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Merged
stephen-riggs merged 8 commits into from
Aug 13, 2026
Merged

Insert tomogram locations in SXT regions of interest #860

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9faef0d
Pixel size and unit conversions for sxt
stephen-riggs Aug 11, 2026
f03329e
Insert tomogram locations into sxt rois
stephen-riggs Aug 11, 2026
8d258b8
Atlas pixel size should be for thumbnail
stephen-riggs Aug 11, 2026
616520b
update tests
stephen-riggs Aug 12, 2026
87d6901
update tests
stephen-riggs Aug 12, 2026
75ef736
update tests
stephen-riggs Aug 12, 2026
f096412
update tests
stephen-riggs Aug 12, 2026
36aaaac
Add comments on units
stephen-riggs Aug 13, 2026
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45 changes: 35 additions & 10 deletions src/murfey/client/contexts/sxt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,7 @@ def register_sxt_data_collection(
"source": str(self._basepath),
"tag": tilt_series,
"pixel_size_on_image": str(
round(data_collection_parameters.get("pixel_size", 100), 2) * 1e-10
data_collection_parameters.get("pixel_size", 100) * 1e-10
), # expected in metres
"image_size_x": data_collection_parameters.get("image_size_x", 0),
"image_size_y": data_collection_parameters.get("image_size_y", 0),
Expand Down Expand Up @@ -210,6 +210,7 @@ def post_transfer(
if xrm_ole.exists("ImageInfo/XPosition") and xrm_ole.exists(
"ImageInfo/YPosition"
):
# Get stage locations in microns
x_tiles = _get_ole_header_value(
xrm_ole, "ImageInfo/XPosition", np.float32
).tolist()
Expand All @@ -220,9 +221,13 @@ def post_transfer(
metadata["y_position"] = y_tiles[int(len(y_tiles) / 2)]

if xrm_ole.exists("ImageInfo/PixelSize"):
metadata["pixel_size"] = _get_ole_header_value(
xrm_ole, "ImageInfo/PixelSize", np.float32
).tolist()[0]
# Pixel size in microns, convert to metres
metadata["pixel_size"] = (
_get_ole_header_value(
xrm_ole, "ImageInfo/PixelSize", np.float32
).tolist()[0]
/ 1e6
)

if xrm_ole.exists("ImageInfo/ImageHeight"):
metadata["height"] = _get_ole_header_value(
Expand Down Expand Up @@ -276,14 +281,20 @@ def post_transfer(

if (
metadata.get("mosaic_size", 1) > 0
and metadata.get("pixel_size", 0) > 0.1
and metadata.get("pixel_size", 0) > 1e-7
):
# Large pixel size, this is an atlas
thumbnail_pixel_size = (
metadata["pixel_size"]
* metadata.get("height", 0)
* metadata["mosaic_rows"]
/ 1024
)
dcg_data = {
"experiment_type_id": 44, # Atlas
"tag": dcg_tag,
"atlas": str(thumbnail_path),
"atlas_pixel_size": round(metadata.get("pixel_size", 0), 2),
"atlas_pixel_size": float(thumbnail_pixel_size),
"atlas_x_stage_position": metadata.get("x_position", None),
"atlas_y_stage_position": metadata.get("y_position", None),
"atlas_height": int(
Expand Down Expand Up @@ -317,7 +328,7 @@ def post_transfer(
"tag": dcg_tag,
"x_stage_position": metadata.get("x_position", None),
"y_stage_position": metadata.get("y_position", None),
"pixel_size": round(metadata.get("pixel_size", 0), 2),
"pixel_size": metadata.get("pixel_size", 0),
"height": int(
metadata.get("height", 0) * metadata["mosaic_rows"]
),
Expand All @@ -342,6 +353,19 @@ def post_transfer(
if txrm_ole.exists("ReferenceData/Image"):
metadata["has_reference"] = True

if txrm_ole.exists("ImageInfo/XPosition") and txrm_ole.exists(
"ImageInfo/YPosition"
):
# Get stage locations in microns
x_tiles = _get_ole_header_value(
txrm_ole, "ImageInfo/XPosition", np.float32
).tolist()
y_tiles = _get_ole_header_value(
txrm_ole, "ImageInfo/YPosition", np.float32
).tolist()
metadata["x_position"] = x_tiles[int(len(x_tiles) / 2)]
metadata["y_position"] = y_tiles[int(len(y_tiles) / 2)]
Comment on lines +360 to +367

@tieneupin tieneupin Aug 12, 2026

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This could be iterated, but works as-is.

