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From: garcia@asu.cas.cz
Subject: Grouping when using epicspeccombine.
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5 followups: 1 2 3 4 5

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Date: Sun, 17 Nov 2019 15:08:13 +0100
From: garcia@asu.cas.cz
To: xmmhelp@sciops.esa.int
Subject: Grouping when using epicspeccombine.
Full_Name: Maria Caballero-Garcia
Submission from: (NULL) (193.147.152.102)


Hi,

I have 3 questions:

1) Is tthe SAS thread
https://www.cosmos.esa.int/web/xmm-newton/sas-thread-epic-merging  valid for
merging epic-pn spectra from single observations? If yes, I get different
individual spectra from setting acceptchanrange=yes or not. In the first case
the spectra has more bins, so it looks better.

2) When to apply "specgroup"? When creating the individual spectra (before
merging them with epicspeccombine) ?

3) Related to the following help-desk question:

http://xmm.esac.esa.int/xmmhelp/EPICpn?id=81582;page=54;user=guest

Why is the EXPOSURE keyword " the average of the individual EXPOSURE values "?
Do we need to correct it to the sum of exposure times MANUALLY?

These questions are important because I get very different merged epic-pn
spectra when assuming different cases (all of what you can imagine
"reasonable").

Best regards,

Maria.


Reply 1

Resend
From: Felix Fuerst <xmmhelp@sciops.esa.int>
To: garcia@asu.cas.cz
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
Date: Mon Nov 18 16:40:57 2019
Dear Maria,

I'm not sure what you mean by "merging epic-pn spectra from single
observations"? Do you want to merge spectra from only the pn camera taken in
different observations? Or do you want to merge MOS and pn spectra from one
single observation? In both cases, you can use epicspeccombine. However, if you
only merge pn spectra and do not change the standard binning, you don't have to
use 'acceptchanrange=yes' in rmfgen.

It is not possible to use 'specgroup' on the combined data, as the camera
information is missing (as described in the SAS thread). Using it before
combining the data is also not recommended, as you will not end up with the same
binning for all data. If you require a certain binning, you can either force
that in 'evselect' during extraction (but then remember to run 'rmfgen' with '
acceptchanrange=yes'), or you could use 'grppha' or similar programs after
combining the data.

The combined spectrum does indeed have the average exposure time in the EXPOSURE
keyword. You shoul not need to correct that, as the created response file has at
the same time uses the average of all ARFs weighted by the relative exposure
time of each observation, so that the resulting countrates are correct.

Hope that helps,
Best,
 Felix


Followup 1

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Date: Mon, 18 Nov 2019 17:39:17 +0100
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
From: "Maria Caballero-Garcia" <garcia@asu.cas.cz>
To: "Felix Fuerst" <xmmhelp@sciops.esa.int>
Hi Felix,

I find this very helpful. Thank you very much for your reply!

Cheers!

Maria.

> Dear Maria,
>
> I'm not sure what you mean by "merging epic-pn spectra from single
> observations"? Do you want to merge spectra from only the pn camera taken
> in
> different observations? Or do you want to merge MOS and pn spectra from
> one
> single observation? In both cases, you can use epicspeccombine. However,
> if you
> only merge pn spectra and do not change the standard binning, you don't
> have to
> use 'acceptchanrange=yes' in rmfgen.
>
> It is not possible to use 'specgroup' on the combined data, as the camera
> information is missing (as described in the SAS thread). Using it before
> combining the data is also not recommended, as you will not end up with
> the same
> binning for all data. If you require a certain binning, you can either
> force
> that in 'evselect' during extraction (but then remember to run 'rmfgen'
> with '
> acceptchanrange=yes'), or you could use 'grppha' or similar programs after
> combining the data.
>
> The combined spectrum does indeed have the average exposure time in the
> EXPOSURE
> keyword. You shoul not need to correct that, as the created response file
> has at
> the same time uses the average of all ARFs weighted by the relative
> exposure
> time of each observation, so that the resulting countrates are correct.
>
> Hope that helps,
> Best,
>  Felix
>
> This message is intended only for the recipient(s) named above. It may
> contain proprietary information and/or
> protected content. Any unauthorised disclosure, use, retention or
> dissemination is prohibited. If you have received
> this e-mail in error, please notify the sender immediately. ESA applies
> appropriate organisational measures to protect
> personal data, in case of data privacy queries, please contact the ESA
> Data Protection Officer (dpo@esa.int).
>
>
>


