Flip the tomogram y coordinates so origin is at top (#643)

Author: stephen-riggs

src/murfey/workflows/tomo/tomo_metadata.py

@@ -329,6 +329,7 @@ def register_batch_position_in_database(
             ]
         )
 
+        # Apply stage corrections to the location
         corrected_vector = np.matmul(
             np.linalg.inv(reference_shift_matrix),
             np.matmul(
@@ -339,7 +340,10 @@ def register_batch_position_in_database(
                 ),
             ),
         )
-        centre_batch_pixel = corrected_vector / search_map.pixel_size + [
+        # Invert y coordinate
+        inverted_corrected_vector = np.matmul([[1, 0], [0, -1]], corrected_vector)
+        # Apply shift from centre
+        centre_batch_pixel = inverted_corrected_vector / search_map.pixel_size + [
             search_map.width / 2,
             search_map.height / 2,
         ]
@@ -354,7 +358,7 @@ def register_batch_position_in_database(
         tilt_series.y_location = (
             (
                 centre_batch_pixel[1]
-                - batch_parameters.y_beamshift / search_map.pixel_size
+                + batch_parameters.y_beamshift / search_map.pixel_size
             )
             * 512
             / search_map.width

tests/workflows/tomo/test_tomo_metadata.py

@@ -249,8 +249,8 @@ def test_register_batch_position_update(murfey_db_session: Session):
 
     # These two should have been updated, values are known as used identity matrices
     bp_final_parameters = murfey_db_session.exec(select(TiltSeries)).one()
-    assert bp_final_parameters.x_location == 880 * 512 / search_map.width
-    assert bp_final_parameters.y_location == 1780 * 512 / search_map.width
+    assert bp_final_parameters.x_location == 880 * 512 / 2000
+    assert bp_final_parameters.y_location == (4000 - 1780) * 512 / 2000
 
 
 def test_register_batch_position_update_skip(murfey_db_session: Session):
@@ -361,5 +361,5 @@ def test_register_batch_position_new(murfey_db_session: Session):
 
     # These two should have been updated, values are known as used identity matrices
     bp_final_parameters = murfey_db_session.exec(select(TiltSeries)).one()
-    assert bp_final_parameters.x_location == 880 * 512 / search_map.width
-    assert bp_final_parameters.y_location == 1780 * 512 / search_map.width
+    assert bp_final_parameters.x_location == 880 * 512 / 2000
+    assert bp_final_parameters.y_location == (4000 - 1780) * 512 / 2000