rfinder 1.1.0

Description:

rfinder 1.1.0

RFInder
Insallation instructions
pip install rfinder

To create a local repository, type:
git clone [email protected]:caracal-pipeline/RFInder.git


Requisites
For a successfull installation make sure to have installed the following packages.

RFInder makes use of the most common python packages (e.g. numpy, scipy, astropy).
The parameter file is in yaml format, hence pyaml, and json packages should be installed,
The logging module is used to print out warnings.
.gif file of multiple plots can be created if ffmpeg is installed.
casacore is utilized to open casa tables.

install it with python_casacore: pip install python-casacore or conda install -c conda-forge python-casacore


texmaker to plot latex fancy formulae
dvipng
python tk
RFInder class rfinder_uzero.py which can be used to solve the u=0 problem makes use of wsclean, which must have been previously installed.


Description
This is a set of tools that have been developed in preparation of the Apertif & MeerKAT surveys.
The main function of rfinder is to identify the presence of RFI in an observation and visualize it according to different parameters. Two are the main functions:

estimate the RFI present in an MS file through a sigma clipping (rms_clip)
read the FLAG column of an MS file (use_flags) and summarize how RFI affects the data products of an observation.

These are the products that rfinder provides and summarizes in an .html file:

presence of RFI per frequency channel and baseline length.
percentage flagged visibilities due to RFI per frequency channel.
increase in noice due to RFI per frequency channel.
estimated noise per frequency channel, assuming natural weighting.

check out the WiKi for a complete illustration of RFInder.

Usage
RFInder takes its variables from a default parameter file and from terminal, if any are given.
From your current working directory typying rfinder this message will be shown:
------ Reading default installation parameter file ------

MSNAME & telescope missing
please edit rfinder_default.yml in your current directory
or run: rfinder -i msname -fl <num> -tel <meerkat,apertif,wsrt>
(assuming the observation is located in your current directory)


------ RFInder out ------

Hence, you have to set the name of the MSfile you wish to analyse. There are two ways to do this. By specifying from terminal the path to the msfile from your current directory, the field number of the source you whish to analyse, and the telescope of the observation:
rfinder -i msname -fl <num> -tel <meerkat,apertif,wsrt>

or, editing the rfinder_default.yml configuration file that has been copied in your current directory (workdir, in the configuration file).
This configuration file is read automatically by RFInder through the command rfinder. A short explanation of the parameters is given in the configuration file, and by typing rfinder -h (see below).
If you wish to use a different configuration file (at your own risk!!), type: rfinder -c <path_to_configuration_file>.
Minimal instructions


Default rfinder will scan the MSfile in chunks of 10 minutes averaging 10 channels together. The output product will be an html file where the gis scan through the time steps to show the identified RFI/flags.


Running rfinder -noCh after rfinder will produce a full_report.html file containing both the analysis over time steps and the analysis of the dataset as a whole.


Running rfinder -noCh -noMov will analyse the full dataset as a whole and generate the full_report.html without embedded movies.


Attention: the option rfinder -noCh will end with a report successfully generated, only if it is run after rfinder. Otherwise run rfinder -noCh -noMov.
(These tutorials show the different capabilities of rfinder. outdated)
Output products
If rfinder runs correctly, you will find the following output products in your current directory:

the folder rfi_pol in your current directory, or in the directory specified by the -odir parameter (pol is the stokes parameters for which you analysed RFI).

Within, there are the .html reports that you wished to generate.


The configuration file rfinder_default.yml contains the parameters of the last run.
A log of the commands run by the program is stored in log-rfinder.log, in your working directory.

Help
rfinder -h will show you a (minimal) help:
usage: rfinder [-h] [-v] [-c CONFIG] [-w WORKING_DIR] [-odir OUTPUT_DIR]
[-i INPUT] [-fl FIELD] [-tel TELESCOPE] [-mode RFIMODE]
[-pol POLARIZATION]
[-fint [FREQUENCY_INTERVAL [FREQUENCY_INTERVAL ...]]]
[-spwAv SPW_AV] [-tStep TIME_STEP] [-sig SIGMA_CLIP]
[-baseCut BASELINE_CUT] [-noCh] [-yesCh] [-noSpw] [-yesSpw]
[-noClp] [-yesClp]

RFInder: package to visualize the flagged RFI in a dataset

version 1.0.3

install path /home/maccagni/programs/RFInder/rfinder

Filippo Maccagni <[email protected]>

optional arguments:
-h, --help Print help message and exit
-v, --version show program's version number and exit
-c CONFIG, --config CONFIG
RFInder configuration file (YAML format)
-idir INPUT_DIR, --input_dir WORKING_DIR
select working directory (MS file assumed to be here)
-odir OUTPUT_DIR, --output_dir OUTPUT_DIR
select output directory
-i INPUT, --input INPUT
input ['MS'] file
-fl FIELD, --field FIELD
select field of MS file to analyze
-tel TELESCOPE, --telescope TELESCOPE
select telescope: meerkat, apertif, wsrt
-mode RFIMODE, --rfimode RFIMODE
select mode where to investigate RFI: use_flags or
rms_clip
-pol POLARIZATION, --polarization POLARIZATION
select stokes parameter: xx, yy, xy, yx, q (also in
CAPS)
-fint [FREQUENCY_INTERVAL [FREQUENCY_INTERVAL ...]], --frequency_interval [FREQUENCY_INTERVAL [FREQUENCY_INTERVAL ...]]
select frequency interval where to measure noise in
GHz
-spwAv SPW_AV, --spw_av SPW_AV
select number of channels to average
-tStep TIME_STEP, --time_step TIME_STEP
select time step in minutes in which divide the
analysis of the MSfile
-sig SIGMA_CLIP, --sigma_clip SIGMA_CLIP
select sigma clip for rms_clip mode to find RFI
-baseCut BASELINE_CUT, --baseline_cut BASELINE_CUT
select cut in baseline lenght [m] for differential RFI
analysis
-noCh, --no_chunks desable chunking in time
-yesCh, --yes_chunks enable chunking in time
-noSpw, --no_spw_av desable averaging in channels
-yesSpw, --yes_spw_av
enable averaging in channels
-noClp, --no_cleanup desable cleanup of intermediate products
-yesClp, --yes_cleanup
enable cleanup of intermediate products

Run a command. This can be:
rfinder
rfinder -c path_to_config_file.yml
rfinder -i <ngc1399.ms> -fl <num> -tel <meerkat/apertif/wsrt>


License
This project is licensed under the GNU General Public License v3.0 - see license for details.

© Filippo M. Maccagni 2018