Synthetic image gen

https://www.notion.so/qim-dtu/Synthetic-image-generation-ee52134828584748bbb36d732c227816?pvs=4

Speed

• For 512^3 takes 35 seconds.
• 512,512,256 takes 18 seconds
• for 128 takes 3 seconds.
• Slow because of large image size. (slow to scale up with scipy.zoom)

qim3d/utils/img.py

@@ -49,12 +49,13 @@ def overlay_rgb_images(background, foreground, alpha=0.5):
     return composite.astype("uint8")
 
 
-def generate_synthetic_volume(shape, dtype=np.float32):
+def generate_synthetic_volume(shape, dtype=np.float32, order=1):
     """Generate a synthetic volume with custom structures.
 
     Args:
         shape (tuple): The shape of the volume in (x, y, z) dimensions.
         dtype (str): The data type of the volume.
+        order (int): The order of interpolation for zooming. (Lower is faster)
 
     Returns:
         numpy.ndarray: The synthetic volume.
@@ -96,7 +97,7 @@ def generate_synthetic_volume(shape, dtype=np.float32):
                                                 k * scale) ) * (1-dist)
 
     # Scale up the volume of organic_shape to size
-    volume = scipy.ndimage.zoom(organic_shape, [s/shape_dim for s in shape])
+    volume = scipy.ndimage.zoom(organic_shape, [s/shape_dim for s in shape], order=order)
 
     # clip the low values of the volume to create a coherent volume
     volume[volume < 0.5] = 0