Add Node of rou_fluo_from_hdf5

frontend/src/components/Workspace/Visualize/VisualizeItem.tsx

@@ -36,7 +36,7 @@ import {
   selectVisualizeDataFilePath,
   selectVisualizeDataNodeId,
   selectVisualizeDataType,
-  selectVisualizeImageItemIdList,
+  selectVisualizeImageAndRoiItemIdList,
   selectVisualizeItemHeight,
   selectVisualizeItemWidth,
 } from "store/slice/VisualizeItem/VisualizeItemSelectors"
@@ -262,7 +262,7 @@ const RefImageItemIdSelect = memo(function RefImageItemIdSelect({
 }: ItemIdProps) {
   const dispatch = useDispatch()
   const itemIdList = useSelector(
-    selectVisualizeImageItemIdList,
+    selectVisualizeImageAndRoiItemIdList,
     arrayEqualityFn,
   )
   const onChangeRefImageItemId = (event: SelectChangeEvent) => {

frontend/src/store/slice/VisualizeItem/VisualizeItemSelectors.ts

@@ -16,6 +16,7 @@ import {
   isHistogramItem,
   isLineItem,
   isPolarItem,
+  isRoiItem,
 } from "store/slice/VisualizeItem/VisualizeItemUtils"
 import { RootState } from "store/store"
 
@@ -30,6 +31,14 @@ export const selectVisualizeImageItemIdList = (state: RootState) =>
       return isImageItem(item) && !item.isWorkflowDialog
     })
 
+export const selectVisualizeImageAndRoiItemIdList = (state: RootState) =>
+  Object.keys(state.visualaizeItem.items)
+    .map(Number)
+    .filter((itemId) => {
+      const item = selectVisualizeItemById(itemId)(state)
+      return !item.isWorkflowDialog && (isImageItem(item) || isRoiItem(item))
+    })
+
 export const selectVisualizeItems = (state: RootState) =>
   state.visualaizeItem.items
 

studio/app/optinist/wrappers/optinist/visualize_utils/__init__.py

@@ -4,6 +4,9 @@
 from studio.app.optinist.wrappers.optinist.visualize_utils.microscope_to_img import (
     microscope_to_img,
 )
+from studio.app.optinist.wrappers.optinist.visualize_utils.roi_fluo_from_hdf5 import (
+    roi_fluo_from_hdf5,
+)
 from studio.app.optinist.wrappers.optinist.visualize_utils.roi_from_hdf5 import (
     roi_from_hdf5,
 )
@@ -21,4 +24,8 @@
         "function": roi_from_hdf5,
         "conda_name": "optinist",
     },
+    "roi_fluo_from_hdf5": {
+        "function": roi_fluo_from_hdf5,
+        "conda_name": "optinist",
+    },
 }

studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml

@@ -0,0 +1 @@
+""

studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py

@@ -0,0 +1,70 @@
+import numpy as np
+
+from studio.app.common.core.logger import AppLogger
+from studio.app.common.dataclass.image import ImageData
+from studio.app.optinist.dataclass.fluo import FluoData
+from studio.app.optinist.dataclass.iscell import IscellData
+from studio.app.optinist.dataclass.roi import RoiData
+
+
+def roi_fluo_from_hdf5(
+    cell_img: ImageData,
+    fluo: FluoData,
+    output_dir: str,
+    iscell: IscellData = None,
+    params: dict = None,
+    **kwargs,
+) -> dict():
+    """
+    Processes ROI and fluorescence data, aligning them, and adds enriched metadata.
+
+    Parameters:
+        cell_img (ImageData): Cell image data containing ROI information.
+        fluo (FluoData): Fluorescence data.
+        output_dir (str): Directory to save the output data.
+        iscell (IscellData): Binary data indicating cell regions (optional).
+        params (dict): Optional parameters for additional processing.
+        **kwargs: Additional keyword arguments.
+
+    Returns:
+        dict: A dictionary containing processed ROI and fluorescence data.
+    """
+    logger = AppLogger.get_logger()
+    logger.info("Starting ROI and fluorescence data processing")
+
+    # Base output data
+    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 iscell is None:
+        return {"all_roi": all_roi, "fluorescence": fluorescence}
+
+    # Extract iscell data
+    iscell_data = iscell.data
+
+    # Process ROI types
+    non_cell_roi = RoiData(
+        np.nanmax(cell_img.data[np.where(iscell_data == 0)], axis=0),
+        output_dir=output_dir,
+        file_name="noncell_roi",
+    )
+
+    cell_roi = RoiData(
+        np.nanmax(cell_img.data[np.where(iscell_data != 0)], axis=0),
+        output_dir=output_dir,
+        file_name="cell_roi",
+    )
+
+    # Construct output dictionary
+    output = {
+        "iscell": IscellData(iscell_data, file_name="iscell"),
+        "all_roi": all_roi,
+        "non_cell_roi": non_cell_roi,
+        "cell_roi": cell_roi,
+        "fluorescence": fluorescence,
+    }
+
+    logger.info("Completed ROI and fluorescence data processing")
+    return output