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CUBISM User Manual

1. 5 4 8 Saving the Background List The background list can be saved to a text bp file using Background gt Save Background Rec s While not strictly necessary this is a useful record of the background records for future reference in other cubes The format is list of unique record IDs DCEID which do not change with updated pipeline processing 5 5 Bad Pixels Hot rogue or bad pixels occur in IRS data with a broad range of intensities and they vary in position and frequency on the array on scales of hours to months Over time damage to the IRS arrays from solar particles has increased the number of these pixels in particular on the two long wavelength arrays Such pixels dominates the noise properties of spectral cubes maps and extracted spectra and if left untreated severely degrade the quality of assembled cubes Cleaning a cube of bad pixels is typically an iterative task mark pixels re build the cube inspect the cube for anomalous spectral or spatial features mark additional pixels etc CUBISM contains a variety of tools for identifying and flagging such pixels which are then ignored when assembling the cube Bad pixels can be identified either manually or automatically or a combination of both As discussed in Section 5 4 Backgrounds page 46 subtracting a background record built from data obtained nearby in time with the same record exposure time can mitigate many rogue pixels which can be
2. 0 02 eee eee 37 AAS AA Pixel Taple Fool cene pct ened ae ered 38 4 4 3 15 Order Mask Tool 2 0 c cece eee eens 38 4 4 3 16 Compass Rose Tool 000 cece eee ee eee 38 AAA COWEDAE 2 55 E Pc ea 38 4 4 5 Status Display Lines 4 20 00 0s des coud e Re sten 38 4 4 6 Bad Pixel Codes 0 cece cece eee eee e AE 38 4 4 7 Image Info Block 0 c cece eee ees 39 4 4 8 WAVSAMP Parme du ed gint bac Er e RE ARR 39 4 QubeSpecz ascendere ee E ach batteh adipatins UR Red nares i 40 ASA Tale BarziciloSeeueeteeteerkte RD Rex DOE ubt e RO e PUE 40 ABD MOTUS PT 41 ASAT RuleMehtas esee EUER Deere EHE EE E 41 4 5 2 2 Maps Ment err RR E RRRRRRR RR OCA 41 4 5 9 JBUULOTS a icseceies eco em y hd rene ne E EY Ee on LR RR ee n 42 4 5 4 Display Panes iere RARE HERE PER Pene 43 4 6 CubeSpec Plot Window 0c cece cece eee eens 43 Cube Assembly sss 44 DL Input Piles eset ue pe e rEPRREPEQeUS OPE n Rp 44 5 2 Build Orde eR EEEE S Cenia R UN ERA gd Ip ge NR ae 45 5 3 Calibration Sets ccetece e Re ERI LODS XR ER rE 46 DA Backgrounds eerie eR Opp RR bera crede Rae RE 46 52b In Situ Background LER RAE Rc AEAEE Rune 4T 5 4 2 Archive Background 0 e cece cee eee eee 47 5 4 3 Background Blend esee bee tese kenn 48 5 44 ID Sky Spectrum ekecesance ua tee eR RR ERR en 48 5 4 5 Combined 1D and 2D B
3. Cubism Manual Load the PDF CUBISM manual Chapter 4 The Tools 20 4 3 3 Data Records A CUBISM projects holds all of the data records often called simply BCDs see below necessary for building a given cube The records either include the data directly or hold a file reference to the data on disk which is loaded on demand In Figure 4 3 two records have been selected In addition to the spectrum data frame each record holds optionally the associated uncertainty frame and the BMASK pixel mask frame 4 3 3 1 Record Info A variety of information is shown for each record and the records can be sorted by individual columns clicking on the column s header The information recorded is ID A hopefully unique ID formed from filename Exp The BCD exposure time in seconds from the headers Observed The date and time the BCD observation GMT Added The date and time this data record was added to the project local time zone Type The type of the record encoded as tMMO_pos with e t The type of data record d for DROOPRES c for COADD f for FLATAP or blank for the by far most common BCD see Section 4 3 3 3 Record Data Types page 21 e MM The module SL SH LL or LH e 0 The targeted order 1 2 or blank for high res or full slit low res e g LLBoth targeting e pos The position within the slit which was targeted cen the slit center a no
4. BackTrackingngc 194SLll Figure 4 8 The backtracking window of CubeView showing contribution from 6 pixels among 2 BCD records to the cube pixel one of which is flagged as a bad pixel The pixel backtracking tool is an advanced cube analysis and verification tool It is enabled only when viewing a single plane of a spectral cube For the pixel under the cursor it displays a list of all the input BCD pixel fragments which contributed to that cube pixel and simultaneously highlights the contributing records in the associated CUBISM Project window The more pixel redundancy built into your map the greater the number of records and record pixels which contributed to a given cube pixel also cubes from the high resolution modules typically have more since there is also overlap among the multiple high res orders The information displayed includes the record ID the pixel within that record and the fractional contribution to the cube pixel being backtracked It also lists the value of the BCD pixel with uncertainty if available the value of the background and the Val BG Chapter 4 The Tools 34 difference At right is any BMASK flag with the same notation as the status line see Section 4 4 5 CubeView Status Display Line page 38 augmented by the flags BP or BP 1 for global and record level bad pixels see Section 5 5 1 Global and Record Level Bad Pixels page 51 Simply turn the tool on and mouse ar
5. Linear Scale image linearly between the clipping limits Square Root Scale image as the square root between the clipping limits Chapter 4 The Tools 24 Logarithmic Scale image logarithmically between the clipping limits Histogram Equalization Scale image between the clipping limits to generate a flat final color histogram Trim 1 5 Before scaling first trim 1 5 from the distribution of pixel values being scaled full image or histogram box Set Scale Range Explicitly set and lock the low and high scale clipping limits Freeze Scaling Lock Unlock the low and high scale clipping limits at their current value This can also be done with SPACE Set Size 256 384 512 768 Set the size of the display image to this width These four sizes can also be selected with 1 4 Wrap Enlarge the display image size to show the entire image at the current zoom up to the size of the monitor This can be selected with 0 4 4 2 3 Tools Menu The tools menu provides an alternative means of selecting among the viewer tools in the tool palette at the top of the CubeView viewer window See Section 4 4 3 CubeView Tools page 24 4 4 3 CubeView Tools The viewer offers a number of individual tools for interacting with the data some of which are generic and always available and others of which are specific to certain data types The tools are accessible via the palette through keyboard shortcuts and via the Tools menu
6. and in the CUBISM Project e g arrow keys to change the record selection RETURN to view it Arrows move the active item and can be accelerated by holding SHIFT or CONTROL SHIFT See Chapter 4 The Tools page 9 for more information and Section 7 1 Mouse and Keyboard Shortcuts page 66 for a handy table 7 Use multiple viewers This allows you to simultaneously scrutinize BCD records the built cube and an AOR visualization image Using color maps to theme them allows viewing data from multiple projects without confusion 8 Use the AOR visualizer to examine in situ backgrounds This lets you quickly check for source contamination ideally using 8 or 24 micron Spitzer image Since the selected records are indicated in white in the AOR visual ization and viewing the background selects the background records it s easy to get a quick view of where the background is being drawn from See Section 4 4 3 13 AOR Visualization Tool page 37 for more 7 3 Troubleshooting Commonly encountered problems and their solutions 1 I get the message Couldn t restore data from file By default to save space CUBISM does not save the BCD and associated data itself in the cpj project file instead recording a file path reference to the files If you ve Chapter 7 Tips and Troubleshooting 71 since moved or modified the BCD files or are loading the project on another system where they are in a different location yo
7. in general extraction apertures recovered from other slits or spectral maps executed at different times will not align with the rows or columns of the cube The aligned apertures are clipped against the cube to generate the partial pixel weighted average over the region The same is true for polygonal and circular apertures which are converted to polygons Regions in DS9 can be defined on any image with valid coordinates which can be useful for extracting areas based on additional information e g an X ray hot spot etc N DS9 REGIONS Only a very specific subset of DS9 region files is supported circles and poly gons of any length The output file format must be set to DS9 WCS coor dinates J2000 FK5 In addition only one polygon or circle per region file is read the first All other region information is quietly ignored Note that self intersecting polygons create multiple polygons in a region file all but the first of which will be quietly ignored Attempting to read any other type of DS9 generated region file will result in an error See DS9 s Region menu and documentation A The name of the file from which the aperture was loaded appears at the top of the CubeSpec window The new spectrum can now be saved in the same manner as described above and its header will contain the file from which its extraction region was drawn Matched extraction can be used to extract Long Low spectra using a region defined in
8. BCD and an NAXIS 3 FITS cube in the primary data unit with WCS header records recording the astrometric positions for the first two celestial dimensions and the third wavelength dimension delineated by a lookup table available in the first cell of the binary table in the single FITS extension This dimension coordinate description follows the lookup table spectral format of Greisen E W et al A amp A 446 2006 5 12 Reading a FITS Cube A saved FITS cube can later be read from disk for immediate display using CubeView see Section 4 4 CubeView page 23 No project window will be displayed instead the cube will be viewed directly in CubeView with a name ending in FITS The associated uncer tainty cube will also be loaded if available Note that most of the features associated with a full CUBISM project will be unavailable when viewing a cube loaded from a FITS file including the CUBISM project interface record and overlay visualization bad pixel lists pixel backtracking see Section 4 4 3 11 Pixel Backtracking Tool page 33 etc Cubes cannot be re built from versions saved as FITS since they do not contain all the infor mation on input data records bad pixels backgrounds calibration settings etc Spectra can be extracted and maps can be created and saved from a FITS cube see See Chapter 6 Cube Analysis page 60 Except for low level analysis of completely validated cubes it is preferable to work with f
9. Normally you would now choose background records among the record set see Section 5 4 Backgrounds page 46 and select bad pixels see Section 5 5 Bad Pixels page 50 In this case we have pre built the background record list and bad pixel list for you Specify the background BCD records to be used by choosing Background gt Load Background Recs and loading ngc3049 sli bgl choosing Average Min Max Trim when prompted Similarly load the prepared bad pixels using BadPix gt Load Bad Pixels choosing ngc3049_s11 bpl1 Choose Edit gt Select All and then Record gt View Record Stack to pop up a viewer displaying an average stack of all the records In the viewer choose Tools gt Scale Image with Histogram and draw a scaling box on the dark part of the image at left by clicking and dragging from top left to bottom right You should see two spectral orders appear with an obvious spectrum in the center Move the scaling box around by click and drag to highlight different features Back in the main CUBISM Project window hit the Build Cube button and watch the build progress You should see the cube build feedback in a window which opens Click the Save button and save the project to disk as a cpj file Congratulations you have completed your first spectral cube 3 3 Visualizing the AORs Before you move on to examine the cube visualize the spectral mapping AOR by choosing Record gt Visualize AORs
10. Other tools accessible below the displayed window will be discussed in the next section Chapter 4 The Tools 25 CubeView ngc5194 SL1 Average of 36 Eee Figure 4 4 CubeView showing a stack of 36 records with an active histogram scaling box and the order WAVSAMP displayed An example CubeView showing a stack average of 36 records is shown Figure 4 4 Chapter 4 The Tools 26 4 4 3 1 Tool Interaction There are two categories of main CubeView tools exclusive tools which require exclusive control of the mouse input and non exclusive tools any number of which can be active at any time These two types are separated in the tool palette with exclusive tools grouped at left and non exclusive tools grouped at right see Figure 4 4 Selecting an exclusive tool enters a mode of operation in which mouse inputs are interpreted by that tool alone Cubeview tools can be toggled on or off by clicking the button selecting the Tools menu item or using the key shortcuts The currently active tool s if any are indicated by depressed buttons in the tool palette and with tick marks in the Tools menu If an exclusive tool is already active toggling it on again as opposed to simply selecting another tool serves as a reset which restores it to its initial state for instance removing any box area which has been defined Other tools which draw marks or annotations on top of the image keep those marks drawn even when they are not ac
11. the SL1 or SL2 cubes thus obtaining a complete spectrum over a single pseudo aperture in the map Since Spitzer is diffraction limited beyond about 6 microns and the IRS modules have different pixel scales users should be very careful to avoid defining critically sampled Chapter 6 Cube Analysis 62 regions at the shortest wavelengths then using these to extract spectra from maps with significantly larger beam sizes This may result in long wavelength spectra generated over areas smaller than the beam Also be aware that diffraction smoothes the angular source distribution to greater degrees at longer wavelength so that a single extraction aperture can probe slightly different physical regions depending on wavelength This effect is particularly pronounced with sharp spatial structures e g an extraction formed inside a small ring of emission at the shortest wavelengths will likely be contaminated by ring emission at longer wavelengths If you read in a region that is larger than your current cube and attempt to extract a spectrum over this region CUBISM will produce a warning message In this case the problem will be obvious as the extraction aperture will extend beyond the edges of your cube in the CubeView window You can still generate the spectrum and save it to disk but you should probably select a smaller aperture if you are attempting to compare or stitch spectra across IRS modules Similarly regions entirely outside the cube will
12. 3 2 4 Memory Requirements sssssssssseeeee eee 4 PEDE CoD EET 4 2 5 1 Running the Source Distribution 000 4 2 5 2 Running the Binary Distribution ssssseessssss 4 2 6 DErAdIDE s 2 enaciseseeiyiaseqens E Re Rede PERI EE D 3 Quick Start Guide ss 6 34 Example Data Set icis reiii i d er Tib E e Y EEG 6 3 2 Building Your First Cube sues esee 7 3 3 Visualizing the AORS 0 ccc ccc cece eee 7 3 4 Navigating the Cube ccc cece cece cece n 8 4 The Pools actaskiqhbe bkn Sua tr anaes 9 4 1 Tool Inter Communication sseeeeee RR 10 4 2 General Interface Tips 0 00 0 cece eee eee eee eee 10 42 L list SelecblOn eet A Ses coarsest ad x andes een 10 4 2 2 Orle rereh ernieren eri ek vate abet lela anaes 10 4 2 3 Mouse shortcuts 20 0 0 ccc cc cece en 11 4D A Fil Selections sve prep ced a DORT UD leaded 11 4 39 ODUBISM PIT6Ject ee ter Rena ninta nis ese ye SRE Gaai 13 ABA Project DWlezniiede tee etes ze ertet oret RE RE RES 14 43 2 Mens di sosset sexe mCRESPSBPUO U UAI a asad d DOS 14 432 L Ele Menus eerie eer poetis 14 432 2 Edi Men 6i Eee deta RPIRLRPRPESD RR EDU 15 4 3 2 9 Record Menik eel RR DID Eee a 15 43324 Cabe MOHBU iiie ESESRDOO Ie hee erra e Ir 43 25 Background Menu ese RR nes 18 4 3 2 6 BadPix Menu ssseeee RII 19 4 3 2 D Info Menu secu ee ERI De bee e
13. AORs found at or below the selected directory BCD Import BCD data flat fielded and straylight corrected DroopRes Import DroopRes data not flat fielded not straylight corrected FlatAp Import FlatAp data flat fielded not straylight corrected Import Data by module Import all records found at or below the selected directory grouped by module independent of any AOR Can be useful for loading archive backgrounds which aren t grouped into mapping AORs see Section 5 4 2 Archive Background page 47 Chapter 4 The Tools 16 BCD Import BCD data flat fielded and straylight corrected The de fault data type CUBISM uses DroopRes Import DroopRes data not flat fielded not straylight corrected FlatAp Import FlatAp data flat fielded not straylight corrected Load Record Masks Load the BMASKSs associated with any newly added records Load Record Uncertainties Load the BCD uncertainty files for any newly added records Switch Record Data Type Prompt for and switch the data type of the selected records among BCD FlatAp and DroopRes Restore All Record Data Recover from file the data for all records these are normally recovered on demand View Record View Stack View the selected record or an average stack of records if more than one is selected using a pre existing viewer window if available Note that double clicking a record or hitting RETURN on a selected record h
14. Arizona by the Spitzer Infrared Nearby Galaxies Survey SINGS team in partial fulfillment of its Spitzer Legacy commitments It is distributed and supported by the Spitzer Science Center at Caltech Pasadena CUBISM consists of three main components which together form the core of its analysis and reduction capabilities CUBISM Project Manage BCD data and track all the various information required to build cubes including calibration data background information bad pixels aperture information etc CubeView General purpose viewer with a variety of tools for interacting with 2D spectral images full spectral cubes and visualization overlay FITS images CubeSpec View and manipulate extracted spectra and create maps from spectral cubes CUBISM is not a general purpose spectral analysis tool The tools it offers are oriented directly towards the task of creating validating and analyzing spectral cubes Since in dividual spectra spectral maps and full spectral cubes can be output from a single cube project other tools can easily be used for higher order analysis of these outputs e g mul tiple Gaussian fitting etc This manual is organized as follows After discussing the installation and requirements of CUBISM in Chapter 2 Installation page 2 we give a quick start guide to building a spectral cube from an example mapping data set in Chapter 3 Quick Start Guide page 6 We then cover in detail the menu options and
15. PR Sample Size 31 620 x 1 000 pixels WS 1 0 03 20 08 0 9620 96 4 Reset r lt 4AShos Edit F iws 1950 F Wrin s File Options Tools 2 l zs o ESEST ESTO TE es CubeSpec Extracted from ngc6946 LL1 107 1 gt 117 7 File Maps F E n pileo rs fii Seng vy Full Cube Mouse XZoom w YZoom w Region fug Nap Equiv Ui ps Lick lian Remove Fit Line Strength 2 7480 01 Fit 33 308 2 837s0 01403 A Lade ai gitad Peak F Renorm FF Valline I Errors Fit Orders 14 tracted from ngc6346 LL1 107 1 Cates mec amp 946 LL1 10x11 Tue May 09 03 59 18 2006 Stack 32 95 34 06 Cont Figure 4 1 The CUBISM tools being used together Chapter 4 The Tools 10 An example of all the CUBISM tools being used together on a single project can be seen in Figure 4 1 Seen in the window are counter clockwise from top left a CUBISM Project window the cube build feedback plot a CubeView tool visualizing the AOR and four selected records a CubeView tool showing the average of 4 records with bad pixels overlayed the CubeSpec tool displaying an extracted spectrum and a 3 component line map a CubeView window showing a line map image built from the LL order 1 cube cube build parameters and header information pane 4 1 Tool Inter Communication The tools which comprise CUBISM constantly communicate w
16. Select the ngc3048_irac_8um fits file and the viewer should fill with an image and some yellow outlines of the AOR regions Click on the histogram scaling tool button second from left and drag to create a histogram scaling box to bring the galaxy into view Click on the zoom tool leftmost and draw a box around these record outlines to zoom in and examine the records overlaid on the 8 micron image Chapter 3 Quick Start Guide 8 3 4 Navigating the Cube Now that the cube is built hit the View Cube button to display the cube in the same viewer window In this window click on the Extract button a cube with a line through it or select Tools gt Extract Spectra and Stack Cubes Click and drag a rectangular extraction region from upper left to lower right on the cube and the CubeSpec window will appear showing you the extracted spectrum Center the purple box on the galaxy seen in the right hand side of the cube In the CubeSpec window click Map and then choose Region Peak Click and release at 11 micron and then 11 8 micron to define a peak region highlighting the 11 3 micron PAH feature This will then be highlighted in red on the spectrum and the image in the CubeView window will change showing a map of NGC 3049 averaged over the wavelength region you have selected Congratulations you have just created your first spectral map with CUBISM By choos ing Region Continuum and setting continuum regions on either sid
17. V Viewing cubes sciscesitaade ere Re ERR Et 28 Viewing maps ip6e eek tieda Re ERE 28 Visualization background selection 50 Visualizing AORS i sees Ree nat 37 Wavelength Weighting 0 64 WAVSAMP ore pees Gen rECTYNU RE PUF PETER UT E 56 Z ZOOMING IMAGES 22 iss seus 9 re LEA REC EE YER 27
18. bad pixels and tips on selecting them It is only available when BCD images are being displayed To use simply left click to set or remove a given bad pixel from the global bad pixel list clicking and dragging to set or unset multiple pixels at once Middle click or CONTROL left click instead to set to record level bad pixels for all of the records being displayed For instance if a stack of 10 records is being displayed setting a single record level bad pixel will add that bad pixel to all 10 records A number of marks are drawn in CubeView to indicate global bad pixels record level bad pixels and various conditions and flags from the pipeline generated mask files BMASK and PMASK The various symbols seen when the Bad Pixel Tool is enabled are Cyan x s Global user defined bad pixels applying to all records Green x s Record level user bad pixels applying to individual records Blue s Locations where the PMASK permanent mask has any bit set The PMASK typically contains a small number of unruly pixels Red diamonds s Non fatal bits set in the BMASK Red x s Fatal bits set in the BMASK These are bits 12 13 and 14 i e none or only one usable sample in the exposure ramp or pixel fatally flagged in the PMASK Chapter 4 The Tools 35 See the IRS Data Handbook for a reference on the individual mask bits which the IRS pipeline applies Note that despite being a fatal mask val
19. build a cube extract a spectrum and build a spectral map leaving all of the important details aside for now These details are covered later in this manual An important note before we begin concerns the scope of a CUBISM project Each CUBISM project pertains to a single IRS slit e g Long Low order 1 LL1 Short Low order 2 SL2 or Short High SH Each of the low res slits are a single spectral order but the high res slits have 10 orders each Just as a reminder there are four IRS modules SL LL SH and LH with each low res module containing two slits and each high res module containing one slit For data sets with mapping observations in all four low resolution orders SL1 SL2 LL1 and LL2 four individual cubes will be built and analyzed as a set A full low res and high res IRS map will therefore produce six spectral cubes the four for low res and two additional for SH and LH and there will be six CUBISM project cpj files 3 1 Example Data Set We have assembled a small example data set using data from the SINGS IRS Short Low order 1 SL1 spectral mapping observations of nearby galaxy NGC 3049 The example data set should be available where you obtained this manual Unpack it and follow along The set includes the following data A directory containing all of the data files ngc3048_irac_8um fits A 8 micron IRAC image of the galaxy ngc3049 s11 bgl The background record list ngc3049 s
20. can have as many instances of the viewer as you want and each can be configured differently By default individual CUBISM projects attempt to target their own set of viewer windows only creating a new window if none is presently available 4 4 1 Title Bar The title bar of CubeView gives an indication of what is currently being displayed An exam ple is Record ngc5194 Average of 36 recs gt This information will change depending on whether a record background record cube map or visualization image is shown The same information is repeated below the line status bar in the image info block 4 4 2 Menus 4 4 2 1 File Menu Save as PNG Save the current image as a PNG file Save Map as FITS Save the current spectral map if available as a FITS file with complete WCS header information Export to Command Line Export the current image as an array variable on the IDL command line Extract Region from File Extract a spectrum from the current cube from the extraction region encoded in the header of an existing extracted spectrum tb1 file or DS9 region reg Save DS9 Region Save the current extraction region whether specified directly or loaded from another file as a DS9 reg region file which can be loaded in D99 to visualize the extraction area Close Close the viewer window 4 4 2 2 Options Menu Colormaps Change the display color map for the image and color bar Scale Image
21. down and the PAGE UP and PAGE DOWN keys skip entire pages full of list items 4 2 2 Scrolling Though not required list items can conveniently be made to respond to mouse scroll wheel input by modifying a set of resources associated with the X11 windows environment To do so add the following to your Xdefaults file XmList baseTranslations augment Shift lt Btn5Down gt ListNextItem n Shift lt Btn4Down gt ListPrevItem n lt Btn5Down gt ListNextPage n lt Btn4Down gt ListPrevPage n XmScrollBar baseTranslations augment lt Btn4Down gt IncrementUpOrLeft 0 IncrementUpOrLeft 1 n lt Btn5Down gt IncrementDownOrRight 0 IncrementDownOrRight 1 n XmText baseTranslations augment Shift lt Btn4Down gt page left n Chapter 4 The Tools 11 Shift lt Btn5Down gt page right n lt Btn4Down gt scroll one line up n lt Btn5Down gt scroll one line down n and restart your X environment 4 2 3 Mouse shortcuts Double clicking on a list item often results in some action being performed on that item e g view a record in the CUBISM Project window The same effect results when RETURN is pressed with a selected item Using the arrow keys and RETURN is a quick way to go through a list viewing each item In graphics windows e g the CubeView window see Section 4 4 CubeView page 23 mouse presses perform specific actions depending on context Typically the left mouse button perfo
22. eS 19 4 3 2 8 Help Meni soca cie chee weed MEI rxer EE PEE 19 4 3 3 Data Records 0c cc cece cc cece m ne 20 433 0 Becord Info 2 Iber A E wrens 20 4 3 8 2 Record Enabled State 0 ccc cee 21 4 3 3 8 Record Data Types 0 0 cece cere eens 21 4 3 3 4 Operating on Records 0 0 cece eee eee ees 21 433 Stas Barera re at ee ii 22 4 3 5 Button Barones ess rr merecen E REA aqu ENI 22 a ME CUIDA ERE 23 AAA lebBatsreexRetRREOPLISPSEISR A Rees reed e RS 23 AAD M mnusa ice eek RR RR SCC aid Pa ue pec ees 23 442 1 Re Mens eere eee reputo e es 23 4 4 2 2 Options Menu scooter er ERE E IRE ERR 23 A ADS Tools Ment i ues e ny aaa awa ennemi Rete een ncn 24 4 4 8 CubeView Tools ccc cece ene ioei 24 449 1 Tool Interaction mee Ie UR ded ea IAM MG 26 2 4 3 2 Box R6glonB8 ire etd de m Sob dutta he erben co 26 4 4 8 8 Tool Overview 0 ccc ccc ccc eee ee 26 AAA Zoom T0012 ib oe RI PHI ep 2 4 4 3 5 Histogram To0l e aee emn RR 28 4 4 3 0 Color Tool 5 ike eR PUES RR A EEEE RORE 28 4 4 3 7 Image Slicing Tool cece einka eee eee 28 4 4 3 8 Box Statisties 601 Rem RR 30 4 4 3 9 Aperture Photometry Tool ssseesssse 32 4 4 3 10 Cube Extraction Tool eeesseeeeeeeese 33 4 4 3 11 Pixel Backtracking Tool 00020 33 4 4 3 12 Bad Pixel Tool 0 cc cece eects 34 4 4 3 13 AOR Visualization Tool
23. eee 38 Cubeanalysisiiss diss ebie ee a esee ne p e nates 60 Cube assembly uere hh RSC PRA ERE 44 Cube menu CUBISM project 17 Cube Building eene ere ORE tEn IES 56 ubeSD6G er erra dp eu Er RE Eee QE PR 40 Cube Vie Ws ssia iemeta EE it cneneleaesan ges fees 23 CUBISM project ise e e ER RC Re 13 Cubism tools 2 220046 000ceeei se e orb 9 D Datarrecords 2 us etre RR tret 20 Debugging CUBISM 005 73 Disabled records 2c rrt nra 21 Display FITS Cube isccanesaceesmoacareaasaass 59 DEOOPRES acd ace sick Rice sep ears ERES PRESS eR RE 21 DS9 Regions veis pe VCI aE a ERTA 61 74 E Edit menu CUBISM project 15 Enabled records sesiesdus roine ineei a Paces 21 Extraction Regions lees 60 F File Menu CubeSpec 2000 ee eee 41 File menu CubeView 2 20 cece eee 23 File menu CUBISM project 14 File names relative cece eee eee 58 File Selections iaip csys atsrenas tas aareesnns we aia tease aus d Files inputs x nreziestemd er PERMDE Exe ROS 44 FITS reading cube from 59 FITS saving c be as secet egpes 59 FITS saving spectral map as suus 23 FFlatAp isses ee ern 21 H Help menu CUBISM project 19 Histogram tool o rer ERPRURRR Y Ree a 28 I Image scaling 2 oe Re EE DER ERN REPRE 28 Iniage slicing tools i 4 berere iniii ERE 28 Info
24. regions are averaged and then subtracted from the average or integral of planes over the peak regions Continuum regions are optional For example if you wish to create a continuum subtracted 11 3 micron PAH map from a SLI cube you can first use the mouse to define the continuum on either side of the PAH feature Once the continuum regions are defined change the selection mode to Peak and select the emission feature with the mouse in the same way For emission line maps select at least three or more pixels around the peak of the line Once the peak region is selected it will show up in a lighter shade of red and the image in the CubeView window will change to reflect the newly defined map This is now the continuum subtracted map of your science target The CubeView window will indicate the type of map being shown the range of peak wavelength coverage SPECTRAL REGION TYPES Though they are called Peak and Continuum the two region types can be used to make arbitrary differential maps averaged over different wavelength intervals Once regions are defined they can be selected by middle clicking SPACE cycles selection among them moved with middle click drag or with the left right arrow keys Up down arrow increase or decrease the width of the region Regions which come in contact with each other are merged When regions are re sized or moved the accompanying map is automatically updated Defining a small peak region several pix
25. s data 8 I get a message about missing calibration files Chapter 7 Tips and Troubleshooting 72 10 11 12 13 14 15 You are probably using another cube built with a version of CUBISM newer than yours and need to update your version See Help gt About Cubism to check the local CUBISM version as well as the version which was used to build the loaded cube project I removed all data records loaded more and built a new cube but something isn t right Remember that a cube project includes saved information on bad pixels background records etc Check Info gt Project Parameters to get a top level view of the settings Set the cube build order and clear bad pixels and background records if necessary or easiest just start from a clean new cube project My source emission disappears when I use outrigger sky data and then click BGSub in the viewed stack Make sure that you are subtracting records with background information in the the correct order You might have inadvertently selected records pointed to the first order for your sky when you actually meant second order for example causing target self subtraction I get a message Failed compiling DLM clipper CUBISM makes heavy use of polygon clipping to map all the partial BCD pixels onto the sky grid so to speed up this crucial operation a small piece of clipping code is written in C and automatically compiled as needed If your system is not
26. selected records prompting for an average of trimmed average combination Load Background Rec s Load a saved list of background records to use from a bg1 file Background Blend Blend data to create background Set and Scale Background A Set the first background in a blend from the selected records spec ifying its fiducial point Set and Scale Background B Set the second background in a blend from the selected records specifying its fiducial point Blend A and B Backgrounds Create a final background by blending backgrounds A and B ac cording to weights calculated from a target fiducial value View Background A View the first blend background and select the records associated with it View Background B View the second blend background and select the records associ ated with it Save Background Rec s Save the list of backgrounds records used as a bg1 file View Background View the record background if any in a pre existing record viewer window if available View Background new viewer View the record background if any in a new record menu Remove Background Remove the assembled background Rebuild Background Recreate background from its associated record data Load Background Spectrum Load a 1D background spectrum from an extracted tb1 file Remove Background Spectrum Remove any loaded 1D background spectrum Chapter 4 The Tools 19 4 3 2 6 Bad
27. thought of as pixels which respond normally to light but have a bright and variable underlying Chapter 5 Cube Assembly 51 dark current component However adjacent in time background subtraction is not always available and even when it is a number of problematic pixels often remain CUBISM has multiple facilities for discovering and flagging out these bad pixels 5 5 1 Global and Record Level Bad Pixels There are two different types of user settable bad pixels in CUBISM Global and Record Level A global bad pixel is a pixel presumed bad in all BCD records Since global bad pixels remain bad throughout the duration or a large portion of the spectral map they produce stripes at individual wavelength planes in the final cube as the pixel is rastered across the map an example of this effect is seen in Figure 5 2 The number of stripes depends on how many steps are executed along the slit Occasionally partial stripes will appear indicating a bad pixel which persisted for only a portion of the map The second type of bad pixel is a record level bad pixel which affects only a single record These can be useful for treating intermittent bad pixels which affect only a single or small number of records rather than discarding that pixel s data for the entire map only the portion affected is removed This is particularly useful for BCD frames with horizontal band artifacts a group of rows with garbled data The number of record leve
28. two sub slits separated by a blocked region When planning low resolution IRS observations you must select where your chosen target position will be placed in the full slit You can choose to have the spacecraft place your chosen target coordinates in the center of the full slit the blocked location in which case your record type will be e g LL Cen Alternatively you might place your target coordinates in the center of one of the sub slits e g SL1_cen Staring mode observations further subdivide each sub slit placing the target at roughly 1 3 and 2 3 along the sub slit these positions are denoted a and b e g SL1_a None of this however has any impact on the order information present in the data themselves If you have placed your target in SL1_cen the other sub slit will still image the sky onto the detector and record a spectrum Each record s data will thus contain both orders as well as the bonus order It is often useful to build a cube from data in the other sub slit s order i e the one not targeted during the map When an object is mapped consecutively with both sub slits using all the data records to build a cube in a given order results in two potentially disjointed regions We often call the region of cube built from the sub slit not being targeted the outrigger Data in the outrigger region can be very useful for improving the statistics for automatic bad pixel selection see Sect
29. 11 bpl The bad pixel list ngc3049_SL1 cpj The pre built cube project ngc3049_SLi_cube fits The pre built cube as a 3D FITS image Chapter 3 Quick Start Guide 7 ngc3049_SL1_cube_unc fits The pre built cube uncertainties as a 3D FITS image 3 2 Building Your First Cube Here we take you through the process of assembling a cube with the pre packaged data set To get going start Cubism see Section 2 5 Running page 4 IDL gt cubism You can either Create New Cube Project to build it from scratch or skip directly to the answer key choosing the pre built cube project file ngc3049_SL1 cpj bundled in the example moving ahead to the next section Once you have chosen to create a new cube project give it a useful name when prompted like NGC3049 SL1 You ll be presented with a blank CUBISM Project window Read in the full example data set by clicking on the Import AOR button at the bottom Select the data directory CUBISM will search for all IRS data files at or beneath that directory and group all discovered data files by object and mapping AOR allowing you to select among them In this case only two AORs are found one for SL1 and one for SL2 Select them both to load data from both mapped orders and all the relevant files will then be loaded into the project When you are warned that no calibration set has been loaded and that the latest is being used simply acknowledge the warning
30. 4 3 1 Project Title The title bar of the CUBISM Project encodes the name of the project surrounded by double arrow brackets if there are unsaved changes as well as the file name the project is saved to in lt gt angle brackets or lt unsaved gt is the project is not yet saved Note that the file name of a saved project and the project name can be distinct though by convention they are usually kept the same 4 3 2 Menus Most of the options for assembling and saving information from the cube are available from the menus of CUBISM Project which are documented here in order of their appearance 4 3 2 1 File Menu New Create a new CUBISM project prompting for the name Open Open an existing CUBISM project or a CUBISM FITS cube for display Save Setup Set the options for saving projects Save Data with Project Save all record data with the project which can greatly increase the project size on disk Relative File Names Modify record filenames to be relative to the project path Use ful for distributing a project file and data set together without including the record data in the project itself Save Clip Accounts with Project Save all clipping information which enables pixel backtracking and rapid cube rebuilds with the project This will increase the project size on disk Save Save the project prompting for a file to save to if not already set Save As Save the project as an alternate fil
31. BISM Project Record Menu page 15 A very common operation is to view a record which is done by simply double clicking it or selecting one or more records and hitting the View Stack button Chapter 4 The Tools 22 4 3 4 Status Bar Beneath the record list a text based status bar gives feedback on the state of completion of the current operation the number of selected records etc 4 3 5 Button Bar The button bar at the base of the CUBISM Project window provides convenient access to common functions also available with menu options or mouse shortcuts Build Cube QuickBuild Re build the cube Enable Enable the selected record s Disable Disable the selected record s View Record View Stack View the selected record or an average stack of the selected records if more than one selected View Cube View the assembled cube if available Import AOR Import BCD records from full mapping AORs found at or beneath the selected directory Save Save the current project prompting for a file if not yet set Close Close the current project prompting to save any unsaved changes Chapter 4 The Tools 23 4 4 CubeView CubeView is a custom viewer with both general purpose and IRS specific tools and config uration options It is used to view BCD records a stack of records special frames like the background frame or full spectral cubes as individual planes or maps created from the cube and AOR visualization images You
32. CUBISM User Manual IRS Spectral Map Analysis and Reduction Edition 1 8 June 2011 by J D Smith Lee Armus Brent Buckalew Danny Dale George Helou Helene Roussel amp Kartik Sheth This is edition 1 8 of the CUBISM User Manual for CUBISM version 1 8 June 2011 Permission is granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 2 or any later version published by the Free Software Foundation with no Invariant Sections with the Front Cover texts being A GNU Manual and with the Back Cover Texts as in a below A copy of the license is included in the section entitled GNU Free Documentation License in the Emacs manual a The FSF s Back Cover Text is You have freedom to copy and modify this GNU Manual like GNU software Copies published by the Free Software Foundation raise funds for GNU development This document is part of a collection distributed under the GNU Free Documentation License If you want to distribute this document separately from the collection you can do so by adding a copy of the license to the document as described in section 6 of the license Table of Contents 1 JIntroducLlOD ve per err er ui aci Par sale 1 2 InsballdblOE ass 4 ood oh cane EE eee we aio S aoe daran 2 2 1 Source Installation sees 2 2 2 Binary Installation 5st ea blah RR rd RAE UR ened 3 2 9 etupi neeieca Re ug er e EERE DEAE EA eR RO OE E ER E NES
33. Fu11 Cube mode select the affected cube plane and look for anomalous stripes or other features Use the backtracking tool to identify and mark bad pixels and re build with QuickBuild 5 5 4 Automatic Bad Pixels UsiNG AvTO BAD Pix Since CUBISM uses the BCD pixel contributions to the cube to discover bad pixels automatically you must first build the cube before the automatic bad pixel options are enabled CUBISM offers a powerful method to automatically discover and mark bad pixels in an assembled cube Selecting BadPix gt Auto Gen Global Bad Pixels or BadPix Auto Gen Record Bad Pixels will show a dialog in which the parameters for the automatic selection are set see Figure 5 3 The method by which bad pixels are automatically discovered is similar in concept to the backtracking method described in the previous section except that all cube pixels are considered simultaneously and statistics are collected on individual BCD pixels which can be used to flag them as bad AuTO BAD PIX WARNING The automatic bad pixel tool must be used with caution It can flag real data such as spectra lines or sharp spatial features e g point sources Always check the resulting bad pixels it finds and avoid very low sigma thresholds or fractions Chapter 5 Cube Assembly 54 An example of the auto badpix parameter dialog is seen in Figure 5 3 The Sigma Trim option sets the rough number of standard deviations a pixel
34. Load all data records from the AOR s which will be built into a single cube 5 Load any additional data records to be used for background subtraction Disable them if they are not intended to appear in the cube see Section 5 1 Input Files page 44 6 Select and set the background records see Section 5 4 Backgrounds page 46 7 Double check the cube build settings under the Cube menu in particular use Set Cube Build Order to select the order for building the cube note that high resolution cubes are typically built using All orders at once 8 Build the cube using Cube gt Build Cube 9 Save the cube project to file 10 Manually or automatically generate bad pixels and re build the cube Iterate as nec essary 11 Enjoy your newly assembled cube extract spectra build maps etc 5 1 Input Files CUBISM works from a set of input BCD or other record level data to produce spectral cubes It reads positional information from the headers loads pipeline mask files and uncertainty images and uses all of this information together to map record level pixels to the sky plane Details of the algorithm employed by CUBISM can be found in Smith et al 2007 PASP submitted CUBISM works best when applied directly to raw AOR directories downloaded from the Spitzer archives To import all data spectra masks uncertaines from all records in a given mapping AOR or set of related AORs simply hit the Import AOR button selec
35. Pix Menu Load Bad Pixels Load a saved list of bad pixels from a bp1 file replacing any existing bad pixels already set Load and Append Bad Pixels Load a saved list of bad pixels from a bp1 file appending to any existing bad pixels already set Save Bad Pixels Save the list of global and record level bad pixels to a bp1 text file Clear Global Bad Pixels Clear all global bad pixels Clear Record Bad Pixels Clear all record specific bad pixels Clear A11 Bad Pixels Clear all global and record level bad pixels Auto Gen Global Bad Pixels Attempt to automatically generate global bad pixels from redundant informa tion in well sampled cubes prompting for detection parameters Auto Gen Record Bad Pixels Attempt to automatically generate record level bad pixels for all records prompting for detection parameters 4 3 2 7 Info Menu Project Parameters Display the currently configured project parameters As Built Parameters Display the project parameters at the time the most recent cube was assembled Calibration Set Details Show the details of the currently loaded calibration set Debug Cubism Enable CUBISM debugging so that errors will halt at the command line with full traceback information see Section 7 4 Debugging CUBISM page 73 4 3 2 8 Help Menu About Cubism Show the current CUBISM version and the version which was used to assemble the loaded cube project if different
36. TAIN 2 setting depending on your window manager this forces IDL to keep track of the contents of windows when they need to be redrawn and is typically required under Linux The binary distribution of CUBISM performs this operation by default Another potential issue relates to the IDL_PATH If you have a source distribution of CUBISM you will need to ensure that the directories containing CUBISM as well as the AstroLib installation are on your IDL_PATH In principle it should not matter where on the path CUBISM is However occasionally two different packages will each define the same routine in two files with the same names a so called name space conflict If you encounter this problem move the directory containing CUBISM higher on your IDL_PATH or use the binary distribution which doesn t suffer such name space conflicts 2 4 Memory Requirements CUBISM is designed to take advantage of the large memory sizes available on modern computers Rather than load a small amount of data from disk operate on it and return it to disk e g as IRAF might do CUBISM attempts to keep most data in memory which enables a variety of features which would not be possible with caching to disk For modest sized cubes with fewer than 100 BCDs contributing this is not a burden For very large cubes many hundreds to many thousands of records CUBISM s use of roughly 0 5 2MB per record at maximum requires at least 1 2GB of RAM to avoid loss of perfor
37. a sets which could contain useful background data Remember that you must decide yourself whether a given BCD record constitutes a valid background frame i e is free from source emission For low resolution data often the safest bet is the outrigger order from a staring mode observation which often target unresolved sources e g SL2 from a SL1 targeted observation The disadvantage of this technique is that the data must be available in the archive which for many program requires waiting for the proprietary period to expire 5 4 3 Background Blend A related technique to the archive background is the Background Blend useful if a set of observations from the archive which closely match the background properties of your source cannot be identified In this method a pair of observations from the archive or else where which bracket the target background are linearly blended together to approximate a local 2D background The same constraints on data of exposure apply ideally all back ground observations would have been obtained within 2 3 days of the target observations to maximize the effectiveness of mitigating rogue pixels the behavior of which drifts on the time scale of days To use this method load the two data background sets ensuring their records are dis abled to avoid having them built into the cube Select the subset of the first which you want to include in the background and select Background gt Background Blen
38. ace the root directory from the file names to fix this issue see Section 7 3 Troubleshooting page 70 another method is to enable this option to specify that all path names will be saved relative to the path of the cpj file itself Then as long as the relative file layout of the project file and data files remains the same all record data should load without problem This has the advantage of allowing cubes to be passed back and forth without needlessly re tranferring all the data but also not requiring any absolute file layout for the data on disk For instance a full directory structure as myproj myproj cpj myproj data ri123456 ch0 bcd myproj inputs myproj bpl myproj inputs myproj bgl myproj myobject 8um viz fits could be distributed as a unit with myproj cpj referencing the data in the data directory a visualization image and even including saved copies of the bad pixel and background list inputs 3 Save Accounts with Project The clipping accounts consist of all the information which maps BCD pixels to the sky grid When the accounts are valid you don t see needs rebuilding in the Info gt Project Parameters page the cube can be rebuilt quickly and pixel backtracking can be used see Section 4 4 3 11 Pixel Backtracking Tool page 33 Saving this account information in the project file gives these benefits to cube projects loaded from disk as well but comes with a steep cost in terms of dis
39. ackground 49 i 5 4 6 No Background 200 c cece eee eee eres 49 5 4 7 Background Selection Using Visualization 50 5 4 8 Saving the Background List 0 e eee eee 50 5 5 Bad Pixel amp sc c 0 peieaeiniesiciedia webiace teases FERE US 50 5 5 1 Global and Record Level Bad Pixels 51 5 5 2 Manual Bad Pixel Selection 0 0 2 cece eee 51 5 5 3 Backtracking to Discover Bad Pixels 000 52 5 5 4 Automatic Bad Pixels 0 0 0 e eee ee 53 5 5 5 Saving Bad Pixels dob ease bende lean es 55 5 6 Cube Build Settings ss liceo ERR pe RR at cde aay 55 5 WAVSAMDP ie RRREERET ERE REA Rp UU P epPIE d SA ds 56 5 8 Building the Cube 5i gem o kinne a Eaa 56 5 9 QuickBulld 2 cote re ERE PER teres E ea teva see DT 5 10 Saving the Project esses esr epe raau sande 57 5 11 Saving the Cube as FITS 0 cee eee eee 59 5 12 Reading a BITS Qube iere p RR anrd cea abe 59 Cube Analysis euis i CHAR CR eite acra gta 60 6 1 Extracting 1D Spectra cee e 60 6 l l Direct Extraction 2 Rb bre eR ERE ERR de 60 6 1 2 Matched Region Extraction 00 0 eee eee eee 60 6 2 Creating 2D Maps Ree iere RR ERRRRERERCES 62 6 2 1 User defined Maps 2 00 cece eee eee eect e nee eee 62 6 2 2 Pre defined Maps 200 c cece cece e cnet e eee eens 63 6 2 3 Map Selen RR RR vet pea keeee ED Ei 64 6 2 4 R
40. alid astrometry DSS 2MASS Spitzer IRAC MIPS etc and the records will be shown as in Figure 4 10 Any selected records in the cube project will be shown in white Disabled records are gray Chapter 4 The Tools 38 When this tool is active records can be selected directly in the image itself Click on a record to activate it at which point it is drawn in white Click and drag to select contiguous records SHIFT click to select the range of records from the last selected and CONTROL click to select non contiguous ranges similar semantics as described in Section 4 2 1 List Selection page 10 Click outside the record overlays to deselect all records Direct selection on the image can be very useful from defining background records directly from an infrared image see Section 5 4 7 Background Selection Using Visualization page 50 4 4 3 14 Pixel Table Tool The pixel table tool can be activated at any time and displays a group of pixel values around the cursor position 4 4 3 15 Order Mask Tool The order mask tool sets to zero all pixels outside the order as defined by the WAVSAMP aperture see Section 5 7 WAVSAMP page 56 It is useful when checking for bad pixels and is only available when BCD record data are displayed 4 4 3 16 Compass Rose Tool The compass rose draws NE compass lines on images data with available astrometry cubes maps and visualization images 4 4 4 Colorbar The colorbar shows the curr
41. and line which should force it to break possibly after generating some input in the GUI The backtrace at this location can be useful for understanding why CUBISM was halted Index Index n as bad pixel cod sccricicereirerisrsrcrress 38 A AOR visualization sessseseeeseeeee 37 Aperture photometry tool 32 B Background menu CUBISM project 18 Background subtraction 00 46 Background archive 00e eee 47 Background blended 54 48 Background 1n SItU cues ee eterne cene 47 Backtracking toolsnii rrd pre Rer RR REOR 33 Bad pixel codes cse rre tn Terrae 38 Bad pixel to0l ios ceci eb ER Deere 34 Bad pixels ise Sabot eased bide ted 50 Bad pixels automatic selection 53 Bad pixels manual selection ol Bad pixels savings iier Reeves 55 BadPix menu CUBISM project 19 pep TE 21 BOD filegz csosonetietemerze back Rh trie eds 44 BCD Fecofds essendo pIE RA 20 Box Statistics tool ssr user r3 RR LR IRR RRMPEE RES 30 Build Ordet i et ee Tr iaie UPPER DES 45 Building C b68 5r rro HerRIRERERECEPRUR 56 Buttons CubeSpec 2 c cece eee ee eee 42 Buttons project window sssesssss 22 C Calibration sets 2 0 cece cece e eens 44 46 ColorbaPj nneecemxrR mer e RAT RULEROSTS 38 Compass rose tool 0c cece eee eee
42. and Troubleshooting T3 7 4 Debugging CUBISM By default CUBISM traps and reports all errors which occur in a dialog The resulting error message may or may not allow you to determine the root of the problem To debug CUBISM yourself or to provide useful information to the SSC help desk to allow them to investigate the problem enable debugging with Info Debug Cubism in the CUBISM Project window This requires access to the IDL command line which will not be available for versions of CUBISM running under the IDLVM see Section 2 2 Binary Installation page 3 After enabling debugging repeat the action which generated the error Instead of trapping the error with a dialog prompt IDL will halt with a full back trace message showing the exact code path which led to the error in the IDL shell This code path might be enough to give you a hint as to the nature of the problem but is also useful for the upstream maintainers for debugging purposes Report problems at the Spitzer Science Center helpdesk including at minimum 1 A brief statement of the problem 2 A detailed description of the steps which can lead to the problem isolated to the smallest necessary number 3 Example inputs which trigger the problem if applicable e g a FITS file which gives trouble 4 The full traceback message reported in the IDL console window after you have enabled Debugging If CUBISM freezes and you cannot make any progress try CONTROL c at the comm
43. ap Save the current map into a map file for later use on other spectra Load Maps Load a spectral map that has been previously saved Reset to Default Maps Re load the default map sets saved in cubism map_sets removing others Set Redshift Set the Redshift of the object spectrum in km s Clear Redshift Clears any entered redshift IRAC 5 8 um Overplots a shaded red area of the IR AC 5 8 micron system response curve IRAC 8 0 um Overplots a shaded red area of the IR AC 8 0 micron system response curve IRS Blue Peak Up 16um Overplots a shaded red area of the IRS Blue Peak Up 16 micron system response curve IRS Red Peak Up 22um Overplots a shaded red area of the IRS Red Peak Up 22 micron system response curve ISOCAM LW2 7um Overplots a shaded red area of the ISOCAM LW2 7 micron system response curve ISOCAM LW3 15um Overplots a shaded red area of the ISOCAM LW3 15 micron system response curve MIPS 24 um Overplots a shaded red area of the MIPS 24 micron system response curve Chapter 4 The Tools 42 4 5 3 Buttons Most of CubeSpec s functionality is accessible in the form of buttons Full Cube Default setting In this mode CubeView sends views of a single wavelength plane of the cube at a time to its associated CubeView viewer Key shortcut u Map In this mode pre defined or custom defined maps see Section 6 2 Creating 2D Maps page 62 are sent to the viewer Key shortcuts p and
44. as the same effect View Record new viewer View Stack new viewer View the selected record or an average stack of records if more than one is selected using a new viewer window View Uncertainty View the associated uncertainty image of the selected record or the quadrature sum of uncertainties if more than one is selected using a pre existing record viewer window if available View Uncertainty new viewer View the associated uncertainty image of the selected record or the quadrature sum of uncertainties if more than one is selected using a new viewer window Delete Delete the selected record s from the project Rename Change the ID of the first select record Disable Disable the selected record s preventing them from being built in the cube Enable Enable the selected record s allowing them to be built in the cube Show Filenames Show the filenames associated with the selected record s Show Header Show the header s of the selected record s Show Keyword Value s Show the value s of a selected FITS header keyword for the selected record s Chapter 4 The Tools 17 Visualize AORs Load a FITS image and visualize the mapping AORs on it using a pre existing visualization viewer window if available Reuse any image which has already been loaded See also Section 4 4 3 13 AOR Visualization Tool page 37 Visualize AORs new viewer Load a FITS image and visualize the mapping AORs on it i
45. c enable this mode for peak or continuum definition respectively ValLine Enable the display of the vertical line in the spectrum plot Errors Pressing this button turns the uncertainty bars on and off in the plot Fit Order 1 2 3 4 or 5 Set the polynomial order for the continuum fit see Fit button Mouse XZoom In this mouse mode when you click the left mouse button in two locations the plot will zoom in on that section of the wavelength range Double clicking the left mouse button in one location or right clicking will return to the full wavelength range Key shortcut x Mouse YZoom In this mouse mode when you click the left mouse button in two locations the plot will zoom in on that section of the flux range Double clicking the left mouse button in one location or right clicking will return to the full wavelength range Key shortcut y Mouse Region Lambda When Full Cube is depressed this button is Lambda a enables sending a single wavelength plane of the cube at a time to the viewer on click When in Map mode the button is Region and enabling it means that clicking a start and finish wavelength range in the spectrum will define a peak or continuum region Continuum Peak This button is used in conjunction with the Region button stated above With Continuum chosen you will select points to use for the continuum With Peak chosen you will select points to use for the emission lines Lam Weight If set the cont
46. can be done without invalidating the accounts 5 9 QuickBuild As a special case of cube rebuild changes to the bad pixel lists global or record level enable a special mode called QuickBuild The Build Cube button and Cube menu items in the project window will change to reflect this In this mode only cube pixels which are affected by dirty BCD pixels those recently added or removed from one or more bad pixel lists are recomputed The status bar mentions the fraction of cube pixels which are being re built This is much faster than a full cube rebuild typically requiring only a second or two even for large projects QuickBuild means that experiments with bad pixels to improve the quality of the cube see Section 5 5 Bad Pixels page 50 can be performed very rapidly This is particu larly powerful with back tracking see Section 5 5 3 Backtracking to Discover Bad Pixels page 52 since you can try out a bad pixel quick build the cube and the cube view and any extracted spectra are automatically updated If the problem isn t solved undo and try again 5 10 Saving the Project Saving the project to a cpj project file records all of the information presented in a CUBISM Project window including data records background settings bad pixels cube build preferences calibration set details etc and allows you to recover a cube project from disk to continue working on it Saving the cube can be accomplished with menu opt
47. capabilities of the three main tools which comprise CUBISM see Chapter 4 The Tools page 9 Then we discuss in greater depth the steps required to build a cube in Chapter 5 Cube Assembly page 44 explain methods of analyzing the cube see Chapter 6 Cube Analysis page 60 and finish with common tips and troubleshooting see Chapter 7 Tips and Troubleshooting page 66 Note that this manual does not include information on planning IRS spectral mapping observations see the IRS Spectral Map HOWTO for information on observation planning CUBISM was based in part on the SCOREX analysis software developed by JD Smith at Cornell Uni versity see Smith J D T PhD Thesis 2001 Chapter 2 Installation 2 2 Installation CUBISM runs under IDL and requires a working version of IDL to function There are two means of installing CUBISM as a set of source pro files which IDL finds on its search path or as a pre compiled binary which can be loaded as a single entity Both versions can be found on the CUBISM home page The advantages of a source installation are e Access to CUBISM s code for bug fixing or examining algorithms e Source level feedback when bugs occur see Section 7 4 Debugging CUBISM page 73 e Should continue to function with all future versions of IDL The disadvantages of the source installation are e Must install the AstroLib dependency library at the required version Some small risk of futur
48. configured with a C compiler typically gcc this can fail generating this message An equivalent fallback IDL native version of the clipping algorithm will take over but it is much slower 10 20x See the documentation for IDL s MAKE DLL to learn more about compiler configuration on your system Selecting He1p Cubism Manual doesn t do anything On Unix systems IDL opens PDF files using its distributed script online help pdf By default this script uses acroread to load the specified file Preview on OSX If you don t have Acrobat reader installed or would prefer to use another reader you can specify another PDF reader by setting the environment variable IDL ONLINE HELP PDF CMD e g in your cshrc setenv IDL ONLINE HELP PDF CMD xpdf I get an IDL compile syntax error like self DR which BCD ptr new readfits file SILENT hdr Syntax error You have an outdated version of AstroLib update it I can t understand the difference between build order and the record order shown under the Type column in the project viewer You need to read Section 5 2 Build Order page 45 All my colors come out red in the viewer cube build visualizer everywhere You are running CUBISM from source and forgot to turn off decomposed color which is usually done in the idl setup See Section 2 3 Setup page 3 Binary versions of CUBISM running under the IDL virtual machine do this for you Chapter 7 Tips
49. cord operati0n8 enlgpeskuemem the pA ER 21 Redshift map creation 0 eee eee 64 Relative file names eee e eee eee 58 Rogue pixels petere RE ET Ree d RA ees 50 Running CUBISM Li ever Er TRIPS 4 Running binary distribution issues 4 Running source distribution 4 S Saving image as PNG se see RR 23 Saying projects soepen eor eruan 43x A RESP EETER 57 Saving with accounts 008 58 Saying With datas cesses eee rt hb RR he ninya 57 Settings cube building 0 55 oetup of CUBISM e srian a v RR Pin 3 75 Shortcut k6y8s sis adie se nrerin en iiaa NU e d 66 oky ID IU MEET 49 Sky 1D spectr umi e cse ent Ree Euer 48 SLOPE iic kg sxtceetee secure p e ERR EE RHEEDAS 55 Slicer tool 2325 he re rrr Pee xe arbre per 28 SMART using CUBISM with 3 Spectra extracting o cecus eee erp Re 60 Spectra fully stitched a x ceteros 60 Spectra Viewing uus usebes rece rese be pius 40 Spectrum plotted ccce neret 43 Statistics amage ssesescoc c Rr Ra Perte err 30 Status line CubeView sseeeesss 38 T uj PH 69 Title bar project coepi Re espis 14 Tool palette CubeView seeeeesse 24 Tools menu CubeView sseesessesse 24 Tools Cube View votre LRL De TPLeP PIE 24 Troubleshooting 4 er meme 66 70 U UPSPACE ep RRIMIe rere aE O mes 5
50. d gt Set and Scale Background A The selected background is displayed with BackgroundA indicated in the image info block see Section 4 4 7 CubeView Image Info Block page 39 Enter a fiducial background value when prompted This value serves as the interpolant for deter mining the weights of the two backgrounds in the blend For SL data it is convenient to use the flux measured in the Peak Up Blue image at 16 microns the lower of the 2 peak up fields visible in all SL BCD images if it is clear of source contamination The box statistics tool can be useful e g use as a fiducial value the 3 sigma clipped average of a large section of the PU field Do the same for BackroundB and then select Background gt Background Blend gt Blend A and B Backgrounds entering a fiducial of your target data set formed in the same way e g in from the PU field statistics Another potentially useful fiducial is the predicted background at the source position and date as available in Spot 5 4 4 1D Sky Spectrum If no 2D BCD level data are available for subtraction some of the same benefits can be obtained by specifying a 1D spectrum to subtract from all the cube planes You can build a cube extract a spectrum from a carefully chosen area believed to be free from source contamination use the visualization if possible see Section 5 4 7 Background Selection Using Visualization page 50 and use this extracted spectrum as a 1D level back
51. d position 1 b nod position 2 Step The step sequence within the map as I X Y where I is the EXPID of this step and X and Y are the row and column positions within the map A secondary page of information is available by clicking on the right angle toggle button at the extreme right edge of the header bar This page includes RA RA targeted by the slit field of view position J2000 DEC DEC targeted by the slit field of view position J2000 DATA Whether the data for this record are loaded rather than just a link to the file Data are loaded on demand Chapter 4 The Tools 21 UNC Whether the associated uncertainty data for this record are loaded These are discovered automatically alongside the primary data products and loaded BMSK Whether the associated BMASK mask data for this record are loaded The BMASKs are discovered automatically alongside the primary data products and loaded ACCT Whether the accounting information for this record is cached mapping BCD pixels to sky pixels BPL How many record level bad pixels exist for this record see Section 5 5 Bad Pixels page 50 The records can be sorted by any of the available data fields by clicking the button associated with each header word e g to sort by RA click RA 4 3 3 2 Record Enabled State All data records can either be enabled or disabled Disabled records have lines drawn through them in the project display see Figure 4 3 Disabled records ca
52. dule gt BCD disable them and Background gt Set Background from Recs For backgrounds which appear among the mapping data set e g as was done in the Chapter 3 Quick Start Guide page 6 simply select these records and choose Background gt Set Background from Recs Using either the average or min max trimmed average is fine These records can be built into the cube directly though by definition they should not contain much source flux or disabled to save time and space 5 4 2 Archive Background If you didn t obtain dedicated sky observations and none of the records in your map are free from source emission you can still recover 2D level BCD maps by borrowing suitable data from the Spitzer archives Useful sky data would have been obtained with the same instrument module using ideally the same exposure time targeted within roughly 10 degrees in ecliptic latitude from your source and within 2 3 days of the target observation Chapter 5 Cube Assembly 48 The efficacy of archive sky subtraction can vary widely and depends on the level of the background at your source and the historical behavior of the IRS detectors at the time of your observations The closer in time and ecliptic coordinate the data the better the subtraction will be both in terms of removing the astrophysical foreground and mitigating the effects of rogue pixels The complete log of all Spitzer observations can be useful for identifying potential dat
53. e Revert to Saved Recover the last saved version of the project from disk discarding current changes Write FITS Cube Write out the assembled cube if any as a FITS cube along with an associated uncertainty cube if built Rename Project Rename the project which does not affect the file to which the project is saved Chapter 4 The Tools 15 Export to Command Line Export the full CUBISM Project object to the IDL command line prompting for the variable name Load New Calibration Set Load an alternate calibration set Close Close the project window prompting to save if changes have been made 4 3 2 2 Edit Menu Select A11 Select all the records Select By Filename Select records with files matching a given expression Select By Keyword Select records with keyword matching a given expression Invert Selection Select an non selected records and de select all selected records Deselect Disabled Deselect any selected record which is disabled Replace File Substring Replace a given substring in the file names of the selected records with another string 4 3 2 3 Record Menu Add Data Add individual data records Useful for data with filenames or organization not following the convention Usually not as convenient as adding full AOR data sets at a time using one of the following commands Import Data from Mapping AOR Import data from entire mapping AORs prompting for selection among the
54. e 2 4 See the IRS Data Handbook for a reference of the BMASK mask bits 4 4 7 Image Info Block Information on the image being displayed is provided here the same as is shown in the title bar see Section 4 4 1 CubeView Title Bar page 23 4 4 8 WAVSAMP Pane Below the image info block when a BCD record is being displayed is the WAVSAMP Pane where the WAVSAMP see Section 5 7 WAVSAMP page 56 can be manipulated Show overlays the current WAVSAMP for the current build order Edit adds handles which can be used to adjust either side or end of the WAVSAMP The normalized aperture coordinates of the 4 corners of the WAVSAMP are shown for each order The Lock toggle controls whether all orders are set to the same WAVSAMP aperture The WvScl toggle creates a WAVSAMP aperture which grows linearly with wavelength The Reset button reset the full aperture Editing the WAVSAMP involves clicking on one of the 6 adjustment handles and dragging When in WvSc1 mode only the central controls adjust the width of the aperture and the central wavelength Otherwise all controls change the width either at one end or both ends together SHIFT click and drag moves both sides of the aperture at once See Section 5 7 WAVSAMP page 56 for more information about when and how to edit the WAVSAMP See Figure 4 4 for an example displayed WAVSAMP Chapter 4 The Tools 40 4 5 CubeSpec CubeSpec i
55. e changes in AstroLib causing problems e Subject to routine name conflicts e g two routines named routine pro on the path so you must carefully set your IDL PATH to be sure CUBISM s files are found first This should not be a common problem but users of the staring mode extraction package SMART may experience routine name conflicts though not for recent versions see Section 2 1 Source Installation page 2 The advantages of installing and running a binary version of CUBISM e All required routines are included in the compiled file at the required version no need to install external libraries e No routine name conflicts should occur e Can be used sans command line with the freely available IDL VM if you don t have access to an IDL license and the disadvantages e No access to source code level debugging feedback when errors occur making it harder to track down problems e More closely tied to the IDL version a given binary may not work with all future versions of IDL though typically binary compatibility between IDL versions within a few versions is quite good 2 1 Source Installation The requirements for installing and running CUBISM from source are 1 A Linux Solaris Unix or MacOSX platform CUBISM may run under the Windows operating system but has not been tested on a Windows platform 2 A licensed copy of IDL version 7 1 or later Download from RSI now ITTVIS 3 The AstroLib library available f
56. e of your peak region you could now create a continuum subtracted spectral map Read on to learn more about the detailed steps for cube assembly and analysis Chapter 4 The Tools 9 4 The Tools CUBISM consists of three main components which are used together for building and analyzing spectral cubes CUBISM Project CubeView and CubeSpec We will give here a description of the purpose and reference of the features of each of these three tools after some general tips on using the interface and background on the communication paths among the tools MF 1906946 LL1 ngc694 t l cp File Edit Record Cube Background BadPix Info M ARA Alec 4T JUNC SESK IAT EPL E M 60 09 08 3 ber fis EE a Tools Qed a Co ES TNI a8 ILS 1 f s Ss 4 records selected Enable Disable Hes von Stack vieu De Inport OR So close 1 ID for the sat o CR files usod 2 OSL 1SH 2 4 Er HIS 2 0965624 103 080 0 nipl ft File nne 05 08 pb e c trin oneg Ihbtasfork cal loaded LL Order 110 BCDs Wari aes Background 20 anak Tus ag 09 E t Reconstructed Bet Pile ble Global 174 bane inge uk bes r puta Rote MEB Loc LLI dr bel WII Orders 0 03 gt 0 03 0 95 0 96 Visualizing noctS4E LLI LLI n amp 946 v5 phot 4 Fits Recordz neess LLt lt Aiverage of 4 recs gt TES 45 720 x 730 000 arcsec 5 080 arcsec pixel 4 Selected
57. e slice to be horizontal vertical or diagonal A plot window with the pixel values along the slice vector is displayed as the slice is made and mousing over it simultaneously highlights the value Chapter 4 The Tools 29 and the corresponding pixel position s within the image SHIFT left click or middle click and drag to define an averaging width perpendicular to the slice line indicated by dashed lines Only full pixels are averaged and the selection heuristic is simple While other tools are active the slice plot window will remain active and continue to indicate the position Creating a new slice replaces the existing line To remove the slice line reset the tool by turning it on twice or destroy the plotting window An example slice plot is shown in Figure 4 5 The image slicing tool s key shortcut is 1 CubeView ngc7793 SL2 SL2 n7793_v5 phot 4 fits Slice 600 1447 to 1247 674 width 296 2 ih k j my A agi 600 Slica Indax Figure 4 5 A plot of a slice through an image Chapter 4 The Tools 4 4 3 8 Box Statistics Tool CubeView ngc5194 SLI 18x1 Tue May V File Options Tools amma fo a SR PR S Cube ngc5194 SL1 18x1 Tue May 09 02 58 53 2006 Waves 11 2594 z Prev Next Plau mu Play Speed Statistics I 51 5 12 x 10 MAX 119 83 HIN 40 243 AVG 60 218 MEDIAN 59 618 STDEY 10 114 3SIG CLIP CNT 117 AVG 59 173 SIEV 7 5043 Figure 4 6 Example CubeVi
