From 33015d9ef007bc36ab619a1982ef7110b6003b15 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 23 Apr 2025 19:08:37 -0700
Subject: [PATCH 01/11] Implementing sfe's image classes with extent

---
 setup.cfg                                     |   2 +
 src/spatialfeatureexperiment/__init__.py      |   3 +-
 .../aligned_spatialimage.py                   | 553 ++++++++++++++++++
 3 files changed, 557 insertions(+), 1 deletion(-)
 create mode 100644 src/spatialfeatureexperiment/aligned_spatialimage.py

diff --git a/setup.cfg b/setup.cfg
index 8fe3837..ae103f6 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -54,6 +54,8 @@ install_requires =
     geopandas
     shapely
     requests
+    rasterio
+    aicsimageio
 
 [options.packages.find]
 where = src
diff --git a/src/spatialfeatureexperiment/__init__.py b/src/spatialfeatureexperiment/__init__.py
index f20782a..31dc947 100644
--- a/src/spatialfeatureexperiment/__init__.py
+++ b/src/spatialfeatureexperiment/__init__.py
@@ -15,4 +15,5 @@
 finally:
     del version, PackageNotFoundError
 
-from .SpatialFeatureExperiment import SpatialFeatureExperiment
+from .aligned_spatialimage import BioFormatsImage, ExtImage, SpatRasterImage
+from .spatialfeatureexperiment import SpatialFeatureExperiment
diff --git a/src/spatialfeatureexperiment/aligned_spatialimage.py b/src/spatialfeatureexperiment/aligned_spatialimage.py
new file mode 100644
index 0000000..33bad91
--- /dev/null
+++ b/src/spatialfeatureexperiment/aligned_spatialimage.py
@@ -0,0 +1,553 @@
+import os
+from pathlib import Path
+from typing import Dict, List, Optional, Union
+from warnings import warn
+
+import biocutils as ut
+import numpy as np
+import rasterio
+import rasterio.transform
+from PIL import Image
+from spatialexperiment.SpatialImage import VirtualSpatialImage
+
+__author__ = "jkanche"
+__copyright__ = "jkanche"
+__license__ = "MIT"
+
+
+def _validate_extent(extent):
+    required_keys = ["xmin", "xmax", "ymin", "ymax"]
+    if not all(k in extent for k in required_keys):
+        raise ValueError(f"Extent must contain keys: {', '.join(required_keys)}.")
+
+    if extent["xmin"] >= extent["xmax"] or extent["ymin"] >= extent["ymax"]:
+        raise ValueError("Invalid extent: xmin must be < xmax and ymin must be < ymax.")
+
+
+class AlignedSpatialImage(VirtualSpatialImage):
+    """Base class for spatial images with extent.
+
+    All images in `SpatialFeatureExperiment` have an extent in spatial coordinates.
+    """
+
+    def __init__(self, metadata: Optional[dict] = None):
+        super().__init__(metadata=metadata)
+
+    def get_extent(self) -> Dict[str, float]:
+        """Get the extent of the image"""
+        raise NotImplementedError("Subclasses must implement `get_extent`")
+
+    def set_extent(self, extent: Dict[str, float], in_place: bool = False):
+        """Set the extent of the image"""
+        raise NotImplementedError("Subclasses must implement `set_extent`")
+
+    @property
+    def extent(self) -> Dict[str, float]:
+        """Alias for :py:attr:`~get_extent`."""
+        return self.get_extent()
+
+    @extent.setter
+    def extent(self, value: Dict[str, float]):
+        """Alias for :py:attr:`~set_extent` with ``in_place = True``.
+
+        As this mutates the original object, a warning is raised.
+        """
+        warn(
+            "Setting property 'extent' is an in-place operation, use 'set_extent' instead",
+            UserWarning,
+        )
+        self.set_extent(value, in_place=False)
+
+
+class SpatRasterImage(AlignedSpatialImage):
+    """`SpatRaster` representation of images in SpatialFeatureExperiment objects.
+
+    This class is a wrapper around rasterio for handling GeoTIFF images.
+    """
+
+    def __init__(
+        self,
+        image: Union[rasterio.DatasetReader, np.ndarray],
+        extent: Optional[Dict[str, float]] = None,
+        metadata: Optional[dict] = None,
+    ):
+        """Initialize a `SpatRasterImage`.
+
+        Args:
+            image:
+                The image data, either as a rasterio dataset or a numpy array.
+
+            extent:
+                The spatial extent of the image, by default None.
+                Must have keys: 'xmin', 'xmax', 'ymin', 'ymax'.
+
+            metadata:
+                Additional image metadata. Defaults to None.
+        """
+        super().__init__(metadata=metadata)
+
+        # Handle numpy array
+        if isinstance(image, np.ndarray):
+            if extent is None:
+                extent = {"xmin": 0, "xmax": image.shape[1], "ymin": 0, "ymax": image.shape[0]}
+
+            # Create a memory-based rasterio dataset
+            self._src = self.numpy_array_to_rasterio(image, extent)
+            self._in_memory = True
+            self._img_source = None
+
+        # Handle rasterio dataset
