def test_writer(self):
"""`WriteImageDataToSGeMS`: check data integrity across I/O"""
writer = WriteImageDataToSGeMS()
filename = os.path.join(self.test_dir, 'test-writer.dat')
writer.SetFileName(filename)
writer.Write(self.GRID)
# Now read that data and compare
reader = SGeMSGridReader()
read = reader.apply(filename)
# Compare data
truedata = self.GRID.GetCellData()
testdata = read.GetCellData()
self.assertEqual(truedata.GetNumberOfArrays(),
testdata.GetNumberOfArrays())
wtbl = dsa.WrapDataObject(self.GRID)
wrd = dsa.WrapDataObject(read)
self.assertEqual(self.GRID.GetDimensions(), wrd.GetDimensions())
self.assertEqual(self.GRID.GetOrigin(), wrd.GetOrigin())
self.assertEqual(self.GRID.GetSpacing(), wrd.GetSpacing())
for i in range(truedata.GetNumberOfArrays()):
self.assertIsNotNone(wtbl.CellData[i])
self.assertIsNotNone(wrd.CellData[i])
self.assertTrue(np.allclose(wtbl.CellData[i], wrd.CellData[i]))
for i in range(self.GRID.GetCellData().GetNumberOfArrays()):
self.assertIsNotNone(wtbl.CellData[i])
self.assertIsNotNone(wrd.CellData[i])
self.assertTrue(np.allclose(wtbl.CellData[i], wrd.CellData[i]))
def test_bad_file(self):
"""`SGeMSGridReader`: check handling of bad input file"""
filename = os.path.join(self.test_dir, 'test_bad.dat')
header = ['Bad header', '%d' % len(self.titles)]
for ln in self.titles:
header.append(ln + '\n')
header = '\n'.join(header)
np.savetxt(filename,
self.data,
delimiter=' ',
header=header,
comments='')
# Set up the reader
reader = SGeMSGridReader()
reader.AddFileName(filename)
# Perform the read
reader.Update()
self.assertTrue(reader.error_occurred())
def setUp(self):
TestBase.setUp(self)
# Create a temporary directory
self.test_dir = tempfile.mkdtemp()
self.n = 100
self.shape = (150, 200, 20)
self.extent = (0, self.shape[0], 0, self.shape[1], 0, self.shape[2])
self.titles = ['Array 1', 'Array 2', 'Array 3']
##### Now generate output for testing ####
filename = os.path.join(self.test_dir, 'test.dat')
self.data = np.random.random((self.n, len(self.titles)))
header = ['%d %d %d' % self.shape, '%d' % len(self.titles)]
for ln in self.titles:
header.append(ln + '\n')
header = '\n'.join(header)
np.savetxt(filename,
self.data,
delimiter=' ',
header=header,
comments='')
# Set up the reader
self.GRID = SGeMSGridReader().apply(filename)
def set_time_delta(self, dt):
SGeMSGridReader.set_time_delta(self, dt)
def set_comments(self, identifier):
SGeMSGridReader.set_comments(self, identifier)
def set_skip_rows(self, skip):
SGeMSGridReader.set_skip_rows(self, skip)
def SetSkipRows(self, skip):
SGeMSGridReader.SetSkipRows(self, skip)
def set_origin(self, ox, oy, oz):
SGeMSGridReader.set_origin(self, ox, oy, oz)
def SetDelimiter(self, deli):
SGeMSGridReader.SetDelimiter(self, deli)
def SetOrigin(self, ox, oy, oz):
SGeMSGridReader.SetOrigin(self, ox, oy, oz)
def SetSpacing(self, dx, dy, dz):
SGeMSGridReader.SetSpacing(self, dx, dy, dz)
def GetTimestepValues(self):
"""This is critical for registering the timesteps"""
return SGeMSGridReader.GetTimestepValues(self)
def SetTimeDelta(self, dt):
SGeMSGridReader.SetTimeDelta(self, dt)
def SetComments(self, identifier):
SGeMSGridReader.SetComments(self, identifier)
def get_time_step_values(self):
"""This is critical for registering the timesteps"""
return SGeMSGridReader.get_time_step_values(self)
def set_spacing(self, dx, dy, dz):
SGeMSGridReader.set_spacing(self, dx, dy, dz)
def __init__(self):
SGeMSGridReader.__init__(self)
class TestSGeMSGridReader(TestBase):
"""
Test the `SGeMSGridReader` and `WriteImageDataToSGeMS`
"""
def setUp(self):
TestBase.setUp(self)
# Create a temporary directory
self.test_dir = tempfile.mkdtemp()
self.n = 100
self.shape = (150, 200, 20)
self.extent = (0, self.shape[0], 0, self.shape[1], 0, self.shape[2])
self.titles = ['Array 1', 'Array 2', 'Array 3']
##### Now generate output for testing ####
filename = os.path.join(self.test_dir, 'test.dat')
self.data = np.random.random((self.n, len(self.titles)))
header = ['%d %d %d' % self.shape, '%d' % len(self.titles)]
for ln in self.titles:
header.append(ln + '\n')
header = '\n'.join(header)
np.savetxt(filename,
self.data,
delimiter=' ',
header=header,
comments='')
# Set up the reader
self.GRID = SGeMSGridReader().apply(filename)
