8. File Formats¶

[FIlesFormat]

This chapter describes the file formats of the intermediate data products generated by the aXe tasks. All files used by the aXe tasks are either ASCII files, FITS binary images with multiple extensions, or FITS binary tables containing multiple extensions. Separate BEAMs are kept by all aXe tasks in separate FITS extensions.

8.1. Input Images¶

[inimage] The input images must be in FITS format. Any FITS file following the FITS standard with binary image extensions can be used as input to the aXe tasks. A WCS (CD matrix) should be present in the header of the FITS extension to be read for some of the aXe tasks to work properly (sex2gol).

All standard pipeline processed input files are multi extension fits-files with the science, error and data quality array(s) in various extensions.

There are two ways to specify a fits extension in an aXe configuration file. One way is to address the fits extension number. Here aXe follows the convention of the CFITSIO library, whereby the primary extension (which is always present) has number 1, the first image extension number 2, the second image number 3 and so on. For an HRC image, the lines

SCIENCE_EXT 2
ERROR_EXT   3
DQ_EXT      4

in an aXe configuration file specify which fits extensions to use as science, error and data quality arrays, respectively. Another way to specify a fits extension in aXe is to use the extension names. In case of an HRC image, the lines

SCIENCE_EXT SCI
ERROR_EXT   ERR
DQ_EXT      DQ

are equivalent to the ones given before.

An aXe configuration file can target only one science array plus its associated error and data quality arrays. For ACS/WFC and WFC3/UVIS images, the data from its two chips is stored in separate extensions. To fully process these images in aXe two processing runs with two different configuration files have to be undertaken. With the fits extension numbers, the extensions can be uniquely specified using the scheme given above. In case that extension names are used, additional information must be provided, since there exist e.g. two extensions with the extension name SCI. In the aXe configuration file this additional information is the chip number, which is specified using the keywords OPTKEY1 and OPTVAL1. For ACS/WFC and WFC3/UVIS data, the chip notation defined by the archive is counterintuitive, since the data from chip 1 is stored at a higher extension number than chip 2 (see ). To specify the data from chip 1, in addition to the extension names, the keywords OPTKEY1 and OPTVAL1 must be set to CCDCHIP and 1, respectively. For chip 2 data the keyword OPTVAL1 must be set to 2. Figure [fits:sub:ext] clarifies the two naming conventions that can be used in the aXe configuration files named WFC.CHIP1.conf and WFC.CHIP2.conf. The configuration files shown in Chapt. [Main Configuration File] also show how the different extensions in the WFC must be addressed.

8.2. Fluxcube file¶

[fcube] The fluxcube files are a necessary input to compute a quantitative contamination extimate with the so called fluxcube emission model. This model is extensively described in Chapt. [quant_cont]. The fluxcube files have the file extension .FLX.fits (a typical fluxcube name is e.g. j8mt20kiq_flt_2.FLX.fits, which is the fluxcube for the grism image j8mt20kiq_flt.fits[sci,1]).

The fluxcube files are generated in the task fcubeprep (see Chapts. [fcubeprep] and [FPREP]) from MultiDrizzled direct images covering the area of the grism images. Fluxcubes are multiextension fits images. The first image extension is a so called Segmentation image. It shows for each pixel the number of the object to which the pixel belongs in the emission model of the corresponding grism image. All other extensions are flux images at different wavelengths. The wavelength of every flux image is indicated in the name of the fits extension (e.g. the fits extension j8mt20kiq_flt_2.FLX.fits[LAMBDA769] is a flux image at \(769\,nm\)).

In the computation of the quantitative contamination with the fluxcube emission model, a fluxcube file must exist for every grism image extension. All extensions cover approximately the identical FoV as the corresponding grism image extension. The keywords XOFFS and YOFFS in the primary fits header mark the offsets between the pixel coordinates in the grism image and in the fluxcube.

8.3. Input Image List¶

[inlist] The Input Image List is a flexible file format used in the High Level Tasks (axeprep, axecore, drzprep, axedrizzle) to specify for each grism image the necessary information for the aXe reduction. The file format is identical for all High Level Tasks. Once the user has produced an Input Image List for a particular data set, it can be used in all High Level Tasks (for the parameter inlist). Each row lists a grism image and the additional filenames and information to reduce the grism image with aXe.

