Merge pull request #564 from arayabrain/feature/cell_numbering

Feature/cell numbering

frontend/src/components/Workspace/Visualize/Editor/ImageItemEditor.tsx

@@ -35,6 +35,7 @@ import {
   selectImageItemRoiAlpha,
   selectImageItemFilePath,
   selectImageItemAlpha,
+  selectImageItemShowRoiLabels,
 } from "store/slice/VisualizeItem/VisualizeItemSelectors"
 import {
   setImageItemShowGrid,
@@ -48,6 +49,7 @@ import {
   resetImageActiveIndex,
   setImageItemRoiAlpha,
   setImageItemAlpha,
+  setImageItemShowRoiLabels,
 } from "store/slice/VisualizeItem/VisualizeItemSlice"
 import { ColorType } from "store/slice/VisualizeItem/VisualizeItemType"
 import { selectCurrentWorkspaceId } from "store/slice/Workspace/WorkspaceSelector"
@@ -71,6 +73,7 @@ export const ImageItemEditor: FC = () => {
         <ShowLine />
         <ShowGrid />
         <ShowScale />
+        <ShowRoiLabels />
         <Zsmooth />
         <Grid container component="label" alignItems="center">
           <Grid item xs={8}>
@@ -225,6 +228,24 @@ const RoiAlpha: FC = () => {
   )
 }
 
+const ShowRoiLabels: FC = () => {
+  const itemId = useContext(SelectedItemIdContext)
+  const showRoiLabels = useSelector(selectImageItemShowRoiLabels(itemId))
+  const dispatch = useDispatch()
+  const toggleChecked = () => {
+    dispatch(
+      setImageItemShowRoiLabels({ itemId, showRoiLabels: !showRoiLabels }),
+    )
+  }
+  return (
+    <ParamSwitch
+      label={"Show ROI labels"}
+      value={showRoiLabels}
+      onChange={toggleChecked}
+    />
+  )
+}
+
 const StartEndIndex: FC = () => {
   const workspaceId = useSelector(selectCurrentWorkspaceId)
   const itemId = useContext(SelectedItemIdContext)

frontend/src/components/Workspace/Visualize/Plot/ImagePlot.tsx

@@ -20,6 +20,7 @@ import {
   PlotData,
   PlotMouseEvent,
   PlotSelectionEvent,
+  Annotations,
 } from "plotly.js"
 
 import { Button, LinearProgress, TextField, Typography } from "@mui/material"
@@ -77,6 +78,7 @@ import {
   selectImageItemAlpha,
   selectRoiItemOutputKeys,
   selectVisualizeItems,
+  selectImageItemShowRoiLabels,
 } from "store/slice/VisualizeItem/VisualizeItemSelectors"
 import {
   incrementImageActiveIndex,
@@ -227,6 +229,7 @@ const ImagePlotChart = memo(function ImagePlotChart({
   const [startDragAddRoi, setStartDragAddRoi] = useState(false)
   const [action, setAction] = useState("")
   const [positionDrag, setChangeSize] = useState<PositionDrag | undefined>()
+  const showRoiLabels = useSelector(selectImageItemShowRoiLabels(itemId))
 
   const outputKey: string | null = useSelector(selectRoiItemOutputKeys(itemId))
 
@@ -300,7 +303,7 @@ const ImagePlotChart = memo(function ImagePlotChart({
         z: roiDataState,
         type: "heatmap",
         name: "roi",
-        hovertemplate: action === ADD_ROI ? "none" : "cell id: %{z}",
+        hovertemplate: action === ADD_ROI ? "none" : "ROI: %{z}",
         // hoverinfo: isAddRoi || pointClick.length ? "none" : undefined,
         colorscale: [...Array(timeDataMaxIndex + 1)].map((_, i) => {
           const new_i = Math.floor(((i % 10) * 10 + i / 10) % 100)
@@ -389,6 +392,57 @@ const ImagePlotChart = memo(function ImagePlotChart({
       dispatch(selectingImageArea({ itemId, range: event.range }))
     }
   })
+
+  const roiLabels = useMemo(() => {
+    if (!showRoiLabels) return []
+    const labels: Annotations[] = []
+    const seen = new Set()
+
+    roiDataState.forEach((row, _y) => {
+      row.forEach((value, _x) => {
+        if (value !== null && !seen.has(value)) {
+          seen.add(value)
+          const points = {
+            x: [] as number[],
+            y: [] as number[],
+            count: 0,
+          }
+          roiDataState.forEach((r, yi) => {
+            r.forEach((v, xi) => {
+              if (v === value) {
+                points.x.push(xi)
+                points.y.push(yi)
+                points.count++
+              }
+            })
+          })
+
+          const centerX = points.x.reduce((a, b) => a + b, 0) / points.count
+          const centerY = points.y.reduce((a, b) => a + b, 0) / points.count
+
+          const annotation: Partial<Annotations> = {
+            x: centerX,
+            y: centerY,
+            text: `${value}`,
+            xref: "x",
+            yref: "y",
+            showarrow: false,
+            font: {
+              color: "black", // Black text
+              size: 10,
+              weight: 700, // Bold text
+            },
+            bgcolor: "rgba(255, 255, 255, 0.6)", // Soft white semi-transparent background (60% opacity)
+            borderpad: 0.5, // Padding around the text
+          }
+
+          labels.push(annotation as Annotations)
+        }
+      })
+    })
+    return labels
+  }, [roiDataState, showRoiLabels])
+
   const layout = useMemo(
     () => ({
       title: {
@@ -412,6 +466,7 @@ const ImagePlotChart = memo(function ImagePlotChart({
         autotick: true,
         ticks: "",
         showticklabels: showticklabels,
+        annotations: roiLabels,
       },
       yaxis: {
         title: meta?.ylabel,
@@ -420,10 +475,11 @@ const ImagePlotChart = memo(function ImagePlotChart({
         showgrid: showgrid,
         showline: showline,
         zeroline: false,
-        autotick: true, // todo
+        autotick: true,
         ticks: "",
-        showticklabels: showticklabels, // todo
+        showticklabels: showticklabels,
       },
+      annotations: roiLabels,
     }),
     //eslint-disable-next-line react-hooks/exhaustive-deps
     [
@@ -435,6 +491,7 @@ const ImagePlotChart = memo(function ImagePlotChart({
       height,
       selectMode,
       action,
+      roiLabels,
     ],
   )
 
