The BIAS system on the SCHMIDT telescope in Brorfelde 23 aug. 1995, Jens Klougart, CUO, Brorfelde Denmark Introduction The BIAS ( == Brorfelde Image Acquisition System ) is a software program running on a PC under the unix-like operating system LINUX. The intension of the software is to give the observer easy control over the CCD camera on the telescope, thus enabling him to make observations effectively, study the data on-line and save his data for later processing. The interaction between the hardware interfacing to the camera electronics and the user interface is performed by this program. This paper describes the user interface and operation of the camera, and the contains the nessesary "howto's" to operate the computer. The Brorfelde Schmidt Camera The camera is a prototype of the Brorfelde camera used on the Danish 1.54 m on La Silla, and on the Nordic Optical Telescope on La Palme (NOT). The PC The PC running Linux and BIAS is a 50 MHz 486, with 20 MByte ram and 2 harddisks of 200 MByte and 500 Mbyte. The first disk (200 Mbyte) contains a MSDOS partition, with a program 'loadlin' to start linux. The second harddisk hold the Linux system, and has room for a number of images aquired by the camera. Booting the PC with Linux The Linux operating system is booted on the PC using a boot program under MSDOS called 'loadlin'. A menu after booting allows you to select either starting linux or MSDOS. When booting linux, a number of messages, mostly for the system administrator, are shown. A login screen appears after a while ( something like this ): Linux n.n.n login: Login as user 'schmidt', with the passwd 'xxxxxx' ( ask the astronomer in charge. At the prompt type: mickey:~$ startx The PC might have the X-windows system started automatically, in that case you get a login window, login as above, but do not issue the 'startx' command. The X windows system is now started. Use the mouse left button, click and hold down in the blue background. Within the pulldown menu choose the 'BIAS' item and release the button. This menu is called the 'ROOT MENU'. BIAS will start within a few seconds, giving you a status window, an image display window, which is the 'Smithsonian Astrophysical Observatory image utility', and a control window where commands are given. Each part will be described in details below. Type 'quit' or 'exit' at the 'BIAS>' promt to leave the BIAS system. Linux shutdown As this is a unix like operating system with an active filesystem, it is important that power is never turned off while the system is running. !! NEVER TURN OFF POWER ON A RUNNING LINUX SYSTEM. To close down from the X-windows system use the following sequence: 1: In case you used 'startx': Choose from the 'ROOT MENU' 'Exit Fvwm' + 'Yes, Really Quit' your non-X login will reappear: mickey:~$ Hold down at the same time: CTRL + ALT + DEL and wait some seconds untill the screen is stable and 'done' is written. The Linux system is now shut down in an orderly fashion. 2: In case you had an X-windows login screen: Hold down at the same time: CTRL + ALT + F1 wait for a stable black screen with a lot of text, then Hold down at the same time: CTRL + ALT + DEL and wait some seconds untill the screen is stable and 'done' is written. The X-windows system This X-windows system uses the fvwm window manager. This gives you a desktop with 6 virtual workspaces, which can be selectes by clicking the left mouse button in the desired workspace in the small window top left. By holding the left mouse button down in the workspace background you get a menu of programs: xterm, xclock, xload ..., with some submenues. All this works in a Motif-window like manner, and as a unix user you should be familiar with most options. In an xterm windows, the standard 'vi' editor is available. In the menu ( root menu ) go to the 'Exit Fvwm' with left button down, release it, and click on the 'Yes, Really Quit' button to logout your session on the Linux machine. IMPORTANT: PLEASE DO NOT KILL WINDOWS, BY CLICKING DESTROY or DELETE FROM THE MENU IN THE UPPER LEFT CORNER OF THE WINDOW. IT LEAVES A LOT OF ZOOMBIE (inactive) PROCESSES ON THE MACHINE. BIAS Starting In an xterm window, type 'startb' ( for start bias ), or use the root menu item 'BIAS'. ( An xterm window is started by selecting 'Xterm (8x16 Font)' in the root menu ). The bias system will start building up a screen of 3 windows: (this will take some seconds as the hardware is checked). SaoImage This window may be familiar to some users. Images from the CCD or from a file on the