From 4dee2946e8ce46705d76e639ba78f6b882e94712 Mon Sep 17 00:00:00 2001 From: tsuchiyama-araya Date: Mon, 10 Feb 2025 13:01:04 +0900 Subject: [PATCH 1/3] Adding Tranpose Parameter --- .../optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml | 2 +- .../wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml index e16c76dff..ca5f01de0 100644 --- a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml +++ b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml @@ -1 +1 @@ -"" +transpose: True diff --git a/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py b/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py index 3d9de2291..036df2fa6 100644 --- a/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py +++ b/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py @@ -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} From af1a4e5174315bfc0e23f489fa37deab4984fedf Mon Sep 17 00:00:00 2001 From: tsuchiyama-araya Date: Tue, 18 Feb 2025 16:31:08 +0900 Subject: [PATCH 2/3] =?UTF-8?q?Params=E3=81=AB=E3=82=B3=E3=83=A1=E3=83=B3?= =?UTF-8?q?=E3=83=88=E8=BF=BD=E5=8A=A0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml index ca5f01de0..0358c8d71 100644 --- a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml +++ b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml @@ -1 +1,3 @@ +# こちらは一時的の対応です。基本的にはTransposeはTrueにしてください。 +# ただし、TransposeがTrueの場合、データの座標が逆になるケースがあります。そのため、画面でFalseに切り替えることもあります。 transpose: True From 2b261cdd726475442e5c8b4a75a3f74972bd9c68 Mon Sep 17 00:00:00 2001 From: tsuchiyama-araya Date: Tue, 18 Feb 2025 17:19:55 +0900 Subject: [PATCH 3/3] =?UTF-8?q?=E3=82=B3=E3=83=A1=E3=83=B3=E3=83=88?= =?UTF-8?q?=E3=82=92=E8=8B=B1=E8=AA=9E=E3=81=AB=E6=9B=B4=E6=96=B0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml index 0358c8d71..e498b8467 100644 --- a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml +++ b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml @@ -1,3 +1,4 @@ -# こちらは一時的の対応です。基本的にはTransposeはTrueにしてください。 -# ただし、TransposeがTrueの場合、データの座標が逆になるケースがあります。そのため、画面でFalseに切り替えることもあります。 +# 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