implement split merge logic (#25)

* initial concept implementation

* implement split/merge logic and corresponding plots

* test fix

* test fix attempt 2

* test fix attempt 3

* attempt to ensure consitant ordering across platforms

* change test to normalize clusterids

* pre-sort test data

* add trackid column to test to fix ordering

* allow filtering and remapping from lineagetracker

* update lint

* fix nPrev issue with merge

* fix nprev

* fister small before split merge apply

* update lineage_plot

arcos4py/plotting/__init__.py

@@ -4,6 +4,6 @@
 __email__ = "[email protected]"
 __version__ = '0.2.5'
 
-from ._plotting import NoodlePlot, dataPlots, plotOriginalDetrended, statsPlots
+from ._plotting import LineagePlot, NoodlePlot, dataPlots, plotOriginalDetrended, statsPlots
 
-__all__ = ["plotOriginalDetrended", "dataPlots", "statsPlots", "NoodlePlot"]
+__all__ = ["plotOriginalDetrended", "dataPlots", "statsPlots", "NoodlePlot", "LineagePlot"]

tests/test_event_detection.py

@@ -8,6 +8,7 @@
 from pandas.testing import assert_frame_equal
 
 from arcos4py import ARCOS
+from arcos4py.tools import track_events_dataframe
 
 
 @pytest.fixture
@@ -279,6 +280,34 @@ def test_split_from_2_objects():
     assert_frame_equal(out, df_true, check_like=True)
 
 
+def test_4_colliding_with_allow_merges():
+    """Test colliding event detection on a simple image."""
+    test_df = pd.read_csv('tests/testdata/4obj_merge_allowed.csv')
+    true_df = pd.read_csv('tests/testdata/4obj_merge_allowed_res.csv')
+    # Sort the test data to ensure consistent order
+    test_df = test_df.sort_values(by=['T', 'X', 'Y', 'track_id']).reset_index(drop=True)
+
+    tracked_df, _ = track_events_dataframe(
+        test_df,
+        eps=2,
+        eps_prev=2,
+        min_clustersize=4,
+        n_prev=1,
+        position_columns=['X', 'Y'],
+        frame_column='T',
+        id_column='track_id',
+        allow_merges=True,
+        stability_threshold=1,
+        allow_splits=True,
+    )
+
+    # Sort by relevant columns
+    tracked_df = tracked_df.sort_values(by=['T', 'X', 'Y', 'track_id']).reset_index(drop=True)
+    true_df = true_df.sort_values(by=['T', 'X', 'Y', 'track_id']).reset_index(drop=True)
+
+    assert_frame_equal(tracked_df, true_df, check_dtype=False)
+
+
 def test_cross_2_objects():
     df_in = pd.read_csv('tests/testdata/2objCross_in.csv')
     df_true = pd.read_csv('tests/testdata/2objCross_res.csv')

tests/test_event_detection_pix.py

@@ -35,6 +35,19 @@ def test_1_split():
     assert_array_equal(tracked_img, true_img)
 
 
+def test_1_split_with_splitting_allowed():
+    """Test split event detection on a simple image."""
+    test_img = imread('tests/testdata/pix/1_split.tif')
+    true_img = imread('tests/testdata/pix/1_split_allowed_true.tif')
+    test_img = np.where(test_img == 255, 0, 1)
+    tracked_img, lineage_tracker = track_events_image(
+        test_img, eps=2, eps_prev=2, min_clustersize=4, dims="TXY", allow_splits=True, stability_threshold=2
+    )
+    cluster_history = lineage_tracker.get_cluster_history(2)  # cluster id 2
+    assert_array_equal(tracked_img, true_img)
+    assert_array_equal([1, 2], [i.cluster_id for i in cluster_history[0]])  # compare cluster history of first parent
+
+
 def test_2_colliding():
     """Test colliding event detection on a simple image."""
     test_img = imread('tests/testdata/pix/2_colliding.tif')
@@ -89,6 +102,27 @@ def test_4_colliding():
     assert_array_equal(tracked_img, true_img)
 
