def file_writer(filename, signal, export_scale=True, extratags=[], **kwds):
"""Writes data to tif using Christoph Gohlke's tifffile library
Parameters
----------
filename: str
signal: a BaseSignal instance
export_scale: bool
default: True
Export the scale and the units (compatible with DM and ImageJ) to
appropriate tags.
If the scikit-image version is too old, use the hyperspy embedded
tifffile library to allow exporting the scale and the unit.
"""
imsave, TiffFile = _import_tifffile_library(export_scale)
data = signal.data
if signal.is_rgbx is True:
data = rgb_tools.rgbx2regular_array(data)
photometric = "rgb"
else:
photometric = "minisblack"
if 'description' in kwds and export_scale:
kwds.pop('description')
# Comment this warning, since it was not passing the test online...
# warnings.warn(
# "Description and export scale cannot be used at the same time, "
# "because of incompability with the 'ImageJ' format")
if export_scale:
kwds.update(_get_tags_dict(signal, extratags=extratags))
_logger.info("kwargs passed to tifffile.py imsave: {0}".format(kwds))
imsave(filename, data,
software="hyperspy",
photometric=photometric,
**kwds)
def file_writer(filename, signal, export_scale=True, extratags=[], **kwds):
"""Writes data to tif using Christoph Gohlke's tifffile library
Parameters
----------
filename: str
signal: a BaseSignal instance
export_scale: bool
default: True
Export the scale and the units (compatible with DM and ImageJ) to
appropriate tags.
If the scikit-image version is too old, use the hyperspy embedded
tifffile library to allow exporting the scale and the unit.
"""
_logger.debug('************* Saving *************')
imsave, TiffFile = _import_tifffile_library(export_scale)
data = signal.data
if signal.is_rgbx is True:
data = rgb_tools.rgbx2regular_array(data)
photometric = "rgb"
else:
photometric = "minisblack"
if 'description' in kwds and export_scale:
kwds.pop('description')
# Comment this warning, since it was not passing the test online...
# warnings.warn(
# "Description and export scale cannot be used at the same time, "
# "because of incompability with the 'ImageJ' format")
if export_scale:
kwds.update(_get_tags_dict(signal, extratags=extratags))
_logger.debug("kwargs passed to tifffile.py imsave: {0}".format(kwds))
if 'date' in signal.metadata['General']:
dt = get_date_time_from_metadata(signal.metadata,
formatting='datetime')
kwds['datetime'] = dt
imsave(filename,
data,
software="hyperspy",
photometric=photometric,
**kwds)
def file_writer(filename, signal, export_scale=True, extratags=[], **kwds):
"""Writes data to tif using Christoph Gohlke's tifffile library
Parameters
----------
filename: str
signal: a BaseSignal instance
export_scale: bool
default: True
Export the scale and the units (compatible with DM and ImageJ) to
appropriate tags.
"""
_logger.debug('************* Saving *************')
data = signal.data
if signal.is_rgbx is True:
data = rgb_tools.rgbx2regular_array(data)
photometric = "RGB"
else:
photometric = "MINISBLACK"
if 'description' in kwds and export_scale:
kwds.pop('description')
_logger.warning(
"Description and export scale cannot be used at the same time, "
"because it is incompability with the 'ImageJ' tiff format")
if export_scale:
kwds.update(_get_tags_dict(signal, extratags=extratags))
_logger.debug("kwargs passed to tifffile.py imsave: {0}".format(kwds))
if 'date' in signal.metadata['General']:
dt = get_date_time_from_metadata(signal.metadata,
formatting='datetime')
kwds['datetime'] = dt
imsave(filename,
data,
software="hyperspy",
photometric=photometric,
**kwds)