ngio 0.4.0a4__py3-none-any.whl → 0.4.1__py3-none-any.whl

ngio/common/_dimensions.py

@@ -15,6 +15,192 @@ from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
 from ngio.utils import NgioValueError
 
 
+def _are_compatible(shape1: int, shape2: int, scaling: float) -> bool:
+    """Check if shape2 is consistent with shape1 given pixel sizes.
+
+    Since we only deal with shape discrepancies due to rounding, we
+    shape1, needs to be larger than shape2.
+    """
+    if shape1 < shape2:
+        return _are_compatible(shape2, shape1, 1 / scaling)
+    expected_shape2 = shape1 * scaling
+    expected_shape2_floor = math.floor(expected_shape2)
+    expected_shape2_ceil = math.ceil(expected_shape2)
+    return shape2 in {expected_shape2_floor, expected_shape2_ceil}
+
+
+def require_axes_match(reference: "Dimensions", other: "Dimensions") -> None:
+    """Check if two Dimensions objects have the same axes.
+
+    Besides the channel axis (which is a special case), all axes must be
+    present in both Dimensions objects.
+
+    Args:
+        reference (Dimensions): The reference dimensions object to compare against.
+        other (Dimensions): The other dimensions object to compare against.
+
+    Raises:
+        NgioValueError: If the axes do not match.
+    """
+    for s_axis in reference.axes_handler.axes:
+        if s_axis.axis_type == "channel":
+            continue
+        o_axis = other.axes_handler.get_axis(s_axis.name)
+        if o_axis is None:
+            raise NgioValueError(
+                f"Axes do not match. The axis {s_axis.name} "
+                f"is not present in either dimensions."
+            )
+    # Check for axes present in the other dimensions but not in this one
+    for o_axis in other.axes_handler.axes:
+        if o_axis.axis_type == "channel":
+            continue
+        s_axis = reference.axes_handler.get_axis(o_axis.name)
+        if s_axis is None:
+            raise NgioValueError(
+                f"Axes do not match. The axis {o_axis.name} "
+                f"is not present in either dimensions."
+            )
+
+
+def check_if_axes_match(reference: "Dimensions", other: "Dimensions") -> bool:
+    """Check if two Dimensions objects have the same axes.
+
+    Besides the channel axis (which is a special case), all axes must be
+    present in both Dimensions objects.
+
+    Args:
+        reference (Dimensions): The reference dimensions object to compare against.
+        other (Dimensions): The other dimensions object to compare against.
+
+    Returns:
+        bool: True if the axes match, False otherwise.
+    """
+    try:
+        require_axes_match(reference, other)
+        return True
+    except NgioValueError:
+        return False
+
+
+def require_dimensions_match(
+    reference: "Dimensions", other: "Dimensions", allow_singleton: bool = False
+) -> None:
+    """Check if two Dimensions objects have the same axes and dimensions.
+
+    Besides the channel axis, all axes must have the same dimension in
+    both images.
+
+    Args:
+        reference (Dimensions): The reference dimensions object to compare against.
+        other (Dimensions): The other dimensions object to compare against.
+        allow_singleton (bool): Whether to allow singleton dimensions to be
+            different. For example, if the input image has shape
+            (5, 100, 100) and the label has shape (1, 100, 100).
+
+    Raises:
+        NgioValueError: If the dimensions do not match.
+    """
+    require_axes_match(reference, other)
+    for r_axis in reference.axes_handler.axes:
+        if r_axis.axis_type == "channel":
+            continue
+        o_axis = other.axes_handler.get_axis(r_axis.name)
+        assert o_axis is not None  # already checked in assert_axes_match
+
+        r_dim = reference.get(r_axis.name, default=1)
+        o_dim = other.get(o_axis.name, default=1)
+
+        if r_dim != o_dim:
+            if allow_singleton and (r_dim == 1 or o_dim == 1):
+                continue
+            raise NgioValueError(
+                f"Dimensions do not match for axis "
+                f"{r_axis.name}. Got {r_dim} and {o_dim}."
+            )
+
+
+def check_if_dimensions_match(
+    reference: "Dimensions", other: "Dimensions", allow_singleton: bool = False
+) -> bool:
+    """Check if two Dimensions objects have the same axes and dimensions.
+
+    Besides the channel axis, all axes must have the same dimension in
+    both images.
+
+    Args:
+        reference (Dimensions): The reference dimensions object to compare against.
+        other (Dimensions): The other dimensions object to compare against.
+        allow_singleton (bool): Whether to allow singleton dimensions to be
+            different. For example, if the input image has shape
+            (5, 100, 100) and the label has shape (1, 100, 100).
+
+    Returns:
+        bool: True if the dimensions match, False otherwise.
+    """
+    try:
+        require_dimensions_match(reference, other, allow_singleton)
+        return True
+    except NgioValueError:
+        return False
+
+
+def require_rescalable(reference: "Dimensions", other: "Dimensions") -> None:
+    """Assert that two images can be rescaled.
+
+    For this to be true, the images must have the same axes, and
+    the pixel sizes must be compatible (i.e. one can be scaled to the other).
+
+    Args:
+        reference (Dimensions): The reference dimensions object to compare against.
+        other (Dimensions): The other dimensions object to compare against.
+
+    """
+    require_axes_match(reference, other)
+    for ax_r in reference.axes_handler.axes:
+        if ax_r.axis_type == "channel":
+            continue
+        ax_o = other.axes_handler.get_axis(ax_r.name)
+        assert ax_o is not None, "Axes do not match."
+        px_r = reference.pixel_size.get(ax_r.name, default=1.0)
+        px_o = other.pixel_size.get(ax_o.name, default=1.0)
+        shape_r = reference.get(ax_r.name, default=1)
+        shape_o = other.get(ax_o.name, default=1)
+        scale = px_r / px_o
+        if not _are_compatible(
+            shape1=shape_r,
+            shape2=shape_o,
+            scaling=scale,
+        ):
+            raise NgioValueError(
+                f"Reference image with shape {reference.shape}, "
+                f"and pixel size {reference.pixel_size}, "
+                f"cannot be rescaled to "
+                f"image with shape {other.shape} "
+                f"and pixel size {other.pixel_size}. "
+            )
+
+
+def check_if_rescalable(reference: "Dimensions", other: "Dimensions") -> bool:
+    """Check if two images can be rescaled.
+
+    For this to be true, the images must have the same axes, and
+    the pixel sizes must be compatible (i.e. one can be scaled to the other).
+
+    Args:
+        reference (Dimensions): The reference dimensions object to compare against.
+        other (Dimensions): The other dimensions object to compare against.
+
+    Returns:
+        bool: True if the images can be rescaled, False otherwise.
+    """
+    try:
+        require_rescalable(reference, other)
+        return True
+    except NgioValueError:
+        return False
+
+
 class Dimensions:
     """Dimension metadata Handling Class.
 
