Date: Fri, 29 Jul 2011 17:36:20 +0200
From: Carolin Dedes 
To: Jun-Hui Zhao 
Subject: Re: scripts

Dear Jun-Hui,

thank you very much for the script and the continuum image!
I will carefully go through it and get back to you if I have any questions regarding the line
processing.
The old smauvspec was not in my installation, but that of a friend, but I will nevertheless try to check
with her if "uvlin" and "invert"  still work on the archive data. 
It just can't be done today anymore, so I will get back to you next week.

Thanks again and good luck for your EVLA proposal!
Carolin
 On Jul 29, 2011, at 5:13 PM, Jun-Hui Zhao wrote:

> 
> Dear Carolin,
>    Sorry, I was interupted by submitting an EVLA proposal which is due
> this week. Back to you now. I have gone through the calibration and
> made a continuum image.
>    Please find attached a script and fig1.ps for the continuum image
> of 06055 showing a complex structure, double with an extension east to
> the primary. The flux density is more than an order magnitude than what
> you expected. You may do us a favor since you have already checked that
> the old smauvspec (CARMA CVS) works for the calibrated archive data.
> Would you please use the same version (CARMA CVS) Miriad to check
> if "uvlin" and "invert" still work for the calibrated archive data?
> It would be great if you can send me a continuum image of your
> target source 06055 made from the calibrated archive data. You
> don't have to do it, completely up to you.
>    I will find time to help you processing the line (CO2-1 as an
> example). Please feel free to ask questions about the scripts.
>    Jun-Hui
> 
> 
> On Thu, 28 Jul 2011, Carolin Dedes wrote:
> 
>> I would have expected some output, like the 06055.map or .beam file, but there is nothing written
out.
>> 
>> Carolin
>> 
>> 
>> On Jul 28, 2011, at 5:29 PM, Jun-Hui Zhao wrote:
>> 
>>> 
>>> 
>>> On Thu, 28 Jul 2011, Carolin Dedes wrote:
>>> 
>>>> sorry, still does not work.
>>>> 
>>>> "line" was  also wrong, but when I corrected it, it still did not work - in the sense that I do not
get the .beam and .map files.
>>>> 
>>>> using "select" gives the same no data  error, and not using "select" gives the following:
>>>> 
>>>> dedesc@columba:/export/data1/sma/data/data_files$ invert vis=101219_040701_06055+2039_lsb
map=06055_lsb.map beam=06055_lsb.beam \
>>>>>       imsize=512,512 cell=0.1 robust=0 line=chan,1,1,6144 \
>>>>>       options=systemp
>>>> Invert: version 1.0 19-apr-09
>>>> Reading the visibility data ...
>>>> Making single plane images
>>>> Visibilities accepted: 9357
>>>> Sidelobe suppression area is 51x51 arcsec
>>>> ... this corresponds to uniform weighting
>>>> Calculating the weights ...
>>>> Applying the weights ...
>>>> Theoretical rms noise: 1.094E-03
>>>> ....
>>> 
>>>    The prompt message from invert seems to me fine. What wrong here, no
>>> image produced? Or invert processing collapsed? Or no source in the map?
>>> 
>>>    Jun-Hui
>>> 
>>> 
>>>> dedesc@columba:/export/data1/sma/data/data_files$ ll -tr
>>>> 
>>>> 
>>>> I also tried the usb data with the other line options you wrote earlier, but it's the same thing.
>>>> 
>>>> Cheers.
>>>> Carolin
>>>> 
>>>> 
>>>> On Jul 28, 2011, at 5:09 PM, Jun-Hui Zhao wrote:
>>>> 
>>>>> 
>>>>> cell=0.1  not cell=0,1
>>>>> 
>>>>>   Try again.
