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== MOPSIC pipeline scripts == ''' defs_general.mopsic '''script: The database pipeline reduction scripts are developed such that they can easily be used for data reduction on your local PC. To do so, you have to edit the''' '''script. Simply change the logical'''foriramdb'''to false: {{{ let foriramdb .false. ! or let foriramdb no }}} This will set the input data directory and the default input list to the directory structure generated by the tar file and all DAFs to defaults, i.e. to the entries defined by MOPSIC_DAFS. The main routines used for the data reduction are '''oo_csf.mopsic''' and '''map_gpd_csf.mopsic''' MOPSIC uses a special method to calculate the chopped signal. This gives much better results than the straight difference of the signals obtained at both chopper positions. The method is described in the __Dec. 2005 IRAM Newsletter__. For some special purposes also special scripts are offered. They are obtained simply by changing some default variables set in '''map_defs''' and/or''' oo_defs''' correspondingly. === Mapping === * '''map_gpd_ncsf.mopsic : ''' (gridded phase difference - no correlated signal filter) map reduction without sky noise subtraction * '''map_gpd_csf.mopsic''' : (gridded phase difference - correlated signal filter general script formap reduction with sky noise subtraction * '''map_gpd_csfdsrmx.mopsic ''': special scripts to reduce maps of relatively compact sources, <200" in diameter; it is not suitable for more extended and structureless sources but should give better sky noise subtraction for relatively compact sources. * '''map_gpd_csf0.mopsic :''' map reduction with sky noise subtraction for sources which are weak (for CSF) and more extended than 0.5*beam_separation; weak for CSF means with peak fluxes < ~5*rms in the final data of one bolometer (i.e. ~5*30 mJy/beam) * '''map_gpd_csfrmn_saa.mopsic''' :(gridded phase difference - correlated signal filter - shift and add) source structure is assumed to be smaller than 0.5*beam_sep. === OnOff === * '''oo_ncsf.mopsic ''' (onoff - no correlated signal filter) reduces onoffs without sky noise subtraction * '''oo_csf.mopsic''' (onoff - correlated signal filter) reduces onoffs with sky noise subtraction Both on-off scripts write the final results to ''''source'.OOxx''' files. For solar system sources ("body") the corresponding scripts '''oo_ncsf_body''' and''' oo_csf_body''' are also within the tar. Note that the only one change between the "body" and the standard on-off scripts is the additional argument body within the oo-command. There is also a script '''oo_csf_csfr_multsou.mopsic''' whic allows to reduce on-offs of many sources. The user has to define the number of sources and the lists with the files. Those can be created from a general lis using the commad find objects write. === Misc === In addition there are also scripts to reduce pointings ('''p_nshav.mopsic '''- without sky noise subtraction, '''p_shav.mopsic''' - with very simple sky noise subtraction), skydips ('''skydips.mopsic''') and to calculate the RCPs (Receiver Channel Parameters) from calibration maps. T he scripts in the subdir '''specials''' are special versions of the general pipeline scripts. They use some other settings than defined in '''map_defs '''(see the corresponding map_defs_*). They are therefore optimized for some special purposes (e.g. subtracting a source distribution before reduction, applying base level corrections subscan by subscan, using polygons to define the base range, ...). In the subdir '''extras''' you will find some scripts useful for checking (e.g. '''chk_rc''') or just displaying the data. The '''snr...''' scripts demonstrate how to calculate a signa-to-noise ratio map. In the subdir '''simple''' you will find a script '''map.mopsi'''c which can be used to reduce maps of simple sources, e.g. compact or extended. It should not be used if the source shows both compact and extended components ! The script '''map_negres.mopsic''' allows to create a map with just the negative residuals of the source due to the shift-and-add restoring. Subtract the map produced by this script from the saa map. For further informations ''read the suggestions'' in README_oo, README_maps, README_glossary, oo_defs.mopsic, map_defs.mopsic. Furthermore, some special suggestions are given in some dedicated scripts (e.g. in mask_subsc_nr.mopsic, oo_oo.mopsic). |
MOPSIC is a software which has been developed and is constantly upgraded by Robert Zylka (IRAM, France). It was created to analyze bolometer data but can be used for much more versatile tasks.
This cookbook is to help in the Mambo2 reduction with the pool. It is largely taken from the READMEs provided by the pool system when downloading the project data. It will give you as well some informations to setup your observations.
General Informations
Tar-file structure of a full download (dafs, scripts, software & data)
If you have downloaded MOPSIC together with the DAFs (Data Associated Files) and the MOPSIC scripts used at the telescope, the tar file will generate six directories:
dafs data logs mopsic scripts work
The dafs directory contains all calibration files and links needed by MOPSIC to calibrate your data. Zenith opacities, receiver channel (i.e. bolometer) parameters, bad receiver channels, flat-field for sky noise filtering and calibration factors are stored in MRT_MAMBO.TAUS, MRT_MAMBO_MB.RCP, MRT_MAMBO_PF.RCP, MRT_MAMBO.DRC, MRT_MAMBO.CSFF and MRT_MAMBO.CAL, ordered by the Julian Date or UT date.
The data directory contains all project observations (scans) as well as pointing, focus, calibration and skydips scans done within one hour from the target observations.