for key, old_path in (("x_position", "ImageInfo/XPosition"), ("y_position", "ImageInfo/YPosition")):
    tiles = _get_ole_header_value(txrm_ole, ole_path, np.float32).tolist()
    metadata[key] = tiles[int(len(tiles) / 2)]

Comment thread
stephen-riggs marked this conversation as resolved.

if txrm_ole.exists("ImageInfo/Angles"):
angles = _get_ole_header_value(
txrm_ole, "ImageInfo/Angles", np.float32
Expand All @@ -350,6 +374,7 @@ def post_transfer(
metadata["maximum_angle"] = max(angles)

if txrm_ole.exists("ImageInfo/PixelSize"):
# Pixel size in microns, converted to angstroms
pixel_size_txrm = _get_ole_header_value(
txrm_ole, "ImageInfo/PixelSize", np.float32
).tolist()
Expand Down Expand Up @@ -492,9 +517,7 @@ def post_transfer(
data={
"tag": tilt_series_tag,
"source": destination_search_dir,
"pixel_size": round(
metadata.get("pixel_size", 100), 2
), # angstroms
"pixel_size": metadata.get("pixel_size", 100), # angstroms
"tilt_offset": midpoint(angles),
"tilt_series_length": metadata.get(
"tilt_series_length", len(angles)
Expand All @@ -503,6 +526,8 @@ def post_transfer(
"xrm_reference": str(reference_file_transferred_to)
if reference_file_transferred_to
else None,
"x_stage_position": metadata.get("x_position", None),
"y_stage_position": metadata.get("y_position", None),
},
)
return True
64 changes: 64 additions & 0 deletions src/murfey/workflows/sxt/process_sxt_tilt_series.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import logging
from pathlib import Path

import numpy as np
from pydantic import BaseModel
from sqlmodel import select
from sqlmodel.orm.session import Session as SQLModelSession
Expand All @@ -15,6 +16,7 @@
DataCollection,
DataCollectionGroup,
ProcessingJob,
SearchMap,
Session,
TiltSeries,
)
Expand All @@ -30,6 +32,8 @@ class SXTTiltSeriesInfo(BaseModel):
pixel_size: float
tilt_offset: int
xrm_reference: str | None
x_stage_position: float | None = None
y_stage_position: float | None = None


def process_sxt_tilt_series(
Expand Down Expand Up @@ -82,6 +86,63 @@ def process_sxt_tilt_series(
instrument_name
]

# Determine pixel location on a roi for display
min_distance: float | None = None
matching_roi: SearchMap | None = None
x_pixel_location: int | None = None
y_pixel_location: int | None = None
if tilt_series_info.x_stage_position and tilt_series_info.y_stage_position:
# Find all rois for this grid
dcg_rois = murfey_db.exec(
select(SearchMap)
.where(SearchMap.session_id == session_id)
.where(SearchMap.tag == tilt_series.rsync_source)
).all()
for roi in dcg_rois:
if roi.x_stage_position is not None and roi.y_stage_position is not None:
# Determine the roi which is closest to this tomogram
roi_distance = np.sqrt(
(tilt_series_info.x_stage_position - roi.x_stage_position) ** 2
+ (tilt_series_info.y_stage_position - roi.y_stage_position) ** 2
)
if min_distance is None or roi_distance < min_distance:
min_distance = roi_distance
matching_roi = roi

# Calculate the position on the roi
if (
matching_roi is not None
and matching_roi.x_stage_position is not None
and matching_roi.y_stage_position is not None
and matching_roi.height
and matching_roi.width
and matching_roi.pixel_size
):
# Convert from stage position to pixel locations
# Stage position in microns, pixel size in metres
x_location_centered = (
(tilt_series_info.x_stage_position - matching_roi.x_stage_position)
/ matching_roi.pixel_size
/ 1e6

@tieneupin tieneupin Aug 12, 2026 •
edited
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Given that on the client side, you have been converting the pixel size to metres, is the /1e6 still needed here?

What are the units of the ..._stage_position and pixel_size attributes at this point?

