def test_4d_data_compute(self):
dask_array = da.random.random((4, 4, 10, 15), chunks=(1, 1, 10, 15))
s = LazyElectronDiffraction2D(dask_array)
s.compute()
assert s.__class__ == ElectronDiffraction2D
assert dask_array.shape == s.data.shape
def load_mib(mib_path, reshape=True, flip=True):
"""Read a .mib file or an h5 stack file using dask and return as a lazy pyXem / hyperspy signal.
Parameters
----------
mib_path : str
The full path of the .mib file to be read.
reshape: boolean
Keyword argument to control reshaping of the stack (default is True).
It attepmts to reshape using the flyback pixel.
flip: boolean
Keyword argument to vertically flip the diffraction signal (default)
or return unchanged. The metadata is updated accordingly.
Returns
-------
data_pxm : pyxem.signals.LazyElectronDiffraction2D
If the data is detected to be STEM is reshaped using two functions, one using the
exposure times appearing on the header and if no exposure times available using the
sum frames and detecting the flyback frames. If TEM data, a single frame or if
reshaping the STEM fails, the stack is returned.
The metadata adds the following domains for STEM mib file:
General
│ └── title =
└── Signal
├── binned = False
├── exposure_time = 0.001
├── flip = True
├── flyback_times = [0.066, 0.071, 0.065, 0.017825]
├── frames_number_skipped = 90
├── scan_X = 256
└── signal_type = STEM
The returned metadata for TEM mib file:
General
│ └── title =
└── Signal
├── binned = False
├── exposure_time = [0.0001]
├── flyback_times = None
├── frames_number_skipped = None
├── scan_X = None
└── signal_type = TEM
"""
hdr_stuff = _parse_hdr(mib_path)
width = hdr_stuff["width"]
height = hdr_stuff["height"]
width_height = width * height
data = _mib_to_daskarr(mib_path)
depth = _get_mib_depth(hdr_stuff, mib_path)
hdr_bits = _get_hdr_bits(hdr_stuff)
if hdr_stuff["Counter Depth (number)"] == 1:
# RAW 1 bit data: the header bits are written as uint8 but the frames
# are binary and need to be unpacked as such.
data = data.reshape(-1, int(width_height / 8 + hdr_bits))
data = data[:, hdr_bits:]
# get the shape axis 1 before unpackbit
s0 = data.shape[0]
s1 = data.shape[1]
data = np.unpackbits(data)
data.reshape(s0, s1 * 8)
else:
data = data.reshape(-1, int(width_height + hdr_bits))
data = data[:, hdr_bits:]
if hdr_stuff["raw"] == "R64":
data = _untangle_raw(data, hdr_stuff, depth)
elif hdr_stuff["raw"] == "MIB":
data = data.reshape(depth, width, height)
# if small mib file read all the exposure times otherwise just the 10% default
if os.stat(mib_path).st_size * 1e9 < 0.1:
exp_times_list = _read_exposures(mib_path, pct_frames_to_read=1.0)
else:
exp_times_list = _read_exposures(mib_path)
data_dict = _STEM_flag_dict(exp_times_list)
if hdr_stuff["Assembly Size"] == "2x2":
# add_crosses expects a dask array object
data = _add_crosses(data)
data_pxm = LazyElectronDiffraction2D(data)
# Tranferring dict info to metadata
if data_dict["STEM_flag"] == 1:
data_pxm.metadata.Signal.signal_type = "STEM"
else:
data_pxm.metadata.Signal.signal_type = "TEM"
data_pxm.metadata.Signal.scan_X = data_dict["scan_X"]
data_pxm.metadata.Signal.exposure_time = data_dict["exposure time"]
data_pxm.metadata.Signal.frames_number_skipped = data_dict[
"number of frames_to_skip"]
data_pxm.metadata.Signal.flyback_times = data_dict["flyback_times"]
if reshape:
# only attempt reshaping if it is not already reshaped!
if len(data_pxm.data.shape) == 3:
try:
if data_pxm.metadata.Signal.signal_type == "TEM":
print(
"This mib file appears to be TEM data. The stack is returned with no reshaping."
)
return data_pxm
# to catch single frames:
if data_pxm.axes_manager[0].size == 1:
print("This mib file is a single frame.")
return data_pxm
# If the exposure time info not appearing in the header bits use reshape_4DSTEM_SumFrames
# to reshape otherwise use reshape_4DSTEM_FlyBack function
if (data_pxm.metadata.Signal.signal_type == "STEM"
and data_pxm.metadata.Signal.exposure_time is None):
print("reshaping using sum frames intensity")
(data_pxm, skip_ind) = reshape_4DSTEM_SumFrames(data_pxm)
data_pxm.metadata.Signal.signal_type = "STEM"
data_pxm.metadata.Signal.frames_number_skipped = skip_ind
else:
print("reshaping using flyback pixel")
data_pxm = reshape_4DSTEM_FlyBack(data_pxm)
except TypeError:
print(
"Warning: Reshaping did not work or TEM data with no exposure info. Returning the stack with no reshaping!"
)
return data_pxm
except ValueError:
print(
"Warning: Reshaping did not work or TEM data with no exposure info. Returning the stack with no reshaping!"
)
return data_pxm
if flip:
data_pxm.data = np.flip(data_pxm.data, axis=2)
data_pxm.metadata.Signal.flip = True
else:
data_pxm.metadata.Signal.flip = False
return data_pxm
def load_mib(mib_filename, reshape=True):
"""Read a .mib file using dask and return as LazyElectronDiffraction2D.
