piXedfit_images

piXedfit.piXedfit_images.EBV_foreground_dust(ra, dec)

Function for estimating E(B-V) dust attenuation due to the foreground Galactic dust attenuation at a given coordinate on the sky.

Parameters

  • ra – Right ascension coordinate in degree.

  • dec – Declination coordinate in degree.

Returns ebv

E(B-V) value.

piXedfit.piXedfit_images.crop_stars_galregion_fits(input_fits, x_cent, y_cent, radius, name_out_fits=None)

Function for cropping foreground stars within a galaxy’s region of interst.

Parameters

  • input_fits – The input FITS file containing the data cube that is produced using the flux_map() funciton in the images_processing class.

  • x_cent – 1D array of x coordinates of the center of the stars.

  • y_cent – 1D array of y coordinates of the center of the stars.

  • radius – 1D array of the estimated circular radii of the stars.

  • name_out_fits – Desired name for the output FITS file. If None, a generic name will be made.

piXedfit.piXedfit_images.dwd_2mass(pos, size=0.1)

A tool to download TwoMASS images from IRSA.

Parameters

  • pos – Target’s coordinate, in the astropy.coordinates form.

  • size – (defaults: 0.1[deg]) Search cone size. Note that this size IS NOT image size.

piXedfit.piXedfit_images.dwd_galex(pos, size=0.1, unzip=True)

A tool to download allwise images from GALEX.

Parameters

  • pos – Target’s coordinate, in the astropy.coordinates form.

  • size – (defaults to 0.1 [deg] ) Search cone size. Note that this size IS NOT image size.

  • unzip – (defaults to True) Whether to unzip the download file.

piXedfit.piXedfit_images.dwd_hst(pos, size=1, save=True, output_fmt='csv')

A tool to download allwise images from Hubble Space Telescope.

Parameters

  • pos – Target’s coordinate, in the astropy.coordinates form.

  • size – (defaults to 1 [arcmin] ) Search cone size. Note that this size IS NOT image size.

  • save – (defaults to True) Whether to save searching result.

  • output_fmt – (defaults to ‘csv’) Search result file extension, by default ‘csv’

Other formats: ‘csv’, ‘votable’, ‘xml’

piXedfit.piXedfit_images.dwd_sdss(pos, bands=['u', 'g', 'r', 'i', 'z'], size=20)

A tool to download images from SDSS.

Parameters

  • pos – Target’s coordinate, in the astropy.coordinates form.

  • bands – (defaults: [‘u’,’g’,’r’,’i’,’z’]) Request image in which filter. Default to download every band

  • size – (defaults: 20[arcsec]) Search cone size. Note that this size IS NOT image size.

piXedfit.piXedfit_images.dwd_spitzer(pos, size=0.008333333333333333)

A tool to download allwise images from Spitzer.

Parameters

  • pos – Target’s coordinate, in the astropy.coordinates form.

  • size – (defaults to 1/120 [deg] ) Search cone size. Note that this size IS NOT image size.

piXedfit.piXedfit_images.dwd_wise(pos, size=0.1, pix=800)

A tool to download allwise images from IRSA.

Parameters

  • pos – Target’s coordinate, in the astropy.coordinates form.

  • size – (defaults: 0.1[deg]) Search cone size. Note that this size IS NOT image size.

  • pix – (defaults to 800) This does crop on the image. If you want to download the whole image from WISE, please set pix = 0 Recommend not to download the original image which is way too large (~60 MB).

class piXedfit.piXedfit_images.images_processing(filters, sci_img, var_img, gal_ra, gal_dec, img_unit=None, img_scale=None, img_pixsizes=None, flag_psfmatch=0, flag_reproject=0, flag_crop=0, kernels=None, gal_z=None, stamp_size=[101, 101], remove_files=True)

A Python class for processing multiband imaging data and producing a data cube containing maps of multiband fluxes that are matched in spatial resolution and sampling. The image processing basically includes the PSF matching to homogenize the spatial resolution of the multiband imaging data and spatial resampling and reprojection to homogenize the spatial sampling (i.e., pixel size) and spatil reprojection of the mulltiband imaging data. A list of imaging data sets that can be handled automatically by this class in the current version of piXedfit can be seen at List of imaging data. However, one need to download convolution kernels from this link and put those inside data/kernels/ within the piXedfit directory ($PIXEDFIT_HOME/data/kernels). These kernels are not included in the piXedfit repository because of the large file sizes. This class can also handle other imaging data. For this, one need to provide kernels for PSF matching. These kernel images should have the same pixel size as the corresponding input images.

