readBrukerParx (my version of readJCAMP) screwed up!

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readBrukerParx (my version of readJCAMP) screwed up! #58

Closed andrewcyung closed 11 years ago

andrewcyung commented 11 years ago

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

             line=re.sub("\\(.*\\)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

DrSAR commented 11 years ago

Shall Firas, Andrew and I meet tomorrow for a git crash course and some chat about scan orientations? Stefan

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

firasm commented 11 years ago

I'm okay after 1 pm tomorrow

DrSAR wrote:

Shall Firas, Andrew and I meet tomorrow for a git crash course and some chat about scan orientations? Stefan

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15257340.

DrSAR commented 11 years ago

Andrew, I think we both missed a trick. There is python parsing module available. pyparsing http://pyparsing.wikispaces.com/ You can define a (recursive) grammar and it parses strings for your. Returns them as lists. The trouble is in understanding grammars but once that is done it looks lovely. Stefan http://pyparsing.wikispaces.com/

firasm mailto:notifications@github.com 21 March, 2013 11:37 I'm okay after 1 pm tomorrow

DrSAR wrote:

Shall Firas, Andrew and I meet tomorrow for a git crash course and some chat about scan orientations? Stefan

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15257340.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15257385.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

firasm commented 11 years ago

^ not to be too forward, but at this point perhaps we could mark such things as "enhancements" and "backburner" in favour of getting some analysis tools developed :P

DrSAR commented 11 years ago

I wasn't suggesting to rewrite the JCAMP reader for the third time. It's more a reminder to think hard before you code something that appears like a generally performed task. Someone else will already have a solution and it;s a matter of deciding whether it's quicker to understand the other persons API or to roll your own...

firasm mailto:notifications@github.com 21 March, 2013 11:49

^ not to be too forward, but at this point perhaps we could mark such things as "enhancements" and "backburner" in favour of getting some analysis tools developed :P

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15258072.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

andrewcyung commented 11 years ago

Yes, let's meet tomorrow, how about 1:30 PM at Hennings this time? I haven't visited your digs yet and since your computers are set up there, maybe it would help me understand everything better if you can show me on your home base computers. I too would like to talk about what your plans are regarding analysis tools. I would really like to get started with developing better registration and segmentation tools to support our comparison between MRI images and histology.

DrSAR commented 11 years ago

Let's do that. Do you have a windows laptop you could bring along. It might benefit you if you can set things up as we go along. Not crucial but nice. (Remote Desktop?) Also, what git client are you using?

andrewcyung mailto:notifications@github.com 21 March, 2013 11:59

Yes, let's meet tomorrow, how about 1:30 PM at Hennings this time? I haven't visited your digs yet and since your computers are set up there, maybe it would help me understand everything better if you can show me on your home base computers. I too would like to talk about what your plans are regarding analysis tools. I would really like to get started with developing better registration and segmentation tools to support our comparison between MRI images and histology.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15258654.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

andrewcyung commented 11 years ago

I am using Git Gui, and tried to use Git Bash but couldn't get very far with the command line.

I do have a busted old laptop that I could set up to remote desktop into my computer at office...

DrSAR commented 11 years ago

We have the computers here to do the remote desktopping (even though it's a mac, VNC should work, correct Firas?) More a question whether your office desktop is open for remote desktop sessions - as I say. not crucial but nice. Let's not spend too much time on that.

andrewcyung mailto:notifications@github.com 21 March, 2013 12:05

I am using Git Gui, and tried to use Git Bash but couldn't get very far with the command line.

I do have a busted old laptop that I could set up to remote desktop into my computer at office...

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15258971.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

firasm commented 11 years ago

coorect, VNC should work.

However, it must be enabled and accessible on your work computer.

It might be better for us to go to the LSC if this becomes too big of a challenge, I know VNC works for stefan and I.

Firas

DrSAR wrote:

We have the computers here to do the remote desktopping (even though it's a mac, VNC should work, correct Firas?) More a question whether your office desktop is open for remote desktop sessions - as I say. not crucial but nice. Let's not spend too much time on that.

andrewcyung mailto:notifications@github.com 21 March, 2013 12:05

I am using Git Gui, and tried to use Git Bash but couldn't get very far with the command line.

I do have a busted old laptop that I could set up to remote desktop into my computer at office...

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15258971.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15259049.

andrewcyung commented 11 years ago

well I installed tightvnc as well as teamviewer, so we can try both. Regardless, even if we can't access my computer during my hennings visit, there will be plenty to talk about and we can figure things out on my end another day.

-andrew

From: firasm [notifications@github.com] Sent: Thursday, March 21, 2013 12:19 PM To: DrSAR/SARlabpy Cc: Yung, Andrew Subject: Re: [SARlabpy] readBrukerParx (my version of readJCAMP) screwed up! (#58)

coorect, VNC should work.

However, it must be enabled and accessible on your work computer.

It might be better for us to go to the LSC if this becomes too big of a challenge, I know VNC works for stefan and I.

Firas

DrSAR wrote:

We have the computers here to do the remote desktopping (even though it's a mac, VNC should work, correct Firas?) More a question whether your office desktop is open for remote desktop sessions - as I say. not crucial but nice. Let's not spend too much time on that.

andrewcyung mailto:notifications@github.com 21 March, 2013 12:05

I am using Git Gui, and tried to use Git Bash but couldn't get very far with the command line.

I do have a busted old laptop that I could set up to remote desktop into my computer at office...

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15258971.

andrewcyung mailto:notifications@github.com 21 March, 2013 11:04

Stefan pointed out that there were problems with my readBrukerParx, regarding its inability to ignore the array size number in a LDR array. I checked my function and there are all kinds of problems. I tracked it down to a line I accidentally deleted when I was cleaning up my code. Insert the following line before line 74 (which is 'line=[line]):

line=re.sub("(.*)", "", line)

This properly strips off the (num) and allows the rest of the code to work properly.

Sorry about that - give it a try to see if it works for you. On another note, I really will need some help figuring out git. I tried to make the changes and commit/push, but git says I have to merge something, but I can't merge something because I have a commit in progress?

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58.

— Reply to this email directly or view it on GitHub https://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15259049.

— Reply to this email directly or view it on GitHubhttps://github.com/DrSAR/SARlabpy/issues/58#issuecomment-15259663.