The standard graphic interface is characterised by several graphic windows and controls used for the display of the spectral data, and by a set of menus, button boxes, and dialogue boxes used for graphic user interaction.
Several graphic windows can be opened at the same time within Gifa. By default, when entering the program, a 1D display and a 2D density display window are opened. Several other graphic windows can also be opened (see CDISP2D, DISP3D, FREEZE). The data held in the working buffers are shown in these windows.
These windows can be closed at any time, re-opening them is performed by issuing the correct command either from the prompt or from the menus (see below). Most of these windows can be resized, to the exception of the 2D density display window which has a fixed size of 512 pixels on each axis. The colours in these windows can also be modified with a set of colour commands.
All the spectral windows can be FREEZEd, either by typing the command, or by selecting the entry in the window menu. A frozen window is just a copy of the current window, just staying here for comparison. It is completely passive, and can only be closed or iconified if needed, the content cannot be changed any-more.
The graphic windows are completely optional, and the effect of a command does not depend on the fact that a graphic window is there or not to display the effect.
A control box should also appear at start-up in the upper right corner of the screen. This box holds controls which permits to zoom and adjust the scale of the display. (If this box disappears, or is absent for any reason, you can make it appear again with the ZM command (also in the Display menu)).
To zoom the display, simply click on the graphic window with the left and middle buttons pressed, and draw a rectangle on the display. You can redraw as many time as wished this rectangle. To zoom into the selected region, simply click in this rectangle with the left and right button of the mouse. You can also use the Zoom in and Zoom out buttons in the control box. The spectrum showed in this box, is the complete spectral region, as was dispayed when you clicked on the Catch Spectrum button. The white rectangle in it, shows the current zoom region.
The four little arrows can be used to move around the zoom region. Each arrow will move the selected region by half the size of the zoom box.
There are five controls to adjust the vertical scale used for displaying the spectra. The Reset button will reset the display to the default, (ABSMAX 0 SCALE 1) where the largest peak in the screen in full size. The four other buttons permit to modify the scale value, raising or lowering the SCALE context by factor of 2 and of 1.2. See below for more details on SCALE.
The pop-up menu Dim, can be used to rapidely switch between the 3 working buffers : 1D, 2D and 3D. Finally, the text above the small spectrum is the current coordinates of the mouse, that you get whenever you click in the display.
The basic-menu graphic user interface is installed in the standard start-up procedure. It is installed whenever the startup.g macro is executed. This macro loads the basic environment, and the 1D and 2D processing menus.
However it is completely optional, and Gifa can work without any menu bar (even without any graphic window !), or with a completely different graphic environment.
The environment macros are found in the /usr/local/gifa/macro directory. Some macros necessitate additional files for interactive processing or for texts, these files are held into the /usr/local/gifa/macro/gm directory.
If a menu is buried below other windows, clicking on the menu name will pop the menu again.
The following menus are usually present whenever the graphic interface is activated, they are independent from the kind or work currently in progress.
If the graphic is missing, try typing the following command env_base.g, which
executes the macro which loads the default menu-bar, from which you can add all
the specific menus.
Some menus are optional or may not be on screen at the same moment, see the Mode Menu.
Entries followed by 3 dots (...) indicates that some input will be asked to the user by the command.
The name of the entries in the menus have been chosen to ressemble as closely as possible to the command name which would realise the same action. This makes the menus a bit cryptic, but ease the process of learning the commands, which can then be used to extend the capabilities of the program by writing macros. These menus implement most of the actions that you will need in regular processing, however there are many more capabilities in Gifa than the ones which are available from this standard menu interface.
This menu gives access to the basic information and documentation.
Will print introduction text, giving the some ideas on the Gifa program, as well as some hints on how getting more information or help.
This button is equivalent to the HELP command without parameter.
Gives access to the text of the History file.
Will prompt you for a command/macro name and will display the help associated with that command/macro.
This button is equivalent to the HELP command with a parameter.
Will prompt you for a word, and will show the name of all the commands/macros that have this word in their help file (case insensitive). Try for instance Fourier or display
This button is equivalent to the apropos macro.
This button launch the Netscape program, with an hyper-text version of the current manual.
