nusPipe -fn SMILE -help
Output:
** SMILE Plugin: Version 2.1 Rev 2019.337.11.19 64-bit **
** NMRPipe System Version 8.9 Rev 2017.150.13.42 64-bit **
SMILE: Sparse Multidimensional Iterative Lineshape Enhanced.
Options:
-nDim dimCount [0] Number of Dimensions (0 for Auto).
-nThread nThread [0] Number of Threads (0 for Auto).
-maxMem maxMem [0.0] Max Allowed Memory in GB (0 for Auto).
-pseudoND Pseudo nD data, n-1 dim spectral series.
SMILE RQD mode for echo-antiEcho (Use -x... -y...):
-xEA Use Echo-AntiEcho (RQD Data Only).
NUS Sampling Schedule:
-sample sName [None] NUS Sampling Schedule File.
-sampleCount sCount [Auto] Number of Valid Samples Measured.
-sampleReverse Reverse Axis Order in Sampling Schedule.
-sampleAverage Average Duplicates in Sampling Schedule.
-sampleOffset sampOff [0 0 ...] Offset Subtracted from Schedule Values.
Phase Correction (Use -x... -y...):
-xP0 xP0 [0.0] Zero Order Phase Correction.
-xP1 xP1 [0.0] First Order Phase Correction.
Zