def file_writer(filename,
signal,
do_async=False,
compressor=None,
clevel=1,
n_threads=None,
**kwds):
import hyperspy.signals
if not isinstance(
signal,
(hyperspy.signals.Signal2D, hyperspy.signals.ComplexSignal2D)):
raise TypeError("MRCZ supports 2D and 3D data only. type(signal) is "
"{}".format(type(signal)))
endianess = kwds.pop('endianess', '<')
mrcz_endian = 'le' if endianess == '<' else 'be'
meta = signal.metadata.as_dictionary()
# Get pixelsize and pixelunits from the axes
pixelunits = signal.axes_manager[-1].units
pixelsize = [signal.axes_manager[I].scale for I in _WRITE_ORDER]
# Strip out voltage from meta-data
voltage = signal.metadata.get_item(
'Acquisition_instrument.TEM.beam_energy')
# There aren't hyperspy fields for spherical aberration or detector gain
C3 = 0.0
gain = signal.metadata.get_item(
"Signal.Noise_properties."
"Variance_linear_model.gain_factor", 1.0)
if do_async:
_mrcz.asyncWriteMRC(signal.data,
filename,
meta=meta,
endian=mrcz_endian,
pixelsize=pixelsize,
pixelunits=pixelunits,
voltage=voltage,
C3=C3,
gain=gain,
compressor=compressor,
clevel=clevel,
n_threads=n_threads)
else:
_mrcz.writeMRC(signal.data,
filename,
meta=meta,
endian=mrcz_endian,
pixelsize=pixelsize,
pixelunits=pixelunits,
voltage=voltage,
C3=C3,
gain=gain,
compressor=compressor,
clevel=clevel,
n_threads=n_threads)
def test_Async(self):
testMage = np.random.uniform(high=10, size=[3, 128, 64]).astype('int8')
meta = {'foo': 5, 'bar': 42}
mrcName = os.path.join(tmpDir, "testMage.mrcz")
pixelsize = [1.2, 5.6, 3.4]
worker = mrcz.asyncWriteMRC(testMage,
mrcName,
meta=meta,
pixelsize=pixelsize,
pixelunits=u"\AA",
voltage=300.0,
C3=2.7,
gain=1.05,
compressor='zstd',
clevel=1,
n_threads=4)
worker.result() # Wait for write to finish
worker = mrcz.asyncReadMRC(mrcName, pixelunits=u"\AA")
rereadMage, rereadHeader = worker.result()
try:
os.remove(mrcName)
except IOError:
log.info("Warning: file {} left on disk".format(mrcName))
assert (np.all(testMage.shape == rereadMage.shape))
assert (testMage.dtype == rereadMage.dtype)
for key in meta:
assert (meta[key] == rereadHeader[key])
npt.assert_array_almost_equal(testMage, rereadMage)
npt.assert_array_equal(rereadHeader['voltage'], 300.0)
npt.assert_array_almost_equal(rereadHeader['pixelsize'], pixelsize)
npt.assert_array_equal(rereadHeader['pixelunits'], u"\AA")
npt.assert_array_equal(rereadHeader['C3'], 2.7)
npt.assert_array_equal(rereadHeader['gain'], 1.05)
pass