DATACUBE — An IFS datacube manipulation package
Contents
1. 5 2006 March 10 Version 1 1 Add gridspec and velmoment and used implementation status MJC 6 2008 July 2 Version 1 2 Added trendview and improved the introduction MJC 7 2010 July 13 Version 1 2 Added pvslice MJC SUN 237 4 Contents 3 SUN 237 4 The Datacube Package 1 The Datacube Package DATACUBE is a collection of C shell scripts layered on top of various pieces of the Starlink Software Collection SSC for the analysis of spectral datacubes such as from integral field spectrometers The scripts permit graphical selection of spatial and spectral regions and features using the cursor DATACUBE provides facilities e to view a white light image of the whole and or part of the spectral range passband e to view a grid of channel maps of defined spectral width to extract individual spectra to extract an arbitrary position spectral slice e to compare spectra to average and compare groups of spectra to plot a grid of spectra with spatial averaging e to build a velocity map from an emission line by line fitting velmap or by intensity weighted moments velmoment or by selecting a cube s voxels using the values of another velocity map as spectral co ordinates mapbyvel e to build an emission line strength map peakmap and to plot multiple spectra from a cube overlaying fitted baselines and spectral feature mask tendview The backbone of the DATACUBE Package is the IFU Data2. Command line Arguments e a Requests that each fit may be inspected then approved or re fit not just the initial reference fit A re fit will change the initial parameter guesses for subsequent fits so it is recommended that you note the co ordinates of spectra to re fit and tackle these individually in the final manual re fit stage FALSE e c number Number of contours in the white light image Set to fewer than 1 means no contours are overlaid 15 e ci index The palette colour index of the contours It should be an integer in the range 0 to 15 It is best to choose an index corresponding to white or black or another dark colour to make the contours stand out from other elements of the plot 0 is the background colour KAPPA GDSTATE will list the current palette colours 0 e f Force the script to accept the first attempt to fit a Gaussian to the line This is a dangerous option if the fit is poor or unobtainable the script may terminate abruptly 15 Notes peakmap SUN 237 4 Descriptions of Individual Applications if it is forced to accept the fit This will additionally suppress manual re fitting of bad pixels at the end of the run of the script FALSE i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input file 1 filename The name of an text log file containing the fitted Gaussian coefficients for each sp
3. p r number s system z z Command line Arguments e b string The number of spectra to block average along the X and Y axes respectively This should be a comma separated list or a single number the latter case applies the same compression factor to both spatial axes The numbers must be positive integers 1 e c number Number of contours in the white light image Set to fewer than one means no contours are overlaid 15 e ci index The palette colour index of the contours It should be an integer in the range 0 to 15 It is best to choose an index corresponding to white or black or another dark colour to make the contours stand out from other elements of the plot 0 is the background colour KAPPA GDSTATE will list the current palette colours 0 e i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input file If there are multiple spectral lines present you should supply an NDF section after the name to restrict the spectral range analysed to a specific line and its environs e o filename The filename for the output NDF of the velocity map e p The script will plot the final image map to the current display as well as saving it to 29 Notes velmoment SUN 237 4 Descriptions of Individual Applications an NDF file Additionally it will over plot the white light image as a contour map for comparison FAL
4. 19 squash SUN 237 4 Descriptions of Individual Applications squash Extracts a two dimensional white light image from a three dimensional IFU NDF Description This shell script reads a three dimensional IFU NDF as input and allows you to extract a specific spectral range from the cube to form a white light image Usage squash i filename 1 number o filename p u number Command line Arguments e i filename The script will use this as its input file the specified file should be a three dimensional NDE by default the script will prompt for the input file e 1 number Lower spectral axis bound of the region of interest e o filename The filename for the output white light or passband image By default the script will prompt for the name of the output file SB The script will plot the extracted image to the current display as well as saving it to an NDF file FALSE e u number Upper spectral axis bound of the region of interest Implementation Status This script invokes a collection of A tasks from the SUN 95 package SUN 237 4 Descriptions of Individual Applications 20 stacker stacker Plots a stack of spectra extracted from a three dimensional IFU NDF Description This shell script reads a three dimensional IFU NDF datacube as input and presents you with a white light image of the cube You can then select a number of X Y position using the cursor The script will then extract and displ
