[SyneRBI/SIRF-Exercises] notebook: `reconstruc_measured_data` does not work if the data is not in the working directory (Issue #260)

[Edoardo Pasca]

paskino created an issue (SyneRBI/SIRF-Exercises#260)

On the STFC cloud the data is available in a read-only filesystem.

The processing works fine if the data is processed in the working directory, but in this case it isn't.

Two fixes need to be made in the cell processing the files:

• #259 (comment)
• the following needs to be added:

# Now add absolute data path to the header file
# This command prepends the data path to the data file so that the header in our working folder points to the data
# You won't need to do this for your own data if the data file is in the same directory.
!sed -i.bak2 -e "s#\(!name of data file:=\)#\\1{data_path}/#" umap.v.hdr
# 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
! cp $data_path/20170809_NEMA_UCL.n .
# !sed -i.bak2 -e "s#\(!name of data file:=\)#\\1{data_path}/#" norm.n.hdr

related issues

• UCL/STIR#1601

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[Kris Thielemans]

Closed #260 as completed via #261.

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