Add tests for XML writer

brainglobe_napari_io/cellfinder/writer_multiple_xml.py

@@ -1,24 +1,15 @@
 from typing import List, Tuple, Dict, Any
+
 from imlib.IO.cells import save_cells
 from imlib.cells.cells import Cell
+from napari.types import FullLayerData
 
 from .utils import convert_layer_to_cells
 
 
-def cellfinder_write_multiple_xml(path: str, layer_types: list):
-    if (
-        isinstance(path, str)
-        and path.endswith(".xml")
-        and all(item == "points" for item in layer_types)
-    ):
-        return write_multiple_points_to_xml
-    else:
-        return None
-
-
 def write_multiple_points_to_xml(
-    path: str, layer_data: List[Tuple[Any, Dict, str]]
-) -> str:
+    path: str, layer_data: List[FullLayerData]
+) -> List[str]:
     cells_to_save = []
     for layer in layer_data:
         data, state, type = layer
@@ -30,4 +21,4 @@ def write_multiple_points_to_xml(
     if cells_to_save:
         save_cells(cells_to_save, path)
 
-    return path
+    return [path]

brainglobe_napari_io/cellfinder/writer_xml.py

@@ -5,21 +5,14 @@
 from .utils import convert_layer_to_cells
 
 
-def cellfinder_write_xml(path, data, meta):
-    if isinstance(path, str) and path.endswith(".xml"):
-        return write_points_to_xml(path, data, meta)
-    else:
-        return None
-
-
-def write_points_to_xml(path, data, metadata):
+def write_points_to_xml(path: str, data: Any, attributes: dict) -> List[str]:
     cells_to_save = []
-    if metadata["metadata"]["point_type"] == Cell.CELL:
+    if attributes["metadata"]["point_type"] == Cell.CELL:
         cells_to_save.extend(convert_layer_to_cells(data))
-    elif metadata["metadata"]["point_type"] == Cell.UNKNOWN:
+    elif attributes["metadata"]["point_type"] == Cell.UNKNOWN:
         cells_to_save.extend(convert_layer_to_cells(data, cells=False))
 
     if cells_to_save:
         save_cells(cells_to_save, path)
 
-    return path
+    return [path]

brainglobe_napari_io/napari.yaml

@@ -16,10 +16,11 @@ contributions:
     python_name: brainglobe_napari_io.cellfinder.reader_xml:cellfinder_read_xml
   - id: brainglobe-napari-io.cellfinder_write_xml
     title: Write Points
-    python_name: brainglobe_napari_io.cellfinder.writer_xml:cellfinder_write_xml
+    python_name: brainglobe_napari_io.cellfinder.writer_xml:write_points_to_xml
   - id: brainglobe-napari-io.cellfinder_write_multiple_xml
     title: Write Multiple Points
-    python_name: brainglobe_napari_io.cellfinder.writer_multiple_xml:cellfinder_write_multiple_xml
+    python_name: brainglobe_napari_io.cellfinder.writer_multiple_xml:write_multiple_points_to_xml
+
   readers:
   - command: brainglobe-napari-io.brainreg_read_dir
     filename_patterns:

brainglobe_napari_io/tests/test_cellfinder_writer.py

@@ -0,0 +1,32 @@
+import pathlib
+
+import numpy as np
+
+from brainglobe_napari_io.cellfinder import (
+    reader_xml,
+    writer_xml,
+    writer_multiple_xml,
+)
+
+test_data_dir = pathlib.Path(__file__) / ".." / "data"
+
+
+def test_xml_roundrip(tmpdir):
+    # Check that a read in XML file can also be written back out
+    xml_file = test_data_dir / "cell_classification.xml"
+    layers = reader_xml.xml_reader(xml_file)
+    layer = layers[0]
+
+    for layer in layers:
+        paths = writer_xml.write_points_to_xml(
+            str(tmpdir / "single.xml"), layer[0], layer[1]
+        )
+        assert len(paths) == 1
+        assert isinstance(paths[0], str)
+
+    paths = writer_multiple_xml.write_multiple_points_to_xml(
+        str(tmpdir / "multiple.xml"), layers
+    )
+    assert len(paths) == 1
+    assert isinstance(paths[0], str)
+    assert reader_xml.is_cellfinder_xml(paths[0])