 |
DIP2000 user manual |
|
DIP2000 user manual |
Previous : Installation of software for the DIP2000 system
#
if ($1 ==’ ‘) then
echo -n ‘Enter a name for your project : ‘
set project = ($<)
else
set project = $1
endif
mkdir $project
cd $project
mkdir images
cp /disk1/people/xdip/DIP2030.DCL ./images
cp /disk1/people/xdip/HKL/coms/site .
cp /disk1/people/xdip/HKL/coms/exp .
cp /disk1/people/xdip/HKL/coms/auto .
cp /disk1/people/xdip/HKL/coms/refine .
cp /disk1/people/xdip/HKL/coms/process .
cp /disk1/people/xdip/HKL/coms/scale .
cd images
format dip 2000 [dip2020(k) with 12 bits ADC]
format dip 2030 [dip2030(k) with 12 bits ADC]
format dip 2000b [dip2020(k) with 16 bits ADC]
format dip 2030b [dip1030 or dip2030(k) with 16bits
ADC]
bad value 40000
reject slope 150 low value 0.5
[source parameters]
Wavelength 1.54178
monochromator graphite [when using a graphite monochromator]
monochromator filter [when using mirrors]
[detector parameters]
[translations]
X beam 100.00 [when using a dip2020(k)]
Y beam 100.00 [when using a dip2020(k)]
X beam 150.00 [when using a dip1030 or dip2030(k)]
Y beam 150.00 [when using a dip1030 or dip2030(k)]
[rotations]
radial offset 0.0
angular offset 0.00
Cassette rotx 0.00 roty 0.00
Film rotation -90
[Spot properties]
spot elliptical .5 .5
background elliptical .6 .6
box 2 2
overlap spot
weak level 3.0
profile fitting radius 30.0
Example of an exp file for denzo
TITLE ' ???? Put here the title of your experiment ???'
[detector parameters]
[translations]
distance ????
[data collection setup]
oscillation start 0.0
oscillation range 1.0 step 1.0
[file names]
raw data file './images/mycompound###.ipf'
film output file ./mycompound###.x
sector 1
[Crystal properties]
space group p1
mosaicity 0.40
resolution limits 20 2.0
Example of an auto file for DENZO
[Indexing parameters & peak file]
longest vector 300
peak search file 'peaks.file'
[start indexing]
fit cell crystal rotx roty rotz x beam y beam
write predictions
go
Example of an input file for scalepack
space group p1
number of zones 10
estimated error 0.02 0.02 0.02 0.02 0.02 0.02 0.02
0.02 0.02 0.02
error scale factor 1.6
[scale restrain 0.01]
[B restrain 0.1]
reference film 1
format denzo_ip
rejection probability 0.0001
postrefine 10
fit crystal a* 1 to 90
fit crystal b* 1 to 90
fit crystal c* 1 to 90
fit crystal alpha* 1 to 90
fit crystal beta* 1 to 90
fit crystal gamma* 1 to 90
fit batch rotx 1 to 90
fit batch roty 1 to 90
fit crystal mosaicity 1 to 90
output file ?????.scaled
[@reject]
write rejection file 0.5
add partials 1 to 90
sector 1 to 90
file 1 ????###.x
Listing of files on a DIP2000 software release
Xdipsys/bin/ConvDIPData, 18664 bytes, 37 blocks
Xdipsys/bin/Dipsetup, 179848 bytes, 352 blocks
Xdipsys/bin/Dipstatus, 150312 bytes, 294 blocks
Xdipsys/bin/MakeCorrectData, 14280 bytes, 28 blocks
Xdipsys/bin/MakeCorrectData_old, 14216 bytes, 28
blocks
