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aXe User Manual version 1.42

1. The recommended reduction strategy is to do a global background subtrac tion and to use aXedrizzle For the typical survey type data this is the best way to reduce ACS grism data In case only individual spectra in crowded fields are to be reduced the reduction with a background PET may have advantages Depending on the reduction strategy different High Level aXe Tasks have to be applied to reduce the spectra Table 3 1 lists the tasks and the order in which to apply them for the various reduction strategies 3 2 2 MultiDrizzle After the reduction strategy has been decided the first reduction step is to run MultiDrizzle on the grism images MultiDrizzle is an interface for perform ing all the tasks necessary for registering dithered HST images The program automatically performs cosmic ray rejection removes geometric distortions and performs the final image combination with drizzle The image combination is done for two reasons 1 the combined image gives a good impression on the quality of the data and the signal to noise level of the various object spectra 2 MultiDrizzle runs a cosmic ray detection algorithm and the dq extention of the flt images is updated with the information on all cosmic rays de tected in the MultiDrizzle run Running MultiDrizzle is therefore a simple way to perform a cosmic ray detection on the grism images While MultiDrizzle can combine slitless grism images no wavelength sen sitive flatfield
2. SPECTRAL EXTRACTION axe User Manual version 1 42 M Kiimmel and J Walsh S Larsen N Pirzkal R Hook 23 June 2005 Contents 1 Description LL WheabisGAer ee A AGM OMe eos eee A 12 Slitless Spectroscopy o sad a de a Ea 1 3 Apertures and Beams 000002 eee 1 4 Pixel Extraction Tables PET L amp Generating ID spectra kk ee eRe a didie A LG Sky Backend casado ee 1 6 1 Global Background Subtraction 1 6 2 Local Background Subtraction ss sa casa ot ef Diss PETE ecos aa Le aXe Wana ee ee a una ee g aa 1 9 Acknowledsement 6 044404848064 a 2 Installing aXe 2 1 Bedienen u 22 453208 248 u ee eb een 2 11 axe Distribution a2 222 2 2 54482 08 8 ar 2 2 Installing from the aXe source distribution 2 3 Installing from the aXe binary distributions 2 4 Validating the aXe installation 23 aXe Mailing List coo coo ee ee OE OS ee eS 20 Re UPPER oaks Ga Bee en men 3 Using aXe Be Ball be hh ES eee ee ew RHA SRE RE LSet Sb SLI PythemfPyRAP 6 664522544444 488 oe oa 312 High Level Tasks ocioso ee Rae ia 313 wReikeele aaa ed ren 3 1 4 Background Subtraction 008 das BLA ACIPS lt a AAA OY 3 2 Preparing the aXe Reduction oo oso creasa csaa pi aaa 3 2 1 Reduction Strategy lt sa aa sse eee BERR o peaa 322 MutiDrizzle ook hh ee a a SES G a ee 323 Input Object List coco s a ee a ee ee a 3 24 luput Image List
3. pixel weight 26 79 preview webpages 17 27 prism wavelength calibration 67 PyRAF 19 26 Python 7 20 25 quadrangle 9 76 reduction strategy 28 reference pixel 8 65 66 REFPIXEL 76 REFX 63 REFY 63 SCIENCE_EXT 62 section point 10 SENSITIVITY 68 sensitivity curve 12 65 68 69 SEX2GOL 48 71 75 sky background 12 slitless image 41 49 52 56 62 slitless spectroscopy 8 Solaris 7 21 84 spectral trace 9 11 12 50 65 67 STAMP 56 81 Stamp Image File 56 81 STSDAS 7 19 26 taxel4 19 TCOUNT 80 TERROR 80 trace distance 11 wavelength bins 11 12 80 81 wavelength calibration 49 67 69 WCS 19 48 WCSLIB 7 WEIGHT 78 80 WIDTH 76 X 77 X IMAGE 74 XI 78 XOFF 66 XS 77 Y Y IMAGE 74 YOFF 66 YS 77 INDEX
4. DRZLAMBO 64 DRZPFRAC 64 DRZPREP 15 45 DRZRESOLA 46 63 DRZROOT 64 DRZSCALE 46 64 DRZXINI 64 DXS 77 DYDX 66 DYDX_ORDER 65 INDEX environment variables 41 61 ERROR 78 80 ERRORS_EXT 62 Example 49 51 57 exposure time 62 63 EXPTIME 63 Extracted Spectra File 11 55 80 FERROR 80 FFNAME 54 63 field dependence 66 67 flat field 54 69 FLUX 80 GAIN 63 GNU CC 19 GOL2AF 49 Grism ACS Program for Extragalac tic Science 27 Grism Object List 48 49 75 grism wavelength calibration 67 GSL 7 19 High Level Tasks 7 26 28 73 HST 7 Hubble Ultra Deep Field 17 27 IGNORE 76 input image 71 Input Image List 26 29 31 73 Input Object List 8 29 31 48 73 INSTRUMENT 62 interpolation 51 LAMBDA 78 80 Linux 7 21 login file 21 Low Level Tasks 7 26 magnitude cutoffs 25 65 mailing list 22 master sky image 13 27 MMAG_ EXTRACT 25 65 MMAG_MARK 25 65 MultiDrizzle 13 27 28 multiple extensions 35 83 N 77 80 NaN 32 74 Note on aXe Input slitless FITS file formats 25 Note on aXe wavelength dependent flat fielding 54 Note on Field Dependent Values 66 Note on How to set up your own BEAM description 68 object orientation 10 object position 66 online parameter 20 51 61 OPTKEY1 63 OPTVALI 63 ORIENT 76 P_X 77 P_Y 77 PET2SPC 55 80 PETCONT 53 81 PETFF 54 Pixel Extraction Table 10 12 52 54 56 77
5. YES extrfwhm 4 0 drzfwhm 0 0 spectr YES rectified YES To execute the script in PyRAF the following command must be given in a PyRAF shell gt pyexecute noaXedrizzle_bpet py 3 4 Computing Time Requirements The aXe tasks are rather expensive in terms of computer time Some of the main factors contributing to a large computational need are e the complete error propagation and the propagation of contamination in formation multiplies the computing effort per science pixel by a factor of 3 since errors as well as contamination are stored and treated similar to the science data e the necessary conversions of data format image PET DPP drizzled im age result in a high demand on input output As a rule of thumb each High Level Task needs around 1 sec of computing time per object and image on a SunBlade 1500 For a typical data set with 10 WFC images and 1000 objects this results in around half a day of pure computing time The minimum RAM requirement is around 150 MB which should not constitute a bottleneck on modern workstations It is our experience that the estimate given in the example can be reduced by a factor 3 for a 2 6 GHz Pentium V Linux system 40 CHAPTER 3 USING AXE Chapter 4 aXe tasks This chapter gives detailed descriptions of each of the aXe tasks and of their parameters Examples of how to run each task are also included as well as de scriptions of the files required and produced b
6. YES backims cr_2 cmb fits cr_1 cmb fits mfwhm 2 0 norm YES histogram YES 36 CHAPTER 3 USING AXE gt axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back NO extr whm 4 0 drzfwhm 3 0 spectr YES rectified YES gt drzprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back NO gt axedrizzle inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf infwhm 4 0 outfwhm 3 0 back NO makespc YES The line breaks are added here for clarity but on the actual command line each command should be given as one string The most convenient way to specify the task parameters is with the IRAF epar mechanism In a python script the same command sequence looks as follows aXedrizzle_mastersky py import os string time from pyraf import iraf from iraf import axei4 stsdas iraf axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr YES backims cr_2 cmb fits cr_1 cmb fits mfwhm 2 0 norm YES histogram YES iraf axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back NO extrfwhm 4 0 drzfwhm 3 0 spectr YES rectified YES iraf drzprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back N0 iraf axedrizzle inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf infwhm 4 0 outfwhm 3 0 back NO makespc YES To execute the script in PyRAF
7. alphabetical sequence A B C follows the sequence of beams defined in the Configuration File Each beam is defined by the coordinates of the quadrangle which contains the pixels that are extracted together to form the spectrum of one dispersion order of an object The beams follow the spectral trace of the spectrum which is defined in the Configuration File While the length of a beam is set by the length of the corresponding dispersion order its width is adapted to the extraction width set 10 CHAPTER 1 DESCRIPTION Extraction direction a an Reference wavelength A o Figure 1 3 The beam geometry in a beam A single wavelength is assigned to each of the pixels within a beam An extraction along an arbitrary direction a with respect to the pixel grid is allowed This optimizes the resolution of the final extracted spectrum In this figure we show a is the orientation of an extended object by the user The left panel in Figure 1 2 shows an HRC grism exposure reduced in the HUDF HRC Parallels Program cleaned from cosmic ray hits In the right panel some of the beams marked and extracted in aXe are indicated The numbers give the spectral order and the letters denote their corresponding character for the configuration file used The bright areas mark regions where beams overlap and contaminate their spectra mutually The different extraction angles for the objects result in differe
8. the following command must be given in a PyRAF shell gt pyexecute aXedrizzle_mastersky py 3 3 5 No aXedrizzle and Global Sky Subtraction Here the background is globally subtracted using master sky images The coad dition of the individual 2D spectra with aXedrizzle is not done The command sequence is a subset of the command sequence in the last example gt axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr YES backims cr_2 cmb fits cr_1 cmb fits mfwhm 2 0 norm YES histogram YES gt axecore inlist aXetest lis 3 3 EXECUTING THE HIGH LEVEL TASKS 37 configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back NO extr whm 3 0 drzfwhm 0 0 spectr YES rectified YES In a python script the same command sequence looks as follows noaXedrizzle_mastersky py import os string time from pyraf import iraf from iraf import axei4 stsdas iraf axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr YES backims cr_2 cmb fits cr_1 cmb fits mfwhm 2 0 norm YES histogram YES iraf axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back NO extrfwhm 4 0 drzfwhm 0 0 spectr YES rectified YES To execute the script in PyRAF the following command must be given in a PyRAF shell gt pyexecute noaXedrizzle_mastersky py 3 3 6 aXedrizzle and Background PET Here the background PETs are generated
9. 10 PETFF This task uses a flat field calibration file to flat field the content of a Pixel Ex traction Table see Chapt 7 7 The wavelength of a pixel is used in conjunction with a flat fielding data cube containing the coefficients of a polynomial which can be used to compute at each pixel x y FF x y 2 ao 2 y ar 2 y a z where T A Ze Amin Amaz a Amin The coefficients ao x y are stored in the first data extension of the flat field cube a x y in the second etc The values for Amar and Amin are in the FITS header keywords WMIN and WMAX The name of the flat field cube is read from the aXe configuration file using the parameter FFNAME Chapter 6 2 gives a detailed description of the flatfield 4 11 PET2SPC 55 4 10 1 Usage petff grism config back ffname 4 10 2 Parameters grism name of the grism image config name of the aXe configuration file back apply FF to the background Pixel Extraction Table BPET ffname overwrite the default input flat field cube name Example petff grism test_grismn fits config SLIM conf test 0 back YES 4 10 3 Output If back NO e Updates SAXE_OUTPUT_PATH slitless filename ext number PET fits If back YES e Updates AXE_OUTPUT_PATH slitless filename _ ext number BPET fits 4 11 PET2SPC This task is used to transform the content of an Object Pixel Extraction Table into a set of 1D binned spectra in an Extra
10. 2 eb ke ee eee as 3 3 3 4 aXe 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 CONTENTS Executing the High Level Tasks 30 3 31 The Input Image List 2 6 ee ee eee sa 31 3 3 2 The Input Object Lists oa c sa ee Rn 31 3 3 3 The aXe Configuration Files 32 3 3 4 aXedrizzle and Global Sky Subtraction 35 3 3 5 No aXedrizzle and Global Sky Subtraction 36 3 3 6 aXedrizzle and Background PET 37 3 3 7 No aXedrizzle and Background PET 38 Computing Time Requirements 39 tasks 41 AREPRED ogrene eae aa parao ARA 41 ALI Usage oc gus re aa 42 AND Parameters 1300 645 sine ine Edw 42 ARECO RE o a Ree es ee de ee es 43 He sape ee ee ee ee neh 43 422 Parameleie ia el 43 lla TIERE ce ee a EP EG 44 IRE REE secem re E ee 45 Bh Pape lt lt ar ee REEL ew es 45 432 Paramelere Lux ee sd nee 46 Ase BU oa de eh ee eee ee EEE ws 46 BEI 000002 a a OR ew We ge ee 46 AAL Mage nennen naar me 47 4 42 Parameters e e e e ana 47 AM OMDAT ios a eds 48 ls ros aoa hk we Da RA 48 AL Pape oca ne ee he ls 49 4 32 Parameters wu 2d be en ee a 49 Wee SWE a ae ee ee et EE aoe 49 LAR ici BRR Eee AA 49 ABI sape naear ee ee a Be a 50 46 2 Paramelere oak aw ee 50 AGS DW 2 8 24 644 a be eh 51 BACKES oia ind ORAR 51 A PaE na a re 52 4 1 2 Paramelere cs ee da we a 52 Ar OUDE copiada srta rra ee ERE a 52 BODEN concave RR aa amp e
11. If drzpath YES e AXE_DRIZZLE_PATH slitless filename ext number STP fits 4 13 DRZ2PET This task produces one object PET background BPET if back YES from a set of images created with AXEDRIZZLE On this PET the task pet2spc can then perform the extraction of the 1D spectra for the drizzled grism images All the necessary input files OAF BAF image list modified configuration file are automatically created by the AXEDRIZZLE task The sequence of the images in the image list must match the sequence of the beams in the OAF Interactive changes to the image list and or the OAF are not recommended The 1D extraction of the 2D drizzled grism spectra is usually done within axedrizzle by calls to the tasks drz2pet and pet2spc The task drz2pet also sets the pixel weights to reflect the different signal to noise S N ratios in each pixel The S N variations are caused by the masking of bad and cosmic ray affected pixels and by the partial coverage of objects on the border of grism object The pixels that will be co added into a single resolution element in the 1D spectra are weighted according to their relative exposure times 58 CHAPTER 4 AXE TASKS 4 13 1 Usage drz2pet imagelist configs back 4 13 2 Parameters inlist ascii list which gives the name of the grism image to be processed as the first item on each line configs name of the aXe configuration file s back boolean to switch on off the creation of back
12. NaN NaN NaN NaN 3 3 EXECUTING THE HIGH LEVEL TASKS 33 New 2nd order dispersion solution and sensitivity New 3rd order dispersion solution and sensitivity SCIENCE_EXT SCI Science extension DQ_EXT DQ DQ extension ERRORS_EXT ERR Error extension OPTKEY1 CCDCHIP OPTVAL1 1 FFNAME WFC flat cube CH1 2 fits DQMASK 16383 DRZRESOLA 40 0 DRZSCALE 0 05 DRZLAMBO 4770 0 DRZXINI 15 0 DRZROOT aXetest First order BEAM A BEAMA 30 160 MMAG_EXTRACT_A 30 0 MMAG_MARK_A 30 0 Trace description ist order DYDX_ORDER_A 1 DYDX_A_O 0 0 0 0 0 0 0 0 0 0 0 0 DYDX_A_1 0 0357549 1 05903e 6 5 09607e 6 9 18057e 11 6 21825e 11 9 56794e 11 X and Y Offsets XOFF_A 0 0 YOFF_A 0 501521 0 000067788 0 000178108 2 52541e 8 1 3043e 7 3 49966e 9 Dispersion solution 2nd order DISP_ORDER_A 2 DLDP_A_O 4771 61 0 0370233 0 000189538 0 0000103637 1 39952e 6 3 20763e 6 DLDP_A_1 36 4556 0 00133904 0 00113125 3 81861e 8 8 88458e 8 1 02802e 7 DLDP_A_2 0 0101197 9 65156e 7 4 33325e 7 2 0178e 10 6 50773e 11 5 05835e 10 SENSITIVITY_A ACS WFC ist sens 5 fits ACS WFC CHIP2 conf INSTRUMENT ACS CAMERA WFC Calibrations for Cycle 11 onward for WFC CHIP 2 released June 2004 based on calibration data taken during SMOV and Cycle 11 Revised 3rd order flat field cube WFC flat cube CH2 2 fits for CHIP2 FH HOH FH Revised ist and 2nd order sensitivity 34 CHAPTER 3 USING AXE New Oth order dispersion solution and
