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

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Merged
stephen-riggs merged 2 commits into from
Jul 24, 2025
Merged

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

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65b9994
Flip the tomogram y coordinates so origin is at top
stephen-riggs Jul 24, 2025
f7c75aa
Beam shift also needs flipping
stephen-riggs Jul 24, 2025
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8 changes: 6 additions & 2 deletions src/murfey/workflows/tomo/tomo_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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,
]
Expand All @@ -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
Expand Down
8 changes: 4 additions & 4 deletions tests/workflows/tomo/test_tomo_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -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