def test_sww_constant(self):
"""Test that constant sww information can be written correctly
(non smooth)
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww' #Remove??
self.domain.smooth = False
sww = SWW_file(self.domain)
sww.store_connectivity()
fid = NetCDFFile(sww.filename, netcdf_mode_r) # Open existing file for append
# Get the variables
x = fid.variables['x']
y = fid.variables['y']
z = fid.variables['elevation']
V = fid.variables['volumes']
assert num.allclose (x[:], self.X.flatten())
assert num.allclose (y[:], self.Y.flatten())
assert num.allclose (z[:], self.F.flatten())
P = len(self.domain)
for k in range(P):
assert V[k, 0] == 3*k
assert V[k, 1] == 3*k+1
assert V[k, 2] == 3*k+2
fid.close()
os.remove(sww.filename)
def test_sww_header(self):
"""Test that constant sww information can be written correctly
(non smooth)
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww' #Remove??
self.domain.smooth = False
sww = SWW_file(self.domain)
sww.store_connectivity()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r) # Open existing file for append
# Get the variables
sww_revision = fid.revision_number
try:
revision_number = get_revision_number()
except:
revision_number = None
assert str(revision_number) == sww_revision
fid.close()
#print "sww.filename", sww.filename
os.remove(sww.filename)
def __init__(self, source, frameDelay=100, frameStep=1):
"""The source parameter is assumed to be a NetCDF sww file.
The frameDelay parameter is the number of milliseconds waited between frames.
"""
Visualiser.__init__(self, source)
self.frameNumber = 0
fin = NetCDFFile(self.source, 'r')
self.maxFrameNumber = fin.variables['time'].shape[0] - 1
fin.close()
#self.frameNumberTkVariable = StringVar()
#self.frameNumberTkVariable.set('Frame - %05g'%self.framNumber)
self.frameDelay = frameDelay
self.xmin = None
self.xmax = None
self.ymin = None
self.ymax = None
self.zmin = None
self.zmax = None
self.frameStep= frameStep
self.vtk_heightQuantityCache = []
for i in range(self.maxFrameNumber + 1): # maxFrameNumber is zero indexed.
self.vtk_heightQuantityCache.append({})
self.paused = False
self.movie = False
def test_ferret2sww_nz_origin(self):
from anuga.coordinate_transforms.redfearn import redfearn
#Call conversion (with nonzero origin)
ferret2sww(self.test_MOST_file, verbose=self.verbose,
origin = (56, 100000, 200000))
#Work out the UTM coordinates for first point
zone, e, n = redfearn(-34.5, 150.66667)
#Read output file 'small.sww'
#fid = NetCDFFile('small.sww', netcdf_mode_r)
fid = NetCDFFile(self.test_MOST_file + '.sww')
x = fid.variables['x'][:]
y = fid.variables['y'][:]
#Check that first coordinate is correctly represented
assert num.allclose(x[0], e-100000)
assert num.allclose(y[0], n-200000)
fid.close()
#Cleanup
os.remove(self.test_MOST_file + '.sww')
def __init__(self, *args, **kwargs):
Visualiser.__init__(self, *args, **kwargs)
fin = NetCDFFile(self.vis_source, 'r')
self.xPoints = array(fin.variables['x'], Float)
self.yPoints = array(fin.variables['y'], Float)
self.quantityCache = {}
fin.close()
def test_boundary_timeII(self):
"""
test_boundary_timeII(self):
Test that starttime can be set in the middle of a boundary condition
"""
boundary_starttime = 0
boundary_filename = self.create_sww_boundary(boundary_starttime)
#print "boundary_filename",boundary_filename
filename = tempfile.mktemp(".sww")
#print "filename",filename
dir, base = os.path.split(filename)
senario_name = base[:-4]
mesh = Mesh()
mesh.add_region_from_polygon([[10, 10], [90, 10], [90, 90], [10, 90]])
mesh.generate_mesh(verbose=False)
domain = pmesh_to_domain_instance(mesh, anuga.Domain)
domain.set_name(senario_name)
domain.set_datadir(dir)
new_starttime = 0.
domain.set_starttime(new_starttime)
# Setup initial conditions
domain.set_quantity('elevation', 0.0)
domain.set_quantity('stage', 0.0)
Bf = anuga.File_boundary(boundary_filename,
domain,
use_cache=False,
verbose=False)
# Setup boundary conditions
domain.set_boundary({'exterior': Bf})
for t in domain.evolve(yieldstep=5, finaltime=9.0):
pass
#print domain.boundary_statistics()
#domain.write_time()
#print "domain.time", domain.time
# do an assertion on the time of the produced sww file
fid = NetCDFFile(filename, netcdf_mode_r) #Open existing file for read
times = fid.variables['time'][:]
stage = fid.variables['stage'][:]
#print stage
#print "times", times
#print "fid.starttime", fid.starttime
assert num.allclose(fid.starttime, new_starttime)
fid.close()
#print "stage[2,0]", stage[2,0]
msg = "This test is a bit hand crafted, based on the output file. "
msg += "Not logic. "
msg += "It's testing that starttime is working"
assert num.allclose(stage[2, 0], 4.85825), msg
# clean up
os.remove(boundary_filename)
os.remove(filename)
def test_ferret2sww_lat_longII(self):
# Test that min lat long works
#The test file has
# LON = 150.66667, 150.83334, 151, 151.16667
# LAT = -34.5, -34.33333, -34.16667, -34 ;
#Read
from anuga.coordinate_transforms.redfearn import redfearn
fid = NetCDFFile(self.test_MOST_file + '_ha.nc')
first_value = fid.variables['HA'][:][0,0,0]
fourth_value = fid.variables['HA'][:][0,0,3]
fid.close()
#Call conversion (with zero origin)
#ferret2sww('small', verbose=self.verbose,
# origin = (56, 0, 0))
try:
ferret2sww(self.test_MOST_file, verbose=self.verbose,
origin = (56, 0, 0), minlat=-34.5, maxlat=-35)
except AssertionError:
pass
else:
self.assertTrue(0 ==1, 'Bad input did not throw exception error!')