@stephen-riggs stephen-riggs Aug 13, 2026

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1e6 is needed as the stage position is microns and the pixel size is metres

)
y_location_centered = (
(tilt_series_info.y_stage_position - matching_roi.y_stage_position)
/ matching_roi.pixel_size
/ 1e6
)

# Scaling from different pixel size of atlas and roi, and atlas thumbnail size
x_pixel_location = int(
x_location_centered * 1024 / matching_roi.width + 512
)
y_pixel_location = int(
512 - y_location_centered * 1024 / matching_roi.height
)
else:
logger.warning(
f"Cannot match ROI {matching_roi.id if matching_roi else None} for {tilt_series_info.tag}"
)

# Find the visit folder and any subfolders needed
parts = [secure_filename(p) for p in Path(tilt_series_info.txrm).parts]
visit_idx = parts.index(visit_name)
Expand Down Expand Up @@ -119,6 +180,9 @@ def process_sxt_tilt_series(
"pixel_size": tilt_series_info.pixel_size,
"manual_tilt_offset": -tilt_series_info.tilt_offset,
"node_creator_queue": machine_config.node_creator_queue,
"search_map_id": matching_roi.id if matching_roi else None,
"x_location": x_pixel_location,
"y_location": y_pixel_location,
},
}
if _transport_object:
Expand Down
18 changes: 14 additions & 4 deletions src/murfey/workflows/sxt/sxt_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,24 +80,34 @@ def register_sxt_roi(
atlas.image_pixels_y,
]
):
# Pixel size of full-size mosaic in metres
original_atlas_pixel_size = atlas.image_pixel_size * 1024 / atlas.image_pixels_x

# Convert from stage position to pixel locations
roi.x_location = (roi.x_stage_position - atlas.pos_x) / atlas.image_pixel_size
roi.y_location = (roi.y_stage_position - atlas.pos_y) / atlas.image_pixel_size
# Stage position in microns, pixel size in metres
roi.x_location = (
(roi.x_stage_position - atlas.pos_x) / original_atlas_pixel_size / 1e6
)
roi.y_location = (
(roi.y_stage_position - atlas.pos_y) / original_atlas_pixel_size / 1e6
)
Comment thread
stephen-riggs marked this conversation as resolved.

# Scaling from different pixel size of atlas and roi, and atlas thumbnail size
roi_parameters.x_location = roi.x_location * (512 / atlas.image_pixels_x) + 256
roi_parameters.y_location = 256 - roi.y_location * (512 / atlas.image_pixels_y)
# Find size in terms of atlas pixels
# Factor of 512 to account for thumbnailing assumption in pato
roi_parameters.width_on_atlas = int(
round(
roi.width
* (roi.pixel_size / atlas.image_pixel_size)
* (roi.pixel_size / original_atlas_pixel_size)
* (512 / atlas.image_pixels_x)
)
)
roi_parameters.height_on_atlas = int(
round(
roi.height
* (roi.pixel_size / atlas.image_pixel_size)
* (roi.pixel_size / original_atlas_pixel_size)
* (512 / atlas.image_pixels_y)
)
)
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Expand Down
34 changes: 22 additions & 12 deletions tests/client/contexts/test_sxt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,9 +83,9 @@ def test_sxt_context_xrm_atlas(mock_ole_file, mock_post, tmp_path):
"experiment_type_id": 44,
"tag": f"{tmp_path}/cm12345-6/grid1",
"atlas": "/path/to/dest/cm12345-6/processed/grid1/example_atlas_Annotated_thumbnail.jpg",
"atlas_pixel_size": 0.3,
"atlas_x_stage_position": 1,
"atlas_y_stage_position": -1,
"atlas_pixel_size": float(float(np.float32(0.3)) / 1e6 * 1000 * 6 / 1024),
"atlas_x_stage_position": 1.0,
"atlas_y_stage_position": -1.0,
"atlas_height": 6000,
"atlas_width": 4500,
},
Expand Down Expand Up @@ -161,9 +161,9 @@ def test_sxt_context_xrm_roi(mock_ole_file, mock_post, tmp_path):
"http://localhost:8000/workflow/sxt/sessions/1/sxt_roi/example_roi",
json={
"tag": f"{tmp_path}/cm12345-6/grid1",
"x_stage_position": 1,
"y_stage_position": -1,
"pixel_size": 0.03,
"x_stage_position": 1.0,
"y_stage_position": -1.0,
"pixel_size": float(np.float32(0.03)) * 1e-6,
"height": 6000,
"width": 4500,
"image": "/path/to/dest/cm12345-6/processed/grid1/example_roi_Annotated_thumbnail.jpg",
Expand All @@ -183,6 +183,8 @@ def test_sxt_context_txrm(mock_ole_file, mock_post, tmp_path):
)
# Metadata encoded arrays
mock_ole_file().__enter__().openstream().getvalue.side_effect = [
np.array([0.01], dtype=np.float32).tobytes(), # X position
np.array([0.02], dtype=np.float32).tobytes(), # Y position
np.array([-55, -25, 5, 35, 65], dtype=np.float32).tobytes(), # Angles
np.array([0.01001], dtype=np.float32).tobytes(), # Pixel size
np.array([1024], dtype=np.int32).tobytes(), # Image Width
Expand Down Expand Up @@ -218,8 +220,8 @@ def test_sxt_context_txrm(mock_ole_file, mock_post, tmp_path):
)

