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Karma User Manual

1. kpvslice interactive position velocity slicing Ol Howto Used iD da A eo ee ee a D 6 1 1 Viewing Profiles 6 2 Extracting Slices From An Image 6 3 Command line Options e e 6 4 Algorithmic Details o o 6 4 1 How the Slice is Computed kslice_3d slicing data cubes delo PLECOMPUtE a a aOR aes Tid Magnifications ur ts a ra a o ee RN kshell looking for expanding shells CONTENTS 9 koords interactive co ordinate fitting 9 1 Centring Algorithm 0 0 200 000 10 kpolar regridding to polar co ordinates 11 Superimposing Images 11 1 Image and Contours 2 20000 000 11 2 Hue and Intensity ae act stk dy a Ste Rea a ok RR 11 3 Intensity and Intensity 12 Command line Tools 12 1 Common Interface aare pai a we ee ie dedos 12 2 Interactive Mode e o 122 1 A CHONS ira A rt as aaa Ss 12 2 2 Scalar Parameters o e eee 12 2 3 Vector Parameters o o e 12 2 4 Choice Parameters o o 00002 eee 12 2 5 Eternal Actions os sota a ann e a e ae de ae 12 2 6 Other Arguments e 12 2 7 Exiting Interactive Mode ouaaa 12 3 Batch Mode sm car porro degen a eid e Boe One e Blas 12 3 1 Passing in Parameters and Actions 12 3 2 Passing in Strings oaaae 12 3
2. 1420 0 1416 5 1418 0 1418 5 Frequeney MHz Figure 2 10 Screen snapshot of profile display window 2 15 COMMON IMAGE DISPLAY FEATURES 31 e Zoom menu this allows you to popup a magnifier or a panner zoom the image in or out 2x or 4x unzoom or popup the lt ZoomPolicy gt widget section 2 7 e Overlays menu this allows you to popup various control panels to control overlay display The following choices are available Axis Labels this will popup controls for the axis labelling section 2 8 Load Annotations this will bring up a file browser to load a file of ASCII overlay commands The file format is described in an ap pendix to the User Manual Editor this will popup the lt OverlayEditorControl gt widget sec tion 2 19 which allows you to interactively draw overlays Remove Last connection this will remove the last overlay object sent via a network connection Remove All connection this will remove all overlay objects sent via a network connection Contours this will pop up a file browser which allows you to load an image and display it as contours You can load an unlimited number of images this way e Export menu you can export data in a variety of formats See section 2 5 e View this will popup a control panel used for displaying two datasets sec tion 4 This is only available in tools like lt kvis gt and lt MultibeamView gt e Edit this will popup the lt ImageEditorContro
3. e Remaining Coordinate Types Menu sets the co ordinate types of the remaining points which define a geometric object See Figure 2 13 for a screen snapshot This widget uses the middle mouse button for its drawing functions Some tools may already be using this button for other purposes in which case the tool should provide a control which allows you to disable the normal use of the middle mouse button For instance the lt kvis gt programme provides such a control through the lt ZoomPolicy gt widget section 2 7 2 20 LOADING OVERLAYS 39 Drawing Rectangles You click down the mouse button to define one corner of the rectangle and move the mouse keeping the button down until you have a rectangle to your liking Once you are happy release the button and the rectangle will be added to the overlay list Drawing Ellipses Click the mouse button to define the centre of the ellipse and move the mouse keeping the button down to change the size and shape of the ellipse If you press and release the r key still with the button down this will toggle rotation mode so that now as you move the mouse the ellipse will rotate To leave rotate mode just press the r key again and you will be back to changing the size and shape of the ellipse Once you have an ellipse you are happy with release the mouse button and it will be added to the overlay list Drawing Polygons Click and release the mouse button to define the first
4. 4 CHAPTER 1 INTRODUCTION e TIFF another popular image format This requires the NetPBM tools to be installed on your machine In addition the automatic decompression of gzipped and bzip2 ed Karma and FITS files is also supported by the file browser lt Filepopup gt widget section 2 1 If your data are not in one of the supported formats you will need to convert it to a supported format like FITS 1 1 1 Converting Other Data Formats to Karma Format A number of command line utilities are provided to convert between other data formats and Karma These are described below e FITS requires the lt fits2karma gt programme which is used fits2karma lt fits file gt lt karma file gt lt fits2karma gt will attempt to trap most deviations from standard FITS and continue gracefully However a truly bizzare FITS file may cause lt fits2karma gt to reject the conversion In this rare case please notify Richard Gooch who will attempt to add a trap so that the data can be converted Also note that lt fits2karma gt will by default truncate axes so that they are divisible by 4 or larger The reason for this is that this then allows the programme to tile the data tiling is a way of organising data so that most ways of accessing it are faster If you really don t want to loose up to 3 co ordinate points along an axis you can run lt fits2karma gt as follows fits2karma allow_truncation off lt fits file gt lt karma file gt
5. But remember for the sake of a little bit of data you may be throwing away enormous speed benefits e Miriad requires the lt miriad2karma gt programme which is used miriad2karma lt miriad file gt lt karma file gt This programme also tries to tile data like lt fits2karma gt does e GIPSY requires the lt gipsy2karma gt programme which is used gipsy2karma lt gipsy file gt lt karma file gt This programme also tries to tile data like lt fits2karma gt does 1 1 2 Converting Between Data Formats There are also command line utilities which allow you to convert between other data formats which are provided as a convenience These are described below 1 2 ADDING YOUR OWN DATA FORMATS 5 e lt miriad2gipsy gt will convert from Miriad format to GIPSY format which is used thus miriad2gipsy lt miriad file gt lt GIPSY file gt This programme is obsoleted by the more general lt ktranslate gt e lt ktranslate gt will convert from any format supported by Karma to another format It is used thus ktranslate lt input file gt lt output file gt The input and output formats are guessed by the programme based on the filename extensions You can force the format if you wish An example of this is ktranslate intype fits outtype miriad lt input file gt lt output file gt The choice of supported output formats is limited to Karma PPM FITS Sun Rasterfile Miriad and GIPSY If possible the conversion p
6. If the opacity for a voxel is zero that voxel becomes completely transparent but also invisible This closely resembles the behaviour of a self radiating cloud of hot gas where gas particles both emit and absorb radiation Regions with high gas particle density will have a higher surface brightness but will also have a higher cross sectional area of absorption The resulting rendered image appears like a cloud of glowing gas which shows both internal and external structure You can use this to make features disappear eg noise The disadvantage is that in order to make the data that you want to see transparent you also make it barely visible Consequently the opacity of data you want to see has to be not too low and as a result one will tend to see only the surface of the emission regions There are a few versions of this implemented differing in whether they do the rendering monochromatically or in colour e Hot Gas substances This works as follows the value range 127 127 of the voxels is divided into a number of subranges typically eight Each subrange has a colour and an opacity associated to it and is called a substance Like every colour in computer displays a colour consists of red green and blue The contribution of a voxel to the colour of the pixel on the display is calculated using the radiative transfer but for each colour red green or blue separately This means that if a blue voxel is behind a red one the bl
7. files are kept You can use the file browser to change directories Byte swapped data are automatically detected and corrected e AIPS this is the format used by the AIPS package Astronom ical Information Processing System not to be confused with AIPS This is a directory based data format like Miriad It is a new package still under development The Karma support for AIPS requires the lt image2fits gt programme to be in your PATH The source code is located somewhere in the AIPS source tree A precompiled binary is available at ftp ftp atnf csiro au pub software karma other packages aips for your convenience e DRAO this is the format produced by the Dominion Radio Astronomy Observatory Penticton B C Canada reduction software This data for mat uses a catalogue file which is automatically scanned by the file browser and each available dataset whether a single image file or a family of files for a cube is given one entry in the browser with the string DRAO shown in the left hand column Unlike the DRAO software Karma re quires no environment variable to cope with byte swapped data they are automatically detected and corrected This format supports loading of partial 3 dimensional datasets section 1 1 3 e FITS this is a popular format amongst astronomers allowing you to move data between many different software packages It is more efficient to use lt fits2karma gt to convert to Karma format f
8. to the resource name First try specifying the particular resource as shown and if that doesn t work prepend the application classname e ZoomPolicy fixAspect this controls whether the aspect ratio will be fixed True or not False e ZoomPolicy integerX ZoomToggle state this controls whether hor izontal zooming will be forced to integer multiples True or not False e ZoomPolicy integerY ZoomToggle state this controls whether ver tical zooming will be forced to integer multiples True or not False e IntensityPolicy resetIntensityToggle state this controls whether the intensity range will be reset upon loading of a new file True or not False e iscaleMenu setChoice this controls the default intensity transforma tion The folowing are supported linear the screen intensity is proportional to the input data values log val min the screen intensity is proportional to the logarithm of the input data values 107 108 APPENDIX C RESOURCES log max val the screen intensity is proportional to the logarithm of the negative input data values sqrt val min the screen intensity is proportional to the square root of the input data values e MagnifierPopup fastPanner this controls whether the magnifier win dow will use a fast large memory mode True or not False panner The default is to use the slower small memory panner In most cases the default mode is quite fast enough unless you enlarge the m
9. 20 TracePopup 28 View2 Datasets 57 ViewDatasets 41 ZoomPolicy 24 WWW site 1 xray 65 zooming 23
10. depending on the type of the parameter If it is a complex value the real and imaginary components must be separated by a space 12 2 3 Vector Parameters A vector parameter is an array of scalar parameters The parameter is displayed with a trailing n m after its name The value n is the minimum number of elements in the array and the value m is the maximum number of elements in the array After typing in the name of the parameter you must type in the array of scalar elements Elements in the array must be separated by a space You must type in at least the minimum number of elements otherwise your input is rejected If you type in more than the maximum number of elements allowed the excess elements are discarded If you wish to append elements to an existing array simply type followed by the parameter name and then followed by the scalar elements If you want to empty out the contents of an array just type the name of the parameter without any elements after it This does not work if the minimum number of elements is greater than 1 12 2 4 Choice Parameters A choice parameter allows you to choose from a selection of possibilities If you wish to see what all the possibilities are type and you will see a list of choices for each choice parameter After typing in the name of the parameter type in your choice You can type the minimum non ambiguous choice string if you wish 12 3 BATCH MODE 97 12 2 5 Eternal Actio
11. maximum and sum value Alternatively you can click left and drag the mouse to a new position still holding the mouse down and press the s key The statistics are computed over the boxed area Af ter you press s you may release the mouse button This feature saves you from having to zoom in and unzoom every time you wish to compute statistics on a sub image Note that the old box remains on the image until something clears it this is useful when you want to know which regions you have already computed statistics over 34 CHAPTER 2 COMMON FEATURES The v key allows you to see the individual image pixel values rather than their statistics This works in a similar fashion to the s key The V key is a variation which shows raw image pixel values Note that if you press v or V without the mouse all the pixels in the subimage being viewed would be printed Since this can take a long time with a large number of pixels a warning message is issued if you attempt this with many pixels If you definately want to display a large number of pixels press the control key at the same time Viewing Header Information in the ImageDisplay Widget Many programmes allow you to inspect the header of the dataset you are cur rently viewing as an image Simply press the h key and the header will be displayed in the terminal window If you press the H key you will get the header without the history Ca
12. 3978 D 4 EXAMPLE ANNOTATION FILE 119 Include another annotation file which has examples of some rotatable objects INCLUDE m42_include ann HHEHHHHEHHAHHHEHHREHHREHHHAEHHAAHRREHHRHHHHREHHHREHRRAH RRR ARR HERR HHH END OF SAMPLE KARMA ANNOTATION FILE M42 ANN HHEHHHHHHHHHHEHHREHHREHHHAEHHAAHRREH HARE PAREADO ARA RORO AREA RRR HRB R HHH R HHH HHEHHHHHHAHHHHHHREHHREHHHAEHHAAHHREH HEHEHE EHHHREHRHRH HR RR HRB RH RRR HHH SAMPLE KARMA ANNOTATION FILE M42_INCLUDE ANN x to be used with M42_ FITS images H H HHH HEHHHHHHHHHEHHHHEHRAHEHAEHHHHEHRAHRHEHAHHAHHEHAEHRAHEHRAHHE HARRAH HE Draw rotated crosses cboxes and ellipses with standard PAs PA STANDARD The W s aren t actually necessary since COORD is still set to W COLOR AQUAMARINE CBOX W 83 72204 5 45408 0 02 0 008 10 CROSS W 83 72204 5 45408 0 02 0 008 10 ELLIPSE W 83 72204 5 45408 0 01 0 004 10 COLOR MAGENTA CBOX R 0 8 0 15 0 05 0 03 10 0 CROSS R 0 8 0 15 0 05 0 03 10 0 CBOX R 0 8 0 15 0 10 0 06 10 0 ELLIPSE R 0 8 0 15 0 05 0 03 10 0 COLOR VIOLET CBOX P 75 200 50 20 10 CROSS P 75 200 50 20 10 ELLIPSE P 75 200 25 10 10 Draw rotated crosses cboxes and ellipses with sky PAs PA SKY COLOR TAN CBOX W 83 7147 5 3007 0 02 0 01 10 120 APPENDIX D ANNOTATION FILE FORMAT CROSS W 83 7147 5 3007 0 02 0 01 10 ELLIPSE W 83 7147 5 3007 0 01 0 005 10 COLOR KHAKI CBOX R 0 88 0 70 0 08 0 04 10 CROSS R 0 88 0 70 0 0
13. Load or File or whatever it is called will show a window with the files that you can load This will be all files with extension kf fts or fits Also subdirectories and the parent directory are shown Clicking on these changes the directory If a directory is in fact a Miriad image dataset clicking on it will load that dataset Note that GIPSY files consist of two files one with a descr extension and another with a image extension Most of the software will simply display a gipsy file instead since that makes the directory browser look less cluttered The lt Filepopup gt widget provides the file browsing interface This wid get allows the user to browse a directory tree and select files All the files and directories the application wants the user to see are displayed Any one of these may be selected by clicking the left mouse button over the filename The D character is used to denote directories while the F character is used to de note ordinary files Above the list of files and directories is shown the current directory for the browser If you edit the text and press return the current directory is changed appropriately The notation is supported as well as other simple Bourne Shell like expansions of environment variables using the variable variable and variable word notations The following controls are provided e close close the window e rescan rescan the directory in case a new file has appeared
14. PPM Data Window export the contents of the window to PPM format Non image data i e axis labels and annotations are also exported The output is at the resolution of the window and yields higher quality than using a separate screen capture tool e Karma whole dataset export the currently viewed dataset to Karma format e FITS whole dataset export the currently viewed dataset to FITS format e Miriad whole dataset export the currently viewed dataset to Miriad Image format e GIPSY whole dataset export the currently viewed dataset to GIPSY format e Karma subset export the currently viewed sub image to Karma for mat If the subimage being viewed is a cube the subcube will be saved e FITS subset export the currently viewed sub image to FITS format If the subimage being viewed is a cube the subcube will be saved e Miriad Image subset export the currently viewed sub image to Miriad Image format If the subimage being viewed is a cube the subcube will be saved e GIPSY subset export the currently viewed sub image to GIPSY for mat If the subimage being viewed is a cube the subcube will be saved 2 6 Zooming Most tools provide a generic 2 dimensional zooming interface This interface is provided by the lt ImageDisplay gt widget section 2 15 24 CHAPTER 2 COMMON FEATURES 2 7 Resizing autoscaling To resize a display window grab the bottom right corner of it and drag to the size that you want The image
15. Pressing the View button will pop up the lt ViewDatasets gt widget This widget provides controls for a display window to manage the display of multiple datasets Most of the controls for data display management are in the lt DataBrowser gt widget The controls provided are e Close this will close the window e Browsers this will pop up the data browser window s for this display window 41 42 CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES e Movie this will pop up the lt AnimateControl gt widget section 2 3 which will allow you to play movies and step through frames In addition the following key bindings are defined for the main display window PgDn go to previous frame PgUp go to next frame Home go to start frame End go to end frame On some keyboards PgDn is marked as Next and PgUp is marked as Prev e Profile Mode Menu this allows you to pop up the lt TracePopup gt widget section 2 11 and choose the profile mode The following modes are available None will pop down the lt TracePopup gt widget Line will show a single profile in the selected direction Box Sum lets you draw a box over the image window using the middle mouse button in a similar way as using the left mouse but ton to zoom and then the sum of all the profiles in that region is displayed Box mode only works for 3 dimensional datasets and will always display a profile along the unseen dimension Box Av
16. access to the following platforms e sparc_SunOS e sparc_Solaris e i386_Linux e mips2_IRIX6 e mips4_IRIX6 e alpha_OSF1 so I make binary distributions for these platforms Karma has also been ported to the following platforms e rs6000_AIX e mips _ULTRIX e hp9000_HPUX e crayPVP_UNICOS e c2_ConvexOS e mipsl IRIX5 e mips2_IRIX5 but since I don t have ready access binary distributions may not be forth coming If you want to run Karma under another operating system I will try to make the executables for it if I can get access to a machine Appendix C Resources All the GUI visualisation tools define a number of resources which control the appearance and functionality of the tools Many of these resources are common to other non visualisation programmes for the X Window system such as the lt xterm gt programme Listed below are those resources which are specific to Karma visualisation tools These resources may be set in your Xdefaults file which is the standard file into which to put your personal resources Some systems use the non standard Xresources file instead although the format is the same On SGI systems you may need to put your Karma resources in a separate file and run xrdb merge lt filename gt in your window system startup script You may also instead on SGI systems need to set resources in your Sgiresources file In some cases you will need to prepend the application classname i e Kvis
17. angle are also printed If you click with the right mouse button near the centre of the slice you can then move the slice centre around whilst the length and position angle is kept constant If instead you clicked the right button near either end of the slice you can change the position angle while the length and centre are kept fixed When moving the cursor in the slice window the coordinates of the cursor are displayed in several ways The natural coordinates of offset from the slice centre and third axis coordinate are shown in the second line The image coordinates corresponding to the offset are shown in the third line The position of the cursor along the slice is also shown by a small circle in the image window If you compute the moments of the cube with lt kpvslice gt both are held in memory so you may switch between them easily The values in the first moment image along the slice are plotted as a red trace in the slice window Note that no smoothing is done before the clipping level is applied so they do not do as good a job of representing weak signals as the standard MOMNT task in AIPS This may be fixed in later versions of the program If the values in the two dimensional image have the same units as the cube s third coordinate axis the values are extracted and displayed as a green trace in the slice window In practice this usually happens when one draws a slice on a velocity field image the velocities from the image
18. are drawn as a green line on the position velocity diagram The position angle is defined as the angle in the corner of a spherical triangle 6 1 1 Viewing Profiles You can also view a profile spectrum of your cube profiles section 2 11 Just press the Z Profile button and move the mouse over the image window If you wish to see a profile along the slice across the image press the I Profile button and another profile window will appear Just don t confuse the two different profile windows 6 2 Extracting Slices From An Image lt kpvslice gt can also extract a one dimensional slice from an image In this case you do not have to load a cube only the image is needed Click on the I Profile button and draw your slice The profile window will show the values in the image which lie along the slice locus 6 3 Command line Options The following command line options are supported by lt kpvslice gt e trace_internal_colour lt colour gt the colour specified by colour is used when displaying the trace taken from the internally computed 1st moment map 6 4 ALGORITHMIC DETAILS 83 e trace_external_colour lt colour gt the colour specified by colour is used when displaying the trace taken from the externally computed loaded Ist moment map 6 4 Algorithmic Details 6 4 1 How the Slice is Computed The slices are interpolated using a weighted average of the nearest four pixels The weighting is inversely proportional to the
19. atnf csiro au pub software karma The programmes available at the moment are e volume rendering of data cubes lt xray gt chapter 5 e play movies of data cubes lt kvis gt chapter 3 e inspecting multiple images and cubes at the same time lt kvis gt chapter 3 e slice a cube lt kslice_3d gt chapter 7 e superimposing images lt kvis gt section 11 2 and lt kvis gt section 11 3 e interactive position velocity slices lt kpvslice gt chapter 6 e look for expanding shells lt kshell gt chapter 8 1 2 CHAPTER 1 INTRODUCTION e interactive co ordinate placement lt koords gt chapter 9 e rectangular to polar gridding of images lt kpolar gt chapter 10 1 1 Supported Data Formats All the visualisation tools support a variety of data formats including e AIPS this is the format used by the AIPS package Astronomical Image Processing System sometimes called Classic AIPS or AIPS1 not to be confused with AIPS which is sometimes called AIPS2 This data format uses a catalogue file which is automatically scanned by the file browser and each available dataset is given an entry in the browser with the string AIPS shown in the left hand column By default all map files in the catalogue are shown You may set the AIPS_ID environment variable to your AIPS user ID to avoid seeing files belonging to other users To see AIPS files on an AIPS disc you will need to change directory to
20. be zoomed To unzoom choose the Unzoom option in the Zoom menu or press the u key while the cursor is in the image window This will show the entire image You can also press the i key zoom in and the image is zoomed 2x with the new centre of the image being the position of the mouse when the i key was pressed You can zoom in as many times as you like To unzoom 2x press the o key zoom out When unzooming it doesn t matter where the mouse is If you press and release the left mouse button without moving the mouse in between the image will be panned so that what is under the mouse cur sor is moved to the centre of the image An extra facility in lt kvis gt and lt MultibeamView gt is the ability to zoom in and out using the middle and right mouse buttons respectively in a similar fashion to using the i and o keys Note that these zoom controls are not available when you place the main window in panning mode 664499 r Another key you can press is which simply refreshes the window without changing the zoom area Image Statistics in the ImageDisplay Widget Many programmes have a facility to compute and display the statistics of the current sub image being viewed Simply press the s key in the display win dow and you will see a summary of the image statistics in the terminal window This summary includes the number of non blank values the standard devi ation the mean minimum