-------------------------------------
( Dr Maria D. Caballero-Garcia, PhD )
ASU-CAS@Prague (CR)
IAA-CSIC@Granada (Spain)
-------------------------------------



Followup 2

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Date: Tue, 19 Nov 2019 17:21:47 +0100
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
From: "Maria Caballero-Garcia" <garcia@asu.cas.cz>
To: "Felix Fuerst" <xmmhelp@sciops.esa.int>
Hi again,

I still have a problem regarding the following point:

> The combined spectrum does indeed have the average exposure time in the
> EXPOSURE
> keyword. You shoul not need to correct that, as the created response file
> has at
> the same time uses the average of all ARFs weighted by the relative
> exposure
> time of each observation, so that the resulting countrates are correct.

since I do NOT get the correct fluxes. It happens that I get lower count
rate for the (combined) spectrum with shorter exposure time. And this
spectrum should have higher count rate (regardless of the exposure time).

I made a selection for some good-time intervals (GTIs), so that may be the
problem of getting wrong spectra for fitting wth XSPEC.

Hope someone can answer to this question.

Maria.

-------------------------------------
( Dr Maria D. Caballero-Garcia, PhD )
ASU-CAS@Prague (CR)
IAA-CSIC@Granada (Spain)
-------------------------------------



Reply 2

Resend
From: Felix Fuerst <xmmhelp@sciops.esa.int>
To: maria.dolores.caballero.garcia@asu.cas.cz
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
Date: Wed Nov 20 15:16:55 2019
Dear Maria,

to answer your question it would be easiest if we can reproduce your extraction.
Could you tell me which observation you are using, which data you want to
combine, and which GTIs you are using?  If you like, you could also share your
extracted data products so we can have a look what is going on.

Thanks,
 Felix


Followup 3

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Date: Thu, 21 Nov 2019 13:20:25 +0100
Subject: ***UNCHECKED*** Re: Grouping when using epicspeccombine. (PR#85857)
From: "Maria Caballero-Garcia" <garcia@asu.cas.cz>
To: "Felix Fuerst" <xmmhelp@sciops.esa.int>
Cc: maria.dolores.caballero.garcia@asu.cas.cz
------=_20191121132025_33043
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: 8bit

Hi Felix,

I provide you with the files I used to produce the PN spectrum from every
single observation. I use GTIs that are shorter than one individual
observation. I do not send to you all the data for all the observations
because this is out of scope. But I send to you a Figure with what I want
to produce well. The black, red and green are the (combined) spectra
obtained after combining 15, 15 and 7 spectra, respectively. But the
problem is that the green spectrum should be brighter than the other two
and it is not.

I hope I explain everything well.

Cheers and many thanks,

Maria.


Example extraction Obs. ID: 0792180601
====================

GTIs file: Attached.
======

Script to produce single spectrum:
=========================

#parameter 1: input events file

in="table=$1.fits:EVENTS"

evselect $in withrateset=yes rateset=rates_b4gti.fits \
timecolumn=TIME makeratecolumn=yes timebinsize=100 maketimecolumn=yes \
expression='#XMMEA_EP && PI in [10000:12000] && (PATTERN==0)'

dsplot table=rates_b4gti.fits x=TIME y=RATE &

evselect $in withrateset=yes rateset=rates_aftergti.fits \
timecolumn=TIME makeratecolumn=yes timebinsize=100 maketimecolumn=yes \
expression='#XMMEA_EP && PI in [200:12000] &&
(PATTERN==0)&&GTI(gtis_HF.fits,TIME)'

dsplot table=rates_aftergti.fits x=TIME y=RATE &

evselect $in withfilteredset=yes filteredset=filtered_pn_HF.fits \
expression='(PATTERN <= 4)&&(FLAG == 0)&&(PI in
[200:12000])&&GTI(gtis_HF.fits,TIME)' \
filtertype=expression keepfilteroutput=yes

#Espectro de la fuente:

evselect table=filtered_pn_HF.fits:EVENTS withspectrumset=yes
spectrumset=spectrum_src_pn_HF.fits energycolumn=PI spectralbinsize=5
withspecranges=yes specchannelmin=0 specchannelmax=20479
expression='(circle(25709.133,27966.33,800,X,Y))'

#Espectro de una region de background:

evselect table=filtered_pn_HF.fits:EVENTS withspectrumset=yes
spectrumset=spectrum_bkg_pn_HF.fits energycolumn=PI spectralbinsize=5
withspecranges=yes specchannelmin=0 specchannelmax=20479
expression='((X,Y) IN box(29907.154,23768.844,2474.5536,4734.5399,131))'

