-	NONIUS KappaCCD
	-	11 july 2001
	-	Server programs for the KappaCCD This describes the set of programs that control the KappaCCD system. It serves several purposes:  to control the system from a console close to the system. Although it is possible to do a full data collection from here it is mainly used for crystal alignment purposes and to have a quick first look at the diffraction quality.  to set-up and initialize the diffractometer hardware and its peripherals (such as remote addressable generators and crystal conditioning devices).  Some test procedures are included for the goniometer and the detector systems  to provide a consistent interface of the system to the outside world (over the network). The system including peripherals is controlled through simple character commands over a standard internet connection. All features present at the local console (excluding the setup of the hardware) are also available remote.           The server program suit consists of 4 communicating programs:  Server This is the main program. It starts up the other executables and monitors the network for incoming requests. All pheripherals are controlled from here. Bitmap utility Display the images from disk or while being collected by the server. Text utility  Displays (and saves) log messages from the server. Crystal viewing utility  Displays a video display of the crystal. Has its own network server to send the resulting images over the network (if so requested).

	Acquisition	The positioning & data collection utilities
	Acquire images	Collect X-ray images. Images can be saved to disk.
	Position goniometer	Position in Kappa- and Eulerian geometry. A number of predefined and user-defined positions are posiible
	Quick scan	Make a (few) quick picture(s) from a crystal. Will optionally set the generator to nominal power and move  the phi or Omega axis.
	Movie mode	'Real time' measurement of a portion of the image, with small readout time.
	Toggle shutter	Open/close the shutter.
	Crystal mounting positions	Crystal viewing utility. Has a set or predefined positions that facilitate the centering of the crystal
	Cancel operation	Abort present operation. The identical function is also available as a button on the main server window
	Grab mastership	Set/release mastership. The Server program can only use the goniometer , detector of any other peripheral is mastership is grabbed (set to "Local"). When mastership is released some other system can request control over the network. In that case mastership is set to "remote". The server program has the overall control; it can take mastership away from a remote system but the reverse is not possible; mastership can only be grabbed by a remote system if mastership is release by the server.  Setup-Network Set-up - "auto master set to network" gives the possibility to automatically grant mastership to a remote system when a request to connect is received(and the mastership setting is "none").

	Experiment	Set the experiment conditions (X-ray, cooling, goniohead, beamstop)
	X-ray generator	Set the X-ray generator. Only relevant if a remote controllable generator (590, 591, microsource) is used.
	Cryostream	Set the crystal cooling device. Only relevant if a remote controllable cryostat (Oxford 600 & 700 series) is used.
	Goniohead	Set the type or properties of the gonometerhead. Relevant for avoidance of collision situations and the calculation of collision situations
	Beam-stop	Set the beamstop size. Relevant for determining the obscured area and to avoid collision situations.

	Set-up	Set-up parameters for the system
	Network set-up	Sets some stuff for the network connection. Gives the possibility to disconnect a remote computer if the connection was cut improperly
	Goniometer set-up	Set-up menus for the goniometer. Also shows the goniometer errors (if any). Has an exercise utility for the goniometer.  Gives the possibility to let the goniometer find its zero position (again). During normal operations this should never be necessary. It is included because the goniometer set-up provides the possibility to never let the goniometer find it's zero position without being requested by the operator. This option is included for installations that require user-intervention in order to move certain axes.
	CCD set-up	Most of the CCD parameters are pre-defined in the KCCD.SET file. Standard use of binned mode and the ADC-readout frequency can be set. Note that the supplied set of calibration files was measured using the standard supplied settings. Also a set of ccd-tests can be  started from here.
	Text screen set-up	Selects whether the log utility should be started when the server is executed. Also sets the types of messages that should be logged. It is probably best to leave everything marked.
	Image display screen setup	Selects whether the image display utility should be started when the server is executed.
	Crystal conditioning setup	Sets the type of cryostat present and the ID of the serial port used. Supported are Oxford cryostream 600 and 700
	X-ray generator set-up	Type of generator used. Also sets the radiation & monochromator type. Supported are the Nonius 590, 591 and the microsource.
	Video microscope	Selects whether the microscope window should be started when the server is executed. Also sets properties for the microscope.
	Calibration	A set of calibration utilities for the goniometer

 
 

	Acquire images	Collect images and (optionally) write them to disk. Pressing Start does the requested scans, Ok saves the requested setup (but does not do the scans) and Cancel cancels any modifications to the menus.
	Scan axis/angle	Angle per scan. Multi axis scan is possible.
	# of scans	Number of successive scans.
	# of iterations	Repetition of the same scan. Default 2 for de-zingering by data evaluating program. All iterations are saved in the same file.
	Scan time	Time per scan in seconds.
	Special scan	Give the possibility to set the readout frequency (see Set-up), partial readout and arbitrary binning factors.
	Save to file	Image files. Default temp###.kcd. The filename is automatically incremented. The program will warn if the filename supplied does not contain sufficient digits to accommodate all scans.
	Check temperature	Check during a scan whether the CCD temperature is OK. If not: wait until proper working conditions are restored, and repeat the last scan. The check can be disabled but the quality of the image cannot be guaranteed.
	Auto dezinger	Dezingers double images and saves the result in a single image. Default not used because the data evaluation program does the dezingering. Zingers are random high intensity spots.
	Shutter open	If not set: a background ("Dark") measurement is made. Automatic set before starting any (set of) scans.

