Fade synthetic objects

The generate_blob and generate_collection functions now take in an argument object_shape that can be either cylinder or tube, which automatically computes the parameters of the fade_mask function such that the blobs will have the desired shape. Examples have been added to the documentation for both the generate_blob and the generate_collection function.

Also, the fade_mask function has been modified to normalize the volume after fading in order to retain the original maximum value of the volume.

qim3d/generate/blob_.py

@@ -2,6 +2,8 @@ import numpy as np
 import scipy.ndimage
 from noise import pnoise3
 
+import qim3d.processing
+
 def blob(
     base_shape: tuple = (128, 128, 128),
     final_shape: tuple = (128, 128, 128),
@@ -11,6 +13,7 @@ def blob(
     max_value: int = 255,
     threshold: float = 0.5,
     smooth_borders: bool = False,
+    object_shape: str = None,
     dtype: str = "uint8",
     ) -> np.ndarray:
     """
@@ -25,6 +28,7 @@ def blob(
         max_value (int, optional): Maximum value for the volume intensity. Defaults to 255.
         threshold (float, optional): Threshold value for clipping low intensity values. Defaults to 0.5.
         smooth_borders (bool, optional): Flag for automatic computation of the threshold value to ensure a blob with no straight edges. If True, the `threshold` parameter is ignored. Defaults to False.
+        object_shape (str, optional): Shape of the object to generate, either 'sphere', 'cylinder', or 'pipe'. Defaults to None.
         dtype (str, optional): Desired data type of the output volume. Defaults to "uint8".
 
     Returns:
@@ -115,4 +119,74 @@ def blob(
         volume, np.array(final_shape) / np.array(base_shape), order=order
     )
 
-    return volume.astype(dtype)
+    # Fade into a shape if specified
+    if object_shape == "sphere":
+        
+        # Arguments for the fade_mask function
+        geometry = "spherical"          # Fade in spherical geometry
+        target_max_normalized_distance = 1.35   # This value ensures that the object will become spherical
+
+        volume = qim3d.processing.operations.fade_mask(volume,
+                                                       geometry = geometry,
+                                                       target_max_normalized_distance = target_max_normalized_distance
+                                                       )
+
+    elif object_shape == "cylinder":
+
+        # Arguments for the fade_mask function
+        geometry = "cylindrical"        # Fade in cylindrical geometry
+        axis = np.argmax(final_shape)   # Fade along the dimension where the object is the largest
+        target_max_normalized_distance = 1.35   # This value ensures that the object will become cylindrical
+
+        print(f"Before fades, volume is dtype: {volume.dtype}, max value: {np.max(volume)}, unique values: {np.unique(volume)}")
+
+        volume = qim3d.processing.operations.fade_mask(volume, 
+                                                       geometry = geometry, 
+                                                       axis = axis, 
+                                                       target_max_normalized_distance = target_max_normalized_distance
+                                                       )
+        
+        print(f"After one fade, volume is dtype: {volume.dtype}, max value: {np.max(volume)}, unique values: {np.unique(volume)}")
+        
+
+    elif object_shape == "pipe":
+
+        # Arguments for the fade_mask function
+        geometry = "cylindrical"        # Fade in cylindrical geometry
+        axis = np.argmax(final_shape)   # Fade along the dimension where the object is the largest
+        target_max_normalized_distance = 1.35   # This value ensures that the object will become cylindrical
+
+        print(f"Before fade, volume is dtype: {volume.dtype}, max value: {np.max(volume)}, unique values: {np.unique(volume)}")
+
+        # Fade once for making the object cylindrical
+        volume = qim3d.processing.operations.fade_mask(volume, 
+                                                       geometry = geometry, 
+                                                       axis = axis,
+                                                       target_max_normalized_distance = target_max_normalized_distance,
+                                                       invert = False
+                                                       )
+        
+        print(f"First fade, volume is dtype: {volume.dtype}, max value: {np.max(volume)}, unique values: {np.unique(volume)}")
+        
+        ratio = 0.3                     # Ratio of the object that will be faded
+        decay_rate = 6                  # Decay rate for the fade operation
+
+        # Fade again with invert = True for making the object a pipe (i.e. with a hole in the middle)
+        volume = qim3d.processing.operations.fade_mask(volume, 
+                                                       geometry = geometry, 
+                                                       axis = axis, 
+                                                    #    ratio = ratio,
+                                                    #    decay_rate = decay_rate,
+                                                       invert = True
+                                                       )
+        
+        print(f"Second fade, volume is dtype: {volume.dtype}, max value: {np.max(volume)}, unique values: {np.unique(volume)}")
+
+    
+    # Convert to desired data type
+    volume = volume.astype(dtype)
+
+    print(f"Final volume is dtype: {volume.dtype}, max value: {np.max(volume)}, unique values: {np.unique(volume)}\n")
+
+    return volume
+