"Measure abundances" on stellar parameters tab is buggy

[maddiecain]

Some of the selected lines won't be included on stellar parameters measurements, and the "measure abundances" button won't measure the line. it happens when i de-select a line then re-select it.

[maddiecain]

Scratch that, it seems like "measure abundances" isn't working at all. If I change a value like micro turbulence and click "measure abundances", nothing changes

[alexji]

Can you paste output from the terminal? Error messages should be showing up there

On Wed, Aug 9, 2017 at 11:47 PM maddiecain notifications@github.com wrote:

Scratch that, it seems like "measure abundances" isn't working at all. If I change a value like micro turbulence and click "measure abundances", nothing changes

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[maddiecain]

Here is the output:

2017-08-10 10:58:47,681 [DEBUG ] Executing MOOG input file: /Users/madelyncain/.smh/tmpRX0VWH/batch.par 2017-08-10 10:58:54,035 [DEBUG ] MOOG at /Users/madelyncain/smhr/moog17scat/moogsilent is version FEB 2017 2017-08-10 10:58:54,035 [INFO ] MOOG executed /Users/madelyncain/.smh/tmpRX0VWH/batch.par successfully 2017-08-10 10:58:54,063 [WARNING ] Temporary working directory should be as short as possible to prevent MOOG(SILENT) from falling over. Current length (33): /Users/madelyncain/.smh/tmpRX0VWH 2017-08-10 10:58:54,098 [DEBUG ] Executing MOOG input file: /Users/madelyncain/.smh/tmpRX0VWH/batch.par 2017-08-10 10:59:00,816 [DEBUG ] MOOG at /Users/madelyncain/smhr/moog17scat/moogsilent is version FEB 2017 2017-08-10 10:59:00,816 [INFO ] MOOG executed /Users/madelyncain/.smh/tmpRX0VWH/batch.par successfully 2017-08-10 10:59:00,820 [WARNING ] No measured transitions to calculate abundances for.

[alexji]

Can you zip the contents of /Users/madelyncain/.smh/tmpRX0VWH/ and e-mail to me?

On Thu, Aug 10, 2017 at 10:59 AM, maddiecain notifications@github.com wrote:

Here is the output:

2017-08-10 10:58:47,681 [DEBUG ] Executing MOOG input file: /Users/madelyncain/.smh/tmpRX0VWH/batch.par 2017-08-10 10:58:54,035 [DEBUG ] MOOG at /Users/madelyncain/smhr/moog17scat/moogsilent is version FEB 2017 2017-08-10 10:58:54,035 [INFO ] MOOG executed /Users/madelyncain/.smh/tmpRX0VWH/batch.par successfully 2017-08-10 10:58:54,063 [WARNING ] Temporary working directory should be as short as possible to prevent MOOG(SILENT) from falling over. Current length (33): /Users/madelyncain/.smh/tmpRX0VWH 2017-08-10 10:58:54,098 [DEBUG ] Executing MOOG input file: /Users/madelyncain/.smh/tmpRX0VWH/batch.par 2017-08-10 10:59:00,816 [DEBUG ] MOOG at /Users/madelyncain/smhr/moog17scat/moogsilent is version FEB 2017 2017-08-10 10:59:00,816 [INFO ] MOOG executed /Users/madelyncain/.smh/tmpRX0VWH/batch.par successfully 2017-08-10 10:59:00,820 [WARNING ] No measured transitions to calculate abundances for.

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[maddiecain]

done

[alexji]

Can you try restarting SMH and trying again? If that doesn't work, can you also send me the SMH file? The error seems to be saying that the EQW are not there (despite the fact that they are definitely there). This appears to be the same problem as #193 but I couldn't reproduce that error later.

The improvements I"m making under-the-hood should eventually resolve this issue, but they aren't ready yet.

