ALFOSC Sequencer Command Documentation

Instrument	: ALFOSC
Observing Mode	: ANY IMA SPEC POL
Command Type	: ANY DATA DET DISP INST TEL
Usage	: BASIC GENERAL STAFF
Description	: SHORT LONG

System	Command	Arguments	Description	Type
alfosc	abort	[-d]	Aborts an ongoing exposure.	DET
alfosc	acquisition	[-c] [-q] [-nofo] <slit> <tt>	Script for ALFOSC-spectroscopy target acquisition for slit <slit> using exposure time <tt>. If optional flag -c is used, a check image of the star on the slit is made. If optional flag -q is used, the user is queried for another iteration. The -nofo flag should be used if no automatic focus-offset should be set.	TEL
alfosc	addtime	[-d] <nn>	Adds <nn> seconds to an ongoing exposure (<nn> can be negative).	DET
alfosc	alfosc-calibs	[-e] [-skip] <date-string>	Script to do biases and spectral flats and arcs for all setups and windows used in a particular night. Per setup, takes 11 biases, 5 spectral flats, and 1 arc for each arc lamp. The date-string argument is expected like 'ALwb13'	DATA
alfosc	allopen	[-e]	Moves all ALFOSC/FASU optical wheels to the OPEN position.	INST
alfosc	ampl	[-d] <x>	Sets the active amplifier to <x>, where <x> can be A, B, C, D, AB, BC, AD, CD or DEFAULT. DEFAULT is amplifier D	DET
alfosc	aperture	[-d] [id] [name] [pos] [ready] [step][orient] <n>	Moves aperture wheel to slot number <n>. [id] returns the NOT ID of the element in the light path. [name] returns the name of the element in the light path. [pos] eturns the position [0-7] of the element in the light path. [ready] returns '0' if the element is moving, '1' if it is ready. [step] returns the step position [0-320000] of the element in the light path. [orient] returns the optical orientation of the element in the light path.	INST
alfosc	autoshow_off	[-d]	Turns off the automatic image display while reading out. If a DS9 is running it will be terminated.	DISP
alfosc	autoshow_on	[-d]	Turns on the automatic image display while reading out. If no DS9 is running one will automatically be started.	DISP
alfosc	bin	[-d] <n>	Sets the binning factor in both X and Y directions to <n>.	DET
alfosc	calibexp	[-e] [-f] [-n <nn>] [-o <ObjName>] [-lmi] <lampID> <tt>	Sets ALFOSC calibration items up for a calibration spectrum with lamp <lampID>, take <nn> calibration images of exposure time <tt>, switch off lamps and, if not -lmi is given, take out mirror. With <lampID>=He/Ne/HeNe/ThAr/Halogen .	DET
alfosc	callamptimes	[-s ] [-xbin N] [-ybin M] <lampID> <grism>	Returns the exposure time needed for calibration exposures, based on lamp and grism choice. The lampID should be one of He/Ne/HeNe/ThAr/Halogen. Slit width [-s] and binning [-xbin][-ybin] can be specified optionally.	INST
alfosc	clearobject	[-d]	Clears the value of the FITS keyword OBJECT.	DATA
alfosc	clearobserver	[-d]	Clears the value of the FITS keyword OBSERVER.	DATA
alfosc	comment	[-d] <text>	Sets the FITS keyword COMMENT to <text>. Will be cleared after each image. FEB 13, 2013: This command is currently unavailable.	DATA
alfosc	dark	[-d] [-t] [-f] [-n]<tt>	Makes a dark exposure of <tt> seconds. If <tt> is set to zero a BIAS exposure is made. If the exposure time is larger then 60 seconds, automatic remnant removal is done before the exposure starts. If the option [-f] (fast mode) is used, the prompt will be returned when the exposure time is over and before the readout begins. If the option [-n] is used, there will be no automatic remnant removal.	DET
alfosc	display	[<file>]	Loads the image <file> into the ALFOSC DS9 display. If no file is specified, the last image obtained will be loaded.	DISP
