Replace correct_drift algorithm with scharr alignment

Stoner/Image/imagefuncs.py

@@ -453,7 +453,7 @@ def convert(image, dtype, force_copy=False, uniform=False, normalise=True):
     return image.astype(dtype)
 
 
-def correct_drift(im, ref, threshold=0.005, upsample_factor=50, box=False, do_shift=True):
+def correct_drift(im, ref, **kargs):
     """Align images to correct for image drift.
 
     Args:
@@ -476,30 +476,15 @@ def correct_drift(im, ref, threshold=0.005, upsample_factor=50, box=False, do_sh
     Adds 'drift_shift' to the metadata as the (x,y) vector that translated the
     image back to it's origin.
     """
-    if isinstance(box, bool) and not box:
-        im = im.clone.crop(box=box)
-    cls = type(im)
-
-    refed = cls(ref, get_metadata=False)
-    refed = refed.crop(box=box)
-    refed = refed.filter_image(sigma=1)
-    refed = refed > refed.threshold_otsu()
-    refed = refed.corner_fast(threshold=threshold)
-
-    imed = im.clone
-    imed = imed.filter_image(sigma=1)
-    imed = imed > imed.threshold_otsu()
-    imed = imed.corner_fast(threshold=threshold)
+    do_shift = kargs.pop("do_shift", True)
+    kargs["scale"] = kargs.pop("upscale", kargs.get("scale", 5.0))
+    kargs.setdefault("meothd", "scharr")
 
-    refed = refed.view(np.ndarray)
-    imed = imed.view(np.ndarray)
-
-    shift = registration.phase_cross_correlation(
-        refed, imed, upsample_factor=upsample_factor, reference_mask=~np.isnan(refered), moving_mask=~np.isnan(imed)
-    )[0]
+    ret = align(im, ref, **kargs)
     if do_shift:
-        im = im.translate(translation=(-shift[1], -shift[0]))  # x,y
-    im.metadata["correct_drift"] = (-shift[1], -shift[0])
+        im = ret
+    im["correct_drift"] = -np.array(ret["tvec"])[::-1]
+
     return im
 
 

tests/Stoner/mixedmetatest.txt

@@ -1,15 +1,15 @@
-TDI Format 1.5	1	2	3	4
-Stoner.class{String}=Data	0	1	2	3
-t0{Boolean}=True	4	5	6	7
-t1{I32}=1	8	9	10	11
-t10{List}=[1, (1, 2), 'abc']
-t11{List}=[[[1]]]
-t12{Void}=None
-t2{Double Float}=0.2
-t3{Cluster (I32,String)}={'a': 1, 'b': 'abc'}
-t4{Cluster (I32,I32)}=(1, 2)
-t5{1D Array (Invalid Type)}=array([0, 1, 2])
-t6{List}=[1, 2, 3]
-t7{String}=abc
-t8{String}=\\abc\cde
-t9{Double Float}=1e-20
+TDI Format 1.5	1	2	3	4
+Stoner.class{String}=Data	0	1	2	3
+t0{Boolean}=True	4	5	6	7
+t1{I32}=1	8	9	10	11
+t10{List}=[1, (1, 2), 'abc']
+t11{List}=[[[1]]]
+t12{Void}=None
+t2{Double Float}=0.2
+t3{Cluster (I32,String)}={'a': 1, 'b': 'abc'}
+t4{Cluster (I32,I32)}=(1, 2)
+t5{1D Array (Invalid Type)}=array([0, 1, 2])
+t6{List}=[1, 2, 3]
+t7{String}=abc
+t8{String}=\\abc\cde
+t9{Double Float}=1e-20