Update reconstruct_measured_data.ipynb for read-only source directory #261
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| "!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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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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also could we ln -s in lieu of cp?
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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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@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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pushed a commit... hopefully fine now.
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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).
KrisThielemans
changed the title
reconstruc_measured_datadoes not work if the data is not in the working directory #260