def test_mrc_header_from_params_defaults(shape, mrc_mode_dtype, ispg_kind):
"""Test the utility function for the minimal required parameters."""
mode, dtype = mrc_mode_dtype
true_ispg, kind = ispg_kind
header = mrc_header_from_params(shape, dtype, kind)
# Check values of all header entries
nx = header['nx']['value']
ny = header['ny']['value']
nz = header['nz']['value']
assert all_equal([nx, ny, nz], shape)
assert header['mode']['value'] == mode
mx = header['mx']['value']
my = header['my']['value']
mz = header['mz']['value']
assert all_equal([mx, my, mz], shape)
cella = header['cella']['value']
assert all_equal(cella, np.ones(3) * shape)
mapc = header['mapc']['value']
mapr = header['mapr']['value']
maps = header['maps']['value']
assert all_equal([mapc, mapr, maps], [1, 2, 3])
dmin = header['dmin']['value']
dmax = header['dmax']['value']
dmean = header['dmean']['value']
rms = header['rms']['value']
assert all_equal([dmin, dmax, dmean, rms], [1.0, 0.0, -1.0, -1.0])
ispg = header['ispg']['value']
assert ispg == true_ispg
nsymbt = header['nsymbt']['value']
assert nsymbt == 0
exttype = header['exttype']['value']
assert np.array_equal(exttype, np.fromstring(' ', dtype='S1'))
nversion = header['nversion']['value']
assert nversion == 20140
origin = header['origin']['value']
assert all_equal(origin, [0, 0, 0])
map = header['map']['value']
assert np.array_equal(map, np.fromstring('MAP ', dtype='S1'))
machst = header['machst']['value']
assert np.array_equal(machst, np.fromiter(b'DD ', dtype='S1'))
nlabl = header['nlabl']['value']
assert nlabl == 0
label = header['label']['value']
assert np.array_equal(label, np.zeros([10, 80], dtype='S1'))
# Check all data types
int32_vars = [nx, ny, nz, mx, my, mz, mapc, mapr, maps, ispg, nsymbt,
nversion, origin, nlabl]
for v in int32_vars:
assert v.dtype == np.dtype('int32')
float32_vars = [cella, dmin, dmax, dmean, rms]
for v in float32_vars:
assert v.dtype == np.dtype('float32')
string_vars = [exttype, map, machst, label]
for v in string_vars:
assert v.dtype == np.dtype('S1')
def test_mrc_io(shape, mrc_mode_dtype, ispg_kind, axis_order):
"""Test reading and writing MRC files and the class properties."""
_, dtype = mrc_mode_dtype
_, kind = ispg_kind
# Data storage shape is the inverse permutation of nx, ny, nz
data_storage_shape = tuple(shape[ax] for ax in np.argsort(axis_order))
header = mrc_header_from_params(shape, dtype, kind,
axis_order=axis_order)
# Test writer properties using standard class construction
with tempfile.NamedTemporaryFile() as named_file:
file = named_file.file
writer = FileWriterMRC(file, header)
assert writer.header_size == 1024 # Standard MRC header size
assert all_equal(writer.data_shape, shape)
assert all_equal(writer.data_storage_shape, data_storage_shape)
assert writer.data_dtype == dtype
assert all_equal(writer.data_axis_order, axis_order)
# Test writing some data (that all data types can represent).
data = np.random.randint(0, 10, size=shape).astype(dtype)
writer.write_data(data)
# Check file size
writer.file.seek(0, 2)
file_size = writer.file.tell()
assert file_size == writer.header_size + data.nbytes
# Check flat arrays
file.seek(1024)
raw_data = np.fromfile(file, dtype=dtype)
flat_data = np.transpose(data, axes=np.argsort(axis_order))
flat_data = flat_data.reshape(-1, order='F')
assert np.array_equal(raw_data, flat_data)
# Write everything using the context manager syntax
with FileWriterMRC(file, header) as writer:
writer.write(data)
# Read from the same file using the reader with standard constructor
reader = FileReaderMRC(file)
reader.read_header()
assert writer.header_size == 1024 # Standard MRC header size
assert all_equal(reader.data_shape, shape)
assert all_equal(reader.data_storage_shape, data_storage_shape)
assert reader.data_dtype == dtype
assert reader.data_kind == kind
assert all_equal(reader.data_axis_order, axis_order)
assert np.allclose(reader.cell_sides_angstrom, 1.0)
assert all_equal(reader.mrc_version, (2014, 0))
assert reader.extended_header_type == ' '
assert reader.labels == ()
def test_mrc_io(shape, mrc_mode_dtype, ispg_kind, axis_order):
"""Test reading and writing MRC files and the class properties."""