+        elif isinstance(image, rasterio.DatasetReader):
+            self._src = image
+            self._in_memory = False
+
+            # Get source path if available
+            try:
+                self._img_source = image.name
+            except Exception as _:
+                self._img_source = None
+
+            # Get extent from transform if not provided
+            if extent is None:
+                bounds = image.bounds
+                extent = {"xmin": bounds.left, "xmax": bounds.right, "ymin": bounds.bottom, "ymax": bounds.top}
+        else:
+            raise ValueError("img must be a rasterio dataset or numpy array.")
+
+        # Store the extent
+        self._extent = extent
+
+    def numpy_array_to_rasterio(self, array, extent):
+        """Convert a numpy array to a rasterio dataset."""
+        from rasterio.io import MemoryFile
+
+        # Handle different dimensions
+        if len(array.shape) == 2:
+            height, width = array.shape
+            count = 1
+        elif len(array.shape) == 3:
+            height, width, count = array.shape
+        else:
+            raise ValueError("Array must be 2D or 3D")
+
+        # Create transform
+        xres = (extent["xmax"] - extent["xmin"]) / width
+        yres = (extent["ymax"] - extent["ymin"]) / height
+        transform = rasterio.transform.from_origin(extent["xmin"], extent["ymax"], xres, yres)
+
+        # Create memory file
+        memfile = MemoryFile()
+        with memfile.open(
+            driver="GTiff",
+            height=height,
+            width=width,
+            count=count,
+            dtype=array.dtype,
+            transform=transform,
+        ) as dataset:
+            if count == 1:
+                dataset.write(array, 1)
+            else:
+                for i in range(count):
+                    dataset.write(array[:, :, i], i + 1)
+
+        return memfile.open()
+
+    def __del__(self):
+        """Clean up resources."""
+        if hasattr(self, "_src") and self._src is not None:
+            self._src.close()
+
+    ##########################
+    ######>> Printing <<######
+    ##########################
+
+    def __repr__(self):
+        """String representation."""
+        shape = self.shape
+
+        output = f"{type(self).__name__}("
+
+        if len(shape) == 3:
+            output += f"{shape[1]} x {shape[0]} x {shape[2]} (width x height x channels)"
+        else:
+            output += f"{shape[1]} x {shape[0]} (width x height)"
+
+        if len(self._metadata) > 0:
+            output += ", metadata=" + ut.print_truncated_dict(self._metadata)
+        output += ")"
+
+        return output
+
+    def __str__(self) -> str:
+        """
+        Returns:
+            A pretty-printed string containing the contents of this object.
+        """
+        output = f"class: {type(self).__name__}\n"
+
+        shape = self.shape
+        if len(shape) == 3:
+            output += f"{shape[1]} x {shape[0]} x {shape[2]} (width x height x channels)\n"
+        else:
+            output += f"{shape[1]} x {shape[0]} (width x height)\n"
+
+        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        return output
+
+    ###########################
+    ######>> accessors <<######
+    ###########################
+
+    def img_source(self) -> str:
+        """Get the source file path if available."""
+        return self._img_source
+
+    def get_extent(self) -> Dict[str, float]:
+        """Get the extent of the image."""
+        return self._extent
+
+    def set_extent(self, extent: Dict[str, float], in_place: bool = False):
+        """Set the extent of the image."""
+        self._extent = extent
+
+        # Update the transform if it's a rasterio dataset
+        if hasattr(self, "_src") and self._src is not None:
+            width = self._src.width
+            height = self._src.height
+            xres = (extent["xmax"] - extent["xmin"]) / width
+            yres = (extent["ymax"] - extent["ymin"]) / height
+            self._src.transform = rasterio.transform.from_origin(extent["xmin"], extent["ymax"], xres, yres)
+
+    def img_raster(self, window: Optional[tuple] = None, out_shape: Optional[tuple] = None, resampling: int = 0):
+        """Load the image.
+
+        Args:
+            window:
+                Window to read, by default None (read entire image).
+
+            out_shape:
+                Output shape, by default None (no resampling).
+
+            resampling:
+                Resampling method, by default 0 (nearest).
+
+        Returns:
+            Image data.
+        """
+        if hasattr(self, "_src") and self._src is not None:
+            return self._src.read(window=window, out_shape=out_shape, resampling=resampling)
+        return None
+
+    @property
+    def shape(self):