58. edshift and Maps 00 0 cece eee eee eee eee eee 64 6 2 5 Integrated Maps cece cece eee eee rn 64 6 2 6 Wavelength Weighting 0 0 cece eee nee ee eee 64 O27 Mine Els bb amie LU LI T has E E eE EP URS 64 6 3 Complex MApS bebe be UP e ge EP WERE S UY e deer 65 Tips and Troubleshooting 66 7 1 Mouse and Keyboard Shortcuts 0 00 e eee eee ees 66 GAL Cube Projecta 22 ener beber he betas sad eene eina 66 FAQ Cube VieW icerum e rer DF PPERE D a Ran 66 eld Cube Spec Re ber ROpeRE RR DeCCp Pb ks 69 17 2 TIpSusesezuekietesessteDegmem E Re koe E E E eek dedo edam 69 To Troubleshooting s acer siratin ien eae ley oh areas rd tS 70 CA Debugging CUBISM ascents zs eta i be edere p dei talent 73 iii Chapter 1 Introduction 1 1 Introduction CUBISM the CUbe Builder for IRS Spectral Mapping is a package which supports the analysis and reduction of spectral maps created with the IRS Spectrograph aboard the Spitzer Space Telescope It is written in the Interactive Data Language IDL CUBISM is designed to allow sets of basic calibrated data BCDs from IRS mapping observations to be combined into single 3D spectral cubes with two spatial and one spectral dimension From these cubes spectra can be extracted over differing apertures and arbitrary maps can be made in spectral features e g a continuum subtracted line image CUBISM was developed at the University of
59. els and then moving it across the spectrum is a good way to get a quick feel for how the cube is changing with wavelength To save any map generated in this way use File gt Save Map as FITS in the CubeView window where it is displayed The FITS file saved in this manner has all the required header keywords to be read into the common FITS readers e g DS9 displayed and aligned with any other FITS image of your science target Using the CubeSpec window any number of spectral regions can be defined and used to make images which can then be saved to FITS from the CubeView window The FITS headers will include the wavelength peak and continuum regions used to generate the map 6 2 2 Pre defined Maps Besides user defined maps CUBISM offers a number of pre defined filter curves available under the Maps menu in the CubeSpec window This will allow you to generate spectral maps in for example any the IRAC 5 8 IRAC 8 MIPS 24 IRS Peakup ISOCAM LW2 or LW3 filters Once selected the spectral ranges will be highlighted on the 1D spectrum in the CubeSpec window and the image in the CubeView window will change to the corresponding 2D map Note these maps are pseudo filter images and are not continuum subtracted and may lie partially outside the wavelength range of the spectra Unlike maps based on wavelength regions maps based on filter curves cannot be directly edited in CubeSpec A selected map will appear at far right in the title of the plo
60. ely available virtual machine Download either from ITTVIS 3 A compiler for C source typically gcc or whatever the IDL routine MAKE_DLL looks for usually available by default Note that running CUBISM from the binary sav file under the free IDL VM does not give you access to an IDL command line so that only the graphical interface to CUBISM is accessible With this setup no analysis can be performed at the command line though all files including spectra maps and cubes can be output as normal Running the binary distribution of CUBISM in a licensed version of IDL does not prevent access to the command line To install the binary version of CUBISM simply unpack the cubism_vX XX_bin tgz file where X XX is the version number in a directory on the IDL path or anywhere else 2 3 Setup CUBISM needs very little setup As long as the binary or source directory structure is left intact CUBISM automatically discovers all the necessary calibration and other files needed One basic setup issue relates to the color mode By default IDL uses DECOMPOSED color in which the RGB value of pixels is directly specified whereas CUBISM and most astronomy software relies on color table indices to specify color To switch modes try adding the following to the IDL startup file specified with the environment variable IDL_ STARTUP Chapter 2 Installation 4 device DECOMPOSED 0 TRUE COLOR 24 RETAIN 2 You may not need the RE
61. ently selected colormap as adjusted by Options gt Colormap menu and the Color tool see Section 4 4 3 6 Color Tool page 28 along with a plot of the current color pixel histogram of the displayed image region and the scale clipping limits See Section 4 4 3 5 Histogram Tool page 28 4 4 5 Status Display Line Below the display window a status display line reports the pixel position and value with uncertainty and depending on the data being viewed 1 BCD images see e g Figure 4 9 Wavelength and order of the cursor position along with a flag code identifying the bad pixel type 2 Cubes and Visualization FITS Images see e g Figure 4 7 Coordinates of the current position from the WCS information 4 4 6 Bad Pixel Codes The flag code at the far right of the status display line indicates the common mask values from the BMASK OR d together when viewing averages of multiple records The pixel was flagged in the PMASK S The pixel was saturated during the read ramp but the value was recovered S The pixel was saturated and uncorrectable F No flat field was applied to the pixel R The pixel suffered a radhit but it was corrected Chapter 4 The Tools 39 0 No samples in the read ramp were valid 1 Only one sample in the read ramp was valid All relevant flags are listed together and for bit values from the BMASK not listed here one or more numeric bit value is listed in brackets lik
62. es 5 4 1 In Situ Background The primary and recommended technique for assembling a background frame is to use dedicated background observations you scheduled along with your mapping AOR or to use data obtained as part of your mapping observations which went far enough off the source to remove all source flux from the slit Finding records in which the full slit is uncontaminated by source emission either within the spectral map itself or as part of a dedicated background AOR grouped with the main observations is the goal This is often aided in maps using the low resolution modules by the fact that each low res slit LL and SL is comprised of two sub slits which define the different spectral orders For small objects less than the size of one sub slit it is common to map first with one sub slit and then with the other e g a SL1 map and separately a SL2 map In this case the outrigger data from those records collected when the source was placed in the other order can be used as a background set Even if the full slit was used to map a source the fact that the two orders extend away from the map center to either side often allow useful background frames to be found at the extremities of the map For a very helpful method for making such selections See Section 5 4 7 Background Selection Using Visualization page 50 For dedicated offset sky observations simply load the records for example with Record gt Import Data by Mo
63. ew statistics computed in the yellow box The statistics tool extends the CubeView window adding a panel of statistics informa tion at the bottom The first two lines list the box size and position as well as the mininum maximum average median and standard deviations within the selected box The 3 sigma trimmed pixel count average and standard deviation in the box are given in the third line 30 Chapter 4 The Tools 31 Simply create or modify a box region see Section 4 4 3 2 Box Regions page 26 to view the statistics within that box The box region for the statistics tool is yellow An example of the tool s output is shown in Figure 4 6 The box statistics tool s key shortcut is s Chapter 4 The Tools 32 4 4 3 9 Aperture Photometry Tool CubeView ngc5194 SL1 18x1 Tue May Bee File Options Tools Eo esta leo ae E 47 6 64 06055 2 85687 13 28 50 793 47 11 38 2 Cube ngc5194 SL1 18x1 Tue May 09 02 53 53 2006 lave 11 2534 E Prev Next Play mE Play Speed Radius 5 00 Sky Width 2 50 J Centroid CEN 57 44 9 73 PHOT TEST 55 0232 Figure 4 7 Example CubeView aperture photometry centered on the centroid found in the box area The aperture photometry tool performs simple circular aperture photometry with a sky annulus It extends the CubeView window to report the photometry results at the bottom This panel includes text fields for entering the primary radius and sky annu
64. generate an error s SPECTRA MISMATCH When comparing spectra extracted from the same physical region flux offsets between modules and orders can occur To minimize this ensure the back ground was subtracted in the same manner for all cubes being compared and that the extraction region was large enough Slight astrometric errors in the final cube astrometry limited by the spacecraft pointing system s precision will compound offsets between matched spectra in very small regions near steep spatial gradients in the source 6 2 Creating 2D Maps Just as the cube can be used to generate 1D spectra over any extraction region so too can the 1D spectra be used to create 2D images slices of the cube averaged or integrated over any specified wavelength interval See Section 4 5 CubeSpec page 40 for more detail on defining regions on the displayed spectrum SAVE MAP AS FITS Any spectral map produced by CubeSpec can be saved to a FITS file by se lecting File gt Save Map as FITS from the CubeView menu 6 2 1 User defined Maps Once a 1D spectrum is visible in the CubeSpec window change the selection from Full Cube to Map and select either Peak or Continuum the convenient key shortcuts p and c set both of these at once and permit quickly switching between peak and continuum region definition A spectral map consists of any number of peak and continuum regions The Chapter 6 Cube Analysis 63 continuum
65. ground Chapter 5 Cube Assembly 49 FLUX UNITS WARNING Note that any fluxed 1D spectrum must be extracted from cubes built with the same flux options e g the SLCF correction as the cube to which it is being applied Spectra extracted from raw cubes in e s units do not have this restriction This method does not help mitigate rogue pixels and is essentially equivalent to ex tracting spectra and differencing them after the fact but operates on the entire cube at once 5 4 5 Combined 1D and 2D Background Occassionally a 2D sky spectrum obtained from the archive in a different region of the sky or from BCD data taken with different exposure times will do a reasonable job mitigating rogue pixels but leave a residual background positive or negative which is obvious in parts of the cube without signal This background offset can have a large effect on sources at or below the absolute residual background flux level The dark areas in a cube where the residual is obvious should of course be smaller than the slit length or else an in situ background could have been used see Section 5 4 1 In Situ Background page 47 Assuming you have located a region within the cube which you feel is free of source emission the residual background can be removed by combining the original 2D level back ground archive or otherwise together with a further 1D correction applied as a separate scalar subtraction to all wa
66. hat record s pixel must satisfy this cut For example if record 20 pixel 40 79 appears 4 times in the cube minbad frac 4 requires at least 2 of these appearances to be outliers at the sigma trim level to consider it a bad pixel Many more bad pixels will be generated by record level auto badpix but each of them will have a much smaller impact on the final cube since they disable that pixel for only a single record Often global bad pixels are sufficient In certain cases record level pixels automatically discovered are very useful for example for very short exposures 6s in which cosmic rays are incompletely identified by the pipeline This results in small 3 4 pixel stripes along rows which can often be identified automatically with record level auto bad pixels Chapter 5 Cube Assembly 55 CLEARING BAD PIXELS Note that by default the bad pixel list is appended to with subsequent runs of auto badpix Clear the bad pixel list first to avoid this and save intermediate results to bp1 files for added flexibility Obviously the amount of redundancy in a spectral map has a major impact on the degree to which outlier pixels can be automatically discovered A 1xn map no steps along the slit offers a minimum amount of pixel redundancy whereas a map stepped many times along the slit placing the same source position at multiple positions along the slit will offer much better redundancy With minimum redu
67. ing CUBISM is simple and requires replacing the source or binary installation di rectories with the newer version and restarting IDL You can always find out what version of CUBISM you are running with the menu Help gt About Cubism in the project window New versions of CUBISM are available at http sings stsci edu cubism Chapter 3 Quick Start Guide 6 3 Quick Start Guide CUBISM has two major functions building cubes from IRS Spectral Mapping data sets and analyzing those cubes Building cubes from collections of mapping data sets is in principle a simple process the correct BCDs are collected together in a project the cube build parameters are adjusted and the cube is built Further refinement of the cube includes identifying bad pixels to exclude from the cube build selecting and creating the appropriate background frames configuring the calibration details and cube build options etc Although straightforward this process can take a good deal of time Users should expect to spend between one half and one hour per IRS slit building and cleaning their cubes flagging and removing bad pixels etc With the assembled cube you can perform a variety of types of analysis including extracting 1D spectra in specific regions and building 2D spectral maps There are many details which can affect the cube assembly process and impact the quality of the final assembled product Here we will quickly go through the basic steps required to
68. inuum subtracted will be based on an average weighted by the distance away in wavelength from the peak to continuum point Normally all continuum planes are averaged with equal weight Only available when both peak and continuum regions are defined Integrate If set an integral over the background subtracted foreground region of f_nu d nu is performed In the case of weight maps e g MIPS 24um the d nu weighted integral int f_nu w d nu int w d nu is performed where w is the weight vector Reset Plot Pressing this button removes all zooms and region selections Chapter 4 The Tools 43 Remove Fit Pressing this button removes any fit generated Fit Perform a fit over the peak and continuum regions which must be defined first The polynomial order of the fit is determined by Fit Order Resulting fit parameters will be displayed at right 4 5 4 Display Panes Two display panes provide information on any line fit and the cursor position Right display box This box displays several values from any fits performed average continuum equivalent width of the line maximum flux maximum wavelength median flux median wavelength and line strength These values will disappear when you press the Remove Fit button Lower Right display box This box gives the wavelength and flux with the uncertainty of the current cursor position 4 6 CubeSpec Plot Window The plot window of CubeSpec is where maps are defined the
69. ion 5 4 Backgrounds All IRS observations are affected at some level by the foreground or background emission of zodiacal dust and Galactic cirrus For faint sources subtracting off a local sky background in the form of a 2D BCD frame constructed from data obtained nearby in position and time is the most effective method for removing the astrophysical background In addition BCD level background subtraction greatly reduces the number of bad or rogue pixels contaminating IRS data especially in the longer wavelength models and effectively reduces residual systematic uncertainties which dominate at low flux intensity often in the form of correlated patterns bands etc BCD level background subtraction is a recommended Chapter 5 Cube Assembly 47 step for all cubes ideally performed with associated background data obtained during the same AOR using the same integration time etc Here we explore a variety of options for background subtraction in decreasing order of preference The degree to which backgrounds must be suppressed also depends on the source flux Very faint sources at or well below the sky brightness level are more affected by residual background and low level systematics which often vary in magnitude and shape among orders and modules IMPROVING CUBES WITH BACKGROUND SUBTRACTION Subtracting a 2D background frame can greatly improve the quality of the assembled cube especially for faint sourc
70. ion File gt Save or File gt Save As to save a version under a different name or with the convenient Save button below the record pane File gt Revert to Saved allows you to discard any changes to the project and restore the version most recently saved to disk Not all of the data is saved with the project by default There are three options related to saving the project file accessible in the File gt Save Setup menu 1 Save Data with Project This saves a copy of all the loaded data including BCD associated masks and uncertainties into the project file This adds approximately 192kB per record to the size of the file and is only necessary when you intend to distribute the file independent of the data directories This can be useful for sharing cpj files with colleagues without access to the Spitzer archives but can result in Chapter 5 Cube Assembly 58 large files when many tens or hundreds of records are involved It is also redundant when the data files themselves are already available 2 Relative File Names By default the absolute paths of the data files are stored in the project and if the data themselves are not stored they will be recalled from disk when needed Unfortunately this makes cube project files non portable leading to errors like Couldn t restore data from file unless the absolute path to the BCD files is fixed on all systems where the cube is loaded While you can easily repl
71. ion 5 5 4 Automatic Bad Pixels page 53 and for confirming the data levels in low signal regions Alternatively for large source the outrigger field can contain interesting data in its own right Chapter 5 Cube Assembly 46 By default CUBISM sets the cube build order to the most common target order among the loaded BCD records Obviously if the full slit center was targeted no individual order is preferred so an arbitrary default is used In general you should check the cube build order to ensure you are building the cube you want In the project window Info gt Project Parameters provides this information and you can set the cube build order with Cube gt Set Cube Build Order Recall that each low resolution cube is built using data from a single IRS order e g SL1 High resolution order wavelengths are much more continuous and are combined directly in the cube 5 3 Calibration Sets CUBISM needs a large number of different pieces of calibration data to perform its tasks including flux calibration functions order positioning and wavelength solutions extended source flux correction functions etc These calibration data are tied directly to those produced by the SSC for point sources although they are extended and supplemented by additional information CUBISM uses the concepts of calibration sets unit bundles of calibration products which snapshot the latest calibration data appropriate for the most recent pipeline pr