#Calculate the area of source and background region used to make the
spectral files. The
#area is written into the header of the SPECTRUM table of the file as
keyword BACKSCAL.

 backscale spectrumset=spectrum_src_pn_HF.fits badpixlocation=PNclean.fits
 backscale spectrumset=spectrum_bkg_pn_HF.fits badpixlocation=PNclean.fits

#Response matrix:

rmfgen spectrumset=spectrum_src_pn_HF.fits
rmfset=spectrum_src_resp_pn_HF.fits \
withenergybins=yes energymin=0.1 energymax=12.0 nenergybins=2400

#Ancilliary response matrix:

arfgen spectrumset=spectrum_src_pn_HF.fits
arfset=spectrum_src_arf_pn_HF.fits withrmfset=yes \
rmfset=spectrum_src_resp_pn_HF.fits badpixlocation=PNclean.fits
detmaptype=psf

Script to combine spectra:
===================

#!/usr/local/bin/bash

epicspeccombine pha="spe_src_HF_0673580101.fits spe_src_HF_0673580401.fits
spe_src_HF_0780561301.fits spe_src_HF_0780561401.fits
spe_src_HF_0780561601.fits spe_src_HF_0792180401.fits
spe_src_HF_0792180601.fits"  \
   bkg="spe_bkg_HF_0673580101.fits spe_bkg_HF_0673580401.fits
spe_bkg_HF_0780561301.fits spe_bkg_HF_0780561401.fits
spe_bkg_HF_0780561601.fits spe_bkg_HF_0792180401.fits
spe_bkg_HF_0792180601.fits"   \
   rmf="spe_rmf_HF_0673580101.fits spe_rmf_HF_0673580401.fits
spe_rmf_HF_0780561301.fits spe_rmf_HF_0780561401.fits
spe_rmf_HF_0780561601.fits spe_rmf_HF_0792180401.fits
spe_rmf_HF_0792180601.fits"  \
   arf="spe_arf_HF_0673580101.fits spe_arf_HF_0673580401.fits
spe_arf_HF_0780561301.fits spe_arf_HF_0780561401.fits
spe_arf_HF_0780561601.fits spe_arf_HF_0792180401.fits
spe_arf_HF_0792180601.fits"   \
   filepha="src_spectrum_HF.fits" \
   filebkg="bkg_spectrum_HF.fits" \
   filersp="response_HF.rmf"


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Message of length 49681 truncated


Followup 4

Compose reply
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Date: Tue, 26 Nov 2019 13:27:18 +0100
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
From: "Maria Caballero-Garcia" <garcia@asu.cas.cz>
To: maria.dolores.caballero.garcia@asu.cas.cz
Cc: "Felix Fuerst" <xmmhelp@sciops.esa.int>
Hi again,

did anyone have time to look at it? I really need to ensure that the
spectra and the count rates I am obtaining are correct. Please feel free
to communicate in private if you do not think this is the right channel of
communication.

Kindly regards,

Maria.

