Consider splits and merges in tdating (#349)

* Ignore 0 in cell match

Since 0 in labels means that no cell was identified in that pixel, we need to
ignore 0 when matching. Otherwise we could have a situation where e.g the
cell overlaps 0.55 with 0 and 0.45 with some cell and it would end up unmatched
(`ID_coverage` would be 0 and a new track would be initialized)

* Get required match overlap frac as parameter

* Store information about splits

If the advected cell overlaps > 10% with more than one cell at next timestep, consider
the advected cell as a split cell. Store information of which IDs the cell split to.
Also for cells at current timestep, mark cells that resulted from splits

* Store information about merges

If the cell at current timestep is overlapped > 10% by more than one advected cell,
consider it merged and store IDs of previous cells.
Also mark cells from previous timestep is they will merge at next timestep.

* Add columns to cell dataframes

* Make splits/merges output optional

* Add options to specify fractions required for matching/splitting/merging

* Update tests to account for split/merge output in tdating

* Fix unused variables code check

* Fix match_frac argument in tracking

* Refactor to avoid chained assignment warnings in pandas

* Add short example

---------

Co-authored-by: Daniele Nerini <daniele.nerini@gmail.com>

Author: ritvje

examples/thunderstorm_detection_and_tracking.py

@@ -90,6 +90,17 @@
 # Properties of one of the identified cells:
 print(cells_id.iloc[0])
 
+###############################################################################
+# Optionally, one can also ask to consider splits and merges of thunderstorm cells.
+# A cell at time t is considered to split if it will verlap more than 10% with more than
+# one cell at time t+1. Conversely, a cell is considered to be a merge, if more
+# than one cells fron time t will overlap more than 10% with it.
+
+cells_id, labels = tstorm_detect.detection(
+    input_image, time=time, output_splits_merges=True
+)
+print(cells_id.iloc[0])
+
 ###############################################################################
 # Example of thunderstorm tracking over a timeseries
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

pysteps/feature/tstorm.py

@@ -58,6 +58,7 @@ def detection(
     minmax=41,
     mindis=10,
     output_feat=False,
+    output_splits_merges=False,
     time="000000000",
 ):
     """
@@ -93,6 +94,10 @@ def detection(
         smaller distance will be merged. The default is 10 km.
     output_feat: bool, optional
         Set to True to return only the cell coordinates.
+    output_split_merge: bool, optional
+        Set to True to return additional columns in the dataframe for describing the
+        splitting and merging of cells. Note that columns are initialized with None,
+        and the information needs to be analyzed while tracking.
     time: string, optional
         Date and time as string. Used to label time in the resulting dataframe.
         The default is '000000000'.
@@ -166,7 +171,15 @@ def detection(
 
     areas, lines = breakup(input_image, np.nanmin(input_image.flatten()), maxima_dis)
 
-    cells_id, labels = get_profile(areas, binary, input_image, loc_max, time, minref)
+    cells_id, labels = get_profile(
+        areas,
+        binary,
+        input_image,
+        loc_max,
+        time,
+        minref,
+        output_splits_merges=output_splits_merges,
+    )
 
     if max_num_features is not None:
         idx = np.argsort(cells_id.area.to_numpy())[::-1]
@@ -225,10 +238,12 @@ def longdistance(loc_max, mindis):
     return new_max
 
