Command-line interface

PySE image configuration options. These can override the values specified in the TOML config file.

usage: pyse [-h] [--config-file CONFIG_FILE] [--pdb] [-v]
            [--interpolate-order INTERPOLATE_ORDER]
            [--median-filter MEDIAN_FILTER] [--mf-threshold MF_THRESHOLD]
            [--rms-filter RMS_FILTER] [--deblend-mincont DEBLEND_MINCONT]
            [--structuring-element STRUCTURING_ELEMENT] [--vectorized]
            [--nr-threads NR_THREADS] [--margin MARGIN] [--radius RADIUS]
            [--back-size-x BACK_SIZE_X] [--back-size-y BACK_SIZE_Y]
            [--eps-ra EPS_RA] [--eps-dec EPS_DEC]
            [--detection-thr DETECTION_THR] [--analysis-thr ANALYSIS_THR]
            [--fdr] [--alpha ALPHA] [--deblend-nthresh DEBLEND_NTHRESH]
            [--grid GRID] [--bmaj BMAJ] [--bmin BMIN] [--bpa BPA]
            [--force-beam] [--detection-image DETECTION_IMAGE]
            [--fixed-posns FIXED_POSNS] [--fixed-posns-file FIXED_POSNS_FILE]
            [--ffbox FFBOX] [--ew-sys-err EW_SYS_ERR]
            [--ns-sys-err NS_SYS_ERR] [--output-dir OUTPUT_DIR] [--skymodel]
            [--csv] [--regions] [--rmsmap] [--sigmap] [--residuals]
            [--islands]
            files [files ...]

Positional Arguments

files

Image files for processing

General

--config-file

TOML file containing default input arguments to PySE. This is especially convenient when swapping between configurations for the same project.

--pdb

Enter debug mode when the application crashes. Meant to be used for more comprehensive debugging.

Default: False

-v, --version

show program’s version number and exit

Image parameters

--interpolate-order

Order of interpolation to use (e.g. 1 for linear).

--median-filter

Size of the median filter to apply to the image. Use 0 to disable.

--mf-threshold

Threshold used with the median filter. Sources below this value are discarded.

--rms-filter

Minimum RMS value to use as filter for the image noise.

--deblend-mincont

Minimum contrast for deblending islands into separate sources (e.g. 0.005).

--structuring-element

Structuring element for morphological operations, provided as a Python-style nested list, e.g. ‘[[1,1,1], [1,1,1], [1,1,1]]’ for 8-connectivity and ‘[[0,1,0], [1,1,1], [0,1,0]]’ for 4-connectivity. This is used for defining the connectivity in connected-component labelling.

--vectorized

Measure sources vectorized, this implies using ‘tweaked moments’ instead of Gaussian fits.

Default: False

--nr-threads

The number of threads used to parallelize Gaussian fits to detected

sources. Note: this does not change numba’s ‘num threads’ for parallel numba operations.

--margin

Margin in pixels to ignore around the edge of the image.

--radius

Radius in pixels around sources to include in analysis.

--back-size-x

Size of the background subimage in the X direction.

--back-size-y

Size of the background subimage in the Y direction.

--eps-ra

RA matching tolerance in arcseconds.

--eps-dec

Dec matching tolerance in arcseconds.

--detection-thr

Detection threshold

--analysis-thr

Analysis threshold

--fdr

Use False Detection Rate algorithm

Default: False

--alpha

FDR Alpha

--deblend-nthresh

Number of deblending subthresholds; 0 to disable

--grid

Background grid segment size

--bmaj

Set beam: Major axis of beam (deg)

--bmin

Set beam: Minor axis of beam (deg)

--bpa

Set beam: Beam position angle (deg)

--force-beam

Force fit axis lengths to beam size

Default: False

--detection-image

Find islands on different image

--fixed-posns

List of position coordinates to force-fit (decimal degrees, JSON, e.g [[123.4,56.7],[359.9,89.9]]) (Will not perform blind extraction in this mode)

--fixed-posns-file

Path to file containing a list of positions to force-fit (Will not perform blind extraction in this mode)

--ffbox

Forced fitting positional box size as a multiple of beam width.

--ew-sys-err

Systematic error in east-west direction

--ns-sys-err

Systematic error in north-south direction

Export parameters

--output-dir

The directory in which to store the output files.

--skymodel

Generate sky model

Default: False

--csv

Generate csv text file for use in programs such as TopCat

Default: False

--regions

Generate DS9 region file(s)

Default: False

--rmsmap

Generate RMS map

Default: False

--sigmap

Generate significance map

Default: False

--residuals

Generate residual maps

Default: False

--islands

Generate island maps

Default: False