Add tracks for automatic tracking results

scripts/automatic_tracks.csv

@@ -0,0 +1,59 @@
+,Cell_ID,Start,End,Parent_ID
+0,1,0,0,0
+1,2,1,6,0
+2,10,1,1,1
+3,3,7,14,0
+4,8,7,8,2
+5,4,15,15,3
+6,6,15,23,3
+7,19,0,4,0
+8,20,5,23,19
+9,22,5,23,19
+10,25,0,3,0
+11,26,4,23,25
+12,28,4,23,25
+13,30,0,1,0
+14,31,2,3,30
+15,33,2,3,30
+16,40,0,22,0
+17,41,23,23,40
+18,43,23,23,40
+19,44,0,3,0
+20,45,4,23,44
+21,47,4,23,44
+22,50,0,4,0
+23,51,5,13,0
+24,62,5,23,50
+25,52,14,15,51
+26,54,14,14,0
+27,55,15,16,0
+28,60,15,15,54
+29,56,17,22,55
+30,58,17,23,55
+31,63,0,5,0
+32,64,6,23,63
+33,66,6,23,63
+34,71,0,0,0
+35,72,1,23,71
+36,74,1,23,71
+37,76,0,8,0
+38,77,9,23,76
+39,79,9,23,76
+40,87,0,2,0
+41,88,3,23,87
+42,90,3,23,87
+43,96,0,14,0
+44,97,15,23,96
+45,99,15,23,96
+46,103,0,3,0
+47,104,4,23,103
+48,106,4,23,103
+49,111,0,12,0
+50,112,13,15,111
+51,114,13,23,111
+52,117,2,2,0
+53,118,3,3,117
+54,120,3,23,117
+55,125,4,13,0
+56,126,14,17,125
+57,128,14,23,125

scripts/measure_for_automatic.py

@@ -6,8 +6,6 @@
 import pandas as pd
 import imageio.v3 as imageio
 
-from deepcell_tracking import isbi_utils
-
 from traccuracy import run_metrics
 from traccuracy.matchers import CTCMatcher
 from traccuracy._tracking_graph import TrackingGraph
@@ -50,7 +48,20 @@ def _get_tracks_to_isbi():
                 'label': daughter_id
             }
 
+    from deepcell_tracking import isbi_utils
     track_df = isbi_utils.trk_to_isbi(track_info)
+    track_df.to_csv("automatic_tracks.csv")
+    return track_df
+
+
+def _get_tracks_df():
+    tracks_path = "automatic_tracks.csv"
+    segmentation = imageio.imread(os.path.join(ROOT, "tracking_result.tif"))
+    breakpoint()
+    if os.path.exists(tracks_path):
+        track_df = pd.read_csv(tracks_path)
+    else:
+        track_df = _get_tracks_to_isbi()
     return segmentation, track_df
 
 
@@ -60,7 +71,7 @@ def _get_metrics_for_autotrack(segmentation, seg_df):
         gt = f['labels'][:]
 
     gt_nodes = _get_node_attributes(gt)
-    gt_df = pd.read_csv(os.path.join(ROOT, "gt_tracks.csv"))
+    gt_df = pd.read_csv("gt_tracks.csv")
     gt_G = ctc_to_graph(gt_df, gt_nodes)
     _check_ctc(gt_df, gt_nodes, gt)
     gt_T = TrackingGraph(gt_G, segmentation=gt, name="DynamicNuclearNet-GT")
@@ -81,7 +92,7 @@ def _get_metrics_for_autotrack(segmentation, seg_df):
 
 
 def main():
-    segmentation, seg_df = _get_tracks_to_isbi()
+    segmentation, seg_df = _get_tracks_df()
     _get_metrics_for_autotrack(segmentation, seg_df)