Parameters

  • filters – List of photometric filters names. To check the filters currently available and manage them (e.g., adding new ones) please see this page. For this input, it is not mandatory to make the input filters in a wavelength order.

  • sci_img – Dictionary containing names of the science images. An example of input: sci_img={‘sdss_u’:’img1.fits’, ‘sdss_g’:’img2.fits’}

  • var_img – Dictionary containing names of the variance images. It has a similar format to sci_img.

  • gal_ra – Right Ascension (RA) coordinate of the target galaxy. This should be in degree.

  • gal_dec – Declination (DEC) coordinate of the target galaxy. This should be in degree.

  • img_unit – (optional) Unit of pixel value in the multiband images. The acceptable format of this input is a python dictionary, similar to that of sci_img. This input is optional. This input will only be considered (and required) if the input images are not among the default list of recognized imaging data in piXedfit (i.e. GALEX, SDSS, 2MASS, WISE, Spitzer, and Herschel). The allowed units are: (1)”erg/s/cm2/A”, (2) “Jy”, and (3) “MJy/sr”.

  • img_scale – (optional) Scale of the pixel value with respect to the unit in img_unit. For instance, if image is in unit of MJy, the img_unit can be set to be “Jy” and img_scale is set to be 1e+6. This input is only relevant if the input images are not among the default list of recognized images in piXedfit. The format of this input should be in python dictionary, similar to sci_img.

  • img_pixsizes – (optional) Pixel sizes (in arcsecond) of the input imaging data. This input should be in dictionary format, similar to sci_img. If not provided, pixel size will be calculated based on the WCS information in the header of the FITS file.

  • flag_psfmatch – (optional) Flag stating whether the multiband imaging data have been PSF-matched or not. The options are: (1) 0 means hasn’t been PSF-matched, and (2)1 means has been PSF-matched.

  • flag_reproject – (optional) Flag stating whether the multiband imaging data have been spatially-resampled and matched in the projection. The options are: (1)0 means not yet, and (2)1 means has been carried out.

  • flag_crop – (optional) Flag stating whether the multiband imaging data have been cropped around the target galaxy. The options are: (1)0 means not yet, and (2)1 means has been cropped. If flag_crop=0, cropping will be done according to the input stamp_size. If flag_crop=1, cropping will not be done.

  • kernels – (optional) Dictionary containing names of FITS files for the kernels to be used for the PSF matching process. If None, internal convolution kernels in piXedfit will be used, given that the imaging data is recognized by piXedfit. Otherwise, input kernels should be supplied. If external kerenels are avaiable, the kernel images should have the same pixel size as the corresponding input images and the this input should be in a dictionary format, which is similar to the input sci_img, but the number of element should be Nb-1, where Nb is the number of photometric bands.

  • gal_z – Galaxy’s redshift. This information will not be used in the image processing and only intended to be saved in the heder of a produced FITS file.

  • stamp_size – Desired size for the reduced maps of multiband fluxes. This is a list data type with 2 elements. Accepted struture is: [dim_y,dim_x]. Only relevant if flag_crop=0.

  • remove_files – If True, the unnecessary image files produced during the image processing will be removed. This can save disk space. If False, those files will not be removed.

flux_map(output_stamps, gal_region, Gal_EBV=None, scale_unit=1e-17, mag_zp_2mass=None, unit_spire='Jy_per_beam', name_out_fits=None)

Function for calculating maps of multiband fluxes from the stamp images produced by the reduced_stamps().

Parameters

  • output_stamps – Dictionary containing reduced multiband images produced by the reduced_stamps() function.

  • gal_region – A 2D array containing the galaxy’s region of interest. It is preferably the output of the gal_region(), but one can also make this input region. The 2D array should has the same size as that of the output stamps and the pixel value is 1 for the galaxy’s region and 0 otherwise.

  • Gal_EBV – The E(B-V) dust attenuation due to the foreground Galactic dust. This is optional parameter. If None, this value will be retrive from the IRSA data server through the astroquery package.

  • scale_unit – Normalized unit for the fluxes in the output fits file. The unit is flux density in erg/s/cm^2/Ang.

