3d removal of background

https://www.notion.so/qim-dtu/3D-remove-background-function-fac8e64da886429eacd9520bc7be0610?pvs=4

implemented into existing filters framework

qim3d/processing/filters.py

@@ -6,6 +6,8 @@ import numpy as np
 from scipy import ndimage
 from skimage import morphology
 
+from qim3d.io.logger import log
+
 __all__ = [
     "Gaussian",
     "Median",
@@ -220,17 +222,18 @@ def tophat(vol, **kwargs):
     Remove background from the volume
     Args:
         vol: The volume to remove background from
-        radius: The radius of the structuring element
-        background_dark: If the background is dark or bright (default: True)
+        radius: The radius of the structuring element (default: 1)
+        background: color of the background, 'dark' or 'bright' (default: 'dark'). If 'bright', volume will be inverted.
     Returns:
         vol: The volume with background removed
     """
-    background_dark =  kwargs["background_dark"] if "background_dark" in kwargs else True
-    radius = kwargs["radius"] if "radius" in kwargs else 3 
-
+    radius = kwargs["radius"] if "radius" in kwargs else 1
+    background = kwargs["background"] if "background" in kwargs else "dark"
+    
+    if background == "bright":
+            log.info("Bright background selected, volume will be inverted.")
+            vol = np.invert(vol)
+    
     selem = morphology.ball(radius)
-    if background_dark:
-        vol = vol - morphology.white_tophat(vol, selem)
-    else:
-        vol = morphology.black_tophat(vol, selem) - vol
+    vol = vol - morphology.white_tophat(vol, selem)
     return vol