5. Product Cookbook SC 16 This includes illustrated examples of the DATACUBE scripts script programming tips and lists of potentially useful applications to manipulate and analyse cubes The C Shell approach was a deliberate design decision which was made for two main reasons first due to the still developing nature of the field it is difficult to pin down exactly visualisation tasks will be necessary and the choice of csh means that the existing scripts can be easily modified by the end user to do exactly the job required second after examining the Starlink Software Collection SSC it was realised that a great deal of the functionality required to analyse IFU data already existed and it would be wasteful to re invent the wheel by re coding large chunks of software Some tasks once mature can and should be re coded in FORTRAN or C mainly for the speed and memory advantages that this will bring For instance the velmap script as implemented is rather slow and memory intensive it seems likely that this will be the first candidate to be re coded in a lower level language Hopefully while I haven t managed to think of everything there is enough ground work here so that the approach to solving your data visualisation or data cube manipulation problem is obvious even if the package doesn t have a script or application to do exactly what you require SUN 237 4 Setting up the applications 4 While this document contains the detailed
6. The schema includes the units and a brief description of each column and the name of the input NDF used The table lists the Gaussian centre peak height the FWHM and integrated flux each with its fitting error o filename The filename for the output NDF of the velocity map P The script will plot the final image map to the current display as well as saving it to an NDF file It will additionally overplot the white light image as a contour map for comparison FALSE r number Rest frame spectral unit of the line being fitted s system The co ordinate system for velocities Allowed values are VRAD radio velocity VOPT optical velocity ZOPT redshift and VELO relativistic velocity If you supply any other value the default is used VOPT V The script will generate a variance array from the line fits and attach it to the velocity map NDF FALSE Z The script will automatically prompt to select a region to zoom before prompting for the region of interest TRUE z The script will not prompt for a zoom before requesting the region of interest FALSE The velocity map display scales between the 2 and 98 percentiles The map uses a false colour spectrum like colour table so that low velocity regions appear in blue and high velocity regions appear in red 27 velmap SUN 237 4 Descriptions of Individual Applications e CURSA CATCOPY may be used to convert the STL log file see the 1
7. default the script will prompt for the input file Z The script will automatically prompt to select a region to zoom before prompting for the region of interest TRUE z The program will not prompt for a zoom before requesting the region of interest FALSE The compression is trimmed so that only compression factor multiples of original pixels are included in the plot The spatial averaging is aligned to obtain the expected number of pixels irrespective of the pixel origin of the input cube Note that this may not be suitable if you wish to preserve alignment with another compressed dataset See KAPPA COMPAVE parameter ALIGN for more details 9 gridspec SUN 237 4 Descriptions of Individual Applications Implementation Status This script invokes a collection of A tasks from the SUN 95 package SUN 237 4 Descriptions of Individual Applications 10 mapbyvel mapbyvel Uses a velocity map to extract values from a velocity cube forming a new map Description This shell script uses a velocity map of a spatial region to create a new velocity map The spatial co ordinates and velocity value at each pixel specify the co ordinates of voxels in a spectral cube The data value in the cube at this voxel becomes the data value in the output map While creating velocity maps is the expected usage for the script it makes no specific tests that the Z co ordinate is velocity or even that the image value is velocity In mathematica
8. descriptions of the shell scripts included with the package the how to information detailing their use can be found in SC 16 I would welcome comments criticisms contributions and corrections to the package once people start to figure out what they want to do with this sort of data Comments can be sent either to the authors atlaalastro ex ac uk or mjcOstar rl ac uk or to the Starlink software librarian starlink jiscmail ac uk 2 Setting up the applications After sourcing the Starlink star etc login and star etc cshrc files the datacube command will make the datacube package scripts available to you the following message or one much like it should appear datacube DATACUBE applications are now available Version 1 2 Support is available by e mailing starlink jiscmail ac uk Type cubehelp for help on DATACUBE commands Type showme sun237 to browse the hypertext documentation or showme sc16 to consult the IFU data product cookbook at this point you can test whether the datacube package has been correctly installed by typing datacube_test which will run the test script for the package If the script does not run correctly you should consult your Starlink system administrator It should be noted that there are a great many useful applications available in other Starlink packages that will assist you in dealing with your IFU data see SC 16 for details so you may at the very minimum wish to setup th
