def test_3d():
grid = RasterField((2, 3, 4), (1., 1., 1.), (0., 0., 0.))
point_data = np.arange(grid.get_point_count())
grid.add_field('var_0', point_data, centering='point')
with cd_temp() as _:
tofile('test-3d', grid)
assert_true(os.path.isfile('test-3d.bov'))
assert_true(os.path.isfile('test-3d.dat'))
data = np.fromfile('test-3d.dat', dtype=int)
assert_array_equal(point_data, data)
with open('test-3d.bov', 'r') as fp:
header = yaml.load(fp)
assert_dict_equal(
header, {
'VARIABLE': 'var_0',
'BRICK_SIZE': '2.0 3.0 4.0',
'DATA_FILE': 'test-3d.dat',
'DATA_SIZE': '2 3 4',
'BRICK_ORIGIN': '0.0 0.0 0.0',
'DATA_FORMAT': 'INT',
'DATA_ENDIAN': sys.byteorder.upper(),
})
def test_2d_cell_fields(self):
# Create a field that looks like this,
#
# (0) --- (1) --- (2)
# | | |
# | 0 | 1 |
# | | |
# (3) --- (4) --- (5)
g = RasterField((2, 3), (1, 2), (0, 0), indexing="ij")
data = np.arange(6)
g.add_field("point_var_1", data, centering="point")
g.add_field("point_var_2", data * 2, centering="point")
data = np.arange(2)
g.add_field("cell_var_1", data, centering="zonal")
g.add_field("cell_var_2", data * 2, centering="zonal")
fields = g.get_cell_fields()
self.assertEqual(len(fields), 2)
self.assertTrue("cell_var_1" in fields)
self.assertTrue("cell_var_2" in fields)
self.assert_field_values(g, "cell_var_1", [0, 1])
self.assert_field_values(g, "cell_var_2", [0, 2])
def test_3d(tmpdir):
grid = RasterField((2, 3, 4), (1., 1., 1.), (0., 0., 0.))
point_data = np.arange(grid.get_point_count())
grid.add_field("var_0", point_data, centering="point")
with tmpdir.as_cwd():
tofile("test-3d", grid)
assert os.path.isfile("test-3d.bov")
assert os.path.isfile("test-3d.dat")
data = np.fromfile("test-3d.dat", dtype=int)
assert np.all(point_data == data)
with open("test-3d.bov", "r") as fp:
header = yaml.load(fp)
assert header == {
"VARIABLE": "var_0",
"BRICK_SIZE": "2.0 3.0 4.0",
"DATA_FILE": "test-3d.dat",
"DATA_SIZE": "2 3 4",
"BRICK_ORIGIN": "0.0 0.0 0.0",
"DATA_FORMAT": "INT",
"DATA_ENDIAN": sys.byteorder.upper(),
}
def test_2d(self):
nc_file = self.temp_file_name(prefix='raster.2d.', suffix='.nc')
field = RasterField((3, 2), (2., 1), (0, 0.5), units=('m', 'km'))
data = np.arange(6.)
field.add_field('Temperature', data * 10, centering='point', units='C')
field.add_field('Elevation', data, centering='point', units='meters')
field.add_field('Velocity', data * 100, centering='point', units='m/s')
field.add_field('Temp', data * 2, centering='point', units='F')
attrs = dict(description='Example nc file', author='Eric')
field_tofile(field, nc_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(nc_file))
root = self.open_as_netcdf(nc_file)
self.assertDataVariableNames(root, [
'mesh', 'Temperature', 'Elevation', 'Velocity', 'Temp', 'x', 'y',
'time'
])
self.assertDimensionsEqual(root, ['x', 'y', 'time'])
self.assertDataVariableArrayEqual(root, 'x', [.5, 1.5])
self.assertDataVariableArrayEqual(root, 'y', [0., 2., 4.])
for name in ['Temperature', 'Elevation', 'Velocity', 'Temp']:
self.assertDataVariableLongNameEqual(root, name, name)
for (name, units) in [('Temperature', 'C'), ('Elevation', 'meters'),
('Velocity', 'm/s'), ('Temp', 'F')]:
self.assertDataVariableUnitsEqual(root, name, units)
root.close()
def test_1d(self):
vtk_file = self.vtk_files['test_1d']
field = RasterField((12, ), (1, ), (-1, ), indexing='ij', units=('m', ))
data = np.arange(12.)
