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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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5 changes: 1 addition & 4 deletions iohub/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -310,10 +310,7 @@ def _get_pos_names(self):
if self.p > 1:
self.pos_names = []
for p in range(self.p):
name = (
self.summary_metadata["StagePositions"][p].get("Label")
or p
)
name = self.reader.stage_positions[p].get("Label") or p
self.pos_names.append(name)
else:
self.pos_names = ["0"]
Expand Down
29 changes: 26 additions & 3 deletions iohub/multipagetiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,12 +55,12 @@ def __init__(self, folder: str, extract_data: bool = False):
# Initialize MM attributes
self.channel_names = []

# Read MM data
self._set_mm_meta()

# Gather index map of file, page, byte offset
self._gather_index_maps()

# Read MM data
self._set_mm_meta()

# if extract data, create all of the virtual zarr stores up front
if extract_data:
for i in range(self.positions):
Expand Down Expand Up @@ -173,6 +173,29 @@ def _set_mm_meta(self):
for ch in self.mm_meta["Summary"]["ChNames"]:
self.channel_names.append(ch)

# Parsing of data acquired with the OpenCell
# acquisition script on the Dragonfly miroscope
elif (
mm_version == "2.0.1 20220920"
and self.mm_meta["Summary"]["Prefix"] == "raw_data"
):
file_names = set(
[(key[0], val[0]) for key, val in self.coord_map.items()]
)

if self.mm_meta["Summary"]["Positions"] > 1:
self._stage_positions = [None] * self.positions

for p_idx, file_name in file_names:
site_idx = int(file_name.split("_")[-1].split("-")[0])
pos = self._simplify_stage_position(
self.mm_meta["Summary"]["StagePositions"][site_idx]
)
self._stage_positions[p_idx] = pos

for ch in self.mm_meta["Summary"]["ChNames"]:
self.channel_names.append(ch)

else:
if self.mm_meta["Summary"]["Positions"] > 1:
self._stage_positions = []
Expand Down
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