def tearDown(self):
# Remove the test data directory after the test
shutil.rmtree(self.test_dir)
TestBase.tearDown(self)
###########################################
def test_data_array_titles(self):
"""`SGeMSGridReader`: data array titles"""
for i, title in enumerate(self.titles):
self.assertEqual(self.GRID.GetCellData().GetArrayName(i), title)
return
def test_shape(self):
"""`SGeMSGridReader`: check output grid shape"""
self.assertEqual(self.GRID.GetExtent(), self.extent)
self.assertEqual(self.GRID.GetNumberOfCells(),
self.extent[1] * self.extent[3] * self.extent[5])
return
def test_data(self, ):
"""`SGeMSGridReader`: data fidelity"""
for i, title in enumerate(self.titles):
arr = nps.vtk_to_numpy(self.GRID.GetCellData().GetArray(i))
self.assertTrue(np.allclose(self.data[:, i], arr, rtol=RTOL))
return
def test_bad_file(self):
"""`SGeMSGridReader`: check handling of bad input file"""
filename = os.path.join(self.test_dir, 'test_bad.dat')
header = ['Bad header', '%d' % len(self.titles)]
for ln in self.titles:
header.append(ln + '\n')
header = '\n'.join(header)
np.savetxt(filename,
self.data,
delimiter=' ',
header=header,
comments='')
# Set up the reader
reader = SGeMSGridReader()
reader.AddFileName(filename)
# Perform the read
reader.Update()
self.assertTrue(reader.error_occurred())
def test_writer(self):
"""`WriteImageDataToSGeMS`: check data integrity across I/O"""
writer = WriteImageDataToSGeMS()
filename = os.path.join(self.test_dir, 'test-writer.dat')
writer.SetFileName(filename)
writer.Write(self.GRID)
# Now read that data and compare
reader = SGeMSGridReader()
read = reader.apply(filename)
# Compare data
truedata = self.GRID.GetCellData()
testdata = read.GetCellData()
self.assertEqual(truedata.GetNumberOfArrays(),
testdata.GetNumberOfArrays())
wtbl = dsa.WrapDataObject(self.GRID)
wrd = dsa.WrapDataObject(read)
self.assertEqual(self.GRID.GetDimensions(), wrd.GetDimensions())
self.assertEqual(self.GRID.GetOrigin(), wrd.GetOrigin())
self.assertEqual(self.GRID.GetSpacing(), wrd.GetSpacing())
for i in range(truedata.GetNumberOfArrays()):
self.assertIsNotNone(wtbl.CellData[i])
self.assertIsNotNone(wrd.CellData[i])
self.assertTrue(np.allclose(wtbl.CellData[i], wrd.CellData[i]))
for i in range(self.GRID.GetCellData().GetNumberOfArrays()):
self.assertIsNotNone(wtbl.CellData[i])
self.assertIsNotNone(wrd.CellData[i])
self.assertTrue(np.allclose(wtbl.CellData[i], wrd.CellData[i]))
def test_sgems_grid_writer_no_data(self):
grid = pyvista.UniformGrid((10, 10, 10), (2, 2, 2))
writer = WriteImageDataToSGeMS()
filename = os.path.join(self.test_dir, 'test-writer-no-data.dat')
writer.SetFileName(filename)
writer.Write(grid)
return
def AddFileName(self, filename):
SGeMSGridReader.AddFileName(self, filename)
def set_delimiter(self, deli):
SGeMSGridReader.set_delimiter(self, deli)
def set_split_on_white_space(self, flag):
SGeMSGridReader.set_split_on_white_space(self, flag)
~~~~~~~~~~~~~~~
Read SGeMS Grid file formats. The examples shown here are downloaded from
`Multiple-point Geostatistics stochastic modeling with training images <http://www.trainingimages.org/training-images-library.html>`_ website.
"""
# sphinx_gallery_thumbnail_number = 2
import pyvista
from pyvista import examples
from PVGeo.gslib import SGeMSGridReader
################################################################################
grid_url = 'http://www.trainingimages.org/uploads/3/4/7/0/34703305/a_wlreferencecat.zip'
filename, _ = examples.downloads._retrieve_file(grid_url,
'A_WLreferenceCAT.sgems.zip')
grid = SGeMSGridReader().apply(filename)
print(grid)
################################################################################
warped = grid.cell_data_to_point_data().warp_by_scalar(scale_factor=5)
warped.plot()
################################################################################
grid_url = 'http://www.trainingimages.org/uploads/3/4/7/0/34703305/maules_creek_3d.zip'
filename, _ = examples.downloads._retrieve_file(grid_url,
'Maules_Creek_3D.SGEMS.zip')
grid = SGeMSGridReader().apply(filename)
grid.plot(categories=True)
################################################################################
def SetUseTab(self, flag):
SGeMSGridReader.SetUseTab(self, flag)
