Breizorro

Image masking and cataloguing suite

Project maintained by ratt-ru Hosted on GitHub Pages — Theme by mattgraham

Breizorro Logo

Breizorro is a flexible software program made to simplify image analysis tasks, including identifying emission islands and generating and modifying image masks, which are frequently used in radio interferometric imaging.

Parameter definition

breizorro [options] --restored-image restored_image

optional arguments:
    -h, --help            show this help message and exit
    -r IMAGE, --restored-image IMAGE
                          Restored image file from which to build mask
    -m MASK, --mask-image MASK
                          Input mask file(s). Either --restored-image or --mask-
                          image must be specfied.
    -t THRESHOLD, --threshold THRESHOLD
                          Sigma threshold for masking (default = 6.5)
    -b BOXSIZE, --boxsize BOXSIZE
                          Box size over which to compute stats (default = 50)
    --savenoise           Enable to export noise image as FITS file (default=do
                          not save noise image)
    --merge MASK(s)|REG(s) [MASK(s)|REG(s) ...]
                          Merge in one or more masks or region files
    --subtract MASK(s)|REG(s) [MASK(s)|REG(s) ...]
                          Subract one or more masks or region files
    --number-islands      Number the islands detected (default=do not number
                          islands)
    --remove-islands N|COORD [N|COORD ...]
                          List of islands to remove from input mask. e.g.
                          --remove-islands 1 18 20 20h10m13s,14d15m20s
    --ignore-missing-islands
                          If an island specified by coordinates does not exist,
                          do not throw an error
    --extract-islands N|COORD [N|COORD ...]
                          List of islands to extract from input mask. e.g.
                          --extract-islands 1 18 20 20h10m13s,14d15m20s
    --minimum-size MINSIZE
                          Remove islands that have areas fewer than or equal to
                          the specified number of pixels
    --make-binary         Replace all island numbers with 1
    --invert              Invert the mask
    --dilate R            Apply dilation with a radius of R pixels
    --erode N             Apply N iterations of erosion
    --fill-holes          Fill holes (i.e. entirely closed regions) in mask
    --sum-peak SUM_PEAK   Sum to peak ratio of flux islands to mask in original
                          image.e.g. --sum-peak 100 will mask everything with a
                          ratio above 100
    -o OUTFILE, --outfile OUTFILE
                          Suffix for mask image (default based on input name
    --gui                 Open mask in gui.

Image Masking and Transformation

Breizorro uses the minimal filter to generate binary masks by replacing each pixel’s value with the lowest value found in its near vicinity. This is incredibly effective at reducing noise and highlighting or smoothing particular regions of an image, such as the regions surrounding bright or small sources. Users can specify a window (or kernel) of a specific size that moves over the image as well as a sigma threshold for masking.

breizorro -t 6.5 -b 50 -r circinus-MFS-image.fits

mypipelinerun_circinus_p3_3-MFS-image fits-mypipelinerun_circinus_p3_3-MFS-image mask fits-image-2024-09-11-10-35-43

breizorro -r circinus-MFS-image.fits --sum-peak 500

mypipelinerun_circinus_p3_3-MFS-image mask fits-mypipelinerun_circinus_p3_3-MFS-image mask fits-image-2024-09-11-13-23-14

Region Generation and Manipulation

Breizorro makes it easier to create and work with regions using image masks. It includes labelling, eliminating, extracting, and filtering regions (islands) based on user-specified criteria. Users can refine their regions of interest using techniques such as erosion, dilation, hole-filling, binary masking, and inversion.

breizorro -r circinus-MFS-image.fits --save-regions circinus.reg

mypipelinerun_circinus_p3_3-MFS-image fits-image-2024-09-11-10-38-15

breizorro -r circinus-MFS-image.fits --merge west.reg --dilate 1 --fill-holes

mypipelinerun_circinus_p3_3-MFS-image mask fits-mypipelinerun_circinus_p3_3-MFS-image mask fits-image-2024-09-11-13-59-39

Cataloguing and Visualization

Breizorro enables catalogue generation from extracted regions, saving source properties to an ASCII/text file. This is particularly useful for analyzing fields dominated by point sources. By efficiently parameterizing and cataloguing compact sources, Breizorro enables rapid cross-matching.

breizorro -r deep2-MFS-image.fits --save-catalog deep2.txt

# processing fits image: deep2-MFS-image.fits
# mean beam size (arcsec): 6.31 
# original image peak flux (Jy/beam): 0.023107271641492844 
# noise out (µJy/beam): 51.62 
# cutt-off flux  (mJy/beam): 0.52 
# freq0 (Hz): 1049833007.8125 
# number of sources detected: 100 
#
#format: name ra_d dec_d i i_err emaj_s emin_s pa_d
src0 60.64975237181635 -79.86348735299585 0.00369 0.0001 11.66 0.0 120.96
src1 60.67140679629887 -80.36126947232378 7e-05 0.0001 0.0 0.0 0.0
src2 60.877334392876136 -79.76691180042988 0.00113 0.0001 8.25 0.0 104.04
src3 60.894387589282964 -79.73476060235502 0.00023 0.0001 0.0 0.0 0.0
src4 60.95196895741357 -79.68021884337942 0.00054 0.0001 0.0 0.0 0.0
src5 61.00657438220518 -80.17745581694626 0.00018 0.0001 0.0 0.0 0.0
src6 61.04136845645677 -80.48097816446368 0.00032 0.0001 0.0 0.0 0.0
src7 61.061502553348895 -79.93907167920088 0.01435 0.0001 21.54 0.0 111.8
src8 61.18650068905602 -80.40952881341589 0.00027 0.0001 0.0 0.0 0.0
src9 61.32594143681846 -79.91488530476678 7e-05 0.0001 0.0 0.0 0.0
src10 61.47462421089555 -79.96912396162651 9e-05 0.0001 0.0 0.0 0.0
src11 61.56419377531346 -80.18249455745902 0.0022 0.0001 10.77 0.0 158.2

Contributors

Thank you to the people who have contributed to this project.

Contributors