ngio 0.4.0a1__tar.gz → 0.4.0a3__tar.gz

{ngio-0.4.0a1 → ngio-0.4.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.0a1
+Version: 0.4.0a3
 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-0.4.0a3}/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-0.4.0a3}/src/ngio/common/_roi.py

@@ -49,7 +49,7 @@ T = TypeVar("T", int, float)
 class GenericRoi(BaseModel, Generic[T]):
     """A generic Region of Interest (ROI) model."""
 
-    name: str
+    name: str | None
     x: T
     y: T
     z: T | None = None
@@ -67,6 +67,38 @@ class GenericRoi(BaseModel, Generic[T]):
         """Calculate the intersection of this ROI with another ROI."""
         return roi_intersection(self, other)
 
+    def _nice_str(self) -> str:
+        if self.t is not None:
+            t_str = f"t={self.t}->{self.t_length}"
+        else:
+            t_str = "t=None"
+        if self.z is not None:
+            z_str = f"z={self.z}->{self.z_length}"
+        else:
+            z_str = "z=None"
+
+        y_str = f"y={self.y}->{self.y_length}"
+        x_str = f"x={self.x}->{self.x_length}"
+
+        if self.label is not None:
+            label_str = f", label={self.label}"
+        else:
+            label_str = ""
+        cls_name = self.__class__.__name__
+        return f"{cls_name}({t_str}, {z_str}, {y_str}, {x_str}{label_str})"
+
+    def get_name(self) -> str:
+        """Get the name of the ROI, or a default if not set."""
+        if self.name is not None:
+            return self.name
+        return self._nice_str()
+
+    def __repr__(self) -> str:
+        return self._nice_str()
+
+    def __str__(self) -> str:
+        return self._nice_str()
+
 
 def _1d_intersection(
     a: T | None, a_length: T | None, b: T | None, b_length: T | None
@@ -113,11 +145,17 @@ def roi_intersection(
     x, x_length = _1d_intersection(
         ref_roi.x, ref_roi.x_length, other_roi.x, other_roi.x_length
     )
+    if x is None and x_length is None:
+        # No intersection
+        return None
     assert x is not None and x_length is not None
 
     y, y_length = _1d_intersection(
         ref_roi.y, ref_roi.y_length, other_roi.y, other_roi.y_length
     )
+    if y is None and y_length is None:
+        # No intersection
+        return None
     assert y is not None and y_length is not None
 
     z, z_length = _1d_intersection(
@@ -127,11 +165,8 @@ def roi_intersection(
         ref_roi.t, ref_roi.t_length, other_roi.t, other_roi.t_length
     )
 
-    if (
-        x_length <= 0
-        or y_length <= 0
-        or (z_length is not None and z_length <= 0)
-        or (t_length is not None and t_length <= 0)
+    if (z_length is not None and z_length <= 0) or (
+        t_length is not None and t_length <= 0
     ):
         # No intersection
         return None
@@ -144,9 +179,14 @@ def roi_intersection(
             )
     label = ref_roi.label or other_roi.label
 
+    if ref_roi.name is not None and other_roi.name is not None:
+        name = f"{ref_roi.name}:{other_roi.name}"
+    else:
+        name = ref_roi.name or other_roi.name
+
     cls_ref = ref_roi.__class__
     return cls_ref(
-        name=f"[{ref_roi.name}_x_{other_roi.name}]",
+        name=name,
         x=x,
         y=y,
         z=z,
@@ -412,6 +452,7 @@ 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 +467,7 @@ def build_roi_numpy_setter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=input_slice_kwargs,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -464,6 +506,7 @@ 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 +521,7 @@ def build_roi_dask_setter(
         axes_order=axes_order,
         transforms=transforms,
         slicing_dict=input_slice_kwargs,
+        remove_channel_selection=remove_channel_selection,
     )
 
 
@@ -504,6 +548,7 @@ 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 +576,7 @@ 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 +595,7 @@ 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 +622,7 @@ 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 +641,7 @@ 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 +668,7 @@ 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 +687,7 @@ 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 +714,5 @@ 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-0.4.0a3}/src/ngio/experimental/iterators/_feature.py

@@ -47,7 +47,7 @@ class FeatureExtractorIterator(AbstractIteratorBuilder):
         self._input = input_image
         self._input_label = input_label
         self._ref_image = input_image
-        self._rois = input_image.build_image_roi_table().rois()
+        self._rois = input_image.build_image_roi_table(name=None).rois()
 
         # Set iteration parameters
         self._input_slicing_kwargs = add_channel_selection_to_slicing_dict(

{ngio-0.4.0a1 → ngio-0.4.0a3}/src/ngio/experimental/iterators/_image_processing.py

