FITMAN Chapter 2.3 - dwong263/MAGIQ GitHub Wiki

*.ges File Format

Overview

The *.ges file is the where the initial guesses for the peak parameters can be specified. Like the *.dat files, *.ges files are ASCII files. The format files of these files are described below.

The "guess" portion of a file must begin with:

****_Guess_File_Begins_****

and end with:

****_Guess_File_Ends_****

Guess File Sections

The guess file contains three distinct sections called:

[Parameters]

[Variables]

[Peaks]

Each section contains specific information that is interpreted by the fitting routine.

[Parameters] Section

The [Parameters] sections contains the following:

Parameter Description Default
number_peaks <n> Specifies the number of peaks used in the fitting. 0
shift_units <s> Specifies the units for the initial guesses of shift values in the guess file. Two choices are available Hz or ppm. ppm

[Variables] Section

The [Variables] section contains the following:

<s>  <n>

where <s> specifies the variable name and <n> specifies the value assigned to it.

[Peaks] Section

Assigning Variables to Peaks

The [Peaks] section contains the following:

;PEAK#  SHIFT   LORENTZIAN WIDTH    AMPLITUDE   PHASE   DELAY   GAUSSIAN WIDTH
1       2.11    6.0                 1.0         0.0     0.0     0.0

repeated for every peak.

The semi-colon identifies a remark and forces the parsing routine to ignore this line.

Units

The following units are used for each peak parameter

Parameter Unit
SHIFT shift_units (in parameter section)
LORENTZIAN WIDTH Hz (FWHM of Lorentzian line)
AMPLITUDE Absolute Units
PHASE Radians
DELAY Seconds
GAUSSIAN WIDTH Hz (FWHM Gaussian line)

Parameters with Offsets

Variables that are specified in the constraints file and contain offsets are resolved so that the initial guess specified in the guess file is the initial value for a particular parameter.

For example suppose the following combination of guess file and constraints file occurred:

****_Constraints_File_Begins_****
.
.
. 
;PEAK#    SHIFT       LORENTZIAN WIDTH     AMPLITUDE    PHASE    DELAY     GAUSSIAN WIDTH
1       {shift1}+0.1  {lorentzian_width1} {amplitude1} {phase1} {delay1}  {Gaussian_width1}

****_Constraints_File_Ends_****

****_Guess_File_Begins_****
.
.
. 
;PEAK#    SHIFT       LORENTZIAN WIDTH     AMPLITUDE    PHASE    DELAY     GAUSSIAN WIDTH
1         2.11        6.0                  1.0          0.0      0.0       0.0

****_Guess_File_Ends_****

In this case, the first peak would have a starting shift of 2.11 ppm. Therefore, the parameter shift1 would be evaluated as shift1=2.01.

Linked Parameters

In the above example further references to shift1 anywhere else in the constraints file would cause the initial guess of that peak’s shift to be evaluated base on the value of shift1=2.01. For example suppose the next peak in the constraints file was specified according to:

2   {shift1}+0.3    {lorentzian_width2}   {amplitude2}    {phase2}    {delay2}    {Gaussian_width2}

The initial guess for the shift of this peak would be evaluated as shift1+0.3 = 2.31 regardless of what the initial guess file specifies for this peak. Since all the other parameters occur for the first time, they would be resolved based on the information in the guess file for that peak.

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