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Register all grid squares and foil holes (#455)
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@d-j-hatton
d-j-hatton authored Jan 22, 2025
1 parent bc3278d commit 9a76bbc
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Showing 2 changed files with 100 additions and 36 deletions.
132 changes: 98 additions & 34 deletions src/murfey/client/contexts/spa_metadata.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import logging
from pathlib import Path
from typing import Optional
from typing import Dict, Optional

import requests
import xmltodict
Expand All @@ -9,13 +9,66 @@
from murfey.client.contexts.spa import _get_source
from murfey.client.instance_environment import MurfeyInstanceEnvironment, SampleInfo
from murfey.util import authorised_requests, capture_post, get_machine_config_client
from murfey.util.spa_metadata import get_grid_square_atlas_positions
from murfey.util.spa_metadata import FoilHoleInfo, get_grid_square_atlas_positions

logger = logging.getLogger("murfey.client.contexts.spa_metadata")

requests.get, requests.post, requests.put, requests.delete = authorised_requests()


def _foil_hole_positions(xml_path: Path, grid_square: int) -> Dict[str, FoilHoleInfo]:
with open(xml_path, "r") as xml:
for_parsing = xml.read()
data = xmltodict.parse(for_parsing)
data = data["GridSquareXml"]
readout_area = data["MicroscopeImage"]["microscopeData"]["acquisition"]["camera"][
"ReadoutArea"
]
pixel_size = data["MicroscopeImage"]["SpatialScale"]["pixelSize"]["x"][
"numericValue"
]
full_size = (int(readout_area["a:width"]), int(readout_area["a:height"]))
serialization_array = data["TargetLocations"]["TargetLocationsEfficient"][
"a:m_serializationArray"
]
required_key = ""
for key in serialization_array.keys():
if key.startswith("b:KeyValuePairOfintTargetLocation"):
required_key = key
break
if not required_key:
return {}
foil_holes = {}
for fh_block in serialization_array[required_key]:
if fh_block["b:value"]["IsNearGridBar"] == "false":
image_paths = list(
(xml_path.parent.parent).glob(
f"Images-Disc*/GridSquare_{grid_square}/FoilHoles/FoilHole_{fh_block['b:key']}_*.jpg"
)
)
image_paths.sort(key=lambda x: x.stat().st_ctime)
image_path: str = str(image_paths[-1]) if image_paths else ""
pix_loc = fh_block["b:value"]["PixelCenter"]
stage = fh_block["b:value"]["StagePosition"]
diameter = fh_block["b:value"]["PixelWidthHeight"]["c:width"]
foil_holes[fh_block["b:key"]] = FoilHoleInfo(
id=int(fh_block["b:key"]),
grid_square_id=grid_square,
x_location=int(float(pix_loc["c:x"])),
y_location=int(float(pix_loc["c:y"])),
x_stage_position=float(stage["c:X"]),
y_stage_position=float(stage["c:Y"]),
readout_area_x=full_size[0] if image_path else None,
readout_area_y=full_size[1] if image_path else None,
thumbnail_size_x=None,
thumbnail_size_y=None,
pixel_size=float(pixel_size) if image_path else None,
image=str(image_path),
diameter=int(float(diameter)),
)
return foil_holes


def _atlas_destination(
environment: MurfeyInstanceEnvironment, source: Path, file_path: Path
) -> Path:
Expand Down Expand Up @@ -109,36 +162,47 @@ def post_transfer(
"atlas_pixel_size": atlas_pixel_size,
}
capture_post(url, json=dcg_data)
registered_grid_squares = (
requests.get(
f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/grid_squares"
)
.json()
.get(str(source), [])
gs_pix_positions = get_grid_square_atlas_positions(
_atlas_destination(environment, source, transferred_file)
/ environment.samples[source].atlas
)
for gs, pos_data in gs_pix_positions.items():
if pos_data:
capture_post(
f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/grid_square/{gs}",
json={
"tag": str(source),
"x_location": pos_data[0],
"y_location": pos_data[1],
"x_stage_position": pos_data[2],
"y_stage_position": pos_data[3],
"width": pos_data[4],
"height": pos_data[5],
"angle": pos_data[6],
},
)

elif transferred_file.suffix == ".dm" and environment:
gs_name = transferred_file.name.split("_")[1]
fh_positions = _foil_hole_positions(transferred_file, int(gs_name))
source = _get_source(transferred_file, environment=environment)
visitless_source = str(source).replace(f"/{environment.visit}", "")
for fh, fh_data in fh_positions.items():
capture_post(
f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/grid_square/{gs_name}/foil_hole",
json={
"name": fh,
"x_location": fh_data.x_location,
"y_location": fh_data.y_location,
"x_stage_position": fh_data.x_stage_position,
"y_stage_position": fh_data.y_stage_position,
"readout_area_x": fh_data.readout_area_x,
"readout_area_y": fh_data.readout_area_y,
"thumbnail_size_x": fh_data.thumbnail_size_x,
"thumbnail_size_y": fh_data.thumbnail_size_y,
"pixel_size": fh_data.pixel_size,
"diameter": fh_data.diameter,
"tag": visitless_source,
"image": fh_data.image,
},
)
if registered_grid_squares:
gs_pix_positions = get_grid_square_atlas_positions(
source_visit_dir / partial_path
)
for gs in registered_grid_squares:
pos_data = gs_pix_positions.get(str(gs["name"]))
if pos_data:
capture_post(
f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/grid_square/{gs['name']}",
json={
"tag": gs["tag"],
"readout_area_x": gs["readout_area_x"],
"readout_area_y": gs["readout_area_y"],
"thumbnail_size_x": gs["thumbnail_size_x"],
"thumbnail_size_y": gs["thumbnail_size_y"],
"pixel_size": gs["pixel_size"],
"image": gs["image"],
"x_location": pos_data[0],
"y_location": pos_data[1],
"x_stage_position": pos_data[2],
"y_stage_position": pos_data[3],
"width": pos_data[4],
"height": pos_data[5],
"angle": pos_data[6],
},
)
4 changes: 2 additions & 2 deletions src/murfey/util/spa_metadata.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import logging
from pathlib import Path
from typing import Dict, NamedTuple, Optional, Tuple
from typing import Dict, NamedTuple, Optional, Tuple, Union

import xmltodict

Expand Down Expand Up @@ -167,7 +167,7 @@ def foil_hole_data(xml_path: Path, foil_hole: int, grid_square: int) -> FoilHole
)
)
image_paths.sort(key=lambda x: x.stat().st_ctime)
image_path: Path | str = image_paths[-1] if image_paths else ""
image_path: Union[Path, str] = image_paths[-1] if image_paths else ""
if image_path:
with open(Path(image_path).with_suffix(".xml")) as fh_xml:
fh_xml_data = xmltodict.parse(fh_xml.read())
Expand Down

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