21. centring algorithm is effectively bypassed and the position you selected will be used for the star position This allows you to position by eye Please note that heavily clipped images have lost information and hence the accuracy of star positions will be limited Chapter 10 kpolar regridding to polar co ordinates This tool allows you to regrid an image using a rectangular to polar trans formation It allows you to see the azimuthal variation of intensity around a given centre This can be useful for looking at the optical structure of galax ies or doing close inspection of a dirty beam quite useful when doing radio astronomy To use this programme all you need is an image file which you load with the Files button Once your image is loaded you need to define an ellipse e Press the right mouse button to define the centre then drag the mouse while keeping the button pressed to define the size and shape of the ellipse e If you press and release the r key still keeping the mouse button down this will toggle on rotation mode so that now when you drag the mouse the ellipse will rotate Press r again to turn off rotation mode so you can continue changing the size and shape of the ellipse e Once you are happy with your ellipse release the mouse button and the polar image will be computed and displayed in the Polar Window The vertical axis is azimuth angle and the horizontal axis is radius Please note this
22. contours can take a long time to display so mistakes are costly e Axis Labelling Title this allows you to change the title placed above the image when axis labelling is enabled Normally the title is automatically generated e ve Contour Width this controls the width of negative contours e ve Contour Width this controls the width of positive contours e Auto Title if enabled the axis labelling title is automatically generated Whenever this is disabled the string specified by Axis Labelling Title is used instead e Show Beam if enabled the dataset headers are searched for BPA BMAJ and BMIN FITS style keywords If these keywords are present a representation of the telescope beam is overlaid on the image e Show Beam Name if enabled the name of the dataset for each beam is placed near the beam representation e Set 1 Beam Xpos controls the horizontal position of the the beam for dataset 1 e Set 1 Beam Ypos controls the vertical position of the the beam for dataset 1 e Set 2 Beam Xpos controls the horizontal position of the the beam for dataset 2 e Set 2 Beam Ypos controls the vertical position of the the beam for dataset 2 In addition if you click the left mouse button in the display window without moving it in between the press and release the image will pan across If you click the middle mouse button the image will zoom in 2x the new centre of the image will be the place where you clicked Click the ri
23. decimating a datacube The user can skip average data values along each dimension as well as extract a subcube The following controls are provided e Cancel close the window e Load load the file using the specified parameters e Abort abort the loading process e Auto Save if enabled the decimated subcube is automatically saved to disc e X Start select the starting position of the subcube in the X dimension e Y Start select the starting position of the subcube in the Y dimension e Z Start select the starting position of the subcube in the Z dimension e X End select the end position of the subcube in the X dimension e Y End select the end position of the subcube in the Y dimension e Z End select the end position of the subcube in the Z dimension e X Skip select the skip factor along the X dimension The default value of 2 will make every 2 input values along X averaged together e Y Skip select the skip factor along the Y dimension The default value of 2 will make every 2 input values along Y averaged together e Z Skip select the skip factor along the Z dimension The default value of 2 will make every 2 input values along Z averaged together e Output filename change this to select the name of the file which is saved to disc Under the first row of buttons the size of the file in data elements is displayed and the memory size required by the decimated subcube is displayed Underneath these the subcube bottom left corner BLC and top
24. default is to use the same projection as the input 12 5 9 ksend This tool allows you to send commands to various GUI tools The commands include loading a file writing PostScript to a file setting display ranges and so on This can be useful for batch processing many different datasets using the same control settings If you wanted to load the files mom0 and momi into the lt kvis gt chapter 3 programme displaying mom0 as an image and mom1 as contours and then write PostScript to the ps file you would first need to start lt kvis gt and set up the controls appropriately to display contours Then you can use the command ksend add_connection unix kvis multi_array load ARRAY FILEO mom0 load ARRAY FILEO momi print ps A variation of this would be to generate a Portable Pixel Map PPM file with name fred ppm ksend add_connection unix kvis multi_array load ARRAY FILEO mom0 load ARRAY FILEO momi ppm fred ppm You can use the above command many times each time specifying different files and hence obtain batch mode operation If you wanted to set the intensity display range to 1 0 and 1 5 for dataset 1 you would do something like this ksend add_connection unix kvis multi_array rclip Dataset 1 1 0 1 5 102 CHAPTER 12 COMMAND LINE TOOLS Alternatively if you wanted to set the intensity display range to 95 of the data you would do something like this ksend add_connection unix kvis multi_array hclip Dataset 1 0
25. e pin enable to force the fileselector window to stay pinned up even if files are selected The default is to close the window once a file is selected 10 CHAPTER 2 COMMON FEATURES e new create a new file browser The current directory will be independent of the original file browser e filter if enabled selected files are not automatically loaded rather the lt LoadAndDecimate gt widget section 2 1 1 is displayed e partial if enabled support loading of partial files This is useful if you want to see a preview of a dataset that is currently being written by an other process See the section on partialdata http www atnf csiro au karma user manual partialdata htmltpubpartialdata data in the Karma User Manual e writable if enabled the file may be modified later ie by the image editing facility e pull change the directory in this browser to match the most recent direc tory change in any browser i e pull the most recent directory change e push change the directory in all other browsers to match the directory for this browser i e push this directory to others Convenience buttons for jumping to commonly used directories may be con figured by the local Karma administrator or by the user The following files are searched e KARMABASE share browser dirbuttons e KARMABASE site share browser dirbuttons e HOME karma browser dirbuttons in that order The format of this file is a sequence of ASCII lines with e
26. for your changes to take effect These leading characters have the following meaning Ispecify channel Indices Thus Imin max 1 selects channels between channel 0 the first and the last channel in single channel increments ie all channels For example if you wanted to display channels 10 to 20 inclusive type 110 20 1 W specify World co ordinates i e velocity in m s or frequency in Hz For example if you wanted to show channels between 1418 and 1420 MHz in 100 KHz steps type W1418e6 1420e6 1e5 e Profile menu The choices are off the array will not be shown as a profile master the array is shown as a profile is drawn on top and controls the axis labels slave the array is shown as a profile and is slaved to the master Dark the colour to use for profile display This must be a dark colour appropriate for display on light backgrounds i e white paper e Light the colour to use for profile display This must be a light colour appropriate for display on dark backgrounds i e a computer monitor Advanced Control Panel This control panel allows you to control some extra aspects of the behaviour of all data browsers The following controls are available e Close this will close the window e Clip Mode menu controls how changes in the low and high clip levels affect display windows The following modes are available 52CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES Image and
27. for a screen snapshot You can also change the intensity control policy by selecting the Intensity Policy option in the Intensity menu This will pop up an lt IntensityPolicy gt widget This widget controls the intensity policy to be used for displaying image data on a drawing canvas The following controls are provided e Close this will close the window e Apply apply control changes and refresh the window e Auto Refresh if enabled each control change is automatically applied and the window refreshed e Auto Intensity Scale if enabled the intensity range of the sub image being viewed is mapped onto the colourmap otherwise the intensity range of the entire image movie is mapped onto the colourmap e Reset Intensity Upon File Load if enabled the intensity scale is reset when a new dataset is loaded it is reset to the full data range If disabled the intensity scale is not changed on file load e Intensity Scale Menu this menu allows you to change between different intensity scales By default the intensity scale is linear but you can select a logarithmic intensity scale or a square root intensity scale If you are using a logarithmic intensity scale you can set the Log Cycles value to control the visible dynamic range in powers of 10 See Figure 2 5 for a screen snapshot 2 3 Sequences of Images If you load a datacube into the lt kvis gt programme you may wish to play it as a movie sequence of images A window to control
28. forwards gt backwards gt forwards gt e Anti Flicker remove the flicker observed when overlays i e contours and or annotations and or axis labels are shown This is normally dis abled because it slows down movie playing and interactive display up dates Also flicker is only noticeable under some conditions complex overlays and or slow display hardware e Frame Interval the time interval between between frame draws A low interval will give fast movies e Skip Factor allows you to skip frames A skip factor of 2 would skip every second frame e Goto Frame jump to the frame number shown in the Current Frame control e Current Frame the current frame number e Starting Frame the starting frame number in the movie loop 20 CHAPTER 2 COMMON FEATURES Y MODE Forward Spin Frame Interval ms gt lt 4 lt o gt Skip Factor Number of frames Current frame o Starting Frame Ea End Frame Figure 2 6 Screen snapshot of movie control panel e End Frame the end frame number in the movie loop You can also step through the cube by clicking left for the previous frame or click right for the next frame in the black rectangle which appears below the Goto Frame button In addition you can click middle and drag in this black rectangle allowing you to dynamically slide through the movie See Figure 2 6 for a screen snapshot 2 4 Hardcopies To make a PostPcript hardcopy of the display click on the menu b
29. is an experimental programme that at present does this transformation in a simpleminded way It works by binning the input image in radius and azimuth directions using a set of concentric elliptical annuli Each annulus has a width of one pixel Some points that you may wish to consider when using this task are listed below e The programme does simple nearest neighbour interpolation to produce the output intensities the absolute flux scale will probably not be per fectly preserved e No world i e angle in degrees radius in arcseconds co ordinate system is attached to the image No allowance is made for images which have different scales on their x and y axes 91 92 CHAPTER 10 KPOLAR REGRIDDING TO POLAR CO ORDINATES e The centre position of the ellipses is not fitted in any way it is exactly where you place it Feedback on improvements to this task including code is welcome Chapter 11 Superimposing Images The lt kvis gt chapter 3 programme allows you to display different images on top of each other while each image has a different colour coding This can be used to display amplitude and phase together in one image or compare different channels from a data cube by superimposing them These visualisation techniques require a 24 bit display 11 1 Image and Contours Note that there is another way to superimpose images which involves drawing one image as a greyscale or false colour image and the other is drawn
30. it is important that the co ordinate system takes the variable pixel size into account so that it tracks the moving object correctly The scaling of the cell size with frequency is accounted for in the coordinate handling within Miriad The correction is quite small for narrow bandwidths e g 4 MHz but quite noticable for cubes with 128 MHz bandwidths at 20cm a 7 pixel shift is not unheard of The FITS convention assumes that pixel sizes are constant The visualisa tion software also makes this assumption Since June 1997 Karma has taken account of this chromatic aberration by adding the new CELLSCAL keyword as it reads in Miriad cubes This keyword is used in the astronomical world co ordinate package to correctly track variable pixel sizes At the same time Miriad was modified to add the CELLSCAL keyword when it writes FITS files Prior to this old FITS cubes 103 104 APPENDIX A CHROMATIC ABERRATION written by Miriad did not have this keyword and hence violated the FITS convention If you have such old cubes you should either regenerate the FITS from the original Miriad cube or else manually edit the FITS header by adding a line such as CELLSCAL 1 F If you use a current version of Miriad and Karma then the co ordinate system will correctly handle the chromatic aberration effects Note that the source object will stil appear to move as you play a movie of channel maps I have been asked to change this but this
31. it should be loaded or just a plain directory which should be entered The tester programme must exit with status 0 if it recognises the dataset otherwise it should exit with some other value If it returns the value 16 no warning will be given It is given the name of the dataset directory as a single argument The file browser described in section 2 1 will show all files which are sup ported by data filters making the loading of extra data formats transparent to the user If you want to write your own data filters see the section on datafilters http www atnf csiro au karma programmer manual datafilters html pubdatafilters in the Karma Programming Manual The converter and tester programmes may be specified with absolute path names or you may give a plain filename and the PATH is searched As well as the normal absolute pathnames i e those with a leading character you may also specify an expression such as KARMABASE site MACHINE_OS bin sdf2karma or alteratively KARMABASE usr local karma site bin sdf2karma which is useful if you want to specify KARMABASE site bin sdf2karma if the KARMABASE environment variable is defined otherwise use usr local karma site bin sdf2karma instead This is a good way of providing a default location 1 3 UNITS y 1 3 Units Karma follows the FITS conventions for units In other words SI units are used Please see the FITS standard for more information 1 4 Co ordinate Sy
32. may not be as good 5 6 Filtering your data Often there will be problems with the data too noisy confusing or bright continuum sources which make it difficult to see your data To help there are a few filtering alogorithms implemented which should help Click on Filter in the main control window and a filtering control panel will pop up The following filtering algorithms are available e simple one of the adaptive filtering algorithms e slow median mask one of the adaptive filtering algorithms e fast median mask one of the adaptive filtering algorithms e 3D one of the adaptive filtering algorithms e subtract continuum the continuum subtraction algorithm 5 6 FILTERING YOUR DATA 75 5 6 1 Adaptive Filtering One problem with volume rendering is that in order to see faint structures in the data cube one has to set the opacities intensity transformation and clips such that also the noise becomes bright As a consequence the emission is visible only through a thick fog of noise and this noise hides a lot of information One solution is to apply adaptive filtering to the data cube the data is smoothed where the emission is faint and extended or absent while the data is left intact if it is stronger or more pointlike There are several techniques to do this At the moment two algorithms are implemented but we are working on other filters The filters are based on work of J L Starck F Murtagh and A Bijaoui with a few extent
33. of data type which are described here There is always a highlighted line which shows which entry you can make changes to using either the mouse buttons or the keyboard The highlighted line is shown by a slightly different background colour You can change the highlighted line by using the mouse or up down arrow keys There is also a selected line which shows which entry has more detail shown in the section s below The list section only shows a summary of the current configuration for each dataset The selected line is shown by using reverse video If the browser is in active mode the default then the selected line is locked to the highlighted line If in passive mode the selected line does not move until you explicitly select an entry If you select an entry while in active mode the browser switches to passive mode If in passive mode and you select the already selected entry the browser switches to active mode As the mouse is moved over the data names one of the names will be highlighted The mouse and keyboard may be pressed to control the settings of the highlighted data The following bindings are available e Left Mouse select the highlighted dataset for display in the sections below and disable active mode If the data is already selected and active mode is disabled active mode is enabled e Spacebar same effect as left mouse button e Up Arrow highlight and select the previous data e Down Arrow highlight and select the n
34. of the emission It is less useful for looking at small details e Minimum voxel The pixel value is the minimum voxel along the line of sight e Maximum voxel The pixel value is the maximum voxel along the line of sight This is a fast way of getting a reasonable image It also allows depending on your data to have a view of the inside of your data the object looks more transparent than with the Voxel sum shader e Front voxel The pixel gets the value of the first voxel along the line of sight above a specified threshold not usually useful the image is very blocky and has many holes You get a control window where you can change the threshold value by clicking the left mouse button 65 66 CHAPTER 5 VOLUME RENDERING A CUBE The second kind of shaders uses an equation of radiative transfer to compute the images These are called hot gas shaders The contribution of a voxel to the pixel on the display is calculated using a simple equation of radiative transfer where a voxel is partly absorbed by voxels that are in front of it Gj G 4 1 0 85 Oj 5 1 where c is the intensity along a line of sight after adding the i voxel in front s the intensity of the voxel added c _ the intensity along the line of sight that is behind the i voxel and o the opacity of the voxel i This calculation is done back to front so voxels in the back of the cube are partly obscured by voxels in the front part of the cube
35. or ZY planes e Profile Axis Menu this allows you to choose along which axis you want the profile to be displayed valid only for line profile mode e Display Mode Menu this allows you to choose how you want to view your two datasets The following choices are available 59 Set 1 gt image view dataset 1 as an image Set 2 gt image view dataset 2 as an image Set 1 gt image Set 2 gt contour view dataset 1 as an image and overlay dataset 2 as contours Set 1 gt contour Set 2 gt image view dataset 2 as an image and overlay dataset 1 as contours Blink between Set 1 and Set 2 enable blinking between the two datasets Link Intensity Scales if this is set then if the intensity scale for either dataset is modified using the lt Dataclip gt section 2 2 widget then the intensity scaling for both datasets is changed This can be useful when blinking between two images Link Frames if this is set then whenever the the current frame number for the image dataset is changed the frame number for the other dataset is also updated to have the same value If the two frame dimensions have the same co ordinate type then the co ordinate values are matched rather than co ordinate indices This feature is often used when displaying a movie of both datasets one as images and one as contours Show Frame in Line Profile if this is set the current frame displayed in the main image window is shown as a vertical red line in the profile w
36. panel This is descibed in section 5 5 e Rescale if you loaded a non byte cube then you can bring up the his togram display using this button and then you can set the data scaling again e Filter this pops up a filtering control panel described in section 5 6 e Quit this will quit the application e Hide Wireframe if disabled a wireframe showing the visible edges of the cube is displayed over the rendered data to show how the data cube is 70 CHAPTER 5 VOLUME RENDERING A CUBE OlHide Hireframe l Stereo Figure 5 1 Screen snapshot of main control panel rotated It also helps the brain to perceive the data as three dimensional If you don t like the wireframe you should enable this toggle Stereo if your are sitting in front of phoenix and you started the window system in stereo mode clicking on Stereo will enable stereo display The way this works is that slightly different images are displayed in your left and right eyes mimicking the way you see depth normally You will hopefully see the rendered cube as a three dimensional object with depth To make use of this you need to wear a pair of Crystal Eyes glasses these fit over most prescription glasses If you want to use this feature please ask the system administrator who will lend you the glasses These things are rather expensive so we don t just leave them lying around Because of a problem with the vendors graphics library it is best to use the stereo option
37. perhaps an optical image and display that as the image This can be useful for comparing optical and radio data You can also view a profile section 2 11 spectrum of your cube Just select select line profile display and a profile window will appear You will note that the profile is drawn in the same colours as the contours 56CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES Chapter 4 Viewing Images and Cubes with the Multibeam Note that this tool will be replaced with the more powerful lt kvis gt chap ter 3 programme The lt MultibeamView gt programme allows you to view two datasets This allows you to compare different datasets in a very easy fashion This programme uses the lt ImageDisplay gt widget section 2 15 to provide the usual interface Pressing the View button will pop up the lt View2Datasets gt widget This widget provides an advanced control for two datasets either two dimensional or three dimensional It allows the user to display one dataset or the other overlay contours of one over the other show profiles along any axis and much more The controls provided are e Close this will close the window e Movie this will pop up the lt AnimateControl gt widget section 2 3 which will allow you to play movies and step through frames In addition the following key bindings are defined for the main display window PgDn go to previous frame PgUp go to next frame Home go to start f
38. right corner TRC co ordinates are displayed and also the pixel increment INC As you change the slider parameters the memory requirement changes as do the BLC TRC and INC values and these are reported to you It is wise to not use more than about half the physical RAM Random Access Memory available in your machine As the file is loaded and decimated a simple progress meter shows you how much longer you have to wait Remember you can always abort See Figure 2 2 for a screen snapshot 2 1 LOADING DATA 13 Figure 2 2 Screen snapshot of decimation control panel 14 CHAPTER 2 COMMON FEATURES 2 2 Intensity Scaling With many images that you display you will want to change the colourtable used The colourtable control appears after selecting the PseudoColour 8 bit option in the Intensity menu in most tools The lt Cmapwinpopup gt widget provides the colourtable control interface This widget controls a colourtable for a PseudoColour display canvas Data values are used to index into a table of colours This is typically used for false colour image display The following controls are provided e Close close the window e Reverse this reverses the colour table the colours of the minimum and maximum are swapped e Invert this inverts every colour e g white becomes black green becomes purple blue becomes yellow and so on e Save this brings up a popup window which allows you to save a colourtable e L
39. same co ordinate grid Once you have loaded your files you simply click with the middle mouse 87 88 CHAPTER 8 KSHELL LOOKING FOR EXPANDING SHELLS button don t let go yet to define the centre of the shell drag the mouse so that you see the expanding circle and release the middle button when you think the radius is sufficiently large such that the entire shell is enclosed Don t make it larger than is really necessary since it will take longer for the programme to compute the radius velocity image After a short time fraction of a second to a few seconds for typical cubes you will see the computed radius velocity image Do you see a nice ellipse in the right window If you move the mouse into the right window you should see the current position in sensible units as well as the averaged intensity at that point You can use the Export menu above the image to write the image with co ordinates in a variety of formats choose one of the whole dataset options A small tip for people looking at data with very high dynamic range such as OHIR masers set intensity scale for the right window to logarithmic see the zooming section 2 6 section otherwise you will only see a few bright blobs Chapter 9 koords interactive co ordinate fitting This tool allows you to quickly place a co ordinate system compute a plate solution onto an image which does not have one This is very useful if you have say a CCD imag
40. some others will automatically display the profile window when you have loaded a cube of floating point data You don t need to press any buttons to update the profile display simply point the mouse at the desired spot The ability to display spectrum profiles is provided by the lt TracePopup gt widget This widget will display a line plot of a single trace of one dimensional data It is fast allowing dynamic display of data and provides zooming and smoothing controls as well as having the ability to display axis labels The controls available are e Close this will close the window e Auto Zoom if enabled the vertical scale is automatically zoomed to the range of the data in the profile e Unzoom this will unzoom the window e Smooth menu to select what kind of smoothing to apply to the data prior to display Both hanning and uniform smoothing kernels are avail able with a range of sizes e Print this will pop up the lt Postscript gt widget section 2 4 e Overlay this allows you to popup various control panels to control overlay display including axis labelling section 2 8 e Save Data this will pop up a dialog widget which allows you to save the data to a file The data is saved in a simple ASCII format with a few comment lines followed by two columns of numbers The first column is for the horizontal axis and the second column is for the vertical axis e Style menu to select the drawing style for the data points The fol
