def get_parsed_metadata(self):
"""Returns the parsed metadata in dictionary form.
Returns:
dict: the parsed metadata
"""
if self._metadata_parsed is not None:
return self._metadata_parsed
frames_per_channel = self._parse_total_images_per_channel()
self._metadata_parsed = {
"height": parse_if_not_none(self.image_attributes, self._parse_height),
"width": parse_if_not_none(self.image_attributes, self._parse_width),
"date": parse_if_not_none(self.image_text_info, self._parse_date),
"fields_of_view": self._parse_fields_of_view(),
"frames": self._parse_frames(),
"z_levels": self._parse_z_levels(),
"z_coordinates": parse_if_not_none(self.z_data, self._parse_z_coordinates),
"total_images_per_channel": frames_per_channel,
"channels": self._parse_channels(),
"pixel_microns": parse_if_not_none(self.image_calibration, self._parse_calibration)
}
self._set_default_if_not_empty('fields_of_view')
self._set_default_if_not_empty('frames')
self._metadata_parsed['num_frames'] = len(self._metadata_parsed['frames'])
self._parse_roi_metadata()
self._parse_experiment_metadata()
self._parse_events()
return self._metadata_parsed
def _parse_z_levels(self):
"""The different levels in the Z-plane.
If they are not available from the _parse_dimension function AND there
is NO 'Dimensions: ' textinfo item in the file, we return a range with
the length of z_coordinates if available, otherwise an empty list.
Returns:
list: the z levels, just a sequence from 0 to n.
"""
# get the dimension text to check if we should apply the fallback or not
dimension_text = self._parse_dimension_text()
# this returns range(len(z_levels))
z_levels = self._parse_dimension(r""".*?Z\((\d+)\).*?""",
dimension_text)
if len(z_levels) > 0 or len(dimension_text) > 0:
# Either we have found the z_levels (first condition) so return, or
# don't fallback, because Z is apparently not in Dimensions, so
# there should be no z_levels
return z_levels
# Not available from dimension, get from z_coordinates
z_levels = parse_if_not_none(self.z_data, self._parse_z_coordinates)
if z_levels is None:
# No z coordinates, return empty list
return []
warnings.warn(
"Z-levels details missing in metadata. Using Z-coordinates instead."
)
return range(len(z_levels))
def _parse_z_levels(self):
"""The different levels in the Z-plane.
Returns:
list: the z levels, just a sequence from 0 to n.
"""
z_levels = self._parse_dimension(r""".*?Z\((\d+)\).*?""")
if 0 == len(z_levels):
z_levels = parse_if_not_none(self.z_data,
self._parse_z_coordinates)
if z_levels is None:
z_levels = []
else:
z_levels = range(len(z_levels))
warnings.warn(
"Z-levels details missing in metadata. Using Z-coordinates instead."
)
return z_levels
