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From: eric@astro.columbia.edu
Subject: xmmextractor fail
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Date: Mon, 8 Jul 2019 20:50:08 +0200
From: eric@astro.columbia.edu
To: xmmhelp@sciops.esa.int
Subject: xmmextractor fail
Full_Name: Eric Gotthelf
Submission from: (NULL) (193.147.152.102)



I just install the latest SAS. I initiated SAS, as usual:

------------------------------------------------------------
mingus:/Users/eric/work/pulsar/cygloop/0722130101$ headas

mingus:/Users/eric/work/pulsar/cygloop/0722130101$ fversion
22Oct2018_V6.25

mingus:/Users/eric/work/pulsar/cygloop/0722130101$ runsas  

sasversion:- Executing (routine): sasversion  -w 1 -V 4
sasversion:- sasversion (sasversion-1.3)  [xmmsas_20190531_1155-18.0.0] started:
 2019-07-08T18:27:59.000
sasversion:- XMM-Newton SAS release and build information:

SAS release: xmmsas_20190531_1155-18.0.0
Compiled on: Sun Jun  2 14:06:47 CEST 2019
Compiled by: sasbuild@xmac01
Platform   : Darwin-16.7.0 64

SAS-related environment variables that are set:

SAS_DIR = /usr/local/sas/xmmsas_20190531_1155
SAS_PATH = /usr/local/sas/xmmsas_20190531_1155
SAS_CCFPATH = /usr/local/sas/ccf
SAS_CCF = ../ODF/ccf.cif
SAS_ODF = ../ODF

sasversion:- sasversion (sasversion-1.3)  [xmmsas_20190531_1155-18.0.0] ended:  
 2019-07-08T18:27:59.000

Do not forget to define SAS_CCFPATH, SAS_CCF and SAS_ODF
--------------------------------------------------------------------

I would like to analysis a point source. I am following the instructions for 
xmmextractor at https://www.cosmos.esa.int/web/xmm-newton/sas-thread-xmmextractor


Is this method still recommended? Seems there is some perl module is missing:

--------------------------------------------------------------------
mingus:/Users/eric/work/pulsar/cygloop/0722130101/PPS$  xmmextractor

Can't locate Switch.pm in @INC (you may need to install the Switch module) (@INC
contains: /usr/local/sas/xmmsas_20190531_1155/lib/perl5
/usr/local/heasoft-6.25/x86_64-apple-darwin15.6.0/lib/perl
/usr/local/heasoft-6.25/x86_64-apple-darwin15.6.0/lib/perl
/Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
/Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18
/Library/Perl/Updates/5.18.2
/System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18
/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.18 .) at
/usr/local/sas/xmmsas_20190531_1155/bin/xmmextractor line 210.
BEGIN failed--compilation aborted at
/usr/local/sas/xmmsas_20190531_1155/bin/xmmextractor line 210.
------------------------------------------------------------------------------

Or should I use epchain, etc... and follow a different method to produe
spectra?

Thank You,
Eric


Reply 1

Resend
From: Ignacio de la Calle <xmmhelp@sciops.esa.int>
To: eric@astro.columbia.edu
Subject: Re: xmmextractor fail (PR#85441)
Date: Tue Jul  9 11:34:31 2019
Dear Eric Gotthelf,

The problem is with your perl installation. It is a bit old and should be
upgraded.
Your version is 5.18 and you should have 5.24.1. Please do,

    # perl -MCPAN -eshell

go into installation mode and install:

    cpan> install Switch.pm

you might need other modules. Just follow the same procedure as for the Switch 
module.

