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 p 
 
 

 pp  - interactive

 sets - up every thing for peak picking and realizes it
 permits peakpicking in a interactive, graphical manner.

 

see also : PEAK

 
 PAGE 
 
 

PAGE plot_file_name
	This command appends code at the end of plot_file_name for page 
ejection; closes the plot file; and send it to the plotter.
 

see also : FORGET PLOT PLOTTER

 
 PCOLOR 
 
 

PCOLOR color_index plot_file_name
	This command permit to change the color mode when plotting on a 
color Postscript printer. On HPGL PCLOR and PEN are equivalent.

color_index is :	1:black  2:red  3:yellow  4:green
		5:cian  6:blue  7:purple  8:white

see also : COLOR PEN PLOT

 
 PEAK 
 
 

PEAK output {radius}
    Will generate a peak-table from the current data set, output can 
be either a file-name or *screen. Peaks are located if their 
intensity lies within the margin defined by the MINIMAX command.
	In 2D, PEAK will prompt you for a "packing radius". Peaks which 
lies within a distance equal or smaller than this packing radius (in 
points) will be ignored in favor of the larger peak in this radius.
	The command SHOWPEAK will show you on the display where the peaks 
have been found. The command PKLIST will list the peak table 
contents.
This is the peak-picker form the PARIS integrator.

see also : INTEG LINEFIT MAX MINIMAX PK->DT PKCLEAN PKCLEAR PKLIST PKPROJ PKREAD PKRESET PKRM PKSELECT PKSYM PKWRITE pp SETPEAK SHOW SIGN_PEAK ZERO_QU

 
 peak_pick 
 
 

 peak_pick  - interactive

 (replaces pp)

 sets - up every thing for peak picking and realizes it
 permits peakpicking in a interactive, graphical manner.


 
 PEN 
 
 

Pen n plot_file_name
Selects the pen number n on the plotter. On a postscript laser 
printer, this corresponds to different line width and dash patterns.
 

see also : PAGE PCOLOR PLOT

 
 PH 
 
 

PH is an interactive 1D phasing module. A button window pops-up 
which permits the user to adjust the 0th and 1st order phase. The 
1st order pivot point is set by clicking in the 1D Spectrum window.
	If you exit by clicking in Ok the phase correction is applied, 
and the phase values becomes then the default values for the PHASE 
command. If you exit with Cancel, no phase correction is applied and 
the original data is restored.
 

see also : apsl HPHASE ph2dc ph2dr PHASE ZM

 
 ph2dc 
 
 

 interactive
 permits to phase a 2D in F1 by interactively selecting columns
 and building a composite 1D

 

see also : colint PH ph2dr rowint

 
 ph2dr 
 
 

 interactive
 permits to phase a 2D in F2 by interactively selecting rows
 and building a composite 1D


 

see also : colint PH ph2dc rowint

 
 PHASE 
 
 

PHASE X Y {dim) 
	Permits to modify the phase of the current displayed spectrum. 
You have to enter zero-order (X) and first-order (Y) corrections, 
and dimension (dim) in 2D. Values are in degree, and first-order 
correction uses center point as pivot.
	For 1D data an interactive phase command is available : PH.
 

see also : apsl HPHASE PH

 
 PK->DT 
 
 

Computes a pseudo-FID from the peaks parameters s held in the PEAK() 
table. Permits to display a spectrum computed by LP analysis.

see also : PEAK RT->PK SHOW

 
 pkadjust 
 
 

 pkadjust line_shape
 with line_shape lorentzian / gaussian

 adjust each peak in the table by fitting around it

 
 PKCLEAN 
 
 

pkclean min_int
Will remove from the pak table entries with intensity less than 
min_int

see also : PEAK PKCLEAR PKRESET PKSELECT RT->PK

 
 PKCLEAR 
 
 

This command remove all entry from the current peak table.

see also : PEAK PKRESET PKRM PKSELECT

 
 PKLIST 
 
 

pklist i j
List the contents of the current peak table, from entry i to entry 
j.

see also : INTEG PEAK PKSELECT RT->PK

 
 PKPROJ 
 
 

PKPROJ axis alogrithm tolerance

Propagates the contents of the 2D peak-table on the 1D peak-table. 
All the 2D peaks will generate an entry in the 1D table. If two (or 
n) peaks are less than tolerance (in Hz) apart during the 
projection, they will be merged into one peak. The intensity of the 
resulting peak will be either the mean value ot the max value of the 
initial peak, depending on the chosen algorithm (Mean or Skyline).
PKPROJ does not modify the spectral parameters (spectral width, 
frequences and offsets), so, if the 1D spectral parameters are 
different from the 2D parameters, strange results can be obtained.

see also : PEAK PKSYM

 
 PKREAD 
 
 

PKREAD file_name yes/no
Reads a peak list file created with PKWRITE into internal peak list. 
Depending on the option, the read values are appended to the current 
value (no) or the peak table is cleared before reading the file.

see also : PEAK PKRESET PKWRITE

 
 PKRESET 
 
 

This command recompute peak intensities from the current data set 
and the current peak table, giving results equivalent to PEAK. 
Usefull when either the data-set or the peak table has changed. Note 
that PKREAD reads in the whole peak table, including intensities, 
thus PKRESET permits to recompute intensities form a stored table.

see also : PEAK PKCLEAR PKLIST PKREAD

 
 PKRM 
 
 

PKRM index
Remove the peak index in the current peak table.

see also : PEAK PKCLEAN PKCLEAR PKRESET pkrmi PKSELECT

 
 pkrmi 
 
 

pkrmi  interactive

 this macro permits to interactively and graphically
 remove peaks from the peak table

 

see also : MONOPOINT PKRM

 
 PKSELECT 
 
 

PKSELECT index()
Select the peaks parameters whose index() are given. To end 
selection, enter the index 0.

see also : PEAK PKCLEAN PKCLEAR PKRESET PKRM

 
 PKSYM 
 
 

PKSYM param tolerance

Symmetrize in the 2D peak-table by either removing (param=0) entries 
in the peak table that do not have a symmetrical counterpart, or by 
adding (param=1) a symmetrical peak in the table. The presence or 
absence of a symmetrical peak is checked within a window of 
tolerance (in Hz) around the peak.
PKSYM does not modify the spectral parameters (spectral width, 
frequences and offsets), so, if they significally different on the 
both axis, strange results can be obtained.

see also : PEAK PKPROJ

 
 PKWRITE 
 
 

PKWRITE file_name
Writes the contents of the peak table on a file. The table can then 
be read with the PKREAD command.

see also : PEAK PKREAD

 
 PLANE 
 
 

PLANE axis index
In 3D only.
Permits to select a plane from the 3D buffer and copies it to the 2D 
buffer. Axis is either F1, F2 or F3 as the axis orthogonal to the 
chosen plane. Thus F1 selects plane F23, etc...

see also : COL DIAG DIM planeint ROW VERT vertint

 
 planeint 
 
 

 interactive
 permits to choose a plane interactively on a 3D by clicking on the 1D
 typically, the 1D should come from a vert command (or equivalent direction)
 and the currently displayed plane determines the direction

see also : COL ph2dc ROW rowint vertint

 
 PLOT 
 
 

plot plot_file_name
Plots the current spectrum on the plotter, using the current value 
of contexts (see PLOT?).
If in 1D, plot the 1D spectrum
If in 2D, plot the contour-plot, as displayed with the CDISP2D 
command.
If in 3D, plot the currently selected plane, as displayed with the 
CDISP2D command.
will create a plot file named file_name, which can later be plotted 
by the command    Gifa> PAGE plot_file_name
If your GIFA program is working in postscript (check with the CONFIG 
command), and if you have a postscript previewer (IBM, Silicon 
Graphics, some X-stations) then you can display the contents of your 
plot-file before sending it to the plotter.
The filename *s
 will send the plot to the  screen rather than to a file or the 
plotter.
The file name *PL will create a temporary plot file that will be 
deleted after plotting.

see also : CDISP2D CX CY DISP1D easyplot GRID LEVEL PAGE PCOLOR PEN PLOT3D PLOTAXIS PLOTAXIS? plotcolordisp PLOTLINE PLOTLINES plotn PLOTOFFSET PLOTPEAKS PLOTTER PLOTTEXT PLOTTEXTS plot_fit STPL STPL? TITLE

 
 PLOT3D 
 
 

plot3d plot_file_name
Equivalent to the PLOT command, will generate a 3D plot, equivalent 
to the display obtained with the DISP3D command.

see also : CHECK3D DISP3D disp3d_form PAGE PLOT

 
 plot? 
 
 

PLOT?
 interactive
 prompt for parameters for plotting

 

see also : easyplot PLOT

 
 PLOTAXIS 
 
 

PLOTAXIS direc output
   This command plots a set of axis on its output. 
The axis are 0.5 cm below the current plotoffset.
If direc=F1 a vertical axis is drawn
If direc=F2 a horizontal axis is drawn
If direc=F12 both axes are drawn
PLOTAXIS uses the current SPECW and OFFSET for the axis calibration.
 

see also : GRID PAGE PLOT

 
 PLOTAXIS? 
 
 

This command prompts you for different parameters that will be used 
by PLOTAXIS : unit (may be different of the UNIT command) and 
separations on x and y axes. The definition is also used for the 
GRID command.

see also : GRID PLOT PLOTAXIS PLOTAXIS? TITLE

 
 plotcolordisp 
 
 

 plotcolordisp <Filename>

 Makes a color contour plot on plotter

 

see also : easyplot PLOT

 
 PLOTLINE 
 
 

PLOTLINE X1 Y1 X2 Y2 plot_file
Draws a line from the X1 Y1 point to the X2 Y2 point (in cm, 
relative to PLOTOFFSET).

see also : PLOT PLOTLINES PLOTTEXT PLOTTEXTS

 
 PLOTLINES 
 
 

PLOTLINES X1 Y1 X2 Y2 plot_file
Draws a line from the X1 Y1 point to the X2 Y2 point (in index unit, 
projected on the CX x CY area, as used by the PLOT command).

see also : PLOT PLOTLINE PLOTPEAKS PLOTTEXT PLOTTEXTS

 
 plotn 
 
 

 plotn total_cx total_cy partial_cx partial_cy  y/n

 plot on several pages to fit size
 permits to build large composite plots on size limited plotters

 

see also : easyplot PLOT

 
 PLOTOFFSET 
 
 

PLOTOFFSET x y
Values are used to offset the (0,0) origin of the plot at (x,y). 
Permits to draw several plots on the same page, or to leave room for 
axes. Default values are 1 1 (in cm).

see also : CX CY PLOT

 
 PLOTPEAKS 
 
 

will plot on the plot file, the contents of the internal peak table, 
thus permitting to plot the result of the PEAK command.

see also : PEAK PLOT PLOTLINE PLOTLINES PLOTTEXT PLOTTEXTS SHOW

 
 PLOTTER 
 
 

PLOTTER H(P-GL) / p(ostscript)
Permits to select which kind of output will be generated ans using 
all the plot commands. HP-GL or postscript code can be selected. If 
the gifaplot shell script has been correctly st-up, the correct 
output should be sent to the correct plotter with no user 
intervention.

see also : CONFIG PAGE PLOT

 
 PLOTTEXT 
 
 

PLOTTEXT string X Y plot_file
Sends the string "string" to the plot_file, at the X, Y position (in 
cm, relative to PLOTOFFSET)

see also : PLOT PLOTLINE PLOTLINES PLOTTEXT

 
 PLOTTEXTS 
 
 

PLOTTEXTS string X Y plot_file
Sends the string "string" to the plot_file, at the X, Y position (in 
index unit, projected on the CX x CY area, as used by the PLOT 
command)

see also : PLOT PLOTLINE PLOTLINES PLOTTEXTS

 
 plot_fit 
 
 

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

 

see also : LINEFIT SHOW show_fit

 
 PLUS 
 
 

Sets to zero the negative part of the data set.

see also : MINUS ONE ZERO

 
 point 
 
 

 interactive mode on screen

 Permit to interactively inspect the content of the data-set,
 using the mouse on the graphic-screen.  Exit when you click
 the 3rd button of the mouse
 Clicked point are stacked onto the POINT_STACK

 

see also : MONOPOINT point_cross point_dump POINT_PUSH ZM

 
 POINT->PK 
 
 

This command will add the point in the point stack (set by the user 
with the last point or MONOPOINT command), into the current peak 
table.

see also : MONOPOINT PEAK PKLIST point POINT_PUSH SETPEAK

 
 POINT_CLEAR 
 
 

clears the point stack

see also : point POINT_PUSH

 
 point_cross 
 
 

 interactive mode on screen

 Permit to interactively inspect the content of the data-set,
 using the mouse on the graphic-screen.  Exit when you click
 the 3rd button of the mouse
 Clicked point are stacked onto the POINT_STACK

 that one draws a little cross

 

see also : MONOPOINT point point_dump POINT_PUSH ZM

 
 point_dump 
 
 

 dumps the containt of the point stack

 

see also : point POINT_PUSH

 
 POINT_INPUT 
 
 

POINT_INPUT F1 {F2}
A point with coordinates F1 (in 1D, or F1,F2 (in 2D) is put on the 
top of the point stack.

see also : point POINT_PUSH

 
 POINT_POP 
 
 

remove one entry from the point stack.

see also : MONOPOINT point POINT_PUSH

 
 POINT_PUSH 
 
 

Add one entry into the point stack.

The point stack contains spectral coordinates, which can be used 
within macros, and are also used by certain commands (typically 
BCORR).

Whithin macros, the content of the point stack can be examined with 
the context variables : $npoint; $pointx[i]; $pointy[i]

The POINT_CLEAR command empties the stack.
The MONOPOINT command sets the top entry on the stack.
The POINT_PUSH command push the entry on the top, thus duplicating 
the entry, and adding an entry in the stack.
The POINT_INPUT command permits to enter a value with determined 
values
The POINT_POP command pops one entry in the stack.
The macro point permits fill the stack by clicking on the spectra
The macro point_dump permits to dump the content of the stack

see also : BCORR BCORRP? MONOPOINT point POINT_CLEAR point_dump POINT_INPUT POINT_POP

 
 pp 
 
 

 pp  - interactive

 sets - up every thing for peak picking and realizes it
 permits peakpicking in a interactive, graphical manner.


 
 PRIMER 
 
 

	The GIFA program is a multi-purpose NMR program. It is designed 
for the processing and the display of 1D and muti-dimensional NMR 
data-sets.
	The program includes sophisticated signal processing methods such 
as Maximum Entropy processing, Linear prediction, line fitting, 
complete control language, or 2D peak integrator as well as more 
classical processing, displaying and plotting of NMR experiments. It 
can handle the complete study of a set of NMR multidimensionnal 
data-sets, from the raw data to plotting, visualisation, and finally 
give some help to the assignment process.
	In contrast with most NMR programs, Gifa tends to do as much data 
processing as possible in memory. Thus a typical processing session 
consists in :
* transfering the raw data-set from the spectrometer to the 
processing computer and converting it to a gifa-compatible format, 
for instance with the ux2gifa shell script.
* loading the data-set in memory with the command READ
* apodizing the data set with EM (exponential), GM (Gaussian), TM 
(trapezoid), SIN (shifted sine bell) or SQSIN (squared shifted sine-
bell).
* changing the size of the data set (zero filling or truncature) 
with CHSIZE.
* realizing the Fourier transform in the acquisition dimension with 
ft_sim (simultaneous acquisition) or ft_seq (sequential 
acquisition); and in the non-classical dimension with ft_tppi (TPPI 
acq.), ft_sh (States-Haberkorn acq.), ft_sh_tppi (mixed mode) or 
ft_phase_modu (phase modulation) (there are als the basic commands : 
FT, RFT, FTBIS, IFT, IRFT, IFTBIS, REVF, INVF).
* correcting the phase with PH (interactive), ph_2dc and ph2dr 
(interactive in 2D), PHASE or HPHASE (batch); or taking the modulus 
with MODULUS.
* eventually correcting the base line with BCORR (see help for that 
command)
* contour plot as well as density plot are available for 2D's. There 
is even an on-screen stacked plot available.
* rows and columns from 2D's can be examined : rowint, colint 
(interactive); ROW, COL, DIAG; as well as planes and lines from 3D's 
planeint, vertint, PLANE, VERT, DIAG.

You should also know that :
o 1D, 2D and 3D processing can be selected
o plots are available on postscript as well as HP-GL
o there is a peak-picker in 1D, 2D and 3D, as well as a line-fitter 
(in 1D so far)
o MaxEnt and Linear Prediction are available with a comprehensive 
set of commands
o you can write your own commands with the command langage
o you can even set-up your own graphic interface with the BUTTONBOX 
command.

Try also :
* HELP a_given_command		/ for instance :  help ft
* apropos a_given_topic		/ for instance :  apropos transform
* reading the manual


 
 PRINT 
 
 

PRINT string
This command permits to issue a string to the user. Permits 
interactivity in command file.

see also : ALERT ERROR FPRINT fprintf PLOTTEXT printf SHOWTEXT sprintf

 
 printf 
 
 

 printf format_string arg1 arg2 ... *

 realises the equivalent of a C  `printf'
 all the remaining of the line  up to the star is taken as arguments 

 

see also : FPRINT fprintf PRINT sprintf

 
 proc2d 
 
 

 proc2d sourcefile destinationfile axis_to_process commands

 this macro processes a 2D file using the cache system (join, getc, putc)
 it permits to handle very large files, which would not fit into memory.

 sourcefile         : is the initial data-set
 destinationfile    : is the result of the process
 axis_to_process    : either F1 or F2 (NOT F12)
 commands           : the commands to be applied to each row/column in 1D notation

 the commands are the regular commands you would used to process a 1D data-set.
 when called without parameters, 'commands' can be several line long, as typed
 when proc2d is called with parameters on the line, then 'commands' should be a single
 command line within quotes.

 e.g.
 proc2 my_ser_file my_F2_processed F2 'sin 0.2  ft_sim  phase 30 -40  real  bcorr 3'
 proc2 my_F2_processed my_F12_processed F1 'sin 0.2  revf ft  phase 0 30  real  bcorr 3'

 would process a whole 2D in 2 steps.

 

see also : easy2d FT JOIN proc3d

 
 proc3d 
 
 

 proc3d sourcefile destinationfile plane_to_process commands

 this macro processes a 3D file using the cache system (join, getc, putc)
 it permits to handle very large files, which would not fit into memory.

 sourcefile         : is the initial data-set
 destinationfile    : is the result of the process
 plane_to_process   : either F1, F2 or F3 (NOT F12 or F123)
 commands           : the commands to be applied to each plane in 2D notation

 the commands are the regular commands you would used to process a 2D data-set.
 when called without parameters, 'commands' can be several line long, as typed
 when proc3d is called with parameters on the line, then 'commands' should be a single
 command line within quotes.

 e.g.
 proc3 ser_file F1_proc F1  'sin 0.2 f12 ft_sim  phase 30 -40 f2 real f12 ft_tppi '
  process axes f3 and f2 as 2D
 proc3 F1_proc full_proc F2 'sin 0.2 f1  ft_tppi real f1  bcorr 3 f1'
  process axis f1

 would process a whole 3D in 2 steps.

 

see also : easy3d FT JOIN proc2d

 
 proc3d_form 
 
 

 prepares a form for proc3d

 

see also : proc3d

 
 PROJ 
 
 

PROJ n a
	Permits to perform a projection of 2D data-set. Projections are 
done either along F1 (n=1) or F2 (n=2) axes, with either skyline 
(a=s) or mean (a=m) technic.
 

see also : DIAG DIM proj3d

 
 proj3d 
 
 

 proj3d file axis algo

 axis is F1, F2 or F3
 algo is M or S

 equivalent to proj in 3D, but on joined file

 

see also : JOIN proc3d PROJ

 
 PUT 
 
 

PUT parameter {n}
 
Moves the content of the current buffer to an other buffer
With parameter equal to:
-DATA:     load the data to be used for MaxEnt processing in 1D

-FILTER:   load the filter used for Deconvolution.  If NCHANNEL is 
greater than 1, then which channel you want to put.  eg.  PUT FILTER 
3.  PUT FILTER 0  will consider the current data set as the 
multichannel filter, and will load the whole filter. Useful when 
associated with GET FILTER to store filters as files.

-WINDOW:   load the window to be used for MaxEnt processing

in 2D only
-ROW  n :  load the 1D buffer in the ROW n
-COL  n :  load the 1D buffer in the COL n
-AMOEBA : the mask definition to be used by the next MSKINTEG 
command

in 3D only
-PLANE Fx n : load the 2D buffer in the plane Fx n
 

see also : APPLY GET SHOW

 
 PUTC 
 
 

syntaxe depends on the dimentionnality of the currently joined data-
set (to) and on the current context dim (from) :
1D to 1D : PUTC left right
1D to 2D : PUTC axis index left right
1D to 3D : PUTC axis index1 index2 left right
2D to 2D : PUTC left1 left2 right1 right2
2D to 3D : PUTC axis index left1 left2 right1 right2
3D to 3D : PUTC left1 left2 left3 right1 right2 right3

Writes into the currently connected file, the area of data as 
described.

see also : dataset GETC JOIN LISTFILEC

 
 PUTHEADER 
 
 

PUTHEADER param_name value
Set the value of a parameter associated to the currently JOINed 
data-set. If the parameter already exists, the value is changed, 
otherwise it is created. Any parameters can be used. Gifa already 
uses the following parameters (as listed with the dataset command) :
Frequency, Freq1, Freq2, Freq3, Specw1, Specw2, Specw3, Offset1, 
Offset2, Offset3, Type, Dim.
But you can use any other parameter name if you wish.

see also : dataset GETHEADER JOIN NEWFILEC

 
 pwd 
 
 

as in unix

 

see also : CD ls more rm SH vi vim vip