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Roi_fluo_from_hdf5 Adding Tranpose Parameter #596

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merged 4 commits into from
Feb 18, 2025
Merged

Roi_fluo_from_hdf5 Adding Tranpose Parameter #596

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4dee294
Adding Tranpose Parameter
tsuchiyama-araya Feb 10, 2025
5caf61b
Merge branch 'develop-main' into feature/roi_fluo_from_hdf5_output_is…
tsuchiyama-araya Feb 14, 2025
af1a4e5
Paramsにコメント追加
tsuchiyama-araya Feb 18, 2025
2b261cd
コメントを英語に更新
tsuchiyama-araya Feb 18, 2025
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5 changes: 4 additions & 1 deletion studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml
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Original file line number Diff line number Diff line change
@@ -1 +1,4 @@
""
# This is a temporary measure. Generally, Transpose should be set to True.
# However, when Transpose is set to True, the data coordinates may sometimes be reversed.
# Therefore, it may be switched to False on the screen.
transpose: True
6 changes: 5 additions & 1 deletion studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py
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Expand Up @@ -36,7 +36,11 @@ def roi_fluo_from_hdf5(
all_roi = RoiData(
np.nanmax(cell_img.data, axis=0), output_dir=output_dir, file_name="all_roi"
)
fluorescence = FluoData(np.transpose(fluo.data), file_name="fluorescence")

if params["transpose"]:
fluorescence = FluoData(np.transpose(fluo.data), file_name="fluorescence")
else:
fluorescence = FluoData(fluo.data, file_name="fluorescence")

if iscell is None:
return {"all_roi": all_roi, "fluorescence": fluorescence}
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