 
-def get_profile(areas, binary, ref, loc_max, time, minref):
+def get_profile(areas, binary, ref, loc_max, time, minref, output_splits_merges=False):
     """
     This function returns the identified cells in a dataframe including their x,y
     locations, location of their maxima, maximum reflectivity and contours.
+    Optionally, the dataframe can include columns for storing information regarding
+    splitting and merging of cells.
     """
     cells = areas * binary
     cell_labels = cells[loc_max]
@@ -255,11 +270,47 @@ def get_profile(areas, binary, ref, loc_max, time, minref):
                 "area": len(x),
             }
         )
+        if output_splits_merges:
+            cells_id[-1].update(
+                {
+                    "splitted": None,
+                    "split_IDs": None,
+                    "merged": None,
+                    "merged_IDs": None,
+                    "results_from_split": None,
+                    "will_merge": None,
+                }
+            )
         labels[cells == cell_labels[n]] = this_id
+
+    columns = [
+        "ID",
+        "time",
+        "x",
+        "y",
+        "cen_x",
+        "cen_y",
+        "max_ref",
+        "cont",
+        "area",
+    ]
+    if output_splits_merges:
+        columns.extend(
+            [
+                "splitted",
+                "split_IDs",
+                "merged",
+                "merged_IDs",
+                "results_from_split",
+                "will_merge",
+            ]
+        )
     cells_id = pd.DataFrame(
         data=cells_id,
         index=range(len(cell_labels)),
-        columns=["ID", "time", "x", "y", "cen_x", "cen_y", "max_ref", "cont", "area"],
+        columns=columns,
     )
-
+    if output_splits_merges:
+        cells_id["split_IDs"] = cells_id["split_IDs"].astype("object")
+        cells_id["merged_IDs"] = cells_id["merged_IDs"].astype("object")
     return cells_id, labels

pysteps/tests/test_feature_tstorm.py

@@ -10,20 +10,29 @@
 except ModuleNotFoundError:
     pass
 
-arg_names = ("source", "output_feat", "dry_input", "max_num_features")
+arg_names = (
+    "source",
+    "output_feat",
+    "dry_input",
+    "max_num_features",
+    "output_split_merge",
+)
 
 arg_values = [
-    ("mch", False, False, None),
-    ("mch", False, False, 5),
-    ("mch", True, False, None),
-    ("mch", True, False, 5),
-    ("mch", False, True, None),
-    ("mch", False, True, 5),
+    ("mch", False, False, None, False),
+    ("mch", False, False, 5, False),
+    ("mch", True, False, None, False),
+    ("mch", True, False, 5, False),
+    ("mch", False, True, None, False),
+    ("mch", False, True, 5, False),
+    ("mch", False, False, None, True),
 ]
 
 
 @pytest.mark.parametrize(arg_names, arg_values)
-def test_feature_tstorm_detection(source, output_feat, dry_input, max_num_features):
+def test_feature_tstorm_detection(
+    source, output_feat, dry_input, max_num_features, output_split_merge
+):
     pytest.importorskip("skimage")
     pytest.importorskip("pandas")
 
@@ -36,7 +45,11 @@ def test_feature_tstorm_detection(source, output_feat, dry_input, max_num_featur
 
     time = "000"
     output = detection(
-        input, time=time, output_feat=output_feat, max_num_features=max_num_features
+        input,
+        time=time,
+        output_feat=output_feat,
+        max_num_features=max_num_features,
+        output_splits_merges=output_split_merge,
     )
 
     if output_feat:
@@ -45,6 +58,40 @@ def test_feature_tstorm_detection(source, output_feat, dry_input, max_num_featur
         assert output.shape[1] == 2
         if max_num_features is not None:
             assert output.shape[0] <= max_num_features
+    elif output_split_merge:
+        assert isinstance(output, tuple)
+        assert len(output) == 2
+        assert isinstance(output[0], DataFrame)
+        assert isinstance(output[1], np.ndarray)
+        if max_num_features is not None:
+            assert output[0].shape[0] <= max_num_features
+        assert output[0].shape[1] == 15
+        assert list(output[0].columns) == [
+            "ID",
+            "time",
+            "x",
+            "y",
+            "cen_x",
+            "cen_y",
+            "max_ref",
+            "cont",
+            "area",
+            "splitted",
+            "split_IDs",
+            "merged",
+            "merged_IDs",
+            "results_from_split",
+            "will_merge",
+        ]
+        assert (output[0].time == time).all()
+        assert output[1].ndim == 2
+        assert output[1].shape == input.shape
+        if not dry_input:
+            assert output[0].shape[0] > 0
+            assert sorted(list(output[0].ID)) == sorted(list(np.unique(output[1]))[1:])
+        else:
+            assert output[0].shape[0] == 0
+            assert output[1].sum() == 0
     else:
         assert isinstance(output, tuple)
         assert len(output) == 2

