Merge pull request #569 from oist/hotfix/fix-roi-edit

fix errors on ROI edit
oist · Sep 29, 2023 · 3db78b0 · 3db78b0
2 parents 6bd688c + cf97b3a
commit 3db78b0
Show file tree

Hide file tree

Showing 17 changed files with 133 additions and 80 deletions.
diff --git a/frontend/src/components/Workspace/Visualize/Plot/ImagePlot.tsx b/frontend/src/components/Workspace/Visualize/Plot/ImagePlot.tsx
@@ -258,9 +258,9 @@ const ImagePlotChart = React.memo<{
         name: 'roi',
         hovertemplate: isAddRoi ? 'none' : 'cell id: %{z}',
         // hoverinfo: isAddRoi || pointClick.length ? 'none' : undefined,
-        colorscale: [...Array(timeDataMaxIndex)].map((_, i) => {
+        colorscale: [...Array(timeDataMaxIndex + 1)].map((_, i) => {
           const new_i = Math.floor(((i % 10) * 10 + i / 10) % 100)
-          const offset: number = i / (timeDataMaxIndex - 1)
+          const offset: number = i / timeDataMaxIndex
           const rgba = colorscaleRoi[new_i]
           const hex = rgba2hex(rgba, roiAlpha)
           return [offset, hex]
@@ -356,7 +356,7 @@ const ImagePlotChart = React.memo<{
         z: Number(point.z),
       })
     }
-    if (point.curveNumber >= 1 && point.z > 0) {
+    if (point.curveNumber >= 1 && point.z >= 0) {
       dispatch(
         setImageItemClikedDataId({
           itemId,
@@ -367,12 +367,12 @@ const ImagePlotChart = React.memo<{
   }
 
   const setSelectRoi = (point: PointClick) => {
-    if (!point.z) return
+    if (typeof point.z !== 'number' || point.z === -1) return
     const newPoints = [...pointClick, point]
     const newRoi = roiDataState.map((roi) => {
       return roi.map((element) => {
         if (newPoints.some((p) => p.z === element)) {
-          return 0
+          return -1
         }
         return element
       })
@@ -480,7 +480,7 @@ const ImagePlotChart = React.memo<{
     dispatch(resetAllOrderList())
     try {
       await mergeRoiApi(roiFilePath, {
-        ids: pointClick.map((point) => point.z - 1),
+        ids: pointClick.map((point) => point.z),
       })
     } catch {}
     setLoadingApi(false)
@@ -495,7 +495,7 @@ const ImagePlotChart = React.memo<{
     dispatch(resetAllOrderList())
     try {
       await deleteRoiApi(roiFilePath, {
-        ids: pointClick.map((point) => point.z - 1),
+        ids: pointClick.map((point) => point.z),
       })
     } catch {}
     setLoadingApi(false)

diff --git a/frontend/src/components/Workspace/Visualize/Plot/TimeSeriesPlot.tsx b/frontend/src/components/Workspace/Visualize/Plot/TimeSeriesPlot.tsx
@@ -130,7 +130,7 @@ const TimeSeriesPlotImple = React.memo(() => {
     return Object.fromEntries(
       dataKeys.map((key) => {
       let y = newDataXrange.map((x) => newTimeSeriesData[key]?.[x])
-      const i = Number(key) - 1
+      const i = Number(key)
       const new_i = Math.floor((i % 10) * 10 + i / 10) % 100
       if (drawOrderList.includes(key) && offset) {
         const activeIdx: number = drawOrderList.findIndex((v) => v === key)

diff --git a/studio/app/common/core/rules/runner.py b/studio/app/common/core/rules/runner.py
@@ -114,13 +114,10 @@ def save_all_nwb(cls, save_path, all_nwbfile):
         timeout = 30  # ロック取得のタイムアウト時間（秒）
         with FileLock(lock_path, timeout=timeout):
             # ロックが取得できたら、ファイルに書き込みを行う
-            try:
-                if os.path.exists(save_path):
-                    overwrite_nwbfile(save_path, nwbconfig)
-                else:
-                    save_nwb(save_path, input_nwbfile, nwbconfig)
-            except Exception as e:
-                print(e)
+            if os.path.exists(save_path):
+                overwrite_nwbfile(save_path, nwbconfig)
+            else:
+                save_nwb(save_path, input_nwbfile, nwbconfig)
 
