Add tests for XML writer

brainglobe_napari_io/cellfinder/writer_xml.py

@@ -1,25 +1,33 @@
 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 napari.utils.notifications import show_info
 
 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_multiple_points_to_xml(
+    path: str, layer_data: List[FullLayerData]
+) -> List[str]:
     cells_to_save = []
-    if metadata["metadata"]["point_type"] == Cell.CELL:
-        cells_to_save.extend(convert_layer_to_cells(data))
-    elif metadata["metadata"]["point_type"] == Cell.UNKNOWN:
-        cells_to_save.extend(convert_layer_to_cells(data, cells=False))
+    for layer in layer_data:
+        data, attributes, type = layer
+        if "point_type" not in attributes["metadata"]:
+            # Not a points layer loaded by brainglobe_napari_io
+            name = attributes["name"]
+            show_info(
+                f'Did not find point type in metadata for "{name}" layer, '
+                "not saving to file."
+            )
+        elif attributes["metadata"]["point_type"] == Cell.CELL:
+            cells_to_save.extend(convert_layer_to_cells(data))
+        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]
+    else:
+        return []

brainglobe_napari_io/napari.yaml

@@ -5,45 +5,47 @@ contributions:
   - id: brainglobe-napari-io.brainreg_read_dir
     title: Brainreg Read Directory
     python_name: brainglobe_napari_io.brainreg.reader_dir:brainreg_read_dir
+
   - id: brainglobe-napari-io.brainreg_read_dir_standard_space
     title: Brainreg Read Directory Standard Space
     python_name: brainglobe_napari_io.brainreg.reader_dir_standard_space:brainreg_read_dir_standard_space
+
   - id: brainglobe-napari-io.cellfinder_read_dir
     title: Cellfinder Read Directory
     python_name: brainglobe_napari_io.cellfinder.reader_dir:cellfinder_read_dir
+
   - id: brainglobe-napari-io.cellfinder_read_xml
     title: Cellfinder Read XML
     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
+
   - 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
+    title: Write Points
+    python_name: brainglobe_napari_io.cellfinder.writer_xml:write_multiple_points_to_xml
+
+
   readers:
   - command: brainglobe-napari-io.brainreg_read_dir
     filename_patterns:
     - '*.tiff'
     accepts_directories: true
+
   - command: brainglobe-napari-io.brainreg_read_dir_standard_space
     filename_patterns:
       - '*.tiff'
     accepts_directories: true
+
   - command: brainglobe-napari-io.cellfinder_read_dir
     filename_patterns:
     - '*.tif'
     accepts_directories: true
+
   - command: brainglobe-napari-io.cellfinder_read_xml
     filename_patterns:
     - '*.xml'
     accepts_directories: false
+
+
   writers:
-  - command: brainglobe-napari-io.cellfinder_write_xml
-    layer_types:
-    - points
-    filename_extensions:
-    - .xml
-    display_name: points
   - command: brainglobe-napari-io.cellfinder_write_multiple_xml
     layer_types:
     - "points+"

brainglobe_napari_io/plugins.py

@@ -3,7 +3,7 @@
 
 from brainglobe_napari_io.brainreg.reader_dir import brainreg_read_dir
 
-from brainglobe_napari_io.cellfinder.writer_multiple_xml import (
+from brainglobe_napari_io.cellfinder.writer_xml import (
+    cellfinder_write_xml,
     cellfinder_write_multiple_xml,
 )
-from brainglobe_napari_io.cellfinder.writer_xml import cellfinder_write_xml

brainglobe_napari_io/tests/test_cellfinder_writer.py

@@ -0,0 +1,24 @@
+import pathlib
+
+import numpy as np
+
+from brainglobe_napari_io.cellfinder import (
+    reader_xml,
+    writer_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)
+    assert len(layers) == 2
+
+    paths = writer_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])