From 256057f8a15f7932315bbe68c370693644ccf1e1 Mon Sep 17 00:00:00 2001
From: Andrew Herzing <andrew.herzing@nist.gov>
Date: Thu, 12 Oct 2023 13:40:52 -0400
Subject: [PATCH] Fixed shift order conflict in stack_register

---
 tomotools/align.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tomotools/align.py b/tomotools/align.py
index 471621aa..3ea12749 100644
--- a/tomotools/align.py
+++ b/tomotools/align.py
@@ -50,7 +50,7 @@ def apply_shifts(stack, shifts):
     for i in range(0, shifted.data.shape[0]):
         shifted.data[i, :, :] =\
             ndimage.shift(shifted.data[i, :, :],
-                          shift=[shifts[i, 1], shifts[i, 0]])
+                          shift=[shifts[i, 0], shifts[i, 1]])
     shifted.metadata.Tomography.shifts = \
         shifted.metadata.Tomography.shifts + shifts
     return shifted
@@ -295,7 +295,7 @@ def calculate_shifts_com(stack, nslice, ratio):
         A[ntilts * j:ntilts * (j + 1), 0:ntilts] = Gam
 
     shifts = np.zeros([stack.data.shape[0], 2])
-    shifts[:, 1] = np.dot(np.linalg.pinv(A), t_select)[:, 0]
+    shifts[:, 0] = np.dot(np.linalg.pinv(A), t_select)[:, 0]
 
     shifts = stack.metadata.Tomography.shifts + shifts
     return shifts
@@ -319,7 +319,7 @@ def calculate_shifts_pc(stack, start, show_progressbar):
     """
     def calc_pc(source, shifted):
         shift = pcc(shifted, source, upsample_factor=3)
-        return shift[0][::-1]
+        return shift[0]
 
     shifts = np.zeros([stack.data.shape[0] - 1, 2])
     if start is None:
@@ -356,7 +356,7 @@ def calculate_shifts_stackreg(stack):
     """
     sr = StackReg(StackReg.TRANSLATION)
     shifts = sr.register_stack(stack.data, reference='previous')
-    shifts = -np.array([i[0:2, 2] for i in shifts])
+    shifts = -np.array([i[0:2, 2][::-1] for i in shifts])
     return shifts
 
 
@@ -395,17 +395,17 @@ def calc_com_cl_shifts(stack, com_ref_index, cl_ref_index, cl_resolution,
 
     """
 
-    def calc_xshifts(stack, com_ref=None):
+    def calc_yshifts(stack, com_ref=None):
         ntilts = stack.data.shape[0]
         aliX = stack.deepcopy()
         coms = np.zeros(ntilts)
-        xhifts = np.zeros_like(coms)
+        yshifts = np.zeros_like(coms)
 
         for i in tqdm.tqdm(range(0, ntilts)):
             im = aliX.data[i, :, :]
             coms[i], _ = ndimage.center_of_mass(im)
-            xhifts[i] = com_ref - coms[i]
-        return xhifts
+            yshifts[i] = com_ref - coms[i]
+        return yshifts
 
     if cl_resolution >= 0.5:
         raise ValueError("Resolution should be less than 0.5")
@@ -415,8 +415,8 @@ def calc_xshifts(stack, com_ref=None):
     logger.info("Common line reference slice: %s" % cl_ref_index)
     xshifts = np.zeros(stack.data.shape[0])
     yshifts = np.zeros(stack.data.shape[0])
-    xshifts = calc_xshifts(stack, com_ref_index)
-    yshifts = calc_shifts_cl(stack, cl_ref_index,
+    yshifts = calc_yshifts(stack, com_ref_index)
+    xshifts = calc_shifts_cl(stack, cl_ref_index,
                              cl_resolution, cl_div_factor)
     shifts = np.stack([yshifts, xshifts], axis=1)
     return shifts
@@ -464,7 +464,7 @@ def align_stack(stack, method, start, show_progressbar, nslice, ratio,
         3-D numpy array containing the tilt series data
     method : string
         Method by which to calculate the alignments. Valid options
-        are 'PC', 'COM', or 'COM-CL'.
+        are 'StackReg', 'PC', 'COM', or 'COM-CL'.
     start : integer
         Position in tilt series to use as starting point for the alignment.
         If None, the central projection is used.