def test_ferret2sww_nz_origin(self):
from anuga.coordinate_transforms.redfearn import redfearn
#Call conversion (with nonzero origin)
ferret2sww(self.test_MOST_file,
verbose=self.verbose,
origin=(56, 100000, 200000))
#Work out the UTM coordinates for first point
zone, e, n = redfearn(-34.5, 150.66667)
#Read output file 'small.sww'
#fid = NetCDFFile('small.sww', netcdf_mode_r)
fid = NetCDFFile(self.test_MOST_file + '.sww')
x = fid.variables['x'][:]
y = fid.variables['y'][:]
#Check that first coordinate is correctly represented
assert num.allclose(x[0], e - 100000)
assert num.allclose(y[0], n - 200000)
fid.close()
#Cleanup
os.remove(self.test_MOST_file + '.sww')
def __init__(self, *args, **kwargs):
Visualiser.__init__(self, *args, **kwargs)
fin = NetCDFFile(self.vis_source, 'r')
self.xPoints = array(fin.variables['x'], Float)
self.yPoints = array(fin.variables['y'], Float)
self.quantityCache = {}
fin.close()
def read_result(fn,
save_pl,
matrix_A,
ele,
quantity_names,
case_num,
time_thinning=1):
fid = NetCDFFile(fn, netcdf_mode_r)
time = fid.variables['time'][:]
upper_time_index = len(time)
quantities = {}
for i, name in enumerate(quantity_names):
quantities[name] = fid.variables[name][:]
quantities[name] = np.array(quantities[name][::time_thinning, :])
fid.close()
for i, t in enumerate(time):
for name in quantity_names:
Q = quantities[name][i, :] # Quantities at timestep i
result = matrix_A * Q
result = np.asarray(result)
result = result.reshape((100, 100))
if name == 'stage':
result = result - ele
save_name = save_pl + case_num + '_' + 'depth' + '_{0}.csv'.format(
i)
else:
save_name = save_pl + case_num + '_' + name + '_{0}.csv'.format(
i)
np.savetxt(save_name, result, delimiter=",")
def test_sww_variable2(self):
"""Test that sww information can be written correctly
multiple timesteps. Use average as reduction operator
"""
import time, os
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
self.domain.reduction = mean
sww = SWW_file(self.domain)
sww.store_connectivity()
sww.store_timestep()
#self.domain.tight_slope_limiters = 1
self.domain.evolve_to_end(finaltime=0.01)
sww.store_timestep()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r)
# Get the variables
x = fid.variables['x']
y = fid.variables['y']
z = fid.variables['elevation']
time = fid.variables['time']
stage = fid.variables['stage']
#Check values
Q = self.domain.quantities['stage']
Q0 = Q.vertex_values[:, 0]
Q1 = Q.vertex_values[:, 1]
Q2 = Q.vertex_values[:, 2]
A = stage[1, :]
assert num.allclose(A[0],
old_div((Q2[0] + Q1[1]), 2),
rtol=1.0e-5,
atol=1.0e-5)
assert num.allclose(A[1],
old_div((Q0[1] + Q1[3] + Q2[2]), 3),
rtol=1.0e-5,
atol=1.0e-5)
assert num.allclose(A[2], Q0[3], rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(A[3],
old_div((Q0[0] + Q1[5] + Q2[4]), 3),
rtol=1.0e-5,
atol=1.0e-5)
#Center point
assert num.allclose(A[4], old_div((Q1[0] + Q2[1] + Q0[2] +\
Q0[5] + Q2[6] + Q1[7]),6), rtol=1.0e-5, atol=1.0e-5)
fid.close()
#Cleanup
os.remove(sww.filename)
def __init__(self, source, frameDelay=100, frameStep=1):
"""The source parameter is assumed to be a NetCDF sww file.
The frameDelay parameter is the number of milliseconds waited between frames.
"""
Visualiser.__init__(self, source)
self.frameNumber = 0
fin = NetCDFFile(self.source, 'r')
self.maxFrameNumber = fin.variables['time'].shape[0] - 1
fin.close()
#self.frameNumberTkVariable = StringVar()
#self.frameNumberTkVariable.set('Frame - %05g'%self.framNumber)
self.frameDelay = frameDelay
self.xmin = None
self.xmax = None
self.ymin = None
self.ymax = None
self.zmin = None
self.zmax = None
self.frameStep = frameStep
self.vtk_heightQuantityCache = []
for i in range(self.maxFrameNumber +
1): # maxFrameNumber is zero indexed.
self.vtk_heightQuantityCache.append({})
self.paused = False
self.movie = False
def sww_merge_parallel(domain_global_name,
np,
verbose=False,
delete_old=False):
output = domain_global_name + ".sww"
swwfiles = [
domain_global_name + "_P" + str(np) + "_" + str(v) + ".sww"
for v in range(np)
]
fid = NetCDFFile(swwfiles[0], netcdf_mode_r)
try: # works with netcdf4
number_of_volumes = len(fid.dimensions['number_of_volumes'])
number_of_points = len(fid.dimensions['number_of_points'])
except: # works with scientific.io.netcdf
number_of_volumes = int(fid.dimensions['number_of_volumes'])
number_of_points = int(fid.dimensions['number_of_points'])
fid.close()
if 3 * number_of_volumes == number_of_points:
_sww_merge_parallel_non_smooth(swwfiles, output, verbose, delete_old)
else:
_sww_merge_parallel_smooth(swwfiles, output, verbose, delete_old)
def test_ferret2sww_lat_longII(self):
# Test that min lat long works
#The test file has
# LON = 150.66667, 150.83334, 151, 151.16667
# LAT = -34.5, -34.33333, -34.16667, -34 ;
#Read
from anuga.coordinate_transforms.redfearn import redfearn
fid = NetCDFFile(self.test_MOST_file + '_ha.nc')
first_value = fid.variables['HA'][:][0, 0, 0]
fourth_value = fid.variables['HA'][:][0, 0, 3]
fid.close()
#Call conversion (with zero origin)
#ferret2sww('small', verbose=self.verbose,
# origin = (56, 0, 0))
try:
ferret2sww(self.test_MOST_file,
verbose=self.verbose,
origin=(56, 0, 0),
minlat=-34.5,
maxlat=-35)
except AssertionError:
pass
else:
self.assertTrue(0 == 1, 'Bad input did not throw exception error!')