alfosc	display-start		Starts an empty ALFOSC DS9 display.	DISP
alfosc	ds9-for-mos		Start a dedicated DS9 display that is used for MOS tweaking	DISP
alfosc	expose	[-d] [-t] [-f] [-n]<tt>	Makes an exposure of <tt> seconds. Remnant removal is made before the exposure starts, if the exposure time is larger then 60 seconds. If the option [-n] is used, no remnant removal is done. If the option [-f] (fast mode) is used, the prompt will be returned when the exposure time is over and before the readout begins. If [-f] is used, make sure that "alfosc.wait-camera-state idle"-command is given before any "alfosc_camera_commands". If the exposure time is larger than 300 seconds, the time left until the rotator reaches its limit will be checked. If there is not time enough to complete the exposure, an error will be generated and the exposure will not start.	DET
alfosc	fasua	[-d] [id] [name] [pos] [ready] <n>	Moves FASU wheel A to position <n>. [id] returns the NOT ID of the element in the light path. [name] returns the name of the element in the light path. [pos] returns the position [0-6] of the element in the light path. [ready] returns '0' if the element is moving, '1' if it is ready.	INST
alfosc	fasub	[-d] [id] [name] [pos] [ready] <n>	Moves FASU wheel B to position <n>. [id] returns the NOT ID of the element in the light path. [name] returns the name of the element in the light path. [pos] returns the position [0-6] of the element in the light path. [ready] returns '0' if the element is moving, '1' if it is ready.	INST
alfosc	filename	[-d] <nn>	Sets the default file name to <nn> (four characters).	DATA
alfosc	filenamestd	[-d]	Sets the filename back to the default file name.	DATA
alfosc	focus	[-e] [-n <N>] [-nodefault] [-t <nn>] [-a <mode>][-filter]	Focuses the telescope. [-n <N>] makes <N> loops. [-t <nn>] sets exposure time to <nn> . [-nodefault] starts from current focus. [-a <mode>] acquisition using <mode>.	TEL
alfosc	focus-offset	[-e] [-d <nn>]	Applies focus offset for optical elements in the light beam. If no offset is known a value of 0 will be assumed. Use [-d] flag to defocus the telescope with <nn> units.	TEL
alfosc	focuspyr		Lets the user interactively examine a Focus Pyramid image to determine the focus offset required to bring the telescope in focus.	DATA
alfosc	focuspyr-auto	[<file>]	Computes the required telescope offset from the Focus Pyramid image <file>. If no file is given, the last image in the data directory will be used.	DATA
alfosc	focuspyr-setup	[-e] [-filter]	Sets ALFOSC up for focusing. If optional argument -filter is used, the filter wheels will be left as they are.	INST
alfosc	focuswindow	[-e]	Sets the ALFOSC CCD to readout only a central 800x800 pixel unbinned window.	DET
alfosc	grism	[-d] [id] [name] [pos] [ready] [step][orient] <n>	Moves the grism wheel to position <n>. [id] returns the NOT ID of the element in the light path. [name] returns the name of the element in the light path. [pos] returns the position [0-6] of the element in the light path. [ready] returns '0' if the element is moving, '1' if it is ready. [step] returns the step position [0-320000] of the element in the light path. [orient] returns the optical orientation of the element in the light path.	INST
alfosc	hicut	<value>	Applies a minmax scaling to the loaded DS9 image and set the highcut to <value>.	DISP
alfosc	imexam		Initiates an IRAF imexam session on the loaded DS9 image.	DATA
alfosc	impath	[-d] <text>	Sets the path of the image saving to <text>.	DATA
alfosc	imtype	[-d] <text>	Sets the FITS keyword IMTYPE to <text>.	DATA
alfosc	killdisplay		Terminates all instances of the ALFOSC DS9 display.	DISP