> Hi Felix,
>
> I provide you with the files I used to produce the PN spectrum from every
> single observation. I use GTIs that are shorter than one individual
> observation. I do not send to you all the data for all the observations
> because this is out of scope. But I send to you a Figure with what I want
> to produce well. The black, red and green are the (combined) spectra
> obtained after combining 15, 15 and 7 spectra, respectively. But the
> problem is that the green spectrum should be brighter than the other two
> and it is not.
>
> I hope I explain everything well.
>
> Cheers and many thanks,
>
> Maria.
>
>
> Example extraction Obs. ID: 0792180601
> ====================
>
> GTIs file: Attached.
> ======
>
> Script to produce single spectrum:
> =========================
>
> #parameter 1: input events file
>
> in="table=$1.fits:EVENTS"
>
> evselect $in withrateset=yes rateset=rates_b4gti.fits \
> timecolumn=TIME makeratecolumn=yes timebinsize=100 maketimecolumn=yes \
> expression='#XMMEA_EP && PI in [10000:12000] &&
(PATTERN==0)'
>
> dsplot table=rates_b4gti.fits x=TIME y=RATE &
>
> evselect $in withrateset=yes rateset=rates_aftergti.fits \
> timecolumn=TIME makeratecolumn=yes timebinsize=100 maketimecolumn=yes \
> expression='#XMMEA_EP && PI in [200:12000] &&
> (PATTERN==0)&&GTI(gtis_HF.fits,TIME)'
>
> dsplot table=rates_aftergti.fits x=TIME y=RATE &
>
> evselect $in withfilteredset=yes filteredset=filtered_pn_HF.fits \
> expression='(PATTERN <= 4)&&(FLAG == 0)&&(PI in
> [200:12000])&&GTI(gtis_HF.fits,TIME)' \
> filtertype=expression keepfilteroutput=yes
>
> #Espectro de la fuente:
>
> evselect table=filtered_pn_HF.fits:EVENTS withspectrumset=yes
> spectrumset=spectrum_src_pn_HF.fits energycolumn=PI spectralbinsize=5
> withspecranges=yes specchannelmin=0 specchannelmax=20479
> expression='(circle(25709.133,27966.33,800,X,Y))'
>
> #Espectro de una region de background:
>
> evselect table=filtered_pn_HF.fits:EVENTS withspectrumset=yes
> spectrumset=spectrum_bkg_pn_HF.fits energycolumn=PI spectralbinsize=5
> withspecranges=yes specchannelmin=0 specchannelmax=20479
> expression='((X,Y) IN box(29907.154,23768.844,2474.5536,4734.5399,131))'
>
> #Calculate the area of source and background region used to make the
> spectral files. The
> #area is written into the header of the SPECTRUM table of the file as
> keyword BACKSCAL.
>
>  backscale spectrumset=spectrum_src_pn_HF.fits badpixlocation=PNclean.fits
>  backscale spectrumset=spectrum_bkg_pn_HF.fits badpixlocation=PNclean.fits
>
> #Response matrix:
>
> rmfgen spectrumset=spectrum_src_pn_HF.fits
> rmfset=spectrum_src_resp_pn_HF.fits \
> withenergybins=yes energymin=0.1 energymax=12.0 nenergybins=2400
>
> #Ancilliary response matrix:
>
> arfgen spectrumset=spectrum_src_pn_HF.fits
> arfset=spectrum_src_arf_pn_HF.fits withrmfset=yes \
> rmfset=spectrum_src_resp_pn_HF.fits badpixlocation=PNclean.fits
> detmaptype=psf
>
> Script to combine spectra:
> ===================
>
> #!/usr/local/bin/bash
>
> epicspeccombine pha="spe_src_HF_0673580101.fits spe_src_HF_0673580401.fits
> spe_src_HF_0780561301.fits spe_src_HF_0780561401.fits
> spe_src_HF_0780561601.fits spe_src_HF_0792180401.fits
> spe_src_HF_0792180601.fits"  \
>    bkg="spe_bkg_HF_0673580101.fits spe_bkg_HF_0673580401.fits
> spe_bkg_HF_0780561301.fits spe_bkg_HF_0780561401.fits
> spe_bkg_HF_0780561601.fits spe_bkg_HF_0792180401.fits
> spe_bkg_HF_0792180601.fits"   \
>    rmf="spe_rmf_HF_0673580101.fits spe_rmf_HF_0673580401.fits
> spe_rmf_HF_0780561301.fits spe_rmf_HF_0780561401.fits
> spe_rmf_HF_0780561601.fits spe_rmf_HF_0792180401.fits
> spe_rmf_HF_0792180601.fits"  \
>    arf="spe_arf_HF_0673580101.fits spe_arf_HF_0673580401.fits
> spe_arf_HF_0780561301.fits spe_arf_HF_0780561401.fits
> spe_arf_HF_0780561601.fits spe_arf_HF_0792180401.fits
> spe_arf_HF_0792180601.fits"   \
>    filepha="src_spectrum_HF.fits" \
>    filebkg="bkg_spectrum_HF.fits" \
>    filersp="response_HF.rmf"
>
>


-------------------------------------
( Dr Maria D. Caballero-Garcia, PhD )
ASU-CAS@Prague (CR)
IAA-CSIC@Granada (Spain)
-------------------------------------



Reply 3

Resend
From: Felix Fuerst <xmmhelp@sciops.esa.int>
To: maria.dolores.caballero.garcia@asu.cas.cz
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
Date: Wed Nov 27 11:59:01 2019
Dear Maria,

thank you for your patience, I understand that this is important for you. I have
looked at the code you send and it all seems fine. However, I currently don't
exactly understand what you try to do. First of all, you are only combining data
from EPIC-pn, and not from any other camera, correct? Are all of these
observations on-axis? 

In the plot you send, I see that the red data have a higher flux than the black
data. You say both are combined from 15 spectra, but obviously these are 15
different spectra. Are they the same 15 observations, only each observation
selected for a different GTI, or 15 completely separate ObsIDs, or a mix of
those two? 