9. will prompt for the input file Implementation Status This script invokes a collection of A tasks from the SUN 95 and FIGARO packages SUN 237 4 Descriptions of Individual Applications 8 gridspec gridspec Averages groups of neighbouring spectra of a three dimensional IFU NDF and then plots these averaged spectra in a grid Description This shell script reads a three dimensional IFU NDF as input and if you request zooming the script presents you with a white light image of the cube You can then select the lower and upper spatial limits to plot using the cursor You can instead supply an NDF section with the filename to define both spatial and spectral limits to plot The script averages spectra in the chosen region by specified compression factors in the spatial domain It then displays the average spectra in a grid where the exterior axes indicate the spatial co ordinates of the averaged spectra and the interior axes the data values against spectra co ordinates Usage gridspec b string i filename z z Command line Arguments Notes b string The number of spectra to block average along the X and Y axes respectively This should be a comma separated list or a single number the latter case applies the same compression factor to both spatial axes The numbers must be positive integers 2 i filename The script will use this as its input file the specified file should be a three dimensional NDF By
10. RAME and or KAPPA WCSATTRIB e It propagates the original variances from the cube but does not account for errors in the input velocity map affecting the values extracted from the cube Implementation Status This script invokes a collection of A tasks from the SUN 95 package SUN 237 4 Descriptions of Individual Applications 12 multistack multistack Averages groups of spectra extracted from a three dimensional IFU NDF and then plots these averaged spectra in a stack Description This shell script reads a three dimensional IFU NDF as input and presents you with a white light image of the cube You can then select a number of X Y positions using the cursor The script will then group these spectra creating an average spectrum for each group It then displays the average spectra in a stack where each group spectrum plotted offset vertically from the previous one in the stack Usage multistack g number i filename n number o number z z Command line Arguments g number The number of spectra in a group i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input file n number The number of groups to extract o number Offset between the spectra in the stack Z The script will automatically prompt to select a region to zoom before prompting for the region of interest TRUE z The program
11. SE r number Rest frame spectral unit of the line being fitted s system The co ordinate system for velocities Allowed values are VRAD radio velocity VOPT optical velocity ZOPT redshift and VELO relativistic velocity If you supply any other value the default is used VOPT Z The script will automatically prompt to select a region to zoom before prompting for the region of interest TRUE z The program will not prompt for a zoom before requesting the region of interest FALSE The compression is trimmed so that only compression factor multiples of original pixels are included in the plot The spatial averaging is aligned to obtain the expected number of pixels irrespective of the pixel origin of the input cube Note that this may not be suitable if you wish to preserve alignment with another compressed dataset See KAPPA COMPAVE parameter ALIGN for more details The velocity map display scales between the 2 and 98 percentiles The map uses a false colour spectrum like colour table so that low velocity regions appear in blue and high velocity regions appear in red If the cube is compressed spatially so is the contour map For NDFs in the UK data cube format where there is no in the WCS Frames the data are first collapsed in their native wave lengths in ngstrom then the pixel values are converted to VOPT using the simple formula c A Ap Ao where A is the intensity weigh
12. SUN 237 4 Starlink Project STARLINK User Note 237 4 A Allan amp Malcolm J Currie 2010 September 7 DATACUBE An IFS datacube manipulation package Version 1 3 User s Manual Wage eT Car Mape Z ZS 2 M mety mp SUN 237 4 Abstract ii DATACUBE is a package which includes the IFU Data Product Cookbook SC 16 and a collection of example shell scripts for IFS data cube manipulation iii SUN 237 4 Contents Contents 1 The Datacube Package 3 2 Setting up the applications 4 6 7 8 10 12 13 14 16 18 19 20 ee de et es Gate a ses huge gies a Gh wees tes eee ee NN 21 Pee ee ee ee eee o Ree eee da 22 de ty vs Ge Bae ok Boag Fee ee ane Soe Sm a be ea ae pe ade eee eS 25 E as ae ee ee A Ae ee Reo es ee a oe 28 B_ Release Notes V1 1 30 B1 New Commands 0 0 0000 ce ESN ENEN ARESE 30 B 2 Modified Commands 0 2 0000 a 30 a Gs odo da Ponies le Seve eas Gee ae E ay 30 31 C1 New Commands ecc g ariar E Ew BS A ee BAS 31 C2 Modified Commands s s sesa Tarira ce ee 31 32 A al bee ee eae Boe oe ee eee oe a 32 D 2 Modified Commands 0 0 00 ee ee ee 32 1 SUN 237 4 Contents Revision history 1 9th November 2000 Version 0 1 Original version AA 2 30th December 2000 Version 0 2 Auto generated code prologs AA 3 2nd January 2001 Version 1 0 Release version AA 4 2005 October 20 Version 1 1 Removed applications and improved scripts MJC