72. ith each other so that up dates in one are immediately reflected in the others For example when selecting bad pixels see Section 4 4 3 12 Bad Pixel Tool page 34 the bad pixel list for the associated CUBISM Project is immediately updated or if a new list is loaded from file the viewer is updated Similar high level communication occurs between all of the sub tools so that you can regard a CUBISM project and all its associated windows and tools as a single consistent state 4 2 General Interface Tips The interactive component of CUBISM is based on IDL widgets which at least on the Unix OSX systems where CUBISM is tested are derived from the Motif widget set As such a variety of common keyboard and mouse shortcuts are available which can simplify interactive operations 4 2 1 List Selection In any list e g the CUBISM Project window see Section 4 3 CUBISM Project page 13 individual list elements can be selected by clicking with the left mouse button A range of elements can be selected by click dragging Alternatively the first element in a range can be selected and then the last element clicked while holding the SHIFT key Non contiguous regions can be selected by holding the CONTROL These methods can be combined e g to select two non adjacent regions click the first scroll to and SHIFT click the second scroll to and CONTROL click the third and finally SHIFT click the last The arrow keys scroll the selection up or
73. iven cube pixel This is a very powerful tool for validating features in a Chapter 5 Cube Assembly 53 cube In particular it is useful for identifying global or persistent record level bad pixels which impress stripes in the cube see Figure 5 2 See Section 4 4 3 11 Pixel Backtracking Tool page 33 for more on using this tool A typical workflow for identifying bad pixels using the backtracking tool is 1 Inspect each wavelength plane of the cube for out of place columns rows Using the left right arrow keys in an extracted spectrum Full Cube view is a quick way to step through the cube 2 Using the backtracking tool select a cube pixel inside a problematic feature e g a stripe 3 Note any pixels in the backtracked data set comparing to other cube pixels along the feature to note record pixels which are consistently outliers 4 Right click a given pixel to mark it as a global or record level bad pixel 5 Re build the cube after one or more pixels are marked to see whether the cube was improved If not undo and try again With QuickBuild see Section 5 9 QuickBuild page 57 this process is very fast even for large cubes The displayed cube and any extracted spectra are automatically updated A related useful technique is to extract spectra in different parts of the cube and look for non physical spectral features typically positive or negative spikes one pixel wide not corresponding to known lines Using CubeSpec s
74. k space approximately 400 700kB per record For distributing CUBISM projects as cpj files it s easiest to save the project without data or accounts the default since this produces the smallest files by far However this requires everyone to have access to the data in the same path for absolute file names or with the same relative path layout for relative file names as on the build host One approach for sharing the data and cube project together is to save the data in the project itself This creates a larger project file but is fully self contained Another reasonable approach is to use relative file names and bundle the cpj together with the data directories and visualization image if any in a single directory for distribution The advantage of the latter is it allows the cpj file to be updated independent of the data themselves For users who simply wish to examine the cube itself extract spectra make maps access to the record data isn t necessary any cpj with an assembled cube will do or even just the FITS Cube see Section 5 12 Reading a FITS Cube page 59 Chapter 5 Cube Assembly 59 5 11 Saving the Cube as FITS The cube can be saved as a 3D FITS file for further analysis using File gt Write FITS Cube If an uncertainty cube exists it will be saved alongside the main cube with _unc fits replacing fits Both FITS files include headers from the first assembled
75. l bad pixels set for a given record can be seen in the secondary pane of information in the CUBISM Project window The total number of bad pixels marked and their sources is given in the project parameters Info Project Parameters CubeView ngc1482 LL1 10x5 Mon Jul 10 08 52 52 2006 Dig Figure 5 2 An example of a global bad pixel impressing stripes in the output cube 5 5 2 Manual Bad Pixel Selection Bad pixels can be selected manually at several levels The most straightforward is at the BCD level simply examine a single or stack of records and mark errant pixels See Chapter 5 Cube Assembly 52 Section 4 4 3 12 Bad Pixel Tool page 34 for more on marking user or record level bad pixels and on the identifying symbols used to mark pixels MULTIPLE RECORD BAD PIXELS AT ONCE Setting record level bad pixels on a stack of more than one record sets that pixel in all the records in the stack A typical workflow for manually marking bad pixels at the BCD level 1 View the stack of relevant BCDs 2 Show the WAVSAMP see Section 4 4 8 CubeView WAVSAMP Panel page 39 3 Click BGSub if available to remove the appearance of many bad pixels using the record level sky background data previously defined 4 Enlarge the stack viewer window see Section 4 4 2 2 CubeView Options Menu page 23 5 Show the user cyan green x bad pixel and pipeline fatal red x
76. lus width for circular photometry A box is drawn blue for this tool and the centroid of the source Chapter 4 The Tools 33 in the box is computed and used to center two circular apertures source and sky If the Centroid option at bottom is de selected the center of the box is used as the center of the circular apertures instead There are actually two centroids computed a standard center of mass style centroid and a refined DAOPhot style vanishing derivatives centroid If the latter is invalid because it falls too far outside the box the former is used and the centroid is marked with an x in addition to a circle Enlarging the search box may help with accurate centroiding The total flux inside the inner circular aperture minus the scaled sky flux reported as the average within the sky annulus is given An example of the tool s output is show in Figure 4 7 The aperture photometry tool s key shortcut is p 4 4 3 10 Cube Extraction Tool The cube extraction tool is used to extract spectra from rectangular regions within a cube and can only be used when a cube is being displayed See Section 4 4 3 2 Box Regions page 26 for more on defining and manipulating a box region which is magenta for this tool Once an extraction region is defined the spectrum is displayed in the CubeSpec tool See Section 4 5 CubeSpec page 40 The cube extraction tool s key shortcut is x 4 4 3 11 Pixel Backtracking Tool
77. mance CUBISM can work with large projects using less memory but performance will suffer dramatically as data is paged to disk Note that data is loaded on demand so for instance viewing a pre built cube without reloading record data will consume only a small amount of memory 2 5 Running How CUBISM is run depends on how it was installed 2 5 1 Running the Source Distribution For source distributions after installation on your IDL path simply type IDL gt cubism and you are prompted to select an existing saved cube project or create a new one 2 5 2 Running the Binary Distribution Running the pre compiled binary version of CUBISM can be accomplished by putting the cubism_vm sav file in your IDL path and using IDL gt cubism_vm Another option allows you to run this binary file from anywhere not necessarily on your IDL path IDL gt restore path to cubism bin cubism_vm sav IDL gt cubism You can also run the compiled file in the free IDL VM which does not require an IDL license Chapter 2 Installation 5 idl vm path to cubism vm sav MacOSX users can accomplish the same thing by optionally using the precompiled wrapper Cubism app application simply double click or double click a cpj CUBISM project file Note that even under OSX CUBISM runs as an X11 application and that Cubism app is simply a wrapper to start IDL in the IDL Virtual Machine and load CU BISM 2 6 Upgrading Upgrad
78. masks only by right clicking two times see Section 4 4 3 12 Bad Pixel Tool page 34 Set the histogram scaling stretch to show only the very brightest pixels Mark gt 4 sigma deviations but ensure you are not marking line data Reset the scaling to show the next brightest set of pixels fer 00 esp m Mark gt 4 sigma deviations 10 Iterate this process until you can clearly see emission lines or other real features in the data to the point where the viewable pixels are no longer gt 4 sigma deviations 11 Save the bad pixel mask see Section 4 3 2 6 CUBISM Project BadPix Menu page 19 12 Re build the cube with this mask uses QuickBuild See Section 5 9 QuickBuild page 57 Note that most BCD records contain a rim of pixels flagged with 7 which appear as red diamonds surrounding each order These are flat field questionable pixels but experience shows that many of these pixels are useful They can be trimmed away by narrowing the WAVSAMP see Section 5 7 WAVSAMP page 56 but aren t considered fatal by default BAD PIXEL TIP When selecting bad pixels in cubes being built with a background be sure to enable the BGSub button before selection since this can mitigate many rogue pixels which would otherwise appear bad 5 5 3 Backtracking to Discover Bad Pixels Backtracking is the term used for listing all the BCD records and pixels within those records contributing to a g
79. menu CUBISM project 19 nput fileg o eor rre a e E VU PHI aere 44 Installation ees rin coe tee E IIR DIOE APIS 2 Installation binary eese 3 Installation from source 0 eee eee eee 2 Integrated maps seeeeeee 64 Interface tips is ne desti nr rb E ees 10 Introduction eerziRie elle pem bk RR sagen ff K Keys Shorteub er siessen ht Rr D RI QU RETE 66 L Dine fibs esseeri a Re p Pan ER SP ADER MURS 64 M Map Sets SAVNE rens ebore S an 64 Maps Menu CubeSpec 0 22 eee e ee 41 Maps Creating oco Ele ies UI D PERDRE 62 Maps integrated ssi en rte RR enn 64 Maps pre defined 2 0 e eee e eee 63 Maps user defined 2 2 c eee eee eee eee 62 Memory Requirements 0 000 4 Index Menus project window ssseeeeeeeese 14 O Options menu CubeView 22005 23 Order mask tool eie ee Rr beet ss 38 P Photometry aperture 2 cece eee eee 32 Pixel backtracking 5 Ra 33 Pixel table tool e tert RR ERERAS 38 PNG saving image as 000 23 Project window buttons 0 00 22 Project window menus 00 085 14 Project CUBIS Mii eio eppDIM minean A crite 13 Q Quick Start ioeoelbel eA DRM RR ede bee ee 6 QuickBuilld i 12er RR ep 57 R Record information seeeeeesese 20 Record menu CUBISM project 15 Re
80. must lie away from the median record pixel value contributing The MinBad Fac lists the minimum fraction of occurrence of a given BCD pixel in which it must deviate to be considered bad For example if sigma trim is 7 and minbad frac is 5 then a given BCD pixel is considered bad if at least 50 of the time it appears in the cube it is 7 sigma from the median pixel value Iv A utoB ad p j x x Figure 5 3 The dialog for setting auto bad pixel parameters The BG button determines whether the test for lying outside the sigma trim threshold is performed on the background subtracted data comparable to using the Val Back column in the backtracking tool This is typically a good idea since many pixels are not outliers when background subtracted The UNC option controls how the fiducial spread of data values is determined If it is set the pipeline estimated uncertainties are used If not a median absolute deviation is used as an estimate for the fiducial sigma value Since the pipeline uncertainties severely under estimate the true spread of data above S N 10 or so for bright sources it is best not to set the UNC option It can be useful for faint sources in particular when the redundancy is small Record level automatic bad pixels are similar to global bad pixels except instead of demanding that a given BCD pixel must deviate at least minbad frac of the time it appears in the cube only t
81. n a new viewer window Load New Visualization Image Load an alternate image for visualizing AORs 4 3 2 4 Cube Menu Build Cube Build the cube from the enable records Reset Accounts Reset the clipping accounts which speed cube re build and enable pixel back tracking View Cube View the cube in a pre existing cube viewer window if available View Cube new viewer View the cube in a new viewer window Show Cube Build Feedback If enabled plot cube build feedback while the cube builds Build Cube with FLUXCON Build the cube using flux calibration Build Cube with SLCF Apply the slit loss correction function to the assembled cube to correct for differential diffractive slit losses for extended sources Subtract Background Subtract the set background from each record when building the cube Trim Wavelengths Trim the unreliable ends of the orders omitting those wavelength planes from the cube Use Reconstructed Positions Use positions reconstructed from the spacecraft telemetry rather than the com manded positions Build Uncertainty Cube Build an associated uncertainty cube if record level uncertainties are available Set Cube Build Order Set the cube build order Aperture s Show the WAVSAMP apertures used for the various orders see Section 5 7 WAVSAMP page 56 Chapter 4 The Tools 18 4 3 2 5 Background Menu Set Background from Rec s Set the record level background from the
82. n be viewed and interacted with normally but are not included in the assembled cube This can be useful to omit the rare frame with garbled data or to include data in the project solely for the purpose of constructing a background Note that failing to disable records which are not associated with the AOR s constituting the map can cause the cube created to be very large or even fail 4 3 3 3 Record Data Types The IRS pipeline produces a variety of different types of output spectral data with differing levels of processing applied The standard product which CUBISM uses is the BCD or basic calibrated data In addition however CUBISM can operate on DroopRes not flat fielded or straylight corrected and FlatAp not straylight corrected data files See the IRS Data Handbook for more information on these different data products Typically they would be used in CUBISM to test results only if problems with the flat field or straylight correction SL were suspected Note that reference to the term BCD throughout this manual is inclusive of the other less commonly used files types FlatAp DroopRes 4 3 3 4 Operating on Records Individual records or groups of records can be examined for header information renamed deleted enabled disabled viewed as an individual or a stack averaged into a background frame and much more Most of these options are accessible from the Record menu see Section 4 3 2 3 CU
83. ndancy the number of record pixel samples mapping into a cube pixel is small and the natural spread of those samples which results from the edges of spectral lines or sharp spatial features falling into a single spectral cube can overwhelm bad pixels Extreme caution must be exercised in this case to avoid marking legitimate pixels at these edges 5 5 5 Saving Bad Pixels The list of global and record level bad pixels can be saved as text in bpl files using BadPix gt Save Bad Pixels This is useful for sharing bad pixel lists among projects and providing a backup of the marked pixels outside of the cube project recommended Bad pixels can be loaded in from bpl files as well either replacing the current set or appending to it The format of the bad pixel file is a list of 1D pixel indices 128 y x prepended in the case of record level bad pixels by a line with two entries the unique record ID DCEID and the number of bad pixels associated with that record The global bad pixel list follows See Section 4 3 2 6 CUBISM Project BadPix Menu page 19 5 6 Cube Build Settings The cube build settings are accessed in the Cube menu of the project window Typically the default values most options enabled are fine but for occasional uses you may prefer to disable some FLUXCON Typically you would build the cube in units of MJy sr using this option It enables use of the extended source flux calibration file
84. ng on the Reset Plot button all the continuum and peak selections will be erased and new spectral regions and their corresponding spectral maps can be defined Such fits are for informational purposes only and do not affect the map displayed Chapter 6 Cube Analysis 65 6 3 Complex Maps CUBISM offers only map creation based on simple averages or wavelength offset weighted averages among planes of the cube For higher order map creation e g to create derived maps by fitting multiple components to at each position it is convenient to export the full cube to the IDL command line or as a separate FITS file See Section 5 11 Saving the Cube as FITS page 59 for more information Chapter 7 Tips and Troubleshooting 66 7 Tips and Troubleshooting Here we document issues which are commonly encountered and provide tips on debugging CUBISM and providing useful feedback to the SSC 7 1 Mouse and Keyboard Shortcuts All collected shortcut keys and mouse actions for all three major tools are assembled here 7 1 1 Cube Project UP DOWN Arrows Move among records PAGEUP PAGEDOWN Move record lists by pages Shift click Select range of records Control click Select additional record Control click drag Select additional range of records Control shift click Select additional range of records from last click RETURN View record same as double clicking 7 1 2 Cube View SPACE Lock the current scaling limits Toggle zo
85. ns from cubes built in different IRS modules or orders will stitch with each other 5 4 7 Background Selection Using Visualization It can be convenient to select suitable records for inclusion in the background frame by using the AOR visualization of an IRAC or MIPS or other zodiacal and or cirrus sensi tive waveband image of the target region See Section 4 4 3 13 AOR Visualization Tool page 37 for more information on the visualization tool Here we describe how to use the outrigger method to select suitable records from a set of low resolution observations in the SL module LL would be similar 1 Load all the relevant SL SL1 SL2 frames which may span more than one AOR Using Import AOR will permit selecting more than one AOR at once Don t mix data taken more than a few days apart to minimize the effects of day to day changes in the pixel response of the detectors 2 Visualize the AORs using e g an 8 micron IRAC image see Section 4 4 3 13 AOR Visualization Tool page 37 After using the histogram box to scale the image such that low level diffuse emission is apparent switch to the visualizer tool To define background BCDs for e g SL1 set the cube build order to 1 Cube gt Set Cube Build Order and see which records are free of source flux Highlight these outriggers with the mouse by click and drag 3 For reference save the resulting record set into a bgl file using Background gt Save Background Recs