def test_boundary_timeII_1_5(self):
"""
test_boundary_timeII(self):
Test that starttime can be set in the middle of a boundary condition
"""
boundary_starttime = 0
boundary_filename = self.create_sww_boundary(boundary_starttime)
# print "boundary_filename",boundary_filename
filename = tempfile.mktemp(".sww")
# print "filename",filename
dir, base = os.path.split(filename)
senario_name = base[:-4]
mesh = Mesh()
mesh.add_region_from_polygon([[10, 10], [90, 10], [90, 90], [10, 90]])
mesh.generate_mesh(verbose=False)
domain = pmesh_to_domain_instance(mesh, anuga.Domain)
domain.set_name(senario_name)
domain.set_datadir(dir)
domain.set_flow_algorithm("1_5")
new_starttime = 0.0
domain.set_starttime(new_starttime)
# Setup initial conditions
domain.set_quantity("elevation", 0.0)
domain.set_quantity("stage", 0.0)
Bf = anuga.File_boundary(boundary_filename, domain, use_cache=False, verbose=False)
# Setup boundary conditions
domain.set_boundary({"exterior": Bf})
for t in domain.evolve(yieldstep=5, finaltime=9.0):
pass
# print domain.boundary_statistics()
# domain.write_time()
# print "domain.time", domain.time
# do an assertion on the time of the produced sww file
fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read
times = fid.variables["time"][:]
stage = fid.variables["stage"][:]
# print stage
# print "times", times
# print "fid.starttime", fid.starttime
assert num.allclose(fid.starttime, new_starttime)
fid.close()
# print "stage[2,0]", stage[2,0]
msg = "This test is a bit hand crafted, based on the output file. "
msg += "Not logic. "
msg += "It's testing that starttime is working"
assert num.allclose(stage[2, 0], 4.88601), msg
# clean up
os.remove(boundary_filename)
os.remove(filename)
def setup_grid(self):
fin = NetCDFFile(self.source, 'r')
self.vtk_cells = vtkCellArray()
N_tri = fin.variables['volumes'].shape[0]
for v in range(N_tri):
self.vtk_cells.InsertNextCell(3)
for i in range(3):
self.vtk_cells.InsertCellPoint(fin.variables['volumes'][v][i])
fin.close()
def setup_grid(self):
fin = NetCDFFile(self.source, 'r')
self.vtk_cells = vtkCellArray()
N_tri = fin.variables['volumes'].shape[0]
for v in range(N_tri):
self.vtk_cells.InsertNextCell(3)
for i in range(3):
self.vtk_cells.InsertCellPoint(fin.variables['volumes'][v][i])
fin.close()
def build_quantity_dict(self):
quantities = {}
fin = NetCDFFile(self.source, 'r')
for q in filter(lambda n:n != 'x' and n != 'y' and n != 'z' and n != 'time' and n != 'volumes', fin.variables.keys()):
if len(fin.variables[q].shape) == 1: # Not a time-varying quantity
quantities[q] = num.ravel(num.array(fin.variables[q], num.float))
else: # Time-varying, get the current timestep data
quantities[q] = num.array(fin.variables[q][self.frameNumber], num.float)
fin.close()
return quantities
def helper_read_msh_file(self, filename):
fid = NetCDFFile(filename, netcdf_mode_r)
mesh = {}
# Get the 'strings' variable
strings = fid.variables['strings'][:]
fid.close()
return char_to_string(strings)
def helper_read_msh_file(self, filename):
fid = NetCDFFile(filename, netcdf_mode_r)
mesh = {}
# Get the 'strings' variable
strings = fid.variables['strings'][:]
fid.close()
return char_to_string(strings)
def get_matrix_A(fn, gauge_name):
# points to read information from
point_reader = reader(file(gauge_name))
points = []
point_name = []
for i, row in enumerate(point_reader):
if i == 0:
for j, value in enumerate(row):
if value.strip() == 'easting': easting = j
if value.strip() == 'northing': northing = j
if value.strip() == 'name': name = j
if value.strip() == 'elevation': elevation = j
else:
#points.append([float(row[easting]),float(row[northing])])
points.append([float(row[easting]), float(row[northing])])
point_name.append(row[name])
points_array = np.array(points, np.float)
dim_gauge = int(np.sqrt(points_array.shape[0]))
interpolation_points = ensure_absolute(points_array)
# read the sww file to extract something
fid = NetCDFFile(fn, netcdf_mode_r)
xllcorner = fid.xllcorner
yllcorner = fid.yllcorner
zone = fid.zone
x = fid.variables['x'][:]
y = fid.variables['y'][:]
triangles = fid.variables['volumes'][:]
x = np.reshape(x, (len(x), 1))
y = np.reshape(y, (len(y), 1))
vertex_coordinates = np.concatenate((x, y), axis=1)
ele = fid.variables['elevation'][:]
fid.close()
vertex_coordinates = ensure_absolute(vertex_coordinates)
triangles = ensure_numeric(triangles)
interpolation_points = ensure_numeric(interpolation_points)
interpolation_points[:, 0] -= xllcorner
interpolation_points[:, 1] -= yllcorner
mesh = Mesh(vertex_coordinates, triangles)
mesh_boundary_polygon = mesh.get_boundary_polygon()
indices = outside_polygon(interpolation_points, mesh_boundary_polygon)
interp = Interpolate(vertex_coordinates, triangles)
matrix_A, inside_poly_indices, outside_poly_indices, centroids = interp._build_interpolation_matrix_A(
interpolation_points, output_centroids=False, verbose=False)
ele = matrix_A * ele
ele = np.asarray(ele)
ele = ele.reshape((100, 100))
return ele, matrix_A
def test_sww_variable(self):
"""Test that sww information can be written correctly
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
self.domain.reduction = mean
sww = SWW_file(self.domain)
sww.store_connectivity()
sww.store_timestep()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename,
netcdf_mode_r) # Open existing file for append
# Get the variables
time = fid.variables['time']
stage = fid.variables['stage']
Q = self.domain.quantities['stage']
Q0 = Q.vertex_values[:, 0]
Q1 = Q.vertex_values[:, 1]
Q2 = Q.vertex_values[:, 2]
A = stage[0, :]
# print stage[0,:]
# print A[0], (Q2[0] + Q1[1])/2
# print A[1], (Q0[1] + Q1[3] + Q2[2])/3
# print A[2], Q0[3]
# print A[3], (Q0[0] + Q1[5] + Q2[4])/3
assert num.allclose(A[0],
old_div((Q2[0] + Q1[1]), 2),
rtol=1.0e-5,
atol=1.0e-5)
assert num.allclose(A[1],
old_div((Q0[1] + Q1[3] + Q2[2]), 3),
rtol=1.0e-5,
atol=1.0e-5)
assert num.allclose(A[2], Q0[3])
assert num.allclose(A[3],
old_div((Q0[0] + Q1[5] + Q2[4]), 3),
rtol=1.0e-5,
atol=1.0e-5)
#Center point
assert num.allclose(A[4], old_div((Q1[0] + Q2[1] + Q0[2] +\
Q0[5] + Q2[6] + Q1[7]),6), rtol=1.0e-5, atol=1.0e-5)
fid.close()
os.remove(sww.filename)
def test_sww_range(self):
"""Test that constant sww information can be written correctly
Use non-smooth to be able to compare to quantity values.