alfosc	killimexam		Terminates all ALFOSC sequencer scripts related to imexam and the ALFOSC DS9 display.	DISP
alfosc	lamp	[-d] [position] <n> <m>	Turns on/off lamp number <n>, <m>=1 is turn on, <m>=0 is turn off. [position] returns a 4 bit pattern corresponding to the state of the 4 lamps.	INST
alfosc	locut	<value>	Applies a minmax scaling to the loaded DS9 image and set the lowcut to <value>.	DISP
alfosc	log-comment	"Comment in quotes" [file1 file2 ...]	Set a comment in the last image (or the specified ones, if any) using the LOGCOMME keyword	DATA
alfosc	mdark	[-t] [-n] [-f]<tt> <nn>	Makes <nn> dark exposures of <tt> seconds. If the [-t] flag is used, a simulated exposure is made. If the exposure time is larger then 60 seconds, automatic remnant removal is done before the exposure starts. If the option [-f] (fast mode) is used, the prompt will be returned when the exposure time is over and before the readout begins. If the option [-n] is used, there will be no automatic remnant removal.	DET
alfosc	mexpose	[-t] [-n] [-f]<tt> <nn> [<imtype>]	Makes <nn> exposures of <tt> seconds. Remnant removal is made before the exposure starts, if the exposure time is larger then 60 seconds. If the option [-n] is used, no remnant removal is done. If the option [-f] (fast mode) is used, the prompt will be returned when the exposure time is over and before the readout begins. If [-f] is used, make sure that "alfosc.wait-camera-state idle"-command is given before any "alfosc_camera_commands". If the exposure time is larger than 300 seconds, the time left until the rotator reaches its limit will be checked. If there is not time enough to complete the exposure, an error will be generated and the exposure will not start.	DET
alfosc	mirror	[-d] [pos] [ready] <n>	Moves calibration mirror in or out, <n>=1 for in and <n>=0 for out. [pos] returns the position of the calibration mirror. '1' is in, '0' is out. [ready] returns '0' if the element is moving, '1' if it is ready.	INST
alfosc	object	[-d] <text>	Sets the FITS keyword OBJECT to <text>.	DATA
alfosc	observer	[-d] <text>	Sets the FITS keyword OBSERVER to <text>.	DATA
alfosc	optics	[-e] [-s <slit>] [-g <grism>] [-f <filterID>] [-d <wheel>] [-m] [-a] [-p] [-o] [-h]	Searches ALFOSC and FASU wheels for optical elements. See the ALFOSC Sequencer Command and Script Reference for a description of the output and a list of all possible <flags>.	INST
alfosc	overlay	[yes|no]	Overlays the loaded DS9 image with seeing information and marks saturated objects.	DISP
alfosc	quickspec	[<file>]	Does a rough spectral extraction for file <file>, or for the last image written to disk if no file is specified, and displays the reduced spectrum interactively.	DATA
alfosc	quickspec-config	[<options>]	Sets parameters used in the quickspec script. See the ALFOSC Sequencer Command and Script Reference for a full list of possible options.	DATA
alfosc	readout	[-d]	Closes the shutter and readout the ccd. The exposure must first be put in the background. Does not work correctly when using a window in Y direction.	DET
alfosc	readspeed	[-d] <readout_speed>	Sets the CCD readout speed to <readout_speed> kpix/second. Valid values for <readout_speed> are 100, 200, 400 or 800.	DET
alfosc	remove_remnants		Remove remnants from the CCD	DET
alfosc	rempath	[-d] <nn>	Sets the remote saving path to <nn>.	DATA
alfosc	remsave_off	[-d]	Turns off remote saving.	DATA
alfosc	remsave_on	[-d]	Turns on remote saving.	DATA
alfosc	remsystem	[-d] <nn>	Sets the remote host computer to <nn>.	DATA
alfosc	reset-log		Resets the talker/obslog and sets it for alfosc	DATA