13. Parameters inlist Input Image List which gives the name of the grism image to be processed as the first item on each line configs name of the aXe configuration file If several image extensions are to be processed e g for WFC images one configuration file per extension must be given in a comma separated list back boolean to switch on the creation of a background DPPs made by processing background PETs Example drzprep inlist axeprep lis configs aXe_config1 conf aXe_config2 conf back ND 4 3 3 Output If back NO e SAXE_DRIZZLE_PATH slitless filename _ ext number DPP fits or If back YES e SAXE_DRIZZLE_PATH slitless filename ext number BCK DPP fits 4 4 AXEDRIZZLE This task takes the DPPs prepared by drzprep as input The extensions for the various objects are extracted from the DPP and the stamp images of each object are drizzled together to form a deep 2D drizzled grism image for each object For a description of the drizzle algorithm see Fruchter A S amp Hook R N 2002 PASP 114 p 144 The drizzle coefficients computed by drzprep for each stamp image are given as header keywords and are computed in such a way that the combined 2D drizzled grism image resembles an ideal grism image with a constant dispersion and a constant pixelscale in the cross dispersion direction The trace of the drizzled spectra is parallel to the x axis of the image The dispersion and the pix
14. aXe We encourage all aXe users to participate and use the mailing list as a discussion forum for aXe and aXe related issues The aXe software package is still evolving and the communication between the software developers and the users is very important to improve the future versions of aXe The subscription to the aXe mailing list is done by sending an email to majordomo stecf org with the content subscribe axe stecf org in the mail body 2 6 AXE SUPPORT 23 To unsubscribe from the aXe mailing list please send an email to majordomo stecf org with the content unsubscribe axe stecf org in the mail body 2 6 aXe Support The ACS group at the Space Telescope European Coordinating Facility STECF is responsible for the support of the spectroscopic modes of ACS The develop ment of the aXe software package and the preparation of calibration products for the reduction are key components of this support To request further help and information concerning aXe or the calibration products please contact us with an email to acsdesk eso org 24 CHAPTER 2 INSTALLING AXE Chapter 3 Using aXe This chapter shows the various ways and strategies to reduce slitless spec troscopy data with aXe The different methods to produce the final calibrated 1D spectra are presented and discussed We also provide example scripts show ing how the various aXe tasks can be applied to reduce a given data set 3 1 aXe 1 4 Version 1 4 of aXe diffe
15. an nt order inverse polynomial which as is the case for the trace description can be field dependent The field dependent format is the same as for the trace description e DISP_ORDER_ int The order of the inverse polynomial of the form A xi a1 a2 2i ao a3 2 a0 e DLDIP_ 0 int Value of the parameter ay which can be a field dependent representation as described for the Trace description e DLDIP_ 1 int Value of the parameter a which can be a field dependent representation as described for the Trace description e DLDIP 2 int Value of the parameter a2 which can be a field dependent representation as described for the Trace description e DLD1P_ _n Value of the parameter an which can be a field dependent representation as described for the trace description e DLDIP_4 PRANGE int int In the form of the dispersion relation given above the singularity at x ay divides the inverse polynomial into the two branches x ay lt 0 and x ag gt 0 The desired solution for the dispersion relation is on only one branch The finite pointspread function and extended sources however request a beam definition which extends from the valid branch over the singularity at x ao partly into the second not valid branch To avoid that pixels from the not valid branch 68 CHAPTER 5 CONFIGURATION OF AXE TASKS enter the PET and the spectra this keyword defines the minimum a
16. direction does not exist It is in fact possible to define a different extraction direction for each object individually by adjusting 1 3 APERTURES AND BEAMS 9 Figure 1 2 A grism image of the HUDF HRC Parallels Program left panel and the aXe beams therein right panel The numbers and characters give the spectral order and the beam label in aXe The bright areas mark the overlap of several beams the wavelength assignment to be constant along the chosen extraction direction see Fig 1 3 In aXe the default action is to set the extraction direction to be parallel to the object position angle as given in the Input Object List The absence of slits and masks also dramatically enhances the probability that spectra of different sources overlap each other Even at large distances along the dispersion direction the different orders of two objects still can overlap and create confusion problems aXe can mark and extract several dispersion orders per object to properly record the source confusion or contamination for every order of each object 1 3 Apertures and Beams The extraction process in aXe is done on the basis of so called BEAMs Each beam comprises one dispersion order of one object The collection of all beams dispersion orders of one object is called the APERTURE The aperture is characterized by the aperture number which is identical to the object number in the Input Object List The beams are named with a single character The
17. eS 7 6 Background Estimate File tat Piel Extraction Table 22 20 4 a 8 8 sa Be ee ee 78 The Drizzle Prepare Pile 2 8 2 2 2 0 44 4 wma nat 7 9 The 2D Drizzled Grism Image ann i a en 7 10 Extracted Spectra Fil o os 665 4200424 06 ea LL Stamp Image File ou 008 2 a a we AAA 7 12 Contamination Pile c saraan ss sera CONTENTS Chapter 1 Description 1 1 What is aXe The aXe software was designed to extract spectra in a consistent manner from all the slitless spectroscopy modes provided by the Advanced Camera for Surveys ACS which was installed on the Hubble Space Telescope in February 2002 What we refer to as aXe is in fact a PyRAF IRAF package with several tasks which can be successively used to produce extracted spectra There exist two classes of aXe tasks see Figure 1 1 1 the Low Level Tasks work on individual grism images All in and output refers to a particular grism image 2 the High Level Tasks work on data sets Their aim is to do certain pro cessing steps for a set of images Often the High Level Tasks use the Low Level Tasks to perform a certain re duction step on each frame see Figure 1 1 The High Level Tasks were designed to cover all steps of the aXe reduction without any restriction in functionality Working with aXe therefore means to apply the four High Level Tasks to a set of data All tasks are controlled through a set of configuration files which can be e
18. extracted from different grism files with axedrizzle The object numbers do not have to start at a particular value and do not need to be consecutive 7 4 Grism Object List This file GOL is usually generated by aXe using the task sex2gol It has exactly the same format as the Input Object List This file can also be edited by hand as long as care is taken to maintain a proper SExtractor 2 x like description of the columns contained in the later part of the Input Object List example 7 5 Aperture File This Aperture File is an ASCII file describing the APERTUREs in the spectro scopic 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 col umn 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 76 CHAPTER 7 FILE FORMATS inside that aperture definition In this manner assuming that the first and sec ond 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
19. from background images which have interpolated pixel values at the beam positions Both the image as well as the background are drizzled to deep 2D grism and background images respectively see Chapt 1 6 2 gt axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr NO norm YES histogram YES gt axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back YES extrfwhm 4 0 drzfwhm 4 0 backfwhm 6 0 spectr YES rectified YES gt drzprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back YES gt axedrizzle inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf infwhm 4 0 outfwhm 3 0 back NO makespc YES gt axedrizzle inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf infwhm 4 0 outfwhm 3 0 back YES makespc YES In a python script the same command sequence looks as follows aXedrizzle_bpet py 38 CHAPTER 3 USING AXE import os string time from pyraf import iraf from iraf import axei4 stsdas iraf axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr NO norm YES histogram YES iraf axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back YES extrfwhm 4 0 drzfwhm 3 0 backfwhm 6 0 spectr YES rectified YES iraf drzprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back YES iraf axedrizzle in
20. objects in the area covered by the grism exposures This basic object catalogue might be taken from an archive or derived via SExtractor from a set of MultiDrizzled direct images In this case STSDAS offers some basic tasks such as tranback traxy or xytosky which can be used in IRAF PyRaf scripts to create an Input Object Lists for each grism exposure see also Note on page 75 Usually there are are several Input Object Lists to reduce a set of grism exposures Care must be taken that each object is assigned an identical object identification number in the various Input Object Lists of the data set since this number is the only way to identify the individual spectra and to derive the coadded deep spectrum of an object It is possible to give an object in the Input Object List a position outside of the area covered by the corresponding grism image In the case that the spectrum of the object falls partly on the grism image but its reference point is outside the spectrum covered by the grism image can still be reduced and contribute to the coadded spectrum of the object 3 2 4 Input Image List After the Input Objects Lists are ready the Input Image List can be prepared The Input Image List is used in all High Level Tasks in the parameter inlist to specify Input Object List s direct image and dmag value for each grism image Its format is extensively described in Chapt 7 2 3 3 Executing the High Level Tasks After all the input files h
21. of the beam are listed in the output such that the user can understand why the pixel information could not be computed 4 14 1 Usage axegps grism config beam_ref xval yval 4 14 2 Parameters grism name of the grism image config name of aXe configuration file used to create the OAF beam_ref the beam to define the spectral solutions xval the x coordinate of the pixel yval the y coordinate of the pixel Example axegps grism j8m822qhg_f1t fits config HUDF HRC conf beam_ref 3A xval 102 yval 588 4 14 3 Output All output is directly printed to the standard output 60 CHAPTER 4 AXE TASKS Chapter 5 Configuration of aXe tasks The aXe tasks are configured in three different ways e Environment Variables e configuration files e online parameters to aXe tasks 5 1 Environment Variables All aXe tasks use the following environment variables e AXE_IMAGE_PATH the path where the input data is located e AXE OUTPUT PATE the path where all aXe outputs except the drizzle related will be directed e AXE_DRIZZLE_PATH the path where the drizzle outputs will be directed e AXE_CONFIG_PATH the path where the aXe configuration files are lo cated These can be set before running the aXe tasks or by a PyRAF script which runs all the aXe tasks in the desired order Using csh tcsh setenv AXE_IMAGE_PATH path to my data setenv AXE_OUTPUT_PATH output directory setenv AXE_DRIZZLE_PATH drizzle directory se
22. spectra with the tasks drz2pet and pet2spc Usually these additional steps are carried out auto matically within axedrizzle if makespc YES To drizzle the background DPPs the task axedrizzle must be run with back YES If the drizzling of the background is done after the drizzling of the object DPPs the background is correctly taken into account in the reduction of the 1D spectra The Input Image List given with the parameter inlist must contain the name of the grism image as the first item on each line The name of the corre sponding DPP file s are then derived from the grism name and the chip as speci fied in the configuration file a Further columns items are neglected Therefore file used as inlist in axecore and axeprep can be reused in axedrizzle again 4 4 1 Usage axedrizzle inlist configs infwhm outfwhm back makespc 4 4 2 Parameters inlist Input Image List with the input grism filename as the first item on each line configs name of the aXe configuration file If several image extensions and therefore DPPs are to be processed e g for WFC images one configuration file per extension must be given in a comma separated list infwhm mfwhm for the input PETs and DPPs outfwhm mfwhm for the extraction of the objects in later steps back boolean to work on background DPPs and produce drizzled backgrounds 48 CHAPTER 4 AXE TASKS makespc boolean to switch on off whether SPCs shall be created directl
23. the 2D drizzled grism images any longslit extraction program can be used All the necessary information for calibration and extraction is given in the aXe configuration file and the various other aXe files Thus aXe users are not restricted to using aXe tasks for the 1D extraction but can also apply alternative extraction methods e g to make use of a more advanced weighting schemes In a pilot study the aXedrizzle reduction scheme was used for the reduction of the Hubble Ultra Deep Field HUDF HRC Parallels data The results can be seen on the preview webpages at http www stecf org UDF HRCpreview html 3 1 4 Background Subtraction Another new feature introduced in aXe 1 4 is the option of using a global back ground subtraction based on a scaled master sky image Our experience with application of this technique to the HUDF HRC Parallels data was very encour aging Also the Grism ACS Program for Extragalactic Science GRAPES PI Sangeeta Malhotra see http www int stsci edu san Grapes and Pirzkal et al 2004 for more details have used this technique to subtract the background prior to the aXe reduction Nevertheless the stability of the grism background and the long term appli cability of the master sky images remain poorly quantified We recommend combining the sky subtracted grism images with the MultiDrizzle task in STSDAS in order to verify that the master sky subtraction went well and resulted in a mean background level clos
