def save(filename, signal, overwrite=None, **kwds):
extension = os.path.splitext(filename)[1][1:]
if extension == '':
extension = \
hyperspy.defaults_parser.preferences.General.default_file_format
filename = filename + '.' + \
hyperspy.defaults_parser.preferences.General.default_file_format
writer = None
for plugin in io_plugins:
if extension.lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
('.%s does not correspond to any supported format. Supported ' +
'file extensions are: %s') %
(extension, strlist2enumeration(default_write_ext)))
else:
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError('Writing to this format is not '
'supported, supported file extensions are: %s ' %
strlist2enumeration(default_write_ext))
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [plugin.format_name for plugin in io_plugins
if plugin.writes is True or
plugin.writes is not False and
(sd, nd) in plugin.writes]
raise ValueError('This file format cannot write this data. '
'The following formats can: %s' %
strlist2enumeration(yes_we_can))
ensure_directory(filename)
if overwrite is None:
overwrite = hyperspy.misc.io.tools.overwrite(filename)
if overwrite is True:
writer.file_writer(filename, signal, **kwds)
print('The %s file was created' % filename)
folder, filename = os.path.split(os.path.abspath(filename))
signal.tmp_parameters.set_item('folder', folder)
signal.tmp_parameters.set_item('filename',
os.path.splitext(filename)[0])
signal.tmp_parameters.set_item('extension', extension)
def save(filename, signal, overwrite=None, **kwds):
extension = os.path.splitext(filename)[1][1:]
if extension == '':
extension = "hspy"
filename = filename + '.' + extension
writer = None
for plugin in io_plugins:
if extension.lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
('.%s does not correspond to any supported format. Supported ' +
'file extensions are: %s') %
(extension, strlist2enumeration(default_write_ext)))
else:
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError('Writing to this format is not '
'supported, supported file extensions are: %s ' %
strlist2enumeration(default_write_ext))
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [
plugin.format_name for plugin in io_plugins
if plugin.writes is True or plugin.writes is not False and
(sd, nd) in plugin.writes
]
raise IOError('This file format cannot write this data. '
'The following formats can: %s' %
strlist2enumeration(yes_we_can))
ensure_directory(filename)
if overwrite is None:
overwrite = overwrite_method(filename)
if overwrite is True:
writer.file_writer(filename, signal, **kwds)
_logger.info('The %s file was created' % filename)
folder, filename = os.path.split(os.path.abspath(filename))
signal.tmp_parameters.set_item('folder', folder)
signal.tmp_parameters.set_item('filename',
os.path.splitext(filename)[0])
signal.tmp_parameters.set_item('extension', extension)
def save(filename, signal, overwrite=None, **kwds):
"""Save hyperspy signal to a file.
A list of plugins supporting file saving can be found here:
http://hyperspy.org/hyperspy-doc/current/user_guide/io.html#supported-formats
Any extra keywords are passed to the corresponding save method in the
io_plugin. For available options, see their individual documentation.
Parameters
----------
filename : None or str or pathlib.Path
The filename to save the signal to.
signal : Hyperspy signal
The signal to be saved to file.
overwrite : None or bool, default None
If None and a file exists the user will be prompted to on whether to
overwrite. If False and a file exists the file will not be written.
If True and a file exists the file will be overwritten without
prompting
Returns
-------
None
"""
filename = Path(filename).resolve()
extension = filename.suffix
if extension == '':
extension = ".hspy"
filename = filename.with_suffix(extension)
writer = None
for plugin in io_plugins:
# Drop the "." separator from the suffix
if extension[1:].lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
f"{extension} does not correspond to any supported format. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError(
"Writing to this format is not supported. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [plugin.format_name for plugin in io_plugins
if plugin.writes is True or
plugin.writes is not False and
(sd, nd) in plugin.writes]
raise IOError(
"This file format does not support this data. "
f"Please try one of {strlist2enumeration(yes_we_can)}"
)
# Create the directory if it does not exist
ensure_directory(filename.parent)
is_file = filename.is_file()
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError(
"`overwrite` parameter can only be None, True or False."
)
if write:
# Pass as a string for now, pathlib.Path not
# properly supported in io_plugins
writer.file_writer(str(filename), signal, **kwds)
_logger.info(f'{filename} was created')
signal.tmp_parameters.set_item('folder', filename.parent)
signal.tmp_parameters.set_item('filename', filename.stem)
signal.tmp_parameters.set_item('extension', extension)
def save(filename, signal, overwrite=None, **kwds):
"""
Save hyperspy signal to a file.