+        """Get the shape of the image (height, width, channels)."""
+        if hasattr(self, "_src") and self._src is not None:
+            return (self._src.height, self._src.width, self._src.count)
+        return None
+
+    @property
+    def in_memory(self):
+        """Check if the image is in memory."""
+        return self._in_memory
+
+    @property
+    def array(self):
+        """Get the image as a numpy array (loads into memory)"""
+        if hasattr(self, "_src") and self._src is not None:
+            if self._src.count == 1:
+                return self._src.read(1)
+            else:
+                # Read all bands and stack
+                return np.dstack([self._src.read(i + 1) for i in range(self._src.count)])
+        return None
+
+
+class BioFormatsImage(AlignedSpatialImage):
+    """On-disk representation of BioFormats images in `SpatialFeatureExperiment` objects.
+
+    This class is designed for OME-TIFF files and other formats supported by aicsimageio.
+    """
+
+    def __init__(
+        self,
+        path: Union[str, Path],
+        extent: Dict[str, float],
+        is_full: bool = True,
+        origin: List[float] = [0.0, 0.0],
+        tranformation: dict = None,
+        metadata: dict = None,
+        validate: bool = False,
+    ):
+        """Initialize the image.
+
+        Args:
+            path:
+                Path to the image file.
+
+            extent:
+                The spatial extent of the image, by default None.
+                Must have keys: 'xmin', 'xmax', 'ymin', 'ymax'.
+
+            is_full:
+                Whether if this the full extent of the image.
+                Defaults to True.
+
+            origin:
+                Origin of the image in spatial coordinates.
+                Defaults to (0, 0).
+
+            tranformation:
+                Affine transformation.
+                Defaults to None.
+
+            metadata:
+                Additional image metadata. Defaults to None.
+
+            validate:
+                Internal use only.
+        """
+        super().__init__(metadata)
+
+        self._path = path
+
+        if extent is None:
+            self._extent = self._get_full_extent()
+        else:
+            self._extent = extent
+
+        self._is_full = is_full
+        self._origin = [0.0, 0.0] if origin is None else origin
+
+        self._transformation = tranformation if tranformation is not None else {}
+
+        if validate:
+            self.validate()
+
+    def validate(self):
+        """Validate the object."""
+
+        # Validate the path
+        if not os.path.exists(self._path):
+            raise FileNotFoundError(f"Image file not found: '{self._path}'.")
+
+        # Validate extent
+        _validate_extent(self._extent)
+
+        # Validate origin
+        if len(self.origin) != 2 or not all(isinstance(x, (int, float)) for x in self.origin):
+            raise ValueError("origin must be a numeric vector of length 2.")
+
+        # Validate transformation
+        if self.transformation:
+            warn("transformations are not validated.")
+
+    def _get_pixel_size(self):
+        """Get the physical pixel size from the metadata."""
+
+        from aicsimageio import AICSImage
+
+        try:
+            with AICSImage(self.path) as img:
+                physical_pixel_size = img.physical_pixel_sizes
+
+                if physical_pixel_size and len(physical_pixel_size) >= 2:
+                    return [physical_pixel_size[0], physical_pixel_size[1]]
+
+            warn("Physical pixel size not found in metadata. Using pixel space.")
+            return [1.0, 1.0]
+        except Exception as e:
+            warn(f"Error reading OME-TIFF metadata: {e}. Using pixel space.")
+            return [1.0, 1.0]
+
+    def _get_full_size(self):
+        """Get the full size of the image in pixels"""
+
+        from aicsimageio import AICSImage
+
+        try:
+            with AICSImage(self.path) as img:
+                shape = img.shape
+
+                if len(shape) >= 2:
+                    # AICSImage returns shape as (t, z, y, x, c)
+                    # We need x (width) and y (height)
+                    return [shape[-2], shape[-3]]  # x, y (width, height)
+
+            warn("Image size not found in metadata.")
+            return [0, 0]
+        except Exception as e:
+            warn(f"Error reading OME-TIFF metadata: {e}.")
+            return [0, 0]
+
+    def _get_full_extent(self):
+        """Get the full extent of the image."""
+        scale_factors = self._get_pixel_size()
+        sfx, sfy = scale_factors
+
+        size_full = self._get_full_size()
+        size_x, size_y = size_full
+
+        return {"xmin": 0, "ymin": 0, "xmax": size_x / sfx, "ymax": size_y / sfy}
+
+    ##########################
+    ######>> Printing <<######