This button launch the Netscape program, directly pointing to the Gifa home page : http://www.cbs.univ-montp1.fr/GIFA/base.html.
Will give all the details on the internal configuration of the program. You will have information on the current version number and the licence of the program, as well as the value of the basic parameters. Some values are hard-wired in the program at compile time, such as the size of the working buffer, or the number of user variables; some values may be modified by the user such as the kind of plotter currently in use (see below).
This button is equivalent to the CONFIG command.
Permits to edit and mail to me (mad@cbs.univ-montp1.fr) a short bug report.
Will quit the Gifa program loosing all data in memory not saved with a WRITE command, and removing the journaling file. If you want to keep the journaling file (a file called gifa.log in your home directory, which holds all the command issued during the Gifa session), you will have to type in the QUIT command directly.
This button is equivalent to the QUIT N command.
This menu holds the basic commands for getting informations on the program, reading and writing data-sets and quitting the program.
Will prompt you for the name of the file to be loaded into memory. The program will switch to 1D, 2D or 3D depending on the data-set itself. File should be in the standard Gifa format.
This button is equivalent to the READ command.
Will prompt you for the name of the file to be written from the data held into memory. The data-set will be created depending on the DIM currently selected (1D, 2D or 3D).
This button is equivalent to the WRITE command.
Are equivalent to Read and Write but a selection box permits to choose among all the supported Gifa file formats. For details, see below in the manual at the READx command
This button calls the shell script ux2cach.sh which permits to convert from a Bruker/UXNMR file format (acquisition data, not the processed data) to the standard Gifa file format. The command first prompt for the directory in which the data resides (for instance /u/data/guest/nmr/your_exp/1 ) and then to the Gifa file format. It will then ask for information which cannot be found in the Bruker files.
Will give you the name of the last read or written file with the READ or WRITE commands (or the Read... or Write... button).
Will give you the detail on the dimension, the sizes, the spectral widths, etc... of the current data-set.
This button is equivalent to the SIZE command.
Will give you the even more details the current data-set, such as the zoom window, the display values, etc...
This button is equivalent to the LIST command.
This menu permit to choose between different interface, already prepared in the standard distribution. Some button will completely change the interface, some, noted with 3 leading points, will add a menu at the end of the menu-bar
Will activate a graphic interface suitable for processing and displaying 1D data-sets only.
Will activate a graphic interface suitable for processing and displaying 2D and 1D data-sets.
Will activate a graphic interface suitable for processing and displaying 3D, 2D and 1D data-sets.
Will activate the assignment module (see assignment documentation)
Will add a menu permitting extended processing, such as baseline correction, water suppression, etc...
Will add a menu permitting to realise MaxEnt processing of the data-sets. (see MaxEnt documentation)
Will add a menu permitting Linear Prediction processing. (see Linear Prediction documentation)
Will add a menu permitting all commands associated to plots.
Will add a menu permitting all commands associated to Peak-picking and Line fitting.
Will add a menu permitting Unix-like commands.
Set the menu bar interface to act as a regular pulldown menus. Also resets the interface to 2D Mode
Set the menu bar interface to act as a set of static button boxes. Also resets the interface to 2D Mode
This menu holds the commands permitting to interact with the display.
Will switch on the graphic window associated to the 1D buffer. Has no effect if the window is already displayed.
This button is equivalent to the DISP1D 1 command.
Will switch on the graphic window associated to the 2D buffer, displaying the density plot. Has no effect if the window is already displayed.
This button is equivalent to the DISP2D 1 command.
Will switch on the graphic window associated to the 2D buffer, displaying the contour plot. Has no effect if the window is already displayed.
By default when entering the program, the DISP1D and DISP2D windows are on but the CDISP2D window is off. This is because the display in contour plot is slower than the density display, and it makes little sense to display a FID in contour plot!
This button is equivalent to the CDISP2D 1 command.
This button will enter a Zoom mode, were you can define a zoom window, zoom in and out, and modify the scale of display. The four little arrows permit to move the zoom window around without modifying its size.
This button is equivalent to the ZM command.
This button will launch a form which permits to control other display parameters such as the state of the contour display window, the display of the negative regions, the number of levels and the spacing algorithm.