     @classmethod
     def execute_function(cls, path, params, nwb_params, output_dir, input_info):

diff --git a/studio/app/optinist/core/edit_ROI/edit_ROI.py b/studio/app/optinist/core/edit_ROI/edit_ROI.py
@@ -107,10 +107,7 @@ def excute(cls, config):
                 last_output_info = cls.__update_pickle_for_roi_edition(
                     last_output_path, func_name, output_info
                 )
-                rule_type = os.path.splitext(os.path.basename(last_output_path))[0]
-                whole_nwb_path = join_filepath(
-                    [workflow_dirpath, f"whole_{rule_type}.nwb"]
-                )
+                whole_nwb_path = join_filepath([workflow_dirpath, "whole.nwb"])
 
                 Runner.save_all_nwb(whole_nwb_path, last_output_info["nwbfile"])
 
@@ -122,7 +119,7 @@ def excute(cls, config):
                 v.save_json(node_dirpath)
 
             if k == "nwbfile":
-                nwb_files = glob(join_filepath([node_dirpath, "*.nwb"]))
+                nwb_files = glob(join_filepath([node_dirpath, "[!tmp_]*.nwb"]))
                 if len(nwb_files) > 0:
                     overwrite_nwb(v, node_dirpath, os.path.basename(nwb_files[0]))
 

diff --git a/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/add_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/add_roi.py
@@ -6,6 +6,9 @@
 def execute_add_ROI(node_dirpath, posx, posy, sizex, sizey):
     import numpy as np
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start caiman add_roi:", function_id)
+
     # load data
     cnmf_data = np.load(f"{node_dirpath}/caiman_cnmf.npy", allow_pickle=True).item()
     is_cell = cnmf_data.get("is_cell")
@@ -48,7 +51,7 @@ def execute_add_ROI(node_dirpath, posx, posy, sizex, sizey):
             file_name="cell_roi",
         ),
         "cnmf_data": CaimanCnmfData(cnmf_data),
-        "nwbfile": set_nwbfile(cnmf_data),
+        "nwbfile": set_nwbfile(cnmf_data, function_id),
     }
 
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/delete_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/delete_roi.py
@@ -5,6 +5,9 @@
 def excute_delete_roi(node_dirpath, ids):
     import numpy as np
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start caiman delete_roi:", function_id)
+
     # load data
     cnmf_data = np.load(f"{node_dirpath}/caiman_cnmf.npy", allow_pickle=True).item()
     is_cell = cnmf_data.get("is_cell")
@@ -30,6 +33,6 @@ def excute_delete_roi(node_dirpath, ids):
             file_name="cell_roi",
         ),
         "cnmf_data": CaimanCnmfData(cnmf_data),
-        "nwbfile": set_nwbfile(cnmf_data),
+        "nwbfile": set_nwbfile(cnmf_data, function_id),
     }
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/merge_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/merge_roi.py
@@ -5,6 +5,9 @@
 def execute_merge_roi(node_dirpath: str, ids: list):
     import numpy as np
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start caiman merge_roi:", function_id)
+
     # load data
     cnmf_data = np.load(f"{node_dirpath}/caiman_cnmf.npy", allow_pickle=True).item()
     is_cell = cnmf_data.get("is_cell")
@@ -49,7 +52,7 @@ def execute_merge_roi(node_dirpath: str, ids: list):
             file_name="cell_roi",
         ),
         "cnmf_data": CaimanCnmfData(cnmf_data),
-        "nwbfile": set_nwbfile(cnmf_data),
+        "nwbfile": set_nwbfile(cnmf_data, function_id),
     }
 
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/utils.py b/studio/app/optinist/core/edit_ROI/wrappers/caiman_edit_roi/utils.py
@@ -1,7 +1,7 @@
 from studio.app.optinist.core.nwb.nwb import NWBDATASET
 
 
-def set_nwbfile(cnmf_data):
+def set_nwbfile(cnmf_data, function_id):
     im = cnmf_data.get("im")
     is_cell = cnmf_data.get("is_cell")
     fluorescence = cnmf_data.get("fluorescence")
@@ -16,11 +16,11 @@ def set_nwbfile(cnmf_data):
         kargs["image_mask"] = im[i, :]
         roi_list.append(kargs)
 
-    nwbfile[NWBDATASET.ROI] = {"roi_list": roi_list}
+    nwbfile[NWBDATASET.ROI] = {function_id: roi_list}
 