harddisk may be viewed in SaoImage. A number of pushbuttons with various function can be used for controlling the displayed image. Note that pixel ( 1,1 ) is in the lower left corner. When the mouse cursor is in the image, the intensity shown ( besides the x,y value ) is scaled back to almost true values from the given highcut and lowcut. There is a manual page for saoimage ( use 'man saoimage' ). This saoimage is controlled by the 'BIAS' program. Other SaoImage's can be started from the command line or the root menu. Status window The status window gives you information about your setup and the condition of the CCD. The screen looks something like this: *************************************************************** *Fri Jan 27 20:58:32 1995 BROR 2K3EB C1 W11/3 * *=============================================================* * * * TOT IM BEG BIN CCD: IDLE * *X 2060 2060 1 1 T.total: 10.0 Mult: 10 * *Y 2060 2060 1 1 * *============================================================ * *CCDtemp: -94.9 C AMPL: A * *REFtemp: -95.0 C GAIN: hi_gain * *AMBtemp: 37.5 C * *============================================================ * *IMPATH: /home/schmidt 125 Mb * *REM_IMPATH: /disk4/images schmidt * *============================================================ * *NEXT_FILE: eh220015 AUTOSAVE:OFF REM_AUTOSAVE: ON * *============================================================ * *FILE: HIGHCUT: 800 LOWCUT: 100 ZOOM:0.50 * *************************************************************** 1. line is date, time and a CCD controller identifier. TOTX and TOTY : Total field size in x and y ( physical dimensions) IMX and IMY : Actual field size chosen. BEGX and BEGY : Starting pixel x and y values. BINX and BINY : Binning selected. The 'CCD IDLE' s the status of the CCD controller, it can be IDLE, INTEGRATING, READOUT or PENDING. PENDING is waiting for the bias program to readout the image. When IDLE the default integration time and multiple int. count is shown. When INTEGRATING the exposure time left is shown, and if multiple integrations are in progress the multip. count and mult. total is shown. During READOUT the linenumber being read out is shown. The next part shows the CCD temperature and its reference temperature, they should match fairly good, if the CCD temperature rises. The ambient temperature ( ?? ). The ' Ampl ' section on the Schmidt ccd is fixed to 'A'. Under this the gain setting (high or low) is shown. The IMPATH is the path where image files and log files are stored. The default value at startup is the current directory. Along with this the remaining diskspace is shown in megabytes. The REM_IMPATH is the path on a remote machine, where images are stored. The 'NEXT_FILE' is the name og the next file being stored, the 'FILE' is the latest stored file, or the file shown in the SaoImage window. If files are being saved automatically after a readout, 'AUTOSAVE' is ON. HIGHCUT, LOWCUT and ZOOM are the values used in displaying the image. The ZOOM value is NOT updated when using the zoom in SaoImage. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx THE .biasrc FILE In the startup directory a file named '.biasrc' controls the initial setting of a number of options. The structure of this file is: KEYWORD VALUE An example is shown beneath: ----------------------------------------------------- STARTUP OFF # # This filename is dynamically updated DO NOT CHANGE # inless you know what you are doing # Omit this to use the default filenaming # FILENAME schm0785 # AMPL A # No mpp mode on the schmidt MPPMODE ON GAINMODE HIGH # AUTOSHOW ON # AUTOSAVE OFF LOCAL_PATH /home/schmidt/data # REMOTE_SAVE ON REMOTE_SYSTEM bro730 REMOTE_PATH /disk4/images/schmidt MIDAS_BATCH ON # GET_INFO ON MAGZERO 30 ----------------------------------------------------- Keywords are: STARTUP ON | OFF Show a BIAS news file at startup. The file is /usr/local/bin/bias/biasnews AUTOSAVE ON | OFF Save the images on the local disk. LOCAL_PATH path The directory to store images in. REMOTE_SAVE ON | OFF Save the images on the REMOTE_SYSTEM REMOTE_SYSTEM machine_name Set the logical name of the workstation connected to this system, and used for storage and possibly running image processing systems. REMOTE_PATH path The directory on the remote machine to store images in. Be sure to have permissions there to write. The user ( here user 'dfosc' ) must have the same UID on this and the remote machine, and have an .rhost file allowing remote shell login without password. GAINMODE HIGH | LOW Select the gain mode AUTOSHOW