Parameters
----------
mib_filename : str
The name of the .mib file to be read.
reshape : boolean
keywork argument to control reshaping of the stack (default is True).
It attepmts to reshape using the flyback pixel.
Returns
-------
data_pxm : pyxem.signals.LazyElectronDiffraction2D
The metadata adds the following domains:
General
│ └── title =
└── Signal
├── binned = False
├── exposure_time = 0.001
├── flyback_times = [0.066, 0.071, 0.065, 0.017825]
├── frames_number_skipped = 90
├── scan_X = 256
└── signal_type = STEM
"""
hdr_stuff = _parse_hdr(mib_filename)
data = _read_mib(mib_filename, hdr_stuff)
exp_times_list = _read_exposures(hdr_stuff, mib_filename)
data_dict = _STEM_flag_dict(exp_times_list)
if hdr_stuff['Assembly Size'] == '2x2':
data = _add_crosses(data)
data_pxm = LazyElectronDiffraction2D(data)
# Tranferring dict info to metadata
if data_dict['STEM_flag'] == 1:
data_pxm.metadata.Signal.signal_type = 'STEM'
else:
data_pxm.metadata.Signal.signal_type = 'TEM'
data_pxm.metadata.Signal.scan_X = data_dict['scan_X']
data_pxm.metadata.Signal.exposure_time = data_dict['exposure time']
data_pxm.metadata.Signal.frames_number_skipped = data_dict[
'number of frames_to_skip']
data_pxm.metadata.Signal.flyback_times = data_dict['flyback_times']
if data_pxm.metadata.Signal.signal_type is 'TEM' and data_pxm.metadata.Signal.exposure_time is not None:
print(
'This mib file appears to be TEM data. The stack is returned with no reshaping.'
)
return data_pxm
try:
if reshape:
# If the exposure time info not appearing in the header bits use reshape_4DSTEM_SumFrames
# to reshape otherwise use reshape_4DSTEM_FlyBack function
if data_pxm.metadata.Signal.exposure_time is None:
data_pxm = reshape_4DSTEM_SumFrames(data_pxm)
else:
data_pxm = reshape_4DSTEM_FlyBack(data_pxm)
except TypeError:
raise ValueError(
'Reshaping did not work. Get the stack by passing reshape=False')
except ValueError:
raise ValueError(
'Reshaping did not work. Get the stack by passing reshape=False')
return data_pxm
def h5stack_to_pxm(h5_path, mib_path, flip=True):
"""
this function reads the saved stack h5 file into a reshaped pyxem.signals.LazyElectronDiffraction2D object
chunks are defined as (100, det_x, det_y)
Parameters
----------
h5_path: str
full path and name of the h5 stack file
mib_path: str
full path and name of the mib file
flip: boolean
Keyword argument to vertically flip the diffraction signal (default)
or return unchanged. The metadata is updated accordingly.
Returns
-------
data_pxm: pyxem.signals.LazyElectronDiffraction2D
"""
hdr_info = _parse_hdr(mib_path)
f = h5py.File(h5_path, "r")
data = f["data_stack"]
data_pxm = LazyElectronDiffraction2D(data)
if hdr_info["Assembly Size"] == "2x2":
data = data_pxm.data
# add_crosses expects a dask array object
data = _add_crosses(data)
data_pxm = LazyElectronDiffraction2D(data)
if os.stat(mib_path).st_size * 1e9 < 0.1:
exp_times_list = _read_exposures(mib_path, pct_frames_to_read=1.0)
else:
exp_times_list = _read_exposures(mib_path)
data_dict = _STEM_flag_dict(exp_times_list)
# Tranferring dict info to metadata
if data_dict["STEM_flag"] == 1:
data_pxm.metadata.Signal.signal_type = "STEM"
else:
data_pxm.metadata.Signal.signal_type = "TEM"
data_pxm.metadata.Signal.scan_X = data_dict["scan_X"]
data_pxm.metadata.Signal.exposure_time = data_dict["exposure time"]
data_pxm.metadata.Signal.frames_number_skipped = data_dict[
"number of frames_to_skip"]
data_pxm.metadata.Signal.flyback_times = data_dict["flyback_times"]
if (data_pxm.metadata.Signal.signal_type == "TEM"
and data_pxm.metadata.Signal.exposure_time != None):
print(
"This mib file appears to be TEM data. The stack is returned with no reshaping."
)
# to catch single frames:
if data_pxm.axes_manager[0].size == 1:
print("This mib file is a single frame.")
try:
# If the exposure time info not appearing in the header bits use reshape_4DSTEM_SumFrames
# to reshape otherwise use reshape_4DSTEM_FlyBack function
if data_pxm.metadata.Signal.exposure_time is None:
(data_pxm, skip_ind) = reshape_4DSTEM_SumFrames(data_pxm)
data_pxm.metadata.Signal.signal_type = "STEM"
data_pxm.metadata.Signal.frames_number_skipped = skip_ind
else:
print("reshaping using flyback pixel")
data_pxm = reshape_4DSTEM_FlyBack(data_pxm)
except TypeError:
print(
"Warning: Reshaping did not work or TEM data with no exposure info. Returning the stack with no reshaping!"
)
except ValueError:
print(
"Warning: Reshaping did not work or TEM data with no exposure info. Returning the stack with no reshaping!"
)
if flip:
data_pxm.data = np.flip(data_pxm.data, axis=2)
data_pxm.metadata.Signal.flip = True
else:
data_pxm.metadata.Signal.flip = False
return data_pxm
