Skip to content

Attempt to fix EpuSession.dm parsing #443

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
d-j-hatton merged 1 commit into from
Jan 13, 2025
Merged

Attempt to fix EpuSession.dm parsing #443

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
34 changes: 12 additions & 22 deletions src/murfey/client/contexts/spa_metadata.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,23 +61,18 @@ def post_transfer(
]["#text"]
visit_index = windows_path.split("\\").index(environment.visit)
partial_path = "/".join(windows_path.split("\\")[visit_index + 1 :])
visitless_path = Path(
str(transferred_file).replace(f"/{environment.visit}", "")
)
visit_index_of_transferred_file = transferred_file.parts.index(
environment.visit
)

source = _get_source(transferred_file, environment)
if not source:
logger.warning(
f"Source could not be indentified for {str(transferred_file)}"
)
return

source_visit_dir = source.parent

atlas_xml_path = list(
(
Path(
"/".join(
transferred_file.parts[
: visit_index_of_transferred_file + 1
]
)
)
/ partial_path
).parent.glob("Atlas_*.xml")
(source_visit_dir / partial_path).parent.glob("Atlas_*.xml")
)[0]
with open(atlas_xml_path, "rb") as atlas_xml:
atlas_xml_data = xmltodict.parse(atlas_xml)
Expand All @@ -88,10 +83,6 @@ def post_transfer(
# need to calculate the pixel size of the downscaled image
atlas_pixel_size = atlas_original_pixel_size * 7.8

source = _get_source(
visitless_path.parent / "Images-Disc1" / visitless_path.name,
environment,
)
sample = None
for p in partial_path.split("/"):
if p.startswith("Sample"):
Expand Down Expand Up @@ -126,8 +117,7 @@ def post_transfer(
)
if registered_grid_squares:
gs_pix_positions = _get_grid_square_atlas_positions(
_atlas_destination(environment, source, transferred_file)
/ environment.samples[source].atlas
source_visit_dir / partial_path
)
for gs in registered_grid_squares:
pos_data = gs_pix_positions.get(str(gs["name"]))
Expand Down
Loading