ON | OFF Show images as soon as they are read out from the CCD. GET_INFO ON | OFF Ask the REMOTE_SYSTEM about additional FITS header information. Uses a shell script called /usr/local/bin/bias/getinfo. This will be used for TCS and other data. F1 filter-1-name Give filters real names. F2 filter-2-name F3 filter-3-name F4 filter-4-name F5 filter-5-name F6 filter-6-name MAGZERO nn.n The magnitude zero value for aperture photometry in 'imexamine'. EXTRA_PHOT ON | OFF When doing aperture photometry, calculate also the ellipticity and position angle of the object. In the directory /usr/local/bin/bias, there is a setup file called 'ccdrc', which contains system wide configuration. An example is shown here: # MAXX 2100 MAXY 2100 # SAOXSIZE 512 SAOYSIZE 512 # # No of samples for making high/low cut SAMPLES 600 # Contrast when making high/low cut CONTRAST 0.30 # SHUTTER_DELAY 0.0 # PCBOARD_BASE 0x500 MEMSIZE 0x1000000 # PIXEL_SCALE 0.175 MAXX, MAXY tells the BIAS program how much room to reserve for images in Ram. This must at least be as large as the largest image, which can be aquired. SAOXSIZE, SAOYSIZE tells the BIAS program the size of the display window SaoImage is started with. PCBOARD_BASE, MEMSIZE tells the BIAS program the I/O address and size of Ram on the interface board. SAMPLES, CONTRAST is used to calculate high- and lowcut for displaying images. SHUTTER_DELAY is the shutter-dealy. PIXEL_SCALE is the size in arcsec of a pixel. Used when calculating FWHM. DIRECTORIES AND FILES The default 'impath' directory is the directory from which the program is started, or your home directory if BIAS is started from the root-menu. When changing the 'impath', your permissions are checked, and you are not allowed to change to a directory where you cannot write. The automatic filenaming mechanism gives you a default filename with the following convension: d j 2 3 0 0 2 5 | | | | | | | | | | | | ----------------- Automatic incremented number | | | | | | ----------------------- Day of the month. | | | -------------------------- Month, a = jan, b = feb, ... | ----------------------------- Year, 1991 = a, 1992 = b, ... These filenames can be overridden, if your filename has a letter in the 1. position, and ends with 4 digits. If some filenames exists when the program is storing, they are not overwritten, but the next free number is found. ( might be confusing if you delete some files, and start over again ). The default filenames are MS-DOS compatible. A logfile called 'logdj23.001' is created with all the input/output on the BIAS screen. The naming cannot be changed. Saving your files As disk space is limited, it might be neccesary to send your files to another computers hard disk during the night. This can be done with FTP to the HP735 or with NFS. A good way to get more diskspace on this machine is to use standard UNIX compress, or GNU's gzip. Files will decrease with 25% - 50%, and are fully recoverable, also on other Unix machines. FITS HEADER The FITS header at the start of the files contains most information about the exposure, view a file with the 'less filename' utility, or with the 'head filename' command from inside BIAS. BIAS COMMANDS At the 'BIAS>' prompt commands are given to the system, with optional data entered either directly on the command line, or bu just entering the command and 'enter'. You will be prompted for data, with the latest value as the default. It is only neccesary to input the number of characters for the system to recognize the command. ( except for 'quit' and 'exit'). Backspace deletes the last character. Arrows and other special keys does not work, they even produce invisible characters, which sometimes gives the message 'Command not found' even if the input looks OK. Try again. The mouse can 'cut' and 'paste' your lines. A few commands does not prompt you for data as they use default values if no parameters are used. These are: exp, mexp, dark, mdark, focus. help This start an xterminal window, which runs the data viewing utility 'less'. Use PgUp , PgDwn and arrow keys to move around. '/' can be used to search for text. Use 'q' to quit the window. If 'BIAS' is stopped, the window remains, please stop it using 'q'. The mouse cursor must be in the window for any keys to work. quit Exit BIAS. alias: 'exit' All windows, except help and head windows are stopped. exp [ T [ F ] ] Start a normal exposure with optional integration time T (in seconds) and filter number F. If no F is specified, the default filter number set with the 'filter' command is used. If