 
+def test_4_colliding_with_allow_merges():
+    """Test colliding event detection on a simple image."""
+    test_img = imread('tests/testdata/pix/4_colliding.tif')
+    true_img = imread('tests/testdata/pix/4_colliding_merge_allowed.tif')
+    test_img = np.where(test_img == 255, 0, 1)
+    tracked_img, lineage_tracker = track_events_image(
+        test_img,
+        eps=2,
+        eps_prev=2,
+        min_clustersize=4,
+        n_prev=1,
+        dims="TXY",
+        allow_merges=True,
+        stability_threshold=1,
+        allow_splits=True,
+    )
+    cluster_history = lineage_tracker.get_cluster_history(5)  # cluster id 5, timepoint 7
+    assert_array_equal([1, 5], [i.cluster_id for i in cluster_history[0]])  # compare cluster history of first parent
+    assert_array_equal(tracked_img, true_img)
+
+
 def test_4_colliding_transportaion():
     """Test colliding event detection on a simple image."""
     test_img = imread('tests/testdata/pix/4_colliding.tif')

tests/testdata/4obj_merge_allowed.csv

@@ -0,0 +1,103 @@
+T,X,Y,track_id
+0,0,6,1
+0,6,0,31
+0,6,12,42
+0,12,6,72
+1,0,6,1
+1,1,5,2
+1,1,6,3
+1,1,7,4
+1,5,1,20
+1,5,11,30
+1,6,0,31
+1,6,1,32
+1,6,11,41
+1,6,12,42
+1,7,1,43
+1,7,11,53
+1,11,5,69
+1,11,6,70
+1,11,7,71
+1,12,6,72
+2,1,5,2
+2,1,6,3
+2,1,7,4
+2,2,5,5
+2,2,6,6
+2,2,7,7
+2,5,1,20
+2,5,2,21
+2,5,10,29
+2,5,11,30
+2,6,1,32
+2,6,2,33
+2,6,10,40
+2,6,11,41
+2,7,1,43
+2,7,2,44
+2,7,10,52
+2,7,11,53
+2,10,5,66
+2,10,6,67
+2,10,7,68
+2,11,5,69
+2,11,6,70
+2,11,7,71
+3,2,5,5
+3,2,6,6
+3,2,7,7
+3,3,4,8
+3,3,8,12
+3,4,3,13
+3,4,9,19
+3,5,2,21
+3,5,10,29
+3,6,2,33
+3,6,10,40
+3,7,2,44
+3,7,10,52
+3,8,3,54
+3,8,9,60
+3,9,4,61
+3,9,8,65
+3,10,5,66
+3,10,6,67
+3,10,7,68
+4,3,5,9
+4,3,6,10
+4,3,7,11
+4,4,4,14
+4,4,8,18
+4,5,3,22
+4,5,9,28
+4,6,3,34
+4,6,9,39
+4,7,3,45
+4,7,9,51
+4,8,4,55
+4,8,8,59
+4,9,5,62
+4,9,6,63
+4,9,7,64
+5,3,6,10
+5,4,5,15
+5,4,6,16
+5,4,7,17
+5,5,4,23
+5,5,8,27
+5,6,4,35
+5,6,8,38
+5,7,4,46
+5,7,8,50
+5,8,5,56
+5,8,6,57
+5,8,7,58
+5,9,6,63
+6,5,5,24
+6,5,6,25
+6,5,7,26
+6,6,5,36
+6,6,7,37
+6,7,5,47
+6,7,6,48
+6,7,7,49