field.add_field('Elevation', data, centering='point')
attrs = dict(description='Example 1D nc file', author='Eric')
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_0d(self):
vtk_file = self.vtk_files["test_0d"]
field = RasterField((1, ), (0, ), (0, ), indexing="ij", units=("m", ))
attrs = dict(description="Example 0D nc file", author="Eric")
for i in range(10):
field.add_field("Elevation", i * 10.0, centering="point")
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_1d(self):
vtk_file = self.vtk_files["test_1d"]
field = RasterField((12,), (1,), (-1,), indexing="ij", units=("m",))
data = np.arange(12.0)
field.add_field("Elevation", data, centering="point")
attrs = dict(description="Example 1D nc file", author="Eric")
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_0d(self):
vtk_file = self.vtk_files["test_0d"]
field = RasterField((1,), (0,), (0,), indexing="ij", units=("m",))
attrs = dict(description="Example 0D nc file", author="Eric")
for i in range(10):
field.add_field("Elevation", i * 10.0, centering="point")
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_2d_point_fields(self):
# Create a field that looks like this,
#
# (0) --- (1) --- (2)
# | | |
# | 0 | 1 |
# | | |
# (3) --- (4) --- (5)
g = RasterField((2, 3), (1, 2), (0, 0), indexing="ij")
data = np.arange(6)
g.add_field("point_var_1", data, centering="point")
g.add_field("point_var_2", data * 2, centering="point")
data = np.arange(2)
g.add_field("cell_var", data, centering="zonal")
fields = g.get_point_fields()
self.assertEqual(len(fields), 2)
self.assertTrue("point_var_1" in fields)
self.assertTrue("point_var_2" in fields)
self.assert_field_values(g, "point_var_1", [0, 1, 2, 3, 4, 5])
self.assert_field_values(g, "point_var_2", [0, 2, 4, 6, 8, 10])
def test_2d_point_fields (self):
# Create a field that looks like this,
#
# (0) --- (1) --- (2)
# | | |
# | 0 | 1 |
# | | |
# (3) --- (4) --- (5)
g = RasterField ((2,3), (1,2), (0, 0), indexing='ij')
data = np.arange (6)
g.add_field ('point_var_1', data, centering='point')
g.add_field ('point_var_2', data*2, centering='point')
data = np.arange (2)
g.add_field ('cell_var', data, centering='zonal')
fields = g.get_point_fields ()
self.assertEqual (len (fields), 2)
self.assertTrue (fields.has_key ('point_var_1'))
self.assertTrue (fields.has_key ('point_var_2'))
self.assert_field_values (g, 'point_var_1', [0, 1, 2, 3, 4, 5])
self.assert_field_values (g, 'point_var_2', [0, 2, 4, 6, 8, 10])
def test_2d_constant_shape(tmpdir):
# Create field and add some data to it that we will write to a
# NetCDF file database.
# nc_file = 'Elevation_time_series_0000.nc'
nc_file = "2d_elevation_time_series.nc"
data = np.arange(6.0)
field = RasterField((2, 3), (1.0, 1.0), (0.0, 0.0), indexing="ij")
field.add_field("Elevation", data, centering="point")
# Create database of 'Elevation' values. Data are written to the
# NetCDF file Elevation_time_series.nc.
with tmpdir.as_cwd():
db = Database()
db.open(nc_file, "Elevation")
db.write(field)
assert os.path.isfile(nc_file)
# Append data to the NetCDF file.
data *= 2.0
db.write(field)
db.close()
try:
root = open_nc_file(nc_file)
except Exception:
raise AssertionError("%s: Could not open" % nc_file)
else:
assert list(root.dimensions.keys()) == ["y", "x", "time"]
assert list(root.variables) == ["mesh", "y", "x", "Elevation", "time"]
assert len(root.dimensions["x"]) == 3
assert len(root.dimensions["y"]) == 2
assert len(root.dimensions["time"]) == 2
assert root.variables["Elevation"].shape == (2, 2, 3)
assert root.variables["Elevation"][0].data == approx(
np.arange(6.0).reshape(2, 3)
)
assert root.variables["Elevation"][1].data == approx(
np.arange(6.0).reshape((2, 3)) * 2.0
)
assert root.variables["y"] == approx([0.0, 1.0])
assert root.variables["x"] == approx([0.0, 1.0, 2.0])
assert root.variables["Elevation"].long_name == "Elevation"
assert root.variables["Elevation"].units == "-"
root.close()
def test_0d(self):
vtk_file = self.vtk_files['test_0d']
field = RasterField((1, ), (0, ), (0, ), indexing='ij',
units=('m', ))
attrs = dict(description='Example 0D nc file', author='Eric')
for i in range(10):
field.add_field('Elevation', i * 10., centering='point')
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_2d_constant_shape(tmpdir):
