How to use the HARPS archive

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How to use the HARPS archive

Post by Shellface on 7th June 2014, 8:23 pm

Though a little later than I had hoped, as promised, I'm here to educate you folks about how to use the HARPS archive. I'll save you the spiel on how it's the greatest resource ever, but know that I had to figure this all out on my own. Manually. Eww.

As a foreword, this guide is designed for windows. Nothing used here is exactly high-tech, though, so doing this on other operating systems shouldn't be too bad.

Things you'll need:

  • Access to the archive (so, uh, an internet connection)
  • The systemic console. You can download it here, and tutorials on how to use it are here.
  • A file unpacker-type thing. For windows, I recommend 7zip.
  • Notepad, or an equivalent program.
  • Microsoft Excel or an equivalent. I use OpenOffice here.

Now, to start off, let's find a suitable star. For the sake of this tutorial, I'll need one which doesn't have too many observations, and is preferably not an RV variable. I can't really know the latter in advance, but it we can make assumptions! Lovis et al. (2011) is quite valuable in this regard, because tables 2 and 3 give a number of observations up to 2011 and an activity level, which can be used to estimate how much stellar variability will influence the RV measurements.


Not too many measurements, and inactive. Seems good. A brief analysis finds that the star is a moderately metal-poor G8 dwarf, so it's not exactly out of the ordinary. Let's head over to the archive!


Upon opening the page, you'll be greeted by this. There's quite a lot there, but we don't have to care about a good deal of it, so we won't. Instead, direct yourself towards these bits:


First, click the "Choose an instrument" dropdown and select HARPS. Unless you want FEROS observations for some reason, you should always select that option. Then, you'll need to type in our target in the "Target" box, which is "HD 224619". The "return max" box isn't relevant for this tutorial, but for stars with larger amounts of observations you'll need to increase that value. 5000 is the maximum.

Once you've done that, hit the green "search" button. You'll be presented by this:


Here we have a list of all the HARPS observations of our star. Take note of the text above the list; before continuing, you'll need an ESO account thing, so go ahead and do that now. The stuff in the orange box isn't relevant for this star, but do watch out for it - I can confirm the data is sometimes (not always) outlying.

Anyway, once you've set up your ESO account, you'll need to select your datasets for request. At the time of writing, all 22 observations of HD 224619 are public, so we can download them all. Hit the "MarkPublic" box above the list, then press "Request Marked Datasets". You'll then be moved over to this:


You don't need to worry about any of the things at the top, so press submit, and the mysterious ESO pixies will process your request. After a short while, you will be moved to a page that looks like this:


Now press "Select All", then "Download Selected". This will open up a new window, and after a few moments, ask you for a directory to download to. It's good to keep these organised, so I have a folder named "HARPS" and then have subfolders for each star. After selecting your directory, the files will start downloading:


The files are quite large, so this will probably take a while. You should probably do something else for a few minutes. If any of the downloads do happen to fail, wait until the rest finish and then press the "Retry failed" button at the bottom-left; that'll fix it.

After the downloads are finished, head over to where you set the files to go. You'll hopefully see something equivalent to this:


I'm pretty sure the file named "defaultSSL.keystore" has no use after the download, so you can delete that. Now you'll be left with a bunch of .tar files. Select them all, and (assuming you're using 7zip) click this:


That'll unpack the .tars into their contents, which are folders of the same name. Go ahead and delete the .tars now. You'll be left with a bunch of folders:


Look inside the first one. You should see six .fits files, but only the first two (the ones that have _bis_ and _ccf_ in their filenames) are important. This is the file format used by all extracted HARPS files which have been DRS'd, so get used to it! (also note that observations after ~September 2010 are nested in additional folders, though the format is the same)

Open up the one with _ccf_ in the name notepad or your equivalent. You should see a big string of text:



search (ctrl+f) for the string "CCF RVC", with the space. You should find one match, which is followed by a value:



That's our first radial velocity! Copy it, open up a second notepad/equivalent file, and paste that number in.

Then, go back to the other file and search for the string "CCF NOISE". Copy the value after it, and paste it in on your second file after the radial velocity. That's your error bar set.

Now search for "DRS BJD". Copy and paste the value before your radial velocity, which gives you your date of observation. Your second file should now look show something equivalent to this:


That's all the information you need from the _ccf_ file, so you can close it. Now, while it isn't strictly necessary, I find it very valuable to take note of the activity indicators that come with the radial velocity. So let's do that; I'll take my preferred activity indicators of the biswidth and the FWHM. Open up the file with _bis_ in the name, and search for "BIS SPAN":


Copy that, and put it somewhere on your other document (I put it after the error). That's the biswidth, in case there was any confusion.

Now search for "CCF FWHM". Copy and paste the value into your other document (I put it after the error and before the biswidth). That's the FWHM. Your second file should look like this now, depending on the order you pasted in your values:


Now go back and repeat the process for every folder. This can take a while, so be ready.

After toiling away, you should have pretty much this (labelled for your convenience)


If you do, then great! That's pretty much the hardest part over. Now, save your file and then open it in Excel or your equivalent - here we do some manual data processing.


We need to do some editing to the raw data because the format's all wrong - systemic needs the series to be in m/s and calibrated around 0, but all of these are in km/s and are all absolute. This is addressed with some simple maths (as in multiplying it by 1000), and an assumption; we assume that γ, which is the offset between the absolute velocity of the star and 0 km/s, is equal to the average value of our time series. systemic can handle datasets where γ is off by a few m/s, so this is a reasonable model assumption.

Space out your columns (right click on the column letter and press "new column"), then find the average radial velocity:


Subtract that value from each individual velocity:


And then multiply both the corrected RVs and the errors by 1000.



Repeat the process for the FWHM and the biswidth. Copy and paste the julian dates in the columns before all three processed datasets, and the errors too (the supplement to Dumusque et al. (2012) indicates errors for the FWHM and biswidth are 2.35 and 2 times the RV error, respectively; from experience, these seem like reasonable approximations). You should end up with these, decimal places notwithstanding:


That's all the external processing we need to do. Copy and paste those into a notepad/ equivalent document, individually:


Save these as .vels files. You should probably have a specific filename format for these - I use [star name]_HARPSCCF for the RVs, and [star name]_HARPSCCF_[FWHM/biswidth], though "HARPSCCF" is a spot redundant for the archive.

Copy and rename a .sys file from the "datafiles" systemic folder (this is important, the format is unique). Open it in notepad/equivalent and replace the requested .vels and the name of the system. You will also need a mass of the star; while you could take one from literature, I recommend using the PARAM interface. Using the Teff and Fe/H from Sousa et al. (2008), the V from Høg et al. (2000) and the parallax from van Leeuwen (2007), the interface outputs a mass of 0.822 ± 0.012 M (also an age of 9.554 ± 1.782 Gyr).

Copy and adjust your new .sys file for the FWHM and the biswidth. Your data is now ready for systemic! Copy and paste all six of your files into your "datafiles" systemic folder, and then open systemic. If all has gone well, you should see these:


As you can see, the biswidth is fairly flat, though a moderate peak appears close to the predicted rotational period (37.6 ± 3.8 d; Lovis et al. (2011)). The FWHM shows a trend (3.26 ± 0.30 m/s) that is similar to other stars, but shows no other distinct residual peak. The radial velocities show moderate excess scatter (1.50 m/s), which does not preclude any periodicities; while the periodogram shows some power, none are distinct, so more data is needed to test the presence of companions.

So, that's my ever-so-slightly rambly tutorial. If you can't get it to work, ask me and I'll probably be able to help.