41. that the Perspective projection is there is that this is quite useful for stereo display Even if you are not using stereo mode you may want to try it anyway It helps for the 3D perception of the images Mode Menu this allows you to choose the rendering mode The process of projecting rays into the data volume and collecting the data along each ray can be quite involved and there are speed quality tradeoffs The Mode Menu allows you to choose between these tradeofts 3 D Cursor Menu this allows you to choose the kind of 3 dimensional cursor available This code is currently in development so things may change rapidly An overlay cursor is available the cursor is drawn over the rendered volume so the cursor will not dissappear behind a feature in the data A proper translucent cursor is also available You can move the position of the 3 D cursor by pressing the left mouse button in any of the three slice windows the ones with the red crosshairs and dragging the mouse Compute this will cause the cube to be rendered using all the current parameters Reset Orientation this will reset the view and then renderer the cube Load Segments this will bring up a file browser which allows you to load files with extension seg These files contain pairs of three dimensional co ordinates each pair defining a line in the world co ordinate system of the volume These 3D lines are drawn through the volume and are obscured by opaque structure in the volum
42. the input datasets are 54CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES Annotation List There is just one column used to display a summary of the configuration The a character is used to indicate whether a annotation file is active visible or not The a key may be used to switch between the two states The middle mouse button has the same effect of switching between the two states Detailed Annotation Information This shows where directory from which the annotation file was loaded the Unload button may be used to unload the annotation file This affects all blink states and display windows Annotation Configuration The Active toggle may be used to switch between active visible and inactive settings for this annotation file 3 4 Command line Options You may pass the names of files to be loaded via the command line You may specify as many files as you desire up to the limit imposed by the operating system 3 5 Intensity Intensity Scatter Plots Earlier in this chapter 3 2 is a brief description of how you can use the c key to compute and display an intensity intensity scatter plot of two images You may also use this facility to display a scatter plot of two channels from the same cube Simply clone the cube i e using the Clone data browser button and select the two channels one from each cube You will need to ensure that the original and cloned cube do not have a master slave movie relationship If th
43. the memory requirement is on the machine you are sitting in front of not the machine that you are running the programme on although for best performance they should be the same 85 86 CHAPTER 7 KSLICE_3D SLICING DATA CUBES 7 2 Magnifications There are three sliders that control the size of the three images If you expand too much lt kslice_3d gt will not display anything i e you will see a blank window Just reduce your expansion factor appropriately until the display re appears If you want to make the images larger than the window would allow you can resize the window drag on the bottom right corner and after this increase the magnifications Chapter 8 kshell looking for expanding shells This tool allows you to browse your datacube searching for expanding shells Since most shells are mostly radially symmetric it is reasonable to azimuthally average concentric annuli around a designated centre What this means is that the programme allows you to define a centre position on the sky and a maximum radius It will then step through a range of radii from zero to the maximum and at each radius will average the values in one velocity map around the circumference of a circle hence azimuthal average This process is repeated for each velocity map and the result is an image with one axis corresponding to radius and the other velocity If you are looking at an expanding shell for each velocity map the aver age ra
44. this sequence is under View gt Animate The lt AnimateControl gt widget provides the animation control interface This widget controls movie loops It allows the user to control the speed and direction of movies as well as the ability to skip frames The following controls are provided e Close close the window e Previous Frame show the previous frame e Next Frame show the next frame e Start Movie start the movie CHAPTER 2 COMMON FEATURES Data Min 358 33 mJy Beam Data Max 110 439 mJy Beam Lower Clip 44 09 mJy Beam Upper Clip 110 49 mJy Beam Cursor pos 358 33 mJy Beam Y Output Type float Filename r m Ca al AN gz A al A E he a a d muy Bear Figure 2 4 Screen snapshot of intensity zoom control panel 2 3 SEQUENCES OF IMAGES Close Apply Auto Refresh O uto Intensity Scale Hu Ko hr Reset Intensity Upon File Load Y Intensity Scale linear Log Cycles 4 l Figure 2 5 Screen snapshot of intensity policy control panel e Stop Movie stop the movie e Sync wait for each frame to be drawn before sending the next draw request Normally this is enabled You can make movies run a little bit faster not much by disabling this but you run the risk of developing a backlog of display requests in the display machinary A large backlog will make the interactive response extremely poor e Spin Mode you can select forward or backward spin or alternatively spin
45. when rendering to 24bit images i e when using the Hot Gas Substances or Hot Gas Continuous shaders 2 D Cursor Menu This menu allows you to switch from the default cursor to an experimental 2 dimensional active cursor The default or dumb cursor will allow you to read image values and positions in the display window in the conventional way The active cursor allows you to point at a feature say a blob on your volume rendered cube and obtain the 3 dimensional position of that feature The horizontal and vertical position information is accurate however the depth position is computed using a heuristic and 5 4 THE MAIN CONTROL WINDOW 71 is less accurate In another window you will see a plot of the cube values versus the position along the line of sight drawn in white A yellow vertical line shows the depth of the feature you are pointing at really the depth the algorithm thinks the feature is at Both the 3 dimensional position information and the plot window are dynamically updated as you move the cursor in the image display window Shader Menu this allows you to select which shader to use See section 5 1 1 Projection Menu this allows you to select a prjection Two projections are available Orthogonal and Perspective If you select the perspec tive projection you can control the distance of the cube i e the amount of perspective with the Distance slider in the control window The main reason
46. would require the visualisation software to regrid the cube Apart from the computational cost involved it is also not the correct approach as subtle artefacts can be introduced The correct approach is to produce a cube in Miriad which does not have a variable pixel size This is possible to do although a little awkward It involves computing each channel image independently This will mean that Miriad computes a beam pattern image for each channel If you manually specify the pixel size each computed image will have the same pixel size After this you clean each image and collect them into a single cube You can make this procedure easier by writing a script Once you have produced such a cube check the header to ensure that you don t have a CELLSCAL keyword with value 1 F Miriad should only do this when a 3 dimensional invert is performed Appendix B Setting up B 1 Environments needed The visualisation software is written using the Karma package a library for networked data processing and visualisation In order to be able to use this library a number of environment variables have to be set There are two ways of doing this 1 is to type source usr local karma login You can also include this in your login file 2 if you are using the standard login file select Karma 105 106 APPENDIX B SETTING UP B 2 Operating Systems All the programs here are available for Unix environments I have ready
47. 3 Loading partial files Adding your own Data Formats UNSL A ee E ahr Tage we Co ordinate Systems 1 0 ee ee 2 Common Features 2 1 2 2 2 3 2 4 2 5 2 6 2 7 2 8 2 9 2 10 2 11 2 12 2 13 2 14 2 15 2 16 2 17 2 18 2 19 2 20 2 21 Loading Data a a de dk Ge a Ee Ee AR a ae 2 1 1 Subsetting Decimation of Array Data Intensity Scaling osito pa ra AS etc abs Ge Sequences of Images 2 o a Hatdcoples sesti are ace te Pe Se ee ie See dae Exporting Data s aa 2 6 Ace eee ad A ee Se a ZOOMING a de Peed Snake Wa oe PaO he ee es Resizing autoscaling 2 42 469 4044e8 8 429 24 68 ee Axis Lapels rir ga A pose oR a ae Magnifying Glass ores ii h ea e E e ea ee Paniers eg ia Wee EE Oh Ae BR A ee ee SY aa A dees Spectrum Profes io geese ao eet a eae Bea He wD Image Statistics 44 4606 ew Xe ne kee a ew be aR ew Viewing Header Information 0 0 4 Freezing Vents a be 2 oe a e ce Bk ew JO RA de aes Common Image Display Features o o Generating Moment Maps o e a Cursor Readout e sie e GO a 2 17 1 Warning for Astronomers GUI Command line Switches o 2 18 1 Avoiding Colourmap Flashing Drawing Overlays 2 2 ee Loading Overlays sas o ee ey ee Rg PR Editing mages i lt 4 820 e o sowie Gee ae ee bc iii 3 8 CONTENTS Viewing and Comparing mu
48. 3 Passing in Negative Values 12 3 4 Passing in Other Arguments 12 4 Saving and Restoring Parameters 12 5 sto Tasks sleeved a eden She ee Re dae Dada 1225 1 clear a A eR oe E 12 5 2 images2karma soc coa a E a p a a ae a a N aa 125 3 karma2ppm 4 4 ie afd Sota be a Po bea 12 54 kdecimate plot tia Poke PR Bok Bos 12 00 IOMA okey teed TOMO Syd ke Bhar SR 12 5 6 kprinthead o e eee LADA TO ag Ge te Ae a wie OI GR ae he ae aD 125 9 krotat 3 dra a ee BR Pa de Ss AA RST grar Te eh ahh arse ase eed deen bean A ies te He i Need oe 12 5 10send contours 1 2 ee A Chromatic Aberration B Setting up B 1 Environments needed aoa a o B 2 Operating Systems 2 eee ee eee C Resources 89 90 91 93 93 93 94 95 95 95 96 96 96 96 97 97 97 97 97 97 98 98 98 98 98 99 99 100 100 100 101 101 101 102 103 105 105 106 107 vi CONTENTS D Annotation File Format 111 DA Usar ia a ORG Bae A ke Gre a ese 111 D 2 Fundamental Syntax ee ee 111 D 3 Annotation Commands 2 0 00 0004 112 D 3 1 Non Graphical Commands 112 D 3 2 Attribute Commands 4 112 D 3 3 Object Commands 00048 113 D 3 4 Position Angle Conventions 115 D 4 Example Annotation File 0 116 E Making Videos 121 E 1 Basic F
49. 8 0 04 10 ELLIPSE R 0 88 0 70 0 04 0 02 10 COLOR GOLD CBOX P 450 220 44 22 10 CROSS P 450 220 44 22 10 ELLIPSE P 450 220 22 11 10 HHEHHHHHHEHHHEHHREHHREHHHAEHHAA HR REH HEHEHE EHHHRE ARA RRR R EHR HHH END OF SAMPLE KARMA ANNOTATION FILE M42_INCLUDE ANN HHEHHHHHHAHHREHHREHHREHHHAEHHAA HERE H HEHEHE EHHH AEH HRH RRR E RRR R HHH R HHH Appendix E Making Videos Sometimes you will want to prepare a video for presentation The procedure to do this depends on the equipment you have available and the desired quality of the production This appendex discusses some options E 1 Basic Facilities at the ATNF The ATNF has video recording equipment connected to the workstation phoenix This equipment is not capable of producing high quality ie broadcast stan dard videos but it has the advantage of being located at the ATNF and so is convient to use Once you have produced your movie you need to purchase a VHS video cassette and use the video recorders supplied When playing the movies it is advisable to use the fullscreen command line option for the kvis chapter 3 and xray chapter 5 tools This will make the image display window take up the entire screen You should see a button labelled Raise somewhere which allows you to place the displayed image above all other windows By clicking the right mouse button you can lower this window again and get back your control panels E 2 Using Sydney University VisLab Facilities T
50. 95 12 5 10 send contours This tool allows you to load an image and compute contour overlays which may then be sent to any GUI programme for display This facility is only useful when you want to add contours to a tool which doesn t already have built in support For each extra dataset you wish to display as contours you need to run a copy of the lt send contours gt programme To start the programme type send contours Once in the tool you will need to specify the desired contours levels This interface is quite primitive requiring you to enter the actual values for each level For example if you have a 1st moment map with interesting contours at 1 419 GHz and 1 420 GHz you would type the following contour_levels 1 419e9 1 420e9 You then need to specify the input file containing the image data in file infile where infile is the input filename Next you need to make a connection from the tool to a GUI tool Typically this will be the lt kvis gt programme which is running on the same machine For example type add connection unix 7605 2D_overlay The number 7605 is the Karma port number of the GUI tool and is dis played in the title bar of the GUI tool Other GUI tools will have different port numbers Once you have done all this setup type go and you should see your new contours The normal GUI functions for zooming are supported You can use the empty_list command to remove the contours and clean up the display Appendix
51. A Chromatic Aberration Radio telescope interferometers exhibit chromatic aberration effects This is because the resolution of the instrument changes with wavelength For low bandwidth spectral line observations these effects are minor and can usually be ignored However for high bandwidth observations say 128 MHz these effects can pose a problem Reduction packages such as AIPS and AIPS will produce a beam pattern image for each frequency channel This allows these packages to compute a spectral line cube which has a pixel size cellsize independent of frequency The chromatic aberration manifests itself in the dirty cubes as a changing antenna pattern In other words if you play a movie of the channel maps you will see the grating ring pattern change Once the cube has been properly cleaned you should no longer see grating rings and hence the cromatic aberration has been effectively corrected Reduction packages such as Miriad will only produce a single beam pattern for a nominal reference frequency channel this approach has the advantage of saving disc space Because of this Miriad produces cubes where the pixel size changes with frequency You can see this when you play a movie of the channel maps an object distant from the phase centre will appear to move although the grating ring pattern will not change it only shifts with the source object This shifting of an object with frequency is of itself not a serious problem however
52. Browser Controls e Close this will close the window e Destroy the blink state that the browser is showing is destroyed It is not possible to destroy the first blink state for the display window e Copy create a new blink state and browser which has the same config uration as the currently viewed blink state In all mode the browser for the new blink state is popped up e Show menu gives control over how the various blink states are displayed The following modes are available all each blink state is viewed in its own browser some each display window has a single browser which can be switched to display any blink state for the display window e Data menu selects which kind of data is displayed in the browser The choices are Arrays gridded array data can be viewed as images or contours 3 3 DATA BROWSER Figure 3 2 Screen snapshot of data browser 46CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES Annotations text and geometric figures which can be overlaid for annotation purposes e Advanced this will raise the advanced control panel section 3 3 e Make Data this will raise the make data control panel section 3 3 Data List Beneath these general controls the list of loaded data appears Each line shows the name and a summary of the configuration settings for that dataset The list section is different for each data type There are common operations that may be performed irrespective
53. DOT 83 81738 5 38494 DOT 83 81875 5 38972 DOT 83 82208 5 38778 CIRCLE 83 81613 5 38706 0 0005 CIRCLE 83 81738 5 38494 0 0005 CIRCLE 83 81875 5 38972 0 0005 Theta 1C Orionis HD 37022 CIRCLE 83 82208 5 38778 0 0005 Theta 1D Orionis HD 37023 CLINES 83 81613 5 38706 83 81738 5 38494 83 82208 5 38778 83 81875 5 38972 83 81613 5 38706 TEXT 83 84 5 38 Trap ezium Theta 1A Orionis HD 37020 Theta 1B Orionis HD 37021 Theta 1C Orionis HD 37022 Theta 1D Orionis HD 37023 Theta 1A Orionis HD 37020 Theta 1B Orionis HD 37021 Indicate the star Theta 1C Orionis source of much of the UV flux ionizing the gas in the nebula Use a mixture of world and relative coordinates to fix the label on the screen when zooming COLOR YELLOW LINE W 83 81875 5 38972 R 0 6 0 1 TEXT R 0 6 0 10 Theta 1C Mark the region imaged by the HST mosaic released in 1995 http oposite stsci edu pubinfo pr 95 45 htm1 COLOR RED BOX 83 86867 5 44977 83 74646 5 31922 TEXT 83 86867 5 31922 HST One transverse light year at a distance of 1500 ly subtends 0 038 degrees At a declination of 5 39 degrees this is 0 0382 Right Ascension degrees COLOR GREEN CBOX 83 91196 5 49598 0 0382 0 038 CROSS 83 91196 5 49598 0 0382 0 038 118 APPENDIX D ANNOTATION FILE FORMAT TEXT 83 88 5 49598 1 1ly 2 Here is a series of disconnected lines for no very good reason The last c
54. IRECTORY dd2fits isdd FITS A directory dataset 6 CHAPTER 1 INTRODUCTION DIRECTORY aips 2fits isaips FITS AIPS Image gif giftopnm PNM GIF Image tga tgatoppm PNM Targa TrueVision This would use the lt iraf2fits gt programme to convert files with imh ex tensions to FITS The FITS data would then be read in with the standard FITS reader in Karma Similarly files with sdf extensions would be con verted to Karma format using the lt sdf2karma gt programme which would write out Karma data Note that it is much more efficient to have a filter which generates Karma than FITS Note the lt giftopnm gt and lt tgatoppm gt filters are both registered as producing PNM files whereas lt tgatoppm gt appears to produce PPM files This is not a problem since PNM Portable aNy Map is the generic format and PPM Portable Pixel Map is a specific subset of PNM The converter programmes are called with a single argument that being the name of the input file The output Karma FITS or PNM data must be written to the standard output You will note that the tester programme supplied for the imh and sdf formats is which means no tester is needed for these formats The special extension name DIRECTORY signifies that this data format is a directory based one examples of such formats are Miriad and AIPS images Directory based formats require a tester programme in order to determine if the directory contains a dataset in which case
55. Karma User Manual Richard Gooch http www safe mbox com rgooch December 26 2006 Copyright 1997 2006 Richard Gooch Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one Permission is granted to copy and distribute translations of this manual into another language under the above conditions for modified versions except that this permission notice must be retained in the English language Permission is granted to provide an additional copy of this permission notice in the language of the translation Richard Gooch may be reached by email at rgooch safe mbox com or on the WWW at http www safe mbox com rgooch The software described in this document is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the im plied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details ii Contents 1 Introduction 1 1 1 2 1 3 1 4 Supported Data Formats a ee eee 1 1 1 Converting Other Data Formats to Karma Format 1 1 2 Converting Between Data Formats 1 1
56. PSY 3 IRAF 3 Karma 3 Miriad 3 PGM 3 PNM 3 PPM 3 Simple FITS 3 Starlink 3 Sun Rasterfile 3 Targa TrueVision 3 TIFF 3 data replacement 48 decimating cubes 10 100 decimating images 10 drawing 39 drawing overlays 38 exporting 21 101 filter clip 76 fitting co ordinate systems 89 fitting gaussians 42 58 flicker removal 19 freezing events 29 hardcopies 20 header viewing 34 histograms image intensity 14 hue intensity display 93 illegal values 100 image formats 2 INDEX image statistics 29 images editing 39 images2karma 99 intensity scaling 14 17 karma 105 Karma WWW site 1 karma2ppm 99 kdecimate 100 key bindings b 57 c 43 54 60 62 control spacebar 29 control v 33 End 42 57 H 34 h 34 Home 42 57 i 33 1 34 o 33 PgDn 42 57 PgUp 42 57 r 33 s 33 spacebar 29 u 33 V 33 v 33 kminmax 100 koords 89 kpolar 91 kprinthead 100 kpvslice 81 switches 82 kregrid 101 krotate 101 ksend 101 kshell 87 kslice_3d 85 magnifications 85 precompute 85 ktranslate 5 kview switches 62 kvis 41 129 command line 54 loading data 9 loading partial data 5 10 magnifying glass 26 making videos 121 maximum of data 100 minimum of data 100 miriad masks 3 miriad2gipsy 5 moment maps generating 34 mosaicing 101 operating systems 106 overlay file format 111 overlays 3D 71 adding annotations 38 axis labels 24 c
57. Profiles the image intensity range and profile vertical range are synchronised and clip level changes affect both Images only only the image intensity range is affected by clip level changes Profiles only only the profile vertical range is affected by clip level changes Both later the image intensity range and profile vertical range are affected by subsequent clip level changes but they are not immedi ately synchronised e Range changes affect all arrays if this is turned on an attempt to change the clip levels of any array dataset will change the clip levels for all array datasets e Make slaved movie on load if this is turned on an array dataset with three or more dimensions will be automatically marked as a movie slave when loaded e Activate annotations on load if this is turned on an annotation dataset is automatically made active i e displayed when loaded e Slave Profile H range to image window if this is turned on the horizontal range of the profile window is set to the same as the horizontal range of the image window if the the axes correspond e Show new data as Image if this is turned on an array dataset is marked as the active image when loaded Make Data Control Panel This control panel allows you to create new array data from existing array data This is useful if you want to combine data together The following controls are available e Close this will close the window e Algorithm menu controls
58. SER 49 e Middle Mouse show as the image the previous image becomes the alternate image If already displayed as the image disable image display e Right Mouse toggle between enabling and disabling contour display e i key same effect as the middle mouse button e control i make the next dataset in the list the currently displayed image This will cycle back to the top of the list when the end is reached e control shift i make the previous dataset in the list the currently dis played image This will cycle back to the end of the list when the top is reached e a key make this image the alternate image e c key same effect as the right mouse button e r key toggle between enabling and disabling Renzogram display e control c enable contours and apply levels e control r enable Renzogram and apply level e M key enable movie controls for this array e m key slave this array to the movie controls e P key display line profiles of this array this array controls the axis labelling and is drawn on top e p key display line profiles of this array Detailed Array Information This shows information about the array such as the directory from where the array was loaded the format of the data i e FITS AIPS Miriad Gipsy and many more the size and dimensionality and the range of data values The following control buttons are available e Histogram pop up a histogram for this array The histogram display can be used to control th
59. ach line containing the name of the button followed by the directory to jump to For example survey nfs survey mydata nfs datal users fred See Figure 2 1 for a screen snapshot 2 1 1 Subsetting Decimation of Array Data Sometimes your image or datacube is too big to handle efficiently If you have a file which is much bigger than your physical memory RAM then most of the visualisation tools will run slower than a lame dog It generally does not make sense to visualise a dataset bigger than RAM To get around this the visualisation tools provide a mechanism whereby you can decimate a 2 dimensional image or 3 dimensional cube array Decimation involves taking every N values along an axis and averaging them together to produce a single output value then jumping to the next group of N input values If you use a decimation factor of 2 for each axis the output cube is 8 times smaller 4 2 1 LOADING DATA Figure 2 1 Screen snapshot of fileselector panel 11 12 CHAPTER 2 COMMON FEATURES times smaller for an image You can also extract a subcube if you are only interested in a small section of the data Note that the decimator allocates some temporary 2 dimensional buffers so when decimating a 2 dimensional array the memory requirements may be significantly higher than reported for the output array The lt LoadAndDecimate gt widget provides the decimation interface This widget controls the process of loading and
60. acilities at the ATNF 121 E 2 Using Sydney University VisLab Facilities 121 F Acknowledgements 123 G Quirks and Unexpected Behaviour 125 H Undocumented Features 127 Index 128 Chapter 1 Introduction Karma is a general purpose programmer s toolkit and contains KarmaLib the structured library and API and a large number of modules applications to perform many standard tasks This manual describes the many visualisation tools which are distributed with the Karma library This document is written for Karma version 1 7 26 which is probably my experimental version Most of this manual will still be relevant to the previously released binary only or beta version since binary releases come every few weeks or so Full public releases come once or twice a year so this document may talk about several new things not available in the last public release of Karma This document is available as compressed PostScript at ftp ftp atnf csiro au pub software karma user manual ps gz You can download a fancy colour front cover for this document at ftp ftp atnf csiro au pub software karma user cover ps gz Separate on line documents the Karma Reference and Programming Man uals may be found via the world wide web at the Karma home page at http www atnf csiro au karma The visualisation tools are available via the Karma home page or you can go directly to the Karma ftp site at ftp ftp