Thanks,

Ignacio de la Calle
XMM-Newton SOC

> Full_Name: Eric Gotthelf
> Submission from: (NULL) (193.147.152.102)
> 
> 
> 
> I just install the latest SAS. I initiated SAS, as usual:
> 
> ------------------------------------------------------------
> mingus:/Users/eric/work/pulsar/cygloop/0722130101$ headas
> 
> mingus:/Users/eric/work/pulsar/cygloop/0722130101$ fversion
> 22Oct2018_V6.25
> 
> mingus:/Users/eric/work/pulsar/cygloop/0722130101$ runsas  
> 
> sasversion:- Executing (routine): sasversion  -w 1 -V 4
> sasversion:- sasversion (sasversion-1.3)  [xmmsas_20190531_1155-18.0.0]
started:
>  2019-07-08T18:27:59.000
> sasversion:- XMM-Newton SAS release and build information:
> 
> SAS release: xmmsas_20190531_1155-18.0.0
> Compiled on: Sun Jun  2 14:06:47 CEST 2019
> Compiled by: sasbuild@xmac01
> Platform   : Darwin-16.7.0 64
> 
> SAS-related environment variables that are set:
> 
> SAS_DIR = /usr/local/sas/xmmsas_20190531_1155
> SAS_PATH = /usr/local/sas/xmmsas_20190531_1155
> SAS_CCFPATH = /usr/local/sas/ccf
> SAS_CCF = ../ODF/ccf.cif
> SAS_ODF = ../ODF
> 
> sasversion:- sasversion (sasversion-1.3)  [xmmsas_20190531_1155-18.0.0]
ended:
 
>  2019-07-08T18:27:59.000
> 
> Do not forget to define SAS_CCFPATH, SAS_CCF and SAS_ODF
> --------------------------------------------------------------------
> 
> I would like to analysis a point source. I am following the instructions
for 
> xmmextractor at
https://www.cosmos.esa.int/web/xmm-newton/sas-thread-xmmextractor
> 
> 
> Is this method still recommended? Seems there is some perl module is
missing:
> 
> --------------------------------------------------------------------
> mingus:/Users/eric/work/pulsar/cygloop/0722130101/PPS$  xmmextractor
> 
> Can't locate Switch.pm in @INC (you may need to install the Switch module)
(@INC
> contains: /usr/local/sas/xmmsas_20190531_1155/lib/perl5
> /usr/local/heasoft-6.25/x86_64-apple-darwin15.6.0/lib/perl
> /usr/local/heasoft-6.25/x86_64-apple-darwin15.6.0/lib/perl
> /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
> /Network/Library/Perl/5.18/darwin-thread-multi-2level
/Network/Library/Perl/5.18
> /Library/Perl/Updates/5.18.2
> /System/Library/Perl/5.18/darwin-thread-multi-2level
/System/Library/Perl/5.18
> /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.18 .) at
> /usr/local/sas/xmmsas_20190531_1155/bin/xmmextractor line 210.
> BEGIN failed--compilation aborted at
> /usr/local/sas/xmmsas_20190531_1155/bin/xmmextractor line 210.
> ------------------------------------------------------------------------------
> 
> Or should I use epchain, etc... and follow a different method to produe
> spectra?
> 
> Thank You,
> Eric
> 
> 


Followup 1

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Subject: Re: xmmextractor fail (PR#85441)
To: Ignacio de la Calle <xmmhelp@sciops.esa.int>
From: Eric Gotthelf <eric@astro.columbia.edu>
Date: Wed, 10 Jul 2019 18:05:08 -0400
Dear Ignacio,

Thank you for you quick reply.

When I run the command "perl -MCPAN -eshell", the result is:

---------------
"Sorry, we have to rerun the configuration dialog for CPAN.pm due to
some missing parameters. Configuration will be written to
 ..<</Users/eric/.cpan/CPAN/MyConfig.pm>>

CPAN.pm requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.

Would you like to configure as much as possible automatically? [yes] "
---------------

However, I hesitate to continue as I fear breaking my current perl set 
up on my compute,
which might break all sort of stuff I know nothing about and could not fix.

Instead I am using an alternative analysis procedure, running epchain 
and emchain
and taking it from there using the FTOOLS and SAS tools to generate 
products.

One question on this front is on adding the two MOS spectrum together. I 
can do this
using:

epicspeccombine pha="seyfert_0722130101M1S001_src.pha 
seyfert_0722130101M2S002_src.pha" bkg="seyfert_0722130101M1S001_bkg.pha 
seyfert_0722130101M2S002_bkg.pha" 
rmf="seyfert_0722130101M1S001_src.pha.rmf 
seyfert_0722130101M2S002_src.pha.rmf"
arf="seyfert_0722130101M1S001_src.pha.arf 
seyfert_0722130101M2S002_src.pha.arf" 
filepha=seyfert_0722130101MOS_src.pha 
filebkg=seyfert_0722130101MOS_bkg.pha filersp=seyfert_0722130101MOS.rsp

However, how do I group the resulting spectral file using specgroup, 
since that requires an RMF and a ARF file to work, not a RSP file?