Also to touch on some subjects while it's relevant:


  • HARPS is not immune to outliers. If you see a RV/FWHM/bis value that is hundreds or more m/s discrepant to others, it is fine to disregard it.
  • For certain stars, the HARPS team adopts an observing strategy designed for nightly bins in order to reduce the effect of short-period oscillations. While this does produce the desired effect, Tuomi et al. (2013) showed that this can suppress peaks in the periodogram. I find it valuable to create time series of both binned and unbinned data from the archive, the former for reduced rms and the latter for more useful information on the data.
  • For solar-type stars, the FWHM consistently shows a positive trend over time, generally on the order of a few m/s/yr. I don't have a very complete sample yet, but they seem to correlate with Teff like so:



  • This implies that the FWHM trend is highest at ~K0 and decreases linearly to ~F5, but also decreases below K0 and is not present for M (the very small errors on two of the lowest points is not exactly real). This relation is not without outliers, though, so be aware of that.

But yeah, Have fun with the archive!

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 8th June 2014, 6:09 pm

I have written a .bat file in C# to automate much of the process above.
http://wikisend.com/download/918952/HARPS_RV_Extract.rar

(Edit: Most up-to-date version here: http://solar-flux.forumandco.com/t1531p15-how-to-use-the-harps-archive#11222 )

It'll probably make your anti-virus software paranoid, considering the file type.

Just drop the .bat file in the root directory of all your unzipped .tar files and it will go through all the sub-directories and try read information from both the bis and ccf files to assemble the relevant .vels files.

Edit: If you want me to send you the source code, send me a pm. Also, this is more than open to revisions.


Last edited by Sirius_Alpha on 6th March 2015, 10:57 pm; edited 4 times in total

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Re: How to use the HARPS archive

Post by Shellface on 8th June 2014, 8:29 pm

Haha, looks like I was right when I said:

I'm sure anyone with basic programming capability would be able to automate the process
A few hundred hours replaced by a .bat, it's poetic!

Anyway, yes, this is excellent. You'll still need to create the .sys files to use them, but this handles the most time-consuming part of the process.

My suggestions are:

  • Truncate the decimal places - six d.p for the julian date and 2 d.p for the velocity and the error are plenty sufficient, and that reduces the file sizes considerably.
  • Outputs for the assumed values of γ would be useful.
  • If there isn't already, some level of automated outlier identification - the DRS occasionally converges on a velocity or activity indicator velocity of several thousand km/s, which is impossible, so rejecting a velocity of >1000 km/s should work to some extent.
  • Similarly, spectra large photon noise values (>10 m/s?) will rarely be useful, as even the faintest typical stars observed by HARPS have ~5 m/s precision. I guess this doesn't really work for the few early-type stars observed by HARPS, though, but that isn't too big of a loss.
  • It might not be feasible, but an option for nightly bins would be valuable, for the reasons I noted in the first post.
  • Just a tiny thing - "biswidth" on the file output should be lowercase.

But yeah. Thanks a million for this!

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 15th June 2014, 5:34 am

Shellface wrote:Outputs for the assumed values of γ would be useful.
You can set the RV offset of the star in Systemic. Are you talking about dγ/dt drifts?

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Re: How to use the HARPS archive

Post by Shellface on 15th June 2014, 10:25 am

I mean the average value from the raw files that is subtracted in the final .vels files.

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 15th June 2014, 12:32 pm

After having played around a bit more and encountered some of the difficulties highlighted by your suggestions earlier, I've rewritten the programme and given the user much more control over the process.

After the data is read by the programme, the user is shown a preview of the dataset as it would appear in Systemic. This is a very simplified rendition, without error bars and graph axis labels and whatnot, and is only designed to assist the user in identifying extreme outliers. The entirety of the dataset is available to the user to be edited before the .vels and .sys files are created.

The user is able to sort the dataset by BJD, RV, Err, FWHM and Biswidth to make finding outliers much easier. The user is also able to normalise the data at any time.

