ngio 0.1.3__tar.gz → 0.1.5__tar.gz

{ngio-0.1.3 → ngio-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.1.3
+Version: 0.1.5
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.1.3 → ngio-0.1.5}/src/ngio/ngff_meta/fractal_image_meta.py

@@ -823,9 +823,7 @@ class Dataset:
             raise ValueError("Spatial axes must have a unit.")
         if return_type not in SpaceUnits.allowed_names():
             raise ValueError(f"Invalid space unit {return_type}.")
-        if isinstance(return_type, str):
-            return_type = SpaceUnits(return_type)
-        return return_type
+        return SpaceUnits(return_type)
 
     @property
     def pixel_size(self) -> PixelSize:
@@ -850,8 +848,7 @@ class Dataset:
         if len(types) == 0:
             return None
         elif len(types) == 1:
-            assert isinstance(types[0], TimeUnits)
-            return types[0]
+            return TimeUnits(types[0])
         else:
             raise ValueError("Multiple time axes found. Only one time axis is allowed.")
 

{ngio-0.1.3 → ngio-0.1.5}/src/ngio/ngff_meta/v04/zarr_utils.py

@@ -110,7 +110,13 @@ def vanilla_omero_v04_to_fractal(omero04: Omero04) -> Omero:
     for channel04 in omero04.channels:
         # Convert the window to a dictionary
         label = channel04.label
-        wavelength_id = channel04.extra_fields.get("wavelength_id", label)
+
+        if "wavelength_id" in channel04.extra_fields:
+            # If the wavelength_id is present, pop it from the extra fields
+            # so that it is not added to the channel_visualisation
+            wavelength_id = channel04.extra_fields.pop("wavelength_id")
+        else:
+            wavelength_id = label
 
         if channel04.window is None:
             window04 = Window04(
@@ -161,6 +167,7 @@ def fractal_omero_to_vanilla_v04(omero: Omero) -> Omero04:
             color=channel.channel_visualisation.color,
             active=channel.channel_visualisation.active,
             window=window04,
+            wavelength_id=channel.wavelength_id,
             **channel.channel_visualisation.extra_fields,
         )
         list_channels04.append(channel04)

{ngio-0.1.3 → ngio-0.1.5}/src/ngio/tables/tables_group.py

@@ -156,14 +156,17 @@ class TableGroup:
 
         list_of_tables = self._get_list_of_tables()
         self._validate_list_of_tables(list_of_tables=list_of_tables)
+
+        all_table_types = ["roi_table", "feature_table", "masking_roi_table"]
+
         if table_type is None:
             return list_of_tables
 
         else:
-            if table_type not in ["roi_table", "feature_table", "masking_roi_table"]:
+            if table_type not in all_table_types:
                 raise ValueError(
                     f"Table type {table_type} not recognized. "
-                    " Allowed values are: 'roi', 'feature', 'masking_roi'."
+                    f" Allowed values are: {all_table_types}"
                 )
             list_of_typed_tables = []
             for table_name in list_of_tables:

{ngio-0.1.3 → ngio-0.1.5}/tests/ngff_meta/test_utils.py

@@ -22,6 +22,7 @@ class TestUtils:
         )
 
         assert meta.channel_labels == ["DAPI", "nanog", "Lamin B1"]
+        assert meta.channel_wavelength_ids == ["A01_C01", "A02_C02", "A03_C03"]
         np.testing.assert_array_equal(meta.pixel_size(idx=0).zyx, [1.0, 1.0, 1.0])
         np.testing.assert_array_equal(meta.scale(idx=0), [1.0, 1.0, 1.0, 1.0, 1.0])
         np.testing.assert_array_equal(meta.pixel_size(path="2").zyx, [1.0, 4.0, 4.0])

{ngio-0.1.3 → ngio-0.1.5}/tests/ngff_meta/test_v04.py

@@ -4,6 +4,36 @@ import pytest
 
 
 class TestOMEZarrHandlerV04:
+    def test_create_image_meta(self, tmp_path):
+        from ngio.ngff_meta import create_image_metadata
+        from ngio.ngff_meta.v04.zarr_utils import (
+            fractal_ngff_image_meta_to_vanilla_v04,
+            vanilla_ngff_image_meta_v04_to_fractal,
+        )
+
+        meta = create_image_metadata(
+            on_disk_axis=("t", "c", "z", "y", "x"),
+            pixel_sizes=None,
+            xy_scaling_factor=2.0,
+            z_scaling_factor=1.0,
+            time_spacing=1.0,
+            time_units="s",
+            levels=5,
+            name="test",
+            channel_labels=["DAPI", "nanog", "Lamin B1"],
+            channel_wavelengths=["A01_C01", "A02_C02", "A03_C03"],
+            channel_visualization=None,
+            omero_kwargs=None,
+            version="0.4",
+        )
+
+        meta04 = fractal_ngff_image_meta_to_vanilla_v04(meta)
+        meta2 = vanilla_ngff_image_meta_v04_to_fractal(meta04)
+        assert meta.channel_labels == meta2.channel_labels
+        assert meta.channel_wavelength_ids == meta2.channel_wavelength_ids
+        assert meta.axes_names == meta2.axes_names
+        assert meta.scale(path="2") == meta2.scale(path="2")
+
     def test_basic_workflow(self, ome_zarr_image_v04_path):
         from ngio.ngff_meta import get_ngff_image_meta_handler
         from ngio.ngff_meta.v04.zarr_utils import NgffImageMeta04