24. the High Level and the Low Level Tasks the aXe webpages at http www stecf org software aXe index html On this webpage we always offer the latest aXe release for download 1 2 Slitless Spectroscopy In conventional spectroscopy slits or masks are used to allow only the light from a small portion of the focal plane of the telescope to enter the dispersing device e g grism grating or prism This results in an unambiguous conversion between pixel coordinates on the detector and wavelength In slitless spectroscopy there is no unique correspondence between pixel co ordinates and wavelength Consequently the spectral reduction on the basis of the spectroscopic data alone is impossible Additional information concerning the positions of the object must be added to facilitate the spectral reduction In aXe this is done by providing Input Object Lists at the beginning of the reduction process In the Input Object List the object positions are given in the image coordinate system or the world coordinate system This allows the determination of the so called reference pixel for every object The reference pixel is the undispersed object position in image coordinates on the grism data For each individual object it is then possible to assign a wavelength to each pixel In conventional spectroscopy the extraction of the 1D spectra from the 2D data is done along the direction of the slit or mask In slitless spectroscopy such a predefined extraction
25. to select the proper chip from a multi extension ACS WFC image for example REFX int The 2D field dependence contained in the configuration file is by default taken to be with respect to pixel 0 0 The parameter REFX and REFY can be set to different values For example these parameters can be used when a 2D field dependence with respect to the center of the image is required REFY int See REFX DRZRESOLA real The dispersion in pixel for the drizzled first order beams 64 CHAPTER 5 CONFIGURATION OF AXE TASKS DRZSCALE real The pixelscale in per pixel in the cross dispersion direction in the drizzled beams DRZLAMBO real The reference wavelength in A which is drizzled to the reference pixel in the drizzled beams DRZXINI real The x value of the reference pixel in the drizzled images The reference wavelength given in DRZLAMO is drizzled to this reference pixel The y value of the reference pixel depends on the object width and the extraction width For a given drizzled beam the y value of the reference pixel is at real ny 2 1 0 where ny is the number of rows in the drizzled beam DRZPFRAC real The pixfrac value used in axedrizzle DRZKERNEL string The drizzle kernel to be used in axedrizzle All kernels available in drizzle v2 92 are allowed Those kernels are square point turbo gaussian tophat lanczos2 lanczos3 DRZROOT string The root name for the output files created in axedrizzle Th
26. 1 cat j8qq18k0q_1 cat j8qq19kgg_1 3 3 2 The Input Object Lists cat cat cat cat cat cat cat j8qq53nkq_flt j8qq54pmq_fl1t j8qq55ntq_fl1t jsqql6ikq_flt j8qq17juq_f1t j8qq18k0q_f1t j8qq19kgq_f1t fits fits fits fits fits fits fits 0 2 0 15 0 4 0 0 0 05 5 0 32 As examples the first lines of the Object Lists j8qq53nkq_1 cat and j8qq54pmq_1 cat both produced by SExtractor are listed below j8qq53nkq_l cat X_IMAGE Y_IMAGE NUMBER X_WORLD Y_WORLD MAG_AUTO A_IMAGE B_IMAGE OMONODOKRWNK 10 A_WORLD 11 B_WORLD 12 THETA_WO 4191 57 323 4266 90 378 4259 20 365 4237 82 374 3991 36 528 4304 72 435 HHH HH HOH HH H OH OF THETA_IMAGE RLD 45 97 97 40 52 51 OON DOH 53 53 53 53 53 53 1655096 1640349 1642830 1643802 1647451 1629142 20 27 27 21 2 7 27 8284792 8288907 8289079 8285958 8245487 8288662 22 27 71 02 28 66 25 19 20 89 28 65 13 w Oowoooo 14 13 6 11 5 NaN NaN 3 0 22 4 NaN NaN 3 0 6 1 NaN NaN 3 0 27 6 NaN NaN 14 3 60 1 NaN NaN 3 0 4 5 NaN NaN NaN NaN NaN NaN NaN NaN 32 CHAPTER 3 USING AXE j8qq54pmq 1 cat X_IMAGE Y_IMAGE NUMBER X_WORLD Y_WORLD MAG_AUTO A_IMAGE B_IMAGE THETA_IMAGE 10 A_WORLD 11 B_WORLD 12 THETA_WORLD 4187 78 312 78 4263 11 368 29 4255 41 355 29 4234 03 363 72 3987 57 517 82 4300 93 424 82 HHH HH HH HOH H OH OF OANA AFPWNHE 53 1655096 27 8284
27. 1 Usage backest grism config np interp mask in_af out_af 4 7 2 Parameters grism name of the grism image config name of the aXe configuration file np the number of pixels used on each side of a beam to compute the median averag fitted background interp the type of interpolation to perform mask create a mask image with the OAF file in_af overwrite the default input aperture filename out_back overwrite the default output background filename Example backest grism test_grismn fits config SLIM conf test 0 np 10 interp 1 4 7 3 Output If mask NO e SAXE_OUTPUT_PATH slitless filename _ ext number BCK fits If mask YES e SAXE OUTPUT PATH slitless filename ext number MSK fits 4 8 AF2PET This task uses the input slitless image together with an Object Aperture File to generate a Pixel Extraction Table PET for the input data The same task should be used with the Background Estimate File and the same Object Aperture File to generate a Background Pixel Extraction Table containing in formation about the spectral background BPET 4 8 1 Usage af2pet grism config back out_pet 4 9 PETCONT 53 4 8 2 Parameters grism name of the grism image config name of the aXe configuration file back generate a PET for a background image using a BAF file instead of a OAF file and using a background image generated by backest out_PET overwrite the default output PET filename Example af2pet g
28. 792 22 71 13 53 1640349 27 8288907 27 02 3 53 1642830 27 8289079 28 66 3 53 1643802 27 8285958 25 19 3 53 1647451 27 8245487 20 89 14 53 1629142 27 8288662 28 65 3 13 6 11 3 22 3 6 3 2l 14 60 3 4 NaN NaN NaN NaN NaN 6 0 0 0 3 0 NaN oo os oaHr Oowooo OrorrA 0 As can be verified from the World coordinates X_WORLD Y WORLD objects with the identical numbers NUMBER in the two Input Object Lists are the same The values NaN in the last column are placeholders and are neglected in aXe 3 3 3 The aXe Configuration Files For each of the two FITS extensions in a WFC image an aXe configura tion file must exist Examples of two such files named ACS WFC CHIP1 conf and ACS WFC CHIP2 conf are listed below To save space the configuration files only include the description of the first beam which is in any case the only beam treated by aXedrizzle The full versions can be retrieved from http www stecf org instruments acs calib all_Cycles WFC ACS WFC CHIP1 conf INSTRUMENT ACS CAMERA WFC Calibrations for Cycle 11 onward for WFC CHIP 1 released Revised 3rd order flat field cube WFC flat cube CH1 2 fits for CHIP1 Revised 1st and 2nd order sensitivity New Oth order dispersion solution and sensitivity HE HH H HH H OF New ist order dispersion solution and sensitivity NaN NaN NaN NaN NaN NaN June 2004 based on calibration data taken during SMOV and Cycle 11 NaN NaN
29. ERA string The name of the camera optional e SCIENCE_EXT string or integer The name of the FITS extension con taining the data array if a string or the number of the extension con taining the data array if an integer e ERRORS_EXT string or integer The name of the FITS extension con taining the error array if a string or the number of the extension con taining the error array if an integer Set to 1 if no error array is to be read in e DQ_EXT string or integer The name of the FITS extension containing the data quality array if a string or the number of the extension containing the data quality array if an integer Set to 1 if no data quality array is to be read in e DQMASK integer This integer value determines which bits in the data quality array must not be set in order that a given pixel is considered 5 2 CONFIGURATION FILES 63 to be good The integer value is logically AND ed with the actual data quality value of each pixel If the result is non zero the pixel will be flagged as bad and ignored in aXe tasks The data quality value assigned to each pixel in calacs and updated in axeprep has different flag values for the various pixel deficiencies see the ACS Data Handbook for the exact codes The flag values for new hot pixels and cosmic ray rejected pixels for example are 16 and 8192 respectively To flag both the new hot pixels and cosmic ray rejected pixels the integer fo
30. H see Chapt 5 1 3 3 EXECUTING THE HIGH LEVEL TASKS 35 j8qq50nkq_fit fits j8qq51pmq_fit fits j8qq52ntq_fit fits j8qq10ikq_fit fits j8qq11juq_flt fits j8qq11k0q_fit fits j8qq12kgq_fit fits j8qq53nkq_2 cat j8qq53nkq_1 cat j8qq54pmq_2 cat j8qq54pmq_1 cat j8qq55ntq_2 cat j8qq55ntq_1 cat j8qq16ikq_2 cat j8qq16ikq_1 cat j8qq17juq_2 cat j8qq17juq_1 cat j8qq18k0q_2 cat j8qq18k0q_1 cat j8qq19kgq_2 cat j8qq19kgq_1 cat gt axeprep inlist aXetest lis j8qq53nkq_fit fits j8qq54pmq_fit fits j8qq55ntq_fit fits j8qq16ikq_fit fits j8qq17juq_fit fits j8qq18k0q_fit fits j8qq19kgq_fit fits configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf dq YES backgr YES backims cr_2 cmb fits cr_1 cmb fits mfwhm 2 0 norm YES histogram YES Figure 3 1 The Input Image List aXetest lis and a High Level aXe 1 4 Task The arrows connect input which refers to the identical science extension 3 3 4 aXedrizzle and Global Sky Subtraction In this reduction scenario the background is subtracted using a mastersky cr_2 cmb fits and cr_1 cmb fits for data in science extension 2 and 1 re spectively For each object the 2D spectra on the individual grism images are combined to a deep 2D grism spectrum with aXedrizzle then the 1D spectrum is extracted from the coadded 2D grism spectrum The sequence of commands interactively applied in PyRAF is gt axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr
31. MAGE can be replaced by NaN NaN or NaN aXe will then try to recompute the missing values using the world coordinate system WCS 2 The Input Object List refers to the grism image Then the parameter use_direct in sex2gol is set to NO In this case the Input Object List must contain at least the following lines NUMBER X_WORLD Y_WORLD A_WORLD B_WORLD THETA_SKY MAG_AUTO In this case sex2gol computes the corresponding IMAGE values from the WORLD values given in the Input Object List using the WCS of the grism image 3 The Input Object List refers to the grism image but in addition to the lines listed in 2 the Input Object List contains also X_IMAGE Y_IMAGE A_IMAGE B_IMAGE THETA_IMAGE 7 4 GRISM OBJECT LIST 75 In this case the MAGE values are taken and copied to the Grism Object List as they are 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 an independent number NUM BER column assigned to it in an Input Object List This is the value which 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 List This is im portant for the combination of spectra
32. R N 2002 PASP 114 p 144 which is available in the STSDAS package within IRAF The advantages of this technique as applied to slitless spectra can be sum marised as follows e Regridding to a uniform wavelength scale and a cross dispersion direction orthogonal to the dispersion direction is achieved in a single step 1 7 DRIZZLING OF PETS 15 Si i extract drizzle Figure 1 6 Drizzling in aXe The object marked in panel a is extracted as a stamp image b The stamp image is drizzled to an image with constant dispersion and constant pixel scale in cross dispersion direction c The deep 2D drizzled image d is then used to extract the 1D spectrum e Weighting of different exposure times per pixel and cosmic ray affected pixels are correctly handled e There is only one linear rebinning step to produce a 2D spectrum e The combined 2D spectra can be viewed to detect any problems These advantages come at the expense of a greater complexity of the reduc tion and significantly longer processing time Also the aXe drizzle reduction currently supports only first order spectra The drizzling within aXe is fully embedded in the aXe reduction flow and uses data products and tasks created and used in the non drizzling part of aXe The input for the drizzle combination consists of flatfielded and wavelength calibrated PETs extracted for each science image which are converted to Drizzle PrePare files DPP using the drzprep
33. R E aa 52 A wee eee eee ee ee m 52 4 82 Parameters a eat Ee ee ee A 53 Aa DUE lb ee a aa ee he a 53 PFPETCONT 2625 4 oat dh 5 Der 53 AJI Page ce ey be ee E ee es 53 402 AN 53 ANS OWU e soas chee ee ica ae a ee t e aa 54 CONTENTS IN PERDER ocios gd a ee he wD Eb A ee AIDI Usage oe kb kkk EM a aaa aaa ee eS os 4 102 Parameters soos ic aa a ee RO a ed E AMA Umpu cos aaa der a 411 PETESPO ace 222 hoe a A we ees LT WAR een a a A12 Patamelere aan as engeren ae LE OMDET na ek AS REESE we RS MIL SADA aid doe Be WOW ee wean ar 412 1 Usar coca ara ee RRR ee 2 122 Poranne ac ce ek ee ee ee eh os LITO RGU Seinen 44 ee 413 DRZIPET osana ee ee aaa ee es Alal Masse oo 2 2er 4 132 Paramelers 224222 ee ee REE EE EE ee es 4138 IN ar oo eS eS EERE ee eS LIA AXEGPS iaa RARER AAA AR RR JA L USARSE ce eh deeded a ae GE Welle do aour drs M Patamele Zu a a eS ee AMAS ARE seno a eher 5 Configuration of aXe tasks 3 1 Barvironment Variables 00 ee eae b a sa ee ee es 52 Conmpuration Wiles 04 444 664 40 te bk Ee EH EEE ws 5 2 1 Main Configuration File 5 2 2 Example of a Main Configuration file 6 aXe Calibration Files 61 Sensitivity Cure ke ek ee nadaa mA Plat Mel eras iaa ates eS RRR dd es 7 File Formats TL Taput IAS ok ee ee PRR RE eee ee 2 pul Image Dist u oo See HRA Rae dee e A To Input Objekt List 2 2 a2 20 22 RAE ARO 7A Grism Object List mmm ea a To APO Pie ooa Sun kungen A A EE
34. _PATH slitless filename ext number OAF If back YES e AXE_OUTPUT PATH slitless filename ext number BAF 4 7 BACKEST This task uses the input slitless image and a Background Aperture File to gen erate a Background Estimate File Chapt 7 6 This task is applicable when a master sky is not used for background subtraction Chapt 1 6 The number of points to use and the order of the interpolation to use to generate the Back ground Estimate File can be set using online parameters The values in the regions within each of the BEAMs listed in the Background Estimate File are replaced by the median average linear or n order polynomial interpolation of pixels which are immediately above and below a BEAM but not within any other BEAM The number of pixels to use for fitting is by default set to 10 on each side below and above the BEAM therefore 20 pixels in total The value given for the np option can be used to change this default value If the number of points is set to a value which is 0 or less then the entire column of an image will be used ignoring any pixels which are within any known BEAM This option allows for a full column background estimate to be created instead of a local background estimate The type of interpolation is controlled by the parameter interp e interp 1 Median e interp 0 Average e interp 1 Linear fit e interp n gt 1 nt order polynomial fit 52 CHAPTER 4 AXE TASKS 4 7