This button will permit you to "freeze" a currently opened window, by duplicating it. It is a bit like taking a snapshot of the window, letting it on screen as long as you wish. There is no way of altering a FREEZEd window but closing it.
This button is equivalent to the FREEZE command.
Clicking this will memorize the current zoom window, it will be possible, at any later time to click on the back to stored zoom to go back to that window.
Jumps back to the last stored zoom window
When in zoom mode, this button will jump to symmetrical zoom region, relative to the diagonal.
This button is equivalent to the RZOOM command.
Creates a form box which permits to display up to 2 additional 1D spectra on the top of the current 1D sprectum held in memory
Equivalent to the super1d macro
Creates a form box which permits to display up to 2 additional 2D spectra on the top of the current 2D sprectum held in memory, and displayed on the contour (CDisp2D on) window.
Equivalent to the super2d macro
This menu holds all the commands permitting to navigate in the different mode of the program, or to move data between the different buffers.
All the processing in Gifa is performed in working buffers. There are 3 main such buffers, the 1D, the 2D and the 3D buffers. The content of the 1D and 2D buffers is directly visualised in the 1D and 2D graphic windows. Only one such working area can be selected at a given time, however switching from one buffer to the other is virtually instantaneous. All commands and actions apply to the currently selected buffer; processing commands (FT, etc..) as well as display commands (SCLAE, ZOOM, etc...).
Choosing a working buffer is completely independent from choosing to display one data space or another.
Switches the active working buffer. Respectively to 1D, 2D and 3D. These buttons are equivalent to the DIM x command
A independent buffer is available, which can hold indifferently a 1D, 2D or 3D data-set. This buffer cannot be processed nor visualised, but can be used as an additional "hand" for processing or comparison.
Loads the DATA buffer with the contents of the currently active buffer. Equivalent to the PUT DATA command.
Brings back the content of the DATA buffer into the working buffer. Equivalent to the GET DATA command. The sequence
Put Data ...any processing... Get Data
can be used as a kind of limited undo facility. Note however that certain commands use the DATA buffer, thus destroying the Get Data capability.
Adds the content of the DATA buffer with the content of the working buffer, and put the result into the working buffer. To make a difference spectra, simply multiply the working buffer by -1 (mult -1) before adding. Equivalent to the ADDDATA command.
Enter an interactive mode, where the coordinates of the cursor are displayed. Click into the text box to exit this mode. Equivalent to the point macro.
Permits to choose the unit in which the coordinates of the cursor are displayed during the Point mode. Unit can be either Index, Hertz or ppm. Equivalent to the UNIT command.
Starts a macro (calib) which permits to calibrate the current spectrum, by clicking on the reference peak, then entering its coordinates.
Starts the macro rowint, which permits to interactively select rows (F2 sections) in the 2D window and display them in the 1D window. You exit this mode by clicking on the right mouse button. The last selected row is copied into the 1D working buffer.
Starts the macro colint, which permits to interactively select columns (F1 sections) in the 2D window and display them in the 1D window. You exit this mode by clicking on the right mouse button. The last selected column is copied into the 1D working buffer.
Permits to copy a 2D row, selected by its index, into the 1D working buffer. Equivalent to the ROW command.
Permits to copy a 2D column, selected by its index, into the 1D working buffer. Equivalent to the COL command.
These menus permit to perform most of the regular processing to be performed on simple NMR spectra.
This menu contains all the operation which are to be applied before the Fourier transform step and is common to all processing modules (1D,2D and 3D), since the apodisation step is the same in all cases. It is installed with the env_proc1d.g macro, along with the Proc 1D menu.
Apply an exponential apodisation to the current data-set. The value of the exponential is in Hertz. There is one parameter for each axis in the data-set (1 in 1D, 2 in 2D, 3 in 3D). Equivalent to the EM command.
Apply an Gaussian apodisation to the current data-set. The value of the Gaussian is in Hertz. There is one parameter for each axis in the data-set (1 in 1D, 2 in 2D, 3 in 3D). Equivalent to the GM command.
Apply a sine-bell apodisation to the current data-set. The first (and only in 1D) parameter is a value ranging from 0.0 to 0.5; the value of the parameter corresponds to the position of the maximum of the filter in your window, thus 0.0 is pure cosine, 0.5 is pure sine, all intermediate values are possible. In 2D or 3D you will be prompted for the axis on which the apodisation should be applied.