61. age plane data and produce a plot of average value versus radius A gaussian is then fitted to the radial profile and overplotted in red and the FWHM full width half max of the gaussian is displayed over the profile You must click the middle mouse button to define the centre of the object of interest then keeping the mouse button down drag out to define the maximum radius of the profile and release the button to display The algorithm automatically adjusts the centre position using a cen troiding operation so you don t have to be too careful about picking the centre of your object More information on the centroidingal gorithm http www atnf csiro au karma user manual centroidingalgorithm html pubc can be found in the Karma User Manual The programme should also work with a photographic negative The centroiding algorithm is automatically modified to look for a trough rather than a peak Boxed Horiz will produce a horizontal profile which is averaged vertically The box is drawn the same way as for the box sum mode The horizontal centroid of the profile is computed and a gaussian is fitted and displayed Boxed Vert will produce a vertical profile which is averaged hori zontally The box is drawn the same way as for the box sum mode The vertical centroid of the profile is computed and a gaussian is fitted and displayed e Slice Direction Menu this allows you to choose how you want to slice your cube You can view XY XZ
62. agnifier window so it nearly fills your screen The reason the default is to use the small memory mode is that if you have a large image say 2k 2k then the fast mode would require 64 MBytes of RAM just to store one copy of the image Unless you have lots of RAM in your computer you will be forced to wait a long time while your machine swaps to disc hence the default e ImageDisplay fastPanner as above but applies to the main image window The default is to use the fast large memory panner This is only of significance when you use panning mode i e select Panner from the Zoom menu e MagnifierPopup showCrosshair this controls whether magnifier win dows should show a crosshair True or not False e displayAxisLabelsToggle state if this is True then most windows which support axis labels will have enabled them by default You also need to set the OverlayMenu createAtInit resource to True see below OverlayMenu createAtInit if this is True then creation of certain control panels is performed at programme startup rather than being de layed until if and when required Normally delayed creation is preferred since it speeds application startup but this prevents some resource specifi cations from taking effect until sometime later Some programmes provide the shorthand create_at_init option e transient if True all popup windows will be iconified if the main window is iconified e AnimateControl pinToggle s
63. and subsequent vertices of the polygon To close terminate the polygon click and release the button twice without moving the mouse Once you have closed the polygon it is added to the overlay list 2 20 Loading Overlays Many tools provide a facility to load overlays annotations from an ASCII file Please see appendix D for details 2 21 Editing Images Many tools provide a facility to edit image data This is provided by the lt ImageEditorControl gt widget This widget allows you to interactively edit images It uses the lt iedit gt package which maintains a list of geometric figures which can be drawn and then applied to data The following controls are provided e Close this will close the window e Undo Last will undo the last edit object that you drew from the list e Undo All will undo all edit objects from the list e Apply apply the edit objects to the data after this you can no longer undo previous edits e Brush Width the width of the paint brush in pixels 40 CHAPTER 2 COMMON FEATURES e Paint Value the data value to paint with e Minimum set the data value to paint with to the current minimum clip value for the display canvas e Middle set the data value to paint with to halfway between the current minimum and maximum clip values for the display canvas e Maximum set the data value to paint with to the current maximum clip value for the display canvas This widget uses the middle mouse button for its dr
64. aset x divide the output dataset by this dataset Hue Intensity combine two datasets into a Hue Intensity array The two datasets may be directly mapped to intensity and hue or they can represent a complex image The real and imaginary com ponents will be in separate datasets and they are converted to am plitude and phase values which are then mapped to intensity and hue The following bindings are available B use this dataset as the brightness intensity component H use this dataset as the hue colour component R use this dataset as the real component I use this dataset as the imaginary component x Left Mouse use this dataset as the brightness component x Middle Mouse use this dataset as the hue component Right Mouse use this dataset as the grid template x use this dataset as the grid template e the dataset list shows the available datasets This is used to mark which datasets are used as inputs to the combining process This list has a similar interface as the dataset list in the data browser Note that in most cases a dataset can only be marked once If you need to mark a dataset for multiple purposes such as to use it for both red and green inputs you will need to clone the dataset first e Name this allows you to specify the name for the new dataset A default name is provided e Make this will create the new dataset based on the selections you have made This could take some time depending on how large
65. awing functions Some tools may already be using this button for other purposes in which case the tool should provide a control which allows you to disable the normal use of the middle mouse button For instance the lt kvis gt programme provides such a control through the lt ZoomPolicy gt widget section 2 7 The drawing interface is the same as for the lt OverlayEditorControl gt widget section 2 19 Chapter 3 Viewing and Comparing multiple Images and Cubes The lt kvis gt programme allows you to view multiple datasets This tool allows you to compare different datasets in a very easy fashion You can display any dataset as an image overlay contours of datasets show pro files along any axis and much more The programme uses the lt ImageDisplay gt widget section 2 15 to provide the usual interface 3 1 Overview The tool is centred around the concept of a blink state which defines how you want to display datasets i e which dataset is shown as the image which datasets are shown as contours how to control movies and profiles and so on A blink state can control the display settings of all datasets that have been loaded into the application Multiple blink states may be created each with a different configuration of what datasets are to be shown By pressing a key the display is switched from one blink state to another Blink states are created and managed using the lt DataBrowser gt widget 3 2 View Control
66. broken operating systems These files are already compressed so further compression is probably not worthwhile Write these images onto a tape or CD ROM and take it to VisLab It is recommended that you attend the video recording session in person in case there are problems You may find that the colour balance intensity or contrast is different on your workstation screen than on the television screen Aborting the process early if there are problems will save you money Rememember it s your video Nobody knows exactly how you want it to appear except you Appendix F Acknowledgements Nearly all of the Karma software and documentation has been written by Richard Gooch formerly of the CSIRO Australia Telescope National Facility and later at the Department of Physics and Astronomy University of Calgary Richard Gooch may be reached by email at rgooch safe mbox com or on the WWW at http www safe mbox com rgooch Some of the early widgets such as the file browser and colourtable con troller were written by Patrick Jordan then with the CSIRO Division of Ra diophysics In addition Patrick contributed through lengthy architectural dis cussions Patrick Jordan may be reached by email at patrick ariel com auor on the WWW at http www ariel com au patrick The anti aliasing image expansion code and the wavelet based filtering code was written by Tom Oosterloo then with the CSIRO Australia Telescope Na tional Facility The f
67. cks if enabled the default the tick marks are placed inside the bounding box otherwise they are placed outside e Grid Lines if enabled the co ordinate grid is shown e Screen Colours pressing this will set the background colour of the win dow to black and the colour of the axis labels to green If a colourmap is associated with the window it s Reverse option is turned off 26 CHAPTER 2 COMMON FEATURES e Paper Colours pressing this will set the background colour of the win dow to white and the colour of the axis labels to black If a colourmap is associated with the window it s Reverse option is turned on e Change Colourmap if enabled the Reverse option for the window colourmap lt Cmapwinpopup gt widget section 2 2 is set when you press either Screen Colours or Paper Colours e Show Colourbar if enabled a colourbar is displayed This shows the mapping between data value and colour Note that currently only linear intensity scales are supported e Font scale this slider allows you to enlarge or shrink the font scale for the labels A further set of controls is provided under the red line most of the time you will not need to use these e Background Colour the background colour of the window You need to press the Apply button for your changes to take effect e Label Colour the colour the labels are drawn in You need to press the Apply button for your changes to take effect e Grid Colour the colour the grid is drawn
68. controls the start of a region of data values which will be blanked e Blank End Slider this controls the end of a region of data values which will be blanked If this value is greater than that of Blank Start Slider 78 CHAPTER 5 VOLUME RENDERING A CUBE raw 1 005311e 02 sc 61 63 mJy Beam Output Substance Arrayfile name Number of Substances 8 Da _ A ah f TA i AAAA N EE a wN Ni AM Figure 5 2 Screen snapshot of hot gas substances control panel 5 8 HOT GAS MONO CONTROL PANEL 79 Intensity Alpha 1 0 Opacity Alpha 1 5 a la __ Blank Start r 128 sc 2 764e 01 mJy Beam Blank End r 128 sc 2 764e 01 mJy Beam Aah i EF fy MN Mun Figure 5 3 Screen snapshot of hot gas mono control panel 80 CHAPTER 5 VOLUME RENDERING A CUBE then some range of data will be blanked The blanking is implemented by setting the opacities for that range to 0 In the display canvas under the controls you will see a log histogram of your data in white as well as a red curve showing the transfer function between data value and intensity see equation 5 3 and a yellow curve showing the transfer function between data value and intensity see equation 5 2 The opacity curve also reflects the blanked range of values 5 9 Hot Gas Continuous control panel This shader is a cross between Hot Gas Substances and Hot Gas Mono It has a similar control as the Hot Gas Mono shader in lt xray gt Also here the exponent of
69. data using the logical mask It inverse transforms this masked difference and adds this filtered difference to the filtered data For the second iteration cycle it again defines a mask takes the difference between the original data and this second filtered data masks the wavelet coefficients and adds the masked difference to the filtered data etc etc The iteration cycle ensures that the wavelet coefficients of the filtered data are identical to those of the original data for those resolutions and positions where there is significant signal An important element of this filter is that it does a median filtering on the logical mask This makes isolated noise peaks disappear and makes the data look more consistent The difference between the fast and slow version of this filter is that in the fast version 2 iterations are done compared to 6 iterations in the 76 CHAPTER 5 VOLUME RENDERING A CUBE slow version The fast filter still leaves some noise blobs in the data but fewer than the simple filter The slow filter gets rid of almost all of them There are two parameters to set for this filtering e levels this specifies the number of wavelet planes to be computed The best values to are either 1 or 2 Using more than 2 planes produces artifacts for the simple filter Usually it is also not necessary to consider more than 2 planes Specifying Levels to 0 the original unfiltered data cube is rendered but with noise clipping appli
70. distance of the point in the slice from the centre of the neighbour pixel So the thickness is basically one spatial pixel but the width of the region that the interpolation is made over varies depending on the angle of the slice with respect to the pixel grid It is least 3 pixels wide when the slice is along the x or y axis of the pixel grid and greatest sqrt 2 3 when the slice is at 45 to the pixel grid The interpolation is made only with respect to the pixel grid so the above numbers are only strictly true if the x and y directions have the same spatial scales Tf the arcsec pixel is different in the x and y directions the width of the slice in arcsec will change from differently as the angle of the slice w r t the pixel grid changes tttt H H H k xx x is the current pixel are the neighbours x is the other pixels in the slice 84CHAPTER 6 KPVSLICE INTERACTIVE POSITION VELOCITY SLICING Chapter 7 kslice_3d slicing data cubes The programme lt kslice_3d gt is the Karma version of an idea of Francois Viallefond a program called 3view Also GIPSY has an implementation of something very similar Because Karma is much more designed for this kind of work lt kslice_3d gt is much faster than the other two versions The program shows 3 images in a window being the data cube sliced along the principle planes The top left image
71. dius of the emission from the centre is approximately constant As you progress from one velocity extreme to the other the radius will change from zero pass through a maximum at the central velocity and go back down to zero So in the computed radius velocity map you should see half an ellipse the signature If you have slightly missed the centre of the expansion you will see a double ellipse so this is a good way of finding the centre If you are not looking at an expanding shell at all you just see a mess so this is also a good way for speculatively searching for shells The lower the expansion veloc ity the more squashed the ellipse becomes vertically of course In fact if you had a static shell you would just see a straight line The power of this tool is that it is both a fast way of browsing for expanding shells because of their charactistic signature and that it is insensitive to fragmentation of shells To drive this programme you need a cube file load with the Cubes button and an image file load with the Images button Actually the image file is optional you can compute an image on the fly from the cube by selecting say the Oth moment option from the Image Mode menu and adjusting the parameters as needed and pressing Apply The reason you need an image is so that you can search for a possible centre of an expanding shell The image is displayed in the left window The image and cube files do not have to lie on the
72. duce the number of colours each tool uses You will need to read the manual for the other tool to see what option controls the colourmap size Summary Examples of things you can do e unix netscape install e Tf running within the CDE or other display tools eg SAOimage unix kvis num_colours 100 and reducing the number of colours in the other tools unix saoimage palette 100 e When running multiple Karma tools at once even on different machines you can do this junior kvis CHAPTER 2 COMMON FEATURES Y Object None Close fi Y First Coordinate Type world Y Remaining Coordinate Types world Figure 2 13 Screen snapshot of overlay editor control panel Port allocated 17545 jumbo xray cmap master junior 17545 2 19 Drawing Overlays Many tools provide a facility to draw overlays This is provided by the lt OverlayEditorControl gt widget This widget allows you to interactively draw overlays on top of an image It uses the lt overlay gt package which maintains a list of geometric figures which should be drawn The following controls are provided e Close this will close the window e Remove Last will remove the last overlay that you drew from the list e Remove All will remove all overlays from the list e Object Menu allows you to choose between the different types of object that you can draw e First Coordinate Type Menu sets the co ordinate type of the first defining point for a geometric object
73. e Show Beam Name if enabled the name of the dataset is placed near the beam representation Beam Xpos controls the horizontal position of the the beam Beam Ypos controls the vertical position of the the beam In addition if you click the left mouse button in the display window without moving it in between the press and release the image will pan across If you click the middle mouse button the image will zoom in 2x the new centre of the image will be the place where you clicked Click the right mouse button to zoom out 2x If the profile mode is box then you can t use the middle mouse button to zoom Pressing the c key in the display window will compute and display a scatter plot of intensity values in the image dataset versus intensity values in the al ternate dataset This is useful for seeing if there is a correlation between the values in two images You can use the left mouse button to define a sub image similarly to zooming in from which the scatter plot is computed See Figure 3 1 for a screen snapshot 44CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES O Freeze Displayed Intensity Range O Track Cursor O Show Frame in Line Profile Auto Title O Show Beam k Show Beam Name P P Figure 3 1 Screen snapshot of view control panel 3 3 Data Browser This widget provides controls for managing the display of multiple datasets See Figure 3 2 for a screen snapshot The controls provided are
74. e Click if enabled clicking the right mouse button will zoom out 2x See Figure 2 8 for a screen snapshot 2 8 Axis Labels All the standard visualisation tools now support axis labelling Most programs have an Axis Labels button which will show the lt DressingControl gt widget which gives you control over how labelling is done This widget controls the way axis labels are drawn onto a canvas The following controls are available e Close this will close the window 2 8 AXIS LABELS 25 Close Apply Auto Refresh br Fix Aspect Allow Truncation Integer X Zoom Integer Y Zoom Zoom In on Middle Mouse Click Vl Zoom Out on Right Mouse Click Figure 2 8 Screen snapshot of zoom policy control panel e Enable if enabled the axis labels are displayed e Apply apply control changes and refresh the window e Auto Refresh if enabled each control change is automatically applied and the window refreshed e Show Labels if enabled the axis names are displayed e Show Scale if enabled the scale values corresponding to major tick marks are displayed e Show Top Tick Marks if enabled the tick marks at the top of the window are displayed e Show Bottom Tick Marks if enabled the tick marks at the bottom of the window are displayed e Show Left Tick Marks if enabled the tick marks at the left of the window are displayed e Show Right Tick Marks if enabled the tick marks at the right of the window are displayed e Internal Ti
75. e data The files are simple ASCII format where each line defines one pair of 3D points Note that the endpoints are projected from 3D to screen co ordinates and then the points are joined by a straight line on the screen For best results your lines in 3D space should be short Roll Slider this controls the roll angle Think of an airplane rotating about it s long axis 72 5 4 1 CHAPTER 5 VOLUME RENDERING A CUBE Pitch Slider this controls the pitch angle The nose of the airplane dips up and down Yaw Slider this controls the yaw angle The nose of the airplane swings left and right Start X Slider this controls the starting X position of the subcube to render Start Y Slider this controls the starting Y position of the subcube to render Start Z Slider this controls the starting Z position of the subcube to render End X Slider this controls the end X position of the subcube to render End Y Slider this controls the end Y position of the subcube to render End Z Slider this controls the end Z position of the subcube to render Distance this changes the distance your viewpoint is from the cube This only has effect when using the Perspective projection Image Expansion Often the image generated by the volume redering software is rather small this is because the original cube was small The software automatically expands the image so that it fills as much as possible the display window using simple pixel replication This resu
76. e file to load and dataname is the name of the data elements to process this is usually the same as the unit name for example JY BEAM or HZ 12 5 6 kprinthead This tool will show the header in a datafile It supports many data formats The general usage for this programme is 12 5 LIST OF TASKS 101 kprinthead infile where infile is the file to print the header for 12 5 7 kregrid This tool will regrid one or more input images or a cube onto an output image or cube It is possible to use this tool to mosaic several images or cubes together onto a new grid The general usage for this programme is kregrid infile where infile is the input file to regrid or is a file containing a list of files to regrid and mosaic The output filename will be kregrid_infile kf 12 5 8 krotate This tool will rotate by regridding an image or cube such that the longitude axis Right Ascension or Galactic Longitude is aligned with the horizontal axis This is often used to rotate images to a more convenient or familiar orientation e g images from the Hubble Space Telescope The general usage for this programme is krotate infile outfile where infile is the input file to rotate and outfile is the name of the output rotated file you wish to create If you specify an extension of fits then a FITS file will be written otherwise a Karma file will be written You may use the projection option to control the output projection the
77. e intensity range for this array e Clone create a virtual copy of the array which will have independent con figuration settings Note that the data are not copied instead a reference is made e Unload unload the array Note that these operations affect all browsers blink states and all display windows 50CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES Array Configuration How to display an array is controlled via this section Some controls are per blink state while others are global and apply to all blink states and all display windows The following controls are per blink state e Image menu The choices are off the array is not selected for image display main the array is selected for normal image display alt the array is the alternate image for computing intensity intensity scatter plots e Contour menu The choices are off the array is not displayed as contours map the array is shown as normal contours renzo the array is shown as a Renzogram e Movie menu The choices are off the array will not be shown as a movie master the array is shown as a movie and controls the frames slave the array is shown as a movie and is slaved to the master The following controls are global to the application and affect all blink states and display windows e Low the low end of the intensity range e High the high end of the intensity range e Map Contour Levels the con
78. e of the output e Auto Increment when enabled existing PostScript files are not over written rather the outfile filename has an incrementing sequence number added to it e Lock Filename when enabled the application will never automatically change the suggested output filename e Output file controls the basename of the output file e Printer queue controls which printer queue to print to The default is taken from the PRINTER environment variable See Figure 2 7 for a screen snapshot 2 5 Exporting Data To save data you are looking at click left and hold the Export button This will show the lt ExportMenu gt widget This widget allows you to export the currently displayed data to some other format The following options are available e PostScript generate hardcopy output of the contents of the drawing canvas This will pop up the lt Postscript gt widget section 2 4 22 CHAPTER 2 COMMON FEATURES Figure 2 7 Screen snapshot of PostScript output control panel 2 6 ZOOMING 23 e SunRasterfile export the currently viewed image to Sun Rasterfile for mat e PPM Data Image export the currently viewed image data to PPM for mat Non image data i e axis labels and annotations are not exported The output is at the resolution of the image data e PPM Data Movie export the currently viewed cube data to PPM for mat similar to PPM Data Image One PPM file is written for each image along the unseen axis e
79. e the list is broken A new parameter or action name with a preceeding will break the list as will a solitary character The solitary character marks the start of remaining other arguments after which there can be no further action or parameters 12 3 2 Passing in Strings If a string contains spaces you should enclose it in quotes on the shell command line If you are familiar with how most shells work you will know that it removes enclosing quotes before passing them onto the programme Karma deals with this by checking if a shell argument has a space in it and if it does it puts a pair of double quotes around the argument again This should be transparent to you unless you start doing esoteric things with embedded quotes 98 CHAPTER 12 COMMAND LINE TOOLS 12 3 3 Passing in Negative Values Passing in a negative number is not a problem because this case is trapped note all parameter or action names must begin with an alphabetic character If you wish to pass in a string with a preceeding then you should type in at the shell command line The double minus will be reduced to a single minus before being used 12 3 4 Passing in Other Arguments If you do not pass in any parameters or actions then you can just type in the other arguments as you would in interactive mode However if you preceed the other arguments with parameters or actions you need to type a solitary between the last argument to the last parameter o