Thanks,
Eric

On 7/9/19 11:34 AM, Ignacio de la Calle wrote:
> Dear Eric Gotthelf,
>
> The problem is with your perl installation. It is a bit old and should be
> upgraded.
> Your version is 5.18 and you should have 5.24.1. Please do,
>
>      # perl -MCPAN -eshell
>
> go into installation mode and install:
>
>      cpan> install Switch.pm
>
> you might need other modules. Just follow the same procedure as for the
Switch
> module.
>
> Thanks,
>
> Ignacio de la Calle
> XMM-Newton SOC
>
>> Full_Name: Eric Gotthelf
>> Submission from: (NULL) (193.147.152.102)
>>
>>
>>
>> I just install the latest SAS. I initiated SAS, as usual:
>>
>> ------------------------------------------------------------
>> mingus:/Users/eric/work/pulsar/cygloop/0722130101$ headas
>>
>> mingus:/Users/eric/work/pulsar/cygloop/0722130101$ fversion
>> 22Oct2018_V6.25
>>
>> mingus:/Users/eric/work/pulsar/cygloop/0722130101$ runsas
>>
>> sasversion:- Executing (routine): sasversion  -w 1 -V 4
>> sasversion:- sasversion (sasversion-1.3)  [xmmsas_20190531_1155-18.0.0]
> started:
>>   2019-07-08T18:27:59.000
>> sasversion:- XMM-Newton SAS release and build information:
>>
>> SAS release: xmmsas_20190531_1155-18.0.0
>> Compiled on: Sun Jun  2 14:06:47 CEST 2019
>> Compiled by: sasbuild@xmac01
>> Platform   : Darwin-16.7.0 64
>>
>> SAS-related environment variables that are set:
>>
>> SAS_DIR = /usr/local/sas/xmmsas_20190531_1155
>> SAS_PATH = /usr/local/sas/xmmsas_20190531_1155
>> SAS_CCFPATH = /usr/local/sas/ccf
>> SAS_CCF = ../ODF/ccf.cif
>> SAS_ODF = ../ODF
>>
>> sasversion:- sasversion (sasversion-1.3)  [xmmsas_20190531_1155-18.0.0]
ended:
>   
>>   2019-07-08T18:27:59.000
>>
>> Do not forget to define SAS_CCFPATH, SAS_CCF and SAS_ODF
>> --------------------------------------------------------------------
>>
>> I would like to analysis a point source. I am following the
instructions for
>> xmmextractor at
https://www.cosmos.esa.int/web/xmm-newton/sas-thread-xmmextractor
>>
>>
>> Is this method still recommended? Seems there is some perl module is
missing:
>>
>> --------------------------------------------------------------------
>> mingus:/Users/eric/work/pulsar/cygloop/0722130101/PPS$  xmmextractor
>>
>> Can't locate Switch.pm in @INC (you may need to install the Switch
module)
> (@INC
>> contains: /usr/local/sas/xmmsas_20190531_1155/lib/perl5
>> /usr/local/heasoft-6.25/x86_64-apple-darwin15.6.0/lib/perl
>> /usr/local/heasoft-6.25/x86_64-apple-darwin15.6.0/lib/perl
>> /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
>> /Network/Library/Perl/5.18/darwin-thread-multi-2level
> /Network/Library/Perl/5.18
>> /Library/Perl/Updates/5.18.2
>> /System/Library/Perl/5.18/darwin-thread-multi-2level
> /System/Library/Perl/5.18
>> /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
>> /System/Library/Perl/Extras/5.18 .) at
>> /usr/local/sas/xmmsas_20190531_1155/bin/xmmextractor line 210.
>> BEGIN failed--compilation aborted at
>> /usr/local/sas/xmmsas_20

Message of length 5783 truncated


Reply 2

Resend
From: Ignacio de la Calle <xmmhelp@sciops.esa.int>
To: eric@astro.columbia.edu
Subject: Re: xmmextractor fail (PR#85441)
Date: Thu Jul 11 15:34:27 2019
Dear Eric Gotthelf,

Sorry for the delay, I was running some tests.

> ---------------
> "Sorry, we have to rerun the configuration dialog for CPAN.pm due to
> some missing parameters. Configuration will be written to
>  ..<</Users/eric/.cpan/CPAN/MyConfig.pm>>
> 
> CPAN.pm requires configuration, but most of it can be done automatically.
> If you answer 'no' below, you will enter an interactive dialog for each
> configuration option instead.
> 
> Would you like to configure as much as possible automatically? [yes] "
> ---------------

It should be safe to do this, but I understand your concern. If you have a
workaround then leave it there. 

