vips reader now supports caching using fetch, memory profiling is nee…

…ded, #8

lazyslide/readers/vips.py

@@ -12,7 +12,6 @@
 except Exception as _:
     pass
 
-
 VIPS_FORMAT_TO_DTYPE = {
     "uchar": np.uint8,
     "char": np.int8,
@@ -38,13 +37,27 @@ def vips2numpy(
     )
 
 
+def buffer2numpy(
+    buffer,
+) -> np.ndarray:
+    """Converts a VIPS image into a numpy array"""
+    return np.ndarray(
+        buffer=buffer,
+        dtype=VIPS_FORMAT_TO_DTYPE[buffer.format],
+        shape=[buffer.height, buffer.width, buffer.bands],
+    )
+
+
 class VipsReader(ReaderBase):
     def __init__(
         self,
         file: Union[Path, str],
+        caching: bool = True,
     ):
         self.file = file
+        self.caching = caching
         self.__level_vips_handler = {}  # cache level handler
+        self.__region_vips_handler = {}  # cache region handler
 
         _vips_img = self._get_vips_level(0)
         _vips_fields = set(_vips_img.get_fields())
@@ -61,47 +74,60 @@ def get_patch(
         top,
         width,
         height,
-        level: int = None,
-        downsample: float = None,
+        level: int = 0,
         fill=255,
     ):
         """Get a patch by x, y from top-left corner"""
         level = self.translate_level(level)
-        img = self._get_vips_level(level)
-        patch = self._get_vips_patch(img, left, top, width, height, fill=fill)
-        if downsample is not None:
-            if downsample != 1:
-                patch = patch.resize(1 / downsample)
-        patch = vips2numpy(patch)
-        return self._rgba_to_rgb(patch)
+        image = self._get_vips_level(level)
+        bg = [fill]
+
+        crop_left, crop_top, crop_w, crop_h, pos = get_crop_left_top_width_height(
+            img_width=image.width,
+            img_height=image.height,
+            left=left,
+            top=top,
+            width=width,
+            height=height,
+        )
+        patch = None
+        if self.caching:
+            cropped = self.__region_vips_handler[level].fetch(
+                crop_left, crop_top, crop_w, crop_h
+            )
+            if pos is None:
+                return np.ndarray(
+                    buffer=cropped,
+                    dtype=VIPS_FORMAT_TO_DTYPE[image.format],
+                    shape=[crop_h, crop_w, image.bands],
+                )
+            else:
+                patch = vips.Image.new_from_buffer(cropped, "").gravity(
+                    pos, width, height, background=bg
+                )
+        else:
+            cropped = image.crop(crop_left, crop_top, crop_w, crop_h)
+            if pos is None:
+                patch = cropped
+            else:
+                patch = cropped.gravity(pos, width, height, background=bg)
+
+        return vips2numpy(patch)  # self._rgba_to_rgb(patch)
 
     def get_level(self, level):
         level = self.translate_level(level)
         img = self._get_vips_level(level)
         img = vips2numpy(img)
-        return self._rgba_to_rgb(img)
+        return img  # self._rgba_to_rgb(img)
 
     def _get_vips_level(self, level=0):
         """Lazy load and load only one for all image level"""
         handler = self.__level_vips_handler.get(level)
         if handler is None:
-            handler = vips.Image.new_from_file(str(self.file), fail=True, level=level)
+            handler = vips.Image.new_from_file(
+                str(self.file), fail=True, level=level, rgb=True
+            )
             self.__level_vips_handler[level] = handler
+            if self.caching:
+                self.__region_vips_handler[level] = vips.Region.new(handler)
         return handler
-
-    @staticmethod
-    def _get_vips_patch(image, left, top, width, height, fill=255):
-        bg = [fill]
-        crop_left, crop_top, crop_w, crop_h, pos = get_crop_left_top_width_height(
-            img_width=image.width,
-            img_height=image.height,
-            left=left,
-            top=top,
-            width=width,
-            height=height,
-        )
-        cropped = image.crop(crop_left, crop_top, crop_w, crop_h)
-        if pos is None:
-            return cropped
-        else:
-            return cropped.gravity(pos, width, height, background=bg)

lazyslide/wsi.py

@@ -200,6 +200,7 @@ def __init__(
         image: Path | str,
         h5_file: Path | str = None,
         reader="auto",  # openslide, vips, cucim
+        reader_options=None,
     ):
         from .utils import check_wsi_path
 
@@ -208,6 +209,7 @@ def __init__(
         if h5_file is None:
             h5_file = self.image.with_suffix(".coords.h5")
 
+        self.reader_options = {} if reader_options is None else reader_options
         self.h5_file = H5File(h5_file)
         self._reader_class = get_reader(reader)
         self._reader = None
@@ -226,7 +228,7 @@ def __repr__(self):
     @property
     def reader(self):
         if self._reader is None:
-            self._reader = self._reader_class(self.image)
+            self._reader = self._reader_class(self.image, **self.reader_options)
         return self._reader
 
     @property