@@ -53,7 +53,7 @@ class ImageProcessingIterator(AbstractIteratorBuilder):
         self._input = input_image
         self._output = output_image
         self._ref_image = input_image
-        self._rois = input_image.build_image_roi_table().rois()
+        self._rois = input_image.build_image_roi_table(name=None).rois()
 
         # Set iteration parameters
         self._input_slicing_kwargs = add_channel_selection_to_slicing_dict(

{ngio-0.4.0a1 → ngio-0.4.0a3}/src/ngio/experimental/iterators/_rois_utils.py

@@ -24,7 +24,7 @@ def grid(
     stride_y: int | None = None,
     stride_z: int | None = None,
     stride_t: int | None = None,
-    base_name: str = "",
+    base_name: str | None = None,
 ) -> list[Roi]:
     """This method is a placeholder for creating a regular grid of ROIs."""
     t_dim = ref_image.dimensions.get("t", default=1)
@@ -49,7 +49,7 @@ def grid(
             for y in range(0, y_dim, stride_y):
                 for x in range(0, x_dim, stride_x):
                     roi = RoiPixels(
-                        name=f"{base_name}({t}, {z}, {y}, {x})",
+                        name=base_name,
                         x=x,
                         y=y,
                         z=z,

{ngio-0.4.0a1 → ngio-0.4.0a3}/src/ngio/experimental/iterators/_segmentation.py

@@ -55,7 +55,7 @@ class SegmentationIterator(AbstractIteratorBuilder):
         self._input = input_image
         self._output = output_label
         self._ref_image = input_image
-        self._rois = input_image.build_image_roi_table().rois()
+        self._rois = input_image.build_image_roi_table(name=None).rois()
 
         # Set iteration parameters
         self._input_slicing_kwargs = add_channel_selection_to_slicing_dict(
@@ -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 → ngio-0.4.0a3}/src/ngio/images/_abstract_image.py

@@ -445,7 +445,7 @@ class AbstractImage(Generic[_image_handler]):
         """
         consolidate_image(image=self, order=order, mode=mode)
 
-    def build_image_roi_table(self, name: str = "image") -> RoiTable:
+    def build_image_roi_table(self, name: str | None = "image") -> RoiTable:
         """Build the ROI table for an image."""
         return build_image_roi_table(image=self, name=name)
 
@@ -467,7 +467,7 @@ def consolidate_image(
     )
 
 
-def build_image_roi_table(image: AbstractImage, name: str = "image") -> RoiTable:
+def build_image_roi_table(image: AbstractImage, name: str | None = "image") -> RoiTable:
     """Build the ROI table for an image."""
     dim_x = image.dimensions.get("x")
     dim_y = image.dimensions.get("y")

{ngio-0.4.0a1 → ngio-0.4.0a3}/src/ngio/images/_ome_zarr_container.py

@@ -589,7 +589,7 @@ class OmeZarrContainer:
             backend=backend,
         )
 
-    def build_image_roi_table(self, name: str = "image") -> RoiTable:
+    def build_image_roi_table(self, name: str | None = "image") -> RoiTable:
         """Compute the ROI table for an image."""
         return self.get_image().build_image_roi_table(name=name)
 

{ngio-0.4.0a1 → ngio-0.4.0a3}/src/ngio/tables/v1/_roi_table.py

@@ -6,6 +6,7 @@ https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
 
 from collections.abc import Iterable
 from typing import Literal
+from uuid import uuid4
 
 import pandas as pd
 from pydantic import BaseModel
@@ -146,7 +147,7 @@ def _rois_to_dataframe(rois: dict[str, Roi], index_key: str | None) -> pd.DataFr
         len_z_micrometer = roi.z_length if roi.z_length is not None else 1.0
 
         row = {
-            index_key: roi.name,
+            index_key: roi.get_name(),
             "x_micrometer": roi.x,
             "y_micrometer": roi.y,
             "z_micrometer": z_micrometer,
@@ -179,8 +180,15 @@ class RoiDictWrapper:
     """A wrapper for a dictionary of ROIs to provide a consistent interface."""
 
     def __init__(self, rois: Iterable[Roi]) -> None:
-        self._rois_by_name = {roi.name: roi for roi in rois}
-        self._rois_by_label = {roi.label: roi for roi in rois if roi.label is not None}
+        self._rois_by_name = {}
+        self._rois_by_label = {}
+        for roi in rois:
+            name = roi.get_name()
+            if name in self._rois_by_name:
+                name = f"{name}_{uuid4().hex[:8]}"
+            self._rois_by_name[name] = roi
+            if roi.label is not None:
+                self._rois_by_label[roi.label] = roi
 
     def get_by_name(self, name: str, default: Roi | None = None) -> Roi | None:
         """Get an ROI by its name."""