Merge pull request #144 from BBQuercus/trackmate_format_update

TrackMate output file changes

Author: BBQuercus

deepblink/cli/_create.py

@@ -184,7 +184,9 @@ def convert_labels(
             df = df.rename(columns={"X": "c", "Y": "r"})[["r", "c"]]
         # TrackMate export format
         elif all(c in df.columns for c in ("POSITION_X", "POSITION_Y")):
-            df = df[~df.index.isna()]  # Remove unused headers for TrackMate v7.0.0+
+            df = df[
+                (~df.index.isna()) & (df.index.str.lower() != "label")
+            ]  # Remove unused headers for TrackMate v7.0.0+
             df = df.rename(columns={"POSITION_X": "c", "POSITION_Y": "r"})[["r", "c"]]
             df = df.reset_index(drop=True)
         else:

tests/data/input_trackmate_post7.csv tests/data/input_trackmate_7.0+.csv

@@ -0,0 +1,10 @@
+LABEL,ID,TRACK_ID,QUALITY,POSITION_X,POSITION_Y,POSITION_Z,POSITION_T,FRAME,RADIUS,VISIBILITY
+Label,Spot ID,Track ID,Quality,X,Y,Z,T,Frame,Radius,Visibility
+Label,Spot ID,Track ID,Quality,X,Y,Z,T,Frame,R,Visibility
+,,,(quality),(micron),(micron),(micron),(sec),,(micron),
+ID2222,2222,,4370.76220703125,30.7670334432784,56.672136700919864,0.0,0.0,0,0.2017290601201014,1
+ID2223,2223,,6644.85693359375,32.286458801647804,59.79454990816701,0.0,0.0,0,0.2017290601201014,1
+ID2225,2225,,4078.255859375,31.736066013414028,70.03157152363852,0.0,0.0,0,0.2017290601201014,1
+ID2226,2226,,4022.391845703125,47.641303205975085,51.394360866478934,0.0,0.0,0,0.2017290601201014,1
+ID2227,2227,,6974.37548828125,46.74081825159567,48.52312950033919,0.0,0.0,0,0.2017290601201014,1
+ID2228,2228,,4659.05810546875,39.851282606785844,54.13192639279647,0.0,0.0,0,0.2017290601201014,1

tests/data/input_trackmate_pre7.csv tests/data/input_trackmate_7.0-.csv

@@ -56,8 +56,9 @@ def test_create():
 
     labels = [
         os.path.join(os.path.dirname(__file__), "./data/input_manual.csv"),
-        os.path.join(os.path.dirname(__file__), "./data/input_trackmate_post7.csv"),
-        os.path.join(os.path.dirname(__file__), "./data/input_trackmate_pre7.csv"),
+        os.path.join(os.path.dirname(__file__), "./data/input_trackmate_7.7+.csv"),
+        os.path.join(os.path.dirname(__file__), "./data/input_trackmate_7.0+.csv"),
+        os.path.join(os.path.dirname(__file__), "./data/input_trackmate_7.0-.csv"),
     ]
     max_size = 100
     image = np.zeros((max_size, max_size))