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.set_store_vertices_uniquely(True)
sww = SWW_file(self.domain)
dqs = self.domain.get_quantity('stage')
dqx = self.domain.get_quantity('xmomentum')
dqy = self.domain.get_quantity('ymomentum')
xmom_min = ymom_min = stage_min = sys.maxint
xmom_max = ymom_max = stage_max = -stage_min
for t in self.domain.evolve(yieldstep = 1, finaltime = 1):
wmax = max(dqs.get_values().flatten())
if wmax > stage_max: stage_max = wmax
wmin = min(dqs.get_values().flatten())
if wmin < stage_min: stage_min = wmin
uhmax = max(dqx.get_values().flatten())
if uhmax > xmom_max: xmom_max = uhmax
uhmin = min(dqx.get_values().flatten())
if uhmin < xmom_min: xmom_min = uhmin
vhmax = max(dqy.get_values().flatten())
if vhmax > ymom_max: ymom_max = vhmax
vhmin = min(dqy.get_values().flatten())
if vhmin < ymom_min: ymom_min = vhmin
# Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r) # Open existing file for append
# Get the variables
range = fid.variables['stage_range'][:]
assert num.allclose(range,[stage_min, stage_max])
range = fid.variables['xmomentum_range'][:]
#print range
assert num.allclose(range, [xmom_min, xmom_max])
range = fid.variables['ymomentum_range'][:]
#print range
assert num.allclose(range, [ymom_min, ymom_max])
fid.close()
os.remove(sww.filename)
def setupGrid(self):
fin = NetCDFFile(self.vis_source, 'r')
nTri = fin.variables['volumes'].shape[0]
insertNextCell = vtkCellArray.InsertNextCell
insertCellPoint = vtkCellArray.InsertCellPoint
for v in range(nTri):
insertNextCell(self.vtk_cells, 3)
for i in range(3):
insertCellPoint(self.vtk_cells, fin.variables['volumes'][v][i])
fin.close()
def getQuantityDict(self):
quantities = {}
fin = NetCDFFile(self.vis_source, 'r')
names = [
k for k in fin.variables.keys() if k != 'x' and k != 'y'
and k != 'z' and k != 'time' and k != 'volumes'
]
argss = [(name, len(fin.variables[name].shape) != 1) for name in names]
fin.close()
for args in argss:
quantities[name] = self.getQuantityPoints(*args)
return quantities
def setupGrid(self):
fin = NetCDFFile(self.vis_source, 'r')
nTri = fin.variables['volumes'].shape[0]
insertNextCell = vtkCellArray.InsertNextCell
insertCellPoint = vtkCellArray.InsertCellPoint
for v in range(nTri):
insertNextCell(self.vtk_cells, 3)
for i in range(3):
insertCellPoint(self.vtk_cells, fin.variables['volumes'][v][i])
fin.close()
def test_sww_variable2(self):
"""Test that sww information can be written correctly
multiple timesteps. Use average as reduction operator
"""
import time, os
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
self.domain.reduction = mean
sww = SWW_file(self.domain)
sww.store_connectivity()
sww.store_timestep()
#self.domain.tight_slope_limiters = 1
self.domain.evolve_to_end(finaltime = 0.01)
sww.store_timestep()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r)
# Get the variables
x = fid.variables['x']
y = fid.variables['y']
z = fid.variables['elevation']
time = fid.variables['time']
stage = fid.variables['stage']
#Check values
Q = self.domain.quantities['stage']
Q0 = Q.vertex_values[:,0]
Q1 = Q.vertex_values[:,1]
Q2 = Q.vertex_values[:,2]
A = stage[1,:]
assert num.allclose(A[0], (Q2[0] + Q1[1])/2, rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(A[1], (Q0[1] + Q1[3] + Q2[2])/3, rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(A[2], Q0[3], rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(A[3], (Q0[0] + Q1[5] + Q2[4])/3, rtol=1.0e-5, atol=1.0e-5)
#Center point
assert num.allclose(A[4], (Q1[0] + Q2[1] + Q0[2] +\
Q0[5] + Q2[6] + Q1[7])/6, rtol=1.0e-5, atol=1.0e-5)
fid.close()
#Cleanup
os.remove(sww.filename)
def test_sww_minimum_storable_height(self):
"""Test that sww information can be written correctly
multiple timesteps using a different reduction operator (min)
"""
import time, os
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
self.domain.reduction = min
self.domain.minimum_storable_height = 100
sww = SWW_file(self.domain)
sww.store_connectivity()
sww.store_timestep()
#self.domain.tight_slope_limiters = 1
self.domain.evolve_to_end(finaltime = 0.01)
sww.store_timestep()
#Check contents
#Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r)
# Get the variables
x = fid.variables['x']
y = fid.variables['y']
z = fid.variables['elevation']
time = fid.variables['time']
stage = fid.variables['stage']
xmomentum = fid.variables['xmomentum']
ymomentum = fid.variables['ymomentum']
#Check values
Q = self.domain.quantities['stage']
Q0 = Q.vertex_values[:,0]
Q1 = Q.vertex_values[:,1]
Q2 = Q.vertex_values[:,2]
A = stage[1,:]
assert num.allclose(stage[1,:], z[:])
assert num.allclose(xmomentum, 0.0)
assert num.allclose(ymomentum, 0.0)
fid.close()
#Cleanup
os.remove(sww.filename)
def build_quantity_dict(self):
quantities = {}
fin = NetCDFFile(self.source, 'r')
for q in filter(
lambda n: n != 'x' and n != 'y' and n != 'z' and n != 'time'
and n != 'volumes', fin.variables.keys()):
if len(fin.variables[q].shape) == 1: # Not a time-varying quantity
quantities[q] = num.ravel(
num.array(fin.variables[q], num.float))
else: # Time-varying, get the current timestep data
quantities[q] = num.array(fin.variables[q][self.frameNumber],
num.float)
fin.close()
return quantities
def test_sync(self):
"""test_sync - Test info stored at each timestep is as expected (incl initial condition)
"""
import time, os
self.domain.set_name('synctest')
self.domain.format = 'sww'
self.domain.smooth = False
self.domain.store = True
self.domain.tight_slope_limiters = True
self.domain.use_centroid_velocities = True
# In this case tight_slope_limiters as default
# in conjunction with protection
# against isolated degenerate timesteps works.
#self.domain.tight_slope_limiters = 1
#self.domain.protect_against_isolated_degenerate_timesteps = True
#print 'tight_sl', self.domain.tight_slope_limiters
#Evolution
for t in self.domain.evolve(yieldstep=1.0, finaltime=4.0):
#########self.domain.write_time(track_speeds=True)
stage = self.domain.quantities['stage'].vertex_values
#Get NetCDF
fid = NetCDFFile(self.domain.writer.filename, netcdf_mode_r)
stage_file = fid.variables['stage']
if t == 0.0:
assert num.allclose(stage,
self.initial_stage,
rtol=1.0e-5,
atol=1.0e-5)
assert num.allclose(stage_file[:],
stage.flatten(),
rtol=1.0e-5,
atol=1.0e-5)
else:
assert not num.allclose(
stage, self.initial_stage, rtol=1.0e-5, atol=1.0e-5)
assert not num.allclose(
stage_file[:], stage.flatten(), rtol=1.0e-5, atol=1.0e-5)
fid.close()
os.remove(self.domain.writer.filename)
def test_boundary_time(self):
"""
test_boundary_time(self):
test that the starttime of a boundary condition is carried thru
to the output sww file.