13. atial pixel The file is written as a Starlink Small Text List STL described in SUN 190 The STL file comprises a schema to locate and describe the columns and store global properties and a formatted table of the coefficients The schema includes the units and a brief description of each column and the name of the input NDF used The table lists the Gaussian centre peak height the FWHM and integrated flux each with its fitting error o filename The filename for the output NDF of the line strength map P The script will plot the final image map to the current display as well as saving it to an NDF file Additionally it will overplot the white light image as a contour map for comparison FALSE V The script will generate a VARIANCE array from the line fits and attach it to the peak intensity map NDF FALSE Z The script will automatically prompt to select a region to zoom before prompting for the region of interest TRUE z The script will not prompt for a zoom before requesting the region of interest FALSE The line strength image map display scales between the 15 and 98 percentiles The map uses a false colour lookup table may be used to convert the STL log file see the 1 option to FITS format for analysis with the likes of TOPCAT provided the STL has the txt file extension If you want just the tabulated data for your own favourite tool the schema can be easily removed manually or with sed excluding the li
14. ay these spectra in a stack with each spectrum plotted offset vertically from the previous one in the stack Usage stacker i filename n number o number z z Command line Arguments i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input file n number Number of spectra to extract o number Offset between the spectra in the stack Z The script will automatically prompt the user to select a region to zoom before prompting for the region of interest TRUE z The program will not prompt for a zoom before requesting the region of interest FALSE Implementation Status This script invokes a collection of A tasks from the SUN 95 package 21 step SUN 237 4 Descriptions of Individual Applications step Steps through the each X Y plane of a three dimensional IFU NDF in the spectral direction using KAPPA DISPLAY to display the output Description This shell script reads a three dimensional IFU NDF as input and allows you to step through the datacube in the spectral direction in slices The output goes to files and optionally to the screen Usage step i filename 1 number p s number u number Command line Arguments i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input
15. bes the contents of the third axis is arbitrary The script clears the graphics database for the current device It then creates two FRAME pictures with labels al and a2 Within each of these DISPLAY creates FRAME and DATA pictures the former holding annotated axes On exit a2 is the current picture The label for the spatial first axis in the slice plot is Offset from start Related Applications KAPPA PROFILE FIGARO SLICE Implementation Status This script invokes a collection of A tasks from the KAPPA package SUN 237 4 Descriptions of Individual Applications 18 ripper ripper Extracts a one dimensional spectrum from a three dimensional IFU NDE Description This shell script reads a three dimensional IFU NDF datacube as input presents you with a white light image of the cube and allows you to select an X Y position using the cursor It then extracts and optionally displays the spectrum for that X Y position Usage ripper i filename o filename p Command line Arguments e i filename be a three dimensional NDF By default the script will prompt for the input file e o filename The filename for the output spectrum By default the script will prompt for the name of the output file P The script will plot the extracted spectrum to the current display as well as saving it to an NDF file FALSE Implementation Status This script invokes a collection of A tasks from the SUN 95 package
16. e KAPPA applications with the kappa command kappa KAPPA commands are now available Version 1 12 Type kaphelp for help on KAPPA commands Type showme sun95 to browse the hypertext documentation NOTE several applications have had major changes made to their parameter lists See the Release Notes section of SUN 95 for details 5 SUN 237 4 Setting up the applications In compiling this document I AA have again depended heavily on the help of many people in the IFS community However special thanks should go to Rachel Johnston Jeremy Allington Smith James Turner and Frank Valdes for their co operation and contributions SUN 237 4 Descriptions of Individual Applications 6 7 compare SUN 237 4 Descriptions of Individual Applications compare Compares multiple extracted spectra from a three dimensional IFU NDF Description This shell script reads a three dimensional IFU NDF as input and presents you with a white light image of the cube You can then select an X Y position using the cursor The script will extract and display this spectrum next to the white light image You can then select another X Y position using the cursor and the script will display this spectrum as well allowing s comparison of the two Usage compare i filename Command line Arguments e i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script