# Create field and add some data to it that we will write to a
# NetCDF file database.
# nc_file = 'Elevation_time_series_0000.nc'
nc_file = "2d_elevation_time_series.nc"
data = np.arange(6.0)
field = RasterField((2, 3), (1.0, 1.0), (0.0, 0.0), indexing="ij")
field.add_field("Elevation", data, centering="point")
# Create database of 'Elevation' values. Data are written to the
# NetCDF file Elevation_time_series.nc.
with tmpdir.as_cwd():
db = Database()
db.open(nc_file, "Elevation")
db.write(field)
assert os.path.isfile(nc_file)
# Append data to the NetCDF file.
data *= 2.0
db.write(field)
db.close()
try:
root = open_nc_file(nc_file)
except Exception:
raise AssertionError("%s: Could not open" % nc_file)
else:
assert list(root.dimensions.keys()) == ["y", "x", "time"]
assert list(
root.variables) == ["mesh", "y", "x", "Elevation", "time"]
assert len(root.dimensions["x"]) == 3
assert len(root.dimensions["y"]) == 2
assert len(root.dimensions["time"]) == 2
assert root.variables["Elevation"].shape == (2, 2, 3)
assert root.variables["Elevation"][0].data == approx(
np.arange(6.0).reshape(2, 3))
assert root.variables["Elevation"][1].data == approx(
np.arange(6.0).reshape((2, 3)) * 2.0)
assert root.variables["y"] == approx([0.0, 1.0])
assert root.variables["x"] == approx([0.0, 1.0, 2.0])
assert root.variables["Elevation"].long_name == "Elevation"
assert root.variables["Elevation"].units == "-"
root.close()
def test_2d_constant_shape():
#Create field and add some data to it that we will write to a
# NetCDF file database.
#nc_file = 'Elevation_time_series_0000.nc'
nc_file = os.path.join(_TMP_DIR, '2d_elevation_time_series.nc')
data = np.arange(6.)
field = RasterField((2, 3), (1., 1.), (0., 0.), indexing='ij')
field.add_field('Elevation', data, centering='point')
#Create database of 'Elevation' values. Data are written to the
# NetCDF file Elevation_time_series.nc.
db = Database()
db.open(nc_file, 'Elevation')
db.write(field)
assert_true(os.path.isfile(nc_file))
# Append data to the NetCDF file.
data *= 2.
db.write(field)
db.close()
try:
root = open_nc_file(nc_file)
except Exception:
raise AssertionError('%s: Could not open' % nc_file)
else:
assert_items_equal(['x', 'y', 'time'], root.dimensions.keys())
assert_items_equal(['Elevation', 'x', 'y', 'time', 'mesh'],
root.variables)
assert_equal(3, len(root.dimensions['x']))
assert_equal(2, len(root.dimensions['y']))
assert_equal(2, len(root.dimensions['time']))
assert_tuple_equal((2, 2, 3), root.variables['Elevation'].shape)
assert_array_equal(
np.arange(6.).reshape(2, 3), root.variables['Elevation'][0])
assert_array_equal(
np.arange(6.).reshape((2, 3)) * 2., root.variables['Elevation'][1])
assert_array_equal([0., 1.], root.variables['y'])
assert_array_equal([0., 1., 2.], root.variables['x'])
assert_equal('Elevation', root.variables['Elevation'].long_name)
assert_equal('-', root.variables['Elevation'].units)
root.close()
def test_clobber(tmpdir):
grid = RasterField((12,), (1.,), (0.,))
var_0_data = np.arange(grid.get_point_count())
grid.add_field("var_0", var_0_data, centering="point")
for fname in ["test-1d.bov", "test-1d.dat"]:
with tmpdir.as_cwd():
with open(fname, "w") as fp:
fp.write("empty_file")
with pytest.raises(FileExists):
tofile("test-1d", grid, no_clobber=True)
tofile("test-1d", grid)
def test_clobber():
grid = RasterField((12, ), (1., ), (0., ))
var_0_data = np.arange(grid.get_point_count())
grid.add_field('var_0', var_0_data, centering='point')
