Back to Alphabetical List

 
 SCALE 
 
 

SCALE x
Changes display scale factor. Default value is 1. The data-set is 
multiplied by SCALE before display. The larger the SCALE, the higher 
the spectrum will be.
Used by all graphical output, either on screen or on plots.
 

see also : CDISP2D DISP1D DISP2D DISP3D LEVEL PLOT ZM

 
 SCALE3D 
 
 

SCALE3D x
This context is used to reduce / expand the drawing during a 3D 
display, usually a value smaller than 1 is needed to fit the whole 
cube within the graphic window.

see also : DISP3D PLOT3D

 
 SCOLOR 
 
 

scolor index
Determines the color used by the SHOW command
index is :	1:white  2:red  3:yellow  4:green
		5:cian  6:blue  7:purple  8:black

see also : COLOR SHOW

 
 SEGM1 
 
 

SEGM1 n

choose the way the first segmentation is done in BCORR 3 .
0 : without.
1 : with a standard deviation algorithm on the data set.
2 : with a standard deviation algorithm on the first derivative
 of the data set.
3 : with thresholds on the data set, and on the first and second 
derivatives.
4 : with a dynamic clusters algorithm.
+10 : with a morphological filtering after the segmentation.

see also : BCORR BCORRP?

 
 SEGM2 
 
 

choose the way the second segmentation is done in BCORR 3. This 
feature is only useful with a polynomial approximation.
0 : without.
1 : interactive.
2 : automatic.
When you choose an interactive second segmentation, you have to 
choose one or several areas with the WINDOW command to allow the 
program to cut the correction in these areas if needed. The 
automatic segmentation uses a window, WINSEGM2, and a threshold, 
LEVELSEGM2.

see also : BCORR BCORRP?

 
 SET 
 
 

SET variable_name = value
SET static_variable := value

Assigns the value of the variable variable_name to value. Creates 
the variable if it does not already exist. Note that you should not 
use a $ sign before variable_name. value can be any kind of value : 
number, string, read from a file, another variable, a calling 
parameter ($_) or an evaluated expression.
If value is missing, or if $_ is used and no parameter are 
available, the user is prompted for input.
When the variable is created during the execution of a macro, the 
first syntax creates a local/volatile variable which value cannot be 
accessed by subsequent called macros, and that will be removed at 
the end of the macro. The second syntax creates a global/static 
variable that can be accessed by any macros, and that will remain 
until explicitly removed with the UNSET command.

see also : DUMP FUNCTIONS MUNSET UNSET VARIABLES

 
 SETPATH 
 
 

SETPATH new_path_string
Permits to change the current GifaPath used for calling macros.
The new_path_string contents all the directories in which macros 
file will searched for, the list is blank separated. The content of 
the current GifaPath is held into the $GIFAPATH context. So the 
following is a very typical use for adding an address

SETPATH ("new_directory"; $GIFAPATH)

see also : MACRO SETPROMPT

 
 SETPEAK 
 
 

SETPEAK index F1 { F2 { F3 } }

Permit to modify directly the content of the peak table. The number 
of entries depends whether you are in 1D, 2D or 3D.
The peak entry at index is modified in the current peak table. Only 
coordinates are given, intensity is taken form the data-set, widthes 
and other parameters are lost.
This is not the way for adding new peaks in the peak table, use 
POINT_INPUT POINT->PK instead.

see also : PEAK PKRESET POINT->PK

 
 SETPROMPT 
 
 

SETPROMPT new_prompt_string

Permits to modify the prompt used in the text window.

see also : MACRO

 
 SETVAL 
 
 

setval i { j {  k } } x
Will set the value of the data point to x. The number of coordinates 
of the point depends of dim. In dim 2 or 3, coordinates are F1 F2 or 
F1 F2 F3. Can be usefully used when associated to the functions 
valnd() to change data point value.

see also : FUNCTIONS SET

 
 SH 
 
 

SH string
Will pass the string to the operating system. For instance, used by 
macros such as pwd, ls, more, etc...
SH alone will enter the Operating system

see also : CD ls more pwd rm vi vim vip

 
 SHIFT 
 
 

This context holds the systematic baseline shift of the current 
data-set,
computed automatically by EVALN.
Used by INTEG.
 

see also : ADDBASE EVALN NOISE

 
 SHOW 
 
 

 SHOW parameter
Displays graphically extra information without disturbing the 
content of the working buffer. Uses the current definition of SCOLOR 
for drawing.

With parameter equal to:
-WINDOW:	display actual window used to compute the chisquare
-FILTER:	display filter used for Deconvolution
-LAMB:	display evolution of Lambda  during MaxEnt iteration
-ENT:		display evolution of Lambda  during MaxEnt iteration
-CHI:		display evolution of Lambda  during MaxEnt iteration
-STEP:	display evolution of Lambda  during MaxEnt iteration
-SUM:	display evolution of Lambda  during MaxEnt iteration
-CONV:	display evolution of Lambda  during MaxEnt iteration
-FT:		display evolution of Lambda  during MaxEnt iteration
-RESIDUE:	displqy the residue of the spectrum after a MaxEnt run
-CURRENT:  moves the current displayed image to the other window
-LINEFIT:	the result of the last line-fitting computation
-AMOEBA: 	the mask used by the last INTEG command
 

see also : APPLY GET PUT SCOLOR SHOWC SHOWLINE SHOWPEAK SHOWPEAKS SHOWTEXT

 
 SHOWC 
 
 

SHOWC scale
display the currently JOINed file using the current zoom window 
(redefined in ppm and used on the JOINed data-set) 
The current parameters are used for the display (VHEIGH, LEVEL, 
etc..) but not SCALE which is passed to the command. In 2D the 
display is only showed in the controur window. The command is not 
implemented in 3D yet.
This command is used by the super1d / super2d macros to display 
several spectra on screen.

see also : JOIN SCOLOR SHOW super1d super2d

 
 SHOWLINE 
 
 

showline x1 y1 x2 y2
Will draw a line on the displayed spectrum. Coordinates are in index 
values. The line will be drawn accordingly to the zoom mode. When in 
2D with density plot and contour plot both on, the contour plot will 
be used for display. Uses the current definition of SCOLOR for 
drawing.

see also : PLOTLINE PLOTLINES SCOLOR SHOWPEAK SHOWPEAKS SHOWTEXT

 
 SHOWPEAK 
 
 

showpeak index
will display on the current graphic, the indexth peak of the peak 
table. Uses the current definition of SCOLOR for drawing.

see also : PEAK PLOTPEAKS SCOLOR SHOWPEAKS

 
 SHOWPEAKS 
 
 

will display on the current graphic, the contents of the internal 
peak table, thus permitting to visualize the result of the PEAK 
command.Uses the current definition of SCOLOR for drawing.
 

see also : PEAK PLOTPEAKS SCOLOR SHOWPEAK

 
 SHOWTEXT 
 
 

SHOWTEXT string X Y 
Displays the string "string" on the displayed spectrum, at the X, Y 
position. Coordinates are in index values. When in 2D with density 
plot and contour plot both on, the contour plot will be used for 
display. Uses the current definition of SCOLOR for drawing.

see also : PLOTTEXT PLOTTEXTS SCOLOR SHOWLINE SHOWPEAK SHOWPEAKS

 
 show_fit 
 
 

 to make a nice multicolored plot out of the fitted line shapes

 

see also : LINEFIT plot_fit SHOW

 
 SIGN 
 
 

SIGN -1 / 0 / 1
	Tells the program how to display 2D data-sets. Used by DISP2D, 
CDSIP2D and PLOT commands
if  1, 2D program will display only positive levels,
if -1, 2D program will display only negative levels,
if  0, 2D program will display both positive and negative levels,
 

see also : CDISP2D DISP2D MINUS PLUS

 
 SIGN_PEAK 
 
 

SIGN_PEAK 1 / -1
Indicates to PEAK and to INTEG to search for positive or negative 
peaks.
 

see also : INTEG PEAK

 
 SimSpect2D 
 
 

 Macro to simulate a 2D spectrum from an intensity file and a DBM ppm file,
 used by SimSpect2D_form

 SimSpect2D dbm_ppm_filename intensity_filename F1_modulation Symetrical_option

 the ppm DBM file can be generated from an ascii ppm file by the
 macro mkdbppm

 the ascii intensity file has the following free-format:

 INT residu_name1 residu_number1 atom_name1 residu_name2 residu_number2 
 atom_name2 intensity_value

 F1_modulation can be either sh_tppi or phase_modu

 if Symetrical_option is sym, then each entry in the intensity file is duplicated on 
 the other side of the spectral diagonal.

 

see also : DBOPEN mkdbppm SimSpect2D_form SIMUN

 
 SimSpect2D_form 
 
 

 SimSpect2D_form args...
 builds and apply a standard action for 2D spectrum simulation

 

see also : DBOPEN SimSpect2D SIMUN

 
 SIMU 
 
 

 Simulate data, works in 1D in 2D and in 3D
You will be prompted for input. SIMU memorizes the last used values 
so SIMU %% is a valid syntax.
 

see also : ADDNOISE READ SimSpect2D SIMUN

 
 SIMUN 
 
 

(1D) simun ampl linecoord linewidth phase

(2D) simun flg ampl linecoordf1 linecoordf2 linewidthf1 \
  linewidthf2 phasef1 phasef2

(3D) simun ampl linecoordf1 linecoordf2 linecoordf3 \
   linewidthf1 linewidthf2 linewidthf3 phasef1 phasef2 phasef3

  Simulate data, works in 1D in 2D and in 3D
 You will be prompted for input. One line is simulated at each run,
 and is added to the data. The line coordinates are entered in PPM,
 Hz or Index, according to the unit value. The line widthes are in 
Hz.
 The 1D and 3D data are complex in all dimensions, the 2D data can 
be 
 phase or amplitude modulated, depending on flg :
 flg = 0 : the data are simulated in phase modulation
 flg = 1 : the data are simulated in amplitude modulation

SIMUN memorizes the last used values 
 so SIMUN %% is a valid syntax.

 

see also : ADDNOISE READ SimSpect2D SIMU ZERO

 
 SIMUNOE 
 
 

This command is now obsolete, it has been superseded by the 
SimSpect2D macro which realizes the same action.
	This command permits to simulate a 2D data set from the result of 
a program computing NOESY intensities (such as CORMA).
	It will prompt you for the filename of the Corma output file,  
the filename of the chemical shift file (generated with the command 
CHEMS), the name of the output file, holding information on 
simulated peaks and for number of data points and spectral windows 
you wish to simulate.
	It generates a time domain data-set which can be subsequently 
processed as a regular FID.

see also : CHEMS SimSpect2D SIMU

 
 SIN 
 
 

 SIN x { axis }
	SIN is used to multiply data by a trigonometric function varying 
continuously from pure sine to pure cosine. It works for 1D 2D and 
3D spectra. You have to enter first the value of the parameter x 
varying continuously from 0 (pure cosine) to 0.5 (pure sine). x 
corresponds to the position of the maximum of the filter in your 
window.  If you are working on a 2D or a 3D spectrum, there is 
another parameter which determines on which axis (axes) the 
apodization will be applies.

see also : EM FILTER GM JMULT SQSIN TM

 
 size 
 
 

 list the size parameters of the current data-set

 

see also : CHSIZE

 
 SLOPE 
 
 

slope n
Will compute a relaxation rate on the current nOe build-up curve by 
using the initial slope method, computed from the first n points of 
the data-set.

see also : METH RELAXRATE

 
 SMOOTH 
 
 

 SMOOTH z   { z2 { z3 }}
where z { z2 { z3 }} is the size of the smoothing window

Permits to smooth a data set by the moving-average technic. Works in 
1D as well as in 2D and 3D.

see also : MEDIAN

 
 SMOOTH1 
 
 

SMOOTH1 n
to be used with BCORR 3
 controls the smoothing of data for the first segmentation
0 : no smoothing.
+1 : moving average of the data set on a window of WINMA points.
+10 : hysteresis smoothing of the data set with the value 
LEVELHYSTE.

see also : BCORR BCORRP?

 
 SNAPSHOT 
 
 

SNAPSHOT file_name
 Permits to store the current graphic display to a UIS file (VMS/VWS 
only) The file can then be displayed with the render command (see 
VWS documentation)
 

 
 SPECW 
 
 

 SPECW x { y { z }}
 Permits to enter the value for the spectral width of the current 
data-set. One parameter will be needed for each dimension of the 
data-set.
When reading a file the spectral width is set to 2000 * 3.1416 if no 
parameter block is available.
The value for spectral width are changed by EXTRACT
 

see also : calib EXTRACT OFFSET size

 
 SPIN 
 
 

SPIN n
Shifts the color table of 2D density image n times. Nice but 
probably useless. (Only VWS )
 

 
 sprintf 
 
 

 sprintf format_string arg1 arg2 ... *

 realises the equivalent of a C  `sprintf'
 all the remaining of the line  up to the star is taken as arguments
 result is returned to the static variable $returned

 only one line can be put into the string, so \n cannot be used

 

see also : FPRINT fprintf PRINT printf

 
 SQSIN 
 
 

 SQSIN x { axis }
	SQSIN is used to multiply data by the square of a trigonometric 
function varying continuously from pure squared sine to pure squared 
cosine. It works for 1D 2D and 3D spectra. You have to enter first 
the value of the parameter x varying continuously from 0 (pure 
square cosine) to 0.5 (pure square sine). x corresponds to the 
position of the maximum of the filter in your window.  If you are 
working on a 2D or a 3D spectrum, there is another parameter which 
determines on which axis (axes) the apodization will be applies.

see also : EM FILTER GM JMULT SIN TM

 
 startup.g 
 
 

 used as a default startup macro

 load the default GUI and preset some default values

 

see also : button.g

 
 STDY 
 
 

Parameter for STPL.
Each new line during STPL is shifted by STDY centimeters on the Y 
axis. Default is 0.1
 

see also : STPL STPL?

 
 STEP 
 
 

Constant used when Maximum Entropy run with no line-minimization.
Algo 1, (1E-6..0.5)  Algo 2 or 3 (0.1 .. 10)
These algorithms are usually highly inefficient.!
 

see also : ALGO MAXENT STEPMAX

 
 STEPMAX 
 
 

This context holds the  maximum extension of the search during the 
line-minimization. Default value is 1.2 for GIFA algorithm, 100 for 
CONJG.
 

see also : ALGO MAXENT STEP

 
 STPL 
 
 

STPL output
This command permits to draw stacked-plots of 2D data-sets. The plot 
is determined by the value of the following parameters:
CX : length in centimeters of a line.
CY : maximum height of a peak in centimeters.
SCALE : scaling applied to the data before plotting, if scale=1 then 
the larger peak on the surface will be CY high, if scale>1 then 
clipping will occur.
STDY : each new line is offsetted by STDY centimeters in the Y axis.
STSKIP : a line every STSKIP line will drawn.
STSHIFT : each new line will shifted right by STSHIFT points, if 
negative then the shift is done on the left. May be fractional.
STSKEW : determine how the horizontal line are skewed during plot, 
if negative skewed to the right, to the right if positive.

output is either a file name or *s for on screen display.
The command STPL? prompts you for all those parameters
 

see also : CX CY PAGE PLOT STDY STSHIFT STSKEW STSKIP

 
 STPL? 
 
 

Prompts for all the parameters of the STPL command (see STPL)

 

see also : STDY STPL STPL? STSHIFT STSKEW STSKIP

 
 STSHIFT 
 
 

Parameter for STPL.
STPL will shift each new by stshift points to the right during the 
plot. May be negative, null or positive; may be fractional.
Default is 0.5.
 

see also : STPL STPL?

 
 STSKEW 
 
 

Determines how the horizontal lines are skewed during a stacked 
plot. If 0 no skewing occurs, if positive the plot is skewed to the 
right, if negative, the plot is skewed to the left.
For instance, a value of -1.0 will skew the horizontal by 45¡ to the 
left. STSKEW gives nice effects in conjunction with STSHIFT. 

see also : STPL STPL?

 
 STSKIP 
 
 

Parameter for STPL.
STPL will skip stskip lines during the plot. Default is 1.
 

see also : STPL STPL?

 
 SUMCONS 
 
 

When set to 1, the program tries to minimize the value of the sum of 
all the points of spectrum during the Maximum Entropy run.
   Should be set whenever a window 1 n is used, or when Antiphase J-
deconvolution is used.
 

see also : ALGO MAXENT

 
 SUMREC 
 
 

SUMREC x1 y1 x2 y2
Realizes the integration under a given area,  value is corrected for 
baseline shift (if any computed with EVALN)

see also : EVALN INTEG sumrec_1d

 
 sumrec_1d 
 
 

 sumrec_1d  radius_of_box
 
 integrate 1D peak on a box around each peak in the peak table

 

see also : INTEG SUMREC

 
 super1d 
 
 

 if called with no argument :
    builds a form which permits to superimpose up to 3 1D in the disp1d window

 if called with proper arguments :
    does actually the display

 

see also : DISP1D JOIN SHOWC super2d

 
 super2d 
 
 

 if called with no argument :
    builds a form which permits to superimpose up to 3 2D in the cdisp2d window

 if called with proper arguments :
    does actually the display

 

see also : CDISP2D JOIN SHOWC super1d

 
 SVD->AR 
 
 

SVD->AR n
Compute the autoregressive coefficients from the singular 
decomposition. This is the second step of the LP-SVD method.
n = 1 : forward autoregressive coefficients
n = 2 : backward autoregressive coefficients
n = 3 : both coefficients

see also : DT->SVD ORDER SVD->DT SVDCLEAN1 SVDLIST svd_rev

 
 SVD->DT 
 
 

Compute back a new data-set from a truncated set (cf SVDCLEAN1) of 
singular values.

see also : DT->SVD ORDER SVD->AR SVDCLEAN1 SVDLIST

 
 SVDCLEAN1 
 
 

SVDCLEAN1 nsignals flag
Keep only the first n signals singular values and put the other to 
0. Use it only if you have a good insight of the number of signals 
in the spectrum. The flag (yes/no) determines wether you want to 
remove the noise power associated with the removed root. 

see also : cadzow DT->SVD ORDER SVD->AR SVD->DT SVDCLEAN2 SVDLIST

 
 SVDCLEAN2 
 
 

SVDCLEAN2 level flag
Keep only the singular values larger than level and put the other to 
0. The flag (yes/no) determines wether you want to remove the noise 
power associated with the removed root.

see also : DT->SVD ORDER SVD->AR SVD->DT SVDCLEAN1 SVDLIST

 
 SVDLIST 
 
 

SVDLIST i j
List the singular values from index i to j.

see also : SVD->AR SVD->DT SVDCLEAN1

 
 svd_rev 
 
 

 svd_rev n_of_point

 reconstruct the missing n_of_point first data points
 using the lp-svd method
 changes order to n_of_point*2

 

see also : BURG burg_rev SVD->AR

 
 SWA 
 
 

SWA {Fx} 
Consider the left part of the data as real and the right part as 
imaginary, and swap them to transform the data set to the internal 
representation of complex data; i.e. odd points real and even points 
imaginary. This is the opposite of USWA.
 

see also : FLIP FLOP REAL USWA

 
 SYM 
 
 

SYM n
Sumetrizes the current 2D data set using either a mean value (n=1) 
or a smallest
value (n=2) algorithm. n=3 corresponds to an algorithm which smootly 
switch from one algorithme to the other depending on the difference 
between the 2 values.

see also : MINDATA TRANSPOSE