frocc Usage

1. Usage

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1. frocc --createConfig --inputMS <path to input.ms>

2. frocc --createScripts

3. frocc --start

4. In one command

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frocc --createConfig --inputMS <path to input.ms> --createScripts --start

3. More advanced

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frocc --inputMS "/my/data/input1.ms, /my/data/input2.mms" --freqRanges '["900-1000", "1300-1500", "1600-1650"]' --imsize 1024 --niter 500 --threshold 0.0001 --smoothbeam 15arcsec --createConfig --createScripts --start

5. Canel slurm jobs

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frocc --cancel

5. Further help

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frocc --readme frocc --help

frocc Readme

1. Installation

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Via source:

source /users/lennart/software/sourcePipeline-stable.sh

Via pip (experimental):

1. git clone git@github.com:idia-astro/frocc.git
2. cd frocc
3. pip install --user .

Via conda:

1. git clone git@github.com:idia-astro/frocc.git

2. cd frocc

3. conda env create

4. Implementation

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frocc takes input measurement set (ms) data and parameters to create channelized data cube in Stokes IQUV.
First CASA split is run to split out visibilities from the input ms into visibilities of the aimed resolution in frequency. Then tclean runs on each of these ms separately and creates .fits-files for each channel. Next, the channel files are put into a data cube. The cube is analysed with an iterative outlier rejection which detects strongly diverging channels by measuring the RMS in Stokes V by fitting a third order polynomial. Bad channels get flagged and the cube .fits-file is converted into a .hdf5-file.
The aforementioned is realized through the following scripts: cube_split.py, cube_tclean.py, cube_buildcube.py, cube_ior_flagging.py

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The input of parameters and setting can be controlled via 3 methods:

1. Command line argument: frocc --inputMS "myData.ms" After calling frocc with --createConfig all settings are written to default_config.txt. (All valid flags can be found in .default_config.template under the [input] section).

2. Standard configuration file: default_config.txt After creating default_config.txt via frocc ... ... --createConfig it can be revised. All parameters in here overwrite the ones in .default_config.template. Do not change anything under the section [data].

3. Fallback configuration file: .default_config.template The pipeline falls back to the values in this file if they have not been specified via one of the previous way. It is also a place where one can lookup explanations for valid flags for frocc. It also includes the section [env]` which can not be controlled via command line flags.

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When calling frocc --createScripts default_config.txt and .default_config.template are read and the python and slurm files are copied to the current directory. The script also tries to calculate the optimal number of slurm taks depending on the input ms spw coverage.

The last step frocc --start submits the slurm files in a dependency chain. Caution: CASA does not always seem to report back its failure state in a correct way. Therefore, the slurm flag --dependency=afterok:... is chosen, which starts the next job in the chain even if the previous one has failed.

Logging

TODO: It's tricky, CASA's logger gets in the way.

3. Known issues

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• About 2% of cube channels show a differend frequency width

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Developed at: IDIA (Institure for Data Intensive Astronomy), Cape Town, ZA Inspired by: https://github.com/idia-astro/image-generator

Lennart Heino

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