Skip to content

Do not in-place mutate in the ispyb functions #853

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
stephen-riggs merged 1 commit into from
Aug 4, 2026
Merged

Do not in-place mutate in the ispyb functions #853

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
106 changes: 44 additions & 62 deletions src/murfey/server/ispyb.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -224,14 +224,15 @@ def do_insert_grid_square(
):
color_flags = color_flags or {}
# most of this is for mypy
pixel_size = grid_square_parameters.pixel_size
if (
grid_square_parameters.pixel_size is not None
pixel_size is not None
and grid_square_parameters.thumbnail_size_x is not None
and grid_square_parameters.readout_area_x is not None
):
# currently hard coding the scale factor because of difficulties with
# guaranteeing we have the atlas jpg and mrc sizes
grid_square_parameters.pixel_size *= (
pixel_size *= (
grid_square_parameters.readout_area_x
/ grid_square_parameters.thumbnail_size_x
)
Expand All @@ -246,7 +247,7 @@ def do_insert_grid_square(
angle=grid_square_parameters.angle,
stageLocationX=grid_square_parameters.x_stage_position,
stageLocationY=grid_square_parameters.y_stage_position,
pixelSize=grid_square_parameters.pixel_size,
pixelSize=pixel_size,
mode=grid_square_parameters.collection_mode,
)
# Optionally insert colour flags
Expand Down Expand Up @@ -281,12 +282,13 @@ def do_update_grid_square(
.filter(GridSquare.gridSquareId == grid_square_id)
.one()
)
pixel_size = grid_square_parameters.pixel_size
if (
grid_square_parameters.pixel_size is not None
pixel_size is not None
and grid_square_parameters.readout_area_x is not None
and grid_square_parameters.thumbnail_size_x is not None
):
grid_square_parameters.pixel_size *= (
pixel_size *= (
grid_square_parameters.readout_area_x
/ grid_square_parameters.thumbnail_size_x
)
Expand All @@ -310,8 +312,8 @@ def do_update_grid_square(
grid_square.stageLocationX = grid_square_parameters.x_stage_position
if grid_square_parameters.y_stage_position:
grid_square.stageLocationY = grid_square_parameters.y_stage_position
if grid_square_parameters.pixel_size:
grid_square.pixelSize = grid_square_parameters.pixel_size
if pixel_size:
grid_square.pixelSize = pixel_size
if grid_square_parameters.collection_mode:
grid_square.mode = grid_square_parameters.collection_mode
# Optionally insert colour flags
Expand Down Expand Up @@ -441,45 +443,34 @@ def do_insert_search_map(
atlas_id: int,
search_map_parameters: SearchMapParameters,
):
pixel_size = search_map_parameters.pixel_size
if (
search_map_parameters.pixel_size
pixel_size
and search_map_parameters.height
and search_map_parameters.height_on_atlas
):
search_map_parameters.pixel_size *= (
pixel_size *= (
search_map_parameters.height / search_map_parameters.height_on_atlas
)
search_map_parameters.height = (
int(search_map_parameters.height / 7.8)
if search_map_parameters.height
else None
)
search_map_parameters.width = (
int(search_map_parameters.width / 7.8)
if search_map_parameters.width
else None
)
search_map_parameters.x_location = (
int(search_map_parameters.x_location / 7.8)
if search_map_parameters.x_location
else None
)
search_map_parameters.y_location = (
int(search_map_parameters.y_location / 7.8)
if search_map_parameters.y_location
else None
)
record = GridSquare(
atlasId=atlas_id,
gridSquareImage=search_map_parameters.image,
pixelLocationX=search_map_parameters.x_location,
pixelLocationY=search_map_parameters.y_location,
height=search_map_parameters.height_on_atlas,
width=search_map_parameters.width_on_atlas,
pixelLocationX=int(search_map_parameters.x_location / 7.8)
if search_map_parameters.x_location
else None,