This isn't a final version, it's open to improvement and revision. I'm not certain exactly how to go about implementing a display for the value of the radial velocity offset γ, since there could be many competing values of it (i.e., a value of γ before outliers are removed and the data is again normalised -- a process that may occur multiple times). I'm certainly open to suggestions.

(Edit: Whoops! No sooner than after posting it do I come across a dataset with values given in scientific notation which, for some reason, the programme was unable to read - this has been fixed now and the link revised).
http://wikisend.com/download/491888/HARPS_RV_Extract_V2.1.rar

The following images show an example using the HD 69830 RV dataset, which has numerous bad datapoints that were removed before generating the .vels and .sys files.




And the result in Systemic.



A few minor annoyances. If you don't click "update dataset" from the trimming tab, it'll undo your changes when you wander off to a different tab. So be sure to do that before re-normalising. I do intend to make it able to do bins by a user-specified duration.

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Re: How to use the HARPS archive

Post by Shellface on 15th June 2014, 8:18 pm

Hey, you got a GUI going! Neat.

I haven't used this version much yet so I'm not going to make my comments, but I'm posting because I've encountered an issue. Attempting to go through HD 192310 results in the program spitting out an error:


(This happens with the first version too)

Sifting through the data indicates the error is caused by the observation on 2008-08-05T02_38_34.898. Though the observation itself is not particularly remarkable, I suspect the error is caused by the format of the biswidth value (-7.04338544395E-05). That is the format used by the DRS output when any value is smaller than |0.0001|, which is pretty rare, so I guess that's the issue?

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 15th June 2014, 8:37 pm

I literally just fixed an issue where it wasn't reading scientific notation properly. I've replaced the link with the fixed version. Try it now?

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 16th June 2014, 11:10 pm

Update. Found another problem. Setting a custom star name changes the file name but not the references to .vels files in the .sys file. I will fix this and upload later.

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Re: How to use the HARPS archive

Post by Shellface on 22nd June 2014, 1:44 pm

Well, I've used v2.1 quite a bit, and it's very smooth! The only issue that I've noticed is that the FWHM errors appear to truncate to 4 d.p, though that is quite minor and easily fixed.

I expect that you will be revising the GUI in future, but again, my suggestions:


  • I would like the "sort" button on the ManualTrim tab to be a dropdown list, as the time it takes for the list to update becomes very long for larger datasets.
  • Is there a reason the "update dataset" and "update plots" buttons could not be combined? I can't think of any reason why you would want to update the dataset without the plot.
  • It's barely of note, but the program name in its window is "Form1". I presume that should be "HARPS RV extractor" or something.

Concerning the γ display, in the context of this interface, perhaps you could show the current values? A paint.net mockup gives the general idea:



Something like those, which updates whenever the relevant data is normalised. Would that work?

On an unrelated note, now that you folks have had two weeks, how has the archive been? Anybody find anything of note? I mean, I hope it isn't just me and Sirius doing this thing!

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 22nd June 2014, 7:30 pm

Programatically, it's simple to do, it's just that I am not sure how to define offsets in the case of datasets with outliers. HD 69830's dataset, for example, I usually normalise my data twice to update the plots to look for outliers. Should the offset be given as the value of the most recent normalisation? If so, it will be skewed significantly by outliers.

The form header text has been fixed. The sort drop down menu can be done. The update dataset and update plot button can indeed be merged into one.

Shellface wrote:On an unrelated note, now that you folks have had two weeks, how has the archive been? Anybody find anything of note? I mean, I hope it isn't just me and Sirius doing this thing!
Indeed! And if anyone else has ideas on improving the RV extract programme, do let me know.

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Re: How to use the HARPS archive

Post by Sirius_Alpha on 22nd June 2014, 8:41 pm

I'm definitely interested in displaying offsets, once I figure out how to go about it, I'll do so, but in the mean time, a new version with suggested improvements.

