 0.0, 0.0
for section_idx, masc_section in enumerate(reach):
section = CrossSection(
masc_section.id,
[(x, y) for x, y in zip(masc_section.x, masc_section.y)],
"Cross-section")
section.coord.values = np.core.records.fromarrays(
np.column_stack((masc_section.z, )).T,
names=VARIABLES_FROM_GEOMETRY)
x, y = masc_section.axis
if section_idx != 0:
dist_proj_axe += sqrt((x - prev_x)**2 + (y - prev_y)**2)
section.dist_proj_axe = dist_proj_axe
prev_x, prev_y = x, y
section_seq.add_section(section)
if len(section_seq) >= 2:
section_seq.check_intersections()
# section_seq.sort_by_dist() is useless because cross-sections are already sorted
constraint_lines = ConstraintLine.get_lines_and_set_limits_from_sections(
section_seq, args.interp_constraint_lines)
mesh_constr = MeshConstructor(section_seq=section_seq,
lat_step=args.lat_step,
nb_pts_lat=args.nb_pts_lat,
interp_values=args.interp_values)
mesh_constr.build_interp(constraint_lines, args.long_step,
args.constant_long_disc)
mesh_constr.build_mesh(in_floworiented_crs=True)
global_mesh_constr.append_mesh_constr(mesh_constr)
else:
logger.error(
"/!\\ Reach %s ignored because it does not contain at least 2 sections"
% reach_id)
if len(global_mesh_constr.points) == 0:
raise ExceptionCrue10("No node in the generated mesh!")
logger.info(global_mesh_constr.summary()
) # General information about the merged mesh
if args.infile_res:
masc_res = MascaretFile(args.infile_res)
masc_res.get_reaches()
nb_section_in_geom = masc_geo.nsections
if masc_res.nsections != nb_section_in_geom:
raise TatooineException(
"The number of sections is different between geometry (%i) and results file (%i)"
% (nb_section_in_geom, masc_res.nsections))
varnames_1d = masc_res.varnames_dict['abbr']
logger.info("Variables 1D available at sections: %s" % varnames_1d)
try:
pos_z = varnames_1d.index('Z')
except ValueError:
raise TatooineException(
"The variable Z must be present in the results file")
additional_variables_id = ['H']
values_geom = global_mesh_constr.interp_values_from_geom()
z_bottom = values_geom[0, :]
with Serafin.Write(args.outfile_mesh, args.lang,
overwrite=True) as resout:
title = '%s (written by TatooineMesher)' % os.path.basename(
args.outfile_mesh)
output_header = Serafin.SerafinHeader(title=title, lang=args.lang)
output_header.from_triangulation(
global_mesh_constr.triangle['vertices'],
global_mesh_constr.triangle['triangles'] + 1)
for var_name in VARIABLES_FROM_GEOMETRY:
if var_name == 'B':
output_header.add_variable_from_ID(var_name)
else:
output_header.add_variable_str(var_name, var_name, '')
for var_id in additional_variables_id:
output_header.add_variable_from_ID(var_id)
for var_name in varnames_1d:
output_header.add_variable_str(var_name, var_name, '')
resout.write_header(output_header)
for idx_time, time in enumerate(masc_res.times):
variables_at_sections = masc_res.get_values(idx_time)[reach.id]
# Interpolate between sections and set in casiers
values_res = global_mesh_constr.interp_values_from_res(
variables_at_sections, None, pos_z)
# Compute water depth: H = Z - Zf and clip below 0m (avoid negative values)
depth = np.clip(values_res[pos_z, :] - z_bottom,
a_min=0.0,
a_max=None)
values = np.vstack((values_geom, depth, values_res))
resout.write_entire_frame(output_header, time, values)
else:
# Write a single frame with only variables from geometry
global_mesh_constr.export_mesh(args.outfile_mesh, lang=args.lang)
t2 = perf_counter()
logger.info("=> Execution time: {}s".format(t2 - t1))
def from_file(filename, label, field_id=None, project_straight_line=False):
section_seq = CrossSectionSequence()
if filename.endswith('.i3s'):
with bk.Read(filename) as in_i3s:
in_i3s.read_header()
for i, line in enumerate(in_i3s.get_open_polylines()):
line_id = i if field_id is None else line.attributes()[
0] # Use `Value` if field is not None
z_array = np.array([(coord[2], )
for coord in line.polyline().coords],
dtype=float_vars('Z'))
line = line.to_2d()
section = CrossSection(line_id,
list(line.polyline().coords), label)
section.coord.values = z_array
section_seq.add_section(section)
elif filename.endswith('.shp'):
shp_type = shp.get_shape_type(filename)
if shp_type in (shapefile.POLYLINEZ, shapefile.POLYLINEM):
field_id_index = get_field_index(filename, field_id)
for i, line in enumerate(shp.get_open_polylines(filename)):
line_id = i if field_id is None else line.attributes(
)[field_id_index]
z_array = np.array([(coord[2], )
for coord in line.polyline().coords],
dtype=float_vars(['Z']))
line = line.to_2d()
section = CrossSection(line_id,
list(line.polyline().coords), label)
section.coord.values = z_array
section_seq.add_section(section)
elif shp_type in (shapefile.POINT, shapefile.POINTZ):
field_id_index = get_field_index(filename, field_id)
field_indexes, field_names = [], []
if shp_type == shapefile.POINTZ:
field_names.append('Z')
for index, name in shp.get_numeric_attribute_names(filename):
if name.startswith('Z'):
field_indexes.append(index)
field_names.append(name)
coords, z_layers = [], []
last_point_id = None
for i, (point, attributes) in enumerate(
shp.get_points(filename,
with_z=shp_type == shapefile.POINTZ)):
point_id = attributes[
field_id_index] # FIXME: should raise exception if field_id_index is None!