>>>>>   Jun-Hui
>>>>> 
>>>>> On Thu, 28 Jul 2011, Carolin Dedes wrote:
>>>>> 
>>>>>> using invert, I get the following error:
>>>>>> 
>>>>>> dedesc@columba:/export/data1/sma/data/data_files$ invert
>>>>> vis=101219_040701_06055+2039_lsb map=06055_lsb.map beam=06055_lsb.beam imsize=512,512 cell=0,1
>>>>> robust=0 options=systemp select='source(06055+2039)' line=chan,1,2500,3644
>>>>>> Invert: version 1.0 19-apr-09
>>>>>> Reading the visibility data ...
>>>>>> Making cubes with 0 planes
>>>>>> ### Fatal Error [invert]:  No data to process
>>>>>> 
>>>>>> 
>>>>>> Cheers,
>>>>>> Carolin
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Jul 28, 2011, at 4:58 PM, Jun-Hui Zhao wrote:
>>>>>> 
>>>>>>> You don't need uvlin since there are no strong lines
>>>>>>> (except for the CO) for your source . Skip uvlin, just using
>>>>>>> invert to get a rough idea what is the flux density and source
>>>>>>> structure.
>>>>>>>    Jun-Hui
>>>>>>> 
>>>>>>> On Thu, 28 Jul 2011, Carolin Dedes wrote:
>>>>>>> 
>>>>>>>> Hi Jun-Hui,
>>>>>>>> 
>>>>>>>> when I try to use uvlin with the archive data, I get the following error:
>>>>>>>> 
>>>>>>>> uvlin vis=101219_040701_06055+2039_lsb out=101219_040701_06055+2039_lsb.ch0 order=1 mode=chan0
options=nowin
>>>>>>>> UvLin: version beta 11jan10
>>>>>>>> ### Fatal Error [uvlin]:
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Cheers,
>>>>>>>> Carolin
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Jul 28, 2011, at 4:36 PM, Jun-Hui Zhao wrote:
>>>>>>>> 
>>>>>>>>> I don't have the calibrated archive data.
>>>>>>>>> What you can do just using USB calibrated archive data
>>>>>>>>> excluding the CO line and make an image, for example, set the input
>>>>>>>>> parameter "line" in invert,
>>>>>>>>>   line=chan,1,2500,3644
>>>>>>>>> Also using all LSB channels
>>>>>>>>>   line=chan,1,1,6144
>>>>>>>>>   Or you can ask someone who calibrated the data to provide you a
>>>>>>>>> map of 06055.
>>>>>>>>>   Jun-Hui
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Thu, 28 Jul 2011, Carolin Dedes wrote:
>>>>>>>>> 
>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>> 
>>>>>>>>>> could you please send me the output of smauvspec for the calibrated SMA archive data, if you
can?
>>>>>>>>>> Otherwise I am not sure where the lines and line free channels are.
>>>>>>>>>> Or shall I assume that all channels are line free? (They are not, but it might be a good
start).
>>>>>>>>>> If I should do that, how many channels are there in the new data?
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> Thanks,
>>>>>>>>>> Carolin
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> On Jul 28, 2011, at 2:56 PM, Jun-Hui Zhao wrote:
>>>>>>>>>> 

>>>>>>>>>>> Dear Carolin,
>>>>>>>>>>> Can you make a continuum map of 06055 from calibrated SMA archive
>>>>>>>>>>> data? What flux density and source structure look like?
>>>>>>>>>>> Thanks.
>>>>>>>>>>> Jun-Hui
>>>>>>>>>>> 
>>>>>>>>>>> On Wed, 27 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>> 
>>>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>>>> 
>>>>>>>>>>>> 06055 is indeed the target source.
>>>>>>>>>>>> The line at 230538.0000 GHz is CO(2-1), and yes, we can start with that one.
>>>>>>>>>>>> The vlsr of 06055 is 9.3 km/s (is that what you meant with red-shift?).
>>>>>>>>>>>> I do not have any idea about the continuum source, but I expect it to be rather compact.
>>>>>>>>>>>> The expected continuum flux was larger 18 mJy, as given in the proposal, if that is any
help.
