Included Richards autofocus plugin in defaults

openflexure_microscope/plugins/default/focus_utils.py

@@ -0,0 +1,21 @@
+import numpy as np
+from scipy import ndimage
+
+def decimate_to(shape, image):
+    """Decimate an image to reduce its size if it's too big."""
+    decimation = np.max(np.ceil(np.array(image.shape, dtype=np.float)[:len(shape)]/np.array(shape)))
+    return image[::int(decimation), ::int(decimation), ...]
+
+def sharpness_sum_lap2(rgb_image):
+    """Return an image sharpness metric: sum(laplacian(image)**")"""
+    #image_bw=np.mean(decimate_to((1000,1000), rgb_image),2)
+    image_bw=np.mean(rgb_image, 2)
+    image_lap=ndimage.filters.laplace(image_bw)
+    return np.mean(image_lap.astype(np.float)**4)
+
+def sharpness_edge(image):
+    """Return a sharpness metric optimised for vertical lines"""
+    gray = np.mean(image.astype(float), 2)
+    n = 20
+    edge = np.array([[-1]*n + [1]*n])
+    return np.sum([np.sum(ndimage.filters.convolve(gray,W)**2) for W in [edge, edge.T]])