17. eakmap Builds a map of emission line strength from a spectral cube NDE Description This shell script reads a three dimensional spectral cube NDF and presents you with a white light image of the cube You can then select an X Y position using the cursor The script will extract and display this reference spectrum You will then be prompted to specify various fitting parameters such as the peak position using the cursor The script will then attempt to fit the emission line The fit will be displayed and you are consulted regarding the goodness of fit If you consider the fit to be good enough the script will attempt to perform similar fits to all spectra within the cube building a two dimensional NDF image of the strength of the line These will use the same initial parameters as the reference spectrum unless option a is selected You may view this image drawn with a key option d and overlay a contour plot with a key of the white light image option c If you do not force the fit to be considered good by using the f command line option the script will offer the opportunity to manually refit the spectral feature for individual pixels such as those that were unsuccessfully fitted by the automatic procedure In this case the line strength map will be plotted and replotted after the new fit regardless of the p option Usage peakmap a c number ci index f i filename 1 logfile o filename p v z z
18. ely absent This is unlikely to cause any hardship while used an exploratory tool However as is normal for a publication graphic some adjustments of the style options may be required See Descriptions of Plotting Attributes in SUN 95 to be used with STYLE parameter SUN 237 4 Descriptions of Individual Applications 24 trendview in the CLINPLOT calls and the margins can be enlarged through the MARGIN parameter Output A composite CLINPLOT plot showing the raw data and the baseline fit and mask from MFITTREND Prior Requirements e The supplied NDFs should be spectral cubes with the spectral being the third e A large display area is recommended if the screen is used for display for instance xmake xwindows width 1200 height 900 that mostly fills the screen The actual width and and height in pixels will depend on your screen s dimensions Also a suitable background colour is needed that will show all four loci for the hardwired colours This should be of mid intensity so that the light and dark curves will both be visible For example palentry 0 steelblue will do this for the original colour scheme 25 velmap SUN 237 4 Descriptions of Individual Applications velmap Builds a velocity map of an emission line from a spectral cube NDF by line fitting Description This shell script reads a three dimensional spectral cube NDF and presents you with a white light image of the cube You can then select an X Y position u
19. ended that you note the co ordinates of spectra to re fit and tackle these individually in the final manual re fit stage FALSE e c number Number of contours in the white light image Set to fewer than 1 means no contours are overlaid 15 e ci index The palette colour index of the contours It should be an integer in the range 0 to 15 It is best to choose an index corresponding to white or black or another dark colour to make the contours stand out from other elements of the plot 0 is the background colour KAPPA GDSTATE will list the current palette colours 0 e f Force the script to accept the first attempt to fit a gaussian to the line This is a SUN 237 4 Descriptions of Individual Applications 26 velmap Notes dangerous option if the fit is poor or unobtainable the script may terminate abruptly if it is forced to accept the fit Additionally this will supress manual re fitting of bad pixels at the end of the run of the script FALSE i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input file 1 filename The name of an text log file containing the fitted Gaussian coefficients for each spatial pixel The file is written as a Starlink Small Text List STL described in SUN 190 The STL file comprises a schema to locate and describe the columns and store global properties and a formatted table of the coefficients
20. file e 1 number Lower spectral axis bound of the region of interest p The script will plot the extracted images to the current display as well as saving it to an NDF file FALSE e s number Spectral axis step size for each passband chunk e u number Upper spectral axis bound of the region of interest Implementation Status This script invokes a collection of A tasks from the SUN 95 package SUN 237 4 Descriptions of Individual Applications 22 trendview trendview Plots multiple spectra from a cube overlaying fitted trends and mask Description This displays whole or part of a spectral cube in a multiple line plot graphic of data values versus spectral co ordinates via In addition to the raw data fitted trends and masks generated PTA NFINREN D are overlaid in different colours for comparison and quality assessment There is an option to also draw the residuals The raw data appear in yellow the fitted trends in darkgreen the mask in red and the residuals in blue The lower left plot has annotated axes of data value against spectral co ordinates For ease of use the baseline and mask files have defined names given by the name argument and suffix arguments See the Notes Usage trendview d device i filename o offset r s suffix y ytopL ybot Command line Arguments e d The device name xwindows e i filename The name of the raw dataset The specified file should be a three dimensi
21. he required NDF that may include spaces q for quiet to prevent the reporting of the filename and its vital statistics e It has also has an improved NDF validation method which allows for NDFs within a container file or NDF extension