80. e to your moving the mouse over the window but not while pressing any mouse buttons or keyboard keys This is useful when you have pointed at a certain place and want to maintain a position or profile display while you move the mouse to some other window perhaps to print the win dow All you need to do is press the spacebar and any further mouse moves are ignored If you press the spacebar again the mouse moves once again do something So that you don t forget that mouse moves are disabled you will hear a quiet beep every time you move the mouse into the window Similar to above except that when pressing any mouse buttons or keyboard keys the freeze position is used rather than the real position of the mouse 2 15 Common Image Display Features Many of the visualisation tools have one or two very similar main windows This is because they are all derived from the lt ImageDisplay gt widget which provides most of the common functionality Most of the tools which use this widget provide the following controls e Setl sometimes labelled as Files or Cubes this will popup up the lt Filepopup gt widget section 2 1 e Intensity menu this will popup widgets to control the colourmap lt Cmapwinpopup gt intensity policy lt IntensityPolicy gt and in tensity scaling section 2 2 ow CHAPTER 2 COMMON FEATURES Close Y Smooth none Print Y Overlay Y Style join x 42 pixel Freq 1419 154 MHz value 122 87 mJy Bean
81. e which does not have a co ordinate system on it All you need is an image of a similar piece of sky which does have a co ordinate system such as an image from the Digital Sky Survey The tool handles flipping and rotation correctly This tool is much faster to use than the various command line driven tools currently available usually less than a minute After you start the tool you will get two windows The left window should be loaded with the reference image the image which has a co ordinate system by pressing Ref Images The right window should be loaded with your target image the image without the co ordinate system by pressing Target Images The programme should also work with a photographic negative The picking algorithm is automatically modified to look for a trough rather than a peak Once you have loaded your images you are now ready to define matching pairs of points stars To do this you must first click middle in the left window near a star and then click middle in the right window near the corresponding star You then go back to the left window and define another star and click on it s mate in the right window You must define at least three pairs of stars As you select a star a green circle is drawn around the fitted centre of the star If at any time you miss the star you can just click again only before going to the other window If you press Undo Pair a pair of stars will be removed from the list As lo
82. ed e filter clip this specifies the clip level to be applied to the wavelet planes in units of the noise level Recommended values are 3 for the simple filter For the median mask filter use 2 or 3 5 6 2 Contintuum Subtraction Often when you observe a spectral line source you may have a confusing contin uum source in the field Your data reduction package should have a programme to subtract the continuum e g uvlin in Miriad The problem with some of these programmes is that in order to compute a fit to the spectrum of the con tinuum source you first have to tell the programme which channels contain the spectral line emission so that it can ignore those channels when computing the fit The problem is how to find out which channels contain the line emission An effective technique is to invert your UV data into a cube before sub tracting the continuum and then using lt xray gt to render it Of course if the continuum source is brighter than your spectral line source it usually is the spectral line source will be washed out This is where you can use the subtract continuum filter This will subtract the average flux in a spectral profile for every point on the sky image This is a good continuum subtraction algorithm to first order it should filter out more than 90 of the continuum source Once you have your first order continuum subtracted cube you can use lt xray gt to find the spectral line emission In particular you s
83. ent gt lt x_width gt lt y_height gt angle Draw a rotatable cross given center coordinates width and height and an optional position angle in degrees D 3 ANNOTATION COMMANDS 115 e CIRCLE coord_type lt x_cent gt lt y_cent gt lt radius gt Draw a circle given center coordinates and radius e ELLIPSE coord_type lt x_cent gt lt y_cent gt lt a gt lt b gt angle Draw a rotatable ellipse given center coords semimajor and semiminor axes and an optional position angle in degrees The semimajor axis must be given before the semiminor axis if adherence to the standard definition of ellipse position angle is desired In order to maintain consistency with the CBOX and CROSS commands the first axis is the one oriented by the position angle regardless of whether it is the largest e TEXT coord_typel lt x_left gt lt y_left gt lt string gt Draw a text string left justified at the given coordinates more precisely these specify the lower left corner of text The string to be used is whatever follows the third argument e g several words separated by spaces and ends with the line of text unless continued onto another line Comment and continuation 1 characters cannot be included in a text string but are acted upon in the usual fashion if found thus text commands can also be extended to multiple lines WARNING At present rotatable figures boxes crosses and ellipses have a tendency to appear distor
84. erage is like the box sum mode except that the average of all profiles is displayed rather than the sum Radial will azimuthally average the image plane data and produce a plot of average value versus radius A gaussian is then fitted to the radial profile and over plotted in red and the FWHM full width half max of the gaussian is displayed over the profile You must click the middle mouse button to define the centre of the object of interest then keeping the mouse button down drag out to define the maximum radius of the profile and release the button to display The algorithm automatically adjusts the centre position using a cen troiding operation so you don t have to be too careful about picking the centre of your object More information on the centroidingal gorithm http www atnf csiro au karma user manual centroidingalgorithm html pubc can be found in the Karma User Manual The programme should also work with a photographic negative The centroiding algorithm is automatically modified to look for a trough rather than a peak Boxed Horiz will produce a horizontal profile which is averaged vertically The box is drawn the same way as for the box sum mode The horizontal centroid of the profile is computed and a gaussian is fitted and displayed 3 2 VIEW CONTROL 43 Boxed Vert will produce a vertical profile which is averaged hori zontally The box is drawn the same way as for the box sum mode The vertical cen
85. ere is a master slave movie relationship then the scatter plot is com puted using the two frames which have corresponding co ordinates for the frame axes This is usually the desired setting when generating scatter plots from frames of two different cubes Note that when computing a scatter plot from two images with a different co ordinate grid the pixels from the unseen image correspond to pixels with the same world co ordinates in the visible image Thus there is no need to re grid either of the images 3 6 Renzograms an alternative to velocity fields A renzogram is a technique for displaying velocity information in a cube in a different better way than velocity fields The technique was pioneered by Renzo Sancisi at the Kapteyn Institute in Groningen A renzogram overlays a single level contour map for every channel in a cube over an image such 3 6 RENZOGRAMS AN ALTERNATIVE TO VELOCITY FIELDS 55 as an optical image or moment map The contour map for each channel is displayed in a different colour typically red blue although this can be changed interactively This has an advantage over velocity fields because it shows multiple peaks in the velocity profile which a velocity field cannot do To use this feature simply load a cube and select it for renzogram display in the data browser You can control the contour level used for the renzogram and the range of channels displayed You may wish to load a separate image
86. ext data e equals sign selects this dataset for replacement section 3 3 copying all data attributes e tilde sign selects this dataset for replacement section 3 3 without attribute copying There are other key bindings which are independent of which dataset the mouse is highlighting e Left Arrow cycle backwards in the list of blink states for the same win dow in Some or One modes Has no effect in A11 mode 3 3 DATA BROWSER 47 Right Arrow as above but cycle forwards Shift Left Arrow similar to Left Arrow but also make the blink state active Shift Right Arrow similar to Right Arrow but also make the blink state active Control Left Arrow cycle backwards to the last browser for the previous display window One mode Has no effect in other modes Control Right Arrow cycle forwards to the first browser for the next display window One mode Has no effect in other modes Shift Control Left Arrow similar to Control Left Arrow but also make the blink state active Shift Control Right Arrow similar to Control Right Arrow but also make the blink state active b key blink the display window to the next browser for this display window B key make the currently viewed blink state active gt key blink the display window to the next browser for this display window lt key blink the display window to the next browser for this display window The list section will show single character codes in a number of col
87. for replacement and these datasets were loaded from the same data source the selected dataset closest to the top of the list is replaced Note that if a data source is removed e g a file browser is destroyed then datasets loaded via that data source can no longer be replaced These datasets can still be explicitly unloaded however Array List There are several columns used to display a summary of the configuration using a simple legend These are described below e Image Column shows which dataset s contribute to the displayed im age These are exclusive settings The legend is I show this array as the image A this array is the alternate image for intensity intensity scatter plot computation hue intensity e Contour Column shows which datasets are displayed as contours These are non exclusive settings The legend is c show this array as a normal contour map r show this array as a Renzogram only for cubes e Movie Column shows which datasets can be shown as a movie The legend is M enable movie controls for this array m slave this array to the movie controls e Profile Column shows which datasets can be shown as profiles The legend is P display line profiles of this array this array controls the axis la belling and is drawn on top p display line profiles of this array The following keyboard and mouse bindings are available to quickly control the configuration 3 3 DATA BROW
88. formed The general usage for the programme is chlen infile dimension name where infile is the input data file and dimension_name is the name of the dimension to change Note that the input file may be of any format 12 5 LIST OF TASKS 99 Examples If you had a spectral line datacube and you wanted to resample the velocity axis to say 600 data pixels the following options would be needed resample_option linear_interpolation option resample num_coordinates 600 and then you would type something like mycube VELO HEL 12 5 2 images2karma This tool will convert multiple images of any format into a Karma cube This tool is not implemented with the lt panel gt and hence does not have settable parameters or an interactive mode The usage for this programme is images2karma infiles outfile The input images must be of the same shape size and type but do not need to be of the same file format 12 5 3 karma2ppm This tool will convert a Karma image or cube file into one or more PPM Portable Pixel Map files The PPM format is a 24bit TrueColour image format A Karma image or cube movie may be either TrueColour or Pseu doColour with an associated colourmap in the file If the input image or cube is greyscale i e no colour information is avail able then it is still possible to write out a PPM file if you supply a colourmap file previously saved with a lt Cmapwinpopup gt widget section 2 2 You specify the colour
89. frame di mensions This is usually the desired setting when generating scatter plots from frames of two different cubes 4 4 INTENSITY INTENSITY SCATTER PLOTS 63 Note that when computing a scatter plot from two images with a different co ordinate grid the pixels from the unseen image correspond to pixels with the same world co ordinates in the visible image Thus there is no need to regrid either of the images 64CHAPTER 4 VIEWING IMAGES AND CUBES WITH THE MULTIBEAM Chapter 5 Volume Rendering a Cube The lt xray gt programme is used to volume render cubes 5 1 How the rendering is done You can think of the way a data cube is rendered as lines of sight going from every pixel of the display through the data cube and the vozels visualisation speak for volume element of the data cube on a line of sight contribute in some way to the colour and intensity of the display pixel To decide how every voxel contributes a number of algorithms called shaders are available 5 1 1 Shaders Below are two lists with the shaders available The first list contains simple shaders The Voxel sum and the Maximum voxel shaders are useful for exploring the data cube because they are relatively fast and give a reasonable display of the data e Voxel sum The value of the display pixel is the sum of all voxel values along the line of sight This is a fast and quite useful way of representing the data With this shader one gets a good global view
90. ft corner of the image Pixel coordinates count screen pixels explicitly in the entire display region includ ing outside any labeled axes beginning in the upper left corner note these are not image pixels but rather the physical pixels of the computer monitor screen Image pixel coordinates are not a usable coordinate type here unless no world coordinates are defined for the image in which case Karma will use the image pixel coordinates in place of world coordinates For most purposes 114 APPENDIX D ANNOTATION FILE FORMAT involving the marking of image features world coordinates are the best choice though relative coordinates are occasionally good for marking a particular part of the display region regardless of image projection Pixel coordinates by their inflexible nature are as a rule not very useful The three coordinate types are specified in an argument list with the letters W R and P In several of the object commands below DOTS LINE CLINES DLINES VECTOR different geometric parameters of the object can be specified in dif ferent coordinate types and so a coordinate type argument may precede more than one coordinate pair in the argument list However all coordinate type arguments are optional they are only necessary to override the current value either one specified earlier in the argument list or the default coordinate type selected with the COORD attribute command e DOT or POINT coord_type lt x_coord gt
91. ght mouse button to zoom out 2x If the profile mode is box then you can t use the middle mouse button to zoom Pressing the c key in the display window will compute and display a scatter plot of intensity values in one image versus intensity values in the other image This is useful for seeing if there is a correlation between the values in the two images You can use the left mouse button to define a sub image similarly to zooming in from which the scatter plot is computed See Figure 4 1 for a screen snapshot 61 Figure 4 1 Screen snapshot of two datasets display control panel 62CHAPTER 4 VIEWING IMAGES AND CUBES WITH THE MULTIBEAM 4 1 Command line Options The following command line options are supported by lt MultibeamView gt e seti lt filename gt this will load the dataset filename as set 1 4 2 Special Movies If you want to play a movie that was made using the Hot Gas Substances section 5 1 1 or the Hot Gas Continuous section 5 1 1 shaders of the xray chapter 5 volume rendering tool you should compress this movie from 24 bit to 8 bit Movies made with the other algorithms do not require compression and can be played directly The compression of 24 bit movies is done with the command conv_24to8 com w max lt max num of colours gt lt inmovie gt The switch com w tells the program that it should compress such that it has the same colourmap for all the images In principle you could
92. has INCLUDE file3 ann Karma will look for file3 ann in the directory containing file1 ann not in subdir Unless all the files are in the same directory it s probably safer to use absolute pathnames or environment variables D 3 2 Attribute Commands Attributes are general properties of objects An attribute command sets one of these properties for all objects drawn after until the attribute is changed by another attribute command Each has an initial value it is assigned when the application first starts D 3 ANNOTATION COMMANDS 113 e COLOR or COLOUR lt name of color gt Sets the color of subsequent objects The color name is a standard sys tem color a list of which can be found for X Windows systems in the file usr lib X11 rgb txt Basic color names include red green yel white etc The default color is green low e FONT lt name of font gt Sets the font of subsequent text objects The font name is a standard system font a list of which can be found for X Windows systems with the command xlsfonts The name of the default font is hershey14 Note font names are case sensitive e COORD lt default coordinate type W R or P gt Sets the default coordinate type of subsequent objects This will apply to any objects which do not have a coordinate type given in their command string Any coordinate type in an object command string takes precedence over the default coordinate type b
93. he 1st moment map e Start Channel the first channel that will be used in the computation 2 17 CURSOR READOUT 35 Figure 2 12 Screen snapshot of moment map generator control panel e End Channel the last channel that will be used in the computation See Figure 2 12 for a screen snapshot 2 17 Cursor Readout Most data display windows have cursor readout facilities simply move the mouse over the display canvas and you will see a few lines of numbers change above the canvas In most cases positions are shown both in data pixel co ordinates as well as real world co ordinates 2 17 1 Warning for Astronomers Most astronomical reduction packages count from 1 so the bottom left corner of an image is at 1 1 This reflects the FORTRAN language from which these packages originated The Karma software is written in the C language and reflects the C convention of counting from 0 This means that the bottom left corner of an image is at 0 0 in Karma 36 CHAPTER 2 COMMON FEATURES 2 18 GUI Command line Switches Many of the Graphical User Interface tools have a number of command line switches which may be used to modify their behaviour These are listed below e private_cmap This option will force the tool to use a private colourmap for its PseudoColour window Otherwise the tool trys to allocate colours from the default colourmap e num_colours This option specifies the number of colour cells that the tool will try to allocate f
94. he University of Sydney has created a commercial visualisation laboratory They are able to make high quality broadcast standard VFS and Betacam videos All you need to do is provide them with a sequence of numbered images in a supported format VisLab also have facilities to convert from many popular image formats to a format their machinery requires but this will cost real money Instead you should produce files in Targa TrueVision format which they will be able to use directly The karma2ppm section 12 5 3 command line utility may be used to produce this format The image size required by VisLab is 720 pixels horizontal and 576 pixels vertical Note that you need to leave a border of 10 inside this otherwise some television screens will chop the outer parts of your movie 121 122 APPENDIX E MAKING VIDEOS You would need to use the following parameters for lt karma2ppm gt converter ppmtotga extension tga out_height 576 out_width 720 You would then type something like karma2ppm mymovie image and you would get a sequence of numbered images starting from 1 such as image_01 tga image_02 tga image_03 tga image_04 tga image_05 tga image_06 tga image_07 tga image_08 tga image_09 tga image_10 tga image_11 tga image_12 tga image_13 tga image_14 tga Try to keep the filenames to 8 3 lengths i e 8 characters for the first part and 3 characters for the extension This avoids any potential problems with some
95. hould find the 3D slicing window very handy since it will give you the 3D co ordinates of a point Be warned that Karma programmes count from 0 whereas most astronomical reduction packages count from 1 If you take a channel index from Karma and put it into Miriad remember to add the value 1 Now that you have identified the spectral line emission you can run a pro gramme like uvlin to do a better job of subtracting the continuum 5 6 3 Other Controls To apply the filtering click on Do Filter The cube is rendered automatically To get back the original data without any filtering click on Undo Filter You may also Save the filtered cube for later use 5 7 HOT GAS SUBSTANCES CONTROL PANEL TT 5 7 Hot Gas Substances control panel See Figure 5 2 for a screen snapshot This controls the settings for the Hot Gas Substances section 5 1 1 You should see a window with a histogram of the data values in the cube actually the logarithm of the distribution and in the bottom part you will see space for the colours of the substances Each colour has a horizontal line on it This is an indicator for the opacity of the substance To change the colour of a substances you have to click left on the space on the bottom of the window that is reserved for the substance This selects the substance To change the colour move the mouse in the upper part of the window and drag middle not left the mouse around until you have the colour you
96. how data arrays are combined The following modes are available RGB combine one two or three datasets into an RGB red green and blue array Each colour component is 8 bits yielding a 24 bit array The input values between the low and high clip are linearly scaled into the output If the clip values on an input array are subsequently changed the RGB image is rescaled The following bindings are available R use this dataset as the red colour component G use this dataset as the green colour component x B use this dataset as the blue colour component 3 3 DATA BROWSER 53 x Left Mouse use this dataset as the red colour component x Middle Mouse use this dataset as the green colour component x Right Mouse use this dataset as the blue colour component x use this dataset as the grid template Arithmetic combine multiple datasets using simple arithmetic ad dition subtraction multiplication or division The output dataset is computed by processing the list of datasets from top to bottom applying the specified arithmetic operations for selected datasets Before processing any datasets the output dataset is initialised to either zeros if the first operator is addition or subtraction or ones if the first operator is multiplication or division The following bindings are available add this dataset to the output dataset x subtract this dataset from the output dataset multiply the output dataset by this dat
97. in Note that the axis labelling currently does not handle co ordinate systems which have rotations close to 90 degrees or 270 degrees See Figure 2 9 for a screen snapshot 2 9 Magnifying Glass Many programmes have a Zoom menu with a Magnifier option which when selected will show a magnifying glass window As you move the mouse cursor over the main image window a zoomed in subsection around the cursor is displayed in the magnifying glass This view is zoomed in four times the scale of the input image If the image in the main window is zoomed in ten times the view in the magnifying glass will actually be smaller This widget is a subclass of the lt SlaveImageDisplayPopup gt widget 2 10 Panner Many programmes have a Zoom menu with a Panner option which when selected will show a panner control window By pressing the left mouse button in this window the image in the main window is panned This widget is a subclass of the lt SlaveImageDisplayPopup gt widget 2 10 PANNER 27 Font scale 1 9 Background Colour black Label Colour Preen Grid Colour pereen Figure 2 9 Screen snapshot of axis labelling control panel 28 CHAPTER 2 COMMON FEATURES 2 11 Spectrum Profiles Many programmes allow you to point at an image and obtain the corresponding profile along the third axis usually a spectrum profile Some programmes provide a Profile button which you need to press first before you will see the profile while
98. indow This marker is only drawn if the profile axis is the unseen axis Contour Levels this controls the contour levels Be careful not to hit return after filling in the levels The syntax for the contour levels is as follows just type the levels you want eg 0 001 0 002 0 003 0 004 levels with a constant increment 0 001 0 004 0 001 means that the first level is 0 001 that this level is incremented with 0 001 until 0 004 is reached So this example gives the same levels as in the first case levels incremented by a factor 0 001 0 016 2 This gives levels 0 001 0 002 0 004 0 008 0 016 levels as percentage of the peak first character should be num bers are taken as percentage the rest of the syntax is as above e g 10 40 10 gives 10 20 30 and 40 of the maximum of the data These options can be mixed i e 0 03 0 01 0 01 0 003 0 1 0 02 0 2 0 3 is interpreted correctly Contour Colour specifies the colour the contours should be drawn in Apply Levels this will apply the contour levels and colour Reset Levels will reset the contour levels to the default 60CHAPTER 4 VIEWING IMAGES AND CUBES WITH THE MULTIBEAM e Auto Apply if this is on then if you load a new dataset over one that is currently being displayed as contours the old contour levels are auto matically applied The reason this is off by default is because the contour levels for one dataset may be incorrect for another An inappropriate set of