86. ocessing By default CUBISM loads the most recent calibration set which is bundled with it Typically you will not need to select a calibration set As long as you are using the most recent IRS pipeline processing version of your data the latest set is appropriate The calibration set used with a given cube is saved in its project file so that future use even after new calibration sets are created will continue to use that data You can see which calibration set you are using and inspect all of the parameters and input calibration files it consists of with Info gt Calibration Set Details New calibration sets cal files can be loaded with File gt Load New Calibration Set All input calibration files in incrementing versions can be found in the cubism calib data ssc directory in your CUBISM distribution Note that the general presumption is that more current calibration data is always better when used with data processed with the most up to date SSC IRS pipeline This is true in general although there is currently one time dependent calibration the input bias volt age for the LH detectors was changed CUBISM automatically uses the appropriate flux calibration values depending on the date of observation Though normally not necessary new calibration sets can be created from the assembled inputs using the included helper routine irs_make_calib_set see cubism calib irs_make_calib_set pro for more informat
87. of interest or simply click and release to double the zoom level and center on the clicked point To zoom out right click All zoom levels are saved onto a zoom stack which is navigated backwards one step at a time when right clicking To zoom all the way out right double click When an image is zoomed in middle click dragging or CONTROL click dragging pans the image smoothly While panning in this way holding SHIFT constrains the pan to be vertical or horizontal Middle click or CONTROL click and release re centers the image on the point clicked if possible If the display canvas is resized either using the Set Size menu item see Section 4 4 2 2 CubeView Options Menu page 23 or by re sizing the entire CubeView window the image is re zoomed The zoom tool s key shortcut is z 4 4 3 5 Histogram Tool The histogram tool is actually an image rescaling tool It allows you to identify a region of the image and rescale the image values to emphasize it Simply create a box area or move and resize an existing box area to the region of interest The scaling mode can be linear square root logarithmic or histogram equalizing with 196 or 596 trimming available in the Uptions Scale Image menu By default the entire image is scaled This tool also draws a histogram of the resulting image colors on the colorbar see Section 4 4 3 6 Color Tool page 28 and gives the scaling range The scale clipping limits can be frozen
88. om tool Click and release Zoom in on region 2x Click drag Zoom in on defined rectangular region Right click Zoom out one level Right double click Zoom out all the way Middle click Recenter on point Control click Recenter on point Middle click drag Pan image if zoomed in Middle click drag Shift Pan image contrained to horizontal or vertical if zoomed in Control click drag Pan image if zoomed in Control click drag Shift Pan image contrained to horizontal or vertical if zoomed in Chapter 7 Tips and Troubleshooting 67 h Toggle box scale histogram tool on twice to reset Click drag Define scaling box On handle resize box Arrows Move box 1 pixel with Shift 5 pixels with Control Shift 10 pixels c Toggle color adjust tool Click drag Change color map up down narrow widen left right shift Right click Reset color map 1 Toggle line slicing tool on twice to reset Click drag Define slice line Control Constrain Slice line to be vertical horizontal or diagonal Right click drag Constrain Slice line to be vertical horizontal or diagonal Middle click Define strip width for averaging Middle click drag Update averaging strip width S Toggle statistics tool Click drag Define statistics box On handle resize box Arrows Move box 1 pixel with Shift 5 pixels with Control Shift 10 pixels p Toggle photometry tool Click drag Define photometry b
89. ound The BCDs which contributed to the given cube pixel are highlighted in the associated CUBISM Project window Left clicking freezes on an individual cube pixel marking it with a green x while right clicking restores the free motion To stop backtracking close the backtrack window or reset the tool by clicking its icon again after it s enabled In the Back Tracking window right clicking on any individual list item pops up a context menu which allows the associated BCD pixel to be set or cleared as a global or record level bad pixel see Section 5 5 1 Global and Record Level Bad Pixels page 51 In addition you can simultaneously set a given BCD pixel as a record level bad pixel in all the listed records contributing that pixel using the Bad Pixel These records context menu option By default the list of contributing pixels is sorted by BCD identifier clicking on the column head buttons toggles sorting by any of the columns which can be useful for example to quickly identify major outliers in the distribution for long lists You can continue to navigate through the cube while backtracking is active The pixel backtracking tool s key shortcut is t 4 4 3 12 Bad Pixel Tool The bad pixel tools marks individual bad pixels either user flagged or pipeline produced and allows global and record level user bad pixels to be added or removed see Section 5 5 Bad Pixels page 50 for more information on different types of user level
90. ox On handle resize box Arrows Move box 1 pixel with Shift 5 pixels with Control Shift 10 pixels x Toggle cube extraction tool on twice to reset viewing cubes only Click drag Define extraction box On handle resize box Arrows Move box 1 pixel with Shift 5 pixels with Control Shift 10 pixels Chapter 7 Tips and Troubleshooting 68 t Toggle cube back tracking tool on twice to reset viewing single cube planes only Click Freeze backtrack on current pixel Right click Release freeze b Toggle bad pixel tool on twice to reset bcd only Click Add remove global bad pixel Middle click Add remove record level bad pixel for all records in stack Control click Add remove record level bad pixel for all records in stack Middle Control Click drag Add remove multiple bad pixels at once add vs remove based on initial point Right click Rotate through the four bad pixel view sets v Toggle AOR visualization tool on twice to reset visualize image only Click Select record will be outlined in white Outside of record overlays select no records Click drag Select range of records Shift click Select range of records from last selected Control click Select additional record Control click drag Select additional range of records Control shift click Select additional range of records t Toggle displaying pixel table W Toggle masking all off order data BCD only 1 4 Set size of vie
91. rms the default options See the documentation for these tools for more infor mation 4 2 4 File Selection Figure 4 2 A file selection dialog Chapter 4 The Tools 12 CUBISM uses a specialized file selection tool throughout which has some common fea tures n example dialog is shown in Figure 4 2 A list of wildcard filters is included relevant to the file being selected for opening or saving and new filters can be added Click on the Filter button for the current list Show A11 shows all files independent of the filter Directories are at left double click to navigate through them Arbitrary directory paths can be entered at the top Files in the current directory are listed at right click to select or double click to accept and return To the left of the Directories and Files header words are two small icons which when clicked pop up a list of recent directory or file selections which can be selected Chapter 4 The Tools 13 4 3 CUBISM Project 2 records selected 000 Build Cube Enable Disable View Stack View Cobe Inport AOR Save Close Figure 4 3 CUBISM Project Main Window with selected and disabled records The CUBISM Project is the central storehouse of all information relating to a single spectral cube This is where the raw spectral data are collected the calibration parameters are loaded and managed preferences are set the cube is assembled and outputs are saved ONE PROJECT PER ORDER A
92. rom NASA Goddard Be sure to include it on your IDL_PATH 4 A compiler for C source typically gcc or whatever the IDL routine MAKE_DLL looks for usually available by default Chapter 2 Installation 3 The compiler is required to auto compile a small piece of C code used to speed up the main cube building algorithm If this compilation fails an IDL version of this algorithm will be used which gives the same results but operates more slowly To install CUBISM from source 1 Unpack the cubism_vX XX_src tgz file where X XX is the version number in a directory on the IDL path e g id1 2 Ensure the irs_cubism directory which is unpacked is on the IDL_PATH e g by setenv IDL PATH lt IDL_DEFAULT gt HOME id1 System wide installation is also possible just install CUBISM in a location accessible by your entire group SMART USERS Users of SMART may experience file name conflicts with CUBISM in partic ular in an IDL session started by SMART As of version 6 2 4 SMART has been modified to avoid such conflicts upgrading to this version or later is highly recommended 2 2 Binary Installation The requirements for CUBISM running as a binary 1 A Linux Solaris Unix or MacOSX platform CUBISM may run under the Windows operating system but has not been tested on a Windows platform 2 A copy of IDL at version 7 1 or later This can either be a fully licensed copy or the IDL VM the fre
93. rum averaged over that region in the units specified in the cube build settings see Section 5 6 Cube Build Settings page 55 If the CubeSpec window was already open the spectrum will change to reflect the newly defined region and the area of extraction in cube pixels is displayed at the top of the CubeSpec window When you move or resize the region the spectrum will update automatically This is an excellent way to quickly see how the IRS spectrum of your source changes with position over the cube or extraction size Remember that the arrow keys allow the selection box to be moved one pixel at a time in CubeView or 5 or 10 with Any extracted spectra can be saved using File gt Save Spectrum As see Section 4 5 2 1 CubeSpec File Menu page 41 The save format is an ASCII file with encoded headers column delimiters and units in the IPAC table format the utility routine read_ipac_table supplied with CUBISM can read this format Any tb1 file saved in this way can also be used to define the region of extraction for another cube see below EXTRACTION APERTURE SIZE Avoid using extraction apertures smaller than roughly 2x2 pixels since over small regions pixel aliasing driven by the undersampled IRS PSF can lead to anomalous continuum sawtooth patterns near high spatial frequency regions within the cube 6 1 2 Matched Region Extraction Matched extraction is the extraction of spectra from a c
94. s Once reason you might prefer to build a cube without fluxcon is to make a 1D background in e s units for loading as a background spectrum see Section 5 4 4 1D Sky Spectrum Background page 48 SLCF The slit loss correction function is used to correct the native IRS pipeline cal ibration tuned for point sources to the case of perfectly extended sources While most sources are not entirely smooth and slit filling this option should be enabled in most cases except for point sources Note that the CUBISM calibration of extended sources is made using the SLCF point source spec trophotometry will be more accurate using SPICE or another single pointing extraction tool Chapter 5 Cube Assembly 56 Subtract Background Only available if a background is set this is usually a good idea unless you d like to create a 1D background spectrum directly or check the cube without background removal Trim Wavelengths Trimming the unreliable order ends is never a bad idea unless you are specif ically interested in the spectrum there Note that some additional trimming may be required this is a conservative trim by default Reconstructed Positions Unless the reconstructed slit positions are thought to be in error use this option Disabling it uses the pre programmed requested slit positions which can be off by several arc seconds Uncertainty Cube Only an option if all your records have uncertainties this builds a full uncer taint
95. s the tool which permits viewing and manipulating extracted spectra and cre ate maps from spectral cubes The CubeSpec tool is a custom viewer used to view one dimensional spectra extracted from a cube see Section 4 4 3 10 Cube Extraction Tool page 33 It is entered by extracting a spectrum from a cube and is always associated with a CubeView window displaying a cube CubeSpec Extracted from ngc0024 LL1 67 2 gt 79 8 Avg Cont v Full Cube Mouse w XZoom w YZoom gt Region Equiv Width Max Flux Map Max Mavez 4 Integrate ti Median Flux CM d Median Wave 34 92 Line Strength 1 5874E 00 27 663 1 04540 02864 F ValLine F Errors Fit Order Extracted from ngc002 Figure 4 11 CubeSpec window showing an extracted spectrum and 4 component map 4 5 1 Title Bar The title bar of CubeSpec gives an indication of what is currently being displayed An example is CubeSpec Extracted from ngc2403_extranuc00 2 1 gt 10 5 This in formation will change depending on the cube extracted and region extracted from The same information is repeated as the title in the plot Chapter 4 The Tools Al 4 5 2 Menus 4 5 2 1 File Menu Save Spectrum as Save the current spectra as a tbl file ASCII text IPAC table format Export Spectrum to Command Line Export the current spectra as an array variable on the IDL command line Close Close the CubeSpec Window 4 5 2 2 Maps Menu Save Current M
96. se files into a new project file and save yourself time if you are breaking a large Project into several smaller project files and they are a useful backup in the case of loss or damage to the cpj file 3 Use auto badpix with care This can be a big time saver but can mark valid data bad if used improperly especially on maps without much cube level redundancy 4 Check spurious spectral features using backtracking Unexpected positive or negative spikes in an extracted spectrum often indicate remain ing bad pixels Use backtracking to track them down see Section 5 5 3 Backtracking to Discover Bad Pixels page 52 Quick build and the cube and spectra are instantly updated 5 Avoid over zealous bad pixel removal Sources with strong high frequency spatial structure e g point sources will necessarily have a broad range of data contributing to some pixels in the cube in particular due to the limited PSF sampling Marking all outliers of any sort bad either by hand or using auto bad pixels will result in depressed or elevated chunks in the spectra with no obvious cause Using backtracking try un setting related global bad pixels and quick building 6 Use keyboard shortcuts to speed up the interface Keyboard shortcuts are available in CubeView e g z to switch to the zoom tool SPACE to freeze the scaling range etc in CubeSpec e g p to enter peak region define mode arrows to move or resize regions etc
97. single CUBISM project contains information for only one spectral cube corresponding to a single IRS module and order This includes sub slits for single IRS modules e g SL1 and SL2 would be two separate cubes There is a separate project window for each open cube For information on how to extract spectra from matched areas in multiple overlapping cubes see Section 6 1 2 Matched Region Extraction page 60 CUBISM projects with all their associated meta data can be saved to and recovered from disk with the default file extension cpj for Cubism Project In a sense the project is the fundamental file type of CUBISM and can be manipulated in a similar way as a document in other applications Open Close Save Revert etc You can have as many CUBISM projects open at once as your memory will allow though all the windows associated with a given project can quickly overwhelm your screen Any given CUBISM project can be read from and saved to disk manipulated from the command line or interacted with via the GUI interface Internally and on disk a full CUBISM project is a single IDL object which contains a rich nested hierarchy of data and Chapter 4 The Tools 14 other information Typically you interact with a project via the graphical interface though it can be manipulated directly from the command line as well The figure above shown an example CUBISM Project window populated with a mapping data set
98. sition feedback E Box Statistics Calculate and report statistics in s box e Aperture Photometry Perform simple circular aperture p photometry on sources E Cube Extraction Extract spectra from rectangular x regions from the cube Pixel Backtracking Backtrack cube pixels to con t tributing BCD pixels Bad Pixel Examine and edit the global and p record level bad pixels Visualization Overlay AOR slit positions and v permit selecting records from the overlay The non exclusive tools are Button Tool Purpose Pixel Table Display a grid of pixel values un der the cursor M Order Mask Mask out all data outside the or ders Compass Rose Display a compass rose Not all tools are active at all times inactive tools are grayed out Among the tools Cube Extraction can only be used when viewing a cube pixel backtracking can only be used when viewing a single cube plane and bad pixels and order masking are enabled only when viewing BCD data Visualization is only possible with a visualization image and the Compass Rose is disabled except with cubes and visualization images i e images with WCS coordinate information 4 4 3 4 Zoom Tool The zoom tool allow arbitrary zooming in on image regions and panning within images By default images are displayed at the maximum integer zoom which fits the entire image Chapter 4 The Tools 28 in the display window To zoom in drag a rectangular region around the area
99. t a directory which contains one or more AORs and CUBISM searches all BCD files contained in that directory or its subdirectories assembling them into constituent AOR sets Select one or more of these AORs to load the associated data sets into the cube project An example can be seen in Figure 5 1 See Section 4 3 3 3 Record Data Types page 21 for more information on non BCD data types which CUBISM can use typically only for debugging problems with the pipeline processing Note that CUBISM projects can contain data from only one IRS module at a time and that CUBISM does not check to see that the data sets you have selected are physically grouped covering a moderate sized region on the sky Chapter 5 Cube Assembly 45 Load Group Figure 5 1 Importing AOR data grouped by AORs found in the selected directory Loading sets of non mapping data for the purpose of background subtraction see Section 5 4 Backgrounds page 46 can be accomplished conveniently using the Record gt Import Data by Module Simply point at a directory containing the data of interest and select the appropriate data sets grouped by object and IRS module 5 2 Build Order For low resolution IRS spectral maps there is a subtle distinction between the build order of a given cube produced by CUBISM and the target order of the observations from which it was built which is worth discussing in detail Each low resolution IRS slit consists of