Xdipsys/bin/MakeNoCorrectData, 14184 bytes, 28 blocks
Xdipsys/bin/Stddip, 298056 bytes, 583 blocks
Xdipsys/bin/calG, 22664 bytes, 45 blocks
Xdipsys/bin/calign, 103536 bytes, 203 blocks
Xdipsys/bin/dcl_demo, 120560 bytes, 236 blocks
Xdipsys/bin/dcl_main, 255704 bytes, 500 blocks
Xdipsys/bin/dclctrl, 141992 bytes, 278 blocks
Xdipsys/bin/dclmsub, 146072 bytes, 286 blocks
Xdipsys/bin/dip2000_init, 158824 bytes, 311 blocks
Xdipsys/bin/dip2000_srv, 86640 bytes, 170 blocks
Xdipsys/bin/dipchange, 21938 bytes, 43 blocks
Xdipsys/bin/dipclean, 4487 bytes, 9 blocks
Xdipsys/bin/dipebterm, 14272 bytes, 28 blocks
Xdipsys/bin/dipterm, 14288 bytes, 28 blocks
Xdipsys/bin/ip_contour, 31976 bytes, 63 blocks
Xdipsys/bin/ip_dsp, 834152 bytes, 1630 blocks
Xdipsys/bin/ip_pks, 101448 bytes, 199 blocks
Xdipsys/bin/ipfuty, 31096 bytes, 61 blocks
Xdipsys/bin/ipss, 14328 bytes, 28 blocks
Xdipsys/bin/repro_pi, 18768 bytes, 37 blocks
Xdipsys/bin/repro_pip, 22928 bytes, 45 blocks
Xdipsys/bin/unico_rf, 23088 bytes, 46 blocks
Xdipsys/conf/DIP.CNF_K_template, 1433 bytes, 3 blocks
Xdipsys/conf/DIP.CNF_template, 1237 bytes, 3 blocks
Xdipsys/conf/DIP2000.CMD, 7144 bytes, 14 blocks
Xdipsys/conf/DIP2000.SUB, 4905 bytes, 10 blocks
Xdipsys/conf/DIP2000K.CMD, 7462 bytes, 15 blocks
Xdipsys/conf/DIP2000K.SUB, 7303 bytes, 15 blocks
Xdipsys/conf/DIP2000K_NW.CMD, 7462 bytes, 15 blocks
Xdipsys/conf/DIP2000K_NW_PA.CMD, 7496 bytes, 15 blocks
Xdipsys/conf/DIP2000K_PA.CMD, 7496 bytes, 15 blocks
Xdipsys/conf/DIP2000K_PA.SUB, 7319 bytes, 15 blocks
Xdipsys/conf/DIP2000_NW.CMD, 7144 bytes, 14 blocks
Xdipsys/conf/DIP2000_NW_PA.CMD, 7178 bytes, 15 blocks
Xdipsys/conf/DIP2000_PA.CMD, 7178 bytes, 15 blocks
Xdipsys/conf/DIP2000_PA.SUB, 4921 bytes, 10 blocks
Xdipsys/conf/DIP2030.CMD, 7144 bytes, 14 blocks
Xdipsys/conf/DIP2030K.CMD, 7462 bytes, 15 blocks
Xdipsys/conf/DIP2030K_NW.CMD, 7462 bytes, 15 blocks
Xdipsys/conf/DIP2030K_NW_PA.CMD, 7496 bytes, 15 blocks
Xdipsys/conf/DIP2030K_PA.CMD, 7496 bytes, 15 blocks
Xdipsys/conf/DIP2030_NW.CMD, 7144 bytes, 14 blocks
Xdipsys/conf/DIP2030_NW_PA.CMD, 7178 bytes, 15 blocks
Xdipsys/conf/DIP2030_PA.CMD, 7178 bytes, 15 blocks
Xdipsys/conf/DIPTYPE_DIP2000L, 15537 bytes, 31 blocks
Xdipsys/conf/DIPTYPE_DIP2000R, 15537 bytes, 31 blocks
Xdipsys/data/DIP_CONV_PARM.1030, 30 bytes, 1 block
Xdipsys/data/DIP_CONV_PARM.2000, 30 bytes, 1 block
Xdipsys/data/DIP_CONV_PARM.2030, 30 bytes, 1 block
Xdipsys/data/DIP_ZERO_COMP, 2 bytes, 1 block
Xdipsys/xv-lib/.text_extras_menu, 703 bytes, 2 blocks
Xdipsys/xv-lib/libolgx.so.3.2, 97128 bytes, 190 blocks
Xdipsys/xv-lib/libxview.so.3.2, 2476984 bytes, 4838
blocks
Xmxpsys/bin/Phaset, 370728 bytes, 725 blocks
Xmxpsys/bin/Premeas, 460168 bytes, 899 blocks
Xmxpsys/bin/XGraphV, 519624 bytes, 1015 blocks
Xmxpsys/bin/Xpress, 99384 bytes, 195 blocks
Xmxpsys/bin/com.out, 120624 bytes, 236 blocks
Xmxpsys/bin/ctdump, 2544 bytes, 5 blocks