On Thu, Aug 10, 2017 at 11:14 AM, maddiecain notifications@github.com wrote:

done

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[maddiecain]

So i restarted, and now when i press "measure abundances" not even the lines show up

Sent you the file

[alexji]

Hi Maddie,

OK the problem is that one of the lines has an insane EQW being written out, and it is messing up our parsing of the results. Line 4407.709 has a poor fit with a large abundance error, and it's breaking MOOG and our MOOG parsing.

Part of the problem is that I haven't solved #249 which also appears to affect profiles so there's no visual cue that this is happening; I'll try to fix this later today.

-Alex

On Thu, Aug 10, 2017 at 11:40 AM, maddiecain notifications@github.com wrote:

So i restarted, and now when i press "measure abundances" not even the lines show up [image: screen shot 2017-08-10 at 11 40 39 am] https://user-images.githubusercontent.com/13720061/29186273-be622ede-7dc0-11e7-97fb-78e975ab20b9.png

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[maddiecain]

Gotcha! Should I just delete that line and that'll fix it?

On Thursday, August 10, 2017, Alex Ji notifications@github.com wrote:

Hi Maddie,

OK the problem is that one of the lines has an insane EQW being written out, and it is messing up our parsing of the results. Line 4407.709 has a poor fit with a large abundance error, and it's breaking MOOG and our MOOG parsing.

Part of the problem is that I haven't solved #249 which also appears to affect profiles so there's no visual cue that this is happening; I'll try to fix this later today.

-Alex

On Thu, Aug 10, 2017 at 11:40 AM, maddiecain <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

So i restarted, and now when i press "measure abundances" not even the lines show up [image: screen shot 2017-08-10 at 11 40 39 am] https://user-images.githubusercontent.com/13720061/29186273-be622ede- 7dc0-11e7-97fb-78e975ab20b9.png

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-- Maddie Cain Department of Computer Science | Department of Physics MIT Class of 2019 mgcain@mit.edu | (512) 656-9661

[alexji]

It will allow you to continue working, but the plotting bug and MOOG parsing big is not fixed yet.

On Thu, Aug 10, 2017 at 1:47 PM, maddiecain notifications@github.com wrote:

Gotcha! Should I just delete that line and that'll fix it?

On Thursday, August 10, 2017, Alex Ji notifications@github.com wrote:

Hi Maddie,

OK the problem is that one of the lines has an insane EQW being written out, and it is messing up our parsing of the results. Line 4407.709 has a poor fit with a large abundance error, and it's breaking MOOG and our MOOG parsing.

Part of the problem is that I haven't solved #249 which also appears to affect profiles so there's no visual cue that this is happening; I'll try to fix this later today.

-Alex

On Thu, Aug 10, 2017 at 11:40 AM, maddiecain <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

So i restarted, and now when i press "measure abundances" not even the lines show up [image: screen shot 2017-08-10 at 11 40 39 am] https://user-images.githubusercontent.com/13720061/29186273-be622ede- 7dc0-11e7-97fb-78e975ab20b9.png

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-- Maddie Cain Department of Computer Science | Department of Physics MIT Class of 2019 mgcain@mit.edu | (512) 656-9661

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[maddiecain]

Gotcha. does the moog parsing bug affect the actual abundances? (like, will I still get accurate abundances when I measure lines?) I noticed the problem with getting crazy off EWs is gone, so I wasn't sure

[alexji]

It should not affect abundances, it is just an bug when trying to read files when they have a crazy EQW (i.e. too many digits to fit in 6 characters or something).

On Thu, Aug 10, 2017 at 1:56 PM, maddiecain notifications@github.com wrote:

Gotcha. does the moog parsing bug affect the actual abundances? (like, will I still get accurate abundances when I measure lines?) I noticed the problem with getting crazy off EWs is gone, so I wasn't sure

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[maddiecain]

Awesome! Yeah, that completely fixed my issue. I have never seen a sigma in the 300,000's so I guess there's a first for everything lol

[alexji]

I did not actually solve the MOOG parsing error, but I have made SMH print the relevant error message to the terminal now; that will have to be good enough.