35. a Background Pixel Extraction Table BPET for all BEAMs in a grism image Thus every PET has its corresponding BPET de rived from the background image with the spectral information of the identical objects and beams in it Finally the BPET is subtracted from the PET and the background subtracted spectra are extracted 1 7 Drizzling of PETs The aXe reduction scheme described up to now produces one spectrum for each individual beam in each science image However datasets such as those obtained with ACS often consist of several images with small position shifts dithers between them The direct approach of co adding the 1D spectra ex tracted from each image to form a combined deep spectrum has several disad vantages e The data is non linearly rebinned twice once when extracting the spec trum from the image and again when combining the individual 1D spectra e A complex weighting scheme is required to flag cosmic ray affected and bad pixels e Low level information on the cross dispersion profile is lost when many 1D extracted spectra are combined to a deep spectrum To circumvent these drawbacks a new reduction scheme is available in aXe 1 4 whereby all the individual 2D spectra of an object are coadded to a single deep 2D spectrum The final deep 1D spectrum is then extracted from this combined 2D spectral image The combination of the individual 2D spectra is done with the Drizzle software Fruchter A S amp Hook
36. ameters of a set of polynomial equations described above which are independent of any field dependent effect Expressing each of the n coefficients of an n order polynomial as an m order 2D x y field dependent polynomial can seem a little awkward at first but allows for a maximum amount of flexibility when calibrating smoothly varying quantities 5 2 CONFIGURATION FILES 67 Wavelength calibration description for grisms The wavelength calibration is handled using an nt order polynomial which as is the case for the Trace description can be field dependent The field dependence format is the same as for the trace description e DISP_ORDER_ int The order of the polynomial of the form A x ao a1 Zi a2 xi which defines the wavelength at a distance x along the spectral trace e DLDP_ _0 int Value of the parameter ay which can be a field de pendent representation as described for the Trace description e DLDP_ 1 int Value of the parameter a which can be a field de pendent representation as described for the Trace description e DLDP 2 int Value of the parameter as which can be a field de pendent representation as described for the Trace description e DLDP_ _n Value of the parameter an which can be a field dependent representation as described for the Trace description Wavelength calibration description for prisms The wavelength calibration is handled using
37. ation of the GSL and the CFITSIO library Follow the instructions given by the configure script to solve problems The configure script generates a Makefile which is used to compile the aXe tasks Type gt make to execute the Makefile and create the tasks The tasks must be installed in the bin directory of the taxel4 package Simply execute gt make install to move the binaries to their proper location On the Python side there exists a similar script to compile the code Go to the Python directory and compile the Python code there with gt cd iraf gt python compileaXe py 2 3 INSTALLING FROM THE AXE BINARY DISTRIBUTIONS 21 If all went well aXe 1 42 is now ready The new package with its tasks must be declared in PyRAF To do this add the following lines near the end of your login cl file or in loginuser cl reset taxel4 your aXel 4 path taxe14 iraf task taxel4 pkg taxel4 taxel4 cl reset helpdb envget helpdb taxe14 lib helpdb mip The next time PyRAF is launched the package taxe14 should be available It can then be loaded as any other package by simply typing its name gt taxel4 The taXe14 software package was developed by the ACS group of the ST ECF It contains the new version 1 42 of the axe software Any questions regarding this software can be directed to mkuemmel eso org taxel4 taf2pet taxegps tdrz2pet tpet2spc tsex2gol taxecore taxeprep tdrzprep tpetcont tstamps taxedrizzle tback
38. ave been prepared the grism spectra now can be reduced by simply executing the High Level aXe Tasks Which set of High Level Tasks have to be used depends strongly on the reduction strategy chosen Table 3 1 gives an overview For the remainder of this section we present the various input files for a typical data set and list the necessary High Level Tasks for the different reduc tion scenarios The High Level Tasks are listed in the correct order in both the 3 3 EXECUTING THE HIGH LEVEL TASKS 31 interactive version as well as the version used in a python script 3 3 1 The Input Image List The Input Image List aXetest lis given in this example is for a data set con sisting of WFC images The Input Image List refers to the direct image listed in the third column There is one Input Object List for each of the two science extensions in the WFC data see Chapt 7 1 and Fig 7 1 for an explanation on chip number versus extension numbers in WFC images All files are ex pected to be located in the directory pointed to by the environment variable AXE_IMAGE_PATH see Chapt 5 1 aXetest lis j8qq50nkq_fl1t jsqqdipmq_flt jsqqd2ntq_flt jsqqloikq_flt j8qqiijug_flt j8qq11k0q_f1t j8qq12kgqg_f1t fits fits fits fits fits fits fits j8qq53nkq_2 j8qq54pmq_2 jSqq55ntq_2 jsqql6ikq_2 j8qqi7juq_2 j8qqi8k0q_2 j8qqi9kgq_2 cat j8qq53nkq_1 cat j8qq54pmq_i cat j8qq55ntq_1i cat j8qqi6ikq_1 cat j8qq17juq_
39. contamination values computed by the petcont task Pixel 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 Index Hi TA ACS 7 63 AF2PET 52 77 APERTURE 9 Aperture File 49 53 65 75 77 78 80 aXe mailing list 22 aXe support 23 aXe tasks 41 61 63 69 aXe test 22 aXe visualization 16 aXe webpage 8 16 19 27 64 aXe 1 4 25 aXe2web 16 75 AXECORE 26 43 AXEDRIZZLE 46 axedrizzle 26 41 47 AXEGPS 27 58 AXEPREP 13 26 41 BACKEST 51 Background 50 Background Estimate File 50 52 77 Background Pixel Extraction Table 14 52 background subtraction 27 BCOUNT 80 BEAM 9 49 51 53 56 62 65 66 BERROR 80 binned spectrum 55 80 calibrated spectrum 12 CAMERA 62 CCDTYPE 63 CFITSIO 7 19 71 82 compilation 20 computing time 39 configuration file 7 32 41 49 50 55 61 63 69 Configuration of aXe tasks 61 CONTAM 78 81 contamination file 81 CORNERS 76 COUNT 78 80 CURVE 76 direct image 41 49 62 66 DISP_ORDER 67 Dispersion Order 65 DIST 77 DLAMBDA 78 DLDIP 67 DLD1P_RANGE 67 DLDP 67 dmag 49 DQ 78 81 DQ_EXT 62 DQMASK 62 drizzle 14 26 46 64 Drizzle PrePare files 15 45 DRZ2PET 57 DRZKERNEL 64
40. ct the X and Y position of the direct object its Right Ascension and Declination a cut out image showing the direct object the spectrum stamp image showing the 2D spectrum a 1D extracted spectrum in counts and the same in flux units The user can set various keywords to influence the html output For example it is possible to sort the objects with respect to an object property such as magnitude or Right Ascension In order to facilitate the navigation within a data set an overview and an index page accompany the object pages The overview page contains for each object the basic information sequence number reference number X Y RA Dec and magnitude The index page includes a table with the ordered reference number of all objects Direct links from both the overview page and the index page guide to the corresponding locations of the objects in the object pages Figure 1 7 is a screenshot taken from Epoch 1 data of the HUDF HRC Paral lels survey and shows the line covering the object whose coadded 2D spectrum is shown in Fig 1 6d The webpages created by aXe2web are located at the preview webpages http www stecf org UDF epoch1 hre_udf html 1 9 Acknowledgement If the aXe software was helpful for your research work the following acknowl edgement would be appreciated 18 CHAPTER 1 DESCRIPTION Chapter 2 Installing aXe 2 1 Requirements The following are required to run aXe e STSDAS 3 2 http www stsci edu resources so
41. cted Spectra File see Chapt 7 10 The binning process is explained in more detail in Chapt 1 5 This task can be used simultaneously with both an Object Pixel Extraction Table and a Back ground Pixel Extraction Table in which case a background subtraction is per formed Care must be taken that both Object and Background Pixel Extraction Tables were created with the same Aperture File Additionally absolute flux calibration can be performed if the proper information is included in the Main Configuration File No time normalization or gain correction is applied to the data since aXe tasks require the input data to be in electron sec An exposure time is used only to compute the count noise level of the data if no error array is specified 4 11 1 Usage pet2spc grism config use_bpet do_flux drzpath oaf opet bpet out_spc 56 CHAPTER 4 AXE TASKS 4 11 2 Parameters grism name of the grism image config name of the aXe configuration file use_bpet use of a BPET file do_flux do flux calibration drzpath use AXE_DRIZZLE_PATH for IN Output oaf overwrite the default input Aperture File name opet overwrite the default input Object PET file name bpet overwrite the default input Background PET file name out_spc overwrite the default output SPC file name Example pet2spc grism test_grismn fits config SLIM conf test 0 use_bpet YES 4 11 3 Output If drzpath NO e AXE_OUTPUT_PATH slitless filename _ ext numb
42. cute gt cd gt python compileaXe py aXe 1 4 is now ready Declare the new package in PyRAF by adding the follow ing lines near the end of your login cl file or in loginuser cl reset taxel4 your aXel1 4 path taxe14 iraf task taxel4 pkg taxel4 taxel4 cl reset helpdb envget helpdb taxe14 lib helpdb mip The next time PyRAF is launched the package taxe14 is available It can be loaded with gt taxe14 from the PyRAF shell 2 4 Validating the aXe installation Test data with grism and prism images can can be obtained from our web site Un zip and un tar the test data file in a clean directory and follow the instructions given in the README file The grism test data consist of a set of science frames taken from the HUDF HRC Parallels program Figs 1 2 1 5 and 1 6 show some of the data products generated during the test reduction The prism test data was taken as part of the calibration proposal 10391 PI S S Larsen Reference spectra generated by running aXe 1 42 on the test data also sup plied as part of the test package If the output obtained by running aXe 1 42 on the test data is identical to these reference spectra the proper working of aXe 1 42 is assured 2 5 aXe Mailing List We have installed an aXe mailing list to keep users informed about new de velopments and updates concerning aXe To the subscribers the mailing list also offers the opportunity to share and discuss their experiences with
43. d stored in the PET This is done by storing for every pixel the so called contamination value which is the number of beams in which the pixels appears This value is 1 for a non contaminated pixel For the pixel in the small white areas on Fig 1 2 this value is 2 since only two beams overlap there In crowded or deep fields larger contamination values are also possible of course During the generation of 1D spectra those contamination values are processed exactly as the pixel values Therefore aXe assigns to each spectral point in the final 1D spectra an associated contamination value which marks the number of contaminations included in the spectral point 1 5 Generating 1D spectra The geometry required to convert the contents of the PET to a set of one dimensional spectra stored in the Extracted Spectra File SPC see Chapt 7 10 is shown in Figure 1 4 The method accounts for the geometrical rotation of the square pixel with respect to the spectral trace and appropriately projects each pixel onto the trace To do this we use a weighting function which is the fractional area of the pixel which when projected onto the trace falls within the bin points e and ea The flux contained in each BEAM pixel is weighted by this weighting function as it is projected onto separate bins o to 1 1 to and ez to ez in Figure 1 4 along the spectral trace The weight is computed by integrating over the length of the segments such a
44. 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 Ay P A ap a Ax ag Ax Az and P Az 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 polynomial parameters int n 1 float WIDTH the number of pixels to extract in the cross dispersion direc tion float ORIENT the orientation in degrees counter clockwise and with re spect to the x axis along which the extraction should proceed float 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 1 BEAM A REFPIXEL1A 500 000 100 000 CORNERS1A 490 79 650 87 650 127 490 119 CURVE1A 2 0 000e 00 3 490e 02 1 000e 04 WIDTH1A 18 200 ORIENTIA 90 000 IGNORE A O0 BEAM END BEAM B REFPIXEL1B 372 328 100 000 CORNERS1B 352 79 392 79 392 120 352 120 CURVE1B 2 0 000e 00 1 000e 9 2 00e 12 WIDTH1B 18 200 ORIENTIB 90 000 IGNORE1B O0 BEAM END APERTURE END 7 6 BACKGROUND ESTIMATE FILE 77 7 6 Background Estimate File This file BEF is a multiple extension FITS f
45. dited by the user and optimized for a given data set The core of the software package is written using ANSI C and Python http www python org and is highly portable from one platform to another aXe uses the third party libraries CFITSIO GSL and WCSLIB which have been used successfully under Linux Solaris and MacOS X aXe is distributed as part of the STSDAS software package Within STS DAS aXe is located under the subpackages hst_calib acs axe As a relatively young software project which is still under active development the changes and improvements introduced with new releases are quite large To give users the possibility to work always with the newest release we also distribute aXe on 7 8 CHAPTER 1 DESCRIPTION High Level Commands Low Level Commands sex2gol generate a grism object list GOL prepare fit files gol2af generate an aperture file AF for aXe axeprep backest compute the background reduce fully generate a pixel extraction table PET flatfielded PET s axecore petcont add contamination to PET apply flatfield to PET prepare PET s for drizzling drzprep drizzle PET s and extract axedrizzle spectra extract 1D spectra pet2spc stamps generate stamp image drz2pet generate PET for drizzled images axegps convert position to lambda Figure 1 1 The list of aXe tasks The arrows indicates the interaction between
46. duction process This removes the background signature from the images so that the remaining signal can be assumed to originate from the sources only and is extracted without further background correction in the aXe reduction The second strategy is to make a local estimate of the sky background for each BEAM by interpolating between the adjacent pixels on either side of the BEAM In this case an individual sky estimate is made for every BEAM in each science image 1 6 SKY BACKGROUND 13 Figure 1 5 Left Panel a The master sky for the HRC The holder for the coronograph results in the arm with low sensitivity at the top Right Panel b Background estimate for the grism image shown in Fig 1 2 with the object regions masked 1 6 1 Global Background Subtraction The homogeneous background of HST grism exposures makes the global back ground subtraction directly from the pipeline processed science images i e fit fits files feasible Master sky images for both the ACS Wide Field Chan nel WFC and the High Resolution Channel HRC are available from the aXe webpages at http www stecf org software aXe inndex html These mas ter sky images were created by combining several hundreds of WFC and HRC grism images from different science programs The object signatures on the science images were removed using several techniques including a two step me dian combination to derive a high signal to noise image of the sky background F