pysteps/tests/test_tracking_tdating.py

@@ -7,22 +7,24 @@
 from pysteps.utils import to_reflectivity
 from pysteps.tests.helpers import get_precipitation_fields
 
-arg_names = ("source", "dry_input")
+arg_names = ("source", "dry_input", "output_splits_merges")
 
 arg_values = [
-    ("mch", False),
-    ("mch", False),
-    ("mch", True),
+    ("mch", False, False),
+    ("mch", False, False),
+    ("mch", True, False),
+    ("mch", False, True),
 ]
 
-arg_names_multistep = ("source", "len_timesteps")
+arg_names_multistep = ("source", "len_timesteps", "output_splits_merges")
 arg_values_multistep = [
-    ("mch", 6),
+    ("mch", 6, False),
+    ("mch", 6, True),
 ]
 
 
 @pytest.mark.parametrize(arg_names_multistep, arg_values_multistep)
-def test_tracking_tdating_dating_multistep(source, len_timesteps):
+def test_tracking_tdating_dating_multistep(source, len_timesteps, output_splits_merges):
     pytest.importorskip("skimage")
 
     input_fields, metadata = get_precipitation_fields(
@@ -37,6 +39,7 @@ def test_tracking_tdating_dating_multistep(source, len_timesteps):
         input_fields[0 : len_timesteps // 2],
         timelist[0 : len_timesteps // 2],
         mintrack=1,
+        output_splits_merges=output_splits_merges,
     )
     # Second half of timesteps
     tracks_2, cells, _ = dating(
@@ -46,6 +49,7 @@ def test_tracking_tdating_dating_multistep(source, len_timesteps):
         start=2,
         cell_list=cells,
         label_list=labels,
+        output_splits_merges=output_splits_merges,
     )
 
     # Since we are adding cells, number of tracks should increase
@@ -67,7 +71,7 @@ def test_tracking_tdating_dating_multistep(source, len_timesteps):
 
 
 @pytest.mark.parametrize(arg_names, arg_values)
-def test_tracking_tdating_dating(source, dry_input):
+def test_tracking_tdating_dating(source, dry_input, output_splits_merges):
     pytest.importorskip("skimage")
     pandas = pytest.importorskip("pandas")
 
@@ -80,7 +84,13 @@ def test_tracking_tdating_dating(source, dry_input):
 
     timelist = metadata["timestamps"]
 
-    output = dating(input, timelist, mintrack=1)
+    cell_column_length = 9
+    if output_splits_merges:
+        cell_column_length = 15
+
+    output = dating(
+        input, timelist, mintrack=1, output_splits_merges=output_splits_merges
+    )
 
     # Check output format
     assert isinstance(output, tuple)
@@ -92,12 +102,12 @@ def test_tracking_tdating_dating(source, dry_input):
     assert len(output[2]) == input.shape[0]
     assert isinstance(output[1][0], pandas.DataFrame)
     assert isinstance(output[2][0], np.ndarray)
-    assert output[1][0].shape[1] == 9
+    assert output[1][0].shape[1] == cell_column_length
     assert output[2][0].shape == input.shape[1:]
     if not dry_input:
         assert len(output[0]) > 0
         assert isinstance(output[0][0], pandas.DataFrame)
-        assert output[0][0].shape[1] == 9
+        assert output[0][0].shape[1] == cell_column_length
     else:
         assert len(output[0]) == 0
         assert output[1][0].shape[0] == 0