+    ##########################
+
+    def __repr__(self):
+        """String representation"""
+        dims = self.dimensions
+
+        output = f"{type(self).__name__}"
+
+        output += f"X: {dims[0]}, Y: {dims[1]}, C: {dims[2]}, Z: {dims[3]}, T: {dims[4]}"
+
+        if len(self._metadata) > 0:
+            output += ", metadata=" + ut.print_truncated_dict(self._metadata)
+        output += ")"
+
+        return output
+
+    def __str__(self) -> str:
+        """
+        Returns:
+            A pretty-printed string containing the contents of this object.
+        """
+        output = f"class: {type(self).__name__}\n"
+
+        dims = self.dimensions
+        output += f"X: {dims[0]}, Y: {dims[1]}, C: {dims[2]}, Z: {dims[3]}, T: {dims[4]}\n"
+
+        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        return output
+
+    ###########################
+    ######>> accessors <<######
+    ###########################
+
+    def img_source(self) -> str:
+        """Get the source file path"""
+        return self.path
+
+    def get_extent(self) -> Dict[str, float]:
+        """Get the extent of the image, applying any transformations"""
+        # if self.transformation:
+        #     return self._transform_bbox(self._extent)
+        return self._extent
+
+    def set_extent(self, extent: Dict[str, float], in_place: bool = False):
+        """Set the extent of the image."""
+        _validate_extent(extent)
+        self._extent = extent
+
+    def to_ext_image(self, resolution=4, channel=None):
+        raise NotImplementedError("Not yet implemented!")
+
+
+class ExtImage(AlignedSpatialImage):
+    """Use the PIL/numpy arrays in SpatialFeatureExperiment objects.
+
+    This class is a wrapper around `PIL.Image` or numpy arrays with spatial extent information.
+    """
+
+    def __init__(
+        self,
+        image: Union[Image.Image, np.ndarray],
+        extent: Optional[Dict[str, float]] = None,
+        metadata: Optional[dict] = None,
+    ):
+        """Initialize an ExtImage.
+
+        Args:
+            image:
+                The image data.
+
+            extent:
+                The spatial extent of the image, by default None.
+                Must have keys: 'xmin', 'xmax', 'ymin', 'ymax'.
+
+            metadata:
+                Additional image metadata. Defaults to None.
+        """
+        super().__init__(metadata=metadata)
+
+        if isinstance(image, np.ndarray):
+            self._array = image
+        elif isinstance(image, Image.Image):
+            self._array = np.array(image)
+        else:
+            raise ValueError("img must be a PIL Image or numpy array")
+
+        if extent is None:
+            raise ValueError("Extent must be specified for ExtImage.")
+
+        _validate_extent(extent)
+        self._extent = extent
+
+    ##########################
+    ######>> Printing <<######
+    ##########################
+
+    def __repr__(self):
+        """String representation."""
+        shape = self.shape
+
+        output = f"{type(self).__name__}("
+
+        if len(shape) == 3:
+            output += f"{shape[1]} x {shape[0]} x {shape[2]} (width x height x channels)"
+        else:
+            output += f"{shape[1]} x {shape[0]} (width x height)"
+
+        if len(self._metadata) > 0:
+            output += ", metadata=" + ut.print_truncated_dict(self._metadata)
+        output += ")"
+
+        return output
+
+    def __str__(self) -> str:
+        """
+        Returns:
+            A pretty-printed string containing the contents of this object.
+        """
+        output = f"class: {type(self).__name__}\n"
+
+        shape = self.shape
+        if len(shape) == 3:
+            output += f"{shape[1]} x {shape[0]} x {shape[2]} (width x height x channels)\n"
+        else:
+            output += f"{shape[1]} x {shape[0]} (width x height)\n"
+
+        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        return output
+
+    ###########################
+    ######>> accessors <<######
+    ###########################
+
+    def img_source(self) -> str:
+        """Get the source file path."""
+        return None
+
+    def get_extent(self) -> Dict[str, float]:
+        """Get the extent of the image."""
+        return self._extent
+
+    def set_extent(self, extent: Dict[str, float], in_place: bool = False):
+        """Set the extent of the image."""
+        _validate_extent(extent)
+        self._extent = extent
+
+    @property
+    def array(self):
+        """Get the image as a numpy array."""
+        return self._array
+
+    @property
+    def shape(self):
+        """Get the shape of the image (height, width, channels)."""
+        return self._array.shape
+
+    def to_pil(self):
+        """Convert to PIL Image."""
+        return Image.fromarray(self._array)

