Skip to content

Update reconstruct_measured_data.ipynb for read-only source directory #261

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

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Update reconstruct_measured_data.ipynb for read-only source directory #261

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9eeb08c
Update reconstruct_measured_data.ipynb
paskino Jul 3, 2025
b25c4c7
some tidy up
casperdcl Jul 3, 2025
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
7 changes: 6 additions & 1 deletion notebooks/PET/reconstruct_measured_data.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -113,11 +113,16 @@
"# umap.v.hdr is the output converted file\n",
"# Also copy the normalisation header for modification below (using a shorter name).\n",
"!cp $data_path/20170809_NEMA_UCL.n.hdr norm.n.hdr\n",
"!convertSiemensInterfileToSTIR.sh $data_path/20170809_NEMA_MUMAP_UCL.v.hdr umap.v.hdr\n",
"# copy to writeable location (https://github.com/UCL/STIR/issues/1600)\n",
"!cp $data_path/20170809_NEMA_MUMAP_UCL.v.hdr tmp_umap.v.hdr\n",
"!convertSiemensInterfileToSTIR.sh tmp_umap.v.hdr umap.v.hdr\n",
"!rm tmp_umap.v.hdr\n",
"\n",
"# These files will sometimes have lines terminated with CR instead of CRLF, fix this\n",
"# This just means, if we see CR<character> and <character> isn't LF, replace it with CRLF<character>\n",
"!sed -i.bak \"s/\\r\\([^\\n]\\)/\\r\\n\\1/g\" norm.n.hdr\n",
"# copy to working directory (https://github.com/UCL/STIR/issues/1601)\n",
"!cp $data_path/20170809_NEMA_UCL.n .\n",
"!sed -i.bak \"s/\\r\\([^\\n]\\)/\\r\\n\\1/g\" umap.v.hdr\n",
"\n",
"# Now add absolute data path to the header file\n",
Expand Down