def test_write_hdf5(self):
"""Test the method to write the mesh in HDF5 format."""
grid = petibmpy.CartesianGrid(config=self.config)
filepath = pathlib.Path('grid.h5')
grid.write_hdf5(filepath)
coords = petibmpy.read_grid_hdf5(filepath, 'vertex')
for x, x2 in zip(grid.get_gridlines(), coords):
self.assertTrue(numpy.allclose(x, x2))
filepath.unlink()
def test_grid_create(self):
"""Create a grid given a configuration."""
grid = petibmpy.CartesianGrid(config=self.config)
self.assertEqual(len(grid.gridlines), 3)
for i, x in enumerate(grid.get_gridlines()):
config = self.config[i]
self.assertAlmostEqual(x[0], config['start'], places=12)
self.assertAlmostEqual(x[-1], config['subDomains'][-1]['end'],
places=12)
def test_num_cells(self):
"""Test the method to get the number of cells."""
start, end, width = -10.0, 10.0, 0.1
num = int(abs(end - start) / width)
subconfig = dict(start=start, subDomains=[dict(end=end, width=width)])
config = []
for dim, direction in zip([1, 2, 3], ['x', 'y', 'z']):
subconfig['direction'] = direction
config.append(copy.deepcopy(subconfig))
grid = petibmpy.CartesianGrid(config=config)
n_cells = grid.get_number_cells()
self.assertEqual(n_cells, num**dim)
def test_write_yaml(self):
"""Test the method to create the YAML configuration file."""
grid = petibmpy.CartesianGrid(config=self.config)
filepath = pathlib.Path('mesh.yaml')
grid.write_yaml(filepath, ndigits=12)
with open(filepath, 'r') as infile:
lines = infile.readlines()
datadir = pathlib.Path(__file__).absolute().parent / 'data'
filepath2 = datadir / 'mesh.yaml'
with open(filepath2, 'r') as infile:
lines2 = infile.readlines()
self.assertEqual(len(lines), len(lines2))
for line, line2 in zip(lines, lines2):
self.assertEqual(line, line2)
filepath.unlink()
show_figure = False
config_x = get_gridline_config(box1.xstart, box2.xstart, box3.xstart,
box3.xend, box2.xend, box1.xend, width2, width3,
1.2, 1.1, 1.03, 1.2)
config_y = get_gridline_config(box1.ystart, box2.ystart, box3.ystart,
box3.yend, box2.yend, box1.yend, width2, width3,
1.2, 1.1, 1.1, 1.2)
config_z = get_gridline_config(box1.zstart, box2.zstart, box3.zstart,
box3.zend, box2.zend, box1.zend, width2, width3,
1.2, 1.1, 1.1, 1.2)
config = [
dict(direction='x', start=box1.xstart, subDomains=config_x),
dict(direction='y', start=box1.ystart, subDomains=config_y),
dict(direction='z', start=box1.zstart, subDomains=config_z)
]
grid = petibmpy.CartesianGrid(config)
print(grid)
simudir = pathlib.Path(__file__).absolute().parents[1]
filepath = simudir / 'mesh.yaml'
grid.write_yaml(filepath, ndigits=10)
grid.print_info()
if show_figure:
fig, ax = grid.plot_gridlines()
fig.tight_layout()
pyplot.show()
ratio = 1.05 # stretching ratio
info = [{'direction': 'x', 'start': xlim[0],
'subDomains': [{'end': xbox[0],
'width': width,
'stretchRatio': ratio,
'reverse': True},
{'end': xbox[1],
'width': width,
'stretchRatio': 1.0},
{'end': xlim[1],
'width': width,
'stretchRatio': ratio}]},
{'direction': 'y', 'start': ylim[0],
'subDomains': [{'end': ybox[0],
'width': width,
'stretchRatio': ratio,
'reverse': True},
{'end': ybox[1],
'width': width,
'stretchRatio': 1.0},
{'end': ylim[1],
'width': width,
'stretchRatio': ratio}]}]
mesh = petibmpy.CartesianGrid(info)
print(mesh)
simudir = pathlib.Path(__file__).absolute().parents[1]
filepath = simudir / 'mesh.yaml'
mesh.write_yaml(filepath, ndigits=10)
'end': ylim[1],
'width': width,
'stretchRatio': 1.3
}]
}, {
'direction':
'z',
'start':
zlim[0],
'subDomains': [{
'end': zbox[0],
'width': width,
'stretchRatio': 1.3,
'reverse': True
}, {
'end': zbox[1],
'width': width,
'stretchRatio': 1.0
}, {
'end': zlim[1],
'width': width,
'stretchRatio': 1.3
}]
}]
mesh = petibmpy.CartesianGrid(config=config)
print(mesh)
simudir = pathlib.Path(__file__).absolute().parents[1]
filepath = simudir / 'mesh.yaml'
mesh.write_yaml(filepath, ndigits=10)