tests/testdata/4obj_merge_allowed_res.csv

@@ -0,0 +1,99 @@
+T,X,Y,track_id,collid,lineage,parent_1,parent_2,parent_3,parent_4
+1,0,6,1,1,1,,,,
+1,1,5,2,1,1,,,,
+1,1,6,3,1,1,,,,
+1,1,7,4,1,1,,,,
+1,5,1,20,2,2,,,,
+1,5,11,30,3,3,,,,
+1,6,0,31,2,2,,,,
+1,6,1,32,2,2,,,,
+1,6,11,41,3,3,,,,
+1,6,12,42,3,3,,,,
+1,7,1,43,2,2,,,,
+1,7,11,53,3,3,,,,
+1,11,5,69,4,4,,,,
+1,11,6,70,4,4,,,,
+1,11,7,71,4,4,,,,
+1,12,6,72,4,4,,,,
+2,1,5,2,1,1,,,,
+2,1,6,3,1,1,,,,
+2,1,7,4,1,1,,,,
+2,2,5,5,1,1,,,,
+2,2,6,6,1,1,,,,
+2,2,7,7,1,1,,,,
+2,5,1,20,2,2,,,,
+2,5,2,21,2,2,,,,
+2,5,10,29,3,3,,,,
+2,5,11,30,3,3,,,,
+2,6,1,32,2,2,,,,
+2,6,2,33,2,2,,,,
+2,6,10,40,3,3,,,,
+2,6,11,41,3,3,,,,
+2,7,1,43,2,2,,,,
+2,7,2,44,2,2,,,,
+2,7,10,52,3,3,,,,
+2,7,11,53,3,3,,,,
+2,10,5,66,4,4,,,,
+2,10,6,67,4,4,,,,
+2,10,7,68,4,4,,,,
+2,11,5,69,4,4,,,,
+2,11,6,70,4,4,,,,
+2,11,7,71,4,4,,,,
+3,2,5,5,1,1,,,,
+3,2,6,6,1,1,,,,
+3,2,7,7,1,1,,,,
+3,3,4,8,1,1,,,,
+3,3,8,12,1,1,,,,
+3,4,3,13,2,2,,,,
+3,4,9,19,3,3,,,,
+3,5,2,21,2,2,,,,
+3,5,10,29,3,3,,,,
+3,6,2,33,2,2,,,,
+3,6,10,40,3,3,,,,
+3,7,2,44,2,2,,,,
+3,7,10,52,3,3,,,,
+3,8,3,54,2,2,,,,
+3,8,9,60,3,3,,,,
+3,9,4,61,4,4,,,,
+3,9,8,65,4,4,,,,
+3,10,5,66,4,4,,,,
+3,10,6,67,4,4,,,,
+3,10,7,68,4,4,,,,
+4,3,5,9,1,1,,,,
+4,3,6,10,1,1,,,,
+4,3,7,11,1,1,,,,
+4,4,4,14,1,1,,,,
+4,4,8,18,1,1,,,,
+4,5,3,22,2,2,,,,
+4,5,9,28,3,3,,,,
+4,6,3,34,2,2,,,,
+4,6,9,39,3,3,,,,
+4,7,3,45,2,2,,,,
+4,7,9,51,3,3,,,,
+4,8,4,55,2,2,,,,
+4,8,8,59,3,3,,,,
+4,9,5,62,4,4,,,,
+4,9,6,63,4,4,,,,
+4,9,7,64,4,4,,,,
+5,3,6,10,5,1,1.0,2.0,3.0,4.0
+5,4,5,15,5,1,1.0,2.0,3.0,4.0
+5,4,6,16,5,1,1.0,2.0,3.0,4.0
+5,4,7,17,5,1,1.0,2.0,3.0,4.0
+5,5,4,23,5,1,1.0,2.0,3.0,4.0
+5,5,8,27,5,1,1.0,2.0,3.0,4.0
+5,6,4,35,5,1,1.0,2.0,3.0,4.0
+5,6,8,38,5,1,1.0,2.0,3.0,4.0
+5,7,4,46,5,1,1.0,2.0,3.0,4.0
+5,7,8,50,5,1,1.0,2.0,3.0,4.0
+5,8,5,56,5,1,1.0,2.0,3.0,4.0
+5,8,6,57,5,1,1.0,2.0,3.0,4.0
+5,8,7,58,5,1,1.0,2.0,3.0,4.0
+5,9,6,63,5,1,1.0,2.0,3.0,4.0
+6,5,5,24,5,1,1.0,2.0,3.0,4.0
+6,5,6,25,5,1,1.0,2.0,3.0,4.0
+6,5,7,26,5,1,1.0,2.0,3.0,4.0
+6,6,5,36,5,1,1.0,2.0,3.0,4.0
+6,6,7,37,5,1,1.0,2.0,3.0,4.0
+6,7,5,47,5,1,1.0,2.0,3.0,4.0
+6,7,6,48,5,1,1.0,2.0,3.0,4.0
+6,7,7,49,5,1,1.0,2.0,3.0,4.0