ngio 0.4.0a1__tar.gz → 0.4.0a2__tar.gz

{ngio-0.4.0a1 → ngio-0.4.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.0a1
+Version: 0.4.0a2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

{ngio-0.4.0a1 → ngio-0.4.0a2}/src/ngio/common/_array_io_pipes.py

@@ -87,6 +87,7 @@ def build_numpy_getter(
         slicing_dict=slicing_dict,
         remove_channel_selection=remove_channel_selection,
     )
+
     return lambda: _numpy_get_pipe(
         zarr_array=zarr_array,
         slicing_ops=slicing_ops,
@@ -285,6 +286,7 @@ def build_masked_numpy_getter(
     label_slicing_dict: dict[str, SlicingInputType] | None = None,
     fill_value: int | float = 0,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[], np.ndarray]:
     """Get a numpy array from the zarr array with the given slice kwargs."""
     slicing_dict = slicing_dict or {}
@@ -296,7 +298,7 @@ def build_masked_numpy_getter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=slicing_dict,
-        remove_channel_selection=False,
+        remove_channel_selection=remove_channel_selection,
     )
 
     label_data_getter = build_numpy_getter(
@@ -379,6 +381,7 @@ def build_masked_dask_getter(
     label_slicing_dict: dict[str, SlicingInputType] | None = None,
     fill_value: int | float = 0,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[], DaskArray]:
     """Get a dask array from the zarr array with the given slice kwargs."""
     slicing_dict = slicing_dict or {}
@@ -390,7 +393,7 @@ def build_masked_dask_getter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=slicing_dict,
-        remove_channel_selection=False,
+        remove_channel_selection=remove_channel_selection,
     )
 
     label_data_getter = build_dask_getter(
@@ -433,6 +436,7 @@ def build_masked_numpy_setter(
     data_getter: Callable[[], np.ndarray] | None = None,
     label_data_getter: Callable[[], np.ndarray] | None = None,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[np.ndarray], None]:
     """Set a numpy array to the zarr array with the given slice kwargs."""
     slicing_dict = slicing_dict or {}
@@ -445,7 +449,7 @@ def build_masked_numpy_setter(
             axes_order=axes_order,
             transforms=transforms,
             slicing_dict=slicing_dict,
-            remove_channel_selection=False,
+            remove_channel_selection=remove_channel_selection,
         )
 
     if label_data_getter is None:
@@ -464,7 +468,7 @@ def build_masked_numpy_setter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=slicing_dict,
-        remove_channel_selection=False,
+        remove_channel_selection=remove_channel_selection,
     )
 
     def set_patch_masked_as_numpy(patch: np.ndarray) -> None:
@@ -498,6 +502,7 @@ def build_masked_dask_setter(
     data_getter: Callable[[], DaskArray] | None = None,
     label_data_getter: Callable[[], DaskArray] | None = None,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[DaskArray], None]:
     """Set a dask array to the zarr array with the given slice kwargs."""
     slicing_dict = slicing_dict or {}
@@ -510,7 +515,7 @@ def build_masked_dask_setter(
             axes_order=axes_order,
             transforms=transforms,
             slicing_dict=slicing_dict,
-            remove_channel_selection=False,
+            remove_channel_selection=remove_channel_selection,
         )
 
     if label_data_getter is None:
@@ -529,7 +534,7 @@ def build_masked_dask_setter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=slicing_dict,
-        remove_channel_selection=False,
+        remove_channel_selection=remove_channel_selection,
     )
 
     def set_patch_masked_as_dask(patch: DaskArray) -> None:

{ngio-0.4.0a1 → ngio-0.4.0a2}/src/ngio/common/_roi.py

@@ -412,6 +412,7 @@ def build_roi_numpy_setter(
     axes_order: Sequence[str] | None = None,
     transforms: Sequence[TransformProtocol] | None = None,
     slicing_dict: dict[str, SlicingInputType] | None = None,
+    remove_channel_selection: bool = False,
 ) -> Callable[[np.ndarray], None]:
     """Prepare slice kwargs for setting an array."""
     input_slice_kwargs = roi_to_slicing_dict(
@@ -426,6 +427,7 @@ def build_roi_numpy_setter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=input_slice_kwargs,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -464,6 +466,7 @@ def build_roi_dask_setter(
     axes_order: Sequence[str] | None = None,
     transforms: Sequence[TransformProtocol] | None = None,
     slicing_dict: dict[str, SlicingInputType] | None = None,
+    remove_channel_selection: bool = False,
 ) -> Callable[[da.Array], None]:
     """Prepare slice kwargs for setting an array."""
     input_slice_kwargs = roi_to_slicing_dict(
@@ -478,6 +481,7 @@ def build_roi_dask_setter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=input_slice_kwargs,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -504,6 +508,7 @@ def build_roi_masked_numpy_getter(
     label_slicing_dict: dict[str, SlicingInputType] | None = None,
     fill_value: int | float = 0,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[], np.ndarray]:
     """Prepare slice kwargs for getting a masked array."""
     input_slice_kwargs = roi_to_slicing_dict(
@@ -531,6 +536,7 @@ def build_roi_masked_numpy_getter(
         label_slicing_dict=label_slice_kwargs,
         fill_value=fill_value,
         allow_scaling=allow_scaling,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -549,6 +555,7 @@ def build_roi_masked_numpy_setter(
     slicing_dict: dict[str, SlicingInputType] | None = None,
     label_slicing_dict: dict[str, SlicingInputType] | None = None,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[np.ndarray], None]:
     """Prepare slice kwargs for setting a masked array."""
     input_slice_kwargs = roi_to_slicing_dict(
@@ -575,6 +582,7 @@ def build_roi_masked_numpy_setter(
         slicing_dict=input_slice_kwargs,
         label_slicing_dict=label_slice_kwargs,
         allow_scaling=allow_scaling,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -593,6 +601,7 @@ def build_roi_masked_dask_getter(
     slicing_dict: dict[str, SlicingInputType] | None = None,
     label_slicing_dict: dict[str, SlicingInputType] | None = None,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[], da.Array]:
     """Prepare slice kwargs for getting a masked array."""
     input_slice_kwargs = roi_to_slicing_dict(
@@ -619,6 +628,7 @@ def build_roi_masked_dask_getter(
         slicing_dict=input_slice_kwargs,
         label_slicing_dict=label_slice_kwargs,
         allow_scaling=allow_scaling,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -637,6 +647,7 @@ def build_roi_masked_dask_setter(
     slicing_dict: dict[str, SlicingInputType] | None = None,
     label_slicing_dict: dict[str, SlicingInputType] | None = None,
     allow_scaling: bool = True,
+    remove_channel_selection: bool = False,
 ) -> Callable[[da.Array], None]:
     """Prepare slice kwargs for setting a masked array."""
     input_slice_kwargs = roi_to_slicing_dict(
@@ -663,4 +674,5 @@ def build_roi_masked_dask_setter(
         slicing_dict=input_slice_kwargs,
         label_slicing_dict=label_slice_kwargs,
         allow_scaling=allow_scaling,
+        remove_channel_selection=remove_channel_selection,
     )

{ngio-0.4.0a1 → ngio-0.4.0a2}/src/ngio/experimental/iterators/_segmentation.py

@@ -103,6 +103,7 @@ class SegmentationIterator(AbstractIteratorBuilder):
             transforms=self._output_transforms,
             pixel_size=self._output.pixel_size,
             roi=roi,
+            remove_channel_selection=True,
         )
 
     def build_dask_getter(self, roi: Roi):
@@ -124,6 +125,7 @@ class SegmentationIterator(AbstractIteratorBuilder):
             transforms=self._output_transforms,
             pixel_size=self._output.pixel_size,
             roi=roi,
+            remove_channel_selection=True,
         )
 
     def post_consolidate(self):
@@ -245,6 +247,7 @@ class MaskedSegmentationIterator(SegmentationIterator):
             axes_order=self._axes_order,
             transforms=self._output_transforms,
             pixel_size=self._output.pixel_size,
+            remove_channel_selection=True,
         )
 
     def build_dask_getter(self, roi: Roi):
@@ -272,6 +275,7 @@ class MaskedSegmentationIterator(SegmentationIterator):
             axes_order=self._axes_order,
             transforms=self._output_transforms,
             pixel_size=self._output.pixel_size,
+            remove_channel_selection=True,
         )
 
     def post_consolidate(self):