mock_ole_file.assert_any_call(str(tmp_path / "cm12345-6/grid1/example.txrm"))
assert mock_ole_file().__enter__().exists.call_count == 10
assert mock_ole_file().__enter__().openstream.call_count == 11 # 9 + 2 above
assert mock_ole_file().__enter__().exists.call_count == 12
assert mock_ole_file().__enter__().openstream.call_count == 13 # 11 + 2 above
mock_ole_file().__enter__().exists.assert_any_call("ReferenceData/Image")
for field_name in [
"ImageInfo/Angles",
Expand Down Expand Up @@ -254,7 +256,7 @@ def test_sxt_context_txrm(mock_ole_file, mock_post, tmp_path):
"data_collection_tag": "example",
"source": f"{tmp_path}/cm12345-6/grid1",
"tag": "example",
"pixel_size_on_image": str(100.1 * 1e-10),
"pixel_size_on_image": str(float(np.float32(0.01001)) * 1e-6),
"image_size_x": 1024,
"image_size_y": 2048,
"magnification": 1000,
Expand All @@ -281,11 +283,13 @@ def test_sxt_context_txrm(mock_ole_file, mock_post, tmp_path):
json={
"tag": "example",
"source": f"{tmp_path}/cm12345-6/grid1",
"pixel_size": 100.1,
"pixel_size": float(np.float32(0.01001)) * 1e4,
"tilt_offset": 5,
"tilt_series_length": 200,
"txrm": str(tmp_path / "destination/cm12345-6/grid1/example.txrm"),
"xrm_reference": None,
"x_stage_position": float(np.float32(0.01)),
"y_stage_position": float(np.float32(0.02)),
},
headers={"Authorization": "Bearer "},
)
Expand All @@ -304,6 +308,8 @@ def test_sxt_context_txrm_external_ref(mock_ole_file, mock_post, tmp_path):
)
# Metadata encoded arrays
mock_ole_file().__enter__().openstream().getvalue.side_effect = [
np.array([0.01], dtype=np.float32).tobytes(), # X position
np.array([0.02], dtype=np.float32).tobytes(), # Y position
np.array([-55, -25, 5, 35, 65], dtype=np.float32).tobytes(), # Angles
np.array([0.01001], dtype=np.float32).tobytes(), # Pixel size
np.array([1024], dtype=np.int32).tobytes(), # Image Width
Expand Down Expand Up @@ -368,7 +374,7 @@ def test_sxt_context_txrm_external_ref(mock_ole_file, mock_post, tmp_path):
"data_collection_tag": "example",
"source": f"{tmp_path}/cm12345-6/grid1",
"tag": "example",
"pixel_size_on_image": str(100.1 * 1e-10),
"pixel_size_on_image": str(float(np.float32(0.01001)) * 1e-6),
"image_size_x": 1024,
"image_size_y": 2048,
"magnification": 1000,
Expand Down Expand Up @@ -405,13 +411,15 @@ def test_sxt_context_txrm_external_ref(mock_ole_file, mock_post, tmp_path):
json={
"tag": "example",
"source": f"{tmp_path}/cm12345-6/grid1",
"pixel_size": 100.1,
"pixel_size": float(np.float32(0.01001)) * 1e4,
"tilt_offset": 5,
"tilt_series_length": 200,
"txrm": str(
tmp_path / "destination/cm12345-6/grid1/example_-60to60@0.5.txrm"
),
"xrm_reference": str(tmp_path / "destination/cm12345-6/grid1/ref.xrm"),
"x_stage_position": float(np.float32(0.01)),
"y_stage_position": float(np.float32(0.02)),
},
headers={"Authorization": "Bearer "},
)
Expand All @@ -430,6 +438,8 @@ def test_sxt_context_txrm_zero_angles(mock_ole_file, mock_post, tmp_path):
)
# Metadata encoded arrays
mock_ole_file().__enter__().openstream().getvalue.side_effect = [
np.array([0.01], dtype=np.float32).tobytes(), # X position
np.array([0.02], dtype=np.float32).tobytes(), # Y position
np.array([0, 0, 0, 0, 0], dtype=np.float32).tobytes(), # Angles
np.array([0.01001], dtype=np.float32).tobytes(), # Pixel size
np.array([1024], dtype=np.int32).tobytes(), # Image Width
Expand Down
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