Fixing pseudo rgb

src/gui/widgets/annotation_canvas_widget.py

@@ -250,12 +250,10 @@ class AnnotationCanvasWidget(QWidget):
             # Get image data in a format compatible with Qt
             if self.current_image.channels in (3, 4):
                 image_data = self.current_image.get_rgb()
-                height, width = image_data.shape[:2]
             else:
-                image_data = self.current_image.get_grayscale()
+                image_data = self.current_image.get_qt_rgb()
-                height, width = image_data.shape
 
-            image_data = np.ascontiguousarray(image_data)
+            height, width = image_data.shape[:2]
             bytes_per_line = image_data.strides[0]
 
             qimage = QImage(
@@ -263,7 +261,7 @@ class AnnotationCanvasWidget(QWidget):
                 width,
                 height,
                 bytes_per_line,
-                self.current_image.qtimage_format,
+                QImage.Format_RGBX32FPx4,  # self.current_image.qtimage_format,
             ).copy()  # Copy so Qt owns the buffer even after numpy array goes out of scope
 
             self.original_pixmap = QPixmap.fromImage(qimage)

src/model/yolo_wrapper.py

@@ -257,17 +257,11 @@ class YOLOWrapper:
             if source_path.is_file():
                 try:
                     img_obj = Image(source_path)
-                    pil_img = img_obj.pil_image
-                    if len(pil_img.getbands()) == 1:
-                        rgb_img = img_obj.convert_grayscale_to_rgb_preserve_range()
-                    else:
-                        rgb_img = pil_img.convert("RGB")
-
                     suffix = source_path.suffix or ".png"
                     tmp = tempfile.NamedTemporaryFile(suffix=suffix, delete=False)
                     tmp_path = tmp.name
                     tmp.close()
-                    rgb_img.save(tmp_path)
+                    img_obj.save(tmp_path)
                     cleanup_path = tmp_path
                     logger.info(
                         f"Converted image {source_path} to RGB for inference at {tmp_path}"

src/utils/image.py

@@ -6,16 +6,49 @@ import cv2
 import numpy as np
 from pathlib import Path
 from typing import Optional, Tuple, Union
-from PIL import Image as PILImage
 
 from src.utils.logger import get_logger
 from src.utils.file_utils import validate_file_path, is_image_file
 
 from PySide6.QtGui import QImage
 
+from tifffile import imread, imwrite
+
 logger = get_logger(__name__)
 
 
+def get_pseudo_rgb(arr: np.ndarray, gamma: float = 0.3) -> np.ndarray:
+    """
+    Convert a grayscale image to a pseudo-RGB image using a gamma correction.
+
+    Args:
+        arr: Input grayscale image as numpy array
+
+    Returns:
+        Pseudo-RGB image as numpy array
+    """
+    if arr.ndim != 2:
+        raise ValueError("Input array must be a grayscale image with shape (H, W)")
+
+    a1 = arr.copy().astype(np.float32)
+    a1 -= np.percentile(a1, 2)
+    a1[a1 < 0] = 0
+    # p999 = np.percentile(a1, 99.9)
+    # a1[a1 > p999] = p999
+    a1 /= a1.max()
+
+    a2 = a1.copy()
+    a2 = a2**gamma
+    a2 /= a2.max()
+
+    a3 = a1.copy()
+    p9999 = np.percentile(a3, 99.99)
+    a3[a3 > p9999] = p9999
+    a3 /= a3.max()
+
+    return np.stack([a1, a2, a3], axis=0)
+
+
 class ImageLoadError(Exception):
     """Exception raised when an image cannot be loaded."""
 