99. ions of our own They consists of making a wavelet transform of each channel in the cube This allows to consider the data locally at different resolutions and modify it such that the signal to noise is improved Note that the wavelet transforms can be 3D and 2D channel by channel The adaptive filtering algorithms available are e Simple this is a very simple filter It is a bit crude but it has the advantage that it is fast the other filters are quite a bit slower It gets rid of most of the noise This filter makes a wavelet transform and in each wavelet plane it clips the wavelet coefficients that are below the noise level defined by the parameter filter clip section 5 6 1 to zero This filter is only slighty more complicated than simple clipping the data below a certain level The fact that it looks at the data with different resolutions makes it more efficient e Median mask fast amp slow the first step of this filter is identical to the simple filter This filter also makes a wavelet transform of the data and makes a logical mask for each wavelet plane defining where there is significant signal for every resolution and inverse transforms only the significant wavelet coefficients Now an iteration cycle begins It transforms the difference between the original data and the filtered data retains only the coefficients of the transform of the differnece for those positions and resolutions where there is significant signal in the
100. irst For the file browser to recognise a FITS file the extension should be either fits fit fts or uppercase versions Files with extension efits are treated specially in that only the header is read These are called empty FITS files 1 1 SUPPORTED DATA FORMATS 3 where the image data are set to all zeros This format supports loading of partial datasets section 1 1 3 GIF another popular image format This requires the NetPBM tools to be installed on your machine GIPSY this is the format for the GIPSY data reduction package It is more efficient to use lt gipsy2karma gt to convert to Karma format first This format supports loading of partial datasets section 1 1 3 IRAF this is the format for the IRAF optical astronomy analysis pack age The current implementation requires IRAF to be installed because it uses the wfits task in IRAF and will create a temporary file which is automatically deleted Karma this is the native data format Reading and writing Karma files is the most efficient These files may be memory mapped upon load which can give enormous speed benefits and reduce swap virtual memory requirements Note that Karma files have the extension kf and that this extension is automatically produced by any Karma software Miriad this is the image format used by the Miriad data reduction package It is more efficient to use lt miriad2karma gt to convert to Karma format first If your Miriad file has no ma
101. irst render using the normal mode and will then build up the cache using the interpolation algorithm in the background Provided you don t change the view or cube parameters once the cache is computed the cube will be rendered again and you will see a refined image Note that if you render the cube with normal mode and then idly change the view or cube parameters and sit back a little while later the cube will suddenly rotate even though you haven t clicked on Apply Orientation 5 4 2 Rotating the cube With the sliders Roll Pitch and Yaw you can rotate the data cube by hand The coordinate axes are defined such that the X axis is horizontal the Y axis vertical and the Z axis pointing into the display The Roll rotation is around the X axis Pitch around the Y axis and Yaw around the Z axis Since rotations do not commute it is important to know that the order of the rotations is Roll first then Pitch and then Yaw To see the cube in the orientation you specify click left on Compute Reset Orientation resets the orientation to face on 74 CHAPTER 5 VOLUME RENDERING A CUBE 5 5 Making a Movie The main problem with volume rendering data cubes is that one does not really get a three dimensional perception of the rendered cube One can display a scene from daily life in a very crude way and still perceive it as a 3D scene But this apparently is not true for data cubes The brain does not recognize the object in the image and theref
102. irst versions of the programme lt khuei gt section were written by Simone Magri of the CSIRO Australia Telescope National Facility Simone Magri may be reached by email at Simone Magri atnf csiro au or on the WWW at http www atnf csiro au smagri The lt kpvslice gt chapter 6 and lt koords gt chapter 9 programmes were a collaborative effort between myself and Vincent McIntyre then with the University of Sydney Vincent McIntyre may be reached by email at Vince McIntyre atnf csiro au or on the WWW at http www atnf csiro au vmcintyr The Starlink to Karma conversion programme lt sdf2karma gt was written by Karl Glazebrook of the Anglo Australian Observatory Karl Glazebrook may be reached by email at kgb pha jhu edu or on the WWW at http www aao gov au local www kgb The annotation file reading code was designed and implemented by Steven Gibson then with the University of Calgary and currently with Arecibo Ob servatory The appendix describing the data format was also written by Steve 123 124 APPENDIX F ACKNOWLEDGEMENTS He may be reached by email at gibson naic edu or on the WWW at http www naic edu gibson Appendix G Quirks and Unexpected Behaviour There are some operations that may not behave in the way you may expect although they are operating according to design These are quirks rather than bugs Below is a list of quirks e When loading a file and Reset Intensity Upon File L
103. is a XY image so for a radio cube this would be a channel the bottom image is XZ so normally a v and the top right ZY v 8 With the mouse one can interactively change the planes that are shown If the mouse is in the XY image the other two images are the XZ and the ZY image corresponding the the x y position of the cursor Alternatively if the mouse is in one of the two other images the XY image shown is the image corresponding to the Z coordinate of the mouse lt kslice_3d gt is fast enough contrary to 3view and GIPSY that if you move the mouse while keeping the left button pressed the images are updated real time Note that the volume rendering programme xray chapter 5 will automati cally display a lt kslice 3d gt window so that you can slice through the cube as well as volume render it There are only a few buttons in lt kslice_3d gt 7 1 Precompute If a cube is loaded the images to display are not computed automatically If next you move the mouse lt kslice_3d gt will have to compute the image that is has to display in real time This makes things a bit slow sometimes Clicking Precompute will make lt kslice_3d gt compute all the images it can display This takes a few seconds but it makes the update of the images very fast Note that to run smoothly lt kslice_3d gt requires quite a bit of memory certainly if you expand the images If this gives problems try running it sitting in front of phoenix Note that
104. is updated automatically Most programs have a menu Zoom which has a selection Zoom Policy which will show the lt ZoomPolicy gt widget which gives you control over how zooming is done This widget controls the policy to be used for displaying image data on a drawing canvas The following controls are provided e Close this will close the window e Apply apply control changes and refresh the window e Auto Refresh if enabled each control change is automatically applied and the window refreshed e Fix Aspect if enabled the image will be expanded shrunk with the same factor in both dimensions to fill the window If disabled the factors are not necessarily the same i e the pixels will not be square but the image will fill the window better e Allow Truncation if enabled and the image is too big for the window and integer zooming is enforced a few rows or columns of data may be discarded to allow the image to be shrunk e Integer X Zoom if enabled force zooming in the horizontal dimension do be done in integer multiples Turning this off allows you to fill the window but can introduce artefacts e Integer Y Zoom if enabled force zooming in the vertical dimension do be done in integer multiples Turning this off allows you to fill the window but can introduce artefacts e Zoom In on Middle Mouse Click if enabled clicking the middle mouse button will zoom in 2x using the mouse click position as the new centre e Zoom Out on Right Mous
105. l gt widget section 2 21 which allows you to interactively edit image data e Quit this will quit the application e Set2 sometimes labelled as Images this will popup up the lt Filepopup gt widget section 2 1 You will also see a few lines of display under the control buttons which gives information about the data under the current cursor position See Figure 2 11 for a screen snapshot The Magnifier Wherever you move the mouse over the main image you will see a magnified portion of that part of the image the magnification is 4x the data resolution You can resize the magnifier window 32 CHAPTER 2 COMMON FEATURES Figure 2 11 Screen snapshot of generic main window 2 15 COMMON IMAGE DISPLAY FEATURES 33 The Panner Simply click with the left mouse button in the panner window and the main window will pan to the desired location The panner window will display a green rectangle showing you where you have panned to relative to the entire image You can resize the panner window When you select the panner from the Intensity menu the panner is popped up and the main window is set to panning mode Zooming in the ImageDisplay Widget To zoom an image click left and drag the mouse still keeping the left button down across the window You will see a rubber banded box stretching be tween the first point and the current mouse cursor position When you release the button the section of the image within the box will
106. le tend to use Netscape less often than a visualisation tool Another more recent and more insidious problem is the CDE the Com mon Desktop Environment which steals not only too much screen space but also a large number of colours Unfortunately users don t get much choice about CDE as the system administrator often blindly enables it when installing the operating system If you start a display tool under CDE the tool will usu ally have to create its own private colourmap in order to get enough colours This would give you that colourmap flashing whenever you move between the image window and the desktop You can try to get around this by using the num_colours option to Karma tools see above Many tools try to allocate 200 colours but you can use 100 instead and it is usually still workable In the long run though it is probably better to get rid of CDE or possibly configure it so it only takes a few colours good luck Another problem can be when you use more than one Karma visualisation tool at the same time The second tool is likely to create its own colourmap because the standard desktop colourmap has few colours left You can either reduce the number of colours required by each tool or you can share colourmaps using the cmap_master host port command line switch see above Finally you may be wanting to use a Karma visualisation tool as well as some other display tool To avoid colourmap flashing you will need to re
107. leave out this switch but that is not recommended Your movie will look awful The switch max lt max num of colours gt gives the maximum number of colours the final movie can have The recommended value to use is max 200 Do not give a higher number than 220 Please note the space between the name of the movie and the minus sign You do not have control over the name of the output file The string conv_24to8_ is prepended to the name of the input file conv_24to8 c w m 200 ugc12441_movie produces a file conv_24to8_ugc12441_movie kf with the compressed movie 4 3 Multiple Contour Images The lt MultibeamView gt programme has special purpose code to display two datasets one as images and the other as contours If you wish to display multiple images or cubes you should use the lt kvis gt chapter 3 programme 4 4 Intensity Intensity Scatter Plots Earlier in this chapter 4 is a brief description of how you can use the c key to compute and display an intensity intensity scatter plot of two images You may also use this facility to display a scatter plot of two channels from the same cube Simply load the same cube in twice i e using the Seti and Set2 file browser buttons and select the two channels one from each cube You will need to ensure that the Link Frames toggle is disabled If the Link Frames toggle is enabled then the scatter plot is computed using the two frames which have corresponding co ordinates for the
108. lowing choices are available join a straight line is drawn from each point to the next hist a centred column is drawn for each point aka histogram style cross a small crosshair is drawn for each point Zooming in TracePopup Widget To zoom a profile click left and drag the mouse still keeping the left button down across the window You will see a rubber banded box stretching be tween the first point and the current mouse cursor position When you release the button the section of the profile within the box will be zoomed To unzoom 2 12 IMAGE STATISTICS 29 choose the Unzoom option in the Zoom menu or press the u key while the cursor is in the profile window This will show the entire image See Figure 2 10 for a screen snapshot 2 12 Image Statistics Many programmes have a facility to compute and display the statistics of the current sub image being viewed This interface is provided by the lt ImageDisplay gt widget section 2 15 2 13 Viewing Header Information Many programmes allow you to inspect the header of the dataset you are cur rently viewing as an image This interface is provided by the lt ImageDisplay gt widget section 2 15 2 14 Freezing Events All drawing operations in Karma tools are performed on a canvas which is usually a big plain black or white rectangle The canvas allows you to freeze mouse move operations i e things which happen in respons
109. lt y_coord gt Draw a single point e DOTS or POINTS coordtype lt x1 gt lt y1 gt coordtype lt x2 gt lt y2 gt Draw a collection of points e LINE coord typel lt x1 gt lt y1 gt coord type lt x2 gt lt y2 gt Draw a line between two points e CLINES coord_typel lt x1 gt lt y1 gt coord_typel lt x2 gt lt y2 gt coord_typel lt x3 gt lt y3 gt Draw a series of connected lines connect the dots e DLINES coord type lt x1 gt lt y1 gt coord_type lt x2 gt lt y2 gt coord_type lt x3 gt lt y3 gt coord_typel lt x4 gt lt y4 gt Draw a collection of disconnected lines e VECTOR coord type lt x_base gt lt y_base gt coord_typel lt x_comp gt lt y_comp gt Draw a vector with specified components at a given location At present this is just a line with no arrowhead drawn However unlike the LINE command which specifies coordinates of both endpoints the arguments for VECTOR are the position of the base and the components of the vector which get added to the base to determine the other endpoint e BOX coord_type lt x1 gt lt y1 gt lt x2 gt lt y2 gt Draw a rectangular box given coordinates of two opposed corners e CBOX coord typel lt x_cent gt lt y_cent gt lt x_width gt lt y_height gt angle Draw a rotatable rectangular box given center coordinates width and height and an optional position angle in degrees e CROSS coord_type lt x_cent gt lt y_c
110. ltiple Images and Cubes Sak OVERVIEW ak sack de de BBS ee we eed ee ee a eh EA 3 2 View Control io uk ye i A AA te od duo Data Browser s s anos 4 A A ee A eS 3 4 Command line Options 2 0004 3 5 Intensity Intensity Scatter Plots 3 6 Renzograms an alternative to velocity fields Viewing Images and Cubes with the Multibeam 4 1 Command line Options 2 0004 4 2 Special Movies eros ae ee Ee Pet 4 3 Multiple Contour Images e e 4 4 Intensity Intensity Scatter Plots Volume Rendering a Cube 5 1 How the rendering isdone A E EnS ari a E bed eke ote oe ce ae 5 2 Starting up the Volume Rendering Tool Bel OPONE rt ges We He A ag ot DS 5 3 Loading Data into xray e 5 4 The main control window 5 4 1 Rendering Modes 5 4 2 Rotating the cube 0 5 5 Making a Movie 5 0 00 ee eee 5 6 Filtering your data e o 5 6 1 Adaptive Filtering 5 6 2 Contintuum Subtraction 08 5 6 3 Other Controls 0 2000000008 5 7 Hot Gas Substances control panel o o 5 8 Hot Gas Mono control panel o 5 9 Hot Gas Continuous control panel o 5 10 Hot Gas Three Colour control panel
111. lts in blocky images which may be undesirable Setting the expansion factor to a value greater than 1 uses an anti aliasing image expansion algorithm which maintains the original smoothness of the image See note on anti alising for more information Setting this to too large a value will result in very large movies which is undesirable Try a vlaue of 2 to start with Eye Separation When viewing the cube in stereo mode it is useful to enhance or diminish the stereo separation The lower the value the closer the left and right eye viewpoints and hence the lesser the stereo effect Rendering Modes The following rendering modes are defined e normal this is the default mode Because rays through the volume will not fall exactly on grid points some approximation of the value has to be made In this mode the ray is snapped to a grid point This can result in aliasing problems but is the fastest mode In most cases the aliasing is not a problem In addition this mode computes a rotated version of the cube in a cache in the background while you are not doing anything the background processing does not slow down normal rendering operations The cube is rotated using the same grid snapping technique so has the same aliasing problems However provided you do not keep changing the 5 4 THE MAIN CONTROL WINDOW 73 view or the cube subsequent render operations such as changing the shader are four to ten times faster Whenever you rota
112. map file using the cmapfile parameter The general usage for this programme is karma2ppm infile outfile where infile is the input Karma file and outfile is the output PPM file If the input file is a 3 dimensional array a sequence of numbered output files will be written Writing other Image Formats You can also use lt karma2ppm gt to write out images in other popular formats such as GIF TIFF Targa TrueVision and so on To do this requires that you have the NetPBM tools installed These tools are freely available and very popular as they allow conversion between many different image formats To use this facility you need to set the converter and extension parameters The converter is the name of the programme which converts PPM PNM images to the image format you desire The extension is the conventional filename extension for that image format For example if you wanted to convert a Karma image or cube to a TIFF image or sequence of images you would need the following settings 100 CHAPTER 12 COMMAND LINE TOOLS converter pnmtotiff extension tiff On the other hand if you wanted to generate GIF images you would need the following settings converter ppmtogif extension gif Notice how the the TIFF converter seems to require PNM files whereas the GIF converter seems to require PPM files This is not a problem since PNM Portable aNy Map is the generic format and PPM Portable Pixel Map is a specific subset of PNM Cha
113. nds is given below with syntaxes and brief de scriptions In the syntax lists the command is given in CAPS with occasional synonyms in parentheses Required arguments follow in lt angle brackets gt and optional arguments or argument groups in square brackets The brack ets are for illustration only and should not be typed D 3 1 Non Graphical Commands At present there is only one of these but it is quite useful e INCLUDE lt name of file gt Includes the contents of another annotation file in the current one The parser acts on the instructions it finds in the included file before moving to the next command in the present one Thus one can include the same file s worth of annotations in several different files without having to maintain multiple copies Furthermore by specifying attributes such as color in the parent file instead of the included file the attributes can be changed from one inclusion to the next The filename can include the notation as well as other simple Borne Shell like expansions of environment variables using the variable variable and variable word notations Note Filenames are case sensitive on many operating systems e g Unix Also when using multi level inclusion including files which in clude other files etc be careful with relative pathnames The parser s working directory remains that of the original file thus if file1 ann has INCLUDE subdir file2 ann and that file
114. ng 2 18 1 Avoiding Colourmap Flashing Standard workstations with 8bit PseudoColour displays only have a single colourmap active at one time If you start two display tools each wanting to use a large number of colours then when you move the mouse between the windows you get that horrible colourmap flashing effect as the window manager updates the hardware colourmap Also since the colours used by one tool are likely to be quite different from those used in another tool the image in one tool will look completely wrong when the mouse is in another tool It is particularly annoying if colourmap flashing occurs when moving between an image window 2 18 GUI COMMAND LINE SWITCHES 37 and the desktop i e normal terminal windows because often you may want to read something in a terminal window while also looking at an image There are a number of ways to get around this One of the most common problems is a WWW browser like Netscape or a display tool like xv or ghostview which is started before you start a display tool You can try to limit the number of colours Netscape uses but I haven t found that to be all that reliable You can also use the install command line switch which will force Netscape to use it s own colourmap rather than stealing colours from the standard one This will of course mean that as you move the mouse into the Netscape window the colours flash but in practice this shouldn t matter so much because peop
115. ng as some visible part of the star is within the circle cursor also known as the capture region when you click middle the tool will find the centroid of the star You might find it helpful to click the Magnifier button to see the magnifier window You will see a crosshair which is centred on the current mouse position in the main window You will also see a green circle which shows the capture region if any part of the star lies within that circle when you click middle the centroid of the star will be picked You can adjust the size of the capture region by clicking with the left mouse button in the magnifier window You 89 90 CHAPTER 9 KOORDS INTERACTIVE CO ORDINATE FITTING will also see a dashed green circle which is slightly larger than the solid green circle The area between the two circles is called the background annulus The magnifier will also show small red crosshairs at the exact centroid positions of selected stars Once you have selected all your star pairs you can click on Compute Co ordinate System and the tool solves for a co ordinate system In your command line window a report of the solution is displayed If you move your mouse around the right window you will see the proper world co ordinates of the pixels Once you are happy with the co ordinate solution you can press the Apply Co ordinate System button and then save the image with the new co ordinate system using the Export menu The coordinate s
116. nge e Output Type Menu change the output type of the array to save not all applications will show this menu e Filename string the name of the file which will be saved This may be changed prior to saving If you click with the left mouse button in the histogram display you define the lower boundary of a region If no region exists one is created If you then click with the right mouse button the upper boundary is defined Once the lower and upper boundaries are defined you will see two vertical lines depicting the boundaries with two diagonal lines joining them You will also see a circle the height of which indicates the width of the region relative to the width of the entire histogram If you click with the middle mouse button the horizontal cursor position will control the midpoint of the region i e change the lower and upper boundaries at the same time and the vertical cursor position changes the width of the region You can drag any of the three mouse buttons to see things continuously change If you have not yet defined a region you may first click with the right button to define the upper boundary The lower boundary is automatically set to the data minimum This is a convenience facility when you want to set the lower 2 3 SEQUENCES OF IMAGES 17 boundary to the data minimum and set the upper boundary manually You can get the same effect by pressing Full Range first and then clicking with the right button See Figure 2 4
117. nging the Output Image Size If you wish to write out images of a different size from your input image cube then you will need to use the out_width and out_height parameters If your input is smaller than this the image will be blank filled and centred onto the desired output image size If the input is larger than this it will be centred and truncated No pixel averaging or replication is performed 12 5 4 kdecimate This tool will decimate a cube averaging a specified number of values along an axis to produce a single value This decimation is performed along all 3 axes This tool provides a simplified version of the lt LoadAndDecimate gt widget section 2 1 1 The only reason to use it is if you are developing batch mode scripts to process large number of datacubes The general usage for this programme is kdecimate infile outfile 12 5 5 kminmax This tool will show the minimum and maximum value in a datafile It will also display the number of blank values TOOBIGs and the number of illegal values Note that illegal values should never occur and are the result of an incorrectly written file Tllegal values will cause problems for Karma programmes such as a segmentation fault or other crash Hence this programme is an excellent diagnostic to determine if the data you are giving to a programme is legal This programme supports many data formats The general usage for this programme is kminmax infile dataname where infile is th
118. ns There are a few actions which are common to all tools which allow you to exit the panel exit the tool with or without saving parameters and others which manipulate the communications infrastructure 12 2 6 Other Arguments Most tools define some other arguments which are not parameters or actions They are usually filenames to process although they can be other things too like dimension to filter along An unlimited number of other arguments may be typed in one line Some tools will show the other arguments by printing General usage followed by the arguments 12 2 7 Exiting Interactive Mode The abort action will abort the tool without saving any parameters The exit and quit actions will exit the tool after saving parameters Pressing control D has the same effect as typing exit 123 Batch Mode Another term for batch mode is shell mode which just means that the tool is started from the shell with arguments and exits when it has completed From the shell you can pass in any number of parameters and actions The limitation in interactive mode of only typing a single parameter or action is removed 12 3 1 Passing in Parameters and Actions You simply need to place the character in front of the name of the parameter or action with no intervening space This marks the start of a new parameter or action All subsequent shell arguments are treated arguments for the action or parameter until th