for fname in ['test-1d.bov', 'test-1d.dat']:
with cd_temp() as _:
with open(fname, 'w') as fp:
fp.write('empty_file')
with assert_raises(FileExists):
tofile('test-1d', grid, no_clobber=True)
tofile('test-1d', grid)
def test_1d(self):
vtk_file = self.vtk_files["test_1d"]
field = RasterField((12, ), (1, ), (-1, ),
indexing="ij",
units=("m", ))
data = np.arange(12.0)
field.add_field("Elevation", data, centering="point")
attrs = dict(description="Example 1D nc file", author="Eric")
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_raster_field_1d(self):
g = RasterField((6,), (1.5,), (0.5,), indexing="ij")
self.assert_point_count(g, 6)
self.assert_cell_count(g, 5)
point_data = np.arange(6.0)
g.add_field("Point Data", point_data, centering="point")
cell_data = np.arange(5.0) * 10.0
g.add_field("Cell Data", cell_data, centering="zonal")
self.assert_field_values(g, "Cell Data", [0.0, 10.0, 20.0, 30.0, 40.0])
self.assert_field_values(g, "Point Data", [0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
def test_raster_field_3d(self):
g = RasterField((4, 3, 2), (1.5, 1.0, 3), (0.5, 0, -0.5), indexing="ij")
self.assert_point_count(g, 24)
self.assert_cell_count(g, 6)
g.add_field("Point Data", g.get_x(), centering="point")
cell_data = np.arange(6.0) * 10.0
g.add_field("Cell Data", cell_data, centering="zonal")
g.get_field("Cell Data")
self.assert_field_values(g, "Cell Data", [0.0, 10.0, 20.0, 30.0, 40.0, 50.0])
self.assert_field_values(
g,
"Point Data",
[
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
-0.5,
2.5,
],
)
self.assert_shape(g, (4, 3, 2))
x = g.get_x()
data = g.get_field("Point Data")
self.assertEqual(x.size, data.size)
def test_2d_changing_shape():
#Create field and add some data to it that we will write to a
# NetCDF file database.
nc_file = os.path.join(_TMP_DIR, 'Temperature_time_series.nc')
data = np.arange(6.)
field = RasterField((3, 2), (1., 1.), (0., 0.))
field.add_field('Temperature', data, centering='point')
db = Database()
db.open(nc_file, 'Temperature')
db.write(field)
assert_true(os.path.isfile(nc_file))
# Create a new field and write the data to the database. Since
# the size of the field has changed, the data will be written
# to a new file, Elevation_time_series_0000.nc.
field = RasterField((3, 3), (1., 1.), (0., 0.))
data = np.arange(9.)
field.add_field('Temperature', data, centering='point')
db.write(field)
assert_true(
os.path.isfile(
os.path.join(_TMP_DIR, 'Temperature_time_series_0000.nc')))
db.close()
try:
nc_file = os.path.join(_TMP_DIR, 'Temperature_time_series_0000.nc')
root = open_nc_file(nc_file)
except Exception:
raise AssertionError('%s: Could not open' % nc_file)
else:
assert_items_equal(['x', 'y', 'time'], root.dimensions.keys())
assert_items_equal(['Temperature', 'x', 'y', 'time', 'mesh'],
root.variables)
assert_equal(3, len(root.dimensions['x']))
assert_equal(3, len(root.dimensions['y']))
assert_equal(1, len(root.dimensions['time']))
assert_tuple_equal((1, 3, 3), root.variables['Temperature'].shape)
assert_array_equal(
np.arange(9.).reshape((3, 3)), root.variables['Temperature'][0])
assert_array_equal([0., 1., 2.], root.variables['x'])
assert_array_equal([0., 1., 2.], root.variables['y'])
assert_equal('Temperature', root.variables['Temperature'].long_name)
assert_equal('-', root.variables['Temperature'].units)
root.close()
def test_3d(self):
vtk_file = self.vtk_files['test_3d']
field = RasterField((2, 3, 4), (1, 2, 3), (-1, 0, 1),
indexing='ij', units=('mm', 'm', 'km'))
data = np.arange(24.)
