Image & DetectedSource Classes

This module defines classes and their methods for Image and DetectedSource objects.

class database.dbclasses.DetectedSource

Bases: object

Class of objects to store elliptical Gaussian fit properties of sources found and measured by PyBDSF. Attribute values are translated from the class of objects output by PyBDSF.

src_id

int – Uniquely identifies the source in a given image.

isl_id

int – Uniquely identifies an island in a given image from which sources are formed.

image_id

int – Uniquely identifies the image the source comes from.

ra

float – Right ascension (degrees).

e_ra

float – Error on the right ascension (degrees).

dec

float – Declination (degrees).

e_dec

float – Error on the declination (degrees).

total_flux

float – Total integrated flux (mJy).

e_total_flux

float – Error on the total integrated flux (mJy).

peak_flux

float – Peak flux density per beam (mJy/beam).

e_peak_flux

float – Error on the peak flux (mJy/beam).

ra_max

float – Right ascension of the source maximum brightness (degrees).

e_ra_max

float – Error on the right ascension of the maximum (degrees).

dec_max

float – Declination of the source maximum brightness (degrees).

e_dec_max

float – Error on the declination of the maximum (degrees).

maj

float – FWHM of the source major axis (arcsec).

e_maj

float – Error on the source major axis size (arcsec).

min

float – FWHM of the source minor axis (arcsec).

e_min

float – Error on the source minor axis size (arcsec).

pa

float – Position angle of the source major axis measured east of north (degrees).

e_pa

float – Error on the source position angle (degrees).

dc_maj

float – FWHM of the deconvolved major axis (arcsec).

e_dc_maj

float – Error on the deconvolved major axis (arcsec).

dc_min

float – FWHM of the deconvolved minor axis (arcsec).

e_dc_min

float – Error on the deconvolved minor axis (arcsec).

dc_pa

float – Position angle of the deconvolved major axis measured east of north (degrees).

e_dc_pa

float – Error on the deconvolved position angle (degrees).

total_flux_isl

float – Total integrated flux density of the island (mJy).

total_flux_islE

float – Error on the total integrated flux density of the island (mJy).

rms_isl

float – Average background rms of the island (mJy/beam).

mean_isl

float – Average background mean of the island (mJy/beam).

resid_rms

float – Average residual background rms of the island (mJy/beam).

resid_mean

float – Average residual background mean of the island (mJy/beam).

code

str – Defines source structure: ‘S’ = isolated single-Gaussian source, ‘C’ = single-Gaussian source in island with other sources, ‘M’ = multi-Gaussian source.

assoc_id

int – Links to associated source in the database assoc_source table.

dist_from_center

float – Angular separation between the source location and image pointing center (degrees).

id

int – Uniquely identifies the source in the assoc_source table.

res_class

str – Resolution class of the image in which the source was found. ‘A’: res <= 15”, ‘B’: 15” < res <= 35”, ‘C’: 35” < res <= 60”, ‘D’: res > 60”.

ndetect

int – Number of times this same source has been detected in other VLITE images.

nmatches

int – Number of catalogs which contain this source.

detected

bool – Whether or not the source was detected in the image (used for the vlite_unique table).

References

Refer to the PyBDSF documentation[1]_ for definitions of their output columns.

[1]	http://www.astron.nl/citt/pybdsm/write_catalog.html#definition-of-output-columns

calc_center_dist(imobj)

Calculates a detected source’s angular distance from the image pointing center in degrees and sets the dist_from_center attribute.

Parameters:imobj (database.dbclasses.Image instance) – Initialized Image object with attribute values set from header info.

cast(origsrc)

Attributes of a bdsf.gaul2srl.Source object output from bdsf.process_image are re-cast to define attributes of a DetectedSource object.

Parameters:origsrc (bdsf.gaul2srl.Source instance) – Object which stores all the measured properties of a source extracted from an image in PyBDSF.

correct_flux(pri_freq)

Applies a 1-D radial correction to all flux measurements from PyBDSF. The correction factor has been empirically derived from flux comparisons of sources as a function of angular distance from the image center. The scale factor increases farther from the pointing center as the beam power decreases.

Parameters:pri_freq (float) – Primary frequency of the observations in GHz.

class database.dbclasses.Image(image)

Bases: object

A class to hold information about the FITS image file.