you specify a filternumber, you must also have given the integration time. If no integration time, T, is given, the default T given with the 'tint' command is used. mexp [ T [ M [ F ] ] ] Start M integrations of each T seconds using filter F. If no F is specified, the default filter number set with the 'filter' command is used. If you specify a filternumber, you must also have given the number of multiple integrations and integration time time. And so forth. Parameters left out will use the defaults set with 'tint', 'mult' and 'filter'. dark [ T [ F ] ] This is for dark exposures. Works as 'exp' with the shutter closed. mdark [ T [ M [ F ] ] ] This is for multiple dark exposures. Works as 'mexp' with the shutter closed. abort Stop an ongoing integration. The data are NOT readout, and can at this time unfortunately not be recovered. Does not work during readout. readout Readout the CCD now and store the image. addtime nn Add 'nn' seconds to the integration time. Negative numbers are allowed. If the resulting integration time is negative the CCD is readout. save Save the image stored in the computer memory and shown in saoImage. Usefull if 'autosave' has been off. head [name] View a file. Starts an xterm window with 'less' on the filename. Works like 'help'. tint [ T ] Set the default integration time in seconds. mult [ M ] Set the default number of multiple integrations. filter [ F ] Set the default filter number. alias 'filt'. xbeg [ X ] Set the xvalue of the first pixel to be read-out from the CCD. The values start with 1. If xbeg + xsize is larger than the CCD's total x-width, xsize is reduced. Default = 1. ybeg [ Y ] As 'xbeg' in the y direction ( lines ). Default = 1. xsize [ XZ ] Set the x size of the image to read-out. Default = 1124. ysize [ YZ ] Set the y size of the image to read-out. Default = 1024. resetxy Reset the size, beg and binning values to the default. gainl Set the CCD preamplifier gain to low. gainh Set the CCD preamplifier gain to high. autosave+ Store the CCD images in the specified 'impath'. When files are stored, there is a check for the remaining diskspace. A warning is given at 10 Mbyte remaining, with 2 Mbyte left the file is not saved. autosave- Do not store images readout. This is often used for a quick look. A warning is given at the start of every integration if autosave is off. Images can manually be stored with 'save'. remsave+ Turn on saving on remote disk. The remote workstation and path must be defined in '.biasrc'. remsave- Turn off saving on remote machine. impath [path] Set the directory ( or path ) where images and logfiles are stored. Default is the startup directory. The specified path is checked for write permissions, and access is denied if the permissions are inadequate. filename [name] Specify the next filename to use. The 1. character must be a letter, the length <= 8 and the last 4 characters must be digits. The last 4 digits are incremented every time an imagefile is stored with a check for the existance of the new filename. When specifying the 4 last digits, any number can be specified as the starting value. autoshow+ Show images in SaoImage. autoshow- Do not show images in SaoImage. ls Unix list 'ls' in the impath directory. ll Unix long list 'ls -l' in the impath directory. imex Start a pseudo Iraf imexamine in the SaoImage window. The plot utility 'gnuplot' is used for graphical output. At this time only a few commands are implemented: a: aperture photometry. Calculates only center, sky and flux. Also FWHM, ellipticity and position angle. z: Print the values of the pixels in a 10x10 box around the cursor. m: Calculate statistics in the aperture. c: Plot the mouse position column across the entire image. l: Plot the mouse position line across the entire image. s: Make a surface plot from a box specified by the command 'imexbox'. e: Make a contour plot from a box specified by the command 'imexbox'. v: Vector plot. The 1. position is where the mouse pointer was when 'v' was typed, 2. position when the next 'v' is typed. u: Vector plot symmetrically around 1. position. 