def _pmesh_to_domain(file_name=None, mesh_instance=None, use_cache=False,
verbose=False):
"""Convert a pmesh file or a pmesh mesh instance to a bunch of lists
that can be used to instantiate a domain object.
"""
from anuga.load_mesh.loadASCII import import_mesh_file
# get data from mesh instance or file
if file_name is None:
mesh_dict = mesh_instance.Mesh2IODict()
else:
mesh_dict = import_mesh_file(file_name)
# extract required data from the mesh dictionary
vertex_coordinates = mesh_dict['vertices']
volumes = mesh_dict['triangles']
vertex_quantity_dict = {}
# num.transpose(None) gives scalar array of value None
point_atts = mesh_dict['vertex_attributes']
point_titles = mesh_dict['vertex_attribute_titles']
geo_reference = mesh_dict['geo_reference']
if point_atts is not None:
point_atts = num.transpose(point_atts)
for quantity, value_vector in map(None, point_titles, point_atts):
vertex_quantity_dict[quantity] = value_vector
tag_dict = pmesh_dict_to_tag_dict(mesh_dict)
tagged_elements_dict = build_tagged_elements_dictionary(mesh_dict)
return (vertex_coordinates, volumes, tag_dict, vertex_quantity_dict,
tagged_elements_dict, geo_reference)
def fit_to_mesh_file(mesh_file,
point_file,
mesh_output_file,
alpha=DEFAULT_ALPHA,
verbose=False,
expand_search=False,
precrop=False,
display_errors=True):
"""
Given a mesh file (tsh) and a point attribute file, fit
point attributes to the mesh and write a mesh file with the
results.
Note: the points file needs titles. If you want anuga to use the tsh file,
make sure the title is elevation.
NOTE: Throws IOErrors, for a variety of file problems.
"""
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file, concatinate_attributelist
try:
mesh_dict = import_mesh_file(mesh_file)
except IOError, e:
if display_errors:
log.critical("Could not load bad file: %s" % str(e))
raise IOError #Could not load bad mesh file.
def fit_to_mesh_file(mesh_file, point_file, mesh_output_file,
alpha=DEFAULT_ALPHA, verbose= False,
expand_search = False,
precrop = False,
display_errors = True):
"""
Given a mesh file (tsh) and a point attribute file, fit
point attributes to the mesh and write a mesh file with the
results.
Note: the points file needs titles. If you want anuga to use the tsh file,
make sure the title is elevation.
NOTE: Throws IOErrors, for a variety of file problems.
"""
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file, concatinate_attributelist
try:
mesh_dict = import_mesh_file(mesh_file)
except IOError, e:
if display_errors:
log.critical("Could not load bad file: %s" % str(e))
raise IOError #Could not load bad mesh file.
def test_fit_to_mesh_file2domain(self):
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file
import tempfile
import os
# create a .tsh file, no user outline
mesh_dic = {}
mesh_dic['vertices'] = [[0.0, 0.0],
[0.0, 5.0],
[5.0, 0.0]]
mesh_dic['triangles'] = [[0, 2, 1]]
mesh_dic['segments'] = [[0, 1], [2, 0], [1, 2]]
mesh_dic['triangle_tags'] = ['']
mesh_dic['vertex_attributes'] = [[], [], []]
mesh_dic['vertiex_attribute_titles'] = []
mesh_dic['triangle_neighbors'] = [[-1, -1, -1]]
mesh_dic['segment_tags'] = ['external',
'external',
'external']
mesh_file = tempfile.mktemp(".tsh")
export_mesh_file(mesh_file,mesh_dic)
# create a points .csv file
point_file = tempfile.mktemp(".csv")
fd = open(point_file,'w')
fd.write("x,y, elevation, stage \n\
1.0, 1.0,2.,4 \n\
1.0, 3.0,4,8 \n\
3.0,1.0,4.,8 \n")
fd.close()
mesh_output_file = tempfile.mktemp(".tsh")
fit_to_mesh_file(mesh_file,
point_file,
mesh_output_file,
alpha = 0.0)
# load in the .tsh file we just wrote
mesh_dic = import_mesh_file(mesh_output_file)
#print "mesh_dic",mesh_dic
ans =[[0.0, 0.0],
[5.0, 10.0],
[5.0,10.0]]
assert num.allclose(mesh_dic['vertex_attributes'],ans)
self.assertTrue(mesh_dic['vertex_attribute_titles'] ==
['elevation','stage'],
'test_fit_to_mesh_file failed')
domain = Domain(mesh_output_file, use_cache=True, verbose=False)
answer = [0., 5., 5.]