47. e BEAMs is set up to be a given number of times the width listed in the Grism Object List Two magnitudes cutoffs are set in the Configuration File Chapt 5 2 Sources which have magnitudes fainter than an extraction cutoff magnitude are flagged so that they are not extracted but will be accounted for when computing spectral contamination and the background estimates Sources which have magnitudes fainter than another cutoff magnitude are marked so that they will be completely ignored The dmag value can be used to globally adjust these to account for 50 CHAPTER 4 AXE TASKS a different signal to noise ratio in one dataset for example without having to resort to editing of the configuration file This task can be used to generate both an Object Aperture File and a Background Aperture File While these files have a similar format it is often desirable to use different Aperture Files for the two cases This is because the former is used to extract counts from pixels which are known to contain flux from the source while the latter can be thought to define a zone to avoid all source flux in the slitless image when computing the background level in the case that a master sky is not used for background subtraction see Chapt 1 6 In practice a larger extraction width multiplier should be used when generating the Background Aperture File so that all the object flux is properly isolated when generating a Background Estimate File Chapt 7 6 With o
48. e P_Y the absolute row coordinate of the pixel e X the relative column coordinate of the pixel with respect to the BEAM reference pixel REFPIXEL in Aperture File e Y the relative row coordinate of the pixel with respect to the BEAM reference pixel REFPIXEL in Aperture File e DIST the projected distance from the center of the pixel to the section point on the trace of the spectrum e XS abscissa of the section point relative to the BEAM reference pixel REFPIXEL in Aperture File e YS ordinate of the section point relative to the BEAM reference pixel REFPIXEL in Aperture File e DXS width of this pixel along the computed trace 78 CHAPTER 7 FILE FORMATS e XI path length of the section point relative to the BEAM reference pixel REFPIXEL in Aperture File along the trace e LAMBDA the average wavelength of the light collected by this pixel e DLAMBDA the wavelength range of the light collected by this pixel e COUNT the number of electron s in this pixel e ERROR the error estimate in electron s in this pixel e WEIGHT the extraction weight assigned to this pixel e 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 CONTAMEN implies that the pixel is present in N 1 BEAMs and that contamination
49. e string hreudf given as DRZROOT would result in the drizzled beams hrcudf ext _1D1 fits hrcudf_ext ID2 fits the OAF BAF hreudf_2 OAF BAF the configuration file hrcudf conf the list of drizzled images hrcudf_2 lis and the dummy image hreudf fits 5 2 CONFIGURATION FILES 65 BEAM configuration There must be a description for each of the BEAMs i e dispersion orders that one would like to extract BEAMs are named using single letter characters CA B OC etc for a maximum number of 26 BEAMs All pixel coordinates and offsets that appear in a BEAM description are in fact offsets from the reference pixel in the BEAM REFPIXEL in Aperture File The following is defined for each BEAM e Magnitude cutoffs e Trace description e Wavelength calibration description e Sensitivity Magnitude cutoffs e MMAG EXTRACT float The maximum magnitude listed in the input object catalog for this BEAM to be extracted during the extraction pro cess Objects fainter than this cutoff magnitude will not be extracted They will however be avoided when computing the background estimate and will be use to flag extracted spectra for contamination unless other wise determined by the MMAG_MARK parameter e MMAG_ MARK float Objects which have an input catalog magnitude greater than this will be completely ignored and not accounted for This BEAM will not be used at all for anything and will not be avoided w
50. e to zero see Chapt 1 6 1 New master sky images as well as the latest information concerning aXe in gen eral and also the background subtraction are posted on the aXe webpages at http www stecf org software aXe index html 3 1 5 aXegps A small but eventually very useful feature of aXe 1 4 is the task axegps see Chapt 4 14 for details This task prints the spectral properties of an individual pixel onto the screen The spectral properties are e g the wavelength at pixel center the dispersion the distance to the trace and the trace distance of the section point closest point on the trace Of course a unique spectral solution can only be derived with respect to a reference beam see Chapt 1 2 28 CHAPTER 3 USING AXE The task axegps assists the user to find important spectral features directly on the unprocessed and undrizzled flt frames On the other hand it is also pos sible to trace back from strange or suspicious features on extracted 1D spectra to the corresponding positions on the original unprocessed images 3 2 Preparing the aXe Reduction 3 2 1 Reduction Strategy Before actually preparing and performing the data reduction the user must de cide which data reduction strategy to follow The main decisions are whether aXedrizzle is used or not and whether the background subtraction is done glob ally with the master background or with a local background for each beam see Chapt 1 6 for a comparison of the two methods
51. elscale in cross dispersion direction are set in the aXe configuration file with the keywords DRZRESOLA and DRZSCALE respectively see Chapt 5 2 At present only the first order beams of images taken with the G800L grism can be drizzled Drizzling usually creates pixels with incomplete coverage at the borders of the drizzle images To avoid those pixels with their lower weight entering the 4 4 AXEDRIZZLE 47 1D extraction the extraction width used in the 1D extraction from the 2D drizzled grism images should be smaller than the extraction width used to gen erate the PETs in axecore The extraction width in multiples of the object fwhm for the 1D extraction must be specified with the parameter outfwhn while the parameter infwhm must be set to the value that was used in axecore to create the PET s and therefore the DPP s infwhm and outfwhm in the task axedrizzle therefore directly correspond in axecore to the parameters extrfwhm and drzfwhm respectively Then the task axedrizzle can recalcu late the extraction width for the 1D extraction Typical value pairs for infwhm outfwhm are 4 0 3 0 or 3 0 2 0 Note however that infwhm and outfwhm must have the same value as extrfwhm and drzfwhm in the task axecore re spectively A wrong value in axecore can not be corrected or changed in the task axedrizzle In addition to the 2D drizzled grism images axedrizzle creates all the necessary files to facilitate the extraction of the 1D
52. ensions 7 1 Input Images 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 CALACS processed ACS input files are multi extension fits files with the science error and data quality array s in its 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 extension 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 71 72 CHAPTER 7 FILE FORMATS primary header Figure 7 1 The naming methods to specify WFC fits extensions in the aXe configuration files named WFC CHIP1 conf and WFC CHIP2 conf are equivalent to the ones given before An aXe configuration file can target only one science array plus its associated error and da
53. er SPC fits If drzpath YES e AXE_DRIZZLE_PATH slitless filename ext number SPC fits 4 12 STAMP This task uses the content of a Pixel Extraction Table see Chapt 7 7 to gener ate a FITS Stamp Image File see Chapt 7 11 containing stamp images of the BEAMs that were extracted This task can output both regular stamp images and rectified stamp images of the BEAM where the spectra are plotted us ing the XI and DIST columns from the Pixel Extraction Table see Chapt 7 7 instead of the X and Y columns This allows one to quickly check that the extraction angle a See Figure 1 3 used to perform the extraction process was the desired one Because this task uses the content of a Pixel Extraction Table and not the original input slitless image it offers a good check of exactly which pixels were used during the extraction process 4 13 DRZ2PET 57 4 12 1 Usage stamp grism config rectified drzpath out_root 4 12 2 Parameters grism name of the grism image config name of the aXe configuration file rectified produces rectified stamp image following the direction of the trace drzpath use AXE_DRIZZLE_PATH for IN Output out_root overwrite the automatically generated path and rootname of the output stamp FITS images Example stamps grism test_grismn fits config SLIM conf test 0 rectified YES 4 12 3 Output If drzpath NO e AXE_OUTPUT_PATH slitless filename ext number STP fits
54. est tgol2af tpetff The message which appears during the loading of the package and the task overview indicate that everything went OK and that the tasks can be used from now on The package can be used by more than one user Other users only have to modify their login cl or loginuser cl as described above to access the aXel 4 package and the tasks within it provided that they have access to the installation directory aXe 1 4 was successfully built and tested under Red Hat Linux 9 and Solaris 2 8 It should be no problem to install aXe 1 4 under other Unix or Unix like operating systems such as HPUX or MacOSX 2 3 Installing from the aXe binary distributions Several distributions of aXe with compiled statically linked C tasks are available for download from the aXe web pages Download the source tarball aXel 42 taxel4src tar gz and then select and download the binary distribution which is appropriate for your platform After downloading the aXe source distribution move it to your preferred location your aXe1 4 path and unpack it there with gt gunzip aXel 42 taxel4src tar gz gt tar xvf aXel 42 taxel4src tar Then move the C binaries to their proper location and unpack them there 22 CHAPTER 2 INSTALLING AXE gt mv aXe1 42 lt arch gt bin tar gz taxe14 iraf bin gt cd taxel4 iraf bin gt gunzip aXe1 42 lt arch gt bin tar gz gt tar xvf aXe1 42 lt arch gt bin tar The Python code must still be compiled To do that exe
55. ext number SPC fits If drzfwhm gt 0 e AXE_OUTPUT PATH slitless filename drzfwhm _ ext number OAF this file is used to recompute the contamination in the PET s using the value specified in drzfwhm as extraction width 4 3 DRZPREP This task produces a set of Drizzle PrePare DPP files for a set of images given in an Input Image List A DPP file is a multi extension fits file with a pixel stamp image an error stamp image and a contamination stamp image for each first order beam in a grism image DRZPREP uses the PET file to derive the pixel error contamination values for the stamp images and the background aperture file BAFs to define a common geometry for the individual objects The need for a common geometry for all stamp images of a single object forces drzprep to be run always on the set of images which later are also coadded with axedrizzle If there is more than one set of PETs for each grism image as in the case of WFC data the configuration files should be given as a comma separated list in the parameter configs The task also derives and stores important keywords for axedrizzle In the Input Image List given with the parameter inlist the first item on each line must be the name of the grism image Further columns items are neglected by drzprep Therefore the file used as inlist in axecore and axeprep can be re used in drzprep again 4 3 1 Usage drzprep imagelist configs back 46 CHAPTER 4 AXE TASKS 4 3 2
56. extensions of the particular object in all DPP files e EXPT the exposure time map for the science extension 80 CHAPTER 7 FILE FORMATS e CON the contamination image drizzled from the contamination extension of the particular object in all DPP files e WHT the weight image for the science extension The weight extension is derived from the exposure time map in the task drz2pet see Chapt 4 13 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 PET 7 10 Extracted Spectra File 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 e N the number of rows in this spectrum e LAMBDA wavelength in A e TCOUNT total number of counts in e s in this wavelength bin e TERROR error in the total number of counts in e s in this wavelength bin 1 e COUNT background
57. files into the corresponding dq extension of the fit files 3 2 3 Input Object List The preparation of the Input Object List is one of the last steps before the actual reduction of the spectra with the High Level aXe Tasks starts The Input Object List see chapter 7 3 for the exact format can refer either to a direct image or to the grism image itself If the third column of the Input Image List see Chapt 7 1 used in the High Level Tasks is a string the entry is interpreted as the name of the direct image to which the Input Object List s 30 CHAPTER 3 USING AXE refer A missing third column or a number means that the Input Object List s refer to the grism image itself In the latter case the format for the Object List is more flexible and the values for the individual objects can be given either in image coordinates pixels or in global coordinates RA DEC If present the pixel coordinates are preferred to the global coordinates However with global coordinates it is possible to use appropriate cutouts from catalogues assembled independently of the grism data Since the requirements and premises of the aXe users concerning the targets and therefore Input Object Lists are quite diverse there exists no standard recipe on how to create an Input Object List We also do not offer an aXe task to perform that job A quite widespread scenario is that there exist a list of grism exposures and a basic object catalogue which comprises all
