def load_mib(filename, scan_size, sum_length=10):
"""Load a medipix hdr/mib file.
Parameters
----------
filename : string
File path and name to .hdr file.
scan_size : int
Scan size in pixels, allows the function to reshape the array into
the right shape.
sum_length : int
Number of lines to sum over to determine scan fly back location.
"""
dpt = load_with_reader(filename=filename, reader=mib_reader)
dpt = ElectronDiffraction(
dpt.data.reshape((scan_size, scan_size, 256, 256)))
trace = dpt.inav[:, 0:sum_length].sum((1, 2, 3))
edge = np.where(trace == max(trace.data))[0][0]
if edge == scan_size - 1:
dp = ElectronDiffraction(dpt.inav[0:edge, 1:])
else:
dp = ElectronDiffraction(
np.concatenate((dpt.inav[edge + 1:, 1:], dpt.inav[0:edge, 1:]),
axis=1))
return dp
def _load_fpd_sum_im(filename):
s = load_with_reader(filename,
reader=emd,
dataset_name="/fpd_expt/fpd_sum_im")
if len(s.axes_manager.shape) == 3:
s = s.isig[0, :, :]
return s
def _load_fpd_emd_file(filename, lazy=False):
s = load_with_reader(filename,
reader=emd,
lazy=lazy,
dataset_name="/fpd_expt/fpd_data")
if len(s.axes_manager.shape) == 5:
s = s.isig[:, :, 0, :, :]
s = s.transpose(signal_axes=(0, 1))
s._lazy = lazy
s_new = signal_to_pixelated_stem(s)
return s_new
def load_single_file(filename, signal_type=None, **kwds):
"""
Load any supported file into an HyperSpy structure
Supported formats: netCDF, msa, Gatan dm3, Ripple (rpl+raw),
Bruker bcf, FEI ser and emi, EDAX spc and spd, hspy (HDF5), and SEMPER unf.
Parameters
----------
filename : string
File name (including the extension)
"""
extension = os.path.splitext(filename)[1][1:]
i = 0
while extension.lower() not in io_plugins[i].file_extensions and \
i < len(io_plugins) - 1:
i += 1
if i == len(io_plugins):
# Try to load it with the python imaging library
try:
from hyperspy.io_plugins import image
reader = image
return load_with_reader(filename,
reader,
signal_type=signal_type,
**kwds)
except BaseException:
raise IOError('If the file format is supported'
' please report this error')
else:
reader = io_plugins[i]
return load_with_reader(filename=filename,
reader=reader,
signal_type=signal_type,
**kwds)
def load_mib(filename, scan_size):
"""
Load medipix file.
Paramters:
filename : string
File path and name
scan_size : int
Scan size in pixels, allows the function to reshape the array into
the right shape.
"""
dpt = load_with_reader(filename=filename, reader=mib_reader)
dpt = ElectronDiffraction(dpt.data.reshape((scan_size, scan_size, 256, 256)))
trace = dpt.inav[:,0:5].sum((1,2,3))
edge = np.where(trace==max(trace.data))[0][0]
if edge==scan_size - 1:
dp = ElectronDiffraction(dpt.inav[0:edge, 1:])
else:
dp = ElectronDiffraction(np.concatenate((dpt.inav[edge + 1:, 1:], dpt.inav[0:edge, 1:]), axis=1))
return dp