@@ -709,8 +766,8 @@ const ImagePlotChart = memo(function ImagePlotChart({
                   action === DELETE_ROI
                     ? "#F84E1B"
                     : action === MERGE_ROI
-                    ? "#6619A9"
-                    : "default",
+                      ? "#6619A9"
+                      : "default",
                 display: "flex",
                 gap: 1,
                 textDecoration: "none",

frontend/src/components/Workspace/Visualize/Plot/RoiPlot.tsx

@@ -92,6 +92,7 @@ const RoiPlotImple = memo(function RoiPlotImple() {
         // zsmooth: zsmooth, // ['best', 'fast', false]
         zsmooth: false,
         showlegend: true,
+        hovertemplate: "ROI: %{z}",
       },
     ],
     [imageData, colorscale],

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

@@ -608,3 +608,13 @@ export const selectImageItemRangeUnit =
       throw new Error("invalid VisualaizeItemType")
     }
   }
+
+export const selectImageItemShowRoiLabels =
+  (itemId: number) => (state: RootState) => {
+    const item = selectVisualizeItemById(itemId)(state)
+    if (isImageItem(item)) {
+      return item.showRoiLabels
+    } else {
+      throw new Error("invalid VisualaizeItemType")
+    }
+  }

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

@@ -80,6 +80,7 @@ const imageItemInitialValue: ImageItem = {
   roiItem: null,
   roiAlpha: 1.0,
   duration: 500,
+  showRoiLabels: false,
 }
 const timeSeriesItemInitialValue: TimeSeriesItem = {
   ...displayDataCommonInitialValue,
@@ -857,6 +858,18 @@ export const visualaizeItemSlice = createSlice({
         targetItem.selectedIndex = action.payload.selectedIndex
       }
     },
+    setImageItemShowRoiLabels: (
+      state,
+      action: PayloadAction<{
+        itemId: number
+        showRoiLabels: boolean
+      }>,
+    ) => {
+      const targetItem = state.items[action.payload.itemId]
+      if (isImageItem(targetItem)) {
+        targetItem.showRoiLabels = action.payload.showRoiLabels
+      }
+    },
   },
   extraReducers: (builder) => {
     builder
@@ -1025,6 +1038,7 @@ export const {
   setHistogramItemBins,
   setLineItemSelectedIndex,
   setPolartemItemSelectedIndex,
+  setImageItemShowRoiLabels,
   resetAllOrderList,
   reset,
 } = visualaizeItemSlice.actions

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

@@ -78,6 +78,7 @@ export interface ImageItem extends DisplayDataItemBaseType {
   roiAlpha: number
   duration: number
   clickedDataId?: string
+  showRoiLabels: boolean
 }
 
 export interface TimeSeriesItem extends DisplayDataItemBaseType {

studio/app/optinist/wrappers/caiman/cnmf.py

@@ -31,10 +31,10 @@ def get_roi(A, roi_thr, thr_method, swap_dim, dims):
         # we compute the cumulative sum of the energy of the Ath component
         # that has been ordered from least to highest
         patch_data = A.data[A.indptr[i] : A.indptr[i + 1]]
-        indx = np.argsort(patch_data)[::-1]
+        idx = np.argsort(patch_data)[::-1]
 
         if thr_method == "nrg":
-            cumEn = np.cumsum(patch_data[indx] ** 2)
+            cumEn = np.cumsum(patch_data[idx] ** 2)
             if len(cumEn) == 0:
                 pars = dict(
                     coordinates=np.array([]),
@@ -48,7 +48,7 @@ def get_roi(A, roi_thr, thr_method, swap_dim, dims):
                 cumEn /= cumEn[-1]
                 Bvec = np.ones(d)
                 # we put it in a similar matrix
-                Bvec[A.indices[A.indptr[i] : A.indptr[i + 1]][indx]] = cumEn
+                Bvec[A.indices[A.indptr[i] : A.indptr[i + 1]][idx]] = cumEn
         else:
             Bvec = np.zeros(d)
             Bvec[A.indices[A.indptr[i] : A.indptr[i + 1]]] = (