58. ftware_hardware stsdas e PyRAF 1 1 1 http www stsci edu resources software hardware pyraf To compile the C code you need e GNU CC 2 95 or later compiler e Gnu Scientific Libraries 1 x http sources redhat com gsl e WCStools 3 x libraries http tdc www harvard edu software westools e CFITSIO 2 x libraries http heasarc gsfe nasa gov docs software fitsio fitsio html 2 1 1 aXe Distribution aXe is distributed as part of the STSDAS software package However as a young software package aXe is still under rapid development and the current version distributed with STSDAS 3 3 is aXe 1 40 New aXe releases incorporate signifi cant improvements over previous versions but the release dates can not always be coordinated with new STSDAS releases We therefore offer the newest aXe 1 4 release for download on the aXe webpages at http www stecf org software aXe index html After the installation aXe 1 4 is loaded and used as the local package taxe14 within PyRAF The new aXe release has tasks with the same names as in previous releases but the implementation e g parameter settings of the tasks may have changed To keep the aXe tasks in your STSDAS distribution separate from the new aXe tasks downloaded from the aXe webpages the aXe tasks distributed via our webpage always start with the letter t For example the task tsex2gol in the 19 20 CHAPTER 2 INSTALLING AXE local taxe14 package corresponds to the task se
59. given in Sect 7 3 For the first two ways to specify object lists the image coordinates of the objects on the grism image will be recomputed using the WCS information of the grism image and the direct image This approach therefore relies on the accuracy of the WCS information given in those images Refer to section 7 3 for a description of what values should be in the the input catalog and which ones can be re constructed by SEX2GOL 4 6 GOL2AF 49 4 5 1 Usage sex2gol grism config in_sex use_direct direct dir_hdu spec_hdu out_sex 4 5 2 Parameters grism name of the grism image to be processed config name of the axe configuration file in_sex name of the object file use_direct boolean to indicate that the Input Object List refers to a direct image direct name of the direct image dir_hdu overwrites the science image extension specified in the configuration file spec_hdu overwrites the science grism prism image specified in the configuration file out_SEX overwrites the default output object catalog name Example sex2gol grism test_grismn fits config SLIM conf test 0 in_sex test_0 cat use_direct NO 4 5 3 Output e AXE_OUTPUT PATH slitless filename ext number cat 4 6 GOL2AF This task generates an Aperture File using an input Grism Object List and a valid configuration file which defines the length wavelength calibration global offsets between direct and slitless images The width of th
60. ground PETs made from drizzled background images Example drz2pet inlist aXedrizzle_2 lis conifgs axedrizzle conf back ND 4 133 Output If back NO e SAXE_DRIZZLE_PATH drizzle root filename _ ext number PET fits If back YES e SAXE_DRIZZLE PATH drizzle root filename ext number BCK PET fits 4 14 AXEGPS This task reports the spectral properties of a single pixel The spectral proper ties for individual pixels can only be assigned with respect to a reference point or reference beam axegps lists e the wavelength at pixel center e the dispersion at pixel center e the trace distance of the section point e the distance of the pixel center to the section point e the data value of the pixel The task axegps works on the OAF file The corresponding OAF file and the reference beam therein must therefore exist before axegps can give a result For numerical reasons a solution can only be guaranteed within the bounding box of the specified beam The extraction width as specified with the parameter extrfwhm in axecore or mfwhm in gol2af has an influence on the bounding box In the case that the desired information for the pixel of interest is not given 4 14 AXEGPS 59 a repetition of axecore or gol2af with a larger value of drzfwhm mfwhm may enlarge the bounding box sufficiently to get a result from axegps Even in case of failure the corner points which define the bounding box
61. hen computing the background estimate Trace description The following items apply to the BEAM The character A through Z should be substituted for e BEAM int int The extent of the spectrum in the row X direction with respect to the reference pixel of this BEAM The location of the reference pixel of this beam with respect to the direct image position is defined by the parameters XOFF and YOFF listed below The beam row extent is measured independently of the position angle and always along the column direction e DYDX_ORDER int The order of the polynomial Ay P Azx ao a1 Az ag Az Az and P Ax which determines the actual location of the trace of the spectrum in this BEAM See description of this process in Chapt 1 3 66 CHAPTER 5 CONFIGURATION OF AXE TASKS e DYDX_40 int For each of the orders n as specified by the DISPLORDER_A an entry of the form DYDX_ _n must exist This can be a field dependent representation as described above e XOFF float A pixel row offset between the reference pixel of this BEAM and the position of the object in the Direct Image This can be a field dependent representation as described below e YOFF float A pixel column offset between the reference pixel of this BEAM and the position of the object in the Direct Image This can be a field dependent representation as described below Note on Field Dependent Values Each co
62. igure 1 5a shows the HRC master sky image Scaling and subtraction of the master sky is done with the aXe task axeprep see Fig 1 1 Before scaling the master sky to the level of each science frame the object spectra are masked out on both the science and the master sky image When reducing a dataset consisting of many individual exposures it may be desirable to check the sky subtraction by co adding all the sky subtracted grism images e g with the MultiDrizzle task The co added image also provides a way to quickly assess the quality of the background subtraction Any deviations from zero in the mean background level of the combined image will also affect the spectra derived with the aXe reduction 14 CHAPTER 1 DESCRIPTION 1 6 2 Local Background Subtraction The second option for handling the sky background is to make a local estimate of the background for each object In this case aXe creates an individual background image for each object on the spectrum image On the background image the pixel values at the positions of the object beams are derived by interpolating in each column between the pixel values on both sides of the beam The number of pixels used in the interpolation as well as the degree of the interpolating polynomial can be chosen by the user Figure 1 5b shows the background image for the grism image displayed in Fig 1 2 The background images are then processed in much the same way as the science images resulting in
63. ile 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 4 7 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 7 7 Pixel Extraction Table 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 1 This file is generated by the af2pet see Chapt 4 8 task Each extension contains the following columns e N the number of pixels in this BEAM e P_X the absolute column coordinate of the pixel
64. ile 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 in list Each row lists a grism image and the additional filenames and information to reduce the grism image with aXe The columns list 1 grism image name mandatory 2 input object list 1 input object list 2 mandatory 3 direct image optional 4 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 4 6 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 jSqq5ipmg_flt fits j8qq54pmq_1 cat j8qq54pmq_2 cat j8qq54pmq_flt fits jsqqd2ntq_flt fits j8qq55ntq_1 cat j8qq55ntq_2 ca
65. ined see parameter mfwhm in gol2af norm boolean to switch on off the exposure time normalization histogram boolean to switch on of the display of an image histogram of the background subtracted image as a quality check Example axeprep inlist imlist lis configs conf1 conf conf2 conf back YES backims back1 fits back2 fits fwhm 2 0 norm YES histogram YES 4 2 AXECORE 43 4 2 AXECORE This aXe task combines the Low Level Tasks sex2gol gol2af af2pet petff petcont pet2spc and stamps and offers the possibility to make a complete aXe reduction based on the individual images in one task This also includes the reduction with background PETs set back YES The parameter list comprises all parameters for the individual tasks and as a consequence is rather long For most of the parameters the default value is appropriate so the actual number of parameters that will normally need to be edited by the user is quite modest In the listing below the axecore parameters are organised according to the low level aXe tasks they affect The Input Image List used in the task axeprep as inlist can be reused again in axecore perhaps extended with individual dmag values for the grism images The sequence of configuration files must correspond to the sequence of Input Object Lists and the sequence of background images in inlist see Fig 3 1 After drizzling beams onto the same deep 2D grism image
66. is applied to the images see Chapt 6 2 Moreover the field dependence of the grism spectra and the field dependent wavelength calibra tion are not taken into account in the combination process It is therefore not recommended to extract the spectra directly from the MultiDrizzle combined grism images It is also possible to use other programs to identify cosmic ray hits on the grism images Information on cosmics should be transported into the dq extension of 3 2 PREPARING THE AXE REDUCTION 29 ae aXedrizzle aXedrizzle aXedrizzle aXedrizzle master sky master sky master sky master sky 1 axeprep axeprep axeprep axeprep 2 axecore axecore axecore axecore 3 drzprep drzprep 4 axedrizzle axedrizzle 5 axedrizzle Table 3 1 The high level aXe tasks to be applied in the different reduction strategies the corresponding flt image aXe can exclude flagged pixels in the dq extention from the reduction In the dq extention cosmic ray affected pixels should be marked by adding the appropriate dq flag 4096 see ACS Data handbook to the original dq value Users with old versions of MultiDrizzle before STSDAS 3 3 will find mask files with the extension flt_sci _mask pl is a placeholder for the extension number In those mask files good pixels have the value 1 and cosmic ray affected one the value 0 Before starting the aXe reduction the user should transport the cosmic ray information from the mask
67. kground is finally subtracted from the grism image e exposure time normalization The input file is normalized by the exposure 41 42 CHAPTER 4 AXE TASKS time to transform the images into counts per second Every processing step can be switched on off independently by associated boolean parameters The file used by axeprep as inlist can be reused again in axecore drzprep and axedrizzle perhaps extended with individual dmag values for the grism images 4 1 1 Usage axeprep inlist configs back backims fwhm norm hist 4 1 2 Parameters inlist Input Image List which gives on each line a the name of the grism image to be processed mandatory b the object catalog s mandatory if back yes comma separated list if there is more than one catalogue c the direct image associated with the grism image optional configs name of the aXe configuration file If several image extensions are to be processed e g for WFC images one configuration file per extension must be given in a comma separated list background boolean to switch on off background subtraction backims name of the background image If several image extensions are to be processed e g for WFC images one background image per extension must be specified in a comma separated list fwhm real number to specify the extent as a multiple of A_IMAGE of the area which is masked out perpendicular to the trace of each object before the background level is determ
68. length of the pixel i j The values for Amaz and Amin are in the FITS header keywords WMIN and WMAX There are no hard limits on the number of extensions in this file i e on the order of the polynomial model The task petff is used to read this file compute and apply the flat field coefficient at each pixel contained in a Pixel Extraction Table This is done by dividing the pixel value by the computed flat field coefficient The structure of this file is shown in figure 6 1 Note that the first extension of this file 0 contains the constant term of the polynomial 69 70 CHAPTER 6 AXE CALIBRATION FILES 19 FITS image and FITS image Ni 3 FITS image SA 4h FITS image sth FITS image 6th FITS image Figure 6 1 The structure of the FITS flat field calibration file which is used by aXe to construct at each pixel coordinate i j a proper flat field coefficient FF i j v ao a1 ag ai x where x is a normalized value obtained with x A Amin Amaz Amin and A is the wavelength of the pixel i j Chapter 7 File Formats This chapter describes the file formats of the intermediate data products gen erated 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 ext
69. list aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf infwhm 4 0 outfwhm 3 0 back NO makespc YES iraf axedrizzle inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf infwhm 4 0 outfwhm 3 0 back YES makespc YES To execute the script in PyRAF the following command must be given in a PyRAF shell gt pyexecute aXedrizzle_bpet py 3 3 7 No aXedrizzle and Background PET This is the old reduction scheme before aXe 1 4 Both object and background spectra are extracted from each grism image individually The background subtraction is done by subtracting the background PET from the object PET pixel by pixel The command sequence is a subset of the command sequence given in the last example gt axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf backgr NO norm YES histogram YES gt axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back YES extrfwhm 4 0 drzfwhm 0 0 backfwhm 6 0 spectr YES rectified YES In a python script the same command sequence looks as follows noa Xedrizzle_bpet py import os string time from pyraf import iraf from iraf import axei4 stsdas iraf axeprep inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf 3 4 COMPUTING TIME REQUIREMENTS 39 backgr NO norm YES histogram YES iraf axecore inlist aXetest lis configs ACS WFC CHIP1 conf ACS WFC CHIP2 conf back
70. m value to specify the extraction width in gol2af drzfwhm mfwhm value to specify the extraction after axedrizzle backfwhm mfwhm value to specify the width of the background PET exclude switch off the listing of faint objects auto_orient enable automatic orientation for the extraction orient enable tilted extraction The following parameters apply to BACKEST np number of points for background estimation interp interpolation type for background determination 1 GLOBAL median 0 local median 1 linear fit 2 quadratic fit The following parameters apply to PET2SPC and STAMPS spectr enable the creation of SPCs and STPs for each of the grism files individually rectified enable the production of rectified stamp images Example axedrizzle inlist imlist lis configs conf1 conf2 back YES extrfwhm 4 0 backfwhm 5 0 exclude NO auto_orient YES np 10 interp 1 spectr YES 4 2 3 Output e AXE_OUTPUT PATH slitless filename ext number cat 4 3 DRZPREP 45 e AXE_OUTPUT PATH slitless filename _ ext number OAF e AXE_OUTPUT PATH slitless filename ext number PET fits If back YES e AXE_OUTPUT PATH slitless filename ext number BAF e SAXE_OUTPUT_PATH slitless filename _ ext number BCK fits e AXE_OUTPUT PATH slitless filename _lext number BCK PET fits If spectr YES e AXE_OUTPUT PATH slitless filename _ ext number STP fits e AXE_OUTPUT PATH slitless filename