field.add_field('Temperature', data * 10, centering='point', units='C')
field.add_field('Elevation', data, centering='point', units='meters')
field.add_field('Velocity', data * 100, centering='point', units='m/s')
field.add_field('Temp', data * 2, centering='point', units='F')
attrs = dict(description='Example 3D nc file', author='Eric')
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_2d_changing_shape(tmpdir):
# Create field and add some data to it that we will write to a
# NetCDF file database.
nc_file = "Temperature_time_series.nc"
data = np.arange(6.0)
field = RasterField((3, 2), (1.0, 1.0), (0.0, 0.0))
field.add_field("Temperature", data, centering="point")
with tmpdir.as_cwd():
db = Database()
db.open(nc_file, "Temperature")
db.write(field)
assert os.path.isfile(nc_file)
# Create a new field and write the data to the database. Since
# the size of the field has changed, the data will be written
# to a new file, Elevation_time_series_0000.nc.
field = RasterField((3, 3), (1.0, 1.0), (0.0, 0.0))
data = np.arange(9.0)
field.add_field("Temperature", data, centering="point")
db.write(field)
assert os.path.isfile("Temperature_time_series_0000.nc")
db.close()
nc_file = "Temperature_time_series_0000.nc"
try:
root = open_nc_file(nc_file)
except Exception:
raise AssertionError("%s: Could not open" % nc_file)
else:
assert list(root.dimensions.keys()) == ["y", "x", "time"]
assert list(
root.variables) == ["mesh", "y", "x", "Temperature", "time"]
assert len(root.dimensions["x"]) == 3
assert len(root.dimensions["y"]) == 3
assert len(root.dimensions["time"]) == 1
assert root.variables["Temperature"].shape == (1, 3, 3)
assert root.variables["Temperature"][0].data == approx(
np.arange(9.0).reshape((3, 3)))
assert root.variables["x"] == approx([0.0, 1.0, 2.0])
assert root.variables["y"] == approx([0.0, 1.0, 2.0])
assert root.variables["Temperature"].long_name == "Temperature"
assert root.variables["Temperature"].units == "-"
root.close()
def test_3d(self):
vtk_file = self.vtk_files["test_3d"]
field = RasterField((2, 3, 4), (1, 2, 3), (-1, 0, 1),
indexing="ij",
units=("mm", "m", "km"))
data = np.arange(24.0)
field.add_field("Temperature", data * 10, centering="point", units="C")
field.add_field("Elevation", data, centering="point", units="meters")
field.add_field("Velocity", data * 100, centering="point", units="m/s")
field.add_field("Temp", data * 2, centering="point", units="F")
attrs = dict(description="Example 3D nc file", author="Eric")
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_3d(self):
nc_file = self.temp_file_name(prefix='raster.3d.', suffix='.nc')
field = RasterField((2, 3, 4), (1, 2, 3), (-1, 0, 1),
indexing='ij',
units=('mm', 'm', 'km'))
data = np.arange(24.)
field.add_field('Temperature', data * 10, centering='point', units='C')
field.add_field('Elevation', data, centering='point', units='meters')
field.add_field('Velocity', data * 100, centering='point', units='m/s')
field.add_field('Temp', data * 2, centering='point', units='F')
attrs = dict(description='Example 3D nc file', author='Eric')
field_tofile(field, nc_file, attrs=attrs, append=True)
self.assertIsFile(nc_file)
def new_raster(self, **kwds):
import random
ndims = kwds.pop('ndims', 1)
shape = np.random.random_integers(2, 101, ndims)
spacing = (1. - np.random.random(ndims)) * 100.
origin = (np.random.random(ndims) - .5) * 100.