	Position goniometer	Position and do collision checks. Start does the requested movement and cancel exits the menu.
	Position goniometer	Position in Kappa or Eulerian geometry. At the point of entrance the present position is filled in.
	Zero & view positions	Some predefined positions (useful for crystal mounting purposes)
	User-definable positions	User-definable positions can be specified in setup->user defined positions
	Kappa-Omega map	Shows on the bitmap utility a map of Kappa-Omega space (Kappa on the vertical axis and Omega on the horizontal axis) at the present setting of DX and Theta. Here the  "forbidden areas" (caused by potential collisions between the moving parts of the goniometer) are shown.
	Show scan ranges	Show which omega scans may be done at the present set position.

	Quick Scan	Used to make a quick picture of a crystal. Start checks whether the generator is at nominal power. Any modifications to the menu are saved.
	DX distance	The DX distance at which the scan is to be done
	scan at phi position	The scan requested can be done at phi=0 or phi=90
	Do phi scan	Either a phi or a omega scan (see below) can be requested
	Do omega scan
	Scan settings	The standard set of scan settings can be requested. Note that it is not possible to save the resulting image(s).
	Start	Start the scan

	Movie mode	Meant to readout a partial image at increased speed. Useful f.i. for alignment of the primary beam. The command can only be stopped by pressing the abort button in the main server window.
	Full image	Use the full image
	central part of image	Just the central part.
	Part of image	The box dimensions can be selected as X and Y of the center of the image and X and Y size.
	Binned mode	The pixels can be binned 2-by-2 in horizontal and vertical directions. Note that the standard setting for the system is set in setup -> CCD-setup -> CCD-parameters.
	Shutter open, integration time	Several standard settings. Note that it is not possible to save the images

	Crystal mounting positions	Crystal mounting utility; The microscope view window will increase in size. The theta axis will move out of the way to improve accessibility to the goniometer-head. The position theta moves to is determined by the setting in setup -> goniometer setup -> goniometer parameters -> crystal mounting
	Window	Left/right clicking of the mouse in an empty area of the window rotates the Phi axis clockwise/counter-clockwise respectively.
	Phi +90 degree	Phi rotates +90 degree from present position.
	Phi +180 degree	Phi rotates +180 degree from present position.
	->	Phi axis horizontal; goniometer access from the left side.
	top	crystal pointing towards the microscope
	<-	Phi axis horizontal; goniometer access from the right side.
	|	Phi axis vertical.
	mount	Kappa at zero.
	Show grid	Show a grid over the centre of the microscope window

	Generator	Does not set anything useful for a non remote controllable generator. The lay-out of the menu differs slightly depending on the generator used; for a RAT generator the bias is added.
	Default setup	Setup for the default settings. The parameters can be saved.
	Apply default	Apply the settings for the default setup.
	Low setup	Setup for the generator settings when not performing data collection. The parameters can be saved.
	Apply low	Apply the settings for the low setup.
	Set generator	Apply the settings to the right of this button. The output fields show the present setting of the generator
	Confirm generator error	Reset any pending error message in the generator.
	Generator on/off	This is a toggle switch.
	Abort	An ongoing operation (started from this menu) can be aborted here.
	OK	Exit this menu

	Cryostream	Set up of an oxford 600 or 700 series cryostream. The menu lay-out differs between both devices.
	Current settings	shows the present status of the cryostream. For the 700-series this display is updated continously, for the 600 series the update-button has to be used.
	Move goniometer when idle	when marked, causes the phi axis to be moved on a regular basis at some high chi angle
	Actions	Set-up the function wanted. The most common used function is  ramp, where the ramp rate and the final temperature is supplied. For the 700 series another much used function is cool. Here just the final temp. is supplied and the controller takes care this temp. is reached as quickly as possible. Some other commands such as hold, ramp and shutdown (600 series) en end (700 series) are self-explanatory. One important difference between the 600 and 700 series is that for the 600 series after shutdown the server cannot regain control over the cryostat; the power on the 600 controller has to be cycled.  On the 700 series cryostat there are stop and restart buttons available.
	start and leave	Start-up the indicated action and leave the cryostream utility after the action has been registered by the crystream controler
	start and wait till finished	Start-up the indicated action and wait until the operation is completed.

 
 

	Goniometer head	For collision avoidance purposes it is important to enter the properties of the goniometer-head used. For this purpose a goniometer head can be described in terms of an intersection between the top-angle of a cone and the radius of the base. In practice the top-angle will depend on things such as the position of the Eulerian cradle and therefore it is advised to use conservative estimates.
	Econ head	The low-cost plastic Nonius goniometer head
	Econ head with extender	Use the head with extender
	Gonio head model 1516.916	The standard Nonius LT-head
	Gonio head hodel 1516.916 with extender
	User defined 1 & 2	In setup -> user defined goniometer heads it is possible to enter name, top angle and base-radius of user-defined gonio-heads.
	Other gonio head	The top-angle and radius of some special head can be entered.

	Beam-stop	The beam-stop size and distance can set here. The parameters are used for  collision avoidance  minimum theta below which reflections are obscured by the beam-stop shadow.  minimum DX during data collection
	Beam catcher distance setting	Defined as the distance between the crystal position and the back of the beam-stop. Note that this distance does not automatically define the minimum DX-distance; when the detector is swinged out (theta not at zero) smaller values of DX may be possible.
	Dx is positioned at the beam catcher setting	This checkbox is provided to provide an easy way to set the beam-stop distance. While theta=0 position the DX such that the beam-stop vane almost touches the collision collar of the detector (use the general position menu for this). The beam-stop position is now known.
	Beam catcher size	The standard set of Nonius supplied beam stops or a user defined beam stop can be entered. Note that a beam stop is defined by a diameter and a length

 
 

	Network set-up	A pull-down menu mostly using check-marks to set network related operations
	Network present	Can be marked when ethernet (TCP/IP) is installed on the computer. For normal (remote) operation this should always be enabled.
	Auto master set to network	If mastership is set to none automatically grant mastership when a remote computer requests connection
	Local mastership	Mimics the setting in the main window
	Server started	When checked, the server program will listen to incoming connection requests from a remote system.
	Disconnect remote user	Disconnect the Host computer. When a remote computer disconnects from the server without using the standard sign-off procedure the server program will probe the client computer when a request for a new connection arrives.  When no response is received the original remote computer will be disconnected. In cases where this does not work this option may be tried to force a sign-off from a remote system.

	Goniometer set-up
	Goniometer present	Checked if a connection the a goniometer has been established. Note that it is still possible to collect images also without goniometer.
	Goniometer parameters	Sets the hardware-related parameters for the goniometer.
	Exercise goniometer	Used to stress-test the system and for demonstration purposes. The positions the goniometer is to move to are recorded in the file excercis.dem. Also scans can be specified. The program will loop to the start of the file when finished until aborted. The file specifies one operation per line : Id Theta Phi Omega Kappa Dx Time Scans Repeats Shutter_flag  Where Id : 1 if a positioning move follows, 2 for a scan Theta, Phi, Omega, Dx : The position for a position line, scan size in case of a scan Time : Scan time (only for a scan) Repeats : multiplicity for each scan (only for a scan) Shutter flag : -1 if shutter is to remain closed, 1 for open (only for scan)
	Goniometer diagnostics	Shows some hardware settings in the goniometer interface and some statistics about the serial communication interface.

	CCD set-up
	CCD present	Checked if the CCD detector was properly initialised.
	CCD parameters	Set-up for the CCD detector. Most parameters are set in the KCCD.SET file.
	CCD test suite	Some tests for the detector

 
 

	X-ray generator setup	Sets generator type, wavelength and monochromator
	Microsource,591,590, other	Set generator type. Note that "Other generator" is not remote addressable
	Target material	Set the type or the wavelength of the target material. UN stands for unknown.
	Monochromator setting	Set the type of monochromator present (if any). None means no monochromator, Perpendicular is commonly used for a sealed tube systen (590), parallel & anti-parallel are the choices for a RAT (depending on at which side of the tube the kappa-CCD is positioned) and Osmic is the choice for Osmic mirrors.

	Calibration
	Beam alignment	Service program, used during X-ray alignment of the goniometer.
	Collimator tool (for mirror alignment)

	Goniometer parameters
	Crystal mounting: access from right/left side	The theta (and therefore the detector) is to move out of the way during crystal mounting to improve accessibility. This determines the direction theta will move to.
	Phi limit switch	Use of a Phi limit switch. This is a special device, mounted at the base of the Kappa block that will cause the Phi to limit its movements to 270 degrees in positive and negative directions. Used with special goniometer heads such as high temperature cells. Do not check if the unit is not mounted; the goniometer will not be able to finish its zeroing procedure in that case.
	Special collar	Use a larger area around the kappa block where collision is predicted. Usable for special gonioheads or if out-of-the-ordinary crashes occur
	Backlash-free positioning of DX	Ensures a final DX positioning move happens always from a higher DX distance. Increases the time for a DX-move but guarantees the highest accuracy.
	No (auto) rezeroing (use with caution)	Some installations might use a very out-of-the-ordinate goniometer-head or might require some special action before some axis may be moved. In such a case it may be impossible to do a zeroing procedure without asking explicit confirmation from the user (during normal operation the goniometer may attempt to re-zero when it thinks it lost its position or when a crash occurs). When this box is checked zeroing always has to be requested explicitly (setup -> goniometer setup -> rezero goniometer) . This is even the case when starting the program. The program will issue a warning when positioning is attempted while the goniometer zero is undetermined.
	Motor stop ID	Sets the positioning philosophy of the goniometer motors. Leave at 3 (meaning tell the server a positioning move is finished once the trajectory is done and leave the motors energised also when idle).
	Position accuracy	The maximum allowable position error during a scan. When this error is exceeded the scan will be aborted and repeated. Default 0.05.
	Min/max Theta	Allowed Theta range. Note that there are also hardware limit switches for theta. These are set to prevent damage to the detector by colliding with the X-ray tube. The software limits should, of course, never exceed the hardware limits. Use the update button in the main server screen to check whether the limits set in software can really be reached.
	Minimum DX	Minimum DX reachable.
	Theta axis	Sets various parameters for the Theta motor of the goniometer. Maximum velocity and acceleration may be changed if required. The motor feedback parameters are better left unchanged unless advised by Nonius.  The Reinit Zero may be used if the zero position of the axis is not correct (this may occur if the detector is remounted). It is supposed the axis is at its new zero position and the goniometer will move a bit to locate this position with respect to its other markings. The new position will be recorded in the Kccd.set file.
	Phi axis	Like theta
	Omega axis	Like theta
	Kappa axis	Like theta
	DX axis	Like theta

 
 