_, dtype = mrc_mode_dtype
_, kind = ispg_kind
# Data storage shape is the inverse permutation of nx, ny, nz
data_storage_shape = tuple(shape[ax] for ax in np.argsort(axis_order))
header = mrc_header_from_params(shape, dtype, kind, axis_order=axis_order)
# Test writer properties using standard class construction
with tempfile.NamedTemporaryFile() as named_file:
file = named_file.file
writer = FileWriterMRC(file, header)
assert writer.header_size == 1024 # Standard MRC header size
assert all_equal(writer.data_shape, shape)
assert all_equal(writer.data_storage_shape, data_storage_shape)
assert writer.data_dtype == dtype
assert all_equal(writer.data_axis_order, axis_order)
# Test writing some data (that all data types can represent).
data = np.random.randint(0, 10, size=shape).astype(dtype)
writer.write_data(data)
# Check file size
writer.file.seek(0, 2)
file_size = writer.file.tell()
assert file_size == writer.header_size + data.nbytes
# Check flat arrays
file.seek(1024)
raw_data = np.fromfile(file, dtype=dtype)
flat_data = np.transpose(data, axes=np.argsort(axis_order))
flat_data = flat_data.reshape(-1, order='F')
assert np.array_equal(raw_data, flat_data)
# Write everything using the context manager syntax
with FileWriterMRC(file, header) as writer:
writer.write(data)
# Read from the same file using the reader with standard constructor
reader = FileReaderMRC(file)
reader.read_header()
assert writer.header_size == 1024 # Standard MRC header size
assert all_equal(reader.data_shape, shape)
assert all_equal(reader.data_storage_shape, data_storage_shape)
assert reader.data_dtype == dtype
assert reader.data_kind == kind
assert all_equal(reader.data_axis_order, axis_order)
assert np.allclose(reader.cell_sides_angstrom, 1.0)
assert all_equal(reader.mrc_version, (2014, 0))
assert reader.extended_header_type == ' '
assert reader.labels == ()
def test_mrc_header_from_params_kwargs():
"""Test the utility function for the minimal required parameters."""
shape = (10, 20, 30)
dtype = np.dtype('int8')
kind = 'projections'
kwargs = {
'extent': [10.0, 1.5, 0.1],
'axis_order': (2, 0, 1),
'dmin': 1.0,
'dmax': 5.0,
'dmean': 2.0,
'rms': 0.5,
'mrc_version': (2014, 1),
'text_labels': ['label 1', ' label 2 ']
}
header = mrc_header_from_params(shape, dtype, kind, **kwargs)
# Check values of the header entries set by kwargs
cella = header['cella']['value']
assert np.allclose(cella, [10.0, 1.5, 0.1])
mapc = header['mapc']['value']
mapr = header['mapr']['value']
maps = header['maps']['value']
assert all_equal([mapc, mapr, maps], (3, 1, 2))
dmin = header['dmin']['value']
dmax = header['dmax']['value']
dmean = header['dmean']['value']
rms = header['rms']['value']
assert all_equal([dmin, dmax, dmean, rms], [1.0, 5.0, 2.0, 0.5])
nversion = header['nversion']['value']
assert nversion == 20141
nlabl = header['nlabl']['value']
assert nlabl == 2
label = header['label']['value']
true_label = np.zeros([10, 80], dtype='S1')
true_label[0] = np.fromstring('label 1'.ljust(80), dtype='S1')
true_label[1] = np.fromstring(' label 2 '.ljust(80), dtype='S1')
assert np.array_equal(label, true_label)
# Check all data types
for v in [mapc, mapr, maps, nversion, nlabl]:
assert v.dtype == np.dtype('int32')
for v in [cella, dmin, dmax, dmean, rms]:
assert v.dtype == np.dtype('float32')
assert label.dtype == np.dtype('S1')
def test_mrc_header_from_params_kwargs():
"""Test the utility function for the minimal required parameters."""
shape = (10, 20, 30)
dtype = np.dtype('int8')
kind = 'projections'
kwargs = {'extent': [10.0, 1.5, 0.1],
'axis_order': (2, 0, 1),
'dmin': 1.0,
'dmax': 5.0,
'dmean': 2.0,
'rms': 0.5,
'mrc_version': (2014, 1),
'text_labels': ['label 1', ' label 2 ']
}
header = mrc_header_from_params(shape, dtype, kind, **kwargs)
# Check values of the header entries set by kwargs
cella = header['cella']['value']
assert np.allclose(cella, [10.0, 1.5, 0.1])
mapc = header['mapc']['value']
mapr = header['mapr']['value']
maps = header['maps']['value']
assert all_equal([mapc, mapr, maps], (3, 1, 2))
dmin = header['dmin']['value']
dmax = header['dmax']['value']
dmean = header['dmean']['value']
rms = header['rms']['value']
assert all_equal([dmin, dmax, dmean, rms], [1.0, 5.0, 2.0, 0.5])
nversion = header['nversion']['value']
assert nversion == 20141
nlabl = header['nlabl']['value']
assert nlabl == 2
label = header['label']['value']
true_label = np.zeros([10, 80], dtype='S1')
true_label[0] = np.fromstring('label 1'.ljust(80), dtype='S1')
true_label[1] = np.fromstring(' label 2 '.ljust(80), dtype='S1')
assert np.array_equal(label, true_label)
# Check all data types
for v in [mapc, mapr, maps, nversion, nlabl]:
assert v.dtype == np.dtype('int32')
for v in [cella, dmin, dmax, dmean, rms]:
assert v.dtype == np.dtype('float32')
assert label.dtype == np.dtype('S1')
def test_mrc_header_from_params_defaults(shape, mrc_mode_dtype, ispg_kind):
"""Test the utility function for the minimal required parameters."""
