diff --git a/docs/source/target.rst b/docs/source/target.rst
index 28f488478c63c500e6375c2b55aa2845bc2e61a6..21d49bf90de405eb701cef9b538314c8e655003e 100644
--- a/docs/source/target.rst
+++ b/docs/source/target.rst
@@ -14,7 +14,7 @@ This chapter will present the specific steps of the target pipeline in more deta
All results (diagnostic plots and calibration solutions) will be stored usually in the ``--outdir`` directory specified with your ``cwltool`` or ``toil`` command.
.. image:: targetscheme.png
-
+
Prepare target, incl. "demixing" (``prep``)
-------------------------------------------
@@ -72,7 +72,7 @@ The workflow ``gsmcal`` consists of:
- wide-band statistical flagging (steps ``ms_concat`` and ``aoflag``)
- checking for bad data chunks (step ``check_unflagged_fraction``)
- perform the self-calibration against the global skymodel (subworkflow ``calibrate_target``, baseline-dependend smoothing (step ``BLsmooth``) if specified ``do_smooth : true``))
-
+
Finalizing the prefactor output (``finalize``)
----------------------------------------------
These steps produce the final data output and many helpful diagnostics.
@@ -89,14 +89,14 @@ The last step also incorporates full `Dysco`_ compression to save disk space. Th
.. note::
All solutions are written in the h5parm file format via the steps ``H5parm_collector`` and called during all the workflows.
-
+
The solutions are stored in the final calibrator solution set ``results/cal_values/cal_solutions.h5``.
Further diagnostics
-------------------
The ``results`` directory will contain all relevant outputs of the current **prefactor** run, once the pipeline has finished:
- - fully calibrated data sets
+ - fully calibrated datasets, concatenated with ``num_SBs_per_group`` subbands per MS file and averaged, if desired (see averaging options below). The DATA column of each MS contains the calibrated data (with the direction-independent solutions applied).
- logfiles in ``results/logs``
- summary file (JSON format) in ``results/summary``
- calibration solutions in ``results/cal_values/cal_solutions.h5``
@@ -112,16 +112,16 @@ The following diagnostic help to assess the quality of the data reduction:
- ``??_uv-coverage_uvdist.png``: fraction of remaining unflagged data versus ``uv``-distance
.. image:: uv-coverage_uvdist.png
- ``??_uv_coverage.png``: the ``uv``-coverage of the final data set
- .. image:: uv-coverage.png
+ .. image:: uv-coverage.png
- ``??_structure.png``: plot of the ionospheric `structure function`_ of the processed target field
.. image:: structure.png
- ``??-MFS-image.fits``: FITS image of the target field
.. image:: target_field.png
-
+
You can also check the calibration solutions for more details::
$ losoto -i results/cal_values/cal_solutions.h5
-
+
Summary of results/cal_values/cal_solutions.h5
Solution set 'calibrator':
@@ -189,11 +189,11 @@ You can also check the calibration solutions for more details::
For an overall summary it is advised to check the summary logfile::
$ cat results/logs/???_summary.log
-
+
*****************************************
*** prefactor target pipeline summary ***
*****************************************
-
+
Field name: P000+00
User-specified baseline filter: [CR]S*&
@@ -208,21 +208,21 @@ For an overall summary it is advised to check the summary logfile::
Amount of flagged solutions per station and solution table:
Station bandpass clock faraday polalign RMextract TGSSphase
- CS001HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
- CS001HBA1 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
- CS002HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
- CS002HBA1 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
- CS003HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
- CS003HBA1 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
- CS004HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
- CS004HBA1 6.05% 0.00% 0.00% 0.00% 0.00% 0.05%
- CS005HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
- CS005HBA1 0.39% 0.00% 0.00% 0.00% 0.00% 0.00%
+ CS001HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
+ CS001HBA1 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
+ CS002HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
+ CS002HBA1 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
+ CS003HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.00%
+ CS003HBA1 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
+ CS004HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
+ CS004HBA1 6.05% 0.00% 0.00% 0.00% 0.00% 0.05%
+ CS005HBA0 0.29% 0.00% 0.00% 0.00% 0.00% 0.05%
+ CS005HBA1 0.39% 0.00% 0.00% 0.00% 0.00% 0.00%
CS006HBA0 0.29% 0.00% 0.00% 0.00% 0.00%
CS006HBA1 0.29% 0.00% 0.00% 0.00% 0.00%
Amount of flagged data per station at a given state:
- Station initial prep Ateam final
+ Station initial prep Ateam final
CS001HBA0 5.13% 5.41% 11.12% 22.74%
CS001HBA1 5.13% 5.41% 11.03% 22.51%
CS002HBA0 5.12% 5.39% 11.39% 23.18%
@@ -235,11 +235,11 @@ For an overall summary it is advised to check the summary logfile::
CS005HBA1 5.12% 15.36% 20.07% 30.09%
CS006HBA0 100.00% 100.00% 100.00%
CS006HBA1 100.00% 100.00% 100.00%
-
+
**********
Summary file is written to: ???_prefactor_target_summary.json
Summary has been created.
-
+
User-defined parameter configuration
------------------------------------