"""
boundary_starttime = 0
boundary_filename = self.create_sww_boundary(boundary_starttime)
filename = tempfile.mktemp(".sww")
dir, base = os.path.split(filename)
senario_name = base[:-4]
mesh = Mesh()
###mesh.add_region_from_polygon([[10,10], [90,10], [90,90], [10,90]])
mesh.add_region_from_polygon([[0, 0], [100, 0], [100, 100], [0, 100]])
mesh.generate_mesh(verbose=False)
domain = pmesh_to_domain_instance(mesh, anuga.Domain)
domain.set_name(senario_name)
domain.set_datadir(dir)
# Setup initial conditions
domain.set_quantity('elevation', 0.0)
domain.set_quantity('stage', 0.0)
Bf = anuga.File_boundary(boundary_filename,
domain,
use_cache=False,
verbose=False)
# Setup boundary conditions
domain.set_boundary({'exterior': Bf})
for t in domain.evolve(yieldstep=5.0, finaltime=10.0):
pass
#print domain.write_time()
#print "domain.time", domain.time
# do an assertion on the time of the produced sww file
fid = NetCDFFile(filename, netcdf_mode_r) #Open existing file for read
times = fid.variables['time'][:]
#print "times", times
#print "fid.starttime", fid.starttime
assert num.allclose(fid.starttime, boundary_starttime)
fid.close()
# clean up
os.remove(boundary_filename)
os.remove(filename)
def test_ferret2sww_2(self):
"""Test that georeferencing etc works when converting from
ferret format (lat/lon) to sww format (UTM)
"""
#The test file has
# LON = 150.66667, 150.83334, 151, 151.16667
# LAT = -34.5, -34.33333, -34.16667, -34 ;
# TIME = 0, 0.1, 0.6, 1.1, 1.6, 2.1 ;
#
# First value (index=0) in small_ha.nc is 0.3400644 cm,
# Fourth value (index==3) is -6.50198 cm
from anuga.coordinate_transforms.redfearn import redfearn
#fid = NetCDFFile('small_ha.nc')
fid = NetCDFFile(self.test_MOST_file + '_ha.nc')
#Pick a coordinate and a value
time_index = 1
lat_index = 0
lon_index = 2
test_value = fid.variables['HA'][:][time_index, lat_index, lon_index]
test_time = fid.variables['TIME'][:][time_index]
test_lat = fid.variables['LAT'][:][lat_index]
test_lon = fid.variables['LON'][:][lon_index]
linear_point_index = lat_index * 4 + lon_index
fid.close()
#Call conversion (with zero origin)
ferret2sww(self.test_MOST_file,
verbose=self.verbose,
origin=(56, 0, 0))
#Work out the UTM coordinates for test point
zone, e, n = redfearn(test_lat, test_lon)
#Read output file 'small.sww'
fid = NetCDFFile(self.test_MOST_file + '.sww')
x = fid.variables['x'][:]
y = fid.variables['y'][:]
#Check that test coordinate is correctly represented
assert num.allclose(x[linear_point_index], e)
assert num.allclose(y[linear_point_index], n)
#Check test value
stage = fid.variables['stage'][:]
assert num.allclose(stage[time_index, linear_point_index],
old_div(test_value, 100))
fid.close()
#Cleanup
import os
os.remove(self.test_MOST_file + '.sww')
def getQuantityDict(self):
quantities = {}
fin = NetCDFFile(self.vis_source, 'r')
names = [ k for k in fin.variables.keys()
if k != 'x'
and k != 'y'
and k != 'z'
and k != 'time'
and k != 'volumes' ]
argss = [ (name, len(fin.variables[name].shape) != 1) for name in names ]
fin.close()
for args in argss:
quantities[name] = self.getQuantityPoints(*args)
return quantities
def test_urs_ungridded_hole (self):
#Zone: 50
#Easting: 240992.578 Northing: 7620442.472
#Latitude: -21 30 ' 0.00000 '' Longitude: 114 30 ' 0.00000 ''
lat_long = [[-20.5, 114.5],
[-20.6, 114.6],
[-20.5, 115.],
[-20.6, 115.],
[-20.5, 115.5],
[-20.6, 115.4],
[-21., 114.5],
[-21., 114.6],
[-21., 115.5],
[-21., 115.4],
[-21.5, 114.5],
[-21.4, 114.6],
[-21.5, 115.],
[-21.4, 115.],
[-21.5, 115.5],
[-21.4, 115.4]
]
time_step_count = 6
time_step = 100
tide = 9000000
base_name, files = self.write_mux(lat_long,
time_step_count, time_step)
#Easting: 292110.784 Northing: 7676551.710
#Latitude: -21 0 ' 0.00000 '' Longitude: 115 0 ' 0.00000 ''
urs_ungridded2sww(base_name, mean_stage=-240992.0,
hole_points_UTM=[ 292110.784, 7676551.710 ])
# now I want to check the sww file ...
sww_file = base_name + '.sww'
#Let's interigate the sww file
# Note, the sww info is not gridded. It is point data.
fid = NetCDFFile(sww_file)
number_of_volumes = fid.variables['volumes']
#print "number_of_volumes",len(number_of_volumes)
assert num.allclose(16, len(number_of_volumes))
fid.close()
self.delete_mux(files)
#print "sww_file", sww_file
os.remove(sww_file)
def test_boundary_time(self):
"""
test_boundary_time(self):
test that the starttime of a boundary condition is carried thru
to the output sww file.
"""
boundary_starttime = 0
boundary_filename = self.create_sww_boundary(boundary_starttime)
filename = tempfile.mktemp(".sww")
dir, base = os.path.split(filename)
senario_name = base[:-4]
mesh = Mesh()
###mesh.add_region_from_polygon([[10,10], [90,10], [90,90], [10,90]])
mesh.add_region_from_polygon([[0, 0], [100, 0], [100, 100], [0, 100]])
mesh.generate_mesh(verbose=False)
domain = pmesh_to_domain_instance(mesh, anuga.Domain)
domain.set_name(senario_name)
domain.set_datadir(dir)
# Setup initial conditions
domain.set_quantity("elevation", 0.0)
domain.set_quantity("stage", 0.0)
Bf = anuga.File_boundary(boundary_filename, domain, use_cache=False, verbose=False)
# Setup boundary conditions
domain.set_boundary({"exterior": Bf})
for t in domain.evolve(yieldstep=5.0, finaltime=10.0):
pass
# print domain.write_time()
# print "domain.time", domain.time
# do an assertion on the time of the produced sww file
fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read
times = fid.variables["time"][:]
# print "times", times
# print "fid.starttime", fid.starttime
assert num.allclose(fid.starttime, boundary_starttime)
fid.close()
# clean up
os.remove(boundary_filename)
os.remove(filename)
def test_small_nxn(self):
most2nc(input_file=FN,output_file='test.nc'\
,inverted_bathymetry = False,verbose = False)
fid = NetCDFFile('test.nc')
elevation = fid.variables['ELEVATION'][:]
fid.close()
z=[[-13., -14., -15., -16.]\
,[-9., -10., -11., -12.]\
,[-5., -6., -7., -8.]\
,[-1., -2., -3., -4.]]
z = num.asarray(z)
assert num.allclose(z, elevation)
import os
os.remove('test.nc')
def helper_write_msh_file(self, filename, l):
# open the NetCDF file
fd = NetCDFFile(filename, netcdf_mode_w)
fd.description = 'Test file - string arrays'
# convert list of strings to num.array
al = num.array(string_to_char(l), num.character)
# write the list
fd.createDimension('num_of_strings', al.shape[0])
fd.createDimension('size_of_strings', al.shape[1])
var = fd.createVariable('strings', netcdf_char,
('num_of_strings', 'size_of_strings'))
var[:] = al
fd.close()
def test_small_nxn(self):
most2nc(input_file=FN,output_file='test.nc'\
,inverted_bathymetry = False,verbose = False)
fid = NetCDFFile('test.nc')
elevation = fid.variables['ELEVATION'][:]
fid.close()
z=[[-13., -14., -15., -16.]\
,[-9., -10., -11., -12.]\
,[-5., -6., -7., -8.]\
,[-1., -2., -3., -4.]]
