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Fixes issue #11

master
Ruben Verweij 5 years ago
parent
commit
cd55b8ffdd
1 changed files with 16 additions and 2 deletions
  1. +16
    -2
      nd2reader/raw_metadata.py

+ 16
- 2
nd2reader/raw_metadata.py View File

@ -43,9 +43,10 @@ class RawMetadata(object):
"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),
"pixel_microns": parse_if_not_none(self.image_calibration, self._parse_calibration)
}
self._set_default_if_not_empty('fields_of_view')
@ -161,6 +162,14 @@ class RawMetadata(object):
"""
return self._parse_dimension(r""".*?Z\((\d+)\).*?""")
def _parse_z_coordinates(self):
"""The coordinate in micron for all z planes.
Returns:
list: the z coordinates in micron
"""
return self.z_data.tolist()
def _parse_dimension_text(self):
"""While there are metadata values that represent a lot of what we want to capture, they seem to be unreliable.
Sometimes certain elements don't exist, or change their data type randomly. However, the human-readable text
@ -492,7 +501,12 @@ class RawMetadata(object):
Returns:
dict: z_data
"""
return read_array(self._fh, 'double', self._label_map.z_data)
try:
return read_array(self._fh, 'double', self._label_map.z_data)
except ValueError:
# Depending on the file format/exact settings, this value is
# sometimes saved as float instead of double
return read_array(self._fh, 'float', self._label_map.z_data)
@property
def roi_metadata(self):


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