.sys files now point to correct .vels files when using a custom star name.
Form title updated.
Update plots and Update dataset functionality merged.
FWHM and Biswidth errors reduced to two significant digits.
Sort button replaced with dropdown box.

http://wikisend.com/download/465818/HARPS_RV_Extractor_v2.3.rar

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Re: How to use the HARPS archive

Post by Lazarus on 26th June 2014, 3:17 pm

Thanks for the tutorial. As regards extracting the data, once the files are in one folder I use the following Python script to generate the .vels file (needs to have Pyfits installed):
Code:

import glob
import pyfits

measurements = []

num_data = 0
mean_rv = 0.0

for f in glob.glob('*_ccf_*.fits'):
    headers = pyfits.getheader(f)

    bjd = headers['ESO DRS BJD']
    rv = headers['ESO DRS CCF RVC'] * 1000.0
    rv_err = headers['ESO DRS CCF NOISE'] * 1000.0

    measurements.append((bjd, rv, rv_err))
   
    num_data += 1
    mean_rv += rv

mean_rv /= num_data

for t in measurements:
    print t[0], t[1] - mean_rv, t[2]
(not on Windows, so Sirius's batch file isn't a possibility for me)

Played around with HD 1461 (the system seems to be a bit of a mess as regards published solutions), HARPS alone slightly prefers an orbital period of 0.85 days (=1/(1 + 1/5.77)) for planet b, combining with the Keck data in there switches it back to the 5.77-day published period. As for additional planets, looks like there are problems with sampling...

Are you using Systemic classic or Systemic 2?
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Re: How to use the HARPS archive

Post by Shellface on 28th June 2014, 3:42 pm

Sirius wrote:Should the offset be given as the value of the most recent normalisation? If so, it will be skewed significantly by outliers.
Yes! It doesn't matter if the initial value is inaccurate as long as it can be corrected.

Have you done anything for binning?

Lazarus wrote:Played around with HD 1461 (the system seems to be a bit of a mess as regards published solutions), HARPS alone slightly prefers an orbital period of 0.85 days (=1/(1 + 1/5.77)) for planet b, combining with the Keck data in there switches it back to the 5.77-day published period.
I haven't been through the data from the most recent release, but what I did go through (up to 2008) seemed in agreement with the solution of Mayor et al., the longer-period signals from Rivera et al. being noticeably related to activity. I didn't check for sub-day aliasing, though!

Lazarus wrote:As for additional planets, looks like there are problems with sampling...
I, uh, doubt that. HD 1461 has some of the best sampling on the GTO sample…

Lazarus wrote:Are you using Systemic classic or Systemic 2?
…There are different versions?

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Re: How to use the HARPS archive

Post by Lazarus on 28th June 2014, 10:02 pm

HD 1461 has a lot of data points, but they are in yearly clumps. This leads to a very strong 1 year peak in the sampling periodogram. The ~400d peak can be found in the data, but converges to a period very close to 1 year, with the most rapid RV shifts occurring between the clumps.

So yeah, I think it's fair to say there are issues with the sampling.
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Re: How to use the HARPS archive

Post by Sunchaser on 3rd July 2014, 11:06 am

Quick question: when doing the first part of the data entry (the columns into notepad) must every available data mentioned be used from the HARPS archive on that star?

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Re: How to use the HARPS archive

Post by Shellface on 3rd July 2014, 5:35 pm

I don't think I'm interpreting your question correctly, but unless it is excessively outlying I don't see why you would want to discard a value.

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Re: How to use the HARPS archive

Post by Sunchaser on 6th July 2014, 8:00 am

What would you define as excessively outlying? A number that seems inconsistent w. the others?

Right now the star I'm working on has, out of 50 files, four RVC values in the negative, a BIS SPAN value of 0, and one line where the CCF NOISE and CCF FWHM values are the same. What effect does this have on the outcome? Or would it have any?

Thanks for putting up with my very non-technical self and equally silly questions.

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Re: How to use the HARPS archive

Post by Shellface on 6th July 2014, 9:59 am

Ah, that sounds like you're dealing with an A/F-star? I've seen these kind of issues several times for early-type stars, which relates to problems using the G2 mask on stars with very different spectra.

