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Scripted plotting
=================
Storing plots that describe the (RFI) quality of an observation can be useful for quality assessment.
Both ``rfigui`` and ``aoqplot`` have options that make it possible to save certain statistics or overview images.
The command-line options of these tools give access to these plotting capabilities from non-interactive pipelines or scripts.
When parameters are given on the command line that save images, the ``rfigui`` and ``aoqplot`` tools will not open their
default window and therefore do not require an X windows system to be running [1]_. In other words, the tools
will run as non-interactive command line programs.
Both ``rfigui`` and ``aoqplot`` provide parameter ``--help``, which will show a list of supported options.
``rfigui``
----------
The ``rfigui`` tool can be used to save time-frequency "heatmap" images, that show the flux of the correlations in a two-dimensional time and frequency display. The syntax is as follows:
.. code-block :: bash
rfigui \
-save-baseline <filename> <ant1> <ant2> <band> <seqindex>
Filename should end with an image extension. Supported formats are ``.png``, ``.pdf`` and ``.svg``. Note that ``.pdf`` and ``.svg`` are of higher quality than ``.png`` files. The created plots will by default be made from the "``DATA``" column. However, a different column can be selected with the option ``-data-column <name>``. The following example will save the correlated data from antennas 1 and 3:
.. code-block :: bash
rfigui \
-data-column CORRECTED_DATA \
-save-baseline WSRT-RT2xRT4.pdf 1 3 0 0 3C196_spw5_sub1.MS/
Which creates the following pdf:
.. image:: images/WSRT-RT2xRT4.png
:alt: Result of rfigui -save-baseline command (WSRT-RT2xRT4)
It is also possible to repeat the '``-save-baseline``' option to save multiple images at once. This saves quite a few computations over saving the baselines one by one with separate ``rfigui`` calls.
``aoqplot``
-----------
The ``aoqplot`` syntax to save plots is as follows:
.. code-block :: bash
aoqplot -save <filename prefix> <statistic name>
Note that unlike ``rfigui``, the ``aoqplot`` tool saves several images at once. The plots created are i) a per-baseline matrix plot; ii) a per antenna plot; iii) a spectrum; iv) a time-plot; and v) a time-frequency heatmap. The statistic name parameter is a case-sensitive name of the statistic that will be plotted over antenna/time/frequency, etc. The common statistics are: ``StandardDeviation``, ``DStandardDeviation`` (=stddev of difference between channels), ``Variance``, ``Mean``, ``RFIPercentage``, ``RFIRatio`` and ``Count`` (=visibility count). A full list of allowed statistics can be retrieved by typing ``aoquality liststats`` on the command line. However, not all allowed statistics are stored by default in a measurement set. This is an example ``aoqplot`` run:
.. code-block :: bash
aoqplot -save aartfaac-stddev StandardDeviation aartfaac-testobs.ms/
(1/1) Adding aartfaac-testobs.ms/ to statistics...
Lowering time resolution...
Lowering frequency resolution...
Integrating baseline statistics to one channel...
Regridding time statistics...
Copying statistics...
Integrating time statistics to one channel...
Opening statistics panel...
Saving aartfaac-stddev-antennas.pdf...
Saving aartfaac-stddev-baselines.pdf...
Saving aartfaac-stddev-baselinelengths.pdf...
Saving aartfaac-stddev-timefrequency.pdf...
Saving aartfaac-stddev-time.pdf...
Saving aartfaac-stddev-frequency.pdf...
This is an example for the produced 'baselines' plot:
.. image:: images/WSRT-stddev-baselines.png
:alt: Result of aoqplot -save command (baseline plot)
As can be seen from this image, antenna index 5 (WSRT RT5) is not working, and the autocorrelations show more power (as they should). Note that ``aoqplot`` uses the quality statistics tables inside the measurement set. These are normally produced by tools like ``DPPP``, ``cotter`` or ``aartfaac2ms``; however, if a measurement set is not produced by one of those tools, it is necessary to create these tables manually. This can be done with the ``aoquality collect <obs.ms>`` command.
.. [1] Older versions of ``rfigui`` and ``aoqplot`` would require an X window system to be running even when running in command line mode. However, that was resolved in AOFlagger [version 2.10](changelog-2.10.0).
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