@@ -54,7 +87,6 @@ class Image:
         """
         self.path = Path(image_path)
         self._data: Optional[np.ndarray] = None
-        self._pil_image: Optional[PILImage.Image] = None
         self._width: int = 0
         self._height: int = 0
         self._channels: int = 0
@@ -85,30 +117,24 @@ class Image:
             )
 
         try:
-            # Load with OpenCV (returns BGR format)
+            if self.path.suffix.lower() in [".tif", ".tiff"]:
-            self._data = cv2.imread(str(self.path), cv2.IMREAD_UNCHANGED)
+                self._data = imread(str(self.path))
+            else:
+                raise NotImplementedError
+                # Load with OpenCV (returns BGR format)
+                self._data = cv2.imread(str(self.path), cv2.IMREAD_UNCHANGED)
 
             if self._data is None:
                 raise ImageLoadError(f"Failed to load image with OpenCV: {self.path}")
 
             # Extract metadata
+            print(self._data.shape)
             self._height, self._width = self._data.shape[:2]
             self._channels = self._data.shape[2] if len(self._data.shape) == 3 else 1
             self._format = self.path.suffix.lower().lstrip(".")
             self._size_bytes = self.path.stat().st_size
             self._dtype = self._data.dtype
 
-            # Load PIL version for compatibility (convert BGR to RGB)
-            if self._channels == 3:
-                rgb_data = cv2.cvtColor(self._data, cv2.COLOR_BGR2RGB)
-                self._pil_image = PILImage.fromarray(rgb_data)
-            elif self._channels == 4:
-                rgba_data = cv2.cvtColor(self._data, cv2.COLOR_BGRA2RGBA)
-                self._pil_image = PILImage.fromarray(rgba_data)
-            else:
-                # Grayscale
-                self._pil_image = PILImage.fromarray(self._data)
-
             logger.info(
                 f"Successfully loaded image: {self.path.name} "
                 f"({self._width}x{self._height}, {self._channels} channels, "
@@ -131,18 +157,6 @@ class Image:
             raise ImageLoadError("Image data not available")
         return self._data
 
-    @property
-    def pil_image(self) -> PILImage.Image:
-        """
-        Get image data as PIL Image (RGB or grayscale).
-
-        Returns:
-            PIL Image object
-        """
-        if self._pil_image is None:
-            raise ImageLoadError("PIL image not available")
-        return self._pil_image
-
     @property
     def width(self) -> int:
         """Get image width in pixels."""
@@ -187,6 +201,7 @@ class Image:
     @property
     def dtype(self) -> np.dtype:
         """Get the data type of the image array."""
+
         if self._dtype is None:
             raise ImageLoadError("Image dtype not available")
         return self._dtype
@@ -206,8 +221,10 @@ class Image:
         elif self._channels == 1:
             if self._dtype == np.uint16:
                 return QImage.Format_Grayscale16
-            else:
+            elif self._dtype == np.uint8:
                 return QImage.Format_Grayscale8
+            elif self._dtype == np.float32:
+                return QImage.Format_BGR30
         else:
             raise ImageLoadError(f"Unsupported number of channels: {self._channels}")
 
@@ -218,6 +235,12 @@ class Image:
         Returns:
             Image data in RGB format as numpy array
         """
+        if self.channels == 1:
+            img = get_pseudo_rgb(self.data)
+            self._dtype = img.dtype
+            return img
+        raise NotImplementedError
+
         if self._channels == 3:
             return cv2.cvtColor(self._data, cv2.COLOR_BGR2RGB)
         elif self._channels == 4:
@@ -225,6 +248,18 @@ class Image:
         else:
             return self._data
 
+    def get_qt_rgb(self) -> np.ascontiguousarray:
+        # we keep data as (C, H, W)
+        _img = self.get_rgb()
+
+        img = np.zeros((self.height, self.width, 4), dtype=np.float32)
+        img[..., 0] = _img[0]  # R gradient
+        img[..., 1] = _img[1]  # G gradient
+        img[..., 2] = _img[2]  # B constant
+        img[..., 3] = 1.0  # A = 1.0 (opaque)
+
+        return np.ascontiguousarray(img)
+
     def get_grayscale(self) -> np.ndarray:
         """
         Get image as grayscale numpy array.
@@ -277,37 +312,18 @@ class Image:
         """
         return self._channels >= 3
 
-    def convert_grayscale_to_rgb_preserve_range(
+    def save(self, path: Union[str, Path], pseudo_rgb: bool = True) -> None:
-        self,
-    ) -> PILImage.Image:
-        """Convert a single-channel PIL image to RGB while preserving dynamic range.
 