z = num.asarray(z)
assert num.allclose(z,elevation)
import os
os.remove('test.nc')
def __init__(self,
swwfile='domain.sww',
plot_dir='_plot',
min_depth=0.01,
minimum_allowed_depth=1.0e-03):
self.plot_dir = plot_dir
self.make_plot_dir()
self.min_depth = min_depth
import matplotlib.tri as tri
import numpy as np
import os
self.name = os.path.splitext(swwfile)[0]
from anuga.file.netcdf import NetCDFFile
p = NetCDFFile(swwfile)
self.x = np.array(p.variables['x'])
self.y = np.array(p.variables['y'])
self.triangles = np.array(p.variables['volumes'])
vols0 = self.triangles[:, 0]
vols1 = self.triangles[:, 1]
vols2 = self.triangles[:, 2]
self.triang = tri.Triangulation(self.x, self.y, self.triangles)
self.xc = (self.x[vols0] + self.x[vols1] + self.x[vols2]) / 3.0
self.yc = (self.y[vols0] + self.y[vols1] + self.y[vols2]) / 3.0
self.xllcorner = p.xllcorner
self.yllcorner = p.yllcorner
self.zone = p.zone
self.elev = np.array(p.variables['elevation_c'])
self.stage = np.array(p.variables['stage_c'])
self.xmom = np.array(p.variables['xmomentum_c'])
self.ymom = np.array(p.variables['ymomentum_c'])
self.depth = np.zeros_like(self.stage)
if (len(self.elev.shape) == 2):
self.depth = self.stage - self.elev
else:
for i in range(self.depth.shape[0]):
self.depth[i, :] = self.stage[i, :] - self.elev
with np.errstate(invalid='ignore'):
self.xvel = np.where(self.depth > minimum_allowed_depth,
self.xmom / self.depth, 0.0)
self.yvel = np.where(self.depth > minimum_allowed_depth,
self.ymom / self.depth, 0.0)
self.speed = np.sqrt(self.xvel**2 + self.yvel**2)
self.time = np.array(p.variables['time'])
def test_sww_variable(self):
"""Test that sww information can be written correctly
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
self.domain.reduction = mean
sww = SWW_file(self.domain)
sww.store_connectivity()
sww.store_timestep()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r) # Open existing file for append
# Get the variables
time = fid.variables['time']
stage = fid.variables['stage']
Q = self.domain.quantities['stage']
Q0 = Q.vertex_values[:,0]
Q1 = Q.vertex_values[:,1]
Q2 = Q.vertex_values[:,2]
A = stage[0,:]
# print stage[0,:]
# print A[0], (Q2[0] + Q1[1])/2
# print A[1], (Q0[1] + Q1[3] + Q2[2])/3
# print A[2], Q0[3]
# print A[3], (Q0[0] + Q1[5] + Q2[4])/3
assert num.allclose(A[0], (Q2[0] + Q1[1])/2, rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(A[1], (Q0[1] + Q1[3] + Q2[2])/3, rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(A[2], Q0[3])
assert num.allclose(A[3], (Q0[0] + Q1[5] + Q2[4])/3, rtol=1.0e-5, atol=1.0e-5)
#Center point
assert num.allclose(A[4], (Q1[0] + Q2[1] + Q0[2] +\
Q0[5] + Q2[6] + Q1[7])/6, rtol=1.0e-5, atol=1.0e-5)
fid.close()
os.remove(sww.filename)
def getQuantityPoints(self, quantityName, dynamic=False):
try:
if dynamic:
q = self.quantityCache[quantityName][self.vis_frame]
else:
q = self.quantityCache[quantityName]
except KeyError:
fin = NetCDFFile(self.vis_source, 'r')
if dynamic:
if not self.quantityCache.has_key(quantityName):
self.quantityCache[quantityName] = {}
q = array(fin.variables[quantityName][self.vis_frame], Float)
self.quantityCache[quantityName][self.vis_frame] = q
else:
q = array(fin.variables[quantityName], Float)
self.quantityCache[quantityName] = q
fin.close()
return q
def getQuantityPoints(self, quantityName, dynamic=False):
try:
if dynamic:
q = self.quantityCache[quantityName][self.vis_frame]
else:
q = self.quantityCache[quantityName]
except KeyError:
fin = NetCDFFile(self.vis_source, 'r')
if dynamic:
if quantityName not in self.quantityCache:
self.quantityCache[quantityName] = {}
q = array(fin.variables[quantityName][self.vis_frame], Float)
self.quantityCache[quantityName][self.vis_frame] = q
else:
q = array(fin.variables[quantityName], Float)
self.quantityCache[quantityName] = q
fin.close()
return q
def test_urs_ungridded2sww_mint_maxtII(self):
#Zone: 50
#Easting: 240992.578 Northing: 7620442.472
#Latitude: -21 30 ' 0.00000 '' Longitude: 114 30 ' 0.00000 ''
lat_long = [[-21.5, 114.5], [-21, 114.5], [-21, 115]]
time_step_count = 6
time_step = 100
tide = 9000000
base_name, files = self.write_mux(lat_long, time_step_count, time_step)
urs_ungridded2sww(base_name,
mean_stage=tide,
origin=(50, 23432, 4343),
mint=0,
maxt=100000)
# now I want to check the sww file ...
sww_file = base_name + '.sww'
#Let's interigate the sww file
# Note, the sww info is not gridded. It is point data.
fid = NetCDFFile(sww_file)
# Make x and y absolute
geo_reference = Geo_reference(NetCDFObject=fid)
points = geo_reference.get_absolute(
list(zip(fid.variables['x'][:], fid.variables['y'][:])))
points = ensure_numeric(points)
x = points[:, 0]
#Check the time vector
times = fid.variables['time'][:]
times_actual = [0, 100, 200, 300, 400, 500]
assert num.allclose(ensure_numeric(times),
ensure_numeric(times_actual))
#Check first value
stage = fid.variables['stage'][:]
assert num.allclose(stage[0], x + tide)
fid.close()
self.delete_mux(files)
os.remove(sww_file)
def test_sync(self):
"""test_sync - Test info stored at each timestep is as expected (incl initial condition)
"""
import time, os
self.domain.set_name('synctest')
self.domain.format = 'sww'