22. l form the output image values are given by the following expression Output x y Cube x y Image x y One application is multi spectral imaging in complex molecular clouds where one opti cally thin spectral line provides a clearer mapping of the cloud and system velocities Using this specie s velocity map traces the varying velocity and thus data observed through different spectral lines can be compared enabling the calculation of cloud parameters such as Opacity Usage mapbyvel i filename m filename o filename Command line Arguments i filename A three dimensional NDF with spatial axes and a third velocity axis By default the script will prompt for the input cube e m filename The name of a two dimensional velocity map where the data values are velocities It should have the same spatial co ordinates as the supplied cube Such a map can be created using velmapjor KAPPA COLLAPSE with the Iwc or Comax estimators By default the script will prompt for the input cube o filename The filename for the output NDF velocity map Notes The script assumes X and Y axes are spatial and Z is spectral Use KAPPA PERMAXES to re orient the cube if that is not the case 11 mapbyvel SUN 237 4 Descriptions of Individual Applications e A further assumption is the cube s Z axis co ordinate matches the data values in the supplied image If that is not the case change the co ordinate system with KAPPA WCSF
23. n to log the Gaussian fit parameters and their errors in a Small Text List file It permits case insensitive responses to prompts except where a prompt requires a file name It now recognises DSBSPECTRUM as a valid spectral domain A number of bugs were fixed the velocity variance is stored in the output NDF VARIANCE previously the velocity error had been supplied the WCS Frame is reset before re plotting in final individual pixel refit loop previously the wrong spectral co ordinate could be plotted and the logic for deciding whether to create or switch WCS Frames is disentangled enabling DSBSPECTRUM data to be used D Release Notes V1 3 D 1 New Commands The following new scripts have been added mapbyvel Form a new image from a cube s voxels using all the data values of a supplied image as the Z co ordinate in the cube The supplied image must span the same X Y region as the cube In practice the cube has RA Dec velocity axes and the input image is a velocity map Extracts and displays position velocity slice from a RA Dec vel cube The slice need not be parallel to either spatial pixel axis and it is defined using the graphics cursor D 2 Modified Commands The following applications have been modified e Internal script checkndf used in all of the public scripts now has new options d to set the required dimensionality 2 or 3 where previously only cubes where tested p to set the prompt string for t
24. nes up to and including the line beginning BEGINTABLE Implementation Status This script invokes a collection of A tasks from the SUN 95 and FIGARO packages SUN 237 4 Descriptions of Individual Applications 16 puslice pvslice Extracts and displays a velocity position slice from an RA Dec vel cube Description This script extracts and displays a slice from a position velocity cube The slice need not be parallel to either spatial pixel axis The script displays a chosen spatial plane from the supplied cube in the left half of the current graphics device You are then invited to select two spatial positions within the displayed plane using the cursor A two dimensional slice is then extracted from the cube that passes through the two selected spatial positions The first axis in this slice measures spatial distance along the line and the second axis is the velocity axis This slice appears in the right hand side of the current graphics device and saved to the specified output NDF Usage pvslice i filename o filename ci index p plane Command line Arguments e ci index The colour or colour index of the annotations on the left hand display indicating the spatial location of the slice An index should be a positive integer no more than 15 normally 2 or 3 to stand out from other elements of the plot If absent the annotations will appear in red e i filename The name of an existing three dimensional RA Dec
25. nge between the upper limit and the offset Examples trendview i ac9_trim y 8 Plots the spectra in NDFs ac9_trim ac9_trim_bsl and ac9_trim_msk between data values 0 4 and 8 trendview i ac9_trim 2 10 4 8 y 0 5 10 As before but the plot range is 0 5 to 10 and display only displays a 10 by 8 spatial pixel region trendview i ac9_trim 2 10 4 8 200 200 y 0 5 10 As the previous example but now only a part 200 to 200 of the spectral range appears in each plot trendview i ac9_trim o _o4 o 7 Plots the spectra in NDFs ac9_trim ac9_trim_bsl_o4 and ac9_trim_msk_o4 be tween data values derived automatically percentiles in ac9_trim with the mask line drawn at value 7 trendview i ac9_trim 2 10 4 8 r y 3 8 As the second example but now the residuals are also plotted The lower data value limit on the plots is 3 to accommodate negative residuals Notes The raw data is given by the i argument the fitted trends or baselines is called lt filename gt _bsl lt suffix gt and the mask is called lt filename gt _msk lt suffix gt where lt filename gt is value of the i option without any section or file extension and lt suffix gt is the value of option s e No key is plotted and the margins are narrow to maximise the plot region However these are not guaranteed to work with all aspect ratios of the graphics device and spatial pixels and for example the title may be clipped or complet