  • mag_zp_2mass – Magnitude zero-points of 2MASS images. Shoud be in 1D array with three elements: [magzp-j,magzp-h,magzp-k]. This is optional parameter. If not given (i.e. None), the values will be taken from the header of the FITS files.

  • unit_spire – Unit of SPIRE images, in case Herschel/SPIRE image is included in the analysis. Therefore, this input is only relevant if Herschel/SPIRE image is among the images that are analyzed. Options are: [‘Jy_per_beam’, ‘MJy_per_sr’, ‘Jy_per_pixel’]

  • name_out_fits – Desired name for the output FITS file. If None, a default name will be adopted.

galaxy_region(segm_maps=None, use_ellipse=False, x_cent=None, y_cent=None, ell=0, pa=45.0, radius_sma=30.0)

Define galaxy’s region of interest for further analysis.

Parameters

  • segm_maps – Input segmentation maps, which are output of the segmentation_sep(). This input argument is required if the galaxy’s region is to be defined based on the segmentation maps obtained with SEP.

  • use_ellipse – Alternative of defining galaxy’s region using elliptical aperture centered at the target galaxy. Set use_ellipse=True if you want to use this option.

  • x_cent – x coordinate of the ellipse center. If x_cent=None, the ellipse center is assumed to be the same as the image center.

  • y_cent – y coordinate of the ellipse center. If y_cent=None, the ellipse center is assumed to be the same as the image center.

  • ell – Ellipticity of the elliptical aperture.

  • pa – Position angle of the elliptical aperture.

  • radius_sma – Radal distance along the semi-major axis of the elliptical aperture. This radius is in pixel unit.

Returns gal_region

Output galaxy’s region of interest.

reduced_stamps()

Run the image processing that includes PSF matching, spatial resampling and reprojection, and cropping around the target galaxy.

Returns output_stamps

Dictionary containing name of postage stamps of reduced multiband images.

segmentation_sep(output_stamps, thresh=1.5, minarea=30, deblend_nthresh=32, deblend_cont=0.005)

Get segmentation maps of a galaxy in multiple bands using the SEP (a Python version of the SExtractor).

Parameters

  • output_stamps – Stamp images output of image processing using the reduced_stamps().

  • thresh – Detection threshold for the source detection and segmentation.

  • minarea – Minimum number of pixels (above threshold) required for an object to be detected.

  • deblend_nthresh – Number of deblending sub-thresholds. Default is 32.

  • deblend_cont – Minimum contrast ratio used for object deblending. Default is 0.005. To entirely disable deblending, set to 1.0.

Returns segm_maps

Output segmentation maps.

piXedfit.piXedfit_images.kpc_per_pixel(z, arcsec_per_pix, cosmo='flat_LCDM', H0=70.0, Om0=0.3)

Function for calculating a physical scale (in kpc) corresponding to a single pixel in an image.

Parameters

  • z – Redshift of the galaxy.

  • arsec_per_pix – Pixel size in arcsecond.

  • cosmo – Choices for the cosmology. The options are: (a)’flat_LCDM’ or 0, (b)’WMAP5’ or 1, (c)’WMAP7’ or 2, (d)’WMAP9’ or 3, (e)’Planck13’ or 4, (f)’Planck15’ or 5, (g)’Planck18’ or 6. These are similar to the choices available in the Astropy Cosmology package.

  • H0 – The Hubble constant at z=0. Only relevant if cosmo=’flat_LCDM’.

  • Om0 – The Omega matter at z=0.0. Only relevant if cosmo=’flat_LCDM’.

Returns kpc_per_pix

Output physical scale in kpc.

piXedfit.piXedfit_images.subtract_background(fits_image, hdu_idx=0, sigma=3.0, box_size=None, mask_region=None, mask_sources=True, var_image=None, thresh=1.5, minarea=5, deblend_nthresh=32, deblend_cont=0.005)

Function for estimating 2D background and subtracting it from the input image. This function also produce RMS image. This function adopts the Background2D function from the photutils package. To estimate 2D background, the input image is gridded and sigma clipping is done to each bin (grid). Then 2D interpolation is performed to construct the 2D background image. A more information can be seen at photutils website.

Parameters

  • fits_image – Input image.

  • hdu_idx – The extension (HDU) where the image is stored. Default is 0 (HDU0).

  • sigma – Sigma clipping threshold value.