>>>>>>>>>>>> 
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Carolin
>>>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>> On Jul 27, 2011, at 9:28 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>> 
>>>>>>>>>>>>> Dear Carolin,
>>>>>>>>>>>>> Is 06055+2039  your target source? What is the redshift?
>>>>>>>>>>>>> There is a very strong line in the upper sideband at sky-frequency
>>>>>>>>>>>>> around 230 GHz. Do you know what is that line? Why do we not start with
>>>>>>>>>>>>> this line? Also do you have any ideas on the continuum source,
>>>>>>>>>>>>> rough number of flux density? and what structure (extended, compact point,
>>>>>>>>>>>>> double, or multiple components)?
>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>> 
>>>>>>>>>>>>> 
>>>>>>>>>>>>> On Tue, 26 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>> 
>>>>>>>>>>>>>> the rest frequency is 220747.2612 MHz.
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> On Jul 26, 2011, at 6:21 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>> What is the rest frequency? Yes, you can reset the rest frequency.
>>>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>> On Tue, 26 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>> maybe start with the CH3CN line.
>>>>>>>>>>>>>>>> Could I then adapt your script to do the rest of the lines?
>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>> On Jul 26, 2011, at 4:27 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>> what is your primary line that you want to image?
>>>>>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>> On Tue, 26 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>> On Tue, 26 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> great - thanks a lot!
>>>>>>>>>>>>>>>>>> What do you need to know?
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> Cheers
>>>>>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> On Jul 25, 2011, at 4:42 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> Dear Carolin,
>>>>>>>>>>>>>>>>>>> Great. I may have a few further questions for you while I work on
>>>>>>>>>>>>>>>>>>> the calibration script.
>>>>>>>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> On Mon, 25 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>>>>>>>>>>>> 

>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> I would appreciate that very much, thanks a lot.
>>>>>>>>>>>>>>>>>>>> My project is  2010B-S031 (I am the PI).
>>>>>>>>>>>>>>>>>>>> Do you want me to send the request for help with calibration as well?
>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> On Jul 25, 2011, at 4:16 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> Dear Carolin,
>>>>>>>>>>>>>>>>>>>>> I understand your concerns for the first time using SMA.
>>>>>>>>>>>>>>>>>>>>> SMA should provide a training course for new users every year.
>>>>>>>>>>>>>>>>>>>>> For your case, I would be happy to provide a calibration script
>>>>>>>>>>>>>>>>>>>>> for you if you allow me to look at your data. Are you the PI
>>>>>>>>>>>>>>>>>>>>> of the SMA project? If not, please ask the PI's permission
>>>>>>>>>>>>>>>>>>>>> (or send us a request to help you calibrate the data).
>>>>>>>>>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> On Mon, 25 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>>>>>> On Mon, 25 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> I am only now reducing the SMA data, and while I started with the
>>>>>>>>>>>>>>>>>>>>>> new miriad version and the scripts provided there, I have some problems
>>>>>>>>>>>>>>>>>>>>>> with the calibration. These are not software related, but rather deal
>>>>>>>>>>>>>>>>>>>>>> with choices to make, such as which data to flag etc. (my first time
>>>>>>>>>>>>>>>>>>>>>> with SMA data), so I did my first round without any flagging.
>>>>>>>>>>>>>>>>>>>>>> That's why I wanted to use the pre-calibrated data from the archive
>>>>>>>>>>>>>>>>>>>>>> (with the new miriad) to get a first overview of the data and be able to
>>>>>>>>>>>>>>>>>>>>>> image it.
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> I will try again to calibrate the data using this time the log from
>>>>>>>>>>>>>>>>>>>>>> the mir reduction as a guideline which data to flag for my data set.
>>>>>>>>>>>>>>>>>>>>>> Do you know of any tutorials that I could use that would show me
>>>>>>>>>>>>>>>>>>>>>> what to watch out for when flagging the sma data?
