update io_sc.py and single_cell.py: add tmp to sc; refactor prep from…

… single label mask case

livecellx/core/io_sc.py

@@ -8,27 +8,9 @@
 from livecellx.core.sc_key_manager import SingleCellMetaKeyManager
 
 
-# TODO: fix the function below
-def process_scs_from_label_mask(label_mask_dataset, dic_dataset, time, bg_val=0, min_contour_len=10):
-    """process single cells from one label mask. Store labels of single cells in their meta data.
-
-    Parameters
-    ----------
-    label_mask_dataset : _type_
-        _description_
-    dic_dataset : _type_
-        _description_
-    time : _type_
-        _description_
-    bg_val : int, optional
-        _description_, by default 0
-
-    Returns
-    -------
-    _type_
-        _description_
-    """
-    label_mask = label_mask_dataset.get_img_by_time(time)
+def process_scs_from_single_label_mask(
+    label_mask, img_dataset, time, bg_val=0, min_contour_len=10, label_mask_dataset=None
+):
     labels = set(np.unique(label_mask))
     if bg_val in labels:
         labels.remove(bg_val)
@@ -75,7 +57,7 @@ def process_scs_from_label_mask(label_mask_dataset, dic_dataset, time, bg_val=0,
         )  # int important here to get rid of numpy.int64 or numpy.int8, etc, to avoid json dump error
         sc = SingleCellStatic(
             timeframe=time,
-            img_dataset=dic_dataset,
+            img_dataset=img_dataset,
             mask_dataset=label_mask_dataset,
             contour=contour,
         )
@@ -84,6 +66,37 @@ def process_scs_from_label_mask(label_mask_dataset, dic_dataset, time, bg_val=0,
     return _scs
 
 
+# TODO: fix the function below
+def process_scs_from_label_mask(label_mask_dataset, img_dataset, time, bg_val=0, min_contour_len=10):
+    """process single cells from one label mask. Store labels of single cells in their meta data.
+
+    Parameters
+    ----------
+    label_mask_dataset : _type_
+        _description_
+    dic_dataset : _type_
+        _description_
+    time : _type_
+        _description_
+    bg_val : int, optional
+        _description_, by default 0
+
+    Returns
+    -------
+    _type_
+        _description_
+    """
+
+    return process_scs_from_single_label_mask(
+        label_mask_dataset.get_mask(time),
+        img_dataset,
+        time,
+        bg_val=bg_val,
+        min_contour_len=min_contour_len,
+        label_mask_dataset=label_mask_dataset,
+    )
+
+
 def process_mask_wrapper(args):
     return process_scs_from_label_mask(*args)
 

livecellx/core/single_cell.py

@@ -49,6 +49,7 @@ def __init__(
         cache: Optional[Dict[str, object]] = None,  # TODO: now only image crop is cached
         update_mask_dataset_by_contour=False,
         empty_cell=False,
+        tmp=None,
     ) -> None:
         """_summary_
 
@@ -125,6 +126,11 @@ def __init__(
             # self.id = SingleCellStatic.id_generator.__next__()
             self.id = uuid.uuid4()
 
+        if tmp is not None:
+            self.tmp = tmp
+        else:
+            self.tmp = dict()
+
     def __repr__(self) -> str:
         return f"SingleCellStatic(id={self.id}, timeframe={self.timeframe}, bbox={self.bbox})"
 
@@ -1734,3 +1740,12 @@ def filter_boundary_cells(scs: List[SingleCellStatic], dist_to_boundary=30):
         ):
             not_boundary_scs.append(sc)
     return not_boundary_scs
+
+
+def create_label_mask_from_scs(scs: List[SingleCellStatic], labels=None, dtype=np.int32):
+    label_mask = np.zeros(scs[0].get_mask().shape, dtype=dtype)
+    if labels is None:
+        labels = list(range(1, len(scs) + 1))  # Bg label is 0
+    for idx, sc in enumerate(scs):
+        label_mask[sc.get_mask()] = labels[idx]
+    return label_mask