Equivalent to the SIN command.
As the Sin button but applies a squared sine-bell. Equivalent to the SQSIN command.
Applies a trapezoidal apodisation. You will be prompted for two parameters, the built function starts from 0.0, raises up to the index entered as the first parameters where it reaches 1.0, the decay from 1.0 to 0.0 starts a the index entered as the second parameter up to the end of the data-set. In 2D or 3D you will be prompted for the axis on which the apodisation should be applied. Equivalent to the TM command.
Correct the first point of the current data set for the quantification bias introduced by the sampling. This is typical correction on 2D-3D data-sets. It partially removes the t1-ridges that are commonly seen. It has less interest in 1D.
Permits to change the size of the current data-set. The operation (reduction or increase) will be realised at once on the data-set. Increasing the size will be realised by adding zeros at the end of the buffer. You will be prompted for a dimension per axis in the data-set.
Equivalent to the CHSIZE command.
This menu, installed with the env_proc1d.g macro, holds the commands for 1D processing.
Extend the size of the current data-set to a size equal to the next power of two.
Realises the Fourier transform suitable for a data set acquired in sequential mode : real and imaginary part alternatively sampled. Equivalent to the ft_seq macro or to the REVF RFT command.
Realises the Fourier transform suitable for a data set acquired in simultaneous mode : real and imaginary part sampled at the same time point, and stored alternatively in the buffer. Equivalent to the ft_sim macro or to the REVF FT command.
Starts the PH command which permits to interactively phase the current spectrum. Pops up a control graphic box, which permits to control zeroth and first order phase corrections, place the pivot (with the middle button of the mouse), and store the phase correction. Zoom and the Zoom Box controls are still active.
Computes a phase correction on the current 1D data-set, using the APSL techniques (A.Heuer J.Magn.Reson. 91 p241 (1991) ). This is equivalent to calling the apsl macro.
Apply to the data-set the last phase correction used. Equivalent to the PHASE %% command.
Remove the imaginary part of the data-set, thus reducing by two the number of buffer points. Equivalent to the REAL command.
Compute the modulus of the spectrum from the real and imaginary parts. Equivalent to the MODULUS command.
This menu, installed with the env_proc2d.g macro, holds the commands for 2D processing. The F1 axis always refers to the non-classical, vertical axis of the 2D, and the F2 axis to the classical, horizontal axis. Some commands are specific to F1 or F2 processing, some commandsprompt for the axis to process, in which case you have to enter either F1, F2 or F12 if you want a processing on both axes.
This button launches a form which simplifies the Fourier transform process. You select the sizes, the apodisation functions, the Fourier, phasing and Baseline correction steps. The set-up can be used for direct computation as well as to store a macro that will realise the process in a latter stage.
Increases the size of the dataset in the F1 or F2 domain up to the next power of 2.
This button permits to use the burg Linear prediction method for extending the data-set. You can see it like a sophisticated zero-filling function.
Realises the Fourier transform in F2 suitable for a data set acquired in sequential mode : real and imaginary part alternatively sampled. Equivalent to the ft_seq macro or to the REVF F2 RFT F2 command.
Realises the Fourier transform in F2 suitable for a data set acquired in simultaneous mode : real and imaginary part sampled same time point, and stored alternatively in the buffer. Equivalent to the ft_sim macro or to the REVF F2 FT F2 command.
Realises the Fourier transform in F1 suitable for a data set acquired in phase modulation mode. Equivalent to the ft_phase_modu macro or to the FLIP REVF F1 FT F1 FLOP command.
Realises the Fourier transform in F1 suitable for a data set acquired in TPPI mode. Equivalent to the ft_tppi macro or to the RFT F1 command.
Realises the Fourier transform in F1 suitable for a data set acquired in Hypercomplex (States-Haberkorn) mode. Equivalent to the ft_sh macro or to the REVF F1 FT F1 command.
Realises the Fourier transform in F1 suitable for a data set acquired in TPPI Hypercomplex (TPPI States-Haberkorn) mode. Equivalent to the ft_sh_tppi macro or to the FT F1 command.