From a6750131ac71a8f40c126bcaa1fc26611cf26f2a Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 23 Apr 2025 21:09:46 -0700
Subject: [PATCH 02/11] Add tests and dimension methods

---
 .github/workflows/run-tests.yml               |  2 +-
 setup.cfg                                     |  1 +
 .../aligned_spatialimage.py                   | 61 ++++++++++++-
 tests/test_image_classes.py                   | 91 +++++++++++++++++++
 4 files changed, 152 insertions(+), 3 deletions(-)
 create mode 100644 tests/test_image_classes.py

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 90aa16a..a9c2506 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     name: Python ${{ matrix.python-version }}
     steps:
diff --git a/setup.cfg b/setup.cfg
index ae103f6..473e85d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -56,6 +56,7 @@ install_requires =
     requests
     rasterio
     aicsimageio
+    numcodecs==0.15.1
 
 [options.packages.find]
 where = src
diff --git a/src/spatialfeatureexperiment/aligned_spatialimage.py b/src/spatialfeatureexperiment/aligned_spatialimage.py
index 33bad91..5637304 100644
--- a/src/spatialfeatureexperiment/aligned_spatialimage.py
+++ b/src/spatialfeatureexperiment/aligned_spatialimage.py
@@ -241,6 +241,9 @@ def img_raster(self, window: Optional[tuple] = None, out_shape: Optional[tuple]
 
     @property
     def shape(self):
+        return self.get_dimensions()
+
+    def get_dimensions(self):
         """Get the shape of the image (height, width, channels)."""
         if hasattr(self, "_src") and self._src is not None:
             return (self._src.height, self._src.width, self._src.count)
@@ -272,7 +275,7 @@ class BioFormatsImage(AlignedSpatialImage):
     def __init__(
         self,
         path: Union[str, Path],
-        extent: Dict[str, float],
+        extent: Dict[str, float] = None,
         is_full: bool = True,
         origin: List[float] = [0.0, 0.0],
         tranformation: dict = None,
@@ -398,7 +401,7 @@ def __repr__(self):
         """String representation"""
         dims = self.dimensions
 
-        output = f"{type(self).__name__}"
+        output = f"{type(self).__name__}("
 
         output += f"X: {dims[0]}, Y: {dims[1]}, C: {dims[2]}, Z: {dims[3]}, T: {dims[4]}"
 
@@ -443,6 +446,48 @@ def set_extent(self, extent: Dict[str, float], in_place: bool = False):
     def to_ext_image(self, resolution=4, channel=None):
         raise NotImplementedError("Not yet implemented!")
 