@@ -23,18 +209,28 @@ class Dimensions:
     such as shape, axes, and properties like is_2d, is_3d, is_time_series, etc.
     """
 
+    require_axes_match = require_axes_match
+    check_if_axes_match = check_if_axes_match
+    require_dimensions_match = require_dimensions_match
+    check_if_dimensions_match = check_if_dimensions_match
+    require_rescalable = require_rescalable
+    check_if_rescalable = check_if_rescalable
+
     def __init__(
         self,
         shape: tuple[int, ...],
+        chunks: tuple[int, ...],
         dataset: Dataset,
     ) -> None:
         """Create a Dimension object from a Zarr array.
 
         Args:
             shape: The shape of the Zarr array.
+            chunks: The chunks of the Zarr array.
             dataset: The dataset object.
         """
         self._shape = shape
+        self._chunks = chunks
         self._axes_handler = dataset.axes_handler
         self._pixel_size = dataset.pixel_size
 
@@ -70,7 +266,12 @@ class Dimensions:
     @property
     def shape(self) -> tuple[int, ...]:
         """Return the shape as a tuple."""
-        return tuple(self._shape)
+        return self._shape
+
+    @property
+    def chunks(self) -> tuple[int, ...]:
+        """Return the chunks as a tuple."""
+        return self._chunks
 
     @property
     def axes(self) -> tuple[str, ...]:
@@ -79,36 +280,36 @@ class Dimensions:
 
     @property
     def is_time_series(self) -> bool:
-        """Return whether the data is a time series."""
+        """Return whether the image is a time series."""
         if self.get("t", default=1) == 1:
             return False
         return True
 
     @property
     def is_2d(self) -> bool:
-        """Return whether the data is 2D."""
+        """Return whether the image is 2D."""
         if self.get("z", default=1) != 1:
             return False
         return True
 
     @property
     def is_2d_time_series(self) -> bool:
-        """Return whether the data is a 2D time series."""
+        """Return whether the image is a 2D time series."""
         return self.is_2d and self.is_time_series
 