	Goniometer diagnostics
	Communication errors	The top part of the windows shows serial line statistics for the PC-goniometer interface. These are listed for packets transmitted, received and as interpreted by the interface. As the communication is robust and may stay up for a long time some errors showing up here is not problematic; all bad communication is retried and all commands from the PC are verified if after some time no response is received.
	Goniometer interface status	The second part of the menu shows the status of the goniometer interface.
	Motor errors	The third part of the menu shows the errors that may occur in the motor drivers. Three types of errors are possible : Position errors; the axis exceeded its maximum allowed position error during a scan. This error may occur; the scan is re-done and the data collection continues. If this error happens often the position accuracy may be too tight or something is mechanically wrong.  Command errors; a bad command was received by the motor controller. This should not happen during normal operation. The command is retried and normal operation continues  Index errors. As the goniometer used optical encoders to sense its position an index-pulse check is build in to ensure no pulses from the encoders are lost. If an error occurs the goniometer will re-do its zero procedure and continue normal operation. This should not happen during normal operation. It generally points to some electronic disturbance or a badly aligned encoder. Note that the errors are cleared if the goniometer interface is reset.

	CCD parameters
	Data CCD	Has the properties of the CCD used and the CCD interface card. Parameters set in KCCD.SET
	Binned	For the 90 mm CCD binned (2x2) is standard. The 135 mm uses unbinned images. A different setup may be chosen but the standard set of calibration files will not fit.
	ADC speed	Default 200 kHz for 90 mm, 100 kHz for 135. A different setup may be chosen but the standard set of calibration files will not fit.

	CCD test suite
	Perfo	Measures the ADC-zero (offset), readout noise and dark current. The output is saved in the log file/window.
	Effic	Measure the efficiency of the X-ray chain. Refer to the technical user manual -> Effic : intensity of the primary beam
	Spot	Measures spot statistics for the primary beam. The beam-stop has to be removed and the attenuator is to be placed on the collimator tip. Calculated are the beam intensity and parameters such as FullWidthHalfMaximum.
	Stat	Calculate some statistics on the basis of a dark image. Also input from file is possible. The image is divided into boxes according to start (pixel nr.), size (of the box), number (of boxes to take into account) and step (number of pixels to step between boxes. Calculated are  the minimum and maximum value when average per box is calculated.  Same for Standard deviation  The standard deviation over all standard deviations  Average Standard deviation  Average over all boxes

 

	Video microscope
	Video microscope present	Checked if the Video microscope image is to be started at server start-up
	Microscope setup	Check and if necessary adjust the horizontal and vertical position of the beam.

 
 

	Microscope setup	Same settings for the video microscope. More (video card-specific) settings can be set in the crystal viewing program itself (select top-left icon)
	Camera type	A Colour or Black & White camera can be selected.
	Microscope size ID	Set the size of the microscope viewing window. The smallest value (1) corresponds to a 80x60  pixel window, the largest value (4) to a 640x480 window.
	image transfer properties	When a microscope image is fetched by a remote computer this will tend to show more noise than the  image on the server PC. This happens because the eye tends to average out the noise from a 'live' image.  In order to overcome this effect it is possible to average several images before transferring them to the remote computer. The number of images to average may be selected as well as the type of image file to write to the remote system (png is a good choice for the collect program)

 
 

	Beam alignment	This utility is used to check the centre of the goniometer. It uses a small vane mounted on a goniometer head. This vane is to be positioned such that it obscures just half of the beam using the regular positioning possibilities of the goniometer. Refer to the technical user manual -> X-ray optics alignment with a sealed tube for detailed information.
	Measure continuously	Measure primary beam intensity using the scan time listed below
	Measure horizontal/vertical direction	Check and if necessary adjust the horizontal and vertical position of the beam.
	Measure open/measure vane	Align the vane on the goniometer head.

Structure of the kccd.set file

 The kccd.set file is located in the same directory as the server executable. It contains all persistent information for the server program. The philosophy of the server program is such that all parameters for the server program that may be changed during normal use of the system are accessible through the GUI of the server program. These may then be committed to the kccd.set file through the file menu of when the server program exits. All other parameters in the kccd.set file are changed rarely if at all. The file may be modified using a standard text editor. The number of items in the file are bound to increase with new releases of the software but should stay upward compatible with the current release. In practice this means that a new release will use the old kccd.set file and will add the new parameters if the user requests a save. The (commented) list of parameters follows :
 
 
 

ID_STRING = FAKE	Id string for the system. It will end up in the header of the image files
DETECTOR_ID = 103	the ID number of the ccd detector. This will be written to the image files. The detector number is Nonius supplied and is checked against the calibration files present
GONIOMETER_ID = 507	the ID number of the goniometer. Nonius supplied
NETWORK_PRESENT	present if setup->network setup->network checked
AUTO_MASTER_SET	setup->network setup-> auto master to network
CCD_PRESENT	setup->CCD setup->CCD present
GONIOMETER_PRESENT	setup->goniometer setup->goniometer present
MICROSCOPE_PRESENT = 2	setup->video microscope->video microscope present and the size from setup->video microscope-> microscope size
MICROSCOPE_DIVISIONS = 41.000000	number of horizontal tick marks on the microscope window. The number of vertical tick marks is relative to this number, taking into account an aspect ration of 3:4
MICROSCOPE_COM_ID = 1	format ID of the microscope images send over the network. 1=bmp, 2=zipped bmp, 3=zipped array
MICROSCOPE_AVERAGING=10	Number of frames to average when sending images over the network
MICROSCOPE_BWCOLOR=1	use color or b/w microscope
SHOW_TEXT_SCREEN	setup->text screen setup->text screen present
TEXT_DISPLAY_LEVEL = 15	bitmap pattern for types of messages to show in setup->text screen setup
SHOW_IMAGE_SCREEN	setup->image display screen setup->image display present
GON_STOP_ID = 1	setup->goniometer setup->goniometer parameters -> motor stop ID
GON_CLOCK_RATE = 22	not used
GON_BAUDRATE = 1200	Baud-rate of the generator connected to the goniometer interface
GON_POS_ACCURACY = 0.009000	setup->goniometer setup->goniometer parameters-> Position accuracy
GON_FLAGS = 11792	a combination of various check marks in setup-> goniometer setup->goniometer parameters and the generator type
GON_EMISSIONLIMIT = 48	not used
GON_THETA_PROPOR = 100 GON_THETA_ACCELERATION =45.000000 GON_THETA_VELOCITY = 500.000000 GON_THETA_INTEGRAL = 100 GON_THETA_DERIVATIVE = 156 GON_THETA_INTEGRATIONLIMIT = 500 GON_THETA_SAMPLINGINTERVAL = 20	the set of parameters for the theta motor in setup->goniometer setup-> goniometer parameters-> theta axis
GON_THETA_OFFSET_FROM_ZERO = -2049 GON_THETA_OFFSET_FROM_INDEX = 3746	the absolute zero position of the theta axis relative to a zero switch and the position encoder. Nonius supplied. These values are modified if the zero position is adapted according to setup->goniometer setup -> goniometer parameters->theta axis -> reinit zero. Both parameters are zero if the axis is not present
GON_THETA_MIN = -45.000000 GON_THETA_MAX = 60. 000000	The theta limits according to setup -> goniometer setup -> goniometer parameters -> max/min theta.
GON_THETA_ASK = 0	non-zero if the user is to be asked permission before moving an axis. setup -> goniometer setup-> goniometer parameters->theta axis -> ask confirmation.
GON_PHI_PROPOR = 100 GON_PHI_ACCELERATION =100.000000 GON_PHI_VELOCITY = 3000.000000 GON_PHI_DERIVATIVE = 150 GON_PHI_INTEGRAL = 150  GON_PHI_INTEGRATIONLIMIT = 1000 GON_PHI_SAMPLINGINTERVAL = 10	the set of parameters for the phi motor in setup->goniometer setup-> goniometer parameters-> phi axis
GON_PHI_OFFSET_FROM_ZERO = -8686  GON_PHI_OFFSET_FROM_INDEX = 121	the absolute zero position of the phi axis relative to a zero switch and the position encoder. Nonius supplied. These values are modified if the zero position is adapted according to setup->goniometer setup -> goniometer parameters->phi axis -> reinit zero. Both parameters are zero if the axis is not present
GON_PHI_MIN = -360.000000 GON_PHI_MAX = 360. 000000	The phi limits. Not accessible through the GUI
GON_PHI_ASK = 0	non-zero if the user is to be asked permission before moving an axis. setup -> goniometer setup-> goniometer parameters->phi axis -> ask confirmation.
GON_OMEGA_PROPOR = 120 GON_OMEGA_ACCELERATION = 180.000000 GON_OMEGA_VELOCITY = 2000.000000 GON_OMEGA_INTEGRAL = 100 GON_OMEGA_DERIVATIVE = 110 GON_OMEGA_INTEGRATIONLIMIT = 1000 GON_OMEGA_SAMPLINGINTERVAL = 12	the set of parameters for the omega motor in setup->goniometer setup-> goniometer parameters-> omega axis
GON_OMEGA_OFFSET_FROM_ZERO = -1561 GON_OMEGA_OFFSET_FROM_INDEX = -429	the absolute zero position of the omega axis relative to a zero switch and the position encoder. Nonius supplied. These values are modified if the zero position is adapted according to setup->goniometer setup -> goniometer parameters->omega axis -> reinit zero. Both parameters are zero if the axis is not present
GON_OMEGA_MIN = -210.000000 GON_OMEGA_MAX = 210.000000	The omega limits. Not accessible through the GUI. The limits given represent the standard omega range
GON_OMEGA_ASK = 0	non-zero if the user is to be asked permission before moving an axis. setup -> goniometer setup-> goniometer parameters-> omega axis -> ask confirmation.
GON_KAPPA_PROPOR = 79 GON_KAPPA_ACCELERATION = 180.000000 GON_KAPPA_VELOCITY = 2000.000000 GON_KAPPA_INTEGRAL = 75 GON_KAPPA_DERIVATIVE = 250 GON_KAPPA_INTEGRATIONLIMIT = 1000 GON_KAPPA_SAMPLINGINTERVAL = 10	the set of parameters for the kappa motor in setup->goniometer setup-> goniometer parameters-> kappa axis
GON_KAPPA_OFFSET_FROM_ZERO = 4469 GON_KAPPA_OFFSET_FROM_INDEX = -1089	the absolute zero position of the kappa axis relative to a zero switch and the position encoder. Nonius supplied. These values are modified if the zero position is adapted according to setup->goniometer setup -> goniometer parameters->kappa axis -> reinit zero. Both parameters are zero if the axis is not present
GON_KAPPA_MIN = -175.000000 GON_KAPPA_MAX = 175.000000	the GUI The kappa limits. Not accessible through the GUI. The limits given represent the standard range.
GON_KAPPA_ASK = 0	non-zero if the user is to be asked permission before moving an axis. setup -> goniometer setup-> goniometer parameters->kappa axis -> ask confirmation.
GON_DX_PROPOR = 125 GON_DX_ACCELERATION = 20.000000 GON_DX_VELOCITY = 2000.000000 GON_DX_INTEGRAL = 150 GON_DX_DERIVATIVE = 600 GON_DX_INTEGRATIONLIMIT = 500 GON_DX_SAMPLINGINTERVAL = 4	the set of parameters for the DX motor in setup->goniometer setup-> goniometer parameters-> DX axis
GON_DX_OFFSET_FROM_ZERO = -23998 GON_DX_OFFSET_FROM_INDEX = 1334	the absolute zero position of the DX axis relative to a zero switch and the position encoder. Nonius supplied. These values are modified if the zero position is adapted according to setup->goniometer setup -> goniometer parameters->DX axis -> reinit zero. Both parameters are zero if the axis is not present
GON_DX_MIN = 25.000000 GON_DX_MAX = 170.000000	the GUI The DX limits. The minimum DX may be set in setup -> goniometer setup -> goniometer parameters -> minimum DX.
GON_DX_ASK = 0	non-zero if the user is to be asked permission before moving an axis to setup -> goniometer setup-> goniometer parameters->phi axis -> ask confirmation.
GON_ALPHA = 50.001888	The kappa block angle. Supplied by Nonius
GON_DX_REFERENCE = 165	The zero position of the goniometer axes are taken relative to some arbitrary position. For all axes this position is 0 degrees except for the DX-axis (dx=0 cannot be reached). This reference position is set here.
GON_GONIOHEAD_ANGLE = 6.000000 GON_GONIOHEAD_RADIUS = 22.000000	The goniometer head properties from experiment -> goniometer head. Note that the half top-angle is saved here.
GON_DX_PHOSPHOR_FRONT = 11.000000	The distance between the phosphor front and the and the front of the detector (meaning the collision ring). Nonius supplied. Used for collision calculations. May be increased if frequent collisions occur between detector and goniometer.
GON_COLLISION_SECURITY = 0.500000	The minimum clearance in degrees that has to be maintained between moving part of the goniometer/detector system. May be increased if frequent collisions occur.
GON_CATCHER_DISTANCE = 24.800001 GON_CATCHER_RADIUS = 0.500000 GON_CATCHER_LENGTH = 6.000000	Setup from experiment -> beam-stop. Note the beam-stop distance saved here is somewhat less than the value from this menu.
GON_DXBACKLASHFREE = 0	The back-lash free DX positioning setting from setup -> goniometer setup -> goniometer parameters -> backlash free positioning of DX
DET_CONTROLERTYPE = 3	The type of CCD controller. Nonius supplied Currently used tpyes are 3 (st138 controller) and 10 (st133)
DET_DETECTORTYPE = 61	The type of CCD-chip in the detector. Nonius supplied. Currently used chips are 61 (90 mm camera) and 88 (135 mm camera)
DET_INTERFACECARD = 20	The type of interface ("TAXI") card in the PC. Used are 4 for an ISA card and 20 for a PCI card.
DET_BASEADDRESS = 2560 DET_CARDINTERRUPT = 10	IO settings for the ISA card. Ignored for the PCI card
DET_DATACOLLECTIONMODE = 1	Not used
DET_APPLICATIONTYPE = 0	Not used
DET_IMAGE_XSIZE = 1250 DET_IMAGE_YSIZE = 1152 DET_IMAGE_XOFF = 0 DET_IMAGE_YOFF = 0	The number of pixels that can be read-out from the CCD detector are fixed for any type of detector ID. Within this area a subset may be defined, set by x- and y-offset and x- and y-size. Nonius supplied.
DET_PIXEL_XSIZE = 55.000000 DET_PIXEL_YSIZE = 55.000000	The approximate size of a (single) pixel in micrometers.
DET_HV = 365 DET_LL = -15552 DET_WD = 1519 DET_GAIN = 0	Not used
DET_PHOTGAIN = 1.700000	The gain in photons/ADU Nonius supplied.
DET_CCDGAIN = 5.000000	The (electronic) gain setting for the CCD detector. Nonius supplied
DET_DEADTIME = 1.000000	Not used
GEN_TARGET = CU  GEN_ALPHA1 = 1.540562  GEN_ALPHA2 = 1.544390  GEN_RATIO = 2.000000	Properties of the target material in the generator according to setup -> Xray generator setup Note that the Alpha1 and alpha2 values are set automatically if the target material is set.
GEN_POLARISATION = OSMIC	Polarisation of the generator monochromator according to setup -> Xray generator setup.
GEN_KV_DEFAULT = 0.00 GEN_MA_DEFAULT = 0.00 GEN_BIAS_DEFAULT = -1	The default setup according to experiment -> X-ray generator -> Default setup.
GEN_KV_LOW = 0.00 GEN_MA_LOW = -1 GEN_BIAS_LOW = -1	The low setup according to experiment -> X-ray generator -> low setup.
COMPORT_NUMBER = 2 COMPORT_BAUDRATE = 9600	Comport number (1=com1, 2=com2 etc.) and baudrate for the RS232 port the goniometer interface is connected to.
ADC_SPEED = 1024	Bit setting for the read-out speed of the CCD detector according to setup -> ccd setup -> ccd parameters -> ADC speed.
CRYO_PRESENT = 2	Identifier for the type of cryostat used according to setup -> crystal conditioning setup -> cryo device setup.
SCINTILLATORTYPE = 1 SCINTILLATORLOAD = 25	The type of scintillation material used for the CCD detector and the load of this materiel. Nonius supplied
QUICK_SCAN_SIZE = 15.000000 QUICK_SCAN_TIME = 5.000000 QUICK_NUMBER_OF_SCANS = 1 QUICK_NUMBER_OF_REPEATS = 1 QUICK_SCAN_DX = 30.000000 QUICK_SCAN_OMEGA_SIZE = 1.000000 QUICK_SCAN_DO_PHI = 1	The quick scan parameters according to acquisition -> Quick scan.
USER_POS1_THETA = 0.000000 USER_POS1_PHI = 0.000000 USER_POS1_OMEGA = 0.000000 USER_POS1_KAPPA = 0.000000 USER_POS1_DX = 0.000000 USER_POS1_TEXT =	The user set special position 1 according to setup -> user defined positions. Used by Acquisition -> position goniometer
USER_POS2_THETA = 0.000000 USER_POS2_PHI = 0.000000 USER_POS2_OMEGA = 0.000000 USER_POS2_KAPPA = 0.000000 USER_POS2_DX = 0.000000 USER_POS2_TEXT =	The user set special position 2 according to setup -> user defined positions. Used by Acquisition -> position goniometer
USER_POS3_THETA = 0.000000 USER_POS3_PHI = 0.000000 USER_POS3_OMEGA = 0.000000 USER_POS3_KAPPA = 0.000000 USER_POS3_DX = 0.000000 USER_POS3_TEXT =	The user set special position 3 according to setup -> user defined positions. Used by Acquisition -> position goniometer
USER_POS4_THETA = 0.000000 USER_POS4_PHI = 0.000000 USER_POS4_OMEGA = 0.000000 USER_POS4_KAPPA = 0.000000 USER_POS4_DX = 0.000000 USER_POS4_TEXT =	The user set special position 4 according to setup -> user defined positions. Used by Acquisition -> position goniometer
FILE_COMPRESSION = 0	File compression ID
USER_HEAD1_ANGLE = 11.000000 USER_HEAD1_RADIUS = 21.000000 USER_HEAD1_TEXT = TEST1	The user-defined goniometer head nr. 1 according to setup -> user defined goniometer heads. Used in experiment -> goniometer head.
USER_HEAD2_ANGLE = 12.000000 USER_HEAD2_RADIUS = 22.000000 USER_HEAD2_TEXT = TEST2	The user-defined goniometer head nr. 1 according to setup -> user defined goniometer heads. Used in experiment -> goniometer head.
GON_GONIOHEAD_ID = 1	The present used goniometer head according to experiment -> goniometer head
NETWORK_TIMEOUT	The maximum number of seconds between 2 packets received before the server will give up on a network connection.

Remote commands :

The server communicates to a client using a simple synchronous ASCII-based protocol. The server posts a prompt (CCD>), the client requests a command and the server will try to supply the requested information or execute the requested command. Commands involving the goniometer and/or the detector are of course possible only when a goniometer and/or detector are present and the user has mastership over the system. If the server cannot execute a command an error is returned (the answer is preceded by the keyword Error: and the error text is followed by the prompt). Another possibility is that a command can temporary  not be executed, in this case a warning (for example Warning: generator down) is generated. Now the server will keep on trying to finish the requested command. Possible commands (as returned by the '"help" command) are :
 

 Exit            (stop this program)
 Filename    [filename] (set filename)
                   (if blank, do not save file)
 Master       (grab mastership)
 Measure    (actively measure present position)
 Pos            [Om=pos] [Th=pos] [Ph=pos] [Ka=pos] [Dx=pos]
 Pos            [Ch=pos] (in this case eulerian coordinates
                  are presumed) (no parameters = show position)
 setccd        [startx=nr] [endx=nr] [starty=nr] [endy=nr]
                  [binning=nr (1 = unbinned)]
                  select a frame area and the binning factor
 Scan         scan-time [number-of-slots] [Sc (shutter closed)]
                  [DZ (de-zinger)] [Rep=nr (number of repeats)]
                  [NC (do not check CCD temperature)] [Th=width]
                  [Ph=width] [Om=width] [Ka=width] [DX=distance]
 Shutter     [Open, Closed] (set shutter (default closed))
 Status       (Status of the system)
 View         [1,2,3] (set one of the view positions
 Generate   [kV=nr] [mA=nr] [Bias=nr] [update (retrieve settings)]
                  [on] [off] [confirm]
                  no parameters = show settings
                  Bias setting only allowed for RAT
 Wait         [time-in-seconds] : wait the time specified
 Zero         drive goniometer to zero
 Gonzero   (Re)zero the goniometer
 Gonquit   Remove the goniometer
 CCDquit  Remove the CCD detector system
 Range      [Om=pos] [Th=pos] [Ph=pos] [Ka=pos] [Dx=pos]
                 display omega scan possible for given position
 Checkpos [Om=pos] [Th=pos] [Ph=pos] [Ka=pos] [Dx=pos]
                 [Scans=nr] display if position can be reached
                 if Scans is supplied check whether scans can be made
 Video       [STATUS]
                 [COM=[1,4,5]] file transfer prototol (bmp,png,ppm/pgm)
                 [SIZE=[1,2,3,4]] microscope window & file size
                 [QUALITY=[1-255]] number of frames to average (file transfer only)
 Cryo        [STATUS] request status (only for Oxford cryostream)
                On,Off (Enables continuous phi motion
                RAMP finaltemp ramprate [wait] : program ramp
                SHUTDOWN finaltemp ramprate [wait] : shutdown after ramp (600 series only)
                HOLD : hold at present temp
                COOL : finaltemp [wait] : go to finaltemp at turbospeed (700 series only)
                END  : ramp-rate [wait] : go to 300K using ramp-rate speed (700 series only)
                WAIT : wait for present command (if any) to finish
                LEAVE : leave slave mode (600 series only)
 Checkgen [mA=nr] [kV=nr]
                returns allowed kv or ma range respectively
                No parameters shows present mA, Kv and Bias (for RAT) range
 Setspeed [NR] set adc speed (in kHz)
                no parameter = show allowed speeds
 