26. onal NDF By default the script will prompt for the input file A section may be defined to home in either or both spatial and spectral regions eo 0O An offset to apply to the mask whose good values are 0 In other words the data value level at which to draw the mask Its purpose is improve mask visibility and to narrow the y plotting range hence see the residuals between the raw data the fitted trends more clearly 0 e r If present the residuals are plotted e 5 The file suffix appended to the baseline and mask file names y ytopl ybot A comma separated list giving the upper and lower data value limits of every spec trum plot in either order A positive lower limit will be ignored if the offset o is not positive too or when residuals are to be plotted r A single value is deemed to be the upper limit and the lower limit is defaulted If this option is not specified the limits derive from the range given by the 1 and 99 percentiles extending by 5 of this range below its minimum and 2 above its 23 trendview SUN 237 4 Descriptions of Individual Applications maximum However a positive lower limit may again be substituted by a default whenever the offset is not positive too or residuals are to be plotted When the lower limit requires a default it is set to negative one twentieth of the upper limit if there is no o offset applied to the mask otherwise it is the offset level minus a twentieth of the ra
27. option to FITS format for analysis with the likes of TOPCAT provided the STL has the txt file extension If you want just the tabulated data for your own favourite tool the schema can be easily removed manually or with sed excluding the lines up to and including the line beginning BEGINTABLE Implementation Status This script invokes a collection of A tasks from the SUN 95 and FIGARO packages SUN 237 4 Descriptions of Individual Applications 28 velmoment velmoment Builds a velocity map from a three dimensional IFU NDF from the intensity weighted spectral co ordinates Description This shell script processes a three dimensional IFU NDF to form a velocity map If you request zooming the script first presents you with a white light image of the cube You can then select the lower and upper spatial limits to plot using the cursor You can instead supply an NDF section with the filename to define both spatial and spectral limits to analyse and from which to create the output velocity map You may average spectra in the chosen region by specifying compression factors in the spatial domain The script then derives the intensity weighted co ordinate of each spatially averaged spectrum and converts the data units into a velocity You may view this image drawn with a key option d and overlay a contour plot of the white light image option c Usage velmoment b string c number ci index i filename o filename
28. sing the cursor The script will extract and display this reference spectrum You will then be prompted to specify various fitting parameters such as the peak position using the cursor The script will then attempt to fit the emission line The fit will be displayed and you are consulted regarding the goodness of fit If you consider the fit to be good enough the script will attempt to perform similar fits to all spectra within the cube building a two dimensional NDF image of the velocity of the line These will use the same initial parameters as the reference spectrum unless option a is selected You may view this image drawn with a key option d and overlay a contour plot with a key of the white light image option c If you do not force the fit to be considered good by using the f command line option the script will offer the opportunity to manually refit the spectral feature for individual pixels such as those that were unsuccessfully fitted by the automatic procedure In this case the velocity map will be plotted and replotted after the new fit regardless of the p option Usage velmap a c number ci index f i filename 1 filename o filename p r number s system v z z Command line Arguments e a Requests that each fit may be inspected then approved or re fit not just the initial reference fit A re fit will change the initial parameter guesses for subsequent fits so it is recomm
29. ted wavelength Ay is the rest frame wavelength for the chosen spectral line and c is the velocity of light in kms Implementation Status This script invokes a collection of A tasks from the SUN 95 package SUN 237 4 Release Notes V1 1 30 B Release Notes V1 1 B 1 New Commands The following new scripts have been added Averages groups of spatially neighbouring spectra of a three dimensional IFU NDF and then plots these averaged spectra in a grid Builds a velocity map from the collapsed intensity weighted spectral co ordinates It supports spatial compression B 2 Modified Commands The following applications have been modified compare has a i option for the input filename for non interactive scripting e multistack and plot ordinate limits now always make visible all the spectra regardless of the chosen offset e does not dump WCS mappings in NDFCOPY Ensured that the plots of spectra use the axis co ordinate system Removed unused r option now has c option to specify the number of contour levels to plot stepjnow plots the image slices in an optimally shaped grid rather than full size in quick succession and thereby permits comparison of the slices velmap generalised the transformation of the measured line displacements from the rest frame co ordinate in the current spectral system into one of four velocity measurements using WCSTRAN Added a SpecFrame to achieve this functionali