71. may therefore be a problem e DQ the data quality of this pixel 7 8 The Drizzle Prepare File This file is a multi extension FITS file with the stamp images of all first order beams in a grism image For each BEAM there are three extensions in the DPP file e the data stamp image with the extension name BEAM _ aperture beam e g BEAM_117A e the error stamp image with the extension name ERR aperture beam e g ERR_117A e the contamination stamp image with the extension name CONT aperture beam e g CONT_117A The Drizzle Prepare File is created in the task drzprep In the task axedrizzle the science error and contamination images are extracted and driz zled to build for each object the various extensions of a 2D drizzled grism image 7 9 THE 2D DRIZZLED GRISM IMAGE 79 7 9 The 2D Drizzled Grism Image The 2D drizzled grism images are multi extension FITS file 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 _ext_ID object number fits e g testaXe_extID105 fits reflects the object number used in the Input Object Lists A 2D drizzled grism image created in axedrizzle has the extensions e SCI the science image drizzled from the science extensions of the partic ular object in all DPP files e ERR the error image drizzled from the error
72. nd maximum values for x ao which are allowed in the PET Thus pixels from the not valid branch can be excluded Sensitivity The absolute sensitivity calibration is handled by applying a sensitivity curve to the electron count rates at each wavelength e SENSITIVITY 4 string The name of a sensitivity FITS file If no sen sitivity is available this keyword can be set to None instead of a real filename 5 2 2 Example of a Main Configuration file See Chapter 3 3 3 Chapter 6 aXe Calibration Files The aXe tasks use several calibration files in addition to the information con tained in the Main Configuration File see Chapt 5 2 1 This section describes these files 6 1 Sensitivity Curve This file is a FITS binary table containing the three columns WAVELENGTH SENSITIVITY ERROR and listing the total system sensitivity in e s per erg cm s7 T as a function of wavelength in A The ERROR column should contain the estimated error in the SENSITIVITY in e s per erg cm s A Note this sensitivity curve should be per A and not per pixel 6 2 Flat field This file is a multiple extension FITS file containing a model of the wavelength dependence of the flat field for each pixel Each extension i of this file contains the nt polynomial coefficient of the relation f i j ao a xx tag 2 a x where x is a normalized value obtained with x A Amin Amar Amin and A is the wave
73. nel a shows one individual grism image with an object marked Panel b displays the stamp image for this object out of the grism image a Panel c shows the drizzled grism stamp image derived from a and the final coadded 2D spectrum for this object is given in panel d Panel d shows an image combined from 112 PETs with a total exposure time of 124 ksec In both panels b and c the holes resulting from the discarded cosmic ray flagged pixels are clearly visible 1 8 aXe Visualization A deep ACS WFC grism image can contain detectable spectra of hundreds to thousands of objects and visual checking of each spectrum is very tedious A quick look facility is highly desirable in order to find interesting objects e g high redshift galaxies SN etc which can be highlighted for further study or interactive spectrum extraction For this reason we developed aXe2web a tool which produces browsable web pages for fast and discerning examination of many hundreds of spectra Since aXe2web requires specific python modules it cannot be included in the STSDAS software package It is therefore distributed via the aXe webpage at http www stecf org software aXe index html in the aXe2html package 1 9 ACKNOWLEDGEMENT 17 aXe2web uses a standard aXe input catalogue and the aXe output files to pro duce an html summary containing a variety of information for each spectrum This includes a reference number magnitude in the magnitude system of the direct obje
74. nfiguration file parameter such as DLDPs DYDXs XOFF or YOFF can be followed by a single float value In this case this unique value is used for the entire image independently of position in the image The same parameter can also be followed by a series of 3 6 m 2 m 2 values in which case these define a 2D field dependent polynomial which is to be used at a given position x y of the image to actually compute the value of the parameter A field dependence of the parameters DLDPs DYDXs XOFF and YOFF can therefore be taken into account if it has been previously calibrated and the field dependence can be fitted by an m order 2D polynomial The 2D field dependent polynomials can be different for every parameter listed in the aXe Configuration File The 2D polynomials are by default taken to be with respect to pixel 0 0 but this behaviour can be changed by setting the parameters REFX and REFY to the appropriate values The REFX and REFY values are first subtracted from the x y coordinates of a pixel before computing values using the 2D field dependent polynomials The order of the coefficients should always be given as shown in the following few examples n 1 a0 n 2 a0 alx X a2xY n 3 a 0 al X a2 Y a3 X 7 a4 X Y ad5 Y n 4a0 al X a2 Y 03x X 04 Xx Y a5bx Y a6x X34 a7 x X xY 08x r Xx Y 09 1 Y where X x REFX and Y y Y REF Note that the set of DLDPs and DYDXs parameters are themselves individual par
75. nt shapes of the marked regions For each beam the description of the spectral trace and the wavelength description is set up and the spectral reduction is done independently 1 4 Pixel Extraction Tables PET An important step in the aXe reduction process is the generation of the so called Pixel Extraction Table PET A PET is a multi extension fits table which stores in each extension the complete spectral description of all pixels of one beam Figure 1 3 illustrates the geometry in a beam and shows various quantities stored in the PET Important pixel information stored in the PET is e the section point defined as the point where the spectral trace intersects a line drawn through the center of the pixel along the extraction direction e the distance to the section point dij 1 5 GENERATING 1D SPECTRA 11 e the trace distance X j of the pixel which is equal to the trace distance of the section point e the wavelength attributed to the pixel derived by inserting the trace dis tance into the dispersion function stored in the configuration file The PETs are read and manipulated by many aXe tasks For example a flat field correction is applied on the pixel values stored in the PETs Since flat fielding is a wavelength dependent operation the assignment of a wavelength to each pixel is required before the correction values derived from a 3D flatfield cube see 6 2 are applied Also the contamination for each pixel is determined an
76. r DQMASK must be set to 8192 16 8208 To flag all non zero values in the data quality array DQMASK must be set to 16383 EXPTIME string or float If set to a string this keyword defines which FITS header keyword will be read in the data array FITS extension in order to define the exposure time of the data If set to a float then this value is used instead If not defined in the configuration file the exposure time is taken to be 1 0s The exposure time is ONLY used to determine the electron noise level it is NOT applied to the input data which is assumed to be in electrons s optional GAIN string or float If set to a string this keyword defines which FITS header keyword will be read in the data array FITS extension in order to define the gain of the data If set to a float then this value is used instead If not defined in the configuration file the gain is taken to be 1 0 This value is only applied to compute proper electron noise of the data and is in no way applied to the input data which is required to be in electrons s optional FFNAME string The name of the configuration file containing the FITS data cube containing the flat field model OPTKEY1 string The name of a keyword to read in the FITS headers to identify the proper extension to read e g CCDTYPE OPTVAL1 string The value that the FITS header keyword defined by OPTKEY1 must have in order to be selected e g 1 The OPTKEY1 OPTVALI pair allow
77. rient YES GOL2AF extracts the beams with an extraction an gle parallel to the semi major axis of the object orient NO forces a vertical extraction perpendicular to the spectral trace of the beam For orient YES and auto_orient YES however GOL2AF adjusts the extraction angle when the desired extraction angle forms too small an angle with the spectral trace la lt 35 Then the extraction angle follows the semi minor axis instead of the semi major axis of the object which results in more pixels being extracted from the slitless image 4 6 1 Usage gol2af grism config mfwhm dmag back auto_orient orient exclude sci_hdu out_af in_gol 4 6 2 Parameters grism name of the grism image config name of the aXe configuration file mfwhm the extraction width multiplicative factor dmag a number to add to the MMAG_EXTRACT and MMAG_MARK values given in the configuration file back to generate a BAF instead of an OAF file orient boolean to switch on off tilted extraction auto_orient boolean to switch on off automatic orientation for the tilted extraction exclude boolean to switch on the removal of faint objects in the result 4 7 BACKEST l out_af overwrites the default output aper filename in_gol overwrites the default input catalog name Example gol2af grims test_grismn fits config SLIM conf test 0 mfwhm 4 0 back YES 4 6 3 Output If back NO e AXE_OUTPUT
78. rism test_grismn fits config SLIM conf test 0 back YES 4 8 3 Output If back NO e AXE_OUTPUT PATH slitless filename ext number PET fits If back YES e AXE_OUTPUT PATH slitless filename ext number BCK PET fits 4 9 PETCONT This task checks whether each pixel listed in each of the BEAMs in a Pixel Extraction Table is a member of more than one of the BEAMs listed in an Aperture File If it is then it is flagged with the number of BEAMs to which this pixel is a member i e a pixel known to not be contaminated by one other aperture is assigned a value of 1 If a pixel is a member of two separate beams i e is in a region where two beams overlap it is assigned a value of 2 and so on A pixel which is not a member of any known beam is assigned a value of 0 If no contamination was computed a value of 1 is assigned by default The right panel of Fig 1 2 is a contamination image which carries the basic information about contamination 4 9 1 Usage petcont grism config cont_map 4 9 2 Parameters grism name of the grism image 54 CHAPTER 4 AXE TASKS config name of the aXe configuration file cont_map write the contamination map into a FITS file Example petcont grism test_grismn fits config SLIM conf test 0 cont_map YES 4 9 3 Output e Updates SAXE_OUTPUT_PATH slitless filename ext number PET fits e SAXE_OUTPUT_PATH slitless filename _ ext number CONT fits 4
79. rs from earlier aXe releases 1 2 or 1 3 in several ways and users who are familiar with previous versions of aXe should be prepared that it may take some time to familiarise themselves with the new look and feel of aXe 1 4 We believe however that the benefits of the new features in aXe by far outweigh the inconvenience of having to learn new tasks In this chapter we present and explain the new features and philosophies that come along with aXe 1 4 3 1 1 Python PyRAF Some of the aXe tasks are now written in Python an interpreted interactive object oriented programming language see http www python org One of 25 26 CHAPTER 3 USING AXE the main reasons for this change was the implementation of the aXedrizzle technique described in Chapt 3 1 3 In Python IRAF commands can be called directly through their PyRAF interfaces and it is therefore easy to use the standard IRAF implementation of drizzle within aXedrizzle The easy access to the standard IRAF tasks also allowed the implementation of the task axeprep which extends aXe to perform some preparatory steps for which users had been required to write their own scripts in previous versions of aXe aXe 1 4 is closely tied to PyRAF the new command language for running IRAF tasks see http www stsci edu resources software_hardware pyraf The aXe versions which are distributed independently of STSDAS see Chapt 2 1 1 also include PyRAF frontends and the normal procedure
80. s l e shown in Figure 1 4 The length of these segments is nonzero from x to x3 reaches a maximum value of 1 sin a and rises and decreases linearly such that it can be described by m x xo if o lt lt zr l a lmaz if T lt T lt T2 m z3 zx ifz2 lt z lt T3 0 otherwise where m lmaz 1 Lo Integration over this function l x to compute w eo 1 w 1 2 and w ez 3 is trivial once one has computed Zo 3 which may be derived from simple trigonometry 12 CHAPTER 1 DESCRIPTION Figure 1 4 How a one dimensional spectrum is created using information from the Pixel Extraction Table see Chapt 7 7 Each pixel in the table is projected onto the trace into separate wavelength bins The number count of each pixel is weighted by the fractional area of that pixel which falls onto a particular bin Once the one dimensional spectra have been generated the final step of flux calibrating can be performed by applying a known sensitivity curve for the observing mode which was used The output product of the aXe extraction process is a FITS binary table containing the set of extracted and calibrated spectra Extracted Spectra File see Chapt 7 10 1 6 Sky Background aXe has two different strategies for removal of the sky background from the spectra The first strategy is to perform a global subtraction of a scaled master sky frame from each input spectrum image at the beginning of the re
81. sensitivity New 1st order dispersion solution and sensitivity New 2nd order dispersion solution and sensitivity New 3rd order dispersion solution and sensitivity SCIENCE_EXT SCI Science extension DQ_EXT DQ DQ extension ERRORS_EXT ERR Error extension OPTKEY1 CCDCHIP OPTVAL1 2 FFNAME WFC flat cube CH2 2 fits DQMASK 16383 DRZRESOLA 40 0 DRZSCALE 0 05 DRZLAMBO 4770 0 DRZXINI 15 0 DRZROOT aXetest First order BEAM A BEAMA 30 160 MMAG_EXTRACT_A 30 0 MMAG_MARK_A 30 0 Trace description ist order DYDX_ORDER_A 1 DYDX_A_0 000 DYDX_A_1 0 0246422 9 28567e 7 5 49754e 6 9 18057e 11 6 21825e 11 9 56794e 11 X and Y offsets XOFF_A O YOFF_A 0 143255 0 00034143 0 000163423 2 52541e 8 1 3043e 7 3 49966e 9 Dispersion solution 2nd order DISP_ORDER_A 2 DLDP_A_O 4786 13 0 0399595 0 0136488 0 0000103637 1 39952e 6 3 20763e 6 DLDP_A_1 39 2815 0 00152543 0 00156261 3 81861e 8 8 88458e 8 1 02802e 7 DLDP_A_2 0 00880236 8 28624e 7 1 68916e 6 2 0178e 10 6 50773e 11 5 05835e 10 SENSITIVITY_A ACS WFC 1st sens 5 fits As can be seen from the two keywords OPTKEY1 and OPTVAL1 the two configuration files ACS WFC CHIP1 conf and ACS WFC CHIP2 conf give the trace description and spectral description for chip 1 and 2 respectively The location of the configuration files also the flatfield sensitivity files and master sky images is the directory pointed to by the environment variable AXE_CONFIG_PAT