assert num.allclose(domain.quantities['elevation'].vertex_values,
answer)
#clean up
os.remove(mesh_file)
os.remove(point_file)
os.remove(mesh_output_file)
def test_fit_to_mesh_file2domain(self):
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file
import tempfile
import os
# create a .tsh file, no user outline
mesh_dic = {}
mesh_dic['vertices'] = [[0.0, 0.0],
[0.0, 5.0],
[5.0, 0.0]]
mesh_dic['triangles'] = [[0, 2, 1]]
mesh_dic['segments'] = [[0, 1], [2, 0], [1, 2]]
mesh_dic['triangle_tags'] = ['']
mesh_dic['vertex_attributes'] = [[], [], []]
mesh_dic['vertiex_attribute_titles'] = []
mesh_dic['triangle_neighbors'] = [[-1, -1, -1]]
mesh_dic['segment_tags'] = ['external',
'external',
'external']
mesh_file = tempfile.mktemp(".tsh")
export_mesh_file(mesh_file,mesh_dic)
# create a points .csv file
point_file = tempfile.mktemp(".csv")
fd = open(point_file,'w')
fd.write("x,y, elevation, stage \n\
1.0, 1.0,2.,4 \n\
1.0, 3.0,4,8 \n\
3.0,1.0,4.,8 \n")
fd.close()
mesh_output_file = tempfile.mktemp(".tsh")
fit_to_mesh_file(mesh_file,
point_file,
mesh_output_file,
alpha = 0.0)
# load in the .tsh file we just wrote
mesh_dic = import_mesh_file(mesh_output_file)
#print "mesh_dic",mesh_dic
ans =[[0.0, 0.0],
[5.0, 10.0],
[5.0,10.0]]
assert num.allclose(mesh_dic['vertex_attributes'],ans)
self.assertTrue(mesh_dic['vertex_attribute_titles'] ==
['elevation','stage'],
'test_fit_to_mesh_file failed')
domain = Domain(mesh_output_file, use_cache=True, verbose=False)
answer = [0., 5., 5.]
assert num.allclose(domain.quantities['elevation'].vertex_values,
answer)
#clean up
os.remove(mesh_file)
os.remove(point_file)
os.remove(mesh_output_file)
def test_fit_to_mesh_fileII(self):
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file
import tempfile
import os
# create a .tsh file, no user outline
mesh_dic = {}
mesh_dic['vertices'] = [[0.0, 0.0],
[0.0, 5.0],
[5.0, 0.0]]
mesh_dic['triangles'] = [[0, 2, 1]]
mesh_dic['segments'] = [[0, 1], [2, 0], [1, 2]]
mesh_dic['triangle_tags'] = ['']
mesh_dic['vertex_attributes'] = [[1,2], [1,2], [1,2]]
mesh_dic['vertex_attribute_titles'] = ['density', 'temp']
mesh_dic['triangle_neighbors'] = [[-1, -1, -1]]
mesh_dic['segment_tags'] = ['external',
'external',
'external']
mesh_file = tempfile.mktemp(".tsh")
export_mesh_file(mesh_file,mesh_dic)
# create a points .csv file
point_file = tempfile.mktemp(".csv")
fd = open(point_file,'w')
fd.write("x,y,elevation, stage \n\
1.0, 1.0,2.,4 \n\
1.0, 3.0,4,8 \n\
3.0,1.0,4.,8 \n")
fd.close()
mesh_output_file = "new_triangle.tsh"
fit_to_mesh_file(mesh_file,
point_file,
mesh_output_file,
alpha = 0.0)
# load in the .tsh file we just wrote
mesh_dic = import_mesh_file(mesh_output_file)
assert num.allclose(mesh_dic['vertex_attributes'],
[[1.0, 2.0,0.0, 0.0],
[1.0, 2.0,5.0, 10.0],
[1.0, 2.0,5.0,10.0]])
self.assertTrue(mesh_dic['vertex_attribute_titles'] ==
['density', 'temp','elevation','stage'],
'test_fit_to_mesh_file failed')
#clean up
os.remove(mesh_file)
os.remove(mesh_output_file)
os.remove(point_file)
def test_fit_to_mesh_fileII(self):
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file
import tempfile
import os
# create a .tsh file, no user outline
mesh_dic = {}
mesh_dic['vertices'] = [[0.0, 0.0],
[0.0, 5.0],
[5.0, 0.0]]
mesh_dic['triangles'] = [[0, 2, 1]]
mesh_dic['segments'] = [[0, 1], [2, 0], [1, 2]]
mesh_dic['triangle_tags'] = ['']
mesh_dic['vertex_attributes'] = [[1,2], [1,2], [1,2]]
mesh_dic['vertex_attribute_titles'] = ['density', 'temp']
mesh_dic['triangle_neighbors'] = [[-1, -1, -1]]
mesh_dic['segment_tags'] = ['external',
'external',
'external']
mesh_file = tempfile.mktemp(".tsh")
export_mesh_file(mesh_file,mesh_dic)
# create a points .csv file
point_file = tempfile.mktemp(".csv")
fd = open(point_file,'w')
fd.write("x,y,elevation, stage \n\
1.0, 1.0,2.,4 \n\
1.0, 3.0,4,8 \n\
3.0,1.0,4.,8 \n")
fd.close()
mesh_output_file = "new_triangle.tsh"
fit_to_mesh_file(mesh_file,
point_file,
mesh_output_file,
alpha = 0.0)