alfosc	resetxy	[-d]	Resets the ccd binning to 1, the X and Y size to maximum and the X and Y beginning to 1.	DET
alfosc	restore-uparm		Restores the uparm parameter files	DATA
alfosc	runselector	<date>	Select current program being observed from the sequencer command line.	DATA
alfosc	runselectorUIF	[alfosc|fies] <date>	Select current program being observed from a graphical user interface	DATA
alfosc	save	[-d]	Saves a read-out image to disk.	DATA
alfosc	setdisplay	[<Xserver>]	Sets the X Server on which the DS9 window will be displayed to <Xserver>. If none is specified, the X Server from which the script is executed will be used.	DISP
alfosc	single-mdark	[-t] <tt> <nn>	Makes <nn> dark exposures of <tt> seconds.	DET
alfosc	single-mexpose	[-t] <tt> <nn> [<imtype>]	Makes <nn> exposures of <tt> seconds.	DET
alfosc	slitoff	[slit=<nn> | xref=<x> yref=<y>]	Calculates the telescope offset needed for slit number <nn>, or for a slit with position (<x>, <y>).	TEL
alfosc	slitrot		Uses the currently loaded DS9 image to compute the TCS field rotation angle required to align two objects (interactively identified by the user) along a slit.	DATA
alfosc	snapshot	[store|restore]	Takes a snapshot of the current instrument and detector setup. [store] stores the snapshot. [restore] restores the latest snapshot.	INST
alfosc	tweakmos	[-e] <MASKfile.fits> <FIELDfile.fits>	Comparison of mask and field positions of the fiducial stars, obtained from subsequent images of the mask and the sky	DATA
alfosc	wait-camera-state	[idle|integrating|readout|not-integrating]	Routine to wait for a given ALFOSC CCD3 camera state.	INST
alfosc	wait_alfosc_ready	[-d]	Waits until all the following items are ready (not moving): FASU A and B, aperture, filter, grism, ALFOSC focus, FAPOL carriage and FAPOL polarizer.	INST
alfosc	wcs-align	[yes|no]	Display the loaded image using world coordinates such that North is up. Called with the [no] option, the image is aligned according to orientation on the detector.	DISP
alfosc	wheels	[-e] [-s <slit>] [-g <grism>] [-c <crossdisp>] [-f <filterID>] [-d <diffuserID>][-nowait] [-forceFASU]	Sets all 5 ALFOSC wheels to the given setup. Default is OPEN. If optional flag -nowait is used, the script exits while wheels are moving.	INST
alfosc	xbeg	[-d] <nn>	Sets the X beginning to <nn>.	DET
alfosc	xbin	[-d] <n>	Sets the binning factor in the X direction to <n>.	DET
alfosc	xsize	[-d] <nn>	Sets the X size to <nn>.	DET
alfosc	ybeg	[-d] <nn>	Sets the Y beginning to <nn>.	DET
alfosc	ybin	[-d] <nn>	Sets the binning factor in the Y direction to <n>.	DET
alfosc	ysize	[-d] <nn>	Sets the Y size to <nn>.	DET
alfosc	zscale		Sets the upper and lower limits of the loaded DS9 image based on the IRAF ZScale algorithm.	DISP

In scripts, the syntax alfosc.<command> should be used.
If a part of a command is written in <angle brackets>, this is an argument that should be replaced with a value.
If a part of a command is written in [square brackets], this is an optional argument or flag.
When available, the optional flag -d will write extended debugging information to the log.
When available, the optional flag -e will show the script on standard output instead of executing the commands.
When available, the optional flag -t will only make a simulated exposure. Useful for testing scripts.

Type definitions:
DATA: All commands related to handling/modifying data (editing fits-headers, post-processing etc.).
DET: Commands related to operations with the detector.
DISP: Commands related to displaying images on the instrument computer.
INST: Commands related to operations with the instrument.
TEL: Commands related to operations with the telescope.