furanku

NMRPipe Processing Functions

MEM ND Maximum Entropy



Command-Line Argument List

 
MEMND: ND Maximum Entropy Calculation.
 -ndim   [1]      Number of Dimensions.
 -sigma  [1.0]    Std Dev of Time-Domain Noise;
                  Use Zero for Auto Estimates.
 -zf     [2]      Zero Fill (Power of 2);
                  (also use -xzf -yzf etc).
Reconstruction Mode Flags:
 -neg             Two Channel (+/-) MEM (Default).
 -pos             Positive-Only MEM.
 -zero            Correct Zero Order Offset (Default).
 -nozero          Suppress Offset Correction.
 -freq            Output Freq-Domain Result (Default).
 -time            Output Time-Domain Result.
Convolution Parameters (also use -x.. -y.. etc);
defines window used on MEM data:
 -conv cFn [None] Convolution Func: EM GM SP.
 -cQ1  cQ1        Convolution Parameter Q1.
 -cQ2  cQ2        Convolution Parameter Q2.
 -cQ3  cQ3        Convolution Parameter Q3.
Deconvolution Parameters (also use -x.. -y.. etc):
defines inverse window used on original data:
 -deco dFn [None] Deconvolution Func: EM GM SP.
 -dQ1  dQ1        Deconvolution Parameter Q1.
 -dQ2  dQ2        Deconvolution Parameter Q2.
 -dQ3  dQ3        Deconvolution Parameter Q3.
Data Clipping and Scaling:
 -ts   tsMode   [0] Time-Domain Scaling Mode:
                    0=None 1=Divergence 2=Always.
 -clip cMode    [0] Freq-Domain Clipping Mode:
                    0=None 1=Pos 2=Neg 3=Both.
 -min  cMin [-1e17] Minimum for Clipping.
 -max  cMax [+1e17] Maximum for Clipping.
MEM Parameters:
 -alpha   [1e-3]  Scale for MEM Update.
 -tScale  [0.5]   Scale for Amplification Threshold.
 -tLimit  [1.5]   Chi Limit for Use of Threshold.
 -cScale  [1e2]   Desired Sigma After Scaling.
 -eScale  [1.0]   Scale (A) for Entropy Calc.
 -lamb    [1e-5]  Initial/Minimum Lambda Value.
 -step    [0.02]  Scale for Lamda Update.
 -x0      [5.0]   Second-Order MEM Threshold.
Convergence Tests:
 -cLim   [1.0]   Chi-Square/N Limit for Convergence;
                 (same as old option -zFact)
 -zLim   [1.0]   Z-Statistic Limit For Convergence.
 -itmax  [50]    Maximum Iteration Count.
 -itmin  [3]     Minimum Iteration Count.
 -div    [3]     Maximum Divergence Count.
 -report [0]     Report Level:
                 0=No Report      1=Final Iteration
                 2=Each Iteration 3=Save F and dC
Notes:
 1. Important options are -ndim -sigma and -alpha.
 2. Underestimate time noise value for -sigma to
    avoid missing peaks.
 3. Use a minimum of 2 zero fills (size*4).
 4. Use -report 2 for statistics of each iterate.
 5. Reduce -alpha value if results diverge.
 6. Chi/N statistic should decrease to 1.0 in a
    good reconstruction.
 7. MEM Z statistic should increase to 1.0 in a
    good reconstruction, but values as small as 0.1
    are not unusual.