pixelLocationY=int(search_map_parameters.y_location / 7.8)
if search_map_parameters.y_location
else None,
height=int(search_map_parameters.height / 7.8)
if search_map_parameters.height
else None,
width=int(search_map_parameters.width / 7.8)
if search_map_parameters.width
else None,
angle=0,
stageLocationX=search_map_parameters.x_stage_position,
stageLocationY=search_map_parameters.y_stage_position,
pixelSize=search_map_parameters.pixel_size,
pixelSize=pixel_size,
)
try:
with ISPyBSession() as db:
Expand All @@ -505,12 +496,13 @@ def do_update_search_map(
.filter(GridSquare.gridSquareId == search_map_id)
.one()
)
pixel_size = search_map_parameters.pixel_size
if (
search_map_parameters.pixel_size
pixel_size
and search_map_parameters.height
and search_map_parameters.height_on_atlas
):
search_map_parameters.pixel_size *= (
pixel_size *= (
search_map_parameters.height
/ search_map_parameters.height_on_atlas
)
Expand All @@ -534,8 +526,8 @@ def do_update_search_map(
grid_square.stageLocationX = search_map_parameters.x_stage_position
if search_map_parameters.y_stage_position:
grid_square.stageLocationY = search_map_parameters.y_stage_position
if search_map_parameters.pixel_size:
grid_square.pixelSize = search_map_parameters.pixel_size
if pixel_size:
grid_square.pixelSize = pixel_size
db.add(grid_square)
db.commit()
return {"success": True, "return_value": grid_square.gridSquareId}
Expand All @@ -552,31 +544,24 @@ def do_insert_sxt_roi(
atlas_id: int,
roi_parameters: SearchMapParameters,
):
if (
roi_parameters.pixel_size
and roi_parameters.height
and roi_parameters.height_on_atlas
):
roi_parameters.pixel_size *= (
roi_parameters.height / roi_parameters.height_on_atlas
)
roi_parameters.x_location = (
int(roi_parameters.x_location) if roi_parameters.x_location else None
)
roi_parameters.y_location = (
int(roi_parameters.y_location) if roi_parameters.y_location else None
)
pixel_size = roi_parameters.pixel_size
if pixel_size and roi_parameters.height and roi_parameters.height_on_atlas:
pixel_size *= roi_parameters.height / roi_parameters.height_on_atlas
record = GridSquare(
atlasId=atlas_id,
gridSquareImage=roi_parameters.image,
pixelLocationX=roi_parameters.x_location,
pixelLocationY=roi_parameters.y_location,
pixelLocationX=int(roi_parameters.x_location)
if roi_parameters.x_location
else None,
pixelLocationY=int(roi_parameters.y_location)
if roi_parameters.y_location
else None,
height=roi_parameters.height_on_atlas,
width=roi_parameters.width_on_atlas,
angle=0,
stageLocationX=roi_parameters.x_stage_position,
stageLocationY=roi_parameters.y_stage_position,
pixelSize=roi_parameters.pixel_size,
pixelSize=pixel_size,
)
try:
with ISPyBSession() as db:
Expand All @@ -598,14 +583,13 @@ def do_update_sxt_roi(self, roi_id, roi_parameters: SearchMapParameters):
grid_square = (
db.query(GridSquare).filter(GridSquare.gridSquareId == roi_id).one()
)
pixel_size = roi_parameters.pixel_size
if (
roi_parameters.pixel_size
pixel_size
and roi_parameters.height
and roi_parameters.height_on_atlas
):
roi_parameters.pixel_size *= (
roi_parameters.height / roi_parameters.height_on_atlas
)
pixel_size *= roi_parameters.height / roi_parameters.height_on_atlas
grid_square.gridSquareImage = (
roi_parameters.image or grid_square.gridSquareImage
)
Expand All @@ -623,9 +607,7 @@ def do_update_sxt_roi(self, roi_id, roi_parameters: SearchMapParameters):
grid_square.stageLocationY = (
roi_parameters.y_stage_position or grid_square.stageLocationY
)
grid_square.pixelSize = (
roi_parameters.pixel_size or grid_square.pixelSize
)
grid_square.pixelSize = pixel_size or grid_square.pixelSize
db.add(grid_square)
db.commit()
return {"success": True, "return_value": grid_square.gridSquareId}
Expand Down