82. sm spectra is probably the most significant addition in aXe 1 4 This is the first implementation of the drizzle code to combine spectral data but the overall methodology presented here can in principle also be applied in other reduction packages for spectral data While the main advantages of aXedrizzle were discussed in Chapt 1 7 a more elaborate discussion of various practical issues is given below The use of drizzle in aXe makes the application of non trivial weights in the extraction of 1D spectra necessary The masking of bad pixels or cosmic ray affected pixels and the incomplete coverage of object beams on individual 3 1 AXE 1 4 27 grism images can result in a very inhomogeneous distribution of exposure times and therefore signal to noise ratio across the 2D drizzled grism images To compensate for the variations in the signal to noise ratio a weight is assigned to each pixel and during the extraction of the 1D spectra the weights are taken into account Within each set of pixels that is coadded to a final 1D spectral element the value assigned to an individual pixel weight is proportional to its relative exposure time see note on page 79 While the use of weights for now is a necessity caused by the irregular coverage of the total field of view this first application opens the door for the implementation of more refined weighting schemes such as optimal extraction in future aXe releases To extract the final 1D spectra from
83. subtracted number of counts in es in this wave length bin e ERROR error in the background subtracted number of counts in es in this wavelength bin e BCOUNT estimate of the number of electron s contributed from the background in this wavelength bin e BERROR error in the estimate of the number of counts in e s con tributed from the background in this wavelength bin e FLUX background subtracted flux in erg cm s A in this wavelength bin e FERROR error in the background subtracted flux in erg cm s7 AT in this wavelength bin e WEIGHT number of pixels binned together into this wavelength bin 7 11 STAMP IMAGE FILE 81 e CONTAM set to 1 0 1 n to give the number of source this bin is contam inated with The value 0 means no contamination if the contamination was not recored every bin has the value 1 e 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 7 11 Stamp Image File 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 This file is generated by the stamp task 7 12 Contamination File This file CONT is a simple FITS image containing the
84. t j8qq55ntq_flt fits j8qqi0ikq_flt fits j8qqi6ikq_1 cat j8qqi6ikgq_2 cat j8qqi6ikq_flt fits j8qq1ijug_f1t fits j8qqi7juq_1 cat j8qqi7jug_2 cat j8qqi7jug_flt fits j8qq11k0q_f1t fits j8qqi8k0q_1 cat j8qqi8k0q_2 cat j8qqi8k0q_flt fits jsqal2kgq_flt fits j8qqi9kgq_1 cat j8qqi9kgq_2 cat j8qqi9kgq_flt fits 7 3 Input Object List 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 image if a filter instead of the G800L grism would have been used The aXe task sex2gol uses the Input Object List plus further image 0 2 0 15 0 4 74 CHAPTER 7 FILE FORMATS information to generate a Grism Object List which contains all the necessary grism image coordinates of the objects There exist three different formats for the Input Object List which allows sex2gol to generate a Grism Object List 1 The Input Object List refers to a direct image The name of the direct image is given in sex2gol with the parameter use_direct set to YES In this case the Input Object List must contain the following lines NUMBER X_IMAGE Y_IMAGE A_IMAGE B_IMAGE THETA_IMAGE X_WORLD Y_WORLD A_WORLD B_WORLD THETA_WORLD MAG_AUTO Values in X_IMAGE Y_I
85. ta quality arrays For WFC images the data from its two chips is stored in separate extensions To fully process WFC images in aXe two pro cessing runs with two different configuration files have to be undertaken With the fits extension numbers WFC extensions can be uniquely specified using the scheme given above In case that extension names are used additional informa tion must be provided since there exist e g two extensions with the extension name SCT In the aXe configuration file this additional information is the chip number which is specified using the keywords OPTKEY1 and OPTVAL For WFC 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 the ACS Data Handbook at http www stsci edu hst acs documents handbooks DataHandbookv2 ACS_longdhbcover html 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 7 1 clari fies 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 3 3 3 also show how the different extensions in the WFC must be addressed 7 2 INPUT IMAGE LIST 73 7 2 Input Image List The Input Image List is a flexible f
86. task Every first order beam in a PET is converted to a stamp image stored as an extension in a DPP The drzprep task also computes the transformation coefficients which are required to drizzle the single stamp images of each object onto a single deep combined 2D spectral image These transformation coefficients are computed such that the combined drizzle image resembles an ideal long slit spectrum with the dispersion direction parallel to the x axis and cross dispersion direction parallel to the y axis The wavelength scale and the pixel scale in the cross dispersion direction can be set by the user with keyword settings in the aXe Configuration File To finally extract the 1D spectrum from the deep 2D spectral image aXe uses an automatically created adapted configuration file that takes into account the 16 CHAPTER 1 DESCRIPTION F axezwen MOZA Build 1D 2UUs11Z5U5 File Cdi view Go Dco lt msrks Tools Mindew Lelp Debug QA 4 a ES E u 8 2 Http Anne steet nrg ID ep or ht aie mare Ap Home 4 vskm ats Figure 1 7 Part of a webpage created by aXe2web The coadded 2D spectrum of the object shown here is displayed in Fig 1 6d modified spectrum of the drizzled images i e orthogonal wavelength and cross dispersion and the pixel and arcsec pixel scales A detailed discussion of the drizzling used in aXe is given in ST ECF Newslet ter 36 p 10 Figure 1 6 illustrates the aXedrizzle process for one object Pa
87. tenv AXE_CONFIG_PATH path to the axe config Using bash 61 62 CHAPTER 5 CONFIGURATION OF AXE TASKS export AXE_IMAGE_PATH path to my data export AXE_OUTPUT_PATH output directory export AXE_DRIZZLE_PATH drizzle directory export AXE_CONFIG_PATH path to the axe config 5 2 Configuration Files 5 2 1 Main Configuration File Many configuration parameters are read in by the aXe tasks from a single text file which serves as the primary means to configure the extraction process for a given mode of an instrument A separate Main Configuration File should be created for each of the spectral modes of each of instruments with which aXe tasks are to be used This configuration file contains a basic geometrical description of where in the slitless image one would expect a given BEAM to be located relative to the position of the source object in a direct image The character can be used to add comments to this file General description of the format of the input data location of the science error and data quality arrays is also included in this file General configuration The following keywords in the Main Configuration file are used to define several parameters such as which extension of the input FITS images contain the data which keywords should be used to determine the exposure time of the input data etc e INSTRUMENT string The name of the instrument to which this config uration file applies optional e CAM
88. the extraction width used then to make the 1D spectra must be smaller than the extraction width used in axecore to create the PET s see Chapt 4 4 The contamination stored in the PET s created in axecore however must reflect the contamination for beam extentions according to the extraction width in axedrizzle in order to derive a consistent result for the object contamination If it is planned to use axedrizzle the extraction width in axedrizzle must be specified in the parameter drzfwhm Then new aperture files and a new contamination for the PET s is computed using the extraction width specified therein In case axedrizzle is not be used then this parameter should be set to 0 0 4 2 1 Usage axecore inlist configs back extrfwhm backfwhm exclude auto_orient orient np interp spectr rectified 4 2 2 Parameters inlist Input Image List which gives on each line a the name of the grism image to be processed mandatory b the object catalog s mandatory c the direct image associated with the grism image optional d dmag value see GOL2AF for the grism image optional 44 CHAPTER 4 AXE TASKS configs name of the axe configuration file If several image extensions are to be processed e g for WFC images one configuration file per extension must be given in a comma separated list back Boolean to switch on off the creation of a background PET with mfwhm backfwhm The following parameters apply to GOL2AF extrfwhm mfwh
89. there is to install aXe as a local PyRAF package rather than running the aXe tasks as separate Unix commands as in previous aXe versions This also makes it straight forward to integrate aXe tasks into IRAF PyRAF scripts aXe tasks no longer have to be applied in external shell scripts but can become an integral part of any data reduction scheme implemented in IRAF PyRAF 3 1 2 High Level Tasks Until aXe 1 3 all aXe tasks performed only a single reduction step on an indi vidual spectrum image The task sex2gol creates a Grism Object List for one grism image Then the task gol2af generates an Aperture File for that grism image af2pet produces a Pixel Extraction Table for that grism image and so on aXe 1 4 introduces a new class of High Level Tasks The High Level Tasks work on Input Image Lists and are designed to perform a reduction step on an entire data set To work on the individual images the High Level Tasks often employ the old Low Level Tasks of aXe see Fig 1 1 Each High Level Task combines several reduction steps e g the whole aXe 1 3 reduction is now executed within the High Level Task axecore This strat egy keeps the number of tasks which the user actually has to use and understand low Although the capabilities of the aXe software have been greatly extended in aXe 1 4 only four High Level Tasks are required to perform a full reduction of a set of ACS grism images with aXe 1 4 3 1 3 aXedrizzle The drizzling of gri
90. x2gol in STSDAS taf2pet in taxe14 corresponds to af2pet in STSDAS and so on While this manual describes aXe 1 42 and the aXe 1 42 tasks distributed via aXe webpages with a t as prefix the tasks are named with the non prefix version throughout the manual If you work with aXe 1 42 tasks don t forget to put a t in front of every command you find in the manual Otherwise you may still use the old aXe 1 40 or even aXe 1 3 equivalent with a different syntax and different behaviour 2 2 Installing from the aXe source distribution After downloading the aXe 1 4 tarball http www stecf org software aXe taxel4_download php move it to the in stallation directory your aXe1 4 path and unpack it there with gt gunzip aXe1 42 taxel4src tar gz gt tar xvf aXel 42 taxei4src tar aXe 1 4 consists of a part written in ANSI C and a second part written in Python www python org For the C part a configure script is included with aXe To configure and then compile the C tasks do the following gt cd taxel4 ccc gt configure For MacsOSX the option build powerpc must be added to the configure command If some libraries used by aXe are not installed in the usual places online parameters must be used to tell the configure script where to find them For example configure with cfitsio prefix your_axelibs cfitsio with gsl prefix your_axelibs gs1l 1 0 with wcstools prefix your_axelibs wcstools 3 0 4 specifies explicitly the loc
91. y from the coadded images by invoking the appropriate tasks Example axedrizzle inlist axegrism lis configs HUDF HRC conf infwhm 4 0 outfwhm 3 0 back NO makespc YES 4 4 3 Output If BACK NO then for an input name drizzle root filename _2 list e AXE_CONFIG_PATH drizzle root filename conf e SAXE_DRIZZLE_PATH drizzle root filename _2 0AF e SAXE _DRIZZLE PATH drizzle root filename TD num fits If BACK YES then for an input name drizzle root filename _2 BCK list e SAXE_CONFIG_PATH drizzle root filename conf e SAXE_DRIZZLE_PATH drizzle root filename _2 BAF e AXE DRIZZLE PATH drizzle root filename TD num BCK fits If makespc YES e SAXE_DRIZZLE_PATH drizzle root filename _2 SPC fits e SAXE_DRIZZLE_PATH drizzle root filename _2 STP fits 4 5 SEX2GOL This task generates a Grism Object List file using an Input Object List as input There are three different kinds of Input Object List that can be fed into aXe e an Input Object List in SExtractor format of objects on a direct image covering roughly the same field as the grism image e an Input Object List in SExtractor format which gives the objects on the grism image in world coordinates RA Dec and theta_sky e an Input Object List in SExtractor format which lists the objects on the grism image in world coordinates and image coordinates x image y image and theta_image A thorough description of the Input Object List is
92. y each task A detailed description of all the output products can be found in Chapt 7 The aXe tasks use Environment Variables see Chapt 5 1 to define the locations of the direct and slitless images In addition all tasks are meant to work on specific FITS extensions in the input images and the output products of each aXe task reflect this by having a _ where is an extension number appended to the original FITS file name e g a grism 1 SPC fits file will be produced if the input slitless FITS file was named grism fits and if the science data of interest was located in extension 1 Selection of the extension to extract is defined in the configuration file Chapt 5 2 1 4 1 AXEPREP This task prepares the science files e g ACS flt files produced by the on the fly pipeline or the calacs task for further processing within aXe axeprep provides important keywords and is mandatory if axedrizzle is to be used later on axeprep provides two different processing steps e background subtraction Provided that an Input Object List is given for the grism image axeprep uses the tasks sex2gol gol2af and backest to mark the beam areas on the grism image as well as on the master background image Using the iraf task imstat with 3 times clipping sources gt 30 the median pixel values are derived for the unmarked pixels on both the grism image and on the master background image The scaled to the level of the grism image master bac

aXe User Manual version 1.42

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