The logs directory contains a project summary listing all target and calibration scans. In mopsic you will find the MOPSIC executable (since June 15 2005 the f95 version).
The scripts directory contains all up-to-date MOPSIC scripts used in the database pipeline reduction (for details see below).
The work directory contains a listing (mydata.LIST) of all scans in the data directory. Such list are use by MOPSIC to find and list data for reduction. Furthermore the directory contains links to the MOPSIC scripts in the script directory. If you are using our standard installation of MOPSIC you should use this directory to reduce the data.
MOPSIC installation
System requirements:
- standard Linux system
- NEW GILDAS ifort version installation required (younger than Oct 18th 2005)
Installation: If you have downloaded together with the MOPSIC software the DAFs-files MOPSIC will know all parameters related to the bolometer array calibration such as the gain parameters, array geometry and the counts per Jansky conversion as well as the zenith optical depths for all data obtained in pooled observations since summer 2001 (the optical depths since Feb 1999). Older DAFs are available under request. We therefore recommend to download the DAFs and to update them regularly. In order to use these parameters on your local MOPSIC installation you have to define the system variable MOPSIC_DAFS by adding the following line to your .cshrc or .tcshrc system file:
setenv MOPSIC_DAFS /YOUR/DOWNLOAD/INSTALLATION/PATH/dafs
or to the.bashrc file:''
export MOPSIC_DAFS=/YOUR/DOWNLOAD/INSTALLATION/PATH/dafs
To run MOPSIC from all directories on your system you furthermore need to add to the same file the path where the MOPSIC executable is located:
in .cshrc or .tcshrc: Of course it is not mandatory to keep MOPSIC and the DAFs in the directories created by the tar. You may put them wherever you want.
defs_general.mopsic script: The database pipeline reduction scripts are developed such that they can easily be used for data reduction on your local PC. To do so, you have to edit the script. Simply change the logicalforiramdbto false: This will set the input data directory and the default input list to the directory structure generated by the tar file and all DAFs to defaults, i.e. to the entries defined by MOPSIC_DAFS. The main routines used for the data reduction are oo_csf.mopsic and map_gpd_csf.mopsic MOPSIC uses a special method to calculate the chopped signal. This gives much better results than the straight difference of the signals obtained at both chopper positions. The method is described in the Dec. 2005 IRAM Newsletter. For some special purposes also special scripts are offered. They are obtained simply by changing some default variables set in map_defs and/or oo_defs correspondingly.
map_gpd_ncsf.mopsic : (gridded phase difference - no correlated signal filter) map reduction without sky noise subtraction map_gpd_csf.mopsic : (gridded phase difference - correlated signal filter general script formap reduction with sky noise subtraction map_gpd_csfdsrmx.mopsic : special scripts to reduce maps of relatively compact sources, <200" in diameter; it is not suitable for more extended and structureless sources but should give better sky noise subtraction for relatively compact sources. map_gpd_csf0.mopsic : map reduction with sky noise subtraction for sources which are weak (for CSF) and more extended than 0.5*beam_separation; weak for CSF means with peak fluxes < ~5*rms in the final data of one bolometer (i.e. ~5*30 mJy/beam) map_gpd_csfrmn_saa.mopsic :(gridded phase difference - correlated signal filter - shift and add) source structure is assumed to be smaller than 0.5*beam_sep.
oo_ncsf.mopsic (onoff - no correlated signal filter) reduces onoffs without sky noise subtraction oo_csf.mopsic (onoff - correlated signal filter) reduces onoffs with sky noise subtraction Both on-off scripts write the final results to 'source'.OOxx files. For solar system sources ("body") the corresponding scripts oo_ncsf_body and oo_csf_body are also within the tar. Note that the only one change between the "body" and the standard on-off scripts is the additional argument body within the oo-command. There is also a script oo_csf_csfr_multsou.mopsic whic allows to reduce on-offs of many sources. The user has to define the number of sources and the lists with the files. Those can be created from a general lis using the commad find objects write.
In addition there are also scripts to reduce pointings (p_nshav.mopsic - without sky noise subtraction, p_shav.mopsic - with very simple sky noise subtraction), skydips (skydips.mopsic) and to calculate the RCPs (Receiver Channel Parameters) from calibration maps. T he scripts in the subdir specials are special versions of the general pipeline scripts. They use some other settings than defined in map_defs (see the corresponding map_defs_*). They are therefore optimized for some special purposes (e.g. subtracting a source distribution before reduction, applying base level corrections subscan by subscan, using polygons to define the base range, ...). In the subdir extras you will find some scripts useful for checking (e.g. chk_rc) or just displaying the data. The snr... scripts demonstrate how to calculate a signa-to-noise ratio map. In the subdir simple you will find a script map.mopsic which can be used to reduce maps of simple sources, e.g. compact or extended. It should not be used if the source shows both compact and extended components ! The script map_negres.mopsic allows to create a map with just the negative residuals of the source due to the shift-and-add restoring. Subtract the map produced by this script from the saa map. For further informations set path path=($path /YOUR/DOWNLOAD/INSTALLATION/PATH/mopsic)
or in .bashrc: PATH=$PATH:/YOUR/DOWNLOAD/INSTALLATION/PATH/mopsic
export PATH
MOPSIC pipeline scripts
let foriramdb .false. ! or let foriramdb no
Mapping
OnOff
Misc