Realises the Fourier transform in F1 suitable for a data set acquired in echo-antiecho mode, with alternated gradients. Equivalent to the ft_n+p macro.
Starts the macro ph2dc which permits to interactively phase a 2D spectrum in F1. You first enter a selection mode, where you click on the 2D window with the left button to visualise the columns, you select them with the middle button, the selected columns are added together. You exit this mode with the right button. You then enter the PH command with a composite 1D spectrum obtained from the selected columns. The phase obtained on this spectrum is then applied on the complete 2D.
Equivalent to ph2dc for the F2 domain.
Apply again the last phase correction in the F1 domain. Equivalent to the PHASE % % F1 command
Apply again the last phase correction in the F2 domain. Equivalent to the PHASE % % F2 command
Remove the imaginary parts of the data-set along each axis, thus reducing the total size of the data-set by four.
Computes the modulus spectrum from the real and imaginary parts. Equivalent to the MODULUS command.
Computes the projection of the 2D dataset along the F1 axis, onto the F2 axis. The command will promt you wether you want a "Skyline" (keep the highest points) or a "Mean" (sum all points) projection. Equivalent to the PROJ F1 command.
Computes the projection of the 2D dataset along the F2 axis, onto the F1 axis. The command will promt you wether you want a "Skyline" (keep the highest points) or a "Mean" (sum all points) projection. Equivalent to the PROJ F2 command.
When 3D processing has been chosen, either with the env_proc23d.g macro, or the Proc 3D option in the Mode menu, 3 additionnal menus are inserted in the menu bar. The first menu is for processing 3D data-sets which can be held into the central memory, the second is specific of 3D display, and the third one is for processing and displaying file which are too big for fitting into the central memory, and thus have to be processed on file.
In 3D processing F3 axis always refer to the acquisition axis, F1 refers to the axis which is stored with the slowest increment, and F2 to the intermediate axis. Thus, 3D can be seen a series of F2-F3 planes. Note that this definition depends only on how the data-set was stored, and not on the order of the incremented delays in the sequence.
Naming of planes is done by giving the axis orthogonal to the plane rather than the axes in the planes; for instance the planes holding the F1 and F3 planes are noted F2 planes.
This menu holds most of the commands for processing 3D experiments in-memory, as it is done for 2Ds. This can be done only for not too big data-sets. In the contrary case, one has to resort to on-file processing (see below). The Gifa central memory is determined at compile time, and several versions of the program, corresponding to differesnt size of the memory, should be available on your machine, check the installation manual.
In the case of in-memory processing, commands are very similar to what is done in 2D.
This button simply call the largest_3d macro which gives you example of data-sets which fit into the memory.
Simply realizes extension of the size in F1, to the next power of two. Done with the CHSIZE command.
Realizes extension of the size in F2, to the next power of two. Done with the CHSIZE command.
Realizes extension of the size in F2, to the next power of two. Done with the CHSIZE command.
Performs the burg extension of the data-set in F1 or F2 using the burg3d macro command.
Performs in the F3 (acquisition) axis, the Fourier transform of a data-set acquired in sequential mode.
Performs in the F3 (acquisition) axis, the Fourier transform of a data-set acquired in simultaneous (complex) mode.
Performs in the F2 or F1 axis, the Fourier transform suitable for data-sets acquired with different protocols, see the Proc 2D menu for details.
Permits to apply a phase correction in a given spectral axis. Equivalent to the PHASE command.
Permits to throw away the imaginary part associated with a given axis (F1, F2 or F3). Equivalent to the REAL command
Permits to throw away all the imaginary part associated to a fully hypercomplex data-set. Equivalent to the REAL F123 command.
Computes the modulus of fully hypercomplex data-set. Equivalent to the MODULUS command.
This menu holds all the functions for displaying the 3D data-set held into memory
Opens the 3D display window, equivalent to the DISP3D 1 command.
Opens a form for setting 3D display parameters. actually calls the disp3d_form macro.
Opens a control box which permit to interactively chose the view point of the 3D display. Equivalent to the CHECK3D 1 command.
This control box permits to change its position and size within the window, to set the orientation of the spectral cube, to change the perspective of the display, and finally to recompute a display with the Refresh button.
