catdagger 0.2.1

**CATDagger**
==============================================================================
A catalog source differential gain tagger based on local noise characteristics

This tool segments regions within residual images that are in need of a differential gain. Preferably the tool is run on stokes V
residuals, which typically contain relatively little real flux and mostly residual calibration errors. In principle it can also be run on Stokes I residuals
if direction independent calibration was successful.

DS9 region maps containing regions and cluster lead information is output by default as shown as example below. Tigger LSM catalogs
can simultaniously be processed and reclustered based on identified dE regions.

.. figure:: https://github.com/bennahugo/catdagger/blob/master/misc/catdagger.png
:width: 250px
:height: 250px
:align: center

Usage
===============================================================================

dagger --help
usage: CATDagger - an automatic differential gain tagger (C) SARAO, Benjamin Hugo 2019
[-h] [--stokes STOKES] [--min-tiles-region MIN_TILES_REGION]
[--input-lsm INPUT_LSM] [--ds9-reg-file DS9_REG_FILE]
[--ds9-tag-reg-file DS9_TAG_REG_FILE] [-s SIGMA]
[--tile-size TILE_SIZE] [--global-rms-percentile GLOBAL_RMS_PERCENTILE]
[--de-tag-name DE_TAG_NAME]
[--min-distance-from-tracking-centre MIN_DISTANCE_FROM_TRACKING_CENTRE]
[--add-custom-exclusion-zone ADD_CUSTOM_EXCLUSION_ZONE [ADD_CUSTOM_EXCLUSION_ZONE ...]]
[--max-region-right-skewness MAX_REGION_RIGHT_SKEWNESS]
[--psf-image PSF_IMAGE]
[--remove-tagged-dE-components-from-model-images REMOVE_TAGGED_DE_COMPONENTS_FROM_MODEL_IMAGES]
[--only-dEs-in-lsm]
[--max-positive-to-negative-flux MAX_POSITIVE_TO_NEGATIVE_FLUX]
[--max-region-abs-skewness MAX_REGION_ABS_SKEWNESS]
noise_map

positional arguments:
noise_map Residual / noise FITS map to use for estimating local
RMS

optional arguments:
-h, --help show this help message and exit
--stokes STOKES Stokes to consider when computing global noise
estimates. Ideally this should be 'V', if available
--min-tiles-region MIN_TILES_REGION
Minimum number of tiles per region. Regions with fewer
tiles will not be tagged as dE
--input-lsm INPUT_LSM
Tigger LSM to recluster and tag. If this is not
specified only DS9 regions will be written out
--ds9-reg-file DS9_REG_FILE
SAODS9 regions filename to write out
--ds9-tag-reg-file DS9_TAG_REG_FILE
SAODS9 regions filename to contain tagged cluster
leads as circles
-s SIGMA, --sigma SIGMA
Threshold to use in detecting outlier regions
--tile-size TILE_SIZE
Number of pixels per region tile axis
--global-rms-percentile GLOBAL_RMS_PERCENTILE
Percentile tiles to consider for global rms
calculations
--de-tag-name DE_TAG_NAME
Tag name to use for tagged sources in tigger LSM
--min-distance-from-tracking-centre MIN_DISTANCE_FROM_TRACKING_CENTRE
Cutoff distance from phase centre in which no tags be
raised.This can be used to effectively exclude the
FWHM of an parabolic reflector-based interferometer.
--add-custom-exclusion-zone ADD_CUSTOM_EXCLUSION_ZONE [ADD_CUSTOM_EXCLUSION_ZONE ...]
Add manual exclusion zone to which no dE tags shall be
added. Expects a tripple of centre X, Y pixel and
radius.
--max-region-right-skewness MAX_REGION_RIGHT_SKEWNESS
The maximum tolerance for right skewness of a pixel
distribution within a region.A large value (tailed
distribution) indicates significant uncleaned flux
remaining in the residual. This can be used to
effectively control detection sensitivity to uncleaned
extended emission, but should be set to 0 if residuals
other than stokes I are used
--psf-image PSF_IMAGE
PSF image from which BPA, BMAJ and BMIN may be
extracted
--remove-tagged-dE-components-from-model-images REMOVE_TAGGED_DE_COMPONENTS_FROM_MODEL_IMAGES
Blank out model images within resolution of tagged LSM
components. Expects list of model FITS files. This
option is useful for hybrid DFT-CLEAN component
modelling as onlyextended / faint clean components
contributes to model.
--only-dEs-in-lsm Only store dE tagged sources in lsm. This option is
useful for hybrid DFT-CLEAN component modelling, as
only bright compact gaussian emission contributes to
dE solutions
--max-positive-to-negative-flux MAX_POSITIVE_TO_NEGATIVE_FLUX
The maximum tolerance for the ratio of positive to
negative flux. Only to be used with stokes I
--max-region-abs-skewness MAX_REGION_ABS_SKEWNESS
The maximum tolerance for absolute skewness of a pixel
distribution within a region.A large value (tailed
distribution) indicates significant uncleaned flux
remaining in the residual. This can be used to
effectively control detection sensitivity to uncleaned
extended emission, but should be set to 0 if residuals
other than stokes Q,U or V are used