mode, dtype = mrc_mode_dtype
true_ispg, kind = ispg_kind
header = mrc_header_from_params(shape, dtype, kind)
# Check values of all header entries
nx = header['nx']['value']
ny = header['ny']['value']
nz = header['nz']['value']
assert all_equal([nx, ny, nz], shape)
assert header['mode']['value'] == mode
mx = header['mx']['value']
my = header['my']['value']
mz = header['mz']['value']
assert all_equal([mx, my, mz], shape)
cella = header['cella']['value']
assert all_equal(cella, np.ones(3) * shape)
mapc = header['mapc']['value']
mapr = header['mapr']['value']
maps = header['maps']['value']
assert all_equal([mapc, mapr, maps], [1, 2, 3])
dmin = header['dmin']['value']
dmax = header['dmax']['value']
dmean = header['dmean']['value']
rms = header['rms']['value']
assert all_equal([dmin, dmax, dmean, rms], [1.0, 0.0, -1.0, -1.0])
ispg = header['ispg']['value']
assert ispg == true_ispg
nsymbt = header['nsymbt']['value']
assert nsymbt == 0
exttype = header['exttype']['value']
assert np.array_equal(exttype, np.fromstring(' ', dtype='S1'))
nversion = header['nversion']['value']
assert nversion == 20140
origin = header['origin']['value']
assert all_equal(origin, [0, 0, 0])
map = header['map']['value']
assert np.array_equal(map, np.fromstring('MAP ', dtype='S1'))
machst = header['machst']['value']
assert np.array_equal(machst, np.fromiter(b'DD ', dtype='S1'))
nlabl = header['nlabl']['value']
assert nlabl == 0
label = header['label']['value']
assert np.array_equal(label, np.zeros([10, 80], dtype='S1'))
# Check all data types
int32_vars = [
nx, ny, nz, mx, my, mz, mapc, mapr, maps, ispg, nsymbt, nversion,
origin, nlabl
]
for v in int32_vars:
assert v.dtype == np.dtype('int32')
float32_vars = [cella, dmin, dmax, dmean, rms]
for v in float32_vars:
assert v.dtype == np.dtype('float32')
string_vars = [exttype, map, machst, label]
for v in string_vars:
assert v.dtype == np.dtype('S1')
np.array_equal(values, data))
# Plot the data to see that it also looks correct. We take the 5th slice
# along the first axis, which is in the middle.
plt.figure()
plt.title('A standing rectangle, middle right')
plt.imshow(data[5], cmap='Greys_r', interpolation='none')
plt.show()
# --- Writing --- #
# Create some data -- float32 is supported by MRC. Data must be 3D.
new_data = np.ones((50, 100, 200), dtype='float32')
# Create a minimal header. All parameters except these here have default
# values.
header = mrc_header_from_params(new_data.shape, new_data.dtype, kind='volume')
# Write the stuff to a temporary (MRC) file
out_file = tempfile.TemporaryFile()
with FileWriterMRC(out_file, header) as writer:
# Write both header and data to the file
writer.write(new_data)
# Check if the file size is consistent with header and data sizes
print('File size ({}) = Header size ({}) + Data size ({})'
''.format(writer.file.seek(0, 2), writer.header_size,
new_data.nbytes))
print('Values from file all equal to manually created array? ',
np.array_equal(values, data))
# Plot the data to see that it also looks correct. We take the 5th slice
# along the first axis, which is in the middle.
plt.figure()
plt.title('A standing rectangle, middle right')
plt.imshow(data[5], cmap='Greys_r', interpolation='none')
plt.show()
# --- Writing --- #
# Create some data -- float32 is supported by MRC. Data must be 3D.
new_data = np.ones((50, 100, 200), dtype='float32')
# Create a minimal header. All parameters except these here have default
# values.
header = mrc_header_from_params(new_data.shape, new_data.dtype, kind='volume')
# Write the stuff to a temporary (MRC) file
out_file = tempfile.TemporaryFile()
with FileWriterMRC(out_file, header) as writer:
# Write both header and data to the file
writer.write(new_data)
# Check if the file size is consistent with header and data sizes
print('File size ({}) = Header size ({}) + Data size ({})'
''.format(writer.file.seek(0, 2), writer.header_size,
new_data.nbytes))