In contrast with the other windows, the 3D display is not automatically refreshed whenever a display parameter changes. This has been chosen because of the time that this refresh might take. Clicking on this button will start the 3D display. Equivalent to the REF3D command, or to the Refresh buttom on the CHECK3D control box.
This button starts the zoom3di macro which permits to interactively choose a zoom window for the current 3D display.
Calls the PLANE command, which loads the 2D buffer with a plane extracted from the 3D.
Calls the DIAG command, which loads the 2D buffer with a diagonal plane extracted from the 3D
Starts the vertint macro which permits to interactively examinate 1D spectra by clicking on a orthogonal 2D plane.
Starts the planeint macro which permits to interactively examinate planes by clicking on a orthogonal 1D spectrum
Compute the projection plane along the corresponding axis. You will get prompted for the projection mode Skyline / Mean.
When a data-set is too big to be processed in-memory, it is possible to realize the processing on-file. This is done with a special set-up in Gifa, the "cache" system, which permits to access files in an optimal fashion, (see below the Working On File rather than In Memory chapter).
3D processing on file is done by having an input file and an output file, planes are loaded from the input ile, processed in memory as regular 2D experiment, and then copied on the output file.
This entry permits to realize the first operation to be done, namely connecting to the input file. This is equivalent to the JOIN command. Once a data-set has been JOINed, it is possible to display internal parameters, load 1D or 2D from it, or even load a 3D region form it. Note that you can issue that command to several files, thus being JOINed to more than one file. However all the command will refer to the last JOINed file.
That button simply runs the dataset macro, which displays all the spectral parameters of the current JOINed data-set. Note that since the header holding all the parameters is in ASCII format, one can simply make more filename to see the value of all the parameters.
This button lists the names of all the files which are currently JOINed.
Once a file have been JOINed it must be DISJOINed in order to release completely the internal memory.
This menu entry permits to load a plane extracted from the currently JOINed 3D dataset. For intance it can usefull to load the first F1 or F2 planes to determines the optimum processing parameters, and phases, before going to full 3D processing. It can used also to look at planes in a processed data-set. It is equivalent to using the GETC command in DIM 2 mode.
This ones permits to load in the central memory a portion of the currently JOINed data-set. You will be prmpted for the coordinates fits point (F1, F2, F3) and then for the coordinates of the last point (F1, F2, F3). It is equivalent to using the GETC command in DIM 3 mode.
This button creates a form which permits to process the 3D data-set on-file. One has to enter the name of the input and output files, the axis along which the processing will be done, and finaly the command line that will be applied to each plane of the 3D. This command line will be executed in 2D mode on each of the planes; thus typical 2D command should be given here. The forms actually calls the proc3d macro.
Compute the projection plane along the corresponding axis. You will get prompted for the projection mode Skyline / Mean
The following optional menus can be accessed from the Mode menu.
Apply a linear baseline correction to the current data-set. You have to click on empty regions of the data-set, from which the baseline correction will be computed. Equivalent to the point and BCORR 1 commands.
Apply a spline baseline correction to the current data-set. You have to click on empty regions of the data-set, from which the baseline correction will be computed. Equivalent to the point and BCORR 2 commands.
Apply an automatic peak detection followed by a polynomial baseline correction. Equivalent to the BCORR 3 command.
Realises the 1D Hilbert transform of the current data-set, that is the current real data-set is transformed to a complex data-set with a reconstructed imaginary part. The operation is done without changing the total number of data points. Is equivalent to
IFTBIS FT
Realises the 1D inverse Hilbert transform of the current data-set, that is the current complex data-set is transformed to a real data-set with all the information of the imaginary part brought back to the real region. The operation is done without changing the total number of data points. Is equivalent to
IFT CHSIZE(%*2) FT REAL
or
IFT FTBIS ; better
These menus realises the direct and inverse Hilbert transform of the 2D data-set.
Starts the rem_h2o macro which remove substantially solvent signal at zero frequency in the FID. It does so by removing any slow varying signal in the FID, using the baseline correction module. Should be applied on the time-domain data-set, before any other processing (before apodisation or Fourier transform).
This menu holds some commands than permit to simply process a 1D or 2D data-set using Maximum Entropy deconvolution. The menus are more or less organised in the order in which you should use them.
