Support standard raster image formats

pyproject.toml

@@ -40,6 +40,7 @@ dependencies = [
     "numpy>=1.26.0",
     "portalocker>=2.8.0",  # Cross-platform file locking
     "metaclass-registry",
+    "imageio>=2.37.0",
     "zarr>=2.18.0,<3.0",  # Required for ZarrStorageBackend
     "ome-zarr>=0.11.0",   # Required for OME-ZARR HCS compliance
 ]
@@ -197,4 +198,4 @@ ignore = [
 ]
 
 [tool.ruff.per-file-ignores]
-"__init__.py" = ["F401"]  # unused imports
+"__init__.py" = ["F401"]  # unused imports

src/polystore/disk.py

@@ -9,6 +9,7 @@
 import logging
 import os
 import shutil
+import importlib
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Set, Union
 
@@ -23,7 +24,7 @@
 
 def optional_import(module_name):
     try:
-        return __import__(module_name)
+        return importlib.import_module(module_name)
     except ImportError:
         return None
 
@@ -44,6 +45,7 @@ def optional_import(module_name):
     cupy = get_cupy()
     tf = get_tf()
 tifffile = optional_import("tifffile")
+imageio = optional_import("imageio.v3")
 
 # Optional arraybridge integration for memory conversion
 try:
@@ -99,6 +101,7 @@ def _register_formats(self):
 
             # Complex formats - use custom handlers
             (FileFormat.TIFF, tifffile, self._tiff_writer, self._tiff_reader),
+            (FileFormat.RASTER_IMAGE, imageio, self._image_writer, self._image_reader),
             (FileFormat.TEXT, True, self._text_writer, self._text_reader),
             (FileFormat.JSON, True, self._json_writer, self._json_reader),
             (FileFormat.CSV, True, self._csv_writer, self._csv_reader),
@@ -164,6 +167,14 @@ def _tiff_reader(self, path):
         else:
             return tifffile.imread(str(path))
 
+    def _image_writer(self, path, data, **kwargs):
+        """Write standard raster images using imageio."""
+        imageio.imwrite(path, np.asarray(data))
+
+    def _image_reader(self, path):
+        """Read standard raster images using imageio."""
+        return imageio.imread(path)
+
     def _text_writer(self, path, data, **kwargs):
         """Write text data to file. Accepts and ignores extra kwargs for compatibility."""
         path.write_text(str(data))
@@ -261,7 +272,7 @@ def load(self, file_path: Union[str, Path], **kwargs) -> Any:
             ext = disk_path.suffix.lower()
 
         if not self.format_registry.is_registered(ext):
-            raise ValueError(f"No writer registered for extension '{ext}'")
+            raise ValueError(f"No reader registered for extension '{ext}'")
 
         try:
             reader = self.format_registry.get_reader(ext)

src/polystore/formats.py

@@ -20,6 +20,7 @@ class FileFormat(Enum):
 
     # Image formats
     TIFF = "tiff"
+    RASTER_IMAGE = "raster_image"
 
     # Data formats
     CSV = "csv"
@@ -44,14 +45,22 @@ def extensions(self):
     FileFormat.TENSORFLOW: [".tf"],
     FileFormat.ZARR: [".zarr"],
     FileFormat.TIFF: [".tif", ".tiff"],
+    FileFormat.RASTER_IMAGE: [".bmp", ".gif", ".jpeg", ".jpg", ".png"],
     FileFormat.CSV: [".csv"],
     FileFormat.JSON: [".json"],
     FileFormat.TEXT: [".txt"],
     FileFormat.ROI: [".roi.zip"],
 }
 
 # Default image extensions
-DEFAULT_IMAGE_EXTENSIONS = {".tif", ".tiff", ".TIF", ".TIFF"}
+DEFAULT_IMAGE_EXTENSIONS = {
+    extension
+    for extensions in (
+        FILE_FORMAT_EXTENSIONS[FileFormat.TIFF],
+        FILE_FORMAT_EXTENSIONS[FileFormat.RASTER_IMAGE],
+    )
+    for extension in extensions
+}
 
 
 def get_format_from_extension(ext: str) -> FileFormat:

src/polystore/memory.py

@@ -139,6 +139,9 @@ def list_files(
         if self._memory_store[dir_key] is not None:
             raise NotADirectoryError(f"Path is not a directory: {directory}")
 
+        lowercase_extensions = (
+            None if extensions is None else {extension.lower() for extension in extensions}
+        )
         result = []
         dir_prefix = dir_key + "/" if not dir_key.endswith("/") else dir_key
 
@@ -159,7 +162,10 @@ def list_files(
                 filename = Path(rel_path).name
                 # If pattern is None, match all files
                 if pattern is None or fnmatch(filename, pattern):
-                    if not extensions or Path(filename).suffix in extensions:
+                    if (
+                        lowercase_extensions is None
+                        or Path(filename).suffix.lower() in lowercase_extensions
+                    ):
                         # Calculate depth for breadth-first sorting
                         depth = rel_path.count('/')
                         result.append((Path(path), depth))

src/polystore/virtual_workspace.py

@@ -210,6 +210,10 @@ def list_files(self, directory: Union[str, Path], pattern: Optional[str] = None,
         logger.info(f"  relative_dir_str='{relative_dir_str}'")
         logger.info(f"  mapping has {len(self._mapping_cache)} entries")
 
+        lowercase_extensions = (
+            None if extensions is None else {ext.lower() for ext in extensions}
+        )
+
         # Filter paths in this directory
         results = []
         for virtual_relative in self._mapping_cache.keys():
@@ -230,7 +234,7 @@ def list_files(self, directory: Union[str, Path], pattern: Optional[str] = None,
             vpath = Path(virtual_relative)
             if pattern and not fnmatch(vpath.name, pattern):
                 continue
-            if extensions and vpath.suffix not in extensions:
+            if lowercase_extensions and vpath.suffix.lower() not in lowercase_extensions:
                 continue
 
             # Return absolute path

tests/test_memory_backend.py

@@ -109,6 +109,17 @@ def test_list_files_with_extension_filter(self):
         npy_files = self.backend.list_files("/test", extensions={".npy"})
         assert len(npy_files) == 2
 
+    def test_list_files_extension_filter_is_case_insensitive(self):
+        """Test extension filtering matches backend contract case-insensitively."""
+        self.backend.save(np.array([1]), "/test/image.TIF")
+        self.backend.save(np.array([2]), "/test/image.tif")
+        self.backend.save("text", "/test/notes.TXT")
+
+        tif_files = self.backend.list_files("/test", extensions={".tif"})
+
+        assert len(tif_files) == 2
+        assert {path.name for path in tif_files} == {"image.TIF", "image.tif"}
+
     def test_list_files_recursive(self):
         """Test recursive file listing."""
         # Create files in multiple levels