119. ntrols are provided e Close close the window e Blank enable to blank data outside specified region not all applications will show this toggle 2 2 INTENSITY SCALING 15 Figure 2 3 Screen snapshot of colourtable control panel 16 CHAPTER 2 COMMON FEATURES e Zoom zoom the histogram display to the range of the current region e Unzoom unzoom the histogram display to the full range of the data e Apply apply any changes made to the regions most applications will then rescale and display their main image e Auto Apply enable this to automatically apply every change as they are made e Subset enable this to use only a subset of the input data This will speed up the histogram computation and may avoid unwanted outlier values e Full Range set the region to the full range of the data e 95 set the region to clip to the inner 95 of the data values i e clip the lower 5 and upper 5 of the data values This is very handy when your data contains outliers small numbers of data values which lie far away from the real data e 98 set the region to clip to the inner 98 of the data values e 99 set the region to clip to the inner 99 of the data values e 99 5 set the region to clip to the inner 99 5 of the data values e 99 9 set the region to clip to the inner 99 9 of the data values e 99 99 set the region to clip to the inner 99 99 of the data values e Save save a new file which has been clipped to the specified ra
120. oad is disabled the intensity range of the previous image will be used However the intensity range that is used is the raw range not the scaled range Thus with images which have different scaling parameters the scaled intensity range will change e When moving between two images such as when blinking or when load ing a new image the display system attempts to retain the old image parameters i e zoom box What is retained are the corners of the zoom box measured in image pixel co ordinates not world co ordinates e Co ordinate positions start from 0 not 1 125 126 APPENDIX G QUIRKS AND UNEXPECTED BEHAVIOUR Appendix H Undocumented Features 127 Index 3D overlays 71 acknowledgements 123 adaptive filtering 74 annotations loading 39 autoscaling 24 axis labels 24 batch processing in GUIs 101 blanked values 100 blinking images 57 capturing co ordinates 34 changing dimension lengths 98 chlen 98 chromatic aberration 103 co ordinate system fitting 89 co ordinate systems 7 colourmap flashing 36 colourtables 14 command line tools 95 ktranslate 5 miriad2gipsy 5 common GUI features 9 common GUI switches 36 contours 41 58 93 levels 50 59 multiple 62 102 crashes 100 cursor readout 35 data converters fits2karma 4 gipsy2karma 4 ktranslate 5 miriad2gipsy 5 miriad2karma 4 data filters 5 128 data formats 2 AIPS 2 AIPS 4 2 DRAO 2 FITS 2 GIF 3 GI
121. oad this brings up a file browser popup which allows you to load a previously saved colourtable You can manipulate the colours in the colourtable by moving the round dot in the big square box left mouse button Usually moving the dot horizontally changes the apparent position of the colours while moving it vertically changes the range of colours There are many colour functions available to set the colourmap the de fault one being Greyscalel Some colour functions produce smoothly varying colourtables while others have sharp boundaries A final way of manipulating the colourtable is provided by the Red Scale Green Scale and Blue Scale sliders With these you can turn down the amount of each primary colour for all the colours in the colourtable See Figure 2 3 for a screen snapshot In many cases you will want to change the intensity scale in an image This may be because the image has a very large dynamic range or has a few outlier values and the control provided by the colourtable is inadequate Most programmes have an Intensity menu with a selection named IScale for Dataset which will pop up a lt Dataclip gt widget This widget allows the user to specify a number of data regions ranges It it most often used to give control over a single region so that an intensity range may be specified The widget displays a histogram of the data values in the array with the vertical axis being logarithmic The following co
122. of whether the coordinate type is W R or P So unlike STANDARD position angles SKY PAs retain their appearance regardless of coordinate type This same system can be used with Ecliptic and Galactic coordinates as well as Equatorial though the PA 0 referent points up in all cases toward the grid s north pole However unless the image projection is flat 116 APPENDIX D ANNOTATION FILE FORMAT PA 0 will only point exactly north at the image projection center but if the image covers a small piece of the sky and is not close to a coordinate pole the error will be small Generalizing this to be correct in all parts of the image is a future project D 4 Example Annotation File Two sample annotation files m42 ann and m42_include ann have been pro vided to illustrate the functions and concepts outlined above To use these ex ample files properly in Karma it is necessary to load the FITS image m42_ha fits to set the world coordinates For best image appearance select a square root intensity scale from the Intensity Policy popup and a 99 99 intensity range from the Scale popup These example files and some image data may be found at ftp ftp atnf csiro au software karma data annotations HHEHHHHHHEHHHHHHREHHREHHHAEHRAAHRREH HEHEHE EHHHAE RRA RRR E HRB HHH RHE SAMPLE KARMA ANNOTATION FILE M42 ANN to be used with M42_ FITS images H H HHH HEHHHHEHAHHEHAHHEHAH HERRERA HEHRRAH HAHAHAHA HE HAHHRAHEHRRRH HERR RHEE Commen
123. ontinuation character is ignored because the following line is empty COLOR LIGHT GRAY DLINES R 0 96 0 05 0 99 0 05 0 96 0 10 0 99 0 10 0 96 0 15 0 99 0 15 0 96 0 20 0 99 0 20 0 96 0 25 0 99 0 25 0 96 0 30 0 99 0 30 0 96 0 35 0 99 0 35 0 96 0 40 0 99 0 40 0 96 0 45 0 99 0 45 0 96 0 50 0 99 0 50 0 96 0 55 0 99 0 55 0 96 0 60 0 99 0 60 0 96 0 65 0 99 0 65 0 96 0 70 0 99 0 70 0 96 0 75 0 99 0 75 0 96 0 80 0 99 0 80 0 96 0 85 0 99 0 85 0 96 0 90 0 99 0 90 0 96 0 95 0 99 0 95 Change default coordinates to relative In the DLINES command above the default was world coordinates so the R was necessary to specify something else COORD R Here are a of couple vectors COLOR CYAN VECTOR 0 1 0 25 0 05 0 05 VECTOR 0 1 0 30 0 05 0 05 COORD W Change back to world coordinates as the default Here are three plain adjacent ellipses No position angle parameter is given so PA 0 However this applies to the first semiaxis given not necessarily the larger of the two With the semiminor axis listed first these ellipses have an effective position angle of 90 degrees in the standard system see below HH H H A COLOR ORANGE ELLIPSE 83 9151 5 3978 0 002 0 005 ELLIPSE 83 9111 5 3978 0 002 0 005 ELLIPSE 83 9071 5 3978 0 002 0 005 Put a dot in the center of all three orange ellipses using a single command DOTS 83 9151 5 3978 83 9111 5 3978 83 9071 5
124. ontours 44 57 58 editing 38 file format 111 loading 39 painting 39 panner 26 panning 43 60 point spread function measuring 42 58 postscript output 20 printing headers 100 printing images 20 profiles area averaged 42 58 area summed 42 58 fitting gaussians 42 58 radial 42 58 spatial 42 58 spectral 28 42 58 programme crashes 100 quirks 125 regridding 98 101 rendering algorithms 65 130 renzogram channels 51 renzograms 54 resizing displays 24 resources 107 rotating 101 saving as PostScript 20 images 21 profiles 28 scatter plots 43 54 60 62 screen snapshots 1 segmentation faults 100 send contours 102 sending commands to GUIs 101 sequences of images 17 setting up 105 shaders front voxel 65 hot gas continuous 67 hot gas mono 67 hot gas substances 66 intensity transformation 67 maximum voxel 65 minimum voxel 65 substances 66 voxel sum 65 statistics images 29 superimposing images 93 undocumented features 127 units 7 viewing headers 29 viewing multiple datasets 41 volume rendering 65 widgets AnimateControl 17 Canvas 29 Cmapwinpopup 14 DataBrowser 44 Advanced 51 Make Data 52 Dataclip 14 DressingControl 24 INDEX ExportMenu 21 Filepopup 9 ImageDisplay 29 ImageEditorControl 39 IntensityPolicy 17 LoadAndDecimate 12 MagnifierPopup 26 Moment Generator 34 OverlayEditorControl 38 PannerPopup 26 Postscript
125. or its PsuedoColour window upon startup If less colours are available it allocates as many as possible minimum 2 e cmap_master host port This option will make the tool use the colourmap of another tool The host portion of the second argument is the Internet hostname or address where another Karma tool is running If this is unix or localhost the tool to connect to is running on the same ma chine The port portion specifies which Karma programme to connect to You may use the port number which is displayed in the other tools title bar or you may use the name of the tool such as kvis and it will connect to the first kvis tool you started on that machine e fullscreen This option will make the image display window take up the entire screen This is useful if you wish to make a video of the data You will need to configure your window manager to cycle the window stacking order when a special key is pressed e g the Back key with the Open Look window manager Alternatively pressing the right mouse button in the image window will place it underneath other windows See also the appendix on making videos appendix E In addition the standard Xt command line switches are supported Read the manual page for xterm for more details In particular the following options are worth noting e display control where the tool is displayed e geometry control the size and postion of the tool e xrm pass a resource stri
126. ore arguments which may be separated with commas spaces or tabs Comments may be placed in the annotation file by using a comment character All text occuring after a comment character on the same line is ignored Blank lines are also ignored The syntax is case insensitive UPPER lower or MiXeD cases are all valid Commands can be extended over more than one line of text by placing a continuation character at the end of each line to be continued Any text appearing after the continuation character on the same line is ignored Continuation characters do not continue comments only command strings therefore any following a is ignored If the line following a continued line is blank or a comment line the continuation is terminated Note The parser ignores any spaces tabs or commas preceding useful text on a command line Consequently a space should be placed prior to the 111 112 APPENDIX D ANNOTATION FILE FORMAT continuation character if the text beginning on the following line is not to be considered part of the last argument on the current continued line The reason for this is to allow a long argument e g a really long font name to be broken up if necessary without being treated as two separate arguments D 3 Annotation Commands There are three types of commands those which draw objects those which change attributes of objects and non graphical commands A complete list of currently implemented comma
127. ore it does not make a three dimensional perception One way to get a three dimensional perception of the data is to make a movie in which the data cube is rotated while it is rendered For making such a movie click left on Make Movie and the movie control window will pop up This window allows you to make a series of images where the data cube is rotated in steps Use the sliders to set the increment in Roll Pitch and Yaw and the number of images you want Start Movie then starts computing this sequence To save a movie type in a filename and click Save Movie Once the movie has been generated an animation control window will appear allowing you to view the movie One consideration is the size of the movie If this is too large i e larger than about 40 Mbyte on phoenix playing the movie will be slow An estimate of the size of a movie is x y 2 7 Nerames N om where x y and z are the size of the axes of the data cube in pixels and Nzoom the zoom factor My experience is that rotating the cube in steps of 10 degrees so the movie is 36 frames is in general sufficient to get a smooth movie It may not be a good idea to make a movie of images with a large Image Expand Factor depending on the sizes of the axes of the cube You will find that when you play such a movie it will be slow because it has to swap images in and out You can always zoom afterwards when you play the movie by resizing the window although the result
128. ors that show up quite well with the rendering software it may be a good idea to take the minimum such that most of this peak is excluded Depending on which voxel algorithm you use in the rendering see later if you include data at the noise level your rendered data cube will have a lot of noise in front of your object of interest and it may just be in the way There are however also other ways see below to hide the noise Consider that with the rendering software you may see faint structures in your data that you were not aware of So you may not want the minimum to be too high either otherwise you may miss interesting features in your data Of course when there is absorption in the data the noise will have to be included Also consider that the because the data is scaled into 127 127 the dy namic range is limited so in some cases it may be a good idea to choose the maximum not too high You will be able to see more detail in the fainter emission 5 4 The main control window See Figure 5 1 for a screen snapshot The following controls are available e Files this pops up a standard lt Filepopup gt widget section 2 1 with which you can load your cube e Show Orientation this pops up a window which shows a wireframe of the cube As you change the cube rotations this is updated immediately This should give you a feel for which way the cube will rotate before you press Compute e Make Movie this pops up a movie control
129. over the top as contours This can be done with lt kvis gt chapter 3 and does not require a 24 bit display You may also use the lt send contours gt section 12 5 10 programme to draw contours over any image This programme is a command line tool how ever and is not normally used since the the GUI tools are much easier to use 11 2 Hue and Intensity With the program lt kvis gt you can superimpose two images where one image is taken to control the intensity and the other the colour This can be used to display amplitude and phase together in one image or line integral and a velocity field To display the images run kvis First load Filel and File2 You should now see the combined images The sliders Start Hue and Stop Hue manipulate the colour of the image the sliders Minimum Intensity and Saturation the intensity By default File1 will control the intensity and File2 the hue You can swap this by choosing Phase Amplitude from the RAW DATA FORM menu If you select Real Imaginary then a rectangular to polar transformation of the data is performed where Filel is real image and File2 is the imaginary image You can swap the sense of this by choosing Imaginary Real After 93 94 CHAPTER 11 SUPERIMPOSING IMAGES the rectangular to polar transformation the amplitude value will control the intensity and the phase value will control the hue 11 3 Intensity and Intensity Another possibility is to overla
130. pturing Co ordinate positions in the ImageDisplay Widget Many programmes allow you to capture the current world co ordinate position of the mouse by pressing the I key in the image window The output is set to the standard output which you may redirect to a file prior to starting the programme 2 16 Generating Moment Maps Some of the programmes allow you to generate quick moment maps This is usually available in tools where you need both a cube and an image of a similar section of sky To save you the trouble of going into an astromonical reduction package to generate the moment maps a menu is provided so that you can generate and view a moment map This is usually the Loaded Image Menu and has entries like Oth moment and 1st moment Selecting either one of these will pop up the lt MomentGenerator gt widget This widget allows the user to generate the Oth total intensity and 1st velocity field moment maps from a cube The following controls are available e Close this will close the window e Apply Parameters this will apply the parameters and compute the moment maps e 1st Moment Algorithm Menu this allows you to choose between a simple weighted mean algorithm or a more robust median algorithm e Lower Clip Level values in the cube lower than this value are not used in the computation of the moments e Sum Clip Level values in the computed Oth moment map lower than this value are not used in the computation of t
131. r action and the first other argument This solitary should be surrounded by at least one space on either side 12 4 Saving and Restoring Parameters Each of the command line tools will look for a file called name defaults where name is the name of the programme This file the defaults file con tains saved parameters which will be read by the tool as it starts First the current working directory is searched and then each parent directory in turn until either a defaults file is found or the root directory is reached If still a de faults file is not found then the tool will look in the karma module defaults directory under the users home directory and then finally it looks in the KARMABASE defaults directory If no defaults file can be found then inter nally hard coded defaults are used Upon normal exit each tool will write its defaults file in the current working directory 12 5 List of Tasks 12 5 1 chlen This tool will change the length of a dimension in a Karma file You can in crease the length of a dimension by zero padding or resampling and decrease the length by truncating windowing or resampling The option parameter con trols whether a dimension is resampled truncated or padded The resampling option is the same as a one dimensional regridding If you have chosen to resample a dimension then the resample_option parameter controls whether a nearest neighbour copy or linear interpolation is per
132. r cells that lt xray gt will try to allocate for its PsuedoColour window upon startup If less colours are available it allocates as many as possible minimum 2 e fullscreen This option will make the image display window take up the entire screen This is useful if you wish to make a video of the data You will need to configure your window manager to cycle the window stacking order when a special key is pressed e g the Back key with the Open Look window manager See also the appendix on making videos appendix E e no_slice_win This option will disable the 3D slicing window similar to what you get in kslice_3d chapter 7 After starting up many windows will appear e the control window with which of course you control the rendering pro gram e aslice window This shows the data cube along the three principle planes XY ZY and XZ By moving the mouse press left the windows will be updated To make things run smoothly click on Precompute This is also available as a stand alone program kslice_3d chapter 7 and is quite useful for inspecting your data This window will appear after you have loaded a cube and possibly converted to bytes Another window that you will see after the first time you render the cube is the image display This window is similar to the display window in many of the other tools see section 2 15 5 3 Loading Data into xray lt xray gt supports many data formats like any other Karma prog
133. rame End go to end frame On some keyboards PgDn is marked as Next and PgUp is marked as Prev Blink if enabled dataset 2 is displayed if the display mode is set to blink if disabled dataset 1 is displayed By repeatedly clicking this the user can blink between the two datasets You can also press the b key in the image window and get the same effect Note that when blinking between two images with non linear co ordinate systems the linear data pixel co ordinates of the canvas boundary are preserved not the non linear world co ordinates This is especially noticable when blinking between two images with a different pixel scale 57 58CHAPTER 4 VIEWING IMAGES AND CUBES WITH THE MULTIBEAM e Profile Mode Menu this allows you to pop up the lt TracePopup gt widget section 2 11 and choose the profile mode The following modes are available None will pop down the lt TracePopup gt widget Line will show a single profile in the selected direction Box Sum lets you draw a box over the image window using the middle mouse button in a similar way as using the left mouse but ton to zoom and then the sum of all the profiles in that region is displayed Box mode only works for 3 dimensional datasets and will always display a profile along the unseen dimension Box Average is like the box sum mode except that the average of all profiles is displayed rather than the sum Radial will azimuthally average the im
134. ramme For reasons of memory use and speed the preferred data format used by lt xray gt is that the data is stored as bytes with values ranging from 127 to 127 the value 128 is used for blank or missing data The values in your data cube will have to be scaled into this range If you load a non byte data cube lt xray gt will display a window showing the histogram of the data values in the cube If you want to use the full range of values in the cube good for a first look at the data click left on the Full Range button If you want to select a sub range of the data click left in the histogram window to define the lower bound and click right to define the upper bound You then click left on Apply to tell lt xray gt to compress the cube to a byte cube You will then be able to click left on the Save button 5 4 THE MAIN CONTROL WINDOW 69 to save the compressed data cube The default filename is scaled but you can change this prior to saving Once you have saved a compressed cube the next time you load it in lt xray gt it will load much faster The proper values for the scaling range of course depend on the data in the cube and on what you want to see in the data but here are some hints Normally the histogram has a large peak around zero The Noise Unless you want to have a look at the noise in your data cube eg because you want to look at subtle calibration errors or errors in the continuum subtraction err
135. rocess is streamed to avoid the need to allocate large amounts of virtual memory 1 1 3 Loading partial files Some data formats support loading of partial datasets With these formats if part of the data are missing the part of the dataset that is available can be loaded if desired This is useful if you want to see a preview of a dataset that is currently being written by another process 1 2 Adding your own Data Formats The visualisation tools also provide a mechanism for you to add support for other data formats not already supported by the Karma library You will need a programme that converts from your data format to either Karma FITS or PNM format and for some data formats in particular directory based formats you will need to provide a tester programme which determines if a dataset is of a particular type To set this up you need to have a file karma data filters which contains rules on how to convert data formats A system wide file maintained by your local Karma installer is also searched and is called KARMABASE site share data filters Finally the file KARMABASE share data filters is scanned to load any filters which come with the Karma distribution Your own data filters override the system data filters which in turn override the Karma distribution filters A typical file would contain Extension Converter Tester Output Format Name imh iraf2fits FITS IRAF Image sdf sdf2karma a Karma Starlink Image D
136. ry the size and placement of the second display window for lt kvis gt The default is 0 0 top right Postscript nameDialog font the name of the font to use in the text entry dialog for the output filename in the lt Postscript gt widget section 2 4 Appendix D Annotation File Format D 1 Usage Karma has a facility to annotate 2 D images with lines boxes and other sim ple figures as well as strings of text Commands to draw these various things are stored in text files which are read in by selecting the Load Annotations option from the Overlays button menu see 2 20 The names of annotation files must have the extension ann or ANN for Karma to recognize them Annotations read from a file can be removed from the image with the Re move buttons in the Annotation File Loader Often the best way to produce a good set of annotations for a particular image is to see what an annotation file produces on the screen then modify the file contents remove the annotations and reload the file until everything appears satisfactory Note the annotations descibed here only work with 2 D images or 2 D slices of 3 D images For information on marking rendered 3 D images with i line segments in lt xray gt see 5 4 D 2 Fundamental Syntax Annotation file syntax is very simple Commands are listed in the order they are to be performed separated by carriage returns Each command is followed by one or m
137. s the last selected entry high lighted i e moving the mouse won t highlight a different entry IntensityPolicy transient as above for the lt IntensityPolicy gt wid get section 2 2 LoadAndDecimate transient as above for the lt LoadAndDecimate gt widget section 2 1 1 MagnifierPopup transient as above for the lt MagnifierPopup gt wid get section 2 9 Moment Generator transient as above for the lt Moment Generator gt widget section 2 16 OverlayEditorControl transient as above for the lt OverlayEditorControl gt widget section 2 19 PannerPopup transient as above for the lt PannerPopup gt widget section 2 10 Postscript transient as above for the lt Postscript gt widget section 2 4 SlaveImageDisplayPopup transient as above for the lt SlaveImageDisplay Popup gt widget TracePopup transient as above for the lt TracePopup gt widget sec tion 2 11 110 APPENDIX C RESOURCES View2Datasets transient as above for the lt View2Datasets gt wid get section 4 ZoomPolicy transient as above for the lt ZoomPolicy gt widget sec tion 2 7 Kvis geometry the size and placement of the main display window for lt kvis gt The default is 0 0 top left Kvis firstDataBrowserShell geometry the size and placement of the first data browser window for lt kvis gt The default is 540 0 to the right of the main display window and at the bottom of the screen Kvis imageDisplayShelll geomet