You should start with a spectrum, phased, baseline corrected, but, ideally, not apodised. You can do processing from an apodised data-set but you will get better results if you start over with a spectrum obtained without any apodisation.
Using this menu, Maximum Entropy can only be applied on a spectrum containing only positive, absorptive spectra.
For a complete understanding of MaxEnt processing, read that part of the manual devoted to MaxEnt.
With this command you first select a small region of the spectrum that you wish to process. You should not use a complete spectrum, but rather concentrate on the interest region with this command.
The command also realizes the inverse Fourier transform step which is necessary to create the pseudo-FID that will be used later on by MaxEnt.
Before running the process you should determine the noise quantity present in the pseudo-FID by zooming, with this command, on the end of FID holding only noise. If the starting data-set had been apodised, the noise quantity will be largely under-estimated; if the pseudo-FID is truncated (total decay is not obtained), the noise quantity will be overestimated. In any case you may want to correct it with the NOISE command.
Before running the process you should determine the deconvolution function, which can be either Lorentzian or Gaussian (other possibility are available from the command level). Line-width is entered in Hz. The line-shape thus defined will be removed from the actual spectrum, thus producing sharer lines. So you should never enter here a line-shape larger than the sharper line present in the spectrum.
Determines the number of iterations that will be used for the starting computation.
Starts the MaxEnt iterations. You are first prompted for the size of the spectrum to be computed, which should larger or equal to the size of the pseudo-FID. Never starts the computation if
* you don't have a FID on screen
* you don't have realised the previous steps
During the iterations you should check the following values : chi2, should be as small as possible, chi2 = 1 means the computation is finished; conv should be as small as possible, a conv larger than 0.1 means that the convergence will never be obtained, probably because the data-set or the deconvolution function are incorrectly chosen.
Continue the processing for 10 more iterations.
Start over the processing with the pseudo-FID.
When the computation is completely finished, you should remove the background that MaxEnt always adds to the spectrum, by running this command and zooming in an empty region of the spectrum. After this operation, the process should be started over. (10 more is not available any more)
This menu holds all the entries for realising simple Linear prediction calculations. (stil experimental - the menu I mean, the commands are fully operationnal)
To fully understand what is going on here, you are supposed to have read the manual (no joking :-). Most (all ?) entries here, are supposed to be applied on untouched (i.e. not apodised) FID.
This menu is built by the env_lin_pred.g macro.
Permits to determine the value of ORDER used for all LP operation. Should be set larger than the number of lines in the spectrum, and smaller than the data-set size. The speed of LP operations usually depend on this setting.(see LP documentation). Equivalent to the ORDER command.
LP commands work only on Complex FIDs, this button transform a Real FID into a Complex one by using a Hilbert transform. Equivalent to the command IFTBIS FT
Extend the current FID using the burg method. Can be used to correct truncated FID. To be used BEFORE any apodisation. Will promt you for the new size.
Equivalent to using the BURG command, or the dt->ar ar->dt size 1 sequence.
Is equivalent to the previous button, but uses the SVD method which is somewhat slower, but more efficient in the case of noisy data. Try this one if burg failed. Equivalent to using the dt->svd % svd->ar 1 ar->dt size 1 sequence
Equivalent to the precedent, but even slower. That one should succeed in all cases. To be used when the previous one failed (typically by transforming your FID into "trumpets" (increasing exponentially towards the end))
Equivalent to using the dt->svd % svd->ar 1 ar->rt 1 rtreflect 1 rt->ar 1 ar->dt size 1 sequence
Uses the burg method to build missing first points. Can be used for instance after a lshift to correct for acoustic ringing.
It is the burg_rev macro
Equivalent to the previous, but with the SVD method. It is the svd_rev macro.
Computes the "urg spectrum" (also called mem1) i.e. an estimate of the power spectrum, based on the burg analysis of the FID.
Prompts you for a size on which the spectrum should be recomputed.
Performs a complete SVD analysis of the current FID. Results are put into the pklist
The same as previous, but uses the Forward & Backward method. Meant to be used on very bas signal/noise cases.
Will prompt you for an exact number of line to keep in the spectm.
Applies the Cadzow procedure to clean up the current FID. Calls the cadow macro.