> epicspeccombine pha="seyfert_0722130101M1S001_src.pha 
> seyfert_0722130101M2S002_src.pha" bkg="seyfert_0722130101M1S001_bkg.pha 
> seyfert_0722130101M2S002_bkg.pha" 
> rmf="seyfert_0722130101M1S001_src.pha.rmf 
> seyfert_0722130101M2S002_src.pha.rmf"
> arf="seyfert_0722130101M1S001_src.pha.arf 
> seyfert_0722130101M2S002_src.pha.arf" 
> filepha=seyfert_0722130101MOS_src.pha 
> filebkg=seyfert_0722130101MOS_bkg.pha filersp=seyfert_0722130101MOS.rsp
> 
> However, how do I group the resulting spectral file using specgroup, 
> since that requires an RMF and a ARF file to work, not a RSP file?

This should work. 

specgroup spectrumset=seyfert_0722130101MOS_src.pha
groupedset=seyfert_0722130101MOS_group.pha
backgndset=seyfert_0722130101MOS_bkg.pha oversample=3 withoversampling=yes
mincounts=25 withCounts=yes rmfset=seyfert_0722130101MOS.rspwithrmfset=yes
arfset=none witharfset=no

However, some assumptions are made. For the combination of MOS1
and MOS2 specgroup assumes the instrumental setup of MOS1. But the task should
run fine and load fine in XSPEC.

Let me know if you have any problems.

Regards,

Ignacio de la Calle
XMM-Newton SOC



Followup 2

Compose reply
Download message
Subject: Re: xmmextractor fail (PR#85441)
To: Ignacio de la Calle <xmmhelp@sciops.esa.int>
From: Eric Gotthelf <eric@astro.columbia.edu>
Date: Sat, 13 Jul 2019 17:04:47 -0400
Dear Ignacio,

On 7/11/19 9:34 PM, Ignacio de la Calle wrote:
> Dear Eric Gotthelf,
>
> Sorry for the delay, I was running some tests.
>
>> ---------------
>> "Sorry, we have to rerun the configuration dialog for CPAN.pm due to
>> some missing parameters. Configuration will be written to
>>   ....<</Users/eric/.cpan/CPAN/MyConfig.pm>>
>>
>> CPAN.pm requires configuration, but most of it can be done
automatically.
>> If you answer 'no' below, you will enter an interactive dialog for each
>> configuration option instead.
>>
>> Would you like to configure as much as possible automatically? [yes] "
>> ---------------
> It should be safe to do this, but I understand your concern. If you have a
> workaround then leave it there.
>
>> epicspeccombine pha="seyfert_0722130101M1S001_src.pha
>> seyfert_0722130101M2S002_src.pha" bkg="seyfert_0722130101M1S001_bkg.pha
>> seyfert_0722130101M2S002_bkg.pha"
>> rmf="seyfert_0722130101M1S001_src.pha.rmf
>> seyfert_0722130101M2S002_src.pha.rmf"
>> arf="seyfert_0722130101M1S001_src.pha.arf
>> seyfert_0722130101M2S002_src.pha.arf"
>> filepha=seyfert_0722130101MOS_src.pha
>> filebkg=seyfert_0722130101MOS_bkg.pha filersp=seyfert_0722130101MOS.rsp
>>
>> However, how do I group the resulting spectral file using specgroup,
>> since that requires an RMF and a ARF file to work, not a RSP file?
> This should work.
>
> specgroup spectrumset=seyfert_0722130101MOS_src.pha
> groupedset=seyfert_0722130101MOS_group.pha
> backgndset=seyfert_0722130101MOS_bkg.pha oversample=3 withoversampling=yes
> mincounts=25 withCounts=yes rmfset=seyfert_0722130101MOS.rspwithrmfset=yes
> arfset=none witharfset=no
>
> However, some assumptions are made. For the combination of MOS1
> and MOS2 specgroup assumes the instrumental setup of MOS1. But the task
should
> run fine and load fine in XSPEC.
>
> Let me know if you have any problems.

That worked just fine (and in this case the two MOSs used the same mode.)

Thanks again,
Eric

>
> Regards,
>
> Ignacio de la Calle
> XMM-Newton SOC
>
>
> 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).
>
>



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