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OpenCell reader extension #197

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merged 4 commits into from
Oct 25, 2023
Merged

OpenCell reader extension #197

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1b6124b
stage positions parsing for opencell datasets
ieivanov Oct 12, 2023
3256e0a
formatting
ieivanov Oct 12, 2023
dfecbe8
don't overwrite frames, slices, and channels in `_set_mm_meta`
ieivanov Oct 24, 2023
cba9038
fix error getting stage position
ieivanov Oct 24, 2023
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14 changes: 8 additions & 6 deletions iohub/multipagetiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -209,15 +209,17 @@ def _set_mm_meta(self):
for ch in self.mm_meta["Summary"]["ChNames"]:
self.channel_names.append(ch)

# dimensions based on mm metadata
# do not reflect final written dimensions
# these will change after data is loaded
self.z_step_size = self.mm_meta["Summary"]["z-step_um"]
self.height = self.mm_meta["Summary"]["Height"]
self.width = self.mm_meta["Summary"]["Width"]
self.frames = self.mm_meta["Summary"]["Frames"]
self.slices = self.mm_meta["Summary"]["Slices"]
self.channels = self.mm_meta["Summary"]["Channels"]

# dimensions based on mm metadata
# do not reflect final written dimensions
# these set in _gather_index_maps
#
# self.frames = self.mm_meta["Summary"]["Frames"]
# self.slices = self.mm_meta["Summary"]["Slices"]
# self.channels = self.mm_meta["Summary"]["Channels"]
Comment on lines +215 to +222
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Thanks for catching this @ziw-liu. I commented out these lines so they don't overwrite the dimensions set by _gather_index_maps


def _simplify_stage_position(self, stage_pos: dict):
"""
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