From 0c19ea2557e2c3e5b81f0b14696b09d42adb40fa Mon Sep 17 00:00:00 2001
From: Martin Laasmaa <martin@sysbio.ioc.ee>
Date: Fri, 16 Jan 2026 10:30:13 +0200
Subject: [PATCH] Updating

---
 src/utils/image.py | 43 ++++++++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/src/utils/image.py b/src/utils/image.py
index c0fdeeb..286ffdf 100644
--- a/src/utils/image.py
+++ b/src/utils/image.py
@@ -37,7 +37,7 @@ def get_pseudo_rgb(arr: np.ndarray, gamma: float = 0.5) -> np.ndarray:
     a1[a1 > p999] = p999
     a1 /= a1.max()
 
-    if 0:
+    if 1:
         a2 = a1.copy()
         a2 = a2**gamma
         a2 /= a2.max()
@@ -47,9 +47,12 @@ def get_pseudo_rgb(arr: np.ndarray, gamma: float = 0.5) -> np.ndarray:
         a3[a3 > p9999] = p9999
         a3 /= a3.max()
 
-    return np.stack([a1, np.zeros(a1.shape), np.zeros(a1.shape)], axis=0)
+    # return np.stack([a1, np.zeros(a1.shape), np.zeros(a1.shape)], axis=0)
     # return np.stack([a2, np.zeros(a1.shape), np.zeros(a1.shape)], axis=0)
-    # return np.stack([a1, a2, a3], axis=0)
+    out = np.stack([a1, a2, a3], axis=0)
+    # print(any(np.isnan(out).flatten()))
+
+    return out
 
 
 class ImageLoadError(Exception):
@@ -122,7 +125,7 @@ class Image:
             if self.path.suffix.lower() in [".tif", ".tiff"]:
                 self._data = imread(str(self.path))
             else:
-                raise NotImplementedError("RGB is not implemented")
+                # raise NotImplementedError("RGB is not implemented")
                 # Load with OpenCV (returns BGR format)
                 self._data = cv2.imread(str(self.path), cv2.IMREAD_UNCHANGED)
 
@@ -246,27 +249,33 @@ class Image:
         if self.channels == 1:
             img = get_pseudo_rgb(self.data)
             self._dtype = img.dtype
-            return img
-        raise NotImplementedError
+            return img, True
 
-        if self._channels == 3:
-            return cv2.cvtColor(self._data, cv2.COLOR_BGR2RGB)
+        elif self._channels == 3:
+            return cv2.cvtColor(self._data, cv2.COLOR_BGR2RGB), False
         elif self._channels == 4:
-            return cv2.cvtColor(self._data, cv2.COLOR_BGRA2RGBA)
+            return cv2.cvtColor(self._data, cv2.COLOR_BGRA2RGBA), False
+
         else:
-            return self._data
+            raise NotImplementedError
+
+        # else:
+        #     return self._data
 
     def get_qt_rgb(self) -> np.ascontiguousarray:
         # we keep data as (C, H, W)
-        _img = self.get_rgb()
+        _img, pseudo = 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)
+        if pseudo:
+            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)
+            return np.ascontiguousarray(img)
+        else:
+            return np.ascontiguousarray(_img)
 
     def get_grayscale(self) -> np.ndarray:
         """