-        Returns:
+        if self.channels == 1:
-            PIL Image in RGB mode with intensities normalized to 0-255.
+            if pseudo_rgb:
-        """
+                img = get_pseudo_rgb(self.data)
-        if self._channels == 3:
+            else:
-            return self.pil_image
+                img = np.repeat(self.data, 3, axis=2)
 
-        grayscale = self.data
-        if grayscale.ndim == 3:
-            grayscale = grayscale[:, :, 0]
-
-        original_dtype = grayscale.dtype
-        grayscale = grayscale.astype(np.float32)
-
-        if grayscale.size == 0:
-            return PILImage.new("RGB", self.shape, color=(0, 0, 0))
-
-        if np.issubdtype(original_dtype, np.integer):
-            denom = float(max(np.iinfo(original_dtype).max, 1))
         else:
-            max_val = float(grayscale.max())
+            raise NotImplementedError("Only grayscale images are supported for now.")
-            denom = max(max_val, 1.0)
 
-        grayscale = np.clip(grayscale / denom, 0.0, 1.0)
+        imwrite(path, data=img)
-        grayscale_u8 = (grayscale * 255.0).round().astype(np.uint8)
-        rgb_arr = np.repeat(grayscale_u8[:, :, None], 3, axis=2)
-        return PILImage.fromarray(rgb_arr, mode="RGB")
 
     def __repr__(self) -> str:
         """String representation of the Image object."""
@@ -322,3 +338,15 @@ class Image:
     def __str__(self) -> str:
         """String representation of the Image object."""
         return self.__repr__()
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--path", type=str, required=True)
+    args = parser.parse_args()
+
+    img = Image(args.path)
+    img.save(args.path + "test.tif")
+    print(img)

src/utils/ultralytics_16bit_patch.py

@@ -32,8 +32,10 @@ def apply_ultralytics_16bit_tiff_patches(*, force: bool = False) -> None:
 
     import cv2
     import numpy as np
-    import tifffile
+
+    # import tifffile
     import torch
+    from src.utils.image import Image
 
     from ultralytics.utils import patches as ul_patches
 
@@ -55,7 +57,7 @@ def apply_ultralytics_16bit_tiff_patches(*, force: bool = False) -> None:
 
         ext = os.path.splitext(filename)[1].lower()
         if ext in (".tif", ".tiff"):
-            arr = tifffile.imread(filename)
+            arr = Image(filename).get_qt_rgb()[:, :, :3]
 
             # Normalize common shapes:
             # - (H, W) -> (H, W, 1)
@@ -71,35 +73,6 @@ def apply_ultralytics_16bit_tiff_patches(*, force: bool = False) -> None:
             if arr.ndim == 2:
                 arr = arr[..., None]
 
-            # Ultralytics expects BGR ordering when `channels=3`.
-            # For grayscale data we replicate channels (no scaling, no quantization).
-            if flags != cv2.IMREAD_GRAYSCALE:
-                if arr.shape[2] == 1:
-                    if pseudo_rgb:
-                        gamma = 0.3
-                        a1 = arr.copy().astype(np.float32)
-                        a1 -= np.percentile(a1, 2)
-                        a1[a1 < 0] = 0
-                        p98 = np.percentile(a1, 98)
-                        a1[a1 > p98] = p98
-                        a1 /= a1.max()
-
-                        a2 = a1.copy()
-                        a2 = a2**gamma
-                        a2 /= a2.max()
-
-                        a3 = a1.copy()
-                        p90 = np.percentile(a3, 90)
-                        a3[a3 > p90] = p90
-                        a3 /= a3.max()
-
-                        arr = np.concatenate([a1, a2, a3], axis=2)
-
-                    else:
-                        arr = np.repeat(arr, 3, axis=2)
-                elif arr.shape[2] >= 3:
-                    arr = arr[:, :, :3]
-
             # Ensure contiguous array for downstream OpenCV ops.
             logger.info(f"Loading with monkey-patched imread: {filename}")
             return np.ascontiguousarray(arr)