ngio 0.4.0a1__py3-none-any.whl → 0.4.0a2__py3-none-any.whl

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/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/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):

{ngio-0.4.0a1.dist-info → ngio-0.4.0a2.dist-info}/METADATA

@@ -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.dist-info → ngio-0.4.0a2.dist-info}/RECORD

@@ -1,11 +1,11 @@
 ngio/__init__.py,sha256=clqwRwmkalSwXvmNLGwtI-385gwvBTnJjohEk3Xp5cE,1463
 ngio/common/__init__.py,sha256=t5FUH7kSTqTT1jHmL_qYiEUCHHwMEKNfcZ6EbrkcpNg,1958
-ngio/common/_array_io_pipes.py,sha256=fCQiiQmJ2IUCiEdTP1Hc45K6YQy3sLQhb_mr00-n924,17930
+ngio/common/_array_io_pipes.py,sha256=zxZIVRtPjWUQ8J09_s5RcwoTgCOHDGmYYrkdPQbOPlM,18221
 ngio/common/_array_io_utils.py,sha256=LktLM2_2LkjYkwzyJXHZ0LyuwrQN4GYTqgpByBxNmlg,16303
 ngio/common/_dimensions.py,sha256=ubBSmnQmZOmen1jUn3LWZlNXCjUuV9FTjZWzUYidOwk,4852
 ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
 ngio/common/_pyramid.py,sha256=ElY_nBcchN3eeD9obLZ31IIo42HVlDn8R-legQpNxzQ,7503
-ngio/common/_roi.py,sha256=CnGHfe0KKkvtPecF_7ZIAOogi8a3tU05XEfYpNjqPDM,20548
+ngio/common/_roi.py,sha256=SJ_YJx5hR35T_OIx7ev9Y-rXInu7B4VEh8VKgcsdkcg,21166
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=p_trkLLrNM6hYvchJQJOHfYpzSlzzdDJmcyTx6K5J1M,6030
 ngio/common/transforms/__init__.py,sha256=Dn8SpMw_e_bg9kx4ZVPrGHJIu_yOK1FkIlePlN_C7FQ,120
@@ -17,7 +17,7 @@ ngio/experimental/iterators/_abstract_iterator.py,sha256=p8ZxQuoqPGLZCp79FprhgV-
 ngio/experimental/iterators/_feature.py,sha256=6uONbB527SS2NLlpiFtL3AVOazH-QpGhETLEt8pykgU,5987
 ngio/experimental/iterators/_image_processing.py,sha256=4U2FCS5pyDes9VJAGbQn7_e8YMs2TU0ocVr2m1QZhYA,6639
 ngio/experimental/iterators/_rois_utils.py,sha256=LfBKk2XEY-UuomT_9uOg-0b0_GUo6IX5h0OJmrbMs4g,4375
-ngio/experimental/iterators/_segmentation.py,sha256=H-hnT2HI45imR02IcAHwvjXHGGlk30Zr4yvXjuUh3Ns,11048
+ngio/experimental/iterators/_segmentation.py,sha256=pCR2eR5LUMV5nouw6vRDjIyIabnvfxp7cE6sukW4GZc,11220
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
 ngio/hcs/_plate.py,sha256=qfRwbCKaoz_AWTi8RDFFwOxy5geSknfJrPcqFVno9zI,44288
 ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
@@ -43,7 +43,7 @@ ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=YKBVVWb3mnuE-5L5k1i85WpHmcrbKl9k5KU2jNqt5yg,15868
 ngio/resources/__init__.py,sha256=Hry2odzDaC471_qgVfAQVnWDMK0Io9F8m9_JBNNm4e0,1633
 ngio/resources/resource_model.py,sha256=0Egs0QAJ5PNknqECHuBd_-ZTdi8EDNirt5VyuPdbg30,835
-ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/mask.png,sha256=Jq18Y5mOwxb46DUco5PL036r2S-00QDo6IWaDmEMFpc,12474
+ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/mask.png,sha256=g3QmxQdmeciAtBe5cTCRfR6yw3keG9cBYfjizMo6EGo,11890
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/nuclei.png,sha256=QhZ4XiFX7r-8-fbX8wSeUymktX85Ap3Nw1MqeOfRrF8,21649
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/raw.jpg,sha256=82lejQAIokj5w9g-qqhysDTWpHtNvJTkdURG_BjqIxQ,37743
 ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
@@ -70,7 +70,7 @@ ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
 ngio/utils/_logger.py,sha256=N5W0a_xwze4blS1MolidBkTMbjTbg8GPguJZNun3mAE,1392
 ngio/utils/_zarr_utils.py,sha256=aYHhjHWGy5Jx7IkPb4nt9N0-HgyvJnyvK9GGqnccZkE,13606
-ngio-0.4.0a1.dist-info/METADATA,sha256=Mpnq5b_yLk5EP4-dGyqTN36m_EvTa1k6dAYDqb1R4bA,5868
-ngio-0.4.0a1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.4.0a1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.4.0a1.dist-info/RECORD,,
+ngio-0.4.0a2.dist-info/METADATA,sha256=Wd5zLtu8OLbjEbgV9Lb5FDlBP9dFT9QU4S8h2358jKc,5868
+ngio-0.4.0a2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.4.0a2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.4.0a2.dist-info/RECORD,,