return RasterField(shape, spacing, origin, **kwds)
def test_all_fields(tmpdir):
grid = RasterField((12,), (1.,), (0.,))
var_0_data = np.arange(grid.get_point_count())
var_1_data = np.arange(grid.get_point_count()) * 10
grid.add_field("var_0", var_0_data, centering="point")
grid.add_field("var_1", var_1_data, centering="point")
with tmpdir.as_cwd():
tofile("test-1d", grid)
assert os.path.isfile("test-1d_var_0.bov")
assert os.path.isfile("test-1d_var_0.dat")
assert os.path.isfile("test-1d_var_1.bov")
assert os.path.isfile("test-1d_var_1.dat")
data = np.fromfile("test-1d_var_0.dat", dtype=int)
assert np.all(var_0_data == data)
data = np.fromfile("test-1d_var_1.dat", dtype=int)
assert np.all(var_1_data == data)
def test_all_fields():
grid = RasterField((12, ), (1., ), (0., ))
var_0_data = np.arange(grid.get_point_count())
var_1_data = np.arange(grid.get_point_count()) * 10
grid.add_field('var_0', var_0_data, centering='point')
grid.add_field('var_1', var_1_data, centering='point')
with cd_temp() as _:
tofile('test-1d', grid)
assert_true(os.path.isfile('test-1d_var_0.bov'))
assert_true(os.path.isfile('test-1d_var_0.dat'))
assert_true(os.path.isfile('test-1d_var_1.bov'))
assert_true(os.path.isfile('test-1d_var_1.dat'))
data = np.fromfile('test-1d_var_0.dat', dtype=int)
assert_array_equal(var_0_data, data)
data = np.fromfile('test-1d_var_1.dat', dtype=int)
assert_array_equal(var_1_data, data)
def test_3d(self):
vtk_file = self.vtk_files["test_3d"]
field = RasterField(
(2, 3, 4), (1, 2, 3), (-1, 0, 1), indexing="ij", units=("mm", "m", "km")
)
data = np.arange(24.0)
field.add_field("Temperature", data * 10, centering="point", units="C")
field.add_field("Elevation", data, centering="point", units="meters")
field.add_field("Velocity", data * 100, centering="point", units="m/s")
field.add_field("Temp", data * 2, centering="point", units="F")
attrs = dict(description="Example 3D nc file", author="Eric")
field_tofile(field, vtk_file, attrs=attrs, append=True)
self.assertTrue(os.path.isfile(vtk_file))
def test_options(tmpdir):
grid = RasterField((12,), (1.,), (0.,))
var_0_data = np.arange(grid.get_point_count())
grid.add_field("var_0", var_0_data, centering="point")
with tmpdir.as_cwd():
tofile("test-1d", grid, options={"foo": "bar"})
with open("test-1d.bov", "r") as fp:
header = yaml.load(fp)
assert header == {
"VARIABLE": "var_0",
"BRICK_SIZE": "12.0 1.0 1.0",
"DATA_FILE": "test-1d.dat",
"DATA_SIZE": "12 1 1",
"BRICK_ORIGIN": "0.0 1.0 1.0",
"DATA_FORMAT": "INT",
"DATA_ENDIAN": sys.byteorder.upper(),
"foo": "bar",
}
def test_1d(self):
nc_file = self.temp_file_name(prefix='raster.1d.', suffix='.nc')
field = RasterField((12, ), (1, ), (-1, ), units=('m', ))
data = np.arange(12.)
field.add_field('Elevation', data, centering='point')
attrs = dict(description='Example 1D nc file', author='Eric')
field_tofile(field, nc_file, attrs=attrs, append=True)
self.assertIsFile(nc_file)
root = self.open_as_netcdf(nc_file)
self.assertDataVariableNames(root, ['mesh', 'Elevation', 'x', 'time'])
self.assertDimensionsEqual(root, ['x', 'time'])
self.assertDataVariableArrayEqual(root, 'x', np.arange(12.) - 1.)
self.assertDataVariableLongNameEqual(root, 'Elevation', 'Elevation')
self.assertDataVariableUnitsEqual(root, 'Elevation', '-')
self.assertDataVariableUnitsEqual(root, 'x', 'm')
root.close()
def test_options():
grid = RasterField((12, ), (1., ), (0., ))
var_0_data = np.arange(grid.get_point_count())
grid.add_field('var_0', var_0_data, centering='point')
with cd_temp() as _:
tofile('test-1d', grid, options={'foo': 'bar'})
with open('test-1d.bov', 'r') as fp:
header = yaml.load(fp)
assert_dict_equal(
header, {
'VARIABLE': 'var_0',
'BRICK_SIZE': '12.0 1.0 1.0',
'DATA_FILE': 'test-1d.dat',
'DATA_SIZE': '12 1 1',
'BRICK_ORIGIN': '0.0 1.0 1.0',
'DATA_FORMAT': 'INT',
'DATA_ENDIAN': sys.byteorder.upper(),
'foo': 'bar',
})
def test_raster(tmpdir, ndims):
if ndims == 0:
shape = (1, )
ndims = 1
else:
shape = np.random.randint(1, 101, ndims)
spacing = np.ones(ndims, dtype=float)
origin = np.zeros(ndims, dtype=float)
units = ["m"] * ndims
field = RasterField(shape, spacing, origin, units=units)
attrs = {
"description":
"Example {ndims}D nc file".format(ndims=ndims, author="pytest")
}
data = np.arange(field.get_point_count())
with tmpdir.as_cwd():
for i in range(10):
field.add_field("Elevation",
data * i,
centering="point",
units="m")
field_tofile(field, "raster.nc", attrs=attrs, append=True)
assert os.path.isfile("raster.nc")
ds = xarray.open_dataset("raster.nc")
assert {"mesh", "Elevation", "time"}.issubset(ds.variables)
assert "time" in ds.dims
assert ds["Elevation"].long_name == "Elevation"
assert ds["Elevation"].units == "m"
def test_bov_database(tmpdir):
data = np.arange(6.)