The columns list:

grism image name (mandatory)
input object list 1, input object list 2, … (mandatory)
direct image (optional)
dmag value (optional)

If the grism image has more than one science extension, the Input Object List corresponding to each science extension must be specified as comma separated list in the second column. If the Input Object Lists refer to a direct image instead of the grism image itself, the name of the grism image should be listed in the third row. The fourth row holds the individual dmag value for the grism image (see task gol2af in Chapt. GOL2AF). The third and fourth columns are optional and can be omitted. A number in the third row will be interpreted as the dmag-value.

The following example shows some rows taken from an Input Image List for a WFC data set.

j8qq50nkq_flt.fits j8qq53nkq_1.cat,j8qq53nkq_2.cat j8qq53nkq_flt.fits 0.2
j8qq51pmq_flt.fits j8qq54pmq_1.cat,j8qq54pmq_2.cat j8qq54pmq_flt.fits 0.15
j8qq52ntq_flt.fits j8qq55ntq_1.cat,j8qq55ntq_2.cat j8qq55ntq_flt.fits -0.4
j8qq10ikq_flt.fits j8qq16ikq_1.cat,j8qq16ikq_2.cat j8qq16ikq_flt.fits 0.0
j8qq11juq_flt.fits j8qq17juq_1.cat,j8qq17juq_2.cat j8qq17juq_flt.fits 0.05
j8qq11k0q_flt.fits j8qq18k0q_1.cat,j8qq18k0q_2.cat j8qq18k0q_flt.fits -.5
j8qq12kgq_flt.fits j8qq19kgq_1.cat,j8qq19kgq_2.cat j8qq19kgq_flt.fits 0.32

8.4. Input Object List¶

sex: This file is a simple ASCII file containing tabulated information about objects to be extracted. It has the same format as a SExtractor 2.x output object catalog. The first few lines contain the name and description of each of the columns in the tabulated portion of this file.

To extract the spectra, aXe must know the exact location the objects would have on the grism/prism image if a filter instead of the grism/prism would have been used. The aXe task sex2gol uses the Input Object Lists plus further image information to generate a Grism Object List, which contains all the necessary grism image coordinates of the objects.

The Input Object List (IOL) and therefore the SExtractor catalogue they are built from, must contain the following columns:

NUMBER
X_IMAGE
Y_IMAGE
A_IMAGE
B_IMAGE
THETA_IMAGE
X_WORLD
Y_WORLD
A_WORLD
B_WORLD
THETA_WORLD
MAG_AUTO

If the IOL refers directly to the grism/prism image and not to a direct image taken at a close position (see Chapt. [IOLprep]), the values in the columns _WORLD are ignored. They can be replaced by ###, NaN, -NaN, or +NaN.

To compute a quantitative contamination estimate with the gaussian emission model presented in Chapt. [quant_cont], the wavelength of the magnitude must be known. aXe decodes the wavelength given in a column name if it is given as:In this notation ? and are single and multiple characters, respectively. Valid magnitude column names instead of MAG_AUTO are therefore e.g. MAG_F906LP, MAG_R710JOHN and MAG_I763SLOAN. Several magnitude columns with the brightness at various wavelengths improve the emission model and therefore the contamination estimate.

Additional columns are ignored and stripped off when generating the Grism Object List. The actual order of the columns in the Input Object List is not important as long as the header of the file properly describes its content. Blank lines and lines starting with a ‘’’ are ignored.

Care should be taken that each object has a unique number (NUMBER column) assigned to it in an Input Object List. This is the value that will be used throughout the extraction process to identify a particular object. If you use several Input Object Lists in your aXe reduction, make sure that an individual object has the same number in all Input Object Lists. This is important for the combination of spectra extracted from different grism files with axedrizzle.

The object numbers must be positive, but do not have to start at a particular value and do not need to be in consecutive order.

With the task iolprep, aXe offers a tool to generate the set of Input Object Lists for standard data sets. This aXe task is described in Chapt. [IOLP]. An example of its use is provided in Chapt. [IOLprep].