A list of plugins supporting file saving can be found here:
http://hyperspy.org/hyperspy-doc/current/user_guide/io.html#supported-formats
Any extra keyword is passed to the corresponding save method in the
io_plugin.
For available options see their individual documentation.
Parameters
----------
filename : None or str
The filename to save the signal to.
signal : Hyperspy signal
The signal to be saved to file
overwrite : None or Bool (default, None)
If None and a file exists the user will be prompted to on whether to
overwrite. If False and a file exists the file will not be written.
If True and a file exists the file will be overwritten without
prompting
"""
extension = os.path.splitext(filename)[1][1:]
if extension == '':
extension = "hspy"
filename = filename + '.' + extension
writer = None
for plugin in io_plugins:
if extension.lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
('.%s does not correspond to any supported format. Supported ' +
'file extensions are: %s') %
(extension, strlist2enumeration(default_write_ext)))
else:
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError('Writing to this format is not '
'supported, supported file extensions are: %s ' %
strlist2enumeration(default_write_ext))
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [
plugin.format_name for plugin in io_plugins
if plugin.writes is True or plugin.writes is not False and
(sd, nd) in plugin.writes
]
raise IOError('This file format cannot write this data. '
'The following formats can: %s' %
strlist2enumeration(yes_we_can))
ensure_directory(filename)
is_file = os.path.isfile(filename)
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError("`overwrite` parameter can only be None, True or "
"False.")
if write:
writer.file_writer(filename, signal, **kwds)
_logger.info('The %s file was created' % filename)
folder, filename = os.path.split(os.path.abspath(filename))
signal.tmp_parameters.set_item('folder', folder)
signal.tmp_parameters.set_item('filename',
os.path.splitext(filename)[0])
signal.tmp_parameters.set_item('extension', extension)
def save(filename, signal, overwrite=None, add_scan=None, **kwargs):
"""Write electron backscatter patterns to file.
Parameters
----------
filename : str
File path including name of new file.
signal : {kikuchipy.signals.EBSD, kikuchipy.lazy_signals.LazyEBSD}
Signal instance.
overwrite : {bool, None}, optional
Whether to overwrite file or not if it already exists.
add_scan : {bool, None}, optional
Whether to add the signal to an already existing h5ebsd file or
not. If the file does not exist the signal is written to a new
file.
**kwargs :
Keyword arguments passed to the writer.
"""
from hyperspy.misc.io.tools import overwrite as overwrite_method
ext = os.path.splitext(filename)[1][1:]
if ext == '': # Will write to HyperSpy's HDF5 format
ext = 'hspy'
filename = filename + '.' + ext
writer = None
for plugin in io_plugins:
if ext.lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
(".%s does not correspond to any supported format. Supported "
"file extensions are: %s") %
(ext, strlist2enumeration(default_write_ext)))
else: # Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError("Writing to this format is not "
"supported, supported file extensions are: %s " %
strlist2enumeration(default_write_ext))
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [
plugin.format_name for plugin in io_plugins
if plugin.writes is True or plugin.writes is not False and
(sd, nd) in plugin.writes
]
raise IOError("This file format cannot write this data. "
"The following formats "
"can: {}".format(strlist2enumeration(yes_we_can)))
# Check possibilities for overwriting file and/or datasets within file
ensure_directory(filename)
is_file = os.path.isfile(filename)
if writer.format_name == 'h5ebsd' and overwrite is not True and is_file:
if add_scan is None:
q = "Add scan to '{}' (y/n)?\n".format(filename)
add_scan = get_input_bool(q)
if add_scan:
overwrite = True # So that the 2nd statement below triggers
kwargs['add_scan'] = add_scan
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError("`overwrite` parameter can only be None, True or "
"False, and not {}".format(overwrite))
if write:
writer.file_writer(filename, signal, **kwargs)
folder, filename = os.path.split(os.path.abspath(filename))
signal.tmp_parameters.set_item('folder', folder)
signal.tmp_parameters.set_item('filename',
os.path.splitext(filename)[0])
signal.tmp_parameters.set_item('extension', ext)
def save(filename, signal, overwrite=None, **kwds):
"""Save hyperspy signal to a file.
A list of plugins supporting file saving can be found here:
http://hyperspy.org/hyperspy-doc/current/user_guide/io.html#supported-formats
Any extra keywords are passed to the corresponding save method in the
io_plugin. For available options, see their individual documentation.
Parameters
----------
filename : None, str, pathlib.Path
The filename to save the signal to.
signal : Hyperspy signal
The signal to be saved to the file.
overwrite : None, bool, optional
If None (default) and a file exists, the user will be prompted whether
to overwrite. If False and a file exists, the file will not be written.