self.domain.smooth = False
self.domain.store = True
self.domain.tight_slope_limiters = True
self.domain.use_centroid_velocities = True
# In this case tight_slope_limiters as default
# in conjunction with protection
# against isolated degenerate timesteps works.
#self.domain.tight_slope_limiters = 1
#self.domain.protect_against_isolated_degenerate_timesteps = True
#print 'tight_sl', self.domain.tight_slope_limiters
#Evolution
for t in self.domain.evolve(yieldstep = 1.0, finaltime = 4.0):
#########self.domain.write_time(track_speeds=True)
stage = self.domain.quantities['stage'].vertex_values
#Get NetCDF
fid = NetCDFFile(self.domain.writer.filename, netcdf_mode_r)
stage_file = fid.variables['stage']
if t == 0.0:
assert num.allclose(stage, self.initial_stage, rtol=1.0e-5, atol=1.0e-5)
assert num.allclose(stage_file[:], stage.flatten(),rtol=1.0e-5, atol=1.0e-5)
else:
assert not num.allclose(stage, self.initial_stage, rtol=1.0e-5, atol=1.0e-5)
assert not num.allclose(stage_file[:], stage.flatten(), rtol=1.0e-5, atol=1.0e-5)
fid.close()
os.remove(self.domain.writer.filename)
def test_urs_ungridded2sww_mint_maxtII (self):
#Zone: 50
#Easting: 240992.578 Northing: 7620442.472
#Latitude: -21 30 ' 0.00000 '' Longitude: 114 30 ' 0.00000 ''
lat_long = [[-21.5,114.5],[-21,114.5],[-21,115]]
time_step_count = 6
time_step = 100
tide = 9000000
base_name, files = self.write_mux(lat_long,
time_step_count, time_step)
urs_ungridded2sww(base_name, mean_stage=tide, origin =(50,23432,4343),
mint=0, maxt=100000)
# now I want to check the sww file ...
sww_file = base_name + '.sww'
#Let's interigate the sww file
# Note, the sww info is not gridded. It is point data.
fid = NetCDFFile(sww_file)
# Make x and y absolute
geo_reference = Geo_reference(NetCDFObject=fid)
points = geo_reference.get_absolute(map(None, fid.variables['x'][:],
fid.variables['y'][:]))
points = ensure_numeric(points)
x = points[:,0]
#Check the time vector
times = fid.variables['time'][:]
times_actual = [0,100,200,300,400,500]
assert num.allclose(ensure_numeric(times),
ensure_numeric(times_actual))
#Check first value
stage = fid.variables['stage'][:]
assert num.allclose(stage[0], x +tide)
fid.close()
self.delete_mux(files)
os.remove(sww_file)
def sww_merge_parallel(domain_global_name, np, verbose=False, delete_old=False):
output = domain_global_name+".sww"
swwfiles = [ domain_global_name+"_P"+str(np)+"_"+str(v)+".sww" for v in range(np)]
fid = NetCDFFile(swwfiles[0], netcdf_mode_r)
try: # works with netcdf4
number_of_volumes = len(fid.dimensions['number_of_volumes'])
number_of_points = len(fid.dimensions['number_of_points'])
except: # works with scientific.io.netcdf
number_of_volumes = int(fid.dimensions['number_of_volumes'])
number_of_points = int(fid.dimensions['number_of_points'])
fid.close()
if 3*number_of_volumes == number_of_points:
_sww_merge_parallel_non_smooth(swwfiles, output, verbose, delete_old)
else:
_sww_merge_parallel_smooth(swwfiles, output, verbose, delete_old)
def sww2obj(filename, size):
""" Convert netcdf based data output to obj
Convert SWW data to OBJ data.
basefilename Stem of filename, needs size and extension added.
size The number of lines to write.
"""
if filename[-4:] != '.sww':
raise IOError('Output file %s should be of type .sww.' % sww_file)
basefilename = filename[:-4]
# Get NetCDF
nc_fname = create_filename('.', basefilename, 'sww', size)
log.critical('Reading from %s' % nc_fname)
fid = NetCDFFile(nc_fname, netcdf_mode_r) #Open existing file for read
# Get the variables
x = fid.variables['x']
y = fid.variables['y']
z = fid.variables['elevation']
time = fid.variables['time']
stage = fid.variables['stage']
M = size #Number of lines
xx = num.zeros((M, 3), num.float)
yy = num.zeros((M, 3), num.float)
zz = num.zeros((M, 3), num.float)
for i in range(M):
for j in range(3):
xx[i, j] = x[i + j * M]
yy[i, j] = y[i + j * M]
zz[i, j] = z[i + j * M]
# Write obj for bathymetry
FN = create_filename('.', basefilename, 'obj', size)
write_obj(FN, xx, yy, zz)
# Now read all the data with variable information, combine with
# x,y info and store as obj
for k in range(len(time)):
t = time[k]
log.critical('Processing timestep %f' % t)
for i in range(M):
for j in range(3):
zz[i, j] = stage[k, i + j * M]
#Write obj for variable data
#FN = create_filename(basefilename, 'obj', size, time=t)
FN = create_filename('.', basefilename[:5], 'obj', size, time=t)
write_obj(FN, xx, yy, zz)
def helper_write_msh_file(self, filename, l):
# open the NetCDF file
fd = NetCDFFile(filename, netcdf_mode_w)
fd.description = 'Test file - string arrays'
# convert list of strings to num.array
al = num.array(string_to_char(l), num.character)
# write the list
fd.createDimension('num_of_strings', al.shape[0])
fd.createDimension('size_of_strings', al.shape[1])
var = fd.createVariable('strings', netcdf_char,
('num_of_strings', 'size_of_strings'))
var[:] = al
fd.close()
def test_triangulation_points_georeference(self):
#
#
filename = tempfile.mktemp("_data_manager.sww")
outfile = NetCDFFile(filename, netcdf_mode_w)
points_utm = num.array([[0.,0.],[1.,1.], [0.,1.]])
volumes = [[0,1,2]]
elevation = [0,1,2]
new_origin = None
points_georeference = Geo_reference(56, 1, 554354)
points_utm = points_georeference.change_points_geo_ref(points_utm)
times = [0, 10]
number_of_volumes = len(volumes)
number_of_points = len(points_utm)
sww = Write_sww(['elevation'], ['stage', 'xmomentum', 'ymomentum'])
sww.store_header(outfile, times, number_of_volumes,
number_of_points, description='fully sick testing',
verbose=self.verbose,sww_precision=netcdf_float)
sww.store_triangulation(outfile, points_utm, volumes,
elevation, new_origin=new_origin,
points_georeference=points_georeference,
verbose=self.verbose)
outfile.close()
fid = NetCDFFile(filename)
x = fid.variables['x'][:]
y = fid.variables['y'][:]
results_georef = Geo_reference()
results_georef.read_NetCDF(fid)
assert results_georef == points_georeference
fid.close()
assert num.allclose(num.array(map(None, x,y)), points_utm)
os.remove(filename)
def test_ferret2sww_2(self):
"""Test that georeferencing etc works when converting from
ferret format (lat/lon) to sww format (UTM)
"""
#The test file has
# LON = 150.66667, 150.83334, 151, 151.16667
# LAT = -34.5, -34.33333, -34.16667, -34 ;
# TIME = 0, 0.1, 0.6, 1.1, 1.6, 2.1 ;
#
# First value (index=0) in small_ha.nc is 0.3400644 cm,
# Fourth value (index==3) is -6.50198 cm
from anuga.coordinate_transforms.redfearn import redfearn
#fid = NetCDFFile('small_ha.nc')
fid = NetCDFFile(self.test_MOST_file + '_ha.nc')
#Pick a coordinate and a value
time_index = 1
lat_index = 0
lon_index = 2
test_value = fid.variables['HA'][:][time_index, lat_index, lon_index]
test_time = fid.variables['TIME'][:][time_index]
test_lat = fid.variables['LAT'][:][lat_index]
test_lon = fid.variables['LON'][:][lon_index]
linear_point_index = lat_index*4 + lon_index
fid.close()
#Call conversion (with zero origin)
ferret2sww(self.test_MOST_file, verbose=self.verbose,
origin = (56, 0, 0))
#Work out the UTM coordinates for test point
zone, e, n = redfearn(test_lat, test_lon)
#Read output file 'small.sww'
fid = NetCDFFile(self.test_MOST_file + '.sww')
x = fid.variables['x'][:]
y = fid.variables['y'][:]
#Check that test coordinate is correctly represented
assert num.allclose(x[linear_point_index], e)
assert num.allclose(y[linear_point_index], n)
#Check test value
stage = fid.variables['stage'][:]
assert num.allclose(stage[time_index, linear_point_index], test_value/100)
fid.close()
#Cleanup
import os
os.remove(self.test_MOST_file + '.sww')
def test_read_NetCDFI(self):
# test if read_NetCDF
from anuga.file.netcdf import NetCDFFile
g = Geo_reference(56,1.9,1.9)
file_name = tempfile.mktemp(".geo_referenceTest")
outfile = NetCDFFile(file_name, netcdf_mode_w)
outfile.xllcorner = g.get_xllcorner()
outfile.yllcorner = g.get_yllcorner()
outfile.zone = g.get_zone()
outfile.close()
in_file = NetCDFFile(file_name, netcdf_mode_r)
new_g = Geo_reference(NetCDFObject=in_file)
in_file.close()
os.remove(file_name)
self.assertTrue(g == new_g, ' failed')
def csv2sts(infile, outfile, latitude = None, longitude = None,
verbose = False):
"""
Take a csv file and convert it to an sts file.