Bitmap utility
 

This displays the images from the Kappa-CCD system. The main display window has 3 areas:

• The left side shows the (binned) image. It is possible to select a part of the image by pressing the left or right button of the mouse and dragging over the area of interest. If the button is released the action as specified by the cursoring menu is executed.
• The bottom-right area has the zoom window. It contains a magnified area of the image as selected by the user.
• The top-right part of the screen has 2 colour bars (one for the main and one for the zoom window) with some control buttons and some special function buttons. When the zoom window is not present the right-most colour bar will be missing. The colour bars show the translation from the integer values in the image file to colours. There are several ways this colour scheme can be manipulated:

- The range of the integer values next to the colour bar may be changed through the scaling-> scaling sub-menu. An alternative way to achieve this is to use the Cursering -> Max-Min Cursering option; this will look up the max. and min. value in the area selected and adapt the colour scale of the whole image to this range of values.

- The colour scheme used can be set-up in the file -> palette manager tool.. Colour schemes can also be read from or saved to a file. The file read at startup is STANDARD.PAL.

- The mouse can be used to manipulate the colours in the colour bars: click inside a colour bar and drag the mouse up or down. A black horizontal line will appear in the selected colour bar and the colours on one side of the bar will compress and broadened at the other side when the bar is moved. The colour scheme of the image will reflect the modified scheme once the mouse button is released. This procedure can be repeated several times with the restriction that a new horizontal bar cannot cross an existing one. It is also possible to pick up an existing bar and re-move it. Use the recalc button to remove the horizontal bars. Use the copy buttons to copy colour bar from the main to the zoom window or vice versa and the reset button to re-set to the original bar.

The Following/freezing toggles between showing the next image from the server if it comes available leave the present image displayed.
The prev/next buttons are shows only if a set of files from disk is displayed and provides the possibility to scroll through the images in a set.
Some info for the present cursor positions is also shows : x-y co-ordinate, value and resolution in angstrom or degrees in theta.

When a double ("binned") image is received from the server the average image is shown. When reading a file from disk the first image is shown by default. The pull-down menu choices are as follows :

 

	Cursoring	Specifies the action when a section of the image is selected.
	Bitmap	Display the selected area at the lower-right corner. Note that if the cursering is done using the right mouse the image is zoomed to the big image; pressing ythe reset button will redisplay the full image. Also note this when the magnification is large enough the program will display the actual decimal values from the image as well.
	3D Render	Displays the intensities of a area in 3-D.
	Line draw	Displays the intensities in a 2-D graph.
	Max-min cursoring	Uses the max. and min. values in the area selected to adjust the colour bars.
	Reflection statistics	Show statistics for the selected area. When one single peak is detected within the area also the peak statistics are shown.
	Resolution in degrees/angstrom	Show the resolution of the present cursor position in either angstrom or degrees.

 

	Scaling	Set the max/min scale in the display (an alternative way is to use max/min cursoring)
	Autoscale	Scales to the min/max value in the image.
	Autoscale to average	Scales to 0%/+50% of the average of the image.
	Manual scale	Manual scale to min/max.
	Min/max	Min/max of the present image or input for manual scale.

 

	Correction
	Correction on	Corrects for bad pixels/lines. Far this option to work the file calibrat.hal must be present (calibrat.ful far an unbinned image). These files can be produced by the next menu choice. Note that corrections are just for display purposes and are never written to file.
	Do correction	Far this utility to work a double shutter-closed file must be on display. This image should have been collected during sufficient time (600 sec. is a good choice). The program calculates average and SD for the image. It then proceeds by selecting all values beyond plus and minus 3 SD from the mean as bad pixels (these max. and min. values are showsn at the top and may be changed). All horizontal lines that contain over 33% bad pixels are marked as bad lines. It is possible to add additional bad pixels by hand.

 

	Various
	Filtering	A 3x3 filter can be applied to the image. Some low- and high-pass filters are pre-defined and it is also possible to define a custom filter.
	Sum image	Sums and averages scans from a set of files.
	Select image	Select images from the file (in case of a file with multiple images). Does not work with images received from the server.
	Image info	Info in the file header. Operates only with files, not with images received from the server.

 
 
 

KappaCCD-Temp.log
 
 

The log-file utility.

 
 
 

	Options
	Find (next)	Text search in the file. It goes to the page with the text, but does not highlight it. Case sensitive.

 
 
 

	Character
	Font	Choosing a font. Default: system, bold, size 12.

 
 
 

Crysview

The microscope viewing program. This does not have its own menus, but settings can be made through the goniohead icon in the top-left corner. It is not necessary to use these menus normal operation; the server program can set the size of the microscope window and can turn the crosshair on and off. However, the settings in Video Format, Video source, Video Display and Choose compressor may be relevant during first time installation. The structure of these menus may differ between the different video cards but the relevant settings are Pal, composite video