added more options to reader plugin

src/in_silico_fate_mapping/_reader.py

@@ -3,7 +3,13 @@
 import numpy as np
 import pandas as pd
 
-TRACKS_HEADER = ("TrackID", "t", "z", "y", "x")
+TRACKS_HEADER = (
+    ("track_id", "TrackID"),
+    ("t", "T"),
+    ("z", "Z"),
+    ("y", "Z"),
+    ("x", "X"),
+)
 
 
 def napari_get_reader(path):
@@ -17,8 +23,8 @@ def napari_get_reader(path):
         return None
 
     header = pd.read_csv(path, nrows=0).columns.tolist()
-    for colname in TRACKS_HEADER:
-        if colname != "z" and colname not in header:
+    for colnames in TRACKS_HEADER:
+        if all(c not in header for c in colnames) and colnames[0] != "z":
             return None
 
     return reader_function
@@ -28,12 +34,15 @@ def read_csv(path: str):
     df = pd.read_csv(path)
 
     data = []
-    for colname in TRACKS_HEADER:
-        try:
-            data.append(df[colname])
-        except KeyError:
-            if colname != "z":
-                raise KeyError(f"{colname} not found in .csv header.")
+    for colnames in TRACKS_HEADER:
+        found = False
+        for c in colnames:
+            if c in df.columns:
+                data.append(df[c])
+                found = True
+                break
+        if not found and colnames[0] != "z":
+            raise KeyError(f"{colnames[0]} not found in .csv header.")
 
     data = np.stack(data).T
 

src/in_silico_fate_mapping/_tests/test_io.py

@@ -25,10 +25,14 @@ def tracks(n_nodes: int = 10) -> pd.DataFrame:
     return pd.DataFrame(tracks_data, columns=["TrackID", "t", "z", "y", "x"])
 
 
-def test_get_reader(tmp_path: Path, tracks: pd.DataFrame) -> None:
+@pytest.mark.parametrize("track_id_col", ["TrackID", "track_id"])
+def test_get_reader(
+    tmp_path: Path, tracks: pd.DataFrame, track_id_col: str
+) -> None:
     path = tmp_path / "good_tracks.csv"
     tracks["NodeID"] = np.arange(len(tracks)) + 1
     tracks["Labels"] = np.random.randint(2, size=len(tracks))
+    tracks.rename(columns={"TrackID": track_id_col}, inplace=True)
     tracks.to_csv(path, index=False)
 
     reader = napari_get_reader(path)
@@ -41,7 +45,7 @@ def test_get_reader(tmp_path: Path, tracks: pd.DataFrame) -> None:
 
     assert np.allclose(props["NodeID"], tracks["NodeID"])
     assert np.allclose(props["Labels"], tracks["Labels"])
-    assert np.allclose(data, tracks[["TrackID", "t", "z", "y", "x"]])
+    assert np.allclose(data, tracks[[track_id_col, "t", "z", "y", "x"]])
 
 
 def test_napari_read(

src/in_silico_fate_mapping/_writer.py

@@ -8,7 +8,8 @@
 
 def napari_write_tracks(path: str, data: np.ndarray, meta: dict) -> List[str]:
 
-    header = list(TRACKS_HEADER)
+    # first position are the default
+    header = list(c[0] for c in TRACKS_HEADER)
     if data.shape[1] == 4:
         header.remove("z")