def test_get_input_variable(self, var_type):
question = "How few are too few coffee cups?"
answer = "1"
with replace_stdin(io.StringIO(answer)):
if isinstance(var_type, int):
with pytest.raises(EOFError):
_ = _get_input_variable(question, var_type)
return 0
else:
returns = _get_input_variable(question, var_type)
assert returns == var_type(answer)
def file_writer(
filename: str,
signal,
add_scan: Optional[bool] = None,
scan_number: int = 1,
**kwargs,
):
"""Write an :class:`~kikuchipy.signals.EBSD` or
:class:`~kikuchipy.signals.LazyEBSD` signal to an existing,
but not open, or new h5ebsd file.
Only writing to kikuchipy's h5ebsd format is supported.
Parameters
----------
filename
Full path of HDF file.
signal : kikuchipy.signals.EBSD or kikuchipy.signals.LazyEBSD
Signal instance.
add_scan
Add signal to an existing, but not open, h5ebsd file. If it does
not exist it is created and the signal is written to it.
scan_number
Scan number in name of HDF dataset when writing to an existing,
but not open, h5ebsd file.
kwargs
Keyword arguments passed to :meth:`h5py:Group.require_dataset`.
"""
# Set manufacturer and version to use in file
from kikuchipy.release import version as ver_signal
man_ver_dict = {"manufacturer": "kikuchipy", "version": ver_signal}
# Open file in correct mode
mode = "w"
if os.path.isfile(filename) and add_scan:
mode = "r+"
try:
f = h5py.File(filename, mode=mode)
except OSError:
raise OSError("Cannot write to an already open file.")
if os.path.isfile(filename) and add_scan:
check_h5ebsd(f)
man_file, ver_file = manufacturer_version(f)
if man_ver_dict["manufacturer"].lower() != man_file.lower():
f.close()
raise IOError(
f"Only writing to kikuchipy's (and not {man_file}'s) h5ebsd "
"format is supported."
)
man_ver_dict["version"] = ver_file
# Get valid scan number
scans_file = [f[k] for k in f["/"].keys() if "Scan" in k]
scan_nos = [int(i.name.split()[-1]) for i in scans_file]
for i in scan_nos:
if i == scan_number:
q = f"Scan {i} already in file, enter another scan number:\n"
scan_number = _get_input_variable(q, int)
if scan_number is None:
raise IOError("Invalid scan number.")
else: # File did not exist
dict2h5ebsdgroup(man_ver_dict, f["/"], **kwargs)
scan_group = f.create_group("Scan " + str(scan_number))
# Create scan dictionary with EBSD and SEM metadata
# Add scan size, image size and detector pixel size to dictionary to write
data_shape = [1] * 4 # (ny, nx, sy, sx)
data_scales = [1] * 4 # (y, x, dy, dx)
nav_extent = [0, 1, 0, 1] # (x0, x1, y0, y1)
am = signal.axes_manager
nav_axes = am.navigation_axes
nav_dim = am.navigation_dimension
if nav_dim == 1:
nav_axis = nav_axes[0]
if nav_axis.name == "y":
data_shape[0] = nav_axis.size
data_scales[0] = nav_axis.scale
nav_extent[2:] = am.navigation_extent
else: # nav_axis.name == "x" or something else
data_shape[1] = nav_axis.size
data_scales[1] = nav_axis.scale
nav_extent[:2] = am.navigation_extent
elif nav_dim == 2:
data_shape[:2] = [i.size for i in nav_axes][::-1]
data_scales[:2] = [i.scale for i in nav_axes][::-1]
nav_extent = am.navigation_extent
data_shape[2:] = am.signal_shape
data_scales[2:] = [i.scale for i in am.signal_axes]
ny, nx, sy, sx = data_shape
scale_ny, scale_nx, scale_sy, _ = data_scales
md = signal.metadata.deepcopy()
sem_node, ebsd_node = metadata_nodes(["sem", "ebsd"])
md.set_item(ebsd_node + ".pattern_width", sx)
md.set_item(ebsd_node + ".pattern_height", sy)
md.set_item(ebsd_node + ".n_columns", nx)
md.set_item(ebsd_node + ".n_rows", ny)
md.set_item(ebsd_node + ".step_x", scale_nx)
md.set_item(ebsd_node + ".step_y", scale_ny)
md.set_item(ebsd_node + ".detector_pixel_size", scale_sy)
# Separate EBSD and SEM metadata
det_str, ebsd_str = ebsd_node.split(".")[-2:] # Detector and EBSD nodes
md_sem = md.get_item(sem_node).copy().as_dictionary() # SEM node as dict
md_det = md_sem.pop(det_str) # Remove/assign detector node from SEM node
md_ebsd = md_det.pop(ebsd_str)
# Phases
if md.get_item("Sample.Phases") is None:
md = _update_phase_info(md, _phase_metadata()) # Add default phase
md_ebsd["Phases"] = md.Sample.Phases.as_dictionary()
for phase in md_ebsd["Phases"].keys(): # Ensure coordinates are arrays
atom_coordinates = md_ebsd["Phases"][phase]["atom_coordinates"]
for atom in atom_coordinates.keys():
atom_coordinates[atom]["coordinates"] = np.array(
atom_coordinates[atom]["coordinates"]
)
scan = {"EBSD": {"Header": md_ebsd}, "SEM": {"Header": md_sem}}
# Write scan dictionary to HDF groups
dict2h5ebsdgroup(scan, scan_group)
# Write signal to file
man_pats = manufacturer_pattern_names()
dset_pattern_name = man_pats["kikuchipy"]
overwrite_dataset(
scan_group.create_group("EBSD/Data"),
signal.data.reshape(nx * ny, sy, sx),
dset_pattern_name,
signal_axes=(2, 1),
**kwargs,
)
nx_start, nx_stop, ny_start, ny_stop = nav_extent
sample_pos = {
"y_sample": np.tile(np.linspace(ny_start, ny_stop, ny), nx),
"x_sample": np.tile(np.linspace(nx_start, nx_stop, nx), ny),
}
dict2h5ebsdgroup(sample_pos, scan_group["EBSD/Data"])
f.close()