  • box_size – The box size for the image gridding. The format is: [ny, nx]. If None, both axes will be divided into 10 grids.

  • mask_region – Region within the image that are going to be excluded. mask_region should be 2D array with the same size as the input image.

  • mask_sources – If True, source detection and segmentation will be performed with SEP (Pyhton version of SExtractor) and the regions associated with the detected sources will be excluded. This help reducing contamination by astronomical sources.

  • var_image – Variance image (in FITS file format) to be used in the sources detection process. This input argument is only relevant if mask_sources=True.

  • thresh – Detection threshold for the sources detection. If variance image is supplied, the threshold value for a given pixel is interpreted as a multiplicative factor of the uncertainty (i.e. square root of the variance) on that pixel. If var_image=None, the threshold is taken to be 2.5 percentile of the pixel values in the image.

  • minarea – Minimum number of pixels above threshold triggering detection.

  • deblend_nthresh – Number of thresholds used for object deblending.

  • deblend_cont – Minimum contrast ratio used for object deblending. To entirely disable deblending, set to 1.0.

piXedfit.piXedfit_images.var_img_2MASS(sci_img, skyrms_img=None, skyrms_value=None, name_out_fits=None)

Function for constructing a variance image from an input 2MASS image. The estimation of flux uncertainty follows the information provided on the 2MASS website.

Parameters

  • sci_img – Input background-subtracted science image.

  • skyrms_img – FITS file of the RMS background image. If skyrms_value=None, this parameter should be provided. The background subtraction and calculation of RMS image can be performed using the subtract_background() function.

  • skyrms_value – Scalar value of median or mean of the RMS background image. This input will be considered when skyrms_img=None.

  • name_out_fits – Desired name for the output FITS file.

piXedfit.piXedfit_images.var_img_GALEX(sci_img, skybg_img, filter_name, name_out_fits=None)

Function for calculating variance image from an input GALEX image

Parameters

  • sci_img – Input GALEX science image (i.e., background subtracted). This type of image is provided in the GALEX website as indicated with “-intbgsub” (i.e., background subtracted intensity map).

  • skybg_img – Input sky background image .

  • filter_name – A string of filter name. Options are: ‘galex_fuv’ and ‘galex_nuv’.

  • name_out_fits – Desired name for the output variance image. If None, a generic name will be used.

piXedfit.piXedfit_images.var_img_WISE(sci_img, unc_img, filter_name, skyrms_img, name_out_fits=None)

Function for constructing variance image from an input WISE image. The uncertainty estimation follows the information from the WISE website

Parameters

  • sci_img – Input background-subtracted science image.

  • unc_img – Input uncertainty image. This type of WISE image is provided in the IRSA website and indicated with ‘-unc-’ keyword.

  • filter_name – The filter name. Options are: ‘wise_w1’, ‘wise_w2’, ‘wise_w3’, and ‘wise_w4’

  • skyrms_img – Input RMS background image. This image is produced in the background subtraction with the subtract_background() function.

  • name_out_fits – (optional, default: None) Desired name for the output FITS file. If None, a generic name will be made.

piXedfit.piXedfit_images.var_img_from_unc_img(unc_image, name_out_fits=None)

Function for constructing a variance image from an input of uncertainty image. This function simply takes square of the uncertainty image and store it into a new FITS file while retaining the header information.

Parameters

  • unc_img – Input uncertainty image.

  • name_out_fits – (optional, default: None) Name of output FITS file. If None, a generic name will be generated.

piXedfit.piXedfit_images.var_img_from_weight_img(wht_image, name_out_fits=None)

Function for constructing a variance image from an input weight (i.e., inverse variance) image. This funciton simply takes inverse of the weight image and store it into a new FITS file while retaining the header information.

Parameters

wht_image – Input of weight image (i.e., inverse variance).

Returns name_out_fits

(optional, default: None) Name of output FITS file. If None, a generic name will be made.

piXedfit.piXedfit_images.var_img_sdss(fits_image, filter_name, name_out_fits=None)

A function for constructing a variance image from an input SDSS image

Parameters

  • fits_image – Input SDSS image (corrected frame type).

  • filter_name – A string of filter name. Options are: ‘sdss_u’, ‘sdss_g’, ‘sdss_r’, ‘sdss_i’, and ‘sdss_z’.

Returns name_out_fits

Name of output FITS file. If None, a generic name will be used.