8.5. Grism Object List¶

::gol This file (GOL) is usually generated by aXe using the task sex2gol. It has exactly the same format as the Input Object List.

8.6. Aperture File¶

aper: This Aperture File is an ASCII file describing the APERTUREs in the spectroscopic image. An APERTURE consists of all BEAMS of an object. A BEAM is defined as the group of pixels in the image which will be extracted and combined to produce a final 1-D spectrum. APERTUREs are numbered (e.g. APERTURE 101) using the same numbers that originally appeared in the NUMBER column of the Input Object List. Each APERTURE itself consists of one or more BEAMs (labelled A, B, C etc..). Usually, each object is assigned one aperture in the APER file and each dispersive order is assigned a different BEAM entry inside that aperture definition. In this manner, assuming that the first and second orders are labelled A and B respectively, the 2nd order of object 101 will be found in APERTURE 101, BEAM B. The aperture file is generated by the task gol2af.

Each BEAM entry in the APER file contains the following information (data format is indicated in ):

REFPIXEL## the position in the image of a reference pixel [2*float, x,y]
CORNERS## the coordinates of a quadrangle defining the region of the image containing the pixel of interest [8*float, x1,y1,x2,y2,x3,y3,x4,y4]
CURVE## a polynomial description of the dispersion relation of the form :math:` {Delta y} = P({Delta x}) = a_0+a_1*{Delta x}+a_2*{Delta x}^2+…`. \(\Delta x^n\) and \(P({\Delta x})\) are the pixel offsets as measured from the coordinates listed in REFPIXEL. The first number following this keyword is the order of the polynomial. It is followed by \((n_1)\) polynomial parameters \([int, (n+1)\*float]\)
WIDTH## the total number of pixels to extract in the cross dispersion direction [float]
ORIENT## the orientation, in degrees counter-clockwise and with respect to the x-axis, along which the extraction should proceed [float]
AWIDTH## the object width as in column A_IMAGE in the Input Object List [float]
BWIDTH## the object width as in column B_IMAGE in the Input Object List [float]
AORIENT## the object angle as in column THETA_IMAGE in the Input Object List [float]
FLUX## the wavelength and the flux values of the object taken from the Input Object List \([2n*float, \lambda_1, flux_1,\lambda_2, flux_2,...\lambda_n, flux_n]\)
IGNORE## followed by either 0 or 1. If set to 1, this BEAM will not be extracted. [int]

The following example shows one APERTURE containing two BEAMs:

APERTURE 2
  BEAM A
     REFPIXEL2A 27.841 712.643
     CORNERS2A  32 714 217 568 208 564 23 710
     CURVE2A    1 0.000e+00 -7.893e-01
     WIDTH2A    2.811
     ORIENT2A   28.083
     AWIDTH2A   1.385
     BWIDTH2A   0.937
     AORIENT2A  -61.917
     FLUX2A     5.55000e+02 4.10993e-20
     IGNORE2A   0
  BEAM END
  BEAM B
     REFPIXEL2B 27.841 712.643
     CORNERS2B  -122 837 -97 817 -106 812 -131 832
     CURVE2B    1 0.000e+00 -7.893e-01
     WIDTH2B    2.811
     ORIENT2B   28.083
     AWIDTH2B   1.385
     BWIDTH2B   0.937
     AORIENT2B  -61.917
     FLUX2B     5.55000e+02 4.10993e-20
     IGNORE2B   1
  BEAM END

8.7. Background Estimate File¶

[BEF] This file (BEF) is a multiple extension FITS file containing a copy of the input slitless data where the regions defined in an Aperture File have been replaced by estimates of the background (see Chapt.[BE]). This file contains one primary data array in the main extension, named SCI, followed by two extensions containing respectively the error array of the Background Estimate (extension ERR), and the Data Quality array of the Background Estimate (extension DQ) where bad pixels are flagged by a non-zero value.

This file is generated by the backest task.

