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DrSAR / SARlabpy

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use Bruker-processed datasets to test readJCAMP and read2dseq #59

Closed andrewcyung closed 11 years ago

andrewcyung commented 11 years ago

I think it would be useful to test BRUKERIO with datasets that result from Bruker calculating the 2dseq, for example a T2* map from raw MGE data, or DTI maps from raw diffusion-weighted images. The corresponding visu_pars files often have elements in some of its string arrays that could mess up our file parsing (for example if a frame group comment has # signs or parentheses in it).

I noticed that readFidTest has a DTI dataset. Can we get Bruker console to calculate the DTI map and add the resultant procno 2 directory?

DrSAR commented 11 years ago

That's exactly the discussion we need. I think you, Andrew, have the widest experience, wrt what BRUKER might throw at us. It might be really handy to get together maybe in front of a virtualbox and design these testcases. we have most of the data: readfidTest is already in place and needs, as you say, additional processing.

Also, I would like to agree with you on a convention for data storage. Firas and I have a failry platform independent way so that we can simply refer to them by their BRUKER names: e1 = Experiment('readfidTest') It would be handy if we can find something similar because then our test code like the one you are mentioning will work out of the box (or rather, the common repo) without having to hunt around for it in some directory...

S

andrewcyung mailto:notifications@github.com 21 March, 2013 11:53

I think it would be useful to test BRUKERIO with datasets that result from Bruker calculating the 2dseq, for example a T2* map from raw MGE data, or DTI maps from raw diffusion-weighted images. The corresponding visu_pars files often have elements in some of its string arrays that could mess up our file parsing (for example if a frame group comment has # signs or parentheses in it).

I noticed that readFidTest has a DTI dataset. Can we get Bruker console to calculate the DTI map and add the resultant procno 2 directory?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/59.

andrewcyung commented 11 years ago

I thought about the data sharing issue as well - it seems to me that the file handling must at least assume that the data is in your home directory in the subdirectory "data"? I think I can set up a data directory in my windows home directory (it would c:\users\ayung), although if there was a way to point it to another directory then that would be better. I don't suppose there is a way to sync data between all of us automatically is there?

From: DrSAR [notifications@github.com] Sent: Thursday, March 21, 2013 11:59 AM To: DrSAR/SARlabpy Cc: Yung, Andrew Subject: Re: [SARlabpy] use Bruker-processed datasets to test readJCAMP and read2dseq (#59)

That's exactly the discussion we need. I think you, Andrew, have the widest experience, wrt what BRUKER might throw at us. It might be really handy to get together maybe in front of a virtualbox and design these testcases. we have most of the data: readfidTest is already in place and needs, as you say, additional processing.

Also, I would like to agree with you on a convention for data storage. Firas and I have a failry platform independent way so that we can simply refer to them by their BRUKER names: e1 = Experiment('readfidTest') It would be handy if we can find something similar because then our test code like the one you are mentioning will work out of the box (or rather, the common repo) without having to hunt around for it in some directory...

S

andrewcyung mailto:notifications@github.com 21 March, 2013 11:53

I think it would be useful to test BRUKERIO with datasets that result from Bruker calculating the 2dseq, for example a T2* map from raw MGE data, or DTI maps from raw diffusion-weighted images. The corresponding visu_pars files often have elements in some of its string arrays that could mess up our file parsing (for example if a frame group comment has # signs or parentheses in it).

I noticed that readFidTest has a DTI dataset. Can we get Bruker console to calculate the DTI map and add the resultant procno 2 directory?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/59.

— Reply to this email directly or view it on GitHubhttps://github.com/DrSAR/SARlabpy/issues/59#issuecomment-15258633.

DrSAR commented 11 years ago

Well, we essentially do that. I use an NFS server that runs on pfeifer and I have $HOME/data pointed to what corresponds to /opt/PV5.1/data/stefan/nmr I can simply change the symbolic link of $HOME/data to some other place it I want to look at mriuser data or jenm etc.

currently BRUKER_classes sets up a dataroot

dataroot = os.path.expanduser('~/data')

which in your case expands to c:\users\ayung\data Is it possible for you to put a symbolic link to point it to a directory that contains those scans?

We might want to rethink our strategy to make it user independent. I.e. scans dataroot would be pointing to the equivalent of /opt/PV5.1/data and then an Experiment has to be defined with the additional naming of a username. We could try to default it to something if the username is not supplied..

E.g. I would (as user stefan) do e1 = Experiment('readfidTest') and you would (as user ayung) do e1 = Experiment('readfidTest', user='stefan') since otherwise you would not see this.

This scheme woudl ensure backwards compatibility. Probably it would be nice to discourage the use of references without the explicit username. There are problems either way... Alternatively, and probably best the code could just look for scans in all dataroot+'/nmr/' directories.

andrewcyung mailto:notifications@github.com 21 March, 2013 12:10 I thought about the data sharing issue as well - it seems to me that the file handling must at least assume that the data is in your home directory in the subdirectory "data"? I think I can set up a data directory in my windows home directory (it would c:\users\ayung), although if there was a way to point it to another directory then that would be better. I don't suppose there is a way to sync data between all of us automatically is there?

From: DrSAR [notifications@github.com] Sent: Thursday, March 21, 2013 11:59 AM To: DrSAR/SARlabpy Cc: Yung, Andrew Subject: Re: [SARlabpy] use Bruker-processed datasets to test readJCAMP and read2dseq (#59)

That's exactly the discussion we need. I think you, Andrew, have the widest experience, wrt what BRUKER might throw at us. It might be really handy to get together maybe in front of a virtualbox and design these testcases. we have most of the data: readfidTest is already in place and needs, as you say, additional processing.

Also, I would like to agree with you on a convention for data storage. Firas and I have a failry platform independent way so that we can simply refer to them by their BRUKER names: e1 = Experiment('readfidTest') It would be handy if we can find something similar because then our test code like the one you are mentioning will work out of the box (or rather, the common repo) without having to hunt around for it in some directory...

S

andrewcyung mailto:notifications@github.com 21 March, 2013 11:53

I think it would be useful to test BRUKERIO with datasets that result from Bruker calculating the 2dseq, for example a T2* map from raw MGE data, or DTI maps from raw diffusion-weighted images. The corresponding visu_pars files often have elements in some of its string arrays that could mess up our file parsing (for example if a frame group comment has # signs or parentheses in it).

I noticed that readFidTest has a DTI dataset. Can we get Bruker console to calculate the DTI map and add the resultant procno 2 directory?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/59.

— Reply to this email directly or view it on GitHubhttps://github.com/DrSAR/SARlabpy/issues/59#issuecomment-15258633.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/59#issuecomment-15259205.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:53

I think it would be useful to test BRUKERIO with datasets that result from Bruker calculating the 2dseq, for example a T2* map from raw MGE data, or DTI maps from raw diffusion-weighted images. The corresponding visu_pars files often have elements in some of its string arrays that could mess up our file parsing (for example if a frame group comment has # signs or parentheses in it).

I noticed that readFidTest has a DTI dataset. Can we get Bruker console to calculate the DTI map and add the resultant procno 2 directory?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/59.

DrSAR commented 11 years ago

I'm closing these (essentially two topics):