Parameters:image (str) – Directory path to the FITS image file location.

id

int – Numerical index. Incremented by PostgreSQL upon insertion into the database image table.

filename

str – Full directory path for the image file.

imsize

str – Image size in pixels – (NAXIS1, NAXIS2).

obs_ra

float – Right ascension of image pointing center (degrees).

obs_dec

float – Declination of image pointing center (degrees).

pixel_scale

float – Spatial conversion from pixel to angular size on the sky (arcseconds / pixel.)

obj

str – Name of observed object in the header.

obs_date

date – Date when observations were taken.

map_date

date – Date when data was imaged.

obs_freq

float – Rest frequency of the observations (MHz).

pri_freq

float – Frequency of the simultaneously acquired primary band data (GHz).

bmaj

float – Size of the beam semi-major axis (arcsec).

bmin

float – Size of the beam semi-minor axis (arcsec).

bpa

float – Beam position angle (degrees).

noise

float – Noise estimate from the image center (mJy/beam).

peak

float – Peak brightness in the image (mJy/beam).

config

str – Very Large Array configuration.

nvis

int – Number of visibilities in the data after calibration.

mjdtime

float – Modified Julian Date (days since 0h Nov 17, 1858).

tau_time

float – Integration time on source in seconds.

duration

float – Total time spanned by the observations in seconds.

nsrc

int – Number of sources extracted during source finding.

rms_box

str – PyBDSF parameter used during source finding. From PyBDSF docs: “The first integer, boxsize, is the size of the 2-D sliding box [in pixels] for calculating the rms and mean over the entire image. The second, stepsize, is the number of pixels by which this box is moved for the next measurement.”

error_id

int – Numerical code assigned when an image fails a quality check. Each number has a corresponding explanation in the database error table.

stage

int – Highest processing stage completed. 1 = read image, 2 = source finding, 3 = source association, 4 = catalog matching.

radius

float – Radius defining the circular field-of-view in which sources were extracted (degrees).

nearest_problem

str – Name of the closest (in angular separation) source which is known to cause difficulties in imaging.

separation

float – Angular separation between the nearest problem source and the image pointing center (degrees).

header_attrs(hdr)

Extracts all keywords of interest from the FITS image header and stores their values as attributes of the initialized Image object. If a header keyword is missing from the image metadata, then that attribute value is set to None. The error_id attribute is also set to 1 if the missing header keyword is deemed important enough.

classmethod image_count()

Returns the number of Image objects initialized.

image_qa(params)

Performs quality checks on the image pre-source finding to flag images with the following issues:

1. missing necessary header keywords (self.error_id = 1)
2. number of visibilities (nvis) < min_nvis
3. noise*sqrt(int. time) <= 0 or > max_sensitivity
4. beam semi-major/semi-minor axis > max_ellip (too elliptical)
5. target is NCP or a planet
6. a known bright radio source is in the field-of-view (Cas A, Cygnus A, Taurus A, Hercules A, Virgo A (M87), Perseus A (3C84), the Sun, the Moon, Jupiter, Galactic Center)

Images that fail checks 1-5 are aborted and do not proceed to source finding. Images are flagged if they fail check 6, but do continue on.

log_attrs(pybdsfdir)

Image object method to assign values to object attributes which come from source finding using info in the PyBDSF output log file. This is useful when source finding has already been run on an image and the results are being recorded after the fact using the PyBDSF output files.

Parameters:pybdsfdir (str) – Directory path to the PyBDSF output files. Returns:

• rms_box (str) – PyBDSF parameter used during source finding.
• gresid_std (float) – Standard deviation of the background in the residual image after removing gaussian fitted sources.
• raw_rms (float) – Estimated noise in the image before source extraction.

read()

Reads FITS image data and header.

set_radius(scale)

Sets the radius attribute of the Image object.

Parameters:scale (float) – Fraction between 0 and 1 of the image radius to use. The full size of the image field-of-view is multiplied by this number.

source_qa(sources, params)

Approximates the expected number of sources in an image based on source counts from WENSS scaled by noise and fitted beam. See EP’s PythonTools.

write(data, header, owrite=False)

Writes FITS image data and header.

database.dbclasses.dict2attr(obj, dictionary)

Converts dictionary key-value pairs to object attributes.

Parameters:

• obj (class instance) – Any object initialized from a class.
• dictionary (dict) – Dictionary key-value pairs become attribute-value pairs.

database.dbclasses.init_image(impath)

Initializes an object of the Image class and sets values for its attributes from the fits file header using the header_attrs object method.

database.dbclasses.translate(img, out)

Method to translate PyBDSF output within the pipeline to DetectedSource objects and update the Image object.

Parameters:

• img (database.dbclasses.Image instance) – Initialized Image object with attribute values set from header info.
• out (bdsf.image.Image instance) – The object output by PyBDSF after running its source finding task process_image(). Contains a list of bdsf.gaul2srl.Source objects which are translated into DetectedSource objects.

Returns:

newsrcs – List of database.dbclasses.DetectedSource objects. Attributes of each object are set from the PyBDSF output object.

Return type:

list

database.dbclasses.translate_from_txtfile(img, pybdsfdir)

Creates a list of DetectedSource objects from reading in a source list text file output by PyBDSF.

Parameters:

• img (database.dbclasses.Image instance) – Initialized Image object with attribute values set from header info.
• pybdsfdir (str) – Directory path to PyBDSF files.

Returns:

• img (database.dbclasses.Image instance) – Initialized Image object with attribute values updated with source finding results.
• sources (list of DetectedSource objects) – DetectedSource objects with attribute values set from PyBDSF output source list text file.