Actually prints the content of the peak table. Equivalent to the PKLIST %% command.
This menu holds all the entries for realising simple plots.
This button launches a from which permits to determine all the parameters for a standard plot, with axes, grid, choice of colours, etc...
Starts the macro plot? which prompts you for some basic parameters associated to plotting : the kind of plotter (postscript or HP-GL), the size of the plot in centimetres, the offset of the plot from the lower left corner of the page, the vertical offset of 1D plots, the rotate state and the parameters for spectral axes. Can used to pre-set the values in Easy Plot
The other menu entries permit to realise more specific plots. Each entry add a element to the current plot, and the final entry Page send this plot to the plotter.
Adds the current display (1D or 2D) to the plot.
Adds a title to the current page. When entering more than one word, put the complete string into quotes (') or double quotes (").
Add an labelled axes on the F1 (y) or F2 (x) direction, as defined with the Plot? command.
Add a grid in the F1 or F2 domain according to the definition of the axis from Plot? command.
Send the current plot to the plotter. On certain platform, the plot file is displayed on screen before being actually sent.
Makes a plot file which can then be read with the NMR analysis Cindy program (see ftp://www.cbs.univ-montp1.fr/pub/Cindy). Equivalent to the FPLOT command.
This menu holds certain facilities for realising peak detection, peak integration and line fitting. All the information is held into an internal table which can be displayed at any time with the PKLIST button.
Asks you to zoom on an empty region, and evaluates noise on the selected region. Uses the EVALN command..
Enter the macro pp which performs a simple peak-picking. You should have evaluated the noise level with the previous button Then zoom on the region to be peak-picked. The peak threshold is evaluated from the noise level.
Permits to add a peak into the table by clicking on the data-set. Equivalent to the point POINT->PK command.
Calls the pkrmi macro which permits to interactively remove a peak on the data-set.
Calls the pkrmz macro which permits to interactively remove a set of peaks on the data-set.
Equivalent to the PKCLEAR command, which removes all peak entries.
Calls the pkrm_diag macro which removes all peaks within a given distance from the diagonal of a homonuclear experiment
Calls the PKSYM command, which "symetrizes" the 2D peak table, you can either remove all peaks with no symmetric counter part or add the missing symetric peak.
Calls the PKPROJ commands which "project" the 2D peak table and produce a corresponding 1D peak table.
Apply the very simple integration scheme which consists in summing all points over a defined rectangle. This is done by calling the pksumrec macro, which is built over the SUMREC command.
Performs a numeric integration of the data-set by computing masks around each peak in the peak table, and integrating over these masks. Equivalent to the INTEG %% command.
Display the masks used by the last INTEG command. Available only in 2D. Equivalent to the SHOW AMOEBA command.
Display graphically the peaks on the current display. Equivalent to the SHOWPEAKS command.
Equivalent to ShowPeaks but on a plot file. Equivalent to the PLOTPEAKS command
Calls the generic line fitter. You are prompted for the line-shape to fit (Lorentz or Gauss). Equivalent to the LINEFIT command.
Equivalent to the SHOW LINEFIT command. Display the content of the curent peak table as a simulated spectrum. Can be used after LINEFIT, but also at any stage.
Graphically displays the content of the peak table (as obtained for instance, from the last line fitting). Equivalent to the show_fit macro.
Display the residue of the last line-fitting. Data can be restored with the GET DATA command.
Lists the content of the internal peak-table. Equivalent to the PKLIST %% command.
Reads the content of the peak table on a text file previously stored with PkWrite. Equivalent to the PKREAD command.
Writes the content of the peak table on a text file. Equivalent to the PKWRITE command.
This button holds some facilities for interacting with the UNIX Operating System. All the buttons are implemented through the generic SH command. All entries have equivalent macros or commands available in text mode.
Realise the Unix counterparts.
Opens an XTerm with the current client and server.
Opens in vi any text file in the current directory.
Opens in vi any text file in the global macro directory (/usr/local/gifa/macro). Macros in this directory are available to all the Gifa users. Equivalent to the vim macro.
Opens in vi any text file in the personal macro directory ($HOME/macro). Macros in this directory are available to you, wherever the directory you are in. Equivalent to the vip macro.