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Fix a bug of parsing channel validity #59

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Fix a bug of parsing channel validity #59

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4abae7d
Fix a bug of parsing channel validity
hayatoikoma Nov 13, 2021
02eeda2
Refactor
hayatoikoma Nov 14, 2021
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15 changes: 12 additions & 3 deletions nd2reader/raw_metadata.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
from collections.abc import Sequence
import re
import xmltodict
import six
Expand Down Expand Up @@ -137,13 +138,21 @@ def _process_channels_metadata(self, metadata):
channels.append('Unknown')
return channels

def _parse_validity(self):
parsed = self.image_metadata[six.b('SLxExperiment')]
for _ in range(2):
parsed = parsed[six.b('ppNextLevelEx')][six.b('')]
if isinstance(parsed, Sequence):
# Old format had this structure.
parsed = parsed[0]
return parsed[six.b('pItemValid')]

def _get_channel_validity_list(self, metadata):
try:
validity = self.image_metadata[six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][
six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')]
validity = self._parse_validity()
except (KeyError, TypeError):
# If none of the channels have been deleted, there is no validity list, so we just make one
validity = [True for _ in metadata]
validity = [True for _ in metadata[six.b('sPlaneNew')]]
return validity

def _parse_fields_of_view(self):
Expand Down