2. position when a second 'u' is typed. = Print on the postscript printer the last plot. The plot screen disappears for a few seconds. q: quit imex, and return to BIAS. Please note that when an integration has just finished you are sent back to the BIAS prompt. imexbox [IB] Specify the box size used for the imex commands s and e. aperture nn The aperture size in pixels. ( adjusted to an uneven number ). disp [name] Display a FITS image in SaoImage from the harddisk. seth [ H ] Set highcut and show the image in SaoImage. setl [ L ] Set lowcut and show the image in SaoImage. z+ Zoom in and out. This zoom works independantly from the z- SaoImage zoom, this means that the zoom shown in the status display might be wrong. z+ and z- has the advantage the zooms of other factors than 2 can be used. object [ Obj ] Specify a text to be put into the FITS header with the keyword OBJECT. The object text is left unchanged until next 'object' command. Maximum no. of characters is 20. comment [text] Comments to put into the FITS header. Maximum 40 characters. The text is cleared after it is used in the header. logon Start a log of BIAS command screen input / output. By default a log file is created. logoff Stop the logging. The 'help' command output BIAS main help page, Using 'less': Use PgUp / PgDn , Cursor keys and Arrows, 'q' to QUIT. /' to search. help Get this screen. quit Exit BIAS. ( alias 'exit' ). exp [ttt.t [i]] Normal expose for 'ttt.t' sec using filter 'filtno'i. mexp [ttt[i[nnn]] nnn multiple exposures of time ttt using filter i. dark [ttt] Dark exposure for 'ttt' sec. mdark [ttt[nnn]] nnn multiple dark exposures of time ttt. abort Stop an ongoing integration or readout. readout Stops an integration and reads the ccd. addt ttt Adds ttt seconds to an integration. 'ttt' can be negative, if the resulting remaining integration time is < 0, the integration is stopped and the ccd is read. save Save the image in next filename. tint [ ttt.t ] set default integration time in sec. mult [ nnn ] set default no. of multiple integrations. filter [ filtno ] set default filter no. xbeg [ nnn ] set start x value of CCD readout ybeg [ nnn ] set start y value of CCD readout. xsize [ nnn ] set x size in true pixel value. ysize [ nnn ] set y size in true pixel value. resetxy reset the CCD geometry values to defaults. gainh, gainl Set gain high or low. autosave+ Turn on automatic saving of images on local disk. autosave- Turn off automatic saving of images on local disk. remsave+ Turn on saving on remote disk. The remote work station and path must be defined in '.biasrc'. remsave- Turn off saving on remote machine impath [ path ] Change the default image directory. Use with care. filename [ filen ] specify the output file names, the length <= 8 char, 1. char must be a letter, last 4 must be numbers. ( Be carefull about this, as the last filename may automatically be updated in '.biasrc'. autoshow+ Show images in SaoImage. autoshow- Do not show images in SaoImage. ls Unix list 'ls' command in impath directory. ll Unix list 'ls -l' command in impath directory. imex Start an Iraf-like imex, valid 'imex' commands are: q: back to BIAS commands. z: print 10x10 box values a: aperture photometry m: show statistics from data in 'imexbox' c: plot total column l: plot total line s: surface plot e: contour plot v-v : vector plot from 'v' is hit till 'v'. u-u : vector plot symmetrically around first 'u'. X : plot sum of all lines. Y : plot sum of all colums. = : print the plot on the laserprinter. imexbox [ nn ] Define the 'aperture' box for surface- and contour plots. aperture nn Set the size of the aperture used in 'imexamine'. The size is adjusted to an uneven value. magzero zz.z Set the magnitude offset for magnitude calculation in the 'imexamine' 'a' function. The value can be fixed at startup in the .biasrc file. disp [filename] Display an image from disk in SaoImage. ( alias 'ld' ) seth [ nnn ] Set highcut for displayed image. ( alias 'z2' ) setl [ nnn ] Set lowcut for displayed image. ( alias 'z1' ) z+, z- Zoom in or out, this works independant of SaoImage. If you zoom with SaoImage buttons, the displayed value in the status window is NOT updated. object text Specify an object name for the FITS header. Max. 20 char. The text is saved untill changed. comment text Comments to put in FITS header. Max. 40 char. The text is cleared after storing in the FITS header. head View the current FITS file header. Use 'q' to quit. logon Start a log of your command screen. Default on. logoff Stop the log. !xxxxxx Execute the Unix command 'xxxxxx'. saoimage Restart saoimage. Miscellaneous commands: sleep nn Wait for nn seconds. ( for use in batch run ). rbias Re-read the '.biasrc'. stat Ask if camera is Busy or Ready. Answers 'B' or 'R'. run filename Run a batch with commands any command ( except this ). xrun command boxsize Goes into SaoImage, when Return or Space is hit, the box is saved in a textfile 'command.data'. The command is then run in an xterm window.