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SyneRBI / SyneRBI_VM

Virtual Machine with pre-installed SyneRBI software
http://www.ccpsynerbi.ac.uk
Apache License 2.0
3 stars 7 forks source link

update ismrmrdtools #193

Open KrisThielemans opened 3 years ago

KrisThielemans commented 3 years ago

we're currently pulling from our own clone https://github.com/SyneRBI/SyneRBI_VM/blob/b09dc990a6d65d5b50ecf8120923d867c609db5c/scripts/UPDATE.sh#L298 which is very much out of date, including python2 errors.

I cannot remember why we didn't pull from https://github.com/ismrmrd/ismrmrd-python-tools

KrisThielemans commented 3 years ago

@johannesmayer @ckolbPTB @DANAJK maybe you could investigate?

KrisThielemans commented 3 years ago

Pinging @johannesmayer @ckolbPTB @DANAJK

johannesmayer commented 3 years ago

Where do we use these tools? For coil sensitivity computation?

KrisThielemans commented 3 years ago

I guess so. We're not using them directly in the exercises as far as I'm aware, but if people use their own data and see that it's installed, they could naturally assume that they will work, and they don't.

I'd be ok with just upgrading, but I'd appreciate a quick look if we did something weird on our own clone. Easiest might be to (in your own VM) merge the upstream master, and then see if there are any difference with upstream master

johannesmayer commented 3 years ago

Alright thanks I will get on it

johannesmayer commented 3 years ago

Easiest might be to (in your own VM) merge the upstream master, and then see if there are any difference with upstream master

I hope I interpreted your comment correctly: I went into the repository that is generated from our clone https://github.com/SyneRBI/ismrmrd-python-tools.git and did:

git add remote ismrmrd https://github.com/ismrmrd/ismrmrd-python-tools.git
git fetch --all
git pull origin master
git diff master..ismrmrd/master

and the differences are things all of the kind to ensure integer division e.g. replacing data.size/data.shape[0] by data.size//data.shape[0], casting to integer, and adding one import and parentheses to a print statement.

Our clone contains basically nothing different, at least nothing was revealed from the git commands that I wrote above.

KrisThielemans commented 3 years ago

I guess I'm interested in

git pull ismrmrd master
git diff master..ismrmrd/master

I hope there will be no differences, in which case we can just update our clone.

johannesmayer commented 3 years ago

alright now I get it, that's much smarter... No difference.

KrisThielemans commented 2 years ago

@paskino, given @johannesmayer 's work, let's just switch to use the normal repo and forget about our clone