+    def img_raster(self, resolution=4, channel=None):
+        """Load the image.
+
+        Returns:
+            Image data.
+        """
+        return self.to_ext_image(resolution=resolution, channel=channel)
+
+    def get_dimensions(self):
+        """Get the dimensions of the image (X, Y, C, Z, T)"""
+
+        from aicsimageio import AICSImage
+
+        try:
+            with AICSImage(self.path) as img:
+                shape = img.shape
+
+                # AICSImage dimensions order is (T, Z, Y, X, C)
+                # Convert to (X, Y, C, Z, T) for compatibility with R's BioFormatsImage
+                if len(shape) == 5:
+                    t, z, y, x, c = shape
+                    return [x, y, c, z, t]
+                elif len(shape) == 4:
+                    # Handle 4D images (assume missing T dimension)
+                    z, y, x, c = shape
+                    return [x, y, c, z, 1]
+                elif len(shape) == 3:
+                    # Handle 3D images (assume missing Z and T dimensions)
+                    y, x, c = shape
+                    return [x, y, c, 1, 1]
+                elif len(shape) == 2:
+                    # Handle 2D images (assume single channel, Z and T)
+                    y, x = shape
+                    return [x, y, 1, 1, 1]
+                else:
+                    warn(f"Unexpected image shape: {shape}")
+                    return [0, 0, 0, 0, 0]
+
+        except Exception as e:
+            warn(f"Error reading OME-TIFF metadata: {e}")
+            return [0, 0, 0, 0, 0]
+
 
 class ExtImage(AlignedSpatialImage):
     """Use the PIL/numpy arrays in SpatialFeatureExperiment objects.
@@ -545,9 +590,21 @@ def array(self):
 
     @property
     def shape(self):
+        """Get the shape of the image (height, width, channels)."""
+        return self.get_dimensions()
+
+    def get_dimensions(self):
         """Get the shape of the image (height, width, channels)."""
         return self._array.shape
 
     def to_pil(self):
         """Convert to PIL Image."""
         return Image.fromarray(self._array)
+
+    def img_raster(self) -> Image.Image:
+        """Load the image.
+
+        Returns:
+            Image data.
+        """
+        return self.to_pil()
diff --git a/tests/test_image_classes.py b/tests/test_image_classes.py
new file mode 100644
index 0000000..9282c56
--- /dev/null
+++ b/tests/test_image_classes.py
@@ -0,0 +1,91 @@
+import os
+import tempfile
+
+import numpy as np
+import pytest
+from aicsimageio.writers import OmeTiffWriter
+
+from spatialfeatureexperiment import BioFormatsImage, ExtImage, SpatialFeatureExperiment, SpatRasterImage
+
+
+# Fixtures
+@pytest.fixture
+def sample_array():
+    width, height = 200, 100
+    x = np.linspace(0, 1, width)
+    y = np.linspace(0, 1, height)
+    xx, yy = np.meshgrid(x, y)
+
+    image_array = np.sin(xx * 10) * np.cos(yy * 10) * 127 + 128
+    return image_array.astype(np.uint8)
+
+
+@pytest.fixture
+def sample_extent():
+    """Create a sample extent dictionary"""
+    return {"xmin": 0, "xmax": 100, "ymin": 0, "ymax": 50}
+
+
+@pytest.fixture
+def ext_image(sample_array, sample_extent):
+    """Create a sample ExtImage"""
+    return ExtImage(sample_array, sample_extent)
+
+
+@pytest.fixture
+def sfe_object():
+    """Create a sample SpatialFeatureExperiment object"""
+    counts = np.random.negative_binomial(5, 0.5, (100, 50))
+    coords = np.random.uniform(0, 1000, (100, 2))
+    return SpatialFeatureExperiment(counts, coords)
+
+
+@pytest.fixture
+def temp_ome_tiff():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        # Create a simple 3D array (TCZYX order)
+        data = np.random.randint(0, 256, (1, 3, 100, 200, 1), dtype=np.uint8)
+
+        # Save as OME-TIFF
+        ome_tiff_path = os.path.join(temp_dir, "dummy.ome.tiff")
+        OmeTiffWriter.save(data, ome_tiff_path, dim_order="TCZYX")
+
+        yield ome_tiff_path
+
+
+# Tests for ExtImage
+def test_create_ext_image(sample_array, sample_extent):
+    img = ExtImage(sample_array, sample_extent)
+    assert img is not None
+    assert img.shape == sample_array.shape
+    assert img.extent == sample_extent
+
+
+# Tests for SpatRasterImage
+def test_create_spat_raster_image(sample_array, sample_extent):
+    img = SpatRasterImage(sample_array, sample_extent)
+    assert img is not None
+    assert img.extent == sample_extent
+
+
+# Tests for BioFormatsImage
+def test_create_bioformats_image(temp_ome_tiff):
+    img = BioFormatsImage(temp_ome_tiff)
+    assert img is not None
+    assert "xmin" in img.extent
+    assert "xmax" in img.extent
+    assert "ymin" in img.extent
+    assert "ymax" in img.extent
+
+
+def test_with_sfe(temp_ome_tiff):
+    bfi = BioFormatsImage(temp_ome_tiff)
+
+    print(bfi)
+
+    sfe = SpatialFeatureExperiment()
+    sfe.add_img(image_source=bfi, scale_factor=False, sample_id="sample1", image_id="ome_tiff", in_place=True)
+
+    img = sfe.get_image_data(sfe, sample_id="sample1", image_id="ome_tiff")
+    assert img is not None
+    assert img.shape == bfi.shape