May be used for timeseries, or any other data.
"""
timeseries_data, col_names = load_csv_as_dict(infile, delimiter=' ')
if not col_names:
raise IOError('csv2sts: file %s is empty or unreadable.' % infile)
if verbose:
log.critical('csv2sts input data:')
for col in col_names:
log.critical('column ' + col + ':')
log.critical(timeseries_data[col])
data_len = len(timeseries_data.values()[0])
if verbose:
log.critical(' data length = %d.' % data_len)
fid = NetCDFFile(outfile, netcdf_mode_w)
fid.createDimension('number_of_timesteps', data_len)
if latitude:
fid.latitude = latitude
if longitude:
fid.longitude = longitude
for col in col_names:
fid.createVariable(col, netcdf_float, ('number_of_timesteps',))
fid.variables[col][:] = timeseries_data[col]
fid.close()
def test_sww_constant_smooth(self):
"""Test that constant sww information can be written correctly
(non smooth)
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
sww = SWW_file(self.domain)
sww.store_connectivity()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename,
netcdf_mode_r) # Open existing file for append
# Get the variables
X = fid.variables['x'][:]
Y = fid.variables['y'][:]
Z = fid.variables['elevation'][:]
V = fid.variables['volumes']
assert num.allclose([X[0], Y[0]], num.array([0.0, 0.0]))
assert num.allclose([X[1], Y[1]], num.array([0.0, 0.5]))
assert num.allclose([X[2], Y[2]], num.array([0.0, 1.0]))
assert num.allclose([X[4], Y[4]], num.array([0.5, 0.5]))
assert num.allclose([X[7], Y[7]], num.array([1.0, 0.5]))
assert Z[4] == -0.5
assert V[2, 0] == 4
assert V[2, 1] == 5
assert V[2, 2] == 1
assert V[4, 0] == 6
assert V[4, 1] == 7
assert V[4, 2] == 3
fid.close()
os.remove(sww.filename)
def test_sww_constant_smooth(self):
"""Test that constant sww information can be written correctly
(non smooth)
"""
self.domain.set_name('datatest' + str(id(self)))
self.domain.format = 'sww'
self.domain.smooth = True
sww = SWW_file(self.domain)
sww.store_connectivity()
# Check contents
# Get NetCDF
fid = NetCDFFile(sww.filename, netcdf_mode_r) # Open existing file for append
# Get the variables
X = fid.variables['x'][:]
Y = fid.variables['y'][:]
Z = fid.variables['elevation'][:]
V = fid.variables['volumes']
assert num.allclose([X[0], Y[0]], num.array([0.0, 0.0]))
assert num.allclose([X[1], Y[1]], num.array([0.0, 0.5]))
assert num.allclose([X[2], Y[2]], num.array([0.0, 1.0]))
assert num.allclose([X[4], Y[4]], num.array([0.5, 0.5]))
assert num.allclose([X[7], Y[7]], num.array([1.0, 0.5]))
assert Z[4] == -0.5
assert V[2,0] == 4
assert V[2,1] == 5
assert V[2,2] == 1
assert V[4,0] == 6
assert V[4,1] == 7
assert V[4,2] == 3
fid.close()
os.remove(sww.filename)
def test_georef_types(self):
'''Ensure that attributes of a georeference are of correct type.
zone int
false_easting int
false_northing int
xllcorner float
yllcorner float
'''
from anuga.file.netcdf import NetCDFFile
# ensure that basic instance attributes are correct
g = Geo_reference(56, 1.8, 1.8)
self.assertTrue(isinstance(g.zone, int),
"geo_ref .zone should be 'int' type, "
"was '%s' type" % type(g.zone))
self.assertTrue(isinstance(g.false_easting, int),
"geo_ref .false_easting should be int type, "
"was '%s' type" % type(g.false_easting))
self.assertTrue(isinstance(g.false_northing, int),
"geo_ref .false_northing should be int type, "
"was '%s' type" % type(g.false_northing))
self.assertTrue(isinstance(g.xllcorner, float),
"geo_ref .xllcorner should be float type, "
"was '%s' type" % type(g.xllcorner))
self.assertTrue(isinstance(g.yllcorner, float),
"geo_ref .yllcorner should be float type, "
"was '%s' type" % type(g.yllcorner))
# now write fikle, read back and check types again
file_name = tempfile.mktemp(".geo_referenceTest")
out_file = NetCDFFile(file_name, netcdf_mode_w)
g.write_NetCDF(out_file)
out_file.close()
in_file = NetCDFFile(file_name, netcdf_mode_r)
new_g = Geo_reference(NetCDFObject=in_file)
in_file.close()
os.remove(file_name)
self.assertTrue(isinstance(new_g.zone, int),
"geo_ref .zone should be 'int' type, "
"was '%s' type" % type(new_g.zone))
self.assertTrue(isinstance(new_g.false_easting, int),
"geo_ref .false_easting should be int type, "
"was '%s' type" % type(new_g.false_easting))
self.assertTrue(isinstance(new_g.false_northing, int),
"geo_ref .false_northing should be int type, "
"was '%s' type" % type(new_g.false_northing))
self.assertTrue(isinstance(new_g.xllcorner, float),
"geo_ref .xllcorner should be float type, "
"was '%s' type" % type(new_g.xllcorner))
self.assertTrue(isinstance(new_g.yllcorner, float),
"geo_ref .yllcorner should be float type, "
"was '%s' type" % type(new_g.yllcorner))