def test_write_hdf5_full(self):
data = phantom.shepp3d(size=32, dtype='float16')
file_io.write_hdf5(data, fname=self.hdf_filename)
# Check that the data were written properly
with h5py.File(self.hdf_filename, mode='r') as h5fp:
self.assertIn('volume', h5fp)
np.testing.assert_array_equal(h5fp['volume'], data)
def test_write_hdf5_partial_overwrite(self):
# Create some existing data to overwrite
with h5py.File(self.hdf_filename, mode='a') as h5fp:
h5fp.create_dataset('volume', data=np.ones((8, 8, 8)))
data = phantom.shepp3d(size=32, dtype='float32')
data_partial = data[10:16]
data_partial_a = data[10:13]
data_partial_b = data[13:16]
# Write the data to the HDF5 file
file_io.write_hdf5(data_partial_a,
fname=self.hdf_filename,
maxsize=data.shape,
dest_idx=slice(10, 13),
overwrite=True)
file_io.write_hdf5(data_partial_b,
fname=self.hdf_filename,
maxsize=data.shape,
dest_idx=slice(13, 16),
overwrite=False)
# Check that the data were written properly
with h5py.File(self.hdf_filename, mode='r') as h5fp:
self.assertIn('volume', h5fp)
# Check that the target data were saved in the right place
np.testing.assert_array_equal(h5fp['volume'][10:16], data_partial)
# Check that the rest of the data are np.nan
self.assertTrue(np.all(np.isnan(h5fp['volume'][:10])))
self.assertTrue(np.all(np.isnan(h5fp['volume'][16:])))
def test_3d_parallel():
phantom = np.squeeze(shepp3d(128))
angles = np.arange(0, 180, 1)
sinogram = astra_fp_3d_parallel(phantom, angles)
rec = astra_recon_3d_parallel(sinogram, angles, [['CGLS3D_CUDA', 10]])
diff = rec - phantom
err = np.sqrt(np.sum(diff**2)) / np.prod(rec.shape)
assert (err < 0.1)
def test_write_hdf5_mismatched_dtypes(self):
"""Try to write partial data with mismatch dtypes should fail."""
# Create some existing data to overwrite
with h5py.File(self.hdf_filename, mode='a') as h5fp:
h5fp.create_dataset('volume', data=np.ones((8, 8, 8)))
data = phantom.shepp3d(size=8, dtype='float32')
# Write the data to the HDF5 file
with self.assertRaises(TypeError):
file_io.write_hdf5(data[10:13],
fname=self.hdf_filename,
maxsize=data.shape,
dest_idx=slice(10, 13),
overwrite=False,
dtype='int')
def test_write_hdf5_partial(self):
data = phantom.shepp3d(size=32, dtype='float16')
data_partial = data[10:16]
# Write the data to the HDF5 file
file_io.write_hdf5(data_partial,
fname=self.hdf_filename,
maxsize=data.shape,
dest_idx=slice(10, 16))
# Check that the data were written properly
with h5py.File(self.hdf_filename, mode='r') as h5fp:
self.assertIn('volume', h5fp)
# Check that the target data were saved in the right place
np.testing.assert_array_equal(h5fp['volume'][10:16], data_partial)
# Check that the rest of the data are zero
self.assertTrue(np.all(np.isnan(h5fp['volume'][:10])))
self.assertTrue(np.all(np.isnan(h5fp['volume'][16:])))
def main():
with h5py.File(h5file, mode='a') as h5fp:
# vol = phantom.shepp3d(vol_size, 'int')
combos = [
('volume', 'float32', 1),
('volume_int', 'int', 16),
('volume_uint', 'uint', 16),
('volume_bool', 'bool', 1.),
]
vol = phantom.shepp3d(vol_size)
for (name, dtype, mult) in combos:
# Delete existing datasets
if name in h5fp.keys():
del h5fp[name]
# Scale the dataset to match the datatype
new_vol = (vol * mult).astype(dtype)
# Save to disk
h5fp.create_dataset(name, data=new_vol)
return 0
def test_shepp3d(self):
assert_equals(shepp3d(size=(6, 8, 10)).dtype, 'float32')
assert_equals(shepp3d(size=(6, 8, 10)).shape, (6, 8, 10))
assert_equals(shepp3d(size=(6, 8, 10)).min(), 0)
assert_equals(shepp3d(size=6).shape, (6, 6, 6))
#!/usr/bin/env python import numpy as np from tomopy.misc.phantom import shepp3d output = 'shepp3d.npy' phantom = shepp3d() np.save(output, phantom)
def main():
vol = phantom.shepp3d(256)
with h5py.File('data/phantom3d_big.h5', mode='a') as h5fp:
h5fp.create_dataset('volume', data=vol)