If True and a file exists, the file will be overwritten without
prompting
Returns
-------
None
"""
if isinstance(filename, MutableMapping):
extension = ".zspy"
else:
filename = Path(filename).resolve()
extension = filename.suffix
if extension == '':
extension = ".hspy"
filename = filename.with_suffix(extension)
writer = None
for plugin in io_plugins:
# Drop the "." separator from the suffix
if extension[1:].lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
f"{extension} does not correspond to any supported format. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError(
"Writing to this format is not supported. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
if writer.writes is not True and (sd, nd) not in writer.writes:
compatible_writers = [
plugin.format_name for plugin in io_plugins
if plugin.writes is True or plugin.writes is not False and
(sd, nd) in plugin.writes
]
raise TypeError(
"This file format does not support this data. "
f"Please try one of {strlist2enumeration(compatible_writers)}")
if not writer.non_uniform_axis and not signal.axes_manager.all_uniform:
compatible_writers = [
plugin.format_name for plugin in io_plugins
if plugin.non_uniform_axis is True
]
raise TypeError("Writing to this format is not supported for "
"non-uniform axes. Use one of the following "
f"formats: {strlist2enumeration(compatible_writers)}")
# Create the directory if it does not exist
if not isinstance(filename, MutableMapping):
ensure_directory(filename.parent)
is_file = filename.is_file() or (
filename.is_dir() and os.path.splitext(filename)[1] == '.zspy')
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError("`overwrite` parameter can only be None, True or "
"False.")
else:
write = True # file does not exist (creating it)
if write:
# Pass as a string for now, pathlib.Path not
# properly supported in io_plugins
signal = _add_file_load_save_metadata('save', signal, writer)
if not isinstance(filename, MutableMapping):
writer.file_writer(str(filename), signal, **kwds)
_logger.info(f'{filename} was created')
signal.tmp_parameters.set_item('folder', filename.parent)
signal.tmp_parameters.set_item('filename', filename.stem)
signal.tmp_parameters.set_item('extension', extension)
else:
writer.file_writer(filename, signal, **kwds)
if hasattr(filename, "path"):
file = Path(filename.path).resolve()
signal.tmp_parameters.set_item('folder', file.parent)
signal.tmp_parameters.set_item('filename', file.stem)
signal.tmp_parameters.set_item('extension', extension)
def _save(
filename: str,
signal,
overwrite: Optional[bool] = None,
add_scan: Optional[bool] = None,
**kwargs,
):
"""Write signal to a file in a supported format.
This function is a modified version of :func:`hyperspy.io.save`.
Parameters
----------
filename
File path including name of new file.
signal : EBSD or LazyEBSD
Signal instance.
overwrite
Whether to overwrite file or not if it already exists.
add_scan
Whether to add the signal to an already existing h5ebsd file or
not. If the file does not exist the signal is written to a new
file.
**kwargs :
Keyword arguments passed to the writer.
"""
ext = os.path.splitext(filename)[1][1:]
if ext == "": # Will write to kikuchipy's h5ebsd format
ext = "h5"
filename = filename + "." + ext
writer = None
for plugin in plugins:
if ext.lower() in plugin.file_extensions and plugin.writes:
writer = plugin
break
if writer is None:
raise ValueError(
f"'{ext}' does not correspond to any supported format. Supported "
f"file extensions are: '{strlist2enumeration(default_write_ext)}'"
)
else:
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is not True and (sd, nd) not in writer.writes:
# Get writers that can write this data
writing_plugins = []
for plugin in plugins:
if (
plugin.writes is True
or plugin.writes is not False
and (sd, nd) in plugin.writes
):
writing_plugins.append(plugin)
raise ValueError(
"This file format cannot write this data. The following "
f"formats can: {strlist2enumeration(writing_plugins)}"
)
ensure_directory(filename)
is_file = os.path.isfile(filename)
# Check if we are to add signal to an already existing h5ebsd file
if writer.format_name == "h5ebsd" and overwrite is not True and is_file:
if add_scan is None:
q = "Add scan to '{}' (y/n)?\n".format(filename)
add_scan = _get_input_bool(q)
if add_scan:
overwrite = True # So that the 2nd statement below triggers
kwargs["add_scan"] = add_scan
# Determine if signal is to be written to file or not
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError(
"overwrite parameter can only be None, True or False, and "
f"not {overwrite}"
)
# Finally, write file
if write:
writer.file_writer(filename, signal, **kwargs)
directory, filename = os.path.split(os.path.abspath(filename))
signal.tmp_parameters.set_item("folder", directory)
signal.tmp_parameters.set_item(
"filename", os.path.splitext(filename)[0]
)
signal.tmp_parameters.set_item("extension", ext)