search

mattyowl / RSSMOSPipeline

Pipeline for reducing both longslit and multi-object spectroscopic data from the Robert Stobie Spectrograph on SALT.
https://rssmospipeline.readthedocs.io
GNU General Public License v3.0
4 stars 2 forks source link

NOREAD mask #24

Closed PKSejake closed 1 year ago

PKSejake commented 1 year ago

Hi Matt,

I have two G4Jy sources where the RSS MOSS Pipeline doesn't do extraction and stacking. These two sources have "NOREAD mask" instead of "PL0200N001". What could be the reason for this, and how can I resolve it?

Kind regards Katlego

mattyowl commented 1 year ago

Hi Katlego,

Sorry, was on holiday last week.

If it's just some weird glitch, and you know the mask was actually PL0200N001 - maybe just try editing the FITS header keyword value. I've never seen this happen before though.

Another thing you can do is to double check the observing logs and/or check if that observing block was accepted by the observatory or not - they always make the data available in case it's useful, even if something went wrong.

Otherwise - you can make an archive of the data and send it to me and I can take a look at what's going on with it.

Cheers Matt

PKSejake commented 1 year ago

Hi Matt,

Thanks for your response.

I did change the mask. The pipeline runs but stops at extracting the stacking step. Here is the output:

2023-04-17 11:52:48,763 - RSSMOSPipeline - INFO - started: 2023-04-17T11:52:48.763268

2023-04-17 11:52:48,763 - RSSMOSPipeline - INFO - parameters: Namespace(excludeMasks='', extensionsList='all', iterativeMethod=False, longslitThreshold='1', maskName='G4Jy 842_NOREAD', rawDir='product', reducedDir='reduced', skipDone=False, subFrac=0.8, threshold=0.1)

2023-04-17 11:52:48,763 - RSSMOSPipeline - INFO - Reading image headers (cache file location: product/imageInfo.pkl)

2023-04-17 11:52:48,771 - RSSMOSPipeline - INFO - Mask: G4Jy 842_NOREAD

2023-04-17 11:52:49,061 - RSSMOSPipeline - INFO - Making masterFlats (it is a good idea to check alignment with object spectra at the cutting stage, and remove any flats which aren't aligned)

2023-04-17 11:52:49,062 - RSSMOSPipeline - INFO - making reduced/G4Jy 842_NOREAD/masterFlat_0.fits (['product/mbxgpP202205260265.fits', 'product/mbxgpP202205260266.fits', 'product/mbxgpP202205260267.fits', 'product/mbxgpP202205260268.fits', 'product/mbxgpP202205260269.fits'])

2023-04-17 11:52:49,988 - RSSMOSPipeline - INFO - It is a good idea to check that for the below the corresponding DS9 .reg file aligns with the slits and that object spectra are actually centred in the slits

2023-04-17 11:52:50,059 - RSSMOSPipeline - INFO - cutting product/mbxgpP202205260263.fits (and arcs, flats) using reduced/G4Jy 842_NOREAD/masterFlat_0.fits for slit definition ...

2023-04-17 11:52:50,247 - RSSMOSPipeline - INFO - cutting product/mbxgpP202205260262.fits (and arcs, flats) using reduced/G4Jy 842_NOREAD/masterFlat_0.fits for slit definition ...

2023-04-17 11:52:50,374 - RSSMOSPipeline - INFO - cutting product/mbxgpP202205260261.fits (and arcs, flats) using reduced/G4Jy 842_NOREAD/masterFlat_0.fits for slit definition ...

2023-04-17 11:52:50,552 - RSSMOSPipeline - INFO - Applying flat field

2023-04-17 11:52:50,583 - RSSMOSPipeline - INFO - Finding 2d wavelength solution

2023-04-17 11:52:50,584 - RSSMOSPipeline - INFO - arc = reduced/G4Jy 842_NOREAD/cmasterFlat_0mbxgpP202205260264.fits

2023-04-17 11:52:50,593 - RSSMOSPipeline - INFO - arc = reduced/G4Jy 842_NOREAD/cmasterFlat_0mbxgpP202205260264.fits

2023-04-17 11:52:50,595 - RSSMOSPipeline - INFO - arc = reduced/G4Jy 842_NOREAD/cmasterFlat_0mbxgpP202205260264.fits

2023-04-17 11:52:50,598 - RSSMOSPipeline - INFO - Applying wavelength calibration and rectifying (reduced/G4Jy 842_NOREAD/cmasterFlat_0mbxgpP202205260264.fits)

2023-04-17 11:52:50,603 - RSSMOSPipeline - INFO - Applying wavelength calibration and rectifying (reduced/G4Jy 842_NOREAD/cmasterFlat_0mbxgpP202205260264.fits)