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> Using SMABLFLAG, axis=time,ampl, in most cases, the bad
>>>>>>>>>>>>>>>>>>>>> visibilities have a large deviations from the normal curve for
>>>>>>>>>>>>>>>>>>>>> a given source on each baseline. Then you should flag them.
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> On Jul 25, 2011, at 3:11 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>> Dear Carolin,
>>>>>>>>>>>>>>>>>>>>>>> I thought that you have reduced your data with the beta Miriad
>>>>>>>>>>>>>>>>>>>>>>> in March/April. Why do you go back to the old system? We will update
>>>>>>>>>>>>>>>>>>>>>>> the Miriad-CVS (CARMA) with the new system soon and obsolete old one.
>>>>>>>>>>>>>>>>>>>>>>> There were many problems on the headers of IDL output data for Miriad.
>>>>>>>>>>>>>>>>>>>>>>> The old system did skip these problems that potentially degrade the
>>>>>>>>>>>>>>>>>>>>>>> quality (precision) of SMA images. With the new system, we can help
>>>>>>>>>>>>>>>>>>>>>>> users to improve the quality of SMA tremendously. Please use the new
>>>>>>>>>>>>>>>>>>>>>>> system if you want to get the best quality of SMA images. This would
>>>>>>>>>>>>>>>>>>>>>>> help us and help you, right?
>>>>>>>>>>>>>>>>>>>>>>> It is completely upto you to choose any system that fits to your
>>>>>>>>>>>>>>>>>>>>>>> purpose. Please let us know if you need any help for handling your data
>>>>>>>>>>>>>>>>>>>>>>> with the updated SMA Miriad.
>>>>>>>>>>>>>>>>>>>>>>> The best.
>>>>>>>>>>>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>> On Mon, 25 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>> we looked at the data with an older version of sma miriad and smauvspec
worked on this file there.
>>>>>>>>>>>>>>>>>>>>>>>> Therefore, I am not sure if it is a format problem with the calibrated
data or the new miriad beta version (I am using the one from March 2011)
>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>> On Jul 21, 2011, at 2:53 PM, Jun-Hui Zhao wrote:
>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>> Dear Carlin,
>>>>>>>>>>>>>>>>>>>>>>>>> There may be format problems for the calibrated data from SMA
>>>>>>>>>>>>>>>>>>>>>>>>> archive. Please use one of the example scripts given on
>>>>>>>>>>>>>>>>>>>>>>>>> http://www.cfa.harvard.edu/sma/miriad/spec/SMAscripts/
>>>>>>>>>>>>>>>>>>>>>>>>> to do the calibration.
>>>>>>>>>>>>>>>>>>>>>>>>> Jun-Hui
>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, 21 Jul 2011, Carolin Dedes wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Jun-Hui,
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> I have downloaded the calibrated miriad file from the sma archives
(101219_04:07:01) for my project and now wanted to do the imaging (both continuum and line cubes)
with miriad.
>>>>>>>>>>>>>>>>>>>>>>>>>> The problem is that I cannot run smauvspec. It does not get stuck or
give error messages, it just does not do anything.
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> smauvspec vis=101219_040701_06055+2039_usb hann=7 \
>>>>>>>>>>>>>>>>>>>>>>>>>>> interval=1000  options=avall,nobase \
>>>>>>>>>>>>>>>>>>>>>>>>>>> axis=freq,both device=/xs nxy=1,1
>>>>>>>>>>>>>>>>>>>>>>>>>> SmaUvSpec: version beta 15-mar-11
>>>>>>>>>>>>>>>>>>>>>>>>>> ....
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> After this, it just goes back to the prompt.
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> I thought that the file from the archive was just a uv file and I cannot
think what else I should try.
>>>>>>>>>>>>>>>>>>>>>>>>>> I could look at the file with smauvplt, so I think that the file is ok
and the pgplot server as well.
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> It would be great if you had any idea what I am doing wrong.
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks a lot,
>>>>>>>>>>>>>>>>>>>>>>>>>> Carolin
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>> 
>