30. tion of files alphabetical ordering of the options documentation of default values of options corrections to gram mar and punctuation avoidance of r aligned output command line rubbish disposal and tab removal Accepts sdf extension and or NDF sections to be supplied through new internal routine checkndf csh Shortened many scripts through use of internal routine getcurpos csh to obtain and mark cursor positions C Release Notes V1 2 C 1 New Commands The following new script has been added Plots multiple spectra from a cube overlaying fitted trends and spectral feature mask It enables assessment of baseline subtraction and feature masking C 2 Modified Commands The following applications have been modified e now has a a option to inspect and approve the fit at each spatial pixel There is also a 1 option to log the Gaussian fit parameters and their errors in a Small Text List file It inteprets a non positive number of contours to mean no contour overlay required There is anew ci option to specify the colour index of contours It permits case insensitive responses to prompts except where a prompt requires a file name A bug has been fixed that caused the peak height error to be stored within the output NDF s VARIANCE component instead of the actual variances SUN 237 4 Release Notes V1 3 32 e velmap now has a a option to inpsect and approve the fit at each spatial pixel There is also a 1 optio
31. ty for UK data cube files Also recognises the SKY DSBSPECTRUM Domain Added the s option to define the co ordinate system of the derived velocities Ensured that the plots of spectra use the axis co ordinate system The script inquires the WCS for the rest frame frequency to avoid unnecessary prompting Changed lower percentile for display from 15 to 2 Use spectrum colour table Added a velocity key Additional c option to specify the number of contours this may be zero to prevent contours be overlaid Added ci option to specify the colour index of contours B 3 General changes The package applications COPYAXIS GETBOUND and PUTAXIS have been withdrawn The scripts that invoked these now call KAPPA SETAXIS setaxis ndf like KAPPA NDFTRACE access FLBND and FUBND output parameters and SETAXIS in WCS mode setaxis ndf dim mode wcs comp Centre for each dimension respectively 31 SUN 237 4 Release Notes V1 2 The scripts have been generalised to spectral co ordinate systems other than Wavelength in Angstrom Units are reported too A bug displacing by 1 pixel negative pixel indices determined by the cursor has been fixed It was present in most of the scripts Spectrum plots now use the histogram style for greater clarity Reset KAPPA DISPLAY parameters in a few scripts so that features enabled in other scripts like a key do not bleed through Tidied the scripts Changes included the silent removal and crea
32. vel cube The script will prompt for the input file if not supplied on the command line e o filename The name of the NDF in which to store the velocity position slice The script will prompt for this NDF if it is not supplied via this option e p plane Velocity or pixel index of the plane to display to enable cursor selection of the slice end points To specify a velocity supply a floating point value such as 2 0 for an index supply an integer 0 Examples pvslice i orion_masked o orion_pvmap This extracts a user selected plane from the cube NDF called orion_masked and saves it to NDF orion_pvmap The slice is shown to the right of the spatial image pvslice i orion_masked o orion_pvmap p 1 5 17 puslice SUN 237 4 Descriptions of Individual Applications As above but slice selection is from the velocity plane at 1 5 as opposed to the middle index Notes The WCS in the returned NDF is somewhat complex it has a degenerate pixel axis and a degenerate WCS axis These could be removed using ndfcopy trim but this would result in a WCS with no inverse transformation from current to pixel which gives problems when displaying it etc Alternatively the AXIS frame can be used by doing wcsframe frame axis To avoid modification of the input cube the script creates a temporary copy in the current directory and deletes the copy upon completion While the script is intended to make position velocity slices from spectral cu
33. will not prompt for a zoom before requesting the region of interest FALSE Implementation Status This script invokes a collection of A tasks from the SUN 95 package 13 passband SUN 237 4 Descriptions of Individual Applications passband Displays multiple passband images from a three dimensional IFU NDE Description This shell script reads a three dimensional IFU NDF as input and presents you with a white light image of the cube You can then select and X Y position using the cursor The script will extract and display this spectrum next to the white light image You can then select a spectral range using the cursor and the script will display a passband image of the cube in that spectral range Usage passband i filename o filename z z Command line Arguments e i filename The script will use this as its input file the specified file should be a three dimensional NDF By default the script will prompt for the input file e o filename An output two dimensional NDF of the passband image By default the output will be displayed only eo Z The script will automatically prompt to select a region to zoom before prompting for the region of interest TRUE z The program will not prompt for a zoom before requesting the region of interest FALSE Implementation Status This script invokes a collection of A tasks from the SUN 95 package SUN 237 4 Descriptions of Individual Applications 14 peakmap p
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