2023-04-17 11:52:50,609 - RSSMOSPipeline - INFO - Applying wavelength calibration and rectifying (reduced/G4Jy 842_NOREAD/cmasterFlat_0mbxgpP202205260264.fits)

2023-04-17 11:52:50,614 - RSSMOSPipeline - INFO - Applying wavelength calibration and rectifying (reduced/G4Jy 842_NOREAD/cmbxgpP202205260263.fits)

2023-04-17 11:52:50,619 - RSSMOSPipeline - INFO - Applying wavelength calibration and rectifying (reduced/G4Jy 842_NOREAD/cmbxgpP202205260262.fits)

2023-04-17 11:52:50,624 - RSSMOSPipeline - INFO - Applying wavelength calibration and rectifying (reduced/G4Jy 842_NOREAD/cmbxgpP202205260261.fits)

2023-04-17 11:52:50,632 - RSSMOSPipeline - INFO - Extracting and stacking

/users/katlego26/PhD_2022_2024/rss_moss/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice.

return _methods._mean(a, axis=axis, dtype=dtype,

/users/katlego26/PhD_2022_2024/rss_moss/lib/python3.8/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide

ret = ret.dtype.type(ret / rcount)

I did check the observation log, and there are no issues reported.

Kind regards

Katlego

On Mon, Apr 17, 2023 at 10:05 AM Matt Hilton @.***> wrote:

Hi Katlego,

Sorry, was on holiday last week.

If it's just some weird glitch, and you know the mask was actually PL0200N001 - maybe just try editing the FITS header keyword value. I've never seen this happen before though.

Another thing you can do is to double check the observing logs and/or check if that observing block was accepted by the observatory or not - they always make the data available in case it's useful, even if something went wrong.

Otherwise - you can make an archive of the data and send it to me and I can take a look at what's going on with it.

Cheers Matt

— Reply to this email directly, view it on GitHub https://github.com/mattyowl/RSSMOSPipeline/issues/24#issuecomment-1510889520, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOY6TPRI6CZRK6PWJVHUJ3TXBT2VLANCNFSM6AAAAAAWZ4AX4E . You are receiving this because you authored the thread.Message ID: @.***>

mattyowl commented 1 year ago

Thanks for sending the data. If you look in the headers you'll see:

MASKTYP = 'MOS '

but your data are long slit. The pipeline assumes the meta data in the headers are correct, so it's trying to find slitlets as if it was MOS data.

To fix it, you should just need to edit the FITS headers and set

MASKTYP = 'LONGSLIT'

and then the pipeline should run without issues.

This is some technical problem at the observatory then.

Cheers Matt

PKSejake commented 1 year ago

Hi Matt,

The pipeline still stops at extracting and stacking step even when I changed MASKTYP to "LONGSLIT". I'll email the SALT help desk and ask why these sources have "NOREAD" MASKID and "MOS" MASKTYP.

Regards Katlego

mattyowl commented 1 year ago

Ok - try deleting imageInfo.pkl after re-running. That wouldn't have been re-made after you edited the headers. It's working for me after I do that.

Cheers Matt

On 18/04/2023 09:08, Precious Katlego Sejake wrote:

Hi Matt,

The pipeline still stops at extracting and stacking step even when I changed MASKTYP to "LONGSLIT". I'll email the SALT help desk and ask why these sources have "NOREAD" MASKID and "MOS" MASKTYP.

Regards Katlego

— Reply to this email directly, view it on GitHub https://github.com/mattyowl/RSSMOSPipeline/issues/24#issuecomment-1512557255, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBC6V7JVLKOOSL7KONEU2TXBY4XFANCNFSM6AAAAAAWZ4AX4E. You are receiving this because you commented.Message ID: @.***>

PKSejake commented 1 year ago

Hi Matt,

It works. Thank you.

Kind regards Katlego

On Tue, Apr 18, 2023 at 9:29 AM Matt Hilton @.***> wrote:

Ok - try deleting imageInfo.pkl after re-running. That wouldn't have been re-made after you edited the headers. It's working for me after I do that.

Cheers Matt

On 18/04/2023 09:08, Precious Katlego Sejake wrote:

Hi Matt,

The pipeline still stops at extracting and stacking step even when I changed MASKTYP to "LONGSLIT". I'll email the SALT help desk and ask why these sources have "NOREAD" MASKID and "MOS" MASKTYP.

Regards Katlego

— Reply to this email directly, view it on GitHub < https://github.com/mattyowl/RSSMOSPipeline/issues/24#issuecomment-1512557255>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACBC6V7JVLKOOSL7KONEU2TXBY4XFANCNFSM6AAAAAAWZ4AX4E . You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/mattyowl/RSSMOSPipeline/issues/24#issuecomment-1512589086, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOY6TPTXGZMQNBVADKIC6K3XBY7EPANCNFSM6AAAAAAWZ4AX4E . You are receiving this because you authored the thread.Message ID: @.***>