The 7 spectra, shown in green, you expect to be brighter than the red ones. Why?
Are they selected with yet another set of GTIs as a sub-set of the red data, but
selected for higher flux? Or are they again completely independent observations?


It would be great if you could provide me with some more details, so I can
better help you identify the problem.

Thanks,
 Felix



Reply 4

Resend
From: Felix Fuerst <xmmhelp@sciops.esa.int>
To: maria.dolores.caballero.garcia@asu.cas.cz
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
Date: Mon Dec  2 10:36:11 2019
Dear Maria,

thanks for sending all the files. I had a look and I think everything is fine.
Here is what I believe is happening:

Epicspeccombine combines spectra in such a way that the total counts are the
*sum* of the combined spectra, the total exposure time is the *average* of the
combined spectra, and the total effective area is also the *sum* of the combined
effective areas. The latter point is bit counter-intuitive when you combine data
from one instrument only. It is also a bit hard to see, because the effective
area has been rolled into the response matrix, but it will give you the correct
result. Combining this in such a way was a decision made when epicspeccombine
was written, and that's what we have to work with now.

Now, because the effective area is the sum of all effective areas you put into
the combined spectrum, the more spectra you use, the higher your resulting
effective area will be. The same goes for the total number of counts of course.
I see that you are using 15 spectra for the low state, but only 7 for the high
state. That means, when you plot in counts/s/keV it might appear that the LF
spectrum is brighter than the HF spectrum. But that is only an effect of the way
it is displayed, as the effective area for LF is about twice as high. I attach a
plot with the effective areas, in black from the LF and in red from the HF.

Therefore, if you plot the unfolded data, the spectra will stack correctly from
LF being the lowest, to HF being the highest. If you fit the data, you will also
find that the HF is indeed brighter and the model will require a higher flux.

Other than that I don't see anything obviously wrong with your scripts.

Hope that helps,
Best,
 Felix


PS: sending this again from the Helpdesk to have a record in the system.


Followup 5

Compose reply
Download message
Date: Mon, 2 Dec 2019 11:01:32 +0100
Subject: Re: Grouping when using epicspeccombine. (PR#85857)
From: "Maria Caballero-Garcia" <garcia@asu.cas.cz>
To: "Felix Fuerst" <xmmhelp@sciops.esa.int>

Thank you, but I do not see the plots...

M.

> Dear Maria,
>
> thanks for sending all the files. I had a look and I think everything is
> fine.
> Here is what I believe is happening:
>
> Epicspeccombine combines spectra in such a way that the total counts are
> the
> *sum* of the combined spectra, the total exposure time is the *average* of
> the
> combined spectra, and the total effective area is also the *sum* of the
> combined
> effective areas. The latter point is bit counter-intuitive when you
> combine data
> from one instrument only. It is also a bit hard to see, because the
> effective
> area has been rolled into the response matrix, but it will give you the
> correct
> result. Combining this in such a way was a decision made when
> epicspeccombine
> was written, and that's what we have to work with now.
>
> Now, because the effective area is the sum of all effective areas you put
> into
> the combined spectrum, the more spectra you use, the higher your resulting
> effective area will be. The same goes for the total number of counts of
> course.
> I see that you are using 15 spectra for the low state, but only 7 for the
> high
> state. That means, when you plot in counts/s/keV it might appear that the
> LF
> spectrum is brighter than the HF spectrum. But that is only an effect of
> the way
> it is displayed, as the effective area for LF is about twice as high. I
> attach a
> plot with the effective areas, in black from the LF and in red from the
> HF.
>
> Therefore, if you plot the unfolded data, the spectra will stack correctly
> from
> LF being the lowest, to HF being the highest. If you fit the data, you
> will also
> find that the HF is indeed brighter and the model will require a higher
> flux.
>
> Other than that I don't see anything obviously wrong with your scripts.
>
> Hope that helps,
> Best,
>  Felix
>
>
> PS: sending this again from the Helpdesk to have a record in the system.
>
> This message is intended only for the recipient(s) named above. It may
> contain proprietary information and/or
> protected content. Any unauthorised disclosure, use, retention or
> dissemination is prohibited. If you have received
> this e-mail in error, please notify the sender immediately. ESA applies
> appropriate organisational measures to protect
> personal data, in case of data privacy queries, please contact the ESA
> Data Protection Officer (dpo@esa.int).
>
>
>


-------------------------------------
( Dr Maria D. Caballero-Garcia, PhD )
ASU-CAS@Prague (CR)
IAA-CSIC@Granada (Spain)
-------------------------------------


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