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

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

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Update reconstruct_measured_data.ipynb
paskino Jul 3, 2025
b25c4c7
some tidy up
casperdcl Jul 3, 2025
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9 changes: 7 additions & 2 deletions notebooks/PET/reconstruct_measured_data.ipynb
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Expand Up @@ -113,12 +113,17 @@
"# 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\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",
"!sed -i.bak \"s/\\r\\([^\\n]\\)/\\r\\n\\1/g\" umap.v.hdr\n",
"# due to https://github.com/UCL/STIR/issues/1601 we copy the data to the working directory which is the same as where the header lives\n",
"! cp $data_path/20170809_NEMA_UCL.n .\n",
"#!sed -i.bak \"s/\\r\\([^\\n]\\)/\\r\\n\\1/g\" umap.v.hdr\n",
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@KrisThielemans KrisThielemans Jul 3, 2025

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why comment this out? It replaces CRLF with LR, which has nothing to do with all the problems you've seen.

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@casperdcl casperdcl Jul 3, 2025

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also could we ln -s in lieu of cp?

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@KrisThielemans KrisThielemans Jul 3, 2025

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would be fine on Unix-type. Not sure about other places. This file is small. I wouldn't bother testing.

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@KrisThielemans KrisThielemans Jul 3, 2025

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@paskino I think you wanted to comment out

!sed -i.bak2 -e \"s#\\(!name of data file:=\\)#\\\\1{data_path}/#\" umap.v.hdr
!sed -i.bak2 -e \"s#\\(!name of data file:=\\)#\\\\1{data_path}/#\" norm.n.hdr

I still need some convincing that this was your problem though.

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@casperdcl casperdcl Jul 3, 2025

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pushed a commit... hopefully fine now.

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@KrisThielemans KrisThielemans Jul 4, 2025

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not yet. we need to change the line below:

!sed -i.bak2 -e \"s#\\(!name of data file:=\\)#\\\\1{data_path}/#\" norm.n.hdr

Likely we don't need it all, i.e. there probably is no path in the norm.n.hdr (there isn't in my copy). Otherwise, we will need to remove the path (which is a more complicated regexp).

"\n",
"# Now add absolute data path to the header file\n",
"# This command prepends the data path to the data file so that the header in our working folder points to the data\n",
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