     # iscellを追加
     nwbfile[NWBDATASET.COLUMN] = {
-        "roi_column": {
+        function_id: {
             "name": "iscell",
             "discription": "two columns - iscell & probcell",
             "data": is_cell,
@@ -30,20 +30,24 @@ def set_nwbfile(cnmf_data):
     # Fluorescence
 
     nwbfile[NWBDATASET.FLUORESCENCE] = {
-        "RoiResponseSeries": {
-            "table_name": "ROIs",
-            "region": list(range(n_cells)),
-            "name": "RoiResponseSeries",
-            "data": fluorescence.T,
-            "unit": "lumens",
-        },
+        function_id: {
+            "Fluorescence": {
+                "table_name": "ROIs",
+                "region": list(range(n_cells)),
+                "name": "Fluorescence",
+                "data": fluorescence.T,
+                "unit": "lumens",
+            },
+        }
     }
 
     # NWB追加
     nwbfile[NWBDATASET.POSTPROCESS] = {
-        "add_roi": cnmf_data.get("add_roi", []),
-        "delete_roi": cnmf_data.get("delete_roi", []),
-        "merge_roi": cnmf_data.get("merge_roi", []),
+        function_id: {
+            "add_roi": cnmf_data.get("add_roi", []),
+            "delete_roi": cnmf_data.get("delete_roi", []),
+            "merge_roi": cnmf_data.get("merge_roi", []),
+        }
     }
 
     return nwbfile
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/add_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/add_roi.py
@@ -8,6 +8,9 @@
 def execute_add_ROI(node_dirpath, posx, posy, sizex, sizey):
     import numpy as np
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start lccd add_roi:", function_id)
+
     lccd_data = np.load(
         os.path.join(node_dirpath, "lccd.npy"), allow_pickle=True
     ).item()
@@ -67,7 +70,9 @@ def execute_add_ROI(node_dirpath, posx, posy, sizex, sizey):
         ),
         "fluorescence": FluoData(timeseries, file_name="fluorescence"),
         "dff": FluoData(timeseries_dff, file_name="dff"),
-        "nwbfile": set_nwbfile(lccd_data, roi_list, fluorescence=timeseries),
+        "nwbfile": set_nwbfile(
+            lccd_data, roi_list, function_id, fluorescence=timeseries
+        ),
     }
 
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/delete_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/delete_roi.py
@@ -7,6 +7,9 @@
 def excute_delete_roi(node_dirpath, ids):
     import numpy as np
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start lccd delete_roi:", function_id)
+
     lccd_data = np.load(
         os.path.join(node_dirpath, "lccd.npy"), allow_pickle=True
     ).item()
@@ -67,7 +70,7 @@ def excute_delete_roi(node_dirpath, ids):
         ),
         "fluorescence": FluoData(timeseries, file_name="fluorescence"),
         "dff": FluoData(timeseries_dff, file_name="dff"),
-        "nwbfile": set_nwbfile(lccd_data, roi_list),
+        "nwbfile": set_nwbfile(lccd_data, roi_list, function_id),
     }
 
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/merge_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/merge_roi.py
@@ -7,6 +7,9 @@
 def execute_merge_roi(node_dirpath, ids):
     import numpy as np
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start lccd merge_roi:", function_id)
+
     lccd_data = np.load(
         os.path.join(node_dirpath, "lccd.npy"), allow_pickle=True
     ).item()
@@ -73,7 +76,9 @@ def execute_merge_roi(node_dirpath, ids):
         ),
         "fluorescence": FluoData(timeseries, file_name="fluorescence"),
         "dff": FluoData(timeseries_dff, file_name="dff"),
-        "nwbfile": set_nwbfile(lccd_data, roi_list, fluorescence=timeseries),
+        "nwbfile": set_nwbfile(
+            lccd_data, roi_list, function_id, fluorescence=timeseries
+        ),
     }
 
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/utils.py b/studio/app/optinist/core/edit_ROI/wrappers/lccd_edit_roi/utils.py
@@ -1,23 +1,26 @@
 from studio.app.optinist.core.nwb.nwb import NWBDATASET
 
 
-def set_nwbfile(lccd_data, roi_list, fluorescence=None):
+def set_nwbfile(lccd_data, roi_list, function_id, fluorescence=None):
     nwbfile = {}
 