138. show only the brighter voxels Also the computation is done on the floating point data not on colours hence the mono This increases the dynamic range of the image very much Images produced by this shaders are floating point An option offered with this shader that the intensity can be transformed before rendering according to a similar function as above sxy 5 3 where s is the value used for the voxel in the radiative transfer and v is the value of the voxel Hot Gas Continuous this shader is a mix between the Hot Gas Sub stances and the Hot Gas Mono shaders There are now 254 substances but the opacity is defined in the same way as in Hot Gas Mono The user interface of this shader is much better than that of hot gas sub stances Also this shader produces 24bit images and to play movies made with this shader you will have to convert the images to 8 bit using the conv24to8 programme section 5 2 Starting up the Volume Rendering Tool To start the rendering software on any workstation type xray 5 2 1 Options lt xray gt supports several command line options which are all documented in the manual page The options of general interest are 68 CHAPTER 5 VOLUME RENDERING A CUBE e private_cmap This option will force lt xray gt to use a private colourmap for its PseudoColour window Otherwise lt xray gt trys to allocate colours from the default colourmap e num_colours This option specifies the number of colou
139. sk attached to it then the file may be memory mapped just like a Karma file which means loading may be just as fast as loading Karma files For this reason it is worthwhile to avoid creating masks for Miriad files if you can help it PNM PPM PGM this is a common image interchange format The format does not support anything fancy like co ordinate systems but it is useful for converting between the many different image formats out there Simple FITS this is a derivative of the FITS format which is easier for the human to manipulate Lines in the header are separated by newline characters rather than having to be padded to 80 characters The data directly follows the END keyword and must be in plain ASCII format a single value per line The blank value for floating point data is 1e30 The filename extension should be sfits Starlink Image this an astronomical reduction package used by many optical astronomers The file extension is sdf and requires the lt sdf2karma gt programme to be in your PATH A precompiled binary is available at ftp ftp atnf csiro au pub software karma other packages starlink for your convenience Sun Rasterfile another popular image format having the distinct ad vantage of not using a patented compression algorithm unfortunately the GIF format uses a patented image compression algorithm Targa TrueVision tga files yet another image format This requires the NetPBM tools to be installed on your machine
140. stems The Karma data format supports simple regular co ordinate systems as well as irregularly spaced co ordinates In addition the curvilinear co ordinate systems i e Right Ascension Declination and Galactic Longitude Galactic Latitude commonly found in astronomy are supported Many common projections for these curvilinear co ordinate systems are supported as is the polynomial based projection used for DSS Digital Sky Survey images The co ordinate system support is tightly integrated with much of the Karma internal infrastructure In general mixing of data with different projec tions is handled correctly For example displaying overlays and contours over a greyscale image will work correctly even if the datasets have different rotations scales and projections Support for mixing different co ordinate systems i e RA DEC overlaid with GLON GLAT is not yet supported nor are data of mixed epochs CHAPTER 1 INTRODUCTION Chapter 2 Common Features Some features of different programmes are the same You may also notice that parts of one programme may also be available as a separate programme or also appear in other programmes This is due to the modular approach provided by Karma Most of the window based control panels you see are in fact widgets and these are reused many times in the same programme or in different programmes 2 1 Loading Data All programmes have the same interface to load data Clicking left on
141. tate this controls whether the anima tion control will be stay popped up when an image is displayed True or will be popped down False e AnimateControl transient as above but specifically only for the lt AnimateControl gt widget section 2 3 e Cmapwinpopup transient as above for the lt Cmapwinpopup gt wid get section 2 2 Dataclip transient as above for the lt Dataclip gt widget section 2 2 109 Dataclip subsetToggle state this controls whether a subset of the input data will be used to compute a histogram for the lt Dataclip gt widget section 2 2 Dialogpopup transient as above for the lt Dialogpopup gt widget DressingControl transient as above for the lt DressingControl gt widget section 2 8 Filepopup transient as above for the lt Filepopup gt widget section 2 1 Filepopup dotsToggle state control whether True or not False hidden files and directories are shown by default in the lt Filepopup gt widget section 2 1 Filewin numLines the desired size of the directory browser in lines The default is that the browser size is automatically configured Filewin list translations may be used to change the file browser mouse behaviour The default is to highlight the entry under the current mouse pointer position If you specify lt Btn1Down gt Set n lt Btn1Up gt Notify then highlighting only occurs when an entry has been selected The only advantage of this behaviour is that it leave
142. te the cube or change it the cache is automatically built up again lt xray gt always uses as much of the cache as it can e smooth cache will build up the cache using a better algorithm when a ray falls between grid points The value computed uses a distance weighted contribution from each of the nearest surrounding values in effect an interpolation This algorithm does not suffer from aliasing The cache takes about four times longer to build up than in normal mode but once it s done rendering is as fast as using the cache that normal mode produces In fact it doesn t matter how complex the cache building process is once it s built rendering times are the same for the same shader of course If the cache is not completed part of the rendering uses the normal mode when you request an update This can lead to the interesting side effect that the lower part of the rendered volume is smoother whilst the upper part is rougher and possibly shows aliasing artefacts always smooth will always render using the interpolation algorithm It does this by waiting for the cache to be built using the interpolation algorithm and then rendering If you don t change your view or cube subsequent rendering operations are still at maximum speed If you find that you are having aliasing problems you should use this option when making a movie otherwise the movie generation process will not wait for the cache to be built up e smooth delayed will f
143. ted from their real appearance in curved world coordinates e g maps of the sky Proper projection of geometric objects into world coordinates is a nontrivial exercise and has been deferred D 3 4 Position Angle Conventions Standard Postition Angles are generally defined in the Cartesian sense where PA 0 specifies X gt 0 Y 0 PA 90 specifies X 0 Y gt 0 and so forth In a coordinate system where X increases from left to right and Y increases from bottom to top PA will increase in a counter clockwise direc tion However this will be reversed if the X increases from right to left or Y from top to bottom though not both So be careful To summarize PA is measured CCW from right in R coords and CW from right in P coords How 1t is measured in W coords depends on the coordinate system in many cases it will be the same as R coords but this is not always true For example most astronomical maps of the sky have the X coordinate increasing toward the left in which case PA will be measured CW from left Sky Position Angles are for the astronomers Usage of this convention in annotations assumes two things 1 a map of the sky is being displayed with the X coordinate increasing from right to left and the Y coordinate increasing from bottom to top i e north up south down east left west right and 2 position angle is measured from north through east up through left The convention is followed regardless
144. the opacity law can be set as well as the values range for valid data The difference is that one can set the connection between voxel value and colour using a colourtable like interface 5 10 Hot Gas Three Colour control panel This shader is an extension of the Hot Gas Continuous shader It allows you to divide the data range into three regions with independant opacity and colour transfer functions for each region This shader is a little esoteric and is designed for rendering data with two or three distinct populations of data values This kind of data does not occur in radio astronomy You may generate this data by combining two datacubes together This shader would allow you to render one dataset in one colour and another dataset in another colour Chapter 6 kpvslice interactive position velocity slicing The lt kpvslice gt programme allows you to use a two dimensional image to define a slice through a three dimensional data cube The image and cube must have two dimensions in common and the coordinate range of those dimensions must partially overlap but the axes need not have the same reference point orientation or scale A typical use is to examine the position velocity diagram for a slice drawn along the major axis of a rotating galaxy The slice is drawn on the total column density or velocity field map and the corresponding position velocity diagram will appear in the other window The slice can be moved around interactivel
145. tour levels for normal contours The syn tax for the contour levels is as follows just type the levels you want e g 0 001 0 002 0 003 0 004 levels with a constant increment 0 001 0 004 0 001 means that the first level is 0 001 that this level is incremented with 0 001 until 0 004 is reached So this example gives the same levels as in the first case levels incremented by a factor 0 001 0 016 2 This gives levels 0 001 0 002 0 004 0 008 0 016 levels as percentage of the peak first character should be num bers are taken as percentage the rest of the syntax is as above e g 10 40 10 gives 10 20 30 and 40 of the maximum of the data the special values min and max indicate the minimum and maximum value 3 3 DATA BROWSER 51 These options can be mixed i e 0 03 0 01 0 01 0 003 0 1 0 02 0 2 0 3 is interpreted correctly You should press the enter key for your changes to take effect ve Cont Width the width of negative contour levels ve Cont Width the width of positive contour levels Colour the colour of negative contour levels Colour the colour of positive contour levels Renzo Contour Levels the contour levels for Renzograms The syntax is the same as for the contour levels e Renzogram Channels the channels along the unseen axis to display in the Renzogram The syntax is similar as for the contour levels except that a leading I or W must be given Again press the enter key
146. troid of the profile is computed and a gaussian is fitted and displayed Slice Direction Menu this allows you to choose how you want to slice your cube You can view XY XZ or ZY planes Profile Axis Menu this allows you to choose along which axis you want the profile to be displayed valid only for line profile mode Freeze Displayed Intensity Range if unset the default the intensity range specified for a dataset is used when that dataset is displayed as an image If set switching from one dataset to the next will not change the displayed intensity range however changing the intensity range for the image dataset will change the displayed intensity range Track Cursor if set the corresponding image display window will lis ten for cursor moves which occur in other image display windows and will draw a red circle at the same world co ordinate position Show Frame in Line Profile if this is set the current frame displayed in the main image window is shown as a vertical red line in the profile window This marker is only drawn if the profile axis is the unseen axis Auto Title if enabled the axis labelling title is automatically generated Whenever this is disabled the string specified by Axis Labelling Title is used instead Show Beam if enabled the dataset headers are searched for BPA BMAJ and BMIN FITS style keywords If these keywords are present a representation of the telescope beam is overlaid on the imag
147. ts are preceded by a character All of the commands names below are given in CAPS for readability but they could just as easily be lower case World coordinates here are decimal degrees of Right Ascension and Declination in accordance with the FITS standard HH HH H OH COORD W These are the attribute settings at startup time PA STANDARD If no annotation files loaded prior to this one COLOR GREEN have changed any attributes then these commands FONT hershey14 are reduntant Label the image near the top Use relative coordinates to fix the position regardless of image zoom COLOR WHITE TEXT R 0 1 0 9 THE ORION NEBULA Change font to something a little smaller for other labels FONT hershey12 Mark the four Trapezium stars with blue circles and connect them D 4 EXAMPLE ANNOTATION FILE 117 Use world coordinates for these markers and name label Since COORD is currently set to W specifying W coords in the argument lists of the objects below is not necessary Note W coords are in degrees for consistency with coordinate information in the FITS image header even though RA is labeled in hours by Karma Note also the TEXT string is continued onto another line The leading space is ignored but a trailing space after Trap would not be The commas in the CLINES command string are not necessary but make it easier for a human to read HH HH HOH H OH FH OF COLOR BLUE DOT 83 81613 5 38706
148. u will then see zero or more values after the parameter name For actions you will not see any values Finally you will see a 4 character usually followed by a short description of the parameter or action To specify a parameter or action type in its name followed by any argu ments required You can type shorter non ambiguous name if you wish You can only specify a single parameter or action on one line 95 96 CHAPTER 12 COMMAND LINE TOOLS 12 2 1 Actions Actions are things that happen when you type their name Some actions require no further arguments such as the exit action while others may require any number of arguments The brief description for the action should indicate what arguments are needed 12 2 2 Scalar Parameters These are parameters which take as argument a single scalar value or string After typing in the name of the parameter followed by a space you must type in the value or string Strings do not need to be enclosed in quotes unless they contain a space You may use either single or double quotes to enclose a string Naturally you must use the same type of quote character to close the string as you used to open it To encase a quote character inside a string just type it if you used the other type of quote character to enclose the string or type the quote character twice if the string is enclosed by the same type of quote Scalar values may be integer or floating point and may be real or complex
149. ue is still visible This makes the data appear more transparent It also means that this shader produces images that are 24 bit deep one byte for every colour and to change colours on the display you will have to manipulate the substances It also means that to play movies made with this shader you may want to convert the images to 8 bit using the conv24to8 programme section A practical disadvantage of this shader is that it is difficult to set the colours and the opacities of the substances exactly as you want there are many many parameters to set It takes quite some time to produce reasonable images with this shader You can save time by only defining 5 2 STARTING UP THE VOLUME RENDERING TOOL 67 a small number of substances say the default eight but then the repre sentation of the data is somewhat schematic If you define the maximum number of substances you can set up a substance table with a smoother colour transition but of course it takes more time for you to set up the table A strong advantage of this shader is it can be useful to display both absorption and emission in a datacube e Hot Gas Mono This shader also uses opacities but the control is much simpler This shader takes o x v 5 2 where o is again the opacity v the value of the voxel By setting you can control which parts of the data are visible opaque A small value of a makes low level emission already quite opaque while a large value will
150. umns to the left of the data entry names Different data types will show a different number of columns and the character codes have different meanings as well However following convention is followed equals sign this dataset has been selected for replacement section 3 3 with data attribute copying tilde sign this dataset has been selected for replacement section 3 3 without attribute copying uppercase this is an exclusive option only one entry may have this option set per blink state lowercase non inclusive option Any number of entries may have this option set Below the list of data more detailed information and configuration settings are shown The appearance depends on the kind of data being shown The configuration controls for the different data types are described below 48CHAPTER 3 VIEWING AND COMPARING MULTIPLE IMAGES AND CUBES Data Replacement As discussed above a dataset may be selected for replacement When a new dataset is loaded the list of already loaded datasets is scanned for a dataset which has been selected for replacement and was loaded from the same data source A typical data source is a file browser but may also include network connections When a dataset is replaced with a new one either all the old settings such as intensity range contour levels etc are retained or none of the settings are retained depending on which replacement mode was selected If more than one dataset is selected
151. ut only applies to that particular object Some objects allow multiple coordinate type arguments in this case each coordinate type given applies only to vertices following it in the argument list until superceded by another coordinate type specification See below for descriptions of the different coordinate types The initial setting of COORD is W e PA lt position angle convention STANDARD or SKY gt Sets the position angle convention for subsequent objects Unlike coordi nate type position angle convention cannot be specified inside an object command but must be set with this attribute command See below for descriptions of the two position angle conventions The initial setting of PA is STANDARD D 3 3 Object Commands Object commands draw specific objects over a displayed image These include text strings as well as figures made up of dots and lines The locations of drawn objects can be specified in three types of coordi nates world W relative R and pixel P World coordinates are those in dicated by axis labeling e g right ascension and declination or velocity in a position velocity map but be careful about coordinate units since anno tations use the units specified by the image header e g the FITS standard default units for right ascension are degrees not hours and for velocity are m s not km s Relative coordinates range from 0 to 1 inside region bounded by the image axes increasing from the lower le
152. utton Ex port in the visualisation tools and select PostScript This will display the lt Postscript gt widget This widget provides controls for generating PostScript hardcopy It supports different orientations and trays and allows you to queue directly to a printer The following controls are available e close this will close the window e save ps save a PostScript file 2 5 EXPORTING DATA 21 e save eps save an Encapsulated PostScript file e print queue directly to a printer e Tray Menu you can choose between default paper or transparency trays e Size Menu you can choose between a variety of media sizes A3 A4 A5 letter and so on The A4 letter size will fit on both A4 and letter size media If you select user defined then you can define the bounding box using the offset and size controls described below The default is taken from the PAPER_SIZE environment variable e Keep Aspect if enabled screen pixels will always be drawn square in the PostScript output e Orientation Menu you can choose between portrait and landscape ori entation or you can let the choice be automatic so that a best fit is made e g a display window that is much wider than it is high would be dis played in landscape mode on A4 size media e hoffset controls the horizontal offset of the output e voffset controls the vertical offset of the output e hsize controls the horizontal size of the output e vsize controls the vertical siz
153. want The saturation of the colour can be changed by moving the mouse around while you drag with the right button To change the opacity put the mouse on the substance and drag with the middle mouse button vertically To change the value ranges for the substances drag left the mouse in the upper part of the window In the upper part there are a few symbols that help to orient yourself The is the setting for the value ranges the O the setting for the substance you have selected and the horizontal line on the left of the window is the saturation of that substance With this window one is only able to change the value ranges in a way similar to a normal colour table control To use the settings you have made click left on Apply and a new image will be calculated The button Save brings up a window to save substances To load a substance table click on Load and select your file 5 8 Hot Gas Mono control panel See Figure 5 3 for a screen snapshot The control window for this allows you to set the opacity law of the Hot Gas Mono section 5 1 1 shader as well as the exponent for the intensity transformation One can also set the range of voxel values that are set to blank The following controls are available e Close this will close the window e Compute this will render the cube e Intensity Alpha this controls the value of 8 in equation 5 3 e Opacity Alpha this controls the value of a in equation 5 2 e Blank Start Slider this
154. y for quick comparison of different regions The fancy colour front cover of this document contains a screen snapshot of this programme 6 1 How to use it You need a cube naturally and a sky map image The image is usually taken to be the total intensity map of the cube but it could just as easily be the velocity field or an optical image As long as the cube and the image have a proper co ordinate system for RA and DEC you re in business To load the cube press the Cubes button in the left window and select a cube file Press the Images button to load the image file The image is displayed in the left window If you then click middle in the image and drag the mouse still keeping the button pressed you will see the position velicity slice in the right window being updated before your very eyes Back in the image window a line is drawn over the image to show where the slice is The horizontal axis in the right window shows position and the vertical axis shows velocity If the machine you are running this on is rather old and slow you can disable Auto Update and the position velocity image will only be computed once you release the middle mouse button The cursor position in RA and DEC is printed to the command shell window whenever the middle button is pressed or released This tells you the endpoints of the slice Also the centre of the slice and it s 81 82 CHAPTER 6 KPVSLICE INTERACTIVE POSITION VELOCITY SLICING position
155. y images so that all images are coded as intensity but in a different colour This you can use to overlay two or three different channels of a data cube and inspect subtle differences The lt kvis gt chapter 3 programme can be used to do this Chapter 12 Command line Tools Karma has a number of command line tools to manipulate data files There are tools for converting from foreign data formats to Karma format tools to convert from Karma to foreign formats as well as tools to manipulate data files in various ways i e regridding 12 1 Common Interface All of the command line tools use the lt panel gt package in the Karma library to implement a common feel This package defines a set of panel items which are simply parameters you can set or actions you can take The tools may be started in interactive mode by giving no arguments to the tool or they may be started in batch mode giving a set of arguments to the tool Once the tool has completed processing it exits 12 2 Interactive Mode To start a tool in interactive mode just type in its name at the shell prompt You should then see a prompt with the name of the tool followed by a gt In this discussion it is assumed that you will press the return key after typing something in Probably the first thing you will want to do is press to see a list of parameters and actions On the left hand side you will see all the parameter and action names For parameters yo
156. ystem is written in the header using the standard CTYPEn CRVALn CDELTn CRPIXn notation The coordinate system is computed under the assumption that the image of the sky has been projected by the telescope optics in a particular way The projection geometry is assumed to be the Rectangular projection denoted by the standard projection name ARC which is used by Schmidt telescopes This may not be always be the appropriate projection to use but the errors should only become noticeable for fields larger than 0 5 degree 9 1 Centring Algorithm The following steps are taken by the picking algorithm e find the brightest pixel within the circle cursor capture region e proceed from that point by walking up the hill searching for a neigh bouring pixel which is of a greater value It continues searching until it finds a pixel with no neighbours with a greater value i e a local maxi mum This is usually the peak pixel e find the half intensity size of the star To do this it needs an estimate of the background value The background is computed by finding the median value inside the background annulus e computes the centroid position by using a two dimensional weighted mean algorithm The centroid is computed out to the half intensity size Note that the centring algorithm will not work with heavily clipped images This is because there is no real peak to work with rather there is only a plateau In these cases the

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