From d5e68188c03ed5dbe82f693cc1c6e8b6dcadd649 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 23 Apr 2025 21:11:23 -0700
Subject: [PATCH 03/11] Fix version for numcodecs

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 473e85d..508177c 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -56,7 +56,7 @@ install_requires =
     requests
     rasterio
     aicsimageio
-    numcodecs==0.15.1
+    numcodecs<=0.15.1
 
 [options.packages.find]
 where = src

From 77e64135dd081fedf36f5472077d2920f080c8ac Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 23 Apr 2025 21:15:18 -0700
Subject: [PATCH 04/11] renaming classes

---
 src/spatialfeatureexperiment/__init__.py                        | 2 +-
 .../{SpatialFeatureExperiment.py => sfe.py}                     | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename src/spatialfeatureexperiment/{SpatialFeatureExperiment.py => sfe.py} (100%)

diff --git a/src/spatialfeatureexperiment/__init__.py b/src/spatialfeatureexperiment/__init__.py
index 31dc947..53158a1 100644
--- a/src/spatialfeatureexperiment/__init__.py
+++ b/src/spatialfeatureexperiment/__init__.py
@@ -16,4 +16,4 @@
     del version, PackageNotFoundError
 
 from .aligned_spatialimage import BioFormatsImage, ExtImage, SpatRasterImage
-from .spatialfeatureexperiment import SpatialFeatureExperiment
+from .sfe import SpatialFeatureExperiment
diff --git a/src/spatialfeatureexperiment/SpatialFeatureExperiment.py b/src/spatialfeatureexperiment/sfe.py
similarity index 100%
rename from src/spatialfeatureexperiment/SpatialFeatureExperiment.py
rename to src/spatialfeatureexperiment/sfe.py

From bac974651bd9bf2240e4c2f4b690ee99bed7fa5a Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 24 Apr 2025 09:00:49 -0700
Subject: [PATCH 05/11] bump version of SPE

---
 setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 508177c..1fcdd45 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,8 +49,8 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    spatialexperiment>=0.0.6
-    pillow>=11.0
+    spatialexperiment>=0.0.8
+    pillow
     geopandas
     shapely
     requests

From 761d5dd3999ad2dec27ff7edfb82dc541ae5a294 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 24 Apr 2025 09:12:35 -0700
Subject: [PATCH 06/11] update method name

---
 tests/test_image_classes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_image_classes.py b/tests/test_image_classes.py
index 9282c56..a6b89ca 100644
--- a/tests/test_image_classes.py
+++ b/tests/test_image_classes.py
@@ -86,6 +86,6 @@ def test_with_sfe(temp_ome_tiff):
     sfe = SpatialFeatureExperiment()
     sfe.add_img(image_source=bfi, scale_factor=False, sample_id="sample1", image_id="ome_tiff", in_place=True)
 
-    img = sfe.get_image_data(sfe, sample_id="sample1", image_id="ome_tiff")
+    img = sfe.get_img(sample_id="sample1", image_id="ome_tiff")
     assert img is not None
     assert img.shape == bfi.shape