     @property
     def is_3d(self) -> bool:
-        """Return whether the data is 3D."""
+        """Return whether the image is 3D."""
         return not self.is_2d
 
     @property
     def is_3d_time_series(self) -> bool:
-        """Return whether the data is a 3D time series."""
+        """Return whether the image is a 3D time series."""
         return self.is_3d and self.is_time_series
 
     @property
     def is_multi_channels(self) -> bool:
-        """Return whether the data has multiple channels."""
+        """Return whether the image has multiple channels."""
         if self.get("c", default=1) == 1:
             return False
         return True
@@ -122,7 +323,7 @@ class Dimensions:
         pass
 
     def get(self, axis_name: str, default: int | None = None) -> int | None:
-        """Return the dimension of the given axis name.
+        """Return the dimension/shape of the given axis name.
 
         Args:
             axis_name: The name of the axis (either canonical or non-canonical).
@@ -132,184 +333,3 @@ class Dimensions:
         if index is None:
             return default
         return self._shape[index]
-
-    def get_index(self, axis_name: str) -> int | None:
-        """Return the index of the given axis name.
-
-        Args:
-            axis_name: The name of the axis (either canonical or non-canonical).
-        """
-        return self.axes_handler.get_index(axis_name)
-
-    def has_axis(self, axis_name: str) -> bool:
-        """Return whether the axis exists."""
-        index = self.axes_handler.get_index(axis_name)
-        if index is None:
-            return False
-        return True
-
-    def require_axes_match(self, other: "Dimensions") -> None:
-        """Check if two Dimensions objects have the same axes.
-
-        Besides the channel axis (which is a special case), all axes must be
-        present in both Dimensions objects.
-
-        Args:
-            other (Dimensions): The other dimensions object to compare against.
-
-        Raises:
-            NgioValueError: If the axes do not match.
-        """
-        require_axes_match(self, other)
-
-    def require_dimensions_match(
-        self, other: "Dimensions", allow_singleton: bool = False
-    ) -> None:
-        """Check if two Dimensions objects have the same axes and dimensions.
-
-        Besides the channel axis, all axes must have the same dimension in
-        both images.
-
-        Args:
-            other (Dimensions): The other dimensions object to compare against.
-            allow_singleton (bool): Whether to allow singleton dimensions to be
-                different. For example, if the input image has shape
-                (5, 100, 100) and the label has shape (1, 100, 100).
-
-        Raises:
-            NgioValueError: If the dimensions do not match.
-        """
-        require_dimensions_match(self, other, allow_singleton)
-
-    def require_can_be_rescaled(self, other: "Dimensions") -> None:
-        """Assert that two images can be rescaled.
-
-        For this to be true, the images must have the same axes, and
-        the pixel sizes must be compatible (i.e. one can be scaled to the other).
-
-        Args:
-            other (Dimensions): The other dimensions object to compare against.
-
-        """
-        require_rescalable(self, other)
-
-
-def _are_compatible(shape1: int, shape2: int, scaling: float) -> bool:
-    """Check if shape2 is consistent with shape1 given pixel sizes.
-
-    Since we only deal with shape discrepancies due to rounding, we
-    shape1, needs to be larger than shape2.
-    """
-    if shape1 < shape2:
-        return _are_compatible(shape2, shape1, 1 / scaling)
-    expected_shape2 = shape1 * scaling
-    expected_shape2_floor = math.floor(expected_shape2)
-    expected_shape2_ceil = math.ceil(expected_shape2)
-    return shape2 in {expected_shape2_floor, expected_shape2_ceil}
-
-
-def require_axes_match(dimensions1: Dimensions, dimensions2: Dimensions) -> None:
-    """Check if two Dimensions objects have the same axes.
-
-    Besides the channel axis (which is a special case), all axes must be
-    present in both Dimensions objects.
-
-    Args:
-        dimensions1 (Dimensions): The first dimensions object to compare against.
-        dimensions2 (Dimensions): The second dimensions object to compare against.
-
-    Raises:
-        NgioValueError: If the axes do not match.
-    """
-    for s_axis in dimensions1.axes_handler.axes:
-        if s_axis.axis_type == "channel":
-            continue