-    nwbfile[NWBDATASET.ROI] = {"roi_list": roi_list}
+    nwbfile[NWBDATASET.ROI] = {function_id: roi_list}
 
     if fluorescence is not None:
-        nwbfile[NWBDATASET.FLUORESCENCE] = {}
-        nwbfile[NWBDATASET.FLUORESCENCE]["Fluorescence"] = {
-            "table_name": "Fluorescence",
-            "region": list(range(len(fluorescence))),
-            "name": "Fluorescence",
-            "data": fluorescence,
-            "unit": "lumens",
+        nwbfile[NWBDATASET.FLUORESCENCE] = {
+            function_id: {
+                "Fluorescence": {
+                    "table_name": "ROIs",
+                    "region": list(range(len(fluorescence))),
+                    "name": "Fluorescence",
+                    "data": fluorescence,
+                    "unit": "lumens",
+                }
+            }
         }
 
     nwbfile[NWBDATASET.COLUMN] = {
-        "roi_column": {
+        function_id: {
             "name": "iscell",
             "discription": "two columns - iscell & probcell",
             "data": lccd_data.get("is_cell"),
@@ -26,9 +29,11 @@ def set_nwbfile(lccd_data, roi_list, fluorescence=None):
 
     # NWB追加
     nwbfile[NWBDATASET.POSTPROCESS] = {
-        "add_roi": lccd_data.get("add_roi", []),
-        "delete_roi": lccd_data.get("delete_roi", []),
-        "merge_roi": lccd_data.get("merge_roi", []),
+        function_id: {
+            "add_roi": lccd_data.get("add_roi", []),
+            "delete_roi": lccd_data.get("delete_roi", []),
+            "merge_roi": lccd_data.get("merge_roi", []),
+        }
     }
 
     return nwbfile
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/suite2p_edit_roi/add_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/suite2p_edit_roi/add_roi.py
@@ -13,6 +13,9 @@
 def execute_add_ROI(node_dirpath, posx, posy, sizex, sizey):
     from suite2p import ROI
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start suite2p add_roi:", function_id)
+
     ops = np.load(os.path.join(node_dirpath, "suite2p.npy"), allow_pickle=True).item()
     iscell = ops.get("iscell")
     stat = ops.get("stat")
@@ -59,6 +62,6 @@ def execute_add_ROI(node_dirpath, posx, posy, sizex, sizey):
         "cell_roi": RoiData(
             np.nanmax(im[iscell], axis=0), output_dir=node_dirpath, file_name="cell_roi"
         ),
-        "nwbfile": set_nwbfile(ops),
+        "nwbfile": set_nwbfile(ops, function_id),
     }
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/suite2p_edit_roi/delete_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/suite2p_edit_roi/delete_roi.py
@@ -9,6 +9,9 @@
 
 
 def excute_delete_roi(node_dirpath, ids):
+    function_id = node_dirpath.split("/")[-1]
+    print("start suite2p delete_roi:", function_id)
+
     ops = np.load(os.path.join(node_dirpath, "suite2p.npy"), allow_pickle=True).item()
     iscell = ops.get("iscell")
     delete_roi = ops.get("delete_roi", [])
@@ -32,7 +35,7 @@ def excute_delete_roi(node_dirpath, ids):
         "cell_roi": RoiData(
             np.nanmax(im[iscell], axis=0), output_dir=node_dirpath, file_name="cell_roi"
         ),
-        "nwbfile": set_nwbfile(ops),
+        "nwbfile": set_nwbfile(ops, function_id),
     }
 
     return info
diff --git a/studio/app/optinist/core/edit_ROI/wrappers/suite2p_edit_roi/merge_roi.py b/studio/app/optinist/core/edit_ROI/wrappers/suite2p_edit_roi/merge_roi.py
@@ -12,6 +12,9 @@ def execute_merge_roi(node_dirpath, ids):
     from suite2p import ROI
     from suite2p.detection.stats import median_pix, roi_stats
 
+    function_id = node_dirpath.split("/")[-1]
+    print("start suite2p merge_roi:", function_id)
+
     ops = np.load(os.path.join(node_dirpath, "suite2p.npy"), allow_pickle=True).item()
     iscell = ops.get("iscell")
     stat_orig = ops.get("stat")
@@ -127,6 +130,6 @@ def execute_merge_roi(node_dirpath, ids):
         "cell_roi": RoiData(
             np.nanmax(im[iscell], axis=0), output_dir=node_dirpath, file_name="cell_roi"
         ),
-        "nwbfile": set_nwbfile(ops),
+        "nwbfile": set_nwbfile(ops, function_id),
     }
     return info