field = RasterField((3, 2), (1., 1.), (0., 0.))
field.add_field("Elevation", data, centering="point")
with tmpdir.as_cwd():
db = Database()
db.open("Bov_database.bov", "Elevation")
# Write the field to the database. Since BOV files only
# store one variable, append the variable name to the file name.
db.write(field)
assert os.path.isfile("Bov_database_0000.bov")
data *= 2.
db.write(field)
assert os.path.isfile("Bov_database_0001.bov")
data *= 2.
db.write(field)
assert os.path.isfile("Bov_database_0002.bov")
db.close()
def test_0d(self):
nc_file = self.temp_file_name(prefix='raster.0d.', suffix='.nc')
field = RasterField((1, ), (0, ), (0, ), units=('m', ))
attrs = dict(description='Example 0D nc file', author='Eric')
for i in range(10):
field.add_field('Elevation', i * 10., centering='point')
field_tofile(field, nc_file, attrs=attrs, append=True)
self.assertIsFile(nc_file)
root = self.open_as_netcdf(nc_file)
self.assertDataVariableNames(root, ['mesh', 'Elevation', 'time'])
self.assertDimensionsEqual(root, ['time'])
self.assertDataVariableLongNameEqual(root, 'Elevation', 'Elevation')
self.assertDataVariableUnitsEqual(root, 'Elevation', '-')
self.assertDataVariableArrayEqual(root, 'Elevation',
10. * np.arange(10))
self.assertDataVariableArrayEqual(root, 'time', range(10))
root.close()
def test_2d_changing_shape(tmpdir):
# Create field and add some data to it that we will write to a
# NetCDF file database.
nc_file = "Temperature_time_series.nc"
data = np.arange(6.0)
field = RasterField((3, 2), (1.0, 1.0), (0.0, 0.0))
field.add_field("Temperature", data, centering="point")
with tmpdir.as_cwd():
db = Database()
db.open(nc_file, "Temperature")
db.write(field)
assert os.path.isfile(nc_file)
# Create a new field and write the data to the database. Since
# the size of the field has changed, the data will be written
# to a new file, Elevation_time_series_0000.nc.
field = RasterField((3, 3), (1.0, 1.0), (0.0, 0.0))
data = np.arange(9.0)
field.add_field("Temperature", data, centering="point")
db.write(field)
assert os.path.isfile("Temperature_time_series_0000.nc")
db.close()
nc_file = "Temperature_time_series_0000.nc"
try:
root = open_nc_file(nc_file)
except Exception:
raise AssertionError("%s: Could not open" % nc_file)
else:
assert list(root.dimensions.keys()) == ["y", "x", "time"]
assert list(root.variables) == ["mesh", "y", "x", "Temperature", "time"]
assert len(root.dimensions["x"]) == 3
assert len(root.dimensions["y"]) == 3
assert len(root.dimensions["time"]) == 1
assert root.variables["Temperature"].shape == (1, 3, 3)
assert root.variables["Temperature"][0].data == approx(
np.arange(9.0).reshape((3, 3))
)
assert root.variables["x"] == approx([0.0, 1.0, 2.0])
assert root.variables["y"] == approx([0.0, 1.0, 2.0])
assert root.variables["Temperature"].long_name == "Temperature"
assert root.variables["Temperature"].units == "-"
root.close()
def test_raster_field_1d(self):
g = RasterField((6, ), (1.5, ), (0.5, ), indexing="ij")
self.assert_point_count(g, 6)
self.assert_cell_count(g, 5)
point_data = np.arange(6.0)
g.add_field("Point Data", point_data, centering="point")
cell_data = np.arange(5.0) * 10.0
g.add_field("Cell Data", cell_data, centering="zonal")
self.assert_field_values(g, "Cell Data", [0.0, 10.0, 20.0, 30.0, 40.0])
self.assert_field_values(g, "Point Data",
[0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
def test_raster_field_1d (self):
g = RasterField ((6, ), (1.5, ), (0.5, ), indexing='ij')
self.assert_point_count (g, 6)
self.assert_cell_count (g, 5)
point_data = np.arange (6.)
