Merge pull request #571 from arayabrain/feature/refactor-edit-roi-code

Refactoring edit roi codes

studio/app/optinist/core/nwb/nwb_creater.py

@@ -22,49 +22,54 @@
 
 class NWBCreater:
     @classmethod
-    def acquisition(cls, config):
-        nwbfile = NWBFile(
+    def acquisition(cls, config: dict):
+        new_nwbfile = NWBFile(
             session_description=config["session_description"],
             identifier=config["identifier"],
             experiment_description=config["experiment_description"],
             session_start_time=datetime.now(tzlocal()),
         )
 
-        # 顕微鏡情報を登録
-        device = nwbfile.create_device(
+        # Create Device (microscope information)
+        device = new_nwbfile.create_device(
             name=config["device"]["name"],
             description=config["device"]["description"],
             manufacturer=config["device"]["manufacturer"],
         )
 
-        # 光チャネルを登録
+        # Create OpticalChannel
         optical_channel = OpticalChannel(
             name=config["optical_channel"]["name"],
             description=config["optical_channel"]["description"],
             emission_lambda=float(config["optical_channel"]["emission_lambda"]),
         )
 
-        # imaging planeを追加
-        imaging_plane = nwbfile.create_imaging_plane(
+        # Create Imaging Plane
+        imaging_plane = new_nwbfile.create_imaging_plane(
             name=config["imaging_plane"]["name"],
             description=config["imaging_plane"]["description"],
-            optical_channel=optical_channel,  # 光チャネル
-            device=device,  # 電極デバイス
-            imaging_rate=float(config["imaging_plane"]["imaging_rate"]),  # 画像の比率Hz
+            optical_channel=optical_channel,  # Optical Channel
+            device=device,  # Electrode Device
+            imaging_rate=float(
+                config["imaging_plane"]["imaging_rate"]
+            ),  # Image Ratio Hz
             excitation_lambda=float(
                 config["imaging_plane"]["excitation_lambda"]
-            ),  # 励起（れいき）波長
-            indicator=config["imaging_plane"]["indicator"],  # カルシウムインジケーター
+            ),  # Excitation Wavelength
+            indicator=config["imaging_plane"]["indicator"],  # Calcium Indicator
             location=config["imaging_plane"]["location"],
         )
 
-        # using internal data. this data will be stored inside the NWB file
+        # Using internal data. this data will be stored inside the NWB file
         if (
             NWBDATASET.IMAGE_SERIES in config
             and "external_file" in config[NWBDATASET.IMAGE_SERIES]
         ):
             external_file = config[NWBDATASET.IMAGE_SERIES]["external_file"]
-            image_path = external_file.path
+            try:
+                image_path = external_file.path
+            except AttributeError:
+                image_path = external_file
 
             starting_frames = (
                 config[NWBDATASET.IMAGE_SERIES]["starting_frame"]
@@ -84,6 +89,7 @@ def acquisition(cls, config):
             elif isinstance(image_path, str):
                 image_path = [image_path]
 
+            # Create Acquisition
             image_series = TwoPhotonSeries(
                 name="TwoPhotonSeries",
                 starting_frame=starting_frames,
@@ -94,16 +100,16 @@ def acquisition(cls, config):
                 unit="normalized amplitude",
                 data=external_file.data if save_raw_image_to_nwb else None,
             )
-            nwbfile.add_acquisition(image_series)
+            new_nwbfile.add_acquisition(image_series)
 
-        nwbfile.create_processing_module(
+        new_nwbfile.create_processing_module(
             name="ophys", description="optical physiology processed data"
         )
+        new_nwbfile.create_processing_module(name="optinist", description="description")
 
-        nwbfile.create_processing_module(name="optinist", description="description")
-        cls.ophys(nwbfile)
+        cls.ophys(new_nwbfile)
 
-        return nwbfile
+        return new_nwbfile
 
     @classmethod
     def ophys(cls, nwbfile):
@@ -123,7 +129,7 @@ def ophys(cls, nwbfile):
         return nwbfile
 