100. that most BCD records contain a rim of pixels flagged with 7 in their BMASK which indicates the flat field is questionable there These are not fatal bad pixels and should not be excluded simply because they are flagged 5 8 Building the Cube Once the data records are assembled backgrounds are set and obvious bad pixels are marked a first pass cube can be assembled Note that disabled records are not included in Chapter 5 Cube Assembly 57 the cube build Frames which are completely garbled a rare occurrence should be disabled as should data records which are used only for setting the background which may be far away on the sky Select Cube gt Build Cube or press the Build Cube button and watch the cube build progress plotted records lain out and clipped against the sky grid and then final cube pixels assembled from the record data Typically several iterations of cube building are performed refining the background and bad pixel selection before the cube is considered complete Once the cube has been built once subsequent builds will proceed much more quickly since the account information which includes all the clipped pixel mapping from BCD to the sky grid is saved Changing the WAVSAMP build order or manually resetting the accounts with Cube gt Reset Accounts will invalidate the accounts which will need to be reconstructed in a slow cube build Changing backgrounds bad pixels etc
101. tive An example is the bad pixel tool which continues to display bad pixel marks even when it is not the active tool i e when mouse clicks don t affect the bad pixel mask To remove these displays reset the tool as described Tool tips identifying the tool its key shortcut and associated mouse operations encoded as left middle right can be displayed by hovering the mouse over the tool button in the tool palette 4 4 3 2 Box Regions Multiple tools make use of box regions for instance to define an area for computing statistics or scaling the image see e g the red box in Figure 4 4 When another tool is activated these tools leave behind corners of the box area to indicate their selection Reactivating the tool restores this preexisting box Click and drag from upper left to lower right to define a box area initially Click and drag within the box to move it or on the handle at lower right to resize it The arrow keys also move the position of the box by one pixel at a time Reset the box as described in Section 4 4 3 1 Tool Interaction page 26 4 4 3 3 Tool Overview The individual exclusive tools with their button icons are Button Tool Purpose Shortcut Zooming Zoom in and out of images Zz Histogram Scaling Re scale image to highlight local h features Color Table Adjust color table end points and c gamma Chapter 4 The Tools 27 Image Slicing Plot data slices through images 1 with po
102. tted spectrum Chapter 6 Cube Analysis 64 6 2 3 Map Sets User defined map sets can be saved for later use using the CubeSpec Maps menu A given set of peak and continuum regions can be saved as a map file using Maps gt Save Current Map and later recovered Once saved or restored it will appear below the default pre defined maps at the bottom of the Maps menu For example a map defined in LL1 on the SilI line with adjacent continuum could be saved as siII map and later re used to create similar SilI image from another LL1 cube To make a map saved in this way one of the default maps move it to the cubism map_sets directory 6 2 4 Redshift and Maps Sources at non negligible redshift can have saved maps automatically shifted into the ob served frame by specifying their redshift cz in km s with Maps Set Redshift The currently set redshift will be displayed at right in the plot title window and will be used to shift any saved map set to the rest frame For example in the SiII map example above specifying a redshift will shift the saved map to track the line in sources at higher redshift Note that pre defined map sets based on filter curves are not shifted in this way since they are meant to define pseudo images simulating direct observation 6 2 5 Integrated Maps By default CubeSpec produces average surface brightness maps typically in units of MJy sr averaged over all foreground
103. u can Edit gt Select A11 then Edit gt Replace File Substring to correct the base pathname you can use regular expressions in the search Another option is to store the data inside of the project or save it with relative pathnames See Section 5 10 Saving the Project page 57 2 I m attempting to upgrade a project from pipeline version S14 to 15 but the project data won t load The SSC increments a version number in the filename for all processed files every time the pipeline processing changes You can use the same technique as in the last tip to e g Find _4_ and replace with _5_ or whatever the relevant version numbers happen to be 3 CUBISM freezes There a number of reasons why CUBISM could freeze but commonly it only appears to be frozen due to a dialog which is awaiting your attention and must be dismissed before the rest of the program is responsive Alternatively if you are using the command line version of CUBISM you may have run other routines at the command line which have halted due to errors Usually retall takes care of these cases and restores response See Section 7 4 Debugging CUBISM page 73 if these are not the problem 4 My CubeView window gets overwritten when I visualize or display cubes or records You can have as many CubeView windows as you want associated with a cube By default however CUBISM recycles CubeView windows to avoid too much clutter on your display If yo
104. u want a new window for instance to visualize an AOR or cube while examining data records use the new viewer version of the view commands See Section 4 3 2 CUBISM Project Menus page 14 5 My cube seems to have skipped some rows or seems to be missing data There are two possible reasons for this One is that you disabled some of your records when making the cube see Section 4 3 3 2 Record Enabled State page 21 The other is that your initial map was not properly sampled We have seen at least one example of a map that was done using full slit spacings which was not contiguous The most likely reason for this is the pointing uncertainty in making the observations If you do full slit spacings it is possible that small gaps may result in your final map To avoid this please see the IRS Spectral Map HOWTO for information on observation planning 6 My cube seems to be built in the wrong spectral order Did you double check the cube build order Cube gt Set Cube Build Order Re member that saving the cube with a different name does not change the cube build order and that the target order of the data does not control the build order see Section 5 2 Build Order page 45 7 I have 4 different projects open and I can t keep track of what is what Look in the title and status bars of each tool for information on the source cube Consider adopting a different color table for all CubeView tools displaying a given project
105. ube in an aperture defined elsewhere All spectra saved by CUBISM include header information giving the celestial coordinates of the region of extraction This aperture can be reused to recover spectra from different cubes built in the same region It is most commonly used to generate single fully stitched Chapter 6 Cube Analysis 61 spectra by matching the physical extraction region between different cubes in different IRS modules or orders e g matching SL1 and SL2 or SL1 with LL1 SH with LH etc and import non rectangular extraction regions defined elsewhere It can also be convenient to recall existing extraction regions from the same cube MATCHED APERTURE SIZE When defining an aperture intended to be matched across multiple IRS mod ules ensure it is large enough to avoid pixel aliasing in all modules being extracted In the CubeView window displaying your cube use File gt Extract Region from File to load a saved region file either in the form of a tbl spectrum file created by CUBISM or a limited subset of reg DS9 region file Once this is done the spatial region will be displayed on your current cube in the CubeView window and a spectrum will automatically appear in a new CubeSpec window Aperture regions loaded from file in this manner are not directly editable Note that since cubes are built with position angle parallel to the IRS slit at the time of observation which rotates throughout the year
106. ue bit 8 in the BMASK not flat fielded is not marked since it occurs everywhere off the orders All BMASK values whether marked or not are indicated in the status display line see Section 4 4 5 CubeView Status Display Line page 38 When viewing and setting bad pixels in CubeView the right mouse button can be used to cycle through 4 settings controlling which bad pixels are indicated 1 All mask and user set bad pixels marks 2 All mask and user set bad pixels marks except for non fatal BMASK marks 3 All fatal BMASK mask and user set bad pixel marks 4 Only user set bad pixel marks SHIF T right click cycles in the opposite direction The bad pixel tool s key shortcut is b Chapter 4 The Tools Ifl Cubeview ngc5194 SL1 Average of 9 r Je J Figure 4 9 A record stack with bad pixels displayed 36 Chapter 4 The Tools 37 4 4 3 13 AOR Visualization Tool CubeView ngc5194 SL1 SLI n5194 v5 BIENES Figure 4 10 A visualization of the records on an IRAC 8 micron image of M51 with 13 records selected It can be useful to view a graphical representation of the AOR layout overlaid of an image of your target The AOR Visualization tool can be activated from the CUBISM Project window by choosing Record gt Visualize AORs see Section 4 3 2 3 CUBISM Project Record Menu page 15 This will prompt for an image to use for visualization if none is set Select a FITS image with v
107. ull cube project files see Section 5 10 Saving the Project page 57 N LoaD FITS CUBES By default when opening a cube from File gt Open or when calling cubism directly only cpj files will be displayed To load a FITS cube select the fil ters list to display fits files and ensure you select a 3D FITS cube generated by CUBISM A Chapter 6 Cube Analysis 60 6 Cube Analysis Once a given cube is fully built and validated it can be used to generate 1D line extractions and build arbitrary 2D spectral maps both of which are straightforward using the CUBISM interface These types of cube analysis can be performed either from a full CUBISM project or from a 3D FITS cube with some limitations 6 1 Extracting 1D Spectra To generate a 1D spectrum you must first identify the spatial region over which the spectral cube is to be averaged This can be done in one of two ways directly defining a rectangular aperture on the cube or from a matched extraction region read in from an existing tb1 spectrum file or DS9 region file 6 1 1 Direct Extraction See Section 4 4 3 10 Cube Extraction Tool page 33 for more information on defining a rectangular extraction aperture on a cube Briefly choose the extraction tool hit x in the CubeView window displaying the cube drag from top left to bottom right to define a rectangular region and a CubeSpec window opens showing the flux intensity spect
108. velength planes in the cube Assemble the 2D background subtracted cube extract the region and save the resulting spectrum to file At this point you might like to load in the spectrum at the command line fit a low order polynomial to it and write it out again to avoid adding noise into the cube Something like IDL gt p read ipac table file tbl h UNITS u IDL gt fit poly fit p wavelength p flux 2 YFIT yf IDL gt p flux yf IDL gt write ipac table file tbl DATA p HEADER h UNITS u will accomplish this Then load this 1D background using Background gt Load Background Spectrum You will recieve a warning that both 1D and 2D record level backgrounds are being applied Re build the cube and extract the same region the spectrum should be near zero with noise EXTENDED SOURCE WARNING CUBISM does not verify that fluxed 1D background spectra have the same extended source corrections applied as the target cube Ensure this yourself 5 4 6 No Background Using no background is a reasonable last resort option for brighter sources though the number of bad pixels in the raw unsubtracted data will be much higher so more work will be required to identify them see Section 5 5 Bad Pixels page 50 The astrophysical Chapter 5 Cube Assembly 50 foreground flux will also of course remain in the final assembled cube which may affect analysis of extracted spectra or maps and the degree to which matched extractio
109. view is modified etc What operations are performed by the mouse is determined by which Mouse mode is selected in the button panes above XZoom YZoom Click twice to zoom in on the wavelength or flux scale Region Lambda Full Cube Clicking on a wavelength plane sends that plane to the viewer The plane can be moved using the arrow keys Holding SHIFT with the arrow keys moves 5 wavelength steps SHIFT and CONTROL together moves by 10 steps Map A Peak or Continuum region is formed by clicking twice once at the start and once at the end of the desired region Middle clicking selects regions SPACE to switch among the selected regions When a region is selected left and right arrows move it up and down increase or decrease its width When defining a region for a map or X YZoom the region can be canceled after the first click by right clicking During region definition a line is left at the location of the first click Chapter 5 Cube Assembly 44 5 Cube Assembly This chapter describes in detail the steps required to assemble a cube from a set of mapping BCDs A quick checklist of these steps is 1 See Chapter 3 Quick Start Guide page 6 for more on starting and running CUBISM 2 Create a new cube project and enter an appropriate name for the project this can be changed later and is not the same as the project s cpj file 3 Accept the default latest calibration set or load a specific set 4
110. w window to 245 384 512 768 pixels 0 Set size of view window to wrap full image at current zoom if possible Chapter 7 Tips and Troubleshooting 69 7 1 3 Cube Spec Click Right click Middle click drag u d SPACE UP DOWN Arrows LEFT RIGHT Arrows 7 2 Tips Define beginning or ending point for region Cancel region selection or zoom out Move peak or continuum regions Full cube mode single wavelength plane at a time Map mode X zoom mouse region click twice to zoom in on wavelength Y zoom mouse region click twice to zoom in on spectrum flux Select wavelength plane mode Select continuum region define mode Select peak region define mode Toggle displaying the value line Delete selected region Select next region Enlarge reduce peak or continuum region size Move selected region or wavelength plane by one step with Shift 5 steps with Control Shift 10 steps Perform line fit peak and continuum regions required Reset plot Close CubeSpec window The most common and useful tips 1 Save Often You can always revert to the file on disk or save multiple versions of a project under different names 2 Save bad pixels and background records Chapter 7 Tips and Troubleshooting 70 You can save your bad pixel and background records in separate files from your project cpj file These are bp1 for bad pixels and bgl for backgrounds You can then load the
111. wavelength planes after optional continuum sub traction If the Integrate button is selected the foreground region s will instead be integrated over 7 f dv which will change from flux density to flux units e g W m 2 sr For weight maps e g the MIPS 24um or IRAC 8um maps the frequency spacing weighted integral 35 f wdv Y wdv is performed instead where w is the weighting vector e g filter transmission function Often this results in only a small difference in the resulting map image 6 2 6 Wavelength Weighting If the Lam Weight button is selected rather than average all continuum planes together CubeSpec preforms a weighted average for each foreground plane with the weight set to 1 1 As Ac where A is the wavelength of the given foreground plane and A is the wavelength of a continuum plane In this way each foreground plane gets a custom background with more weight given to the closest continuum regions This can be useful when averaging multiple peaks with a strongly varying continuum 6 2 7 Line Fits The CubeSpec window can also be used to measure simple line parameters before or after the line map is made By selecting the Fit button a polynomial fit as defined by the Fit Order will be performed between the continuum points and the basic parameters e g line equivalent width line flux average continuum flux density etc will be displayed in the box in the upper right of the CubeSpec menu By clicki
112. with SPACE or specified directly using Options gt Set Scale Range It can be convenient to reset the histogram tool to remove it s box area and define a new one in particular if you are zoomed in on a different region of the image To quickly reset and turn it back on hit the key shortcut twice The box region for the statistics tool is red and can be seen in Figure 4 4 The histogram tool s key shortcut is h 4 4 3 6 Color Tool The histogram tool provides a much more direct means to bring out detail in a given image area but the color tool allows one to use palettes similar to those found in SAOImage DS9 One can use the click and drag method for adjusting the color map directly Simply left click hold and drag around the window Moving down narrows the color map and up widens it changing the contrast Moving left shifts the upper and lower cutoffs to lower color values and right shifts them to higher values Right clicking resets the color map If you find yourself using this tool often to bring out detail in different regions of an image try out the histogram tool instead and see if you prefer it The color tool s key shortcut is c 4 4 3 7 Image Slicing Tool The image slicing tool allows slices to be taken through any image at arbitrary angles either a single pixel wide or averaged over a given width Just left click and drag to define a slice at any angle or hold down CONTROL or right click and drag to constrain th
113. y cube in parallel PIPELINE UNCERTAINTIES Note that pipeline uncertainties are statistical ramp uncertainties only valid only in the low S N limit Above S N 10 20 systematic uncertainties not accounted for by CUBISM dominate 5 7 WAVSAMP The WAVSAMP is the set of pseudo rectangles which define the spectral order s location on the array the tilted locus of constant wavelength and the wavelength calibration see e g Figure 4 4 CUBISM uses a custom built version of the WAVSAMP which differs slightly from that used by the SSC The exact position and size of the WAVSAMP changes with new SSC calibrations and it typically includes a small amount 1 2 pixels of spurious data at the extremities of the slit For spectral maps without any stepping along the slit 1xn maps leaving this crust of spurious data will have little impact since it can be ignored when extracting spectra and making maps For maps with along the slit redundancy however it is important to exclude this data directly See Section 4 4 8 CubeView WAVSAMP Panel page 39 for more information on editing the WAVSAMP Typically the WAVSAMP is edited and the central handle is used to drag each side in by 2 5 the reported WAVSAMP coordinates are in normalized units 0 0 1 0 to exclude the bulk of the spurious data at the slit ends Non uniform edits different normalized range at each end of the order are not recommended Note

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