if i > 0 and point_id != last_point_id:
z_array = np.array(z_layers,
dtype=float_vars(field_names))
section = CrossSection(last_point_id, coords, label)
section.coord.values = z_array
section_seq.add_section(section)
coords, z_layers = [], []
coords.append(point[:2])
if shp_type == shapefile.POINTZ:
z_layers.append((point[2], ) +
tuple(attributes[index]
for index in field_indexes))
else:
z_layers.append(
tuple(attributes[index]
for index in field_indexes))
last_point_id = point_id
z_array = np.array(z_layers, dtype=float_vars(field_names))
section = CrossSection(last_point_id, coords, label)
section.coord.values = z_array
section_seq.add_section(section)
else:
raise TatooineException(
"The type of file %s is not POINT[Z] or POLYLINEZ[M]" %
filename)
else:
raise NotImplementedError(
"Only shp and i3s formats are supported for cross-sections")
if project_straight_line:
for section in section_seq:
section.project_straight_line()
return section_seq
def build_interp(self, constraint_lines, long_step, constant_long_disc):
"""
Build interpolation, add points and segments
@param constraint_lines <[ConstraintLine]>: list of constraint lines
@param long_step <float>: longitudinal space step
@param constant_long_disc <bool>
"""
nb_pts_inter = 0
self.build_initial_profiles()
# LOOP ON ZONES (between 2 consecutive cross-sections)
logger.info("~> Building mesh per zone and then per bed")
for i, (prev_section, next_section) in enumerate(
zip(self.section_seq, self.section_seq[1:])):
logger.debug("> Zone n°{} : between {} and {}".format(
i, prev_section, next_section))
if constant_long_disc:
nb_pts_inter = prev_section.compute_nb_pts_inter(
next_section, long_step)
Xp_adm_list = np.linspace(0.0, 1.0, num=nb_pts_inter + 2)[1:-1]
# Looking for common limits between cross-sections
common_limits_id = prev_section.common_limits(
next_section.limits.keys())
logger.debug("Common limits: {}".format(list(common_limits_id)))
if len(common_limits_id) < 2:
raise TatooineException(
"No interpolation in the interval %i, between %s and %s (%i common limits)"
% (i, prev_section, next_section, len(common_limits_id)))
else:
first_bed = True
# LOOP ON BEDS
for j, (id1, id2) in enumerate(
zip(common_limits_id, common_limits_id[1:])):
pt_list_L1 = []
pt_list_L2 = []
logger.debug("Bed {}-{}".format(id1, id2))
# Extraction of cross-section portions (= beds)
bed_1 = prev_section.extract_bed(id1, id2)
bed_2 = next_section.extract_bed(id1, id2)
# Curvilinear abscissa along constraint lines
(Xp_profil1_L1,
Xp_profil1_L2) = prev_section.get_Xt_lines(id1, id2)
(Xp_profil2_L1,
Xp_profil2_L2) = next_section.get_Xt_lines(id1, id2)
dXp_L1 = Xp_profil2_L1 - Xp_profil1_L1
dXp_L2 = Xp_profil2_L2 - Xp_profil1_L2
if dXp_L1 < 0:
raise TatooineException(
"The constraint line {} is not oriented correctly".
format(id1))
if dXp_L2 < 0:
raise TatooineException(
"The constraint line {} is not oriented correctly".
format(id2))
if not constant_long_disc:
nb_pts_inter = math.ceil(
min(dXp_L1, dXp_L2) / long_step) - 1
Xp_adm_list = np.linspace(0.0,
1.0,
num=nb_pts_inter + 2)[1:-1]
L1_coord_int = constraint_lines[
id1].coord_sampling_along_line(Xp_profil1_L1,
Xp_profil2_L1,
Xp_adm_list)
L2_coord_int = constraint_lines[
id2].coord_sampling_along_line(Xp_profil1_L2,
Xp_profil2_L2,
Xp_adm_list)
# LOOP ON INTERMEDIATE CROSS-SECTIONS
for k in range(nb_pts_inter):
Xp = Xp_adm_list[k]
P1 = Point(tuple(L1_coord_int[k]))
P2 = Point(tuple(L2_coord_int[k]))
if self.nb_pts_lat is None:
nb_pts_lat = math.ceil(
P1.distance(P2) / self.lat_step) + 1
else:
nb_pts_lat = self.nb_pts_lat
array = bed_1.interp_coord_linear(
bed_2, Xp, nb_pts_lat)
bed_int = Bed(array, ['Xt', 'xt'])
bed_int.move_between_targets(P1, P2)
coord_int = bed_int.array[[
'X', 'Y', 'xt', 'Xt_upstream', 'Xt_downstream'
]] # Ignore `Xt`
pt_list_L1.append(self.i_pt + 1)
if not first_bed:
# ignore first point because the constraint line was already considered
coord_int = coord_int[1:]
self.add_points(coord_int, i, Xp, j)
pt_list_L2.append(self.i_pt)
pt_list_L2 = np.array(
[prev_section.get_limit_by_id(id2)['id_pt']] +
pt_list_L2 +
[next_section.get_limit_by_id(id2)['id_pt']])
self.add_segments_from_node_list(pt_list_L2)
if first_bed:
pt_list_L1 = np.array(
[prev_section.get_limit_by_id(id1)['id_pt']] +
pt_list_L1 +
[next_section.get_limit_by_id(id1)['id_pt']])
self.add_segments_from_node_list(pt_list_L1)
first_bed = False