     @classmethod
-    def add_plane_segmentation(cls, nwbfile, function_id):
+    def plane_segmentation(cls, nwbfile, function_id):
         image_seg = nwbfile.processing["ophys"].data_interfaces["ImageSegmentation"]
         if "TwoPhotonSeries" in nwbfile.acquisition:
             reference_images = nwbfile.acquisition["TwoPhotonSeries"]
@@ -189,7 +195,7 @@ def motion_correction(cls, nwbfile, function_id, mc_data, xy_trans_data):
 
     @classmethod
     def roi(cls, nwbfile, function_id, roi_list):
-        nwbfile = cls.add_plane_segmentation(nwbfile, function_id)
+        nwbfile = cls.plane_segmentation(nwbfile, function_id)
         image_seg = nwbfile.processing["ophys"].data_interfaces["ImageSegmentation"]
         plane_seg = image_seg.plane_segmentations[function_id]
 
@@ -284,14 +290,15 @@ def postprocess(cls, nwbfile, function_id, data):
         return nwbfile
 
     @classmethod
-    def reaqcuisition(cls, nwbfile):
+    def re_acquisition(cls, nwbfile: NWBFile):
         new_nwbfile = NWBFile(
             session_description=nwbfile.session_description,
             identifier=nwbfile.identifier,
             experiment_description=nwbfile.experiment_description,
             session_start_time=nwbfile.session_start_time,
         )
 
+        # Create Device (microscope information)
         devices = []
         for key in nwbfile.devices.keys():
             device = new_nwbfile.create_device(
@@ -301,6 +308,7 @@ def reaqcuisition(cls, nwbfile):
             )
             devices.append(device)
 
+        # Create OpticalChannel
         old_optical_channel = nwbfile.imaging_planes["ImagingPlane"].optical_channel[0]
         optical_channels = []
         for old_optical_channel in nwbfile.imaging_planes[
@@ -313,26 +321,28 @@ def reaqcuisition(cls, nwbfile):
             )
             optical_channels.append(optical_channel)
 
+        # Create Imaging Plane
         imaging_planes = []
         for key in nwbfile.imaging_planes.keys():
             imaging_plane = new_nwbfile.create_imaging_plane(
                 name=nwbfile.imaging_planes[key].name,
                 description=nwbfile.imaging_planes[key].description,
-                optical_channel=optical_channels,  # 光チャネル
-                device=devices[0],  # 電極デバイス
+                optical_channel=optical_channels,  # Optical Channel
+                device=devices[0],  # Electrode Device
                 imaging_rate=float(
                     nwbfile.imaging_planes["ImagingPlane"].imaging_rate
-                ),  # 画像の比率Hz
+                ),  # Image Ratio Hz
                 excitation_lambda=float(
                     nwbfile.imaging_planes["ImagingPlane"].excitation_lambda
-                ),  # 励起（れいき）波長
+                ),  # Excitation Wavelength
                 indicator=nwbfile.imaging_planes[
                     "ImagingPlane"
-                ].indicator,  # カルシウムインディケーター
+                ].indicator,  # Calcium Indicator
                 location=nwbfile.imaging_planes["ImagingPlane"].location,
             )
             imaging_planes.append(imaging_plane)
 
+        # Create Acquisition
         image_series = TwoPhotonSeries(
             name="TwoPhotonSeries",
             starting_frame=nwbfile.acquisition["TwoPhotonSeries"].starting_frame,
@@ -342,14 +352,15 @@ def reaqcuisition(cls, nwbfile):
             rate=nwbfile.acquisition["TwoPhotonSeries"].rate,
             unit=nwbfile.acquisition["TwoPhotonSeries"].unit,
         )
-
         new_nwbfile.add_acquisition(image_series)
 
         new_nwbfile.create_processing_module(
             name="ophys", description="optical physiology processed data"
         )
         new_nwbfile.create_processing_module(name="optinist", description="description")
+
         cls.ophys(new_nwbfile)
+
         return new_nwbfile
 
 
@@ -432,7 +443,7 @@ def overwrite_nwb(config, save_path, nwb_file_name):
     with NWBHDF5IO(nwb_path, "r") as io:
         nwbfile = io.read()
         # acquisition を元ファイルから作成する
-        new_nwbfile = NWBCreater.reaqcuisition(nwbfile)
+        new_nwbfile = NWBCreater.re_acquisition(nwbfile)
         new_nwbfile = set_nwbconfig(new_nwbfile, config)
 
         with NWBHDF5IO(tmp_nwb_path, "w") as io: