-
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
setfont
-
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
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
pkrm_diag
PKSELECT
-
pkrmi
-
pkrmi interactive
this macro permits to interactively and graphically
remove peaks from the peak table
see also : MONOPOINT
PKRM
pkrmz
pkrm_diag
-
pkrmz
-
pkrmz
permits to remove all the peaks within a given zone
see also : PKRM
pkrmi
pkrm_diag
-
pkrm_diag
-
removes all peaks along the diagonal
asks for the width of the diagonal to remove.
see also : PKRM
pkrmi
pkrmz
-
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
-
pksumrec
-
pksumrec { height(F1) width(F2)}
permit to integrate all the peaks in the current peak table
over a given rectangle.
if called with no argument, build a graphic interface,
if called with arguments, uese them as the width and the height of the box
(n means -n +n range, e.g. 2 means integrate over 5 points)
see also : INTEG
SUMREC
-
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
setfont
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
PLOTTEXT
setfont
-
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
setfont
-
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
setfont
-
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
ZEROING
-
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
-
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.
Gifa can be operated either form the menus or from the command
line. Both are strictly equivalent, since the menu buttons simply
internally call commands and macros.
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, (
ux2cach utility for the Bruker case, Varian cab be read directly
with READV).
* loading the data-set in memory (Load menu; READ command)
* apodizing (Apod. menu; commands 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)
(Proc1D/Proc2D menus; or CHSIZE command)
* 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) (in the Mode/Advanced proc menu)
* contour plot as well as density plot are available for 2D's. There
is even an on-screen stacked plot available. (Display menu)
* rows and columns from 2D's can be examined : (Move menu; 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.
o macros are case-sensitive, but commands are not even though
commands are always given in UPPERCASE in the documentation.
o the command to get out of it is 'exit n'
Try also :
* help a_given_command / for instance : help ft
* apropos a_given_topic / for instance : apropos hilbert
* reading the manual / try Documentation in the File
menu.
-
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
-
PULLDOWNMENU
-
PULLDOWNMENU 0/1
Permit to choose the aspect of the BUTTONBOX graphic interface.
The user can choose between classic pulldown menu mode (1) and menus
as static boxes, remaining on screen (0).
Setto 1 in the standard startup.g
see also : BUTTONBOX
startup.g
-
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