From d2d755cc706f1dcd7a0bcf4151683ae5bf600e61 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 24 Apr 2025 09:15:59 -0700
Subject: [PATCH 07/11] add missing shape prop

---
 src/spatialfeatureexperiment/aligned_spatialimage.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/spatialfeatureexperiment/aligned_spatialimage.py b/src/spatialfeatureexperiment/aligned_spatialimage.py
index 5637304..b691a90 100644
--- a/src/spatialfeatureexperiment/aligned_spatialimage.py
+++ b/src/spatialfeatureexperiment/aligned_spatialimage.py
@@ -488,6 +488,9 @@ def get_dimensions(self):
             warn(f"Error reading OME-TIFF metadata: {e}")
             return [0, 0, 0, 0, 0]
 
+    @property
+    def shape(self):
+        return self.get_dimensions()
 
 class ExtImage(AlignedSpatialImage):
     """Use the PIL/numpy arrays in SpatialFeatureExperiment objects.

From cb943c387524dc65f534ba5e0eb22c8af4079c59 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 24 Apr 2025 16:16:16 +0000
Subject: [PATCH 08/11] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spatialfeatureexperiment/aligned_spatialimage.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/spatialfeatureexperiment/aligned_spatialimage.py b/src/spatialfeatureexperiment/aligned_spatialimage.py
index b691a90..406a39f 100644
--- a/src/spatialfeatureexperiment/aligned_spatialimage.py
+++ b/src/spatialfeatureexperiment/aligned_spatialimage.py
@@ -492,6 +492,7 @@ def get_dimensions(self):
     def shape(self):
         return self.get_dimensions()
 
+
 class ExtImage(AlignedSpatialImage):
     """Use the PIL/numpy arrays in SpatialFeatureExperiment objects.
 

From d7420e96ab82346ed38ba555832f166efd73b07a Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 24 Apr 2025 09:17:23 -0700
Subject: [PATCH 09/11] update changelog

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7cbbb61..e210a78 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,6 @@
 # Changelog
 
-## Version 0.1
+## Version 0.1 - 0.1.1
 
 - Migrating the class from the SpatialExperiment package
+- Adding the image classes specific to SFE with 'extent'.

From 8d810cf6b2747cc17becb8b5dfde9f9fb62fec84 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 24 Apr 2025 13:30:27 -0700
Subject: [PATCH 10/11] fixes

---
 tests/test_image_classes.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/test_image_classes.py b/tests/test_image_classes.py
index a6b89ca..0a3e527 100644
--- a/tests/test_image_classes.py
+++ b/tests/test_image_classes.py
@@ -22,19 +22,16 @@ def sample_array():
 
 @pytest.fixture
 def sample_extent():
-    """Create a sample extent dictionary"""
     return {"xmin": 0, "xmax": 100, "ymin": 0, "ymax": 50}
 
 
 @pytest.fixture
 def ext_image(sample_array, sample_extent):
-    """Create a sample ExtImage"""
     return ExtImage(sample_array, sample_extent)
 
 
 @pytest.fixture
 def sfe_object():
-    """Create a sample SpatialFeatureExperiment object"""
     counts = np.random.negative_binomial(5, 0.5, (100, 50))
     coords = np.random.uniform(0, 1000, (100, 2))
     return SpatialFeatureExperiment(counts, coords)

From 14f7656d07abb878cff1a4147f3c112cd6880020 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 24 Apr 2025 13:32:38 -0700
Subject: [PATCH 11/11] remove prints

---
 tests/test_image_classes.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/test_image_classes.py b/tests/test_image_classes.py
index 0a3e527..ebb66f1 100644
--- a/tests/test_image_classes.py
+++ b/tests/test_image_classes.py
@@ -78,8 +78,6 @@ def test_create_bioformats_image(temp_ome_tiff):
 def test_with_sfe(temp_ome_tiff):
     bfi = BioFormatsImage(temp_ome_tiff)
 
-    print(bfi)
-
     sfe = SpatialFeatureExperiment()
     sfe.add_img(image_source=bfi, scale_factor=False, sample_id="sample1", image_id="ome_tiff", in_place=True)