-        o_axis = dimensions2.axes_handler.get_axis(s_axis.name)
-        if o_axis is None:
-            raise NgioValueError(
-                f"Axes do not match. The axis {s_axis.name} "
-                f"is not present in either dimensions."
-            )
-    # Check for axes present in the other dimensions but not in this one
-    for o_axis in dimensions2.axes_handler.axes:
-        if o_axis.axis_type == "channel":
-            continue
-        s_axis = dimensions1.axes_handler.get_axis(o_axis.name)
-        if s_axis is None:
-            raise NgioValueError(
-                f"Axes do not match. The axis {o_axis.name} "
-                f"is not present in either dimensions."
-            )
-
-
-def require_dimensions_match(
-    dimensions1: Dimensions, dimensions2: Dimensions, allow_singleton: bool = False
-) -> None:
-    """Check if two Dimensions objects have the same axes and dimensions.
-
-    Besides the channel axis, all axes must have the same dimension in
-    both images.
-
-    Args:
-        dimensions1 (Dimensions): The first dimensions object to compare against.
-        dimensions2 (Dimensions): The second dimensions object to compare against.
-        allow_singleton (bool): Whether to allow singleton dimensions to be
-            different. For example, if the input image has shape
-            (5, 100, 100) and the label has shape (1, 100, 100).
-
-    Raises:
-        NgioValueError: If the dimensions do not match.
-    """
-    require_axes_match(dimensions1, dimensions2)
-    for s_axis in dimensions1.axes_handler.axes:
-        if s_axis.axis_type == "channel":
-            continue
-        o_axis = dimensions2.axes_handler.get_axis(s_axis.name)
-        assert o_axis is not None  # already checked in assert_axes_match
-
-        i_dim = dimensions1.get(s_axis.name, default=1)
-        o_dim = dimensions2.get(o_axis.name, default=1)
-
-        if i_dim != o_dim:
-            if allow_singleton and (i_dim == 1 or o_dim == 1):
-                continue
-            raise NgioValueError(
-                f"Dimensions do not match for axis "
-                f"{s_axis.name}. Got {i_dim} and {o_dim}."
-            )
-
-
-def require_rescalable(dimensions1: Dimensions, dimensions2: Dimensions) -> None:
-    """Assert that two images can be rescaled.
-
-    For this to be true, the images must have the same axes, and
-    the pixel sizes must be compatible (i.e. one can be scaled to the other).
-
-    Args:
-        dimensions1 (Dimensions): The first dimensions object to compare against.
-        dimensions2 (Dimensions): The second dimensions object to compare against.
-
-    """
-    require_axes_match(dimensions1, dimensions2)
-    for ax1 in dimensions1.axes_handler.axes:
-        if ax1.axis_type == "channel":
-            continue
-        ax2 = dimensions2.axes_handler.get_axis(ax1.name)
-        assert ax2 is not None, "Axes do not match."
-        px1 = dimensions1.pixel_size.get(ax1.name, default=1.0)
-        px2 = dimensions2.pixel_size.get(ax2.name, default=1.0)
-        shape1 = dimensions1.get(ax1.name, default=1)
-        shape2 = dimensions2.get(ax2.name, default=1)
-        scale = px1 / px2
-        if not _are_compatible(
-            shape1=shape1,
-            shape2=shape2,
-            scaling=scale,
-        ):
-            raise NgioValueError(
-                f"Image1 with shape {dimensions1.shape}, "
-                f"and pixel size {dimensions1.pixel_size}, "
-                f"cannot be rescaled to "
-                f"Image2 with shape {dimensions2.shape}, "
-                f"and pixel size {dimensions2.pixel_size}. "
-            )

ngio/common/_roi.py

@@ -40,7 +40,7 @@ T = TypeVar("T", int, float)
 class GenericRoi(BaseModel):
     """A generic Region of Interest (ROI) model."""
 
-    name: str | None
+    name: str | None = None
     x: float
     y: float
     z: float | None = None
@@ -327,7 +327,7 @@ def zoom_roi(roi: Roi, zoom_factor: float = 1) -> Roi:
             If the zoom factor is 1 the ROI will not be changed.
     """
     if zoom_factor <= 0:
-        raise ValueError("Zoom factor must be greater than 0.")
+        raise NgioValueError("Zoom factor must be greater than 0.")
 
     # the zoom factor needs to be rescaled
     # from the range [-1, inf) to [0, inf)

ngio/experimental/iterators/__init__.py

@@ -7,8 +7,6 @@ from ngio.experimental.iterators._segmentation import (
     SegmentationIterator,
 )
 
-# from ngio.experimental.iterators._builder import IteratorBuilder
-
 __all__ = [
     "FeatureExtractorIterator",
     "ImageProcessingIterator",