8.8. Pixel Extraction Table¶

[PET] This file (PET) is a FITS file containing FITS binary table extensions. The primary extension is empty and its header contains information from the header of the original FITS data file from which the PET was generated. Each of these extensions correspond to a single BEAM (as listed in the Aperture File). Each extension can be accessed using its name which is ##” (e.g. 1A for the first BEAM of APERTURE 1). Each extension contains the information extracted using the task af2pet for every pixel contained in the corresponding BEAM. It is in essence a table listing all the pixels in BEAM and some of the values computed for each pixel. A description of the geometry involved can be found in Chapt. [soft description].

This file is generated by the af2pet task (see Chapt.[AF2PET]).

Each extension contains the following columns :

N, the number of pixels in this BEAM
P_X, the absolute column coordinate of the pixel
P_Y, the absolute row coordinate of the pixel
X, the relative column coordinate of the pixel with respect to the BEAM reference pixel (REFPIXEL## in Aperture File)
Y, the relative row coordinate of the pixel with respect to the BEAM reference pixel (REFPIXEL## in Aperture File)
DIST, the projected distance from the center of the pixel to the section point on the trace of the spectrum
XS, abscissa of the section point relative to the BEAM reference pixel (REFPIXEL## in Aperture File)
YS, ordinate of the section point relative to the BEAM reference pixel (REFPIXEL## in Aperture File)
DXS, width of this pixel along the computed trace
XI, path length of the section point relative to the BEAM reference pixel (REFPIXEL## in Aperture File) along the trace
LAMBDA, the average wavelength of the light collected by this pixel
DLAMBDA, the wavelength range of the light collected by this pixel
COUNT, the number of electron/s in this pixel
ERROR, the error estimate in electron/s in this pixel
WEIGHT, the extraction weight assigned to this pixel
CONTAM, the contamination flag. Set to \(-1\) if no contamination was computed (the task petcont was not run) or to the number of BEAMs in which the pixel is included. CONTAM=1 implies that the pixel is a member of exactly one BEAM and therefore not contaminated, while CONTAM\(=\)N implies that the pixel is present in N-1 BEAMs, and that contamination may therefore be a problem.
MODEL, the signal (electron/s) in this pixel according to the quantitative contamination model.
DQ, the data quality of this pixel.

8.9. The Drizzle Prepare File¶

This file is a multi-extension FITS file containing the stamp images of all first order beams in a grism image. For each BEAM there are up to five extensions in the DPP-file:

the data stamp image with the extension name “BEAM_[aperture][beam] (e.g. BEAM_117A)
the error stamp image with the extension name ERR_[aperture][beam] (e.g. ERR_117A)
the contamination stamp image with the extension name CONT_[aperture][beam] (e.g. CONT_117A)
the grism model stamp image with the extension name MOD_[aperture][beam] (e.g. MOD_117A)
the variance stamp image with the extension name VAR_[aperture][beam] (e.g. VAR_117A)

The Drizzle Prepare File is created by the task drzprep. In the task axedrizzle, the science, error and contamination images are extracted and drizzled to build for each object the various extensions of a 2D drizzled grism image.

8.10. The 2D Drizzled Grism Image¶

[mef:sub:file] The 2D drizzled grism images are multi-extension FITS files created in the task axedrizzle. There exists one 2D drizzled grism image for every object in the Input Object Lists used to start the aXe reduction. Its name is [DRZROOT-keyword]_mef_ID[object number].fits (e.g. testaXe_mef_ID105.fits) and reflects the object number used in the Input Object Lists. A 2D drizzled grism image created in axedrizzle has the extensions:

SCI: the science image drizzled from the science extensions of the particular object in all DPP files
ERR: the error image drizzled from the error extensions of the particular object in all DPP files
EXPT: the exposure time map for the science extension
CON: the contamination image drizzled from the contamination extensions of the particular object in all DPP files
MOD: the grism model drizzled from the model extensions of the particular object in all DPP files
VAR: the variance image drizzled from the variance extensions of the particular object in all DPP files
SCIBCK: the drizzled background image (exists only if background drizzling was used)
ERRBCK: the error of the drizzled background image (exists only if background drizzling was used)
WHT: the weight image for the science extension

The weight extension is derived from the exposure time map in the task drz2pet (see Chapt. [DRZ2PET] on how the weights are computed). In axedrizzle the task drz2pet is used to generates a PET from the set of 2D grism images and to extract 1D spectra for those drizzle-coadded PETs.