Xmxpsys/bin/dp, 128232 bytes, 251 blocks
Xmxpsys/bin/emstop, 43832 bytes, 86 blocks
Xmxpsys/bin/envedit, 111784 bytes, 219 blocks
Xmxpsys/bin/icon, 69016 bytes, 135 blocks
Xmxpsys/bin/mnctrl, 107688 bytes, 211 blocks
Xmxpsys/bin/plot.out, 14168 bytes, 28 blocks
Xmxpsys/bin/xpress, 959 bytes, 2 blocks
Xmxpsys/data/AutoInf, 100 bytes, 1 block
Xmxpsys/data/Status, 4112 bytes, 9 blocks
Xmxpsys/data/Winpos, 988 bytes, 2 blocks
Xmxpsys/data/instr, 71360 bytes, 140 blocks
Xmxpsys/data/wavef, 225 bytes, 1 block
Xmxpsys/man/XGraphV, 23589 bytes, 47 blocks
env/.Sgiresources, 84 bytes, 1 block
env/.Xdefaults, 114 bytes, 1 block
env/.cshrc, 1247 bytes, 3 blocks
env/.desktop-indy/4DWm, 298 bytes, 1 block
env/.desktop-indy/4Dwmdeskname, 9 bytes, 1 block
env/.desktop-indy/4Dwmdesks, 326 bytes, 1 block
env/.desktop-indy/4Dwmdesks.bak, 620 bytes, 2 blocks
env/.desktop-indy/4Dwmsession, 411 bytes, 1 block
env/.desktop-indy/configchecks/checksgisession, 2
bytes, 1 block
env/.desktop-indy/configchecks/checkversion, 2 bytes,
1 block
env/.desktop-indy/log, 0 bytes, 0 blocks
env/.insightrc, 1756 bytes, 4 blocks
env/.login, 597 bytes, 2 blocks
env/.profile, 722 bytes, 2 blocks
env/.sgisession, 137 bytes, 1 block
env/.sgisession.bak, 137 bytes, 1 block
env/.workspace/.tmLockIRIS.0.0, 6 bytes, 1 block
env/.workspace/.wsLockIRIS.0.0, 6 bytes, 1 block
env/.workspace/_+dev, 10143 bytes, 20 blocks
env/.workspace/ctrTimeFile, 20 bytes, 1 block
env/.workspace/currentTransferDevice, 38 bytes, 1
block
env/.workspace/database, 1353 bytes, 3 blocks
env/.workspace/saveFiles, 52 bytes, 1 block
env/.workspace/timeFile, 10 bytes, 1 block
env/4DWm, 3685 bytes, 8 blocks
env/dist_table, 1984 bytes, 4 blocks
installation_notes_d2000, 5929 bytes, 12 blocks
Example of a DIP2000 .cshrc file
#
# The commands in this file are executed each time
a new csh shell
# is started.
#
# $Revision: 1.9 $
#
# Remember last 100 commands
set history = 100
set path = (. ~/bin /usr/bin /usr/sbin /usr/bsd /bin /etc /usr/bin/X11 /usr/etc /usr/local/bin)
if ( `whoami` == "root" ) then
set pst="#"
else
set pst="%"
endif
alias ls 'ls -CF'
alias ll 'ls -lAt \!*|more'
alias cd 'cd \!*;set prompt="`hostname -s`:`pwd`${pst}
"'
alias rm 'rm -i'
alias cp 'cp -pi'
alias mv 'mv -i'
alias m more
alias h history
alias df 'df -k \!*'
alias du 'du -k \!*'
alias dipprep 'source /disk4/xdip/DIPprep'
alias disp '/usr/local/bin/xdisp dip 2030b'
alias denzo /usr/local/bin/denzo
alias scalepack /usr/local/bin/scalepack
setenv DIPHOME /diskb/xdip/xdip2030/Xdipsys
setenv MXPHOME /diskb/xdip/xdip2030/Xmxpsys
setenv XPRESSHOME /diskb/xdip/xdip2030/Xmxpsys
setenv LD_LIBRARY_PATH $DIPHOME/xv-lib
setenv EXTRASMENU $LD_LIBRARY_PATH/.text_extras_menu
setenv LINEEYE ON
set path = ($DIPHOME/bin $MXPHOME/bin $path)
if ( $?DISPLAY ) then
xset fp= /usr/lib/X11/fonts/75dpi/,/usr/lib/X11/fonts/100dpi/,/usr/lib/X11/fonts/misc/
endif
cd .
Listing of LINEEYE RS232 commands
All commands in the winterm window have the following structure:
Command-code
AK Command-code (acknowledge command) or NK (not acknowledge command)
CE Command-code
E.g. for erasing the sequence would be:
ER
AKER
CEER
The following commands are possible:
| 1 | SP | Stop the command which is being executed |
| 2 | DT | Set each axis to zero (Datum position) |
| 3 | PO | Positioning for an axis |
| 4 | GR | Goniometer Readout of position for an axis |
| 5 | CL | Calibration for an axis |
| 6 | PI | Oscillation Phi or Omega axis |
| 7 | WE | Weissenberg operation |
| 8 | LA | Setting the mode for the Laser arm axis |
| 9 | ER | Erasing |
| 10 | IR | Image Plate Rotation |
| 11 | HL | Halogen Lamp |
| 12 | SL | Solenoid for IP lock |
| 13 | IT | IP readout and Transfer of information |
| 14 | UL | UpLoad of information |
| 15 | GS | Goniometer Shutter |
| 16 | CS | Counting with the Scintillation counter |
| 17 | HV | Setting High Voltage for the scintillation counter |
| 18 | BL | Setting Base level for the scintillation couter |
| 19 | WI | Setting the Window for the pulse height analysis |
| 20 | PH | Setting the mode for the pulse height analysis |
| 21 | HS | Scanning for High Voltage |
| 22 | BS | Scanning for Base level |
| 23 | EC | disconnect nEtwork Connection with the host |
| Error code | Description |
|
1280
|
A new command has been issued before completion of the previous command (Busy). Incomplete recovery from the previous problem. Please report to Nonius or software developers. |
|
1536
|
The zeroing procedure (Setup start) has not been completed |
|
1792
|
Limiter switch activated. Press setup start to put axes to zero again. |
|
2048
|
IP locking has not completed within one minute. Problems with lock solenoid or IP rotation |
|
15616
|
Network connection failure. Check IP address in computer & controller or check Ethernet cables. |
|
15872
|
Failure of uploading the image file from the controller to the computer. Check the IP addresses in computer or check Ethernet cables. |
|
16128
|
Network disconnected |
|
16384
|
No network response from computer |
|
16640
|
Data reception has been refused by the computer |
|
16896
or 17152 |
DMAC (Controller) data overrun. Buffer memory has been filled up due to delay of data reception by the computer. Too slow connection (writing to nfs mounted disk?), computer too busy or memory too small. |
Description
of the format of a DIP2000 image
| machine | DIP2020 series | DIP2030 series |
| file size | 12501024 bytes | 18001024 bytes |
| pixel size | 80*80 [um^2] | 100*100 [um^2] |
| number of pixels | 2500*2500 | 3000*3000 |
| bytes per pixel | 2 | 2 |
| size of tailer info | 1024 | 1024 |
Intensity values are encoded differently according to type of ADC : 12bit or 16 bits. Refer to the following codes to decode these values. The type of encoding scheme can be known from the tail information by displaying the "Info." window, where Data type value greater than 100 indicates 16 bit ADC type.
(in case of dual 12 ADC type)
short iipf; /* encoded value read from image
file */
long jint; /* decoded true intensity
value */
if(iipf>=0) jint=(long)iipf;
else jint=((long)(~iipf)<<8)+32768;
(in case of dual 16 ADC type) --- this is present type
short iipf; /* encoded value read from image
file */
long jint; /* decoded true intensity
value */
if(iipf>=0) jint=(long)iipf;
else jint=((long)(~iipf)<<5);
Description of the tail of a DIP2000 image
#ifndef _tailer_h_
#define _tailer_h_
/********************TAILER STRUCTURE**************************************/
typedef struct _CO_TAIL{
char
id[4];
/* data mark (general = DIP0)
*/
long
m_type1;
/* machine reading mode:
*/
/* == 0:line
*/
/* else:spiral(IP diameter[0.1mm] */
long
m_type2;
/* 0: flat cassette
*/
/* 1: Cylindrical cassette (Para) */
/* 2: Cylindrical cassette (Perp) */
long
dtype;
/* 0: short integer(4+12bits)
*/
/* 1: unsigned short(16bits)
*/
/* 2: short integer(1+15bits)
*/
/* n ... ... ... ... ... ... ... */
long
pixelsize; /* pixel
size (main) (um)
*/
long
pixelsize2; /* pixel size
(sub) (um)
*/
float radius;
/* radius of cylinder (mm)
*/
long
xsize;
/* Number of pixels along x coord */
long
ysize;
/* Number of pixels along y coord */
long
ipno;
/* imaging plate No.(1/2)
*/
char
comment[80]; /* comment message
*/
float x_lamda;
/* X-ray wave length (A)
*/
float cdist;
/* camera distance (mm)
*/
char
monochro[32]; /* monochro parameter
*/
float pttheta;
/* 2Theta angle (deg)
*/
/* in Weissenberg configuration */
/* this is used to define mu angle */
long
ipx;
/* P position (x) of pixel adress */
long
ipy;
/* P position (y) of pixel adress */
float exposure;
/* Exposure time (sec)
*/
float kv;
/* X.G. voltage (kv)
*/
float ma;
/* X.G. current (mA)
*/
float collimator;
/* collimator diameter (mm)
*/
float coupling;
/* == 0: No weissenberg motion
*/
/* not 0: Weissenberg motion
*/
/* for DIP2000 unit: deg/deg
*/
/* for DIP3000 orcylindrical
*/
/* type unit:
mm/deg */
float
phi1;
/* Phi start angle (deg)
*/
float
phi2;
/* Phi ended angle (deg)
*/
float
phispeed; /* Phi
speed (deg/min)
*/
long
repet;
/* repetition number
*/
long
osc_axis; /* oscillation
axis
*/
/* 0: phi
*/
/* 1: omega
*/
/* 2: kappa
*/
float
g_omega; /*
omega angle (deg)
*/
float
g_kappa; /*
kappa angle (deg)
*/
float
g_phi;
/* phi angle (deg)
*/
long
xstart;
/* start pixel position along x coord */
long
ystart;
/* start pixel position along y coord */
char
dummy[152]; /* for fist part
(384 bytes) */
}CO_TAIL;
typedef struct _SR_TAIL{
long colour;
/* Current color mode
*/
long max_val;
/* Current Max_Show_Value
*/
long min_val;
/* Current Min_Show_Value
*/
long start_x;
/* AOI start point ipx value */
long start_y;
/* AOI start point ipy value */
long AOI_w;
/* AOI width (in IP pixel) */
long AOI_h;
/* AOI width (in IP pixel) */
long f1x;
/* Fiducial point 1 in x
*/
long f1y;
/* Fiducial point 1 in y
*/
long f2x;
/* Fiducial point 2 in x
*/
long f2y;
/* Fiducial point 2 in y
*/
char dummy[596];
/* part 2 for screen parameters */
}SR_TAIL;
typedef struct _TAILER{
CO_TAIL part1;
/* part1 284 bytes
*/
SR_TAIL part2;
/* part2 640 bytes
*/
/* Total 1024 bytes
*/
}TAILER;
#endif _tailer_h_
#define NULL 0
A single spiral image can be made with the Basic Operations menu of the xpress software.
If you do not want this image to be correct for non-uniformity, the file CorrectData should be changed to another file, normally called NoCorrectData. This can be done as follows:
Open a winterm window and rename the file CorrectData to e.g. CorrectData.save
% cd $DIPHOME/data
% mv CorrectData CorrectData.save
Make a new file CorrectData with the following command :
% MakeNoCorrectData > $DIPHOME/data/CorrectData
By having made this change, all image files written, will be uncorrected !!! Do not forget to "mv"the files back again if you want to go back to the normal siuation!
Prepare the experiment, by checking the generator settings, sample to plate distance, optional presence of an attenuator or Ni filter in the mirror optics, collimator and sample mount. Open the generator shutter.
Unlock the IP rotation:
Converting a spiral to a Cartesian image
A spiral image can be converted in to a cartesian window in a winterm window by running a conversion program as follows:
% ConvDIPData test.spi test.ipf $DIPHOME/data/ConvData
This will write a cartesian image file, however without the tail information. The size of the .ipf file will therefore be 1024 bytes too small. The tail can be added as follows:
Click the pencil icon with the right mouse: Application software --> IP display.
Display test.ipf.
This will pop up a message: No tailer structure.
Press info
Add the tailer information
For a 20 cm image plate :
Set pixelsize (major scan) to 80
Set pixelsize (minor scan) to 80
Set # of pixels (major scan) to 2500
Set # of pixels (minor scan) to 2500
For a 30 cm image plate :
Set pixelsize (major scan) to 100
Set pixelsize (minor scan) to 100
Set # of pixels (major scan) to 3000
Set # of pixels (minor scan) to 3000
Set the dtype to 21 for 12bit ADC systems and to 306 for 16bit ADC systems.
Optionally the other values and comments can also be filled in.
Click Apply & Storage.
Close the window.
Click Display and the image will appear.