g.add_field ('Point Data', point_data, centering='point')
cell_data = np.arange (5.)*10.
g.add_field ('Cell Data', cell_data, centering='zonal')
self.assert_field_values (g, 'Cell Data',
[0., 10., 20., 30., 40.])
self.assert_field_values (g, 'Point Data',
[0., 1., 2., 3., 4., 5.])
def test_2d(self):
# Create a field that looks like this,
#
# (0) --- (1) --- (2)
# | | |
# | 0 | 1 |
# | | |
# (3) --- (4) --- (5)
g = RasterField((2, 3), (1, 2), (0, 0), indexing="ij")
self.assert_cell_count(g, 2)
self.assert_point_count(g, 6)
data = np.arange(6)
g.add_field("var0", data, centering="point")
self.assert_field_values(g, "var0", [0, 1, 2, 3, 4, 5])
data = np.arange(6)
data.shape = (2, 3)
g.add_field("var0", data, centering="point")
self.assert_field_values(g, "var0", [0, 1, 2, 3, 4, 5])
# If the size or shape doesn't match, it's an error.
with self.assertRaises(DimensionError):
data = np.arange(2)
g.add_field("bad var", data, centering="point")
# DimensionError: (3, 2) != (2, 3)
with self.assertRaises(DimensionError):
data = np.ones((3, 2))
g.add_field("bad var", data, centering="point")
data = np.arange(2)
g.add_field("var1", data, centering="zonal")
self.assert_field_values(g, "var1", [0.0, 1.0])
# DimensionError: (2, 1) != (1, 2)
with self.assertRaises(DimensionError):
data = np.ones((2, 1))
g.add_field("bad var", data, centering="zonal")
# DimensionError: 3 != 2
with self.assertRaises(DimensionError):
data = np.arange(3)
g.add_field("bad var", data, centering="zonal")
# DimensionError: 1 != 2
with self.assertRaises(DimensionError):
data = np.array(3)
g.add_field("bad var", data, centering="zonal")
def test_2d(self):
# Create a field that looks like this,
#
# (0) --- (1) --- (2)
# | | |
# | 0 | 1 |
# | | |
# (3) --- (4) --- (5)
g = RasterField((2, 3), (1, 2), (0, 0), indexing="ij")
self.assert_cell_count(g, 2)
self.assert_point_count(g, 6)
data = np.arange(6)
g.add_field("var0", data, centering="point")
self.assert_field_values(g, "var0", [0, 1, 2, 3, 4, 5])
data = np.arange(6)
data.shape = (2, 3)
g.add_field("var0", data, centering="point")
self.assert_field_values(g, "var0", [0, 1, 2, 3, 4, 5])
# If the size or shape doesn't match, it's an error.
with self.assertRaises(DimensionError):
data = np.arange(2)
g.add_field("bad var", data, centering="point")
# DimensionError: (3, 2) != (2, 3)
with self.assertRaises(DimensionError):
data = np.ones((3, 2))
g.add_field("bad var", data, centering="point")
data = np.arange(2)
g.add_field("var1", data, centering="zonal")
self.assert_field_values(g, "var1", [0.0, 1.0])
# DimensionError: (2, 1) != (1, 2)
with self.assertRaises(DimensionError):
data = np.ones((2, 1))
g.add_field("bad var", data, centering="zonal")
# DimensionError: 3 != 2
with self.assertRaises(DimensionError):
data = np.arange(3)
g.add_field("bad var", data, centering="zonal")
# DimensionError: 1 != 2
with self.assertRaises(DimensionError):
data = np.array(3)
g.add_field("bad var", data, centering="zonal")