8.11. Extracted Spectra File¶

[SPC] This file (SPC) is a FITS file containing FITS binary table extensions. The primary extension is empty and its header contains information from the header of the original FITS data file from which the SPC was generated. Each of these extensions correspond to a single BEAM (as listed in the Aperture File). Each extension can be accessed using its name which is ’”BEAM_##” (e.g. ”BEAM_1A” for the first BEAM of APERTURE 1).

This file is generated by the pet2spc task. Each extension contains an extracted, binned, spectrum as produce by the task pet2spc. Each extension contains the following columns :

N, the number of rows in this spectrum
LAMBDA, wavelength in A
TCOUNT, total number of counts in e s\(^{-1}\) in this wavelength bin.
TERROR, error in the total number of counts in e s\(^{-1}\) in this wavelength bin.
COUNT, background subtracted number of counts in e s\(^{-1}\) in this wavelength bin.
ERROR, error in the background subtracted number of counts in e s\(^{-1}\) in this wavelength bin.
BCOUNT, estimate of the number of counts in electron/s contributed from the background in this wavelength bin.
BERROR, error in the estimate of the number of counts in e s\(^{-1}\) contributed from the background in this wavelength bin.
FLUX, background subtracted flux in erg cm\(^{-2}\) s\(^{-1}\) A\(^{-1}\) in this wavelength bin.
FERROR, error in the background subtracted flux in erg cm\(^{-2}\) s\(^{-1}\) A\(^{-1}\) in this wavelength bin.
WEIGHT, number of pixels binned together into this wavelength bin.[wcolumn]
CONTAM, for quantitative contamination (see Chapt. [quant_cont]) this column gives an estimate on the contaminating flux from other objects to the spectrum. For geometrical contamination the values are set to -1,0,1..n to give the number of source this bin is contaminated with. The value 0 means no contamination. If the contamination was not recovered, every bin has the value -1.
DQ, the propagated data quality at this wavelength. This is computed by simply summing all the individual DQ values from the pixels contributing to this wavelength.

8.12. Stamp Image File¶

[STP] This file (STP) is a multi-extension FITS file containing stamp images of the BEAMs that were extracted. The primary extension of this file is empty. Each following extension contains the image of a single extracted BEAM. Extensions are named BEAM_[aperture][beam] (e.g. BEAM_1A). The STP-file is similar to the drizzled grism image explained in Chapt. [mef_file]. The STP-file contains all stamp images in a slitless image, and the drizzled grism image the stamp image of one object as combined from all slitless images. Also the drizzled grism images all have a WCS in wavelength and spatial direction.

8.13. Weight Image File¶

[WHT] The weight image file is produced in the optimal weighted extraction of spectra from individual grism images. Its file name extension is _opt.WHT.fits, corresponding to the _opt.SPC.fits of the optimal extracted spectra file.

The weight image file is a multi extension fits file which contains images of the weights applied to the PET pixels during the optimal weighted extraction. The weights are computed acording to Eqn. [opt_noise] in Chapt. [optimal weighting]. The weight images have trace length and trace distance as x- and y-axes, respectively. The extensions are named WHT_[aperture][beam] (e.g. WHT_1A).

8.14. Contamination File¶

[CONT] This file (CONT) is a simple FITS image containing the contamination estimate computed by the petcont task.

If quantitative contamination (see Chapt. [quant_cont]) was deployed, the contamination image contains the sum of all modelled beams. It is therefore a complete, quantitative model of the corresponding grism/prism image. Blinking the contamination image against the slitless image is a very good method to check whether the contaimation estimates are reasonable. The contamination image should have pixel values comparable to the background subtracted slitless image.

In geometrical contamination, pixels which are not within any known beams are assigned a value of 0. Pixels which are within a single beam (i.e. not contaminated by higher spectral orders and/or other objects in the field) are assigned a value of 1. Pixels contaminated by n beams are given a value of n+1.