Issue #68 swapped rotation and translation vectors in return from get…

… smooth frame

sksurgerycore/baseclasses/tracker.py

@@ -54,7 +54,8 @@ def get_smooth_frame(self, port_handles):
 
             tracking : list of 4x4 tracking matrices, rotation and position,
             or if use_quaternions is true, a list of tracking quaternions,
-            column 0-2 is x,y,z column 3-6 is the rotation as a quaternion.
+            column 0-3 is the rotation as a quaternion (qw, qx, qy, qz),
+            column 4-6 is the translation (x,y,z).
 
             tracking_quality : list the tracking quality, one per tool.
         """
@@ -75,8 +76,8 @@ def get_smooth_frame(self, port_handles):
 
                 if self.use_quaternions:
                     output_matrix = np.full((7,1), np.nan)
-                    output_matrix[0:3,0] = mean_tvec
-                    output_matrix[3:7,0] = mean_quat
+                    output_matrix[0:4,0] = mean_quat
+                    output_matrix[4:7,0] = mean_tvec
                     smth_tracking.append(output_matrix)
 
                 else:
@@ -155,7 +156,8 @@ def get_frame(self):
 
             tracking : list of 4x4 tracking matrices, rotation and position,
             or if use_quaternions is true, a list of tracking quaternions,
-            column 0-2 is x,y,z column 3-6 is the rotation as a quaternion.
+            column 0-3 is the rotation as a quaternion (qw, qx, qy, qz),
+            column 4-6 is the translation (x,y,z).
 
             tracking_quality : list the tracking quality, one per tool.
             """

tests/baseclasses/test_tracker.py

@@ -210,8 +210,8 @@ def test_tracker_quaternions():
     assert frame_numbers[test_index] == 0
     transform = np.full((7,1), np.nan)
     rotation = _rvec_to_quaternion([1.0, 0.0, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [0.0, 100.0, 200.0]
+    transform[0:4,0] = rotation
+    transform[4:7,0] = [0.0, 100.0, 200.0]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 0.5
 
@@ -244,8 +244,8 @@ def test_tracker_quaternions():
     assert frame_numbers[test_index] == 1
 
     rotation = _rvec_to_quaternion([0.6, 0.0, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [5.0, 75.0, 200.0]
+    transform[0:4,0] = rotation
+    transform[4:7,0] = [5.0, 75.0, 200.0]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 0.65
 
@@ -254,8 +254,8 @@ def test_tracker_quaternions():
     assert frame_numbers[test_index] == 0
 
     rotation = _rvec_to_quaternion([0.0, 0.0, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [50.0, -100.0, 70.0]
+    transform[0:4,0] = rotation
+    transform[4:7,0] = [50.0, -100.0, 70.0]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 1.0
 
@@ -284,8 +284,8 @@ def test_tracker_quaternions():
     assert time_stamps[test_index] == 1.4
     assert frame_numbers[test_index] == 2
     rotation = _rvec_to_quaternion([0.0, 0.45, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [50.0, -100.0, 70.0]
+    transform[4:7,0] = [50.0, -100.0, 70.0]
+    transform[0:4,0] = rotation
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 1.0
 
@@ -300,7 +300,7 @@ def test_tracker_quaternions():
     assert math.isclose(time_stamps[test_index],1.4)
     assert frame_numbers[test_index] == 2
     rotation = _rvec_to_quaternion([0.6, 0.00, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [3.333333, 83.33333, 166.666667]
+    transform[0:4,0] = rotation
+    transform[4:7,0] = [3.333333, 83.33333, 166.666667]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 0.6