I can't really make much of a diagnostic from here, but if you could direct me to the star I could try to judge which spectra are not useful. Based on previous experience, probably more than a few of them…

Thanks for putting up with my very non-technical self and equally silly questions.
All for a good cause![citation needed]

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Re: How to use the HARPS archive

Post by Sunchaser on 6th July 2014, 1:21 pm

PSI Cap, HD 197692, Pazhan, or whatever else you choose to call it....it's an F5V.

Thanks.

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Re: How to use the HARPS archive

Post by Shellface on 7th July 2014, 6:28 pm

Alright. First thing, the last three spectra of the 50 are actually of Vesta (as indicated by the name of the files) - the asteroid is often used to take a spectrum of the Sun, and looking in Celestia at the date of observation shows that Vesta was quite close to Psi Cap. So ignore those three.

Now, to preface: literature indicates the radial velocity of the star is about 26 km/s, give or take a couple, and Lagrange et al. found a radial velocity RMS of 30 m/s (0.03 km/s) based on a subset of these spectra (but analysed with their own program)

This is what I got from the 47 spectra, format equal to that in the first post in this thread and split into nights. As you can see, very few of the RVs are in the vicinity of 26 km/s; the first two are definitely unphysical because such high velocities are impossible, while the others are unusually high. Also, the RV scatter is in excess of 50 km/s, which is very inconsistent Lagrange et al.'s result (again, based on the same spectra). The activity indicators are also peculiar; the FWHM is generally less than 10 km/s (though it does correlate with v sin i, and this star is a fast rotator) and the biswidth is always close to 0 km/s and rarely more than a few km/s. The only spectrum which seems to be normal is the second-to-last one, but even then the other one from the same night does not have a convergent biswidth. In all, the series is not representative of the real behaviour of the star.

This is, again, related to problems with using the G2 mask (the earliest that HARPS has) for a spectrum that is significantly different. The problems seen here do seem to stop at some point for other stars; for example, Iota Crateris' spectra from 2006 do not have convergent biswidths, but those from afterwards do - so for the Lagrange et al. sample observations before 2007 are not useful when analysed with the HARPS DRS.

Peculiarly, early-type stars observed by other groups do not seem to have this issue, so it isn't strictly due to the instrument. However, it seems to be a locally persistent problem, so my best advice here is to not bother with any spectra before 2007 for stars observed by Lagrange et al. (you can check the observing group by clicking what's in the "ProgId" column in the archive query results). Their program (which is not publicly available) does not seem to suffer from these issues, but the DRS most certainly does.

So yeah. Sorry for the none-too-positive result, but the DRS was not designed for stars earlier than F7 or so. However, I can assure you that it works wonderfully for any sensible star later than that!

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Re: How to use the HARPS archive

Post by Sunchaser on 7th July 2014, 7:47 pm

I'm sure that there are plenty of others I can take a stab at...Thanks for your help!

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Re: How to use the HARPS archive

Post by Sunchaser on 8th July 2014, 7:38 pm

Another question(s): Are the FWHM and BISWIDTH columns also averaged? Are they also multiplied by 1000?

Thanks (again)

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Re: How to use the HARPS archive

Post by Shellface on 8th July 2014, 8:48 pm

They are on an absolute scale, so yes, you need to adjust them by their average: they are in km/s, so yes, they need to be multiplied by 1000 (after correcting for the average).

Are you also unable to use Sirius' extractor? It's a lot quicker than doing it manually, as I will never stop saying.

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Re: How to use the HARPS archive

Post by Sunchaser on 9th July 2014, 7:11 am

I tried the most recent link and it said the file is no longer available...argh. It looks like it would be most useful for those really big files. Right now I'm working on Gliese 511, and despite the smaller number of files, it's still taking a while.

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Re: How to use the HARPS archive

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