# load in the .tsh file we just wrote
mesh_dic = import_mesh_file(mesh_output_file)
assert num.allclose(mesh_dic['vertex_attributes'],
[[1.0, 2.0,0.0, 0.0],
[1.0, 2.0,5.0, 10.0],
[1.0, 2.0,5.0,10.0]])
self.assertTrue(mesh_dic['vertex_attribute_titles'] ==
['density', 'temp','elevation','stage'],
'test_fit_to_mesh_file failed')
#clean up
os.remove(mesh_file)
os.remove(mesh_output_file)
os.remove(point_file)
#Just a small triangle
#print "We shoulnd't get here"
removeable.append(i)
except ValueError:
#must be corrupt
removeable.append(i)
return len(corrupt) + len(fixable) + len(inflatable) + len(removeable)
#START
fixable = []
inflatable = []
removeable = []
corrupt = []
counter = 0
mesh = loadASCII.import_mesh_file('output.msh')
fo1 = open("foo.geojson", "rw+")
fo1.write('{"type": "FeatureCollection","features":[\n')
#do first check
wrongs = check(mesh)
print 'Fixable: ', len(fixable)
print 'Inflatable: ', len(inflatable)
print 'Corrupt: ', len(corrupt)
print 'Removeable: ', len(removeable)
#keep looping until fixed
while wrongs > 0:
print '-----', counter
#inflate()
skew()
#fix()
def fit_to_mesh_file(mesh_file,
point_file,
mesh_output_file,
alpha=DEFAULT_ALPHA,
verbose=False,
expand_search=False,
precrop=False,
display_errors=True):
"""
Given a mesh file (tsh) and a point attribute file, fit
point attributes to the mesh and write a mesh file with the
results.
Note: the points file needs titles. If you want anuga to use the tsh file,
make sure the title is elevation.
NOTE: Throws IOErrors, for a variety of file problems.
"""
from anuga.load_mesh.loadASCII import import_mesh_file, \
export_mesh_file, concatinate_attributelist
try:
mesh_dict = import_mesh_file(mesh_file)
except IOError as e:
if display_errors:
log.critical("Could not load bad file: %s" % str(e))
raise IOError # Could not load bad mesh file.
vertex_coordinates = mesh_dict['vertices']
triangles = mesh_dict['triangles']
if isinstance(mesh_dict['vertex_attributes'], num.ndarray):
old_point_attributes = mesh_dict['vertex_attributes'].tolist()
else:
old_point_attributes = mesh_dict['vertex_attributes']
if isinstance(mesh_dict['vertex_attribute_titles'], num.ndarray):
old_title_list = mesh_dict['vertex_attribute_titles'].tolist()
else:
old_title_list = mesh_dict['vertex_attribute_titles']
if verbose:
log.critical('tsh file %s loaded' % mesh_file)
# load in the points file
try:
geo = Geospatial_data(point_file, verbose=verbose)
except IOError as e:
if display_errors:
log.critical("Could not load bad file: %s" % str(e))
raise IOError # Re-raise exception
point_coordinates = geo.get_data_points(absolute=True)
title_list, point_attributes = concatinate_attributelist(
geo.get_all_attributes())
if 'geo_reference' in mesh_dict and \
not mesh_dict['geo_reference'] is None:
mesh_origin = mesh_dict['geo_reference'].get_origin()
else:
mesh_origin = None
if verbose:
log.critical("points file loaded")
if verbose:
log.critical("fitting to mesh")
f = fit_to_mesh(point_coordinates,
vertex_coordinates,
triangles,
None,
point_attributes,
alpha=alpha,
verbose=verbose,
data_origin=None,
mesh_origin=mesh_origin)
if verbose:
log.critical("finished fitting to mesh")
# convert array to list of lists
new_point_attributes = f.tolist()
# FIXME have this overwrite attributes with the same title - DSG
# Put the newer attributes last
if old_title_list != []:
old_title_list.extend(title_list)
# FIXME can this be done a faster way? - DSG
for i in range(len(old_point_attributes)):
old_point_attributes[i].extend(new_point_attributes[i])
mesh_dict['vertex_attributes'] = old_point_attributes
mesh_dict['vertex_attribute_titles'] = old_title_list
else:
mesh_dict['vertex_attributes'] = new_point_attributes
mesh_dict['vertex_attribute_titles'] = title_list
if verbose:
log.critical("exporting to file %s" % mesh_output_file)
try:
export_mesh_file(mesh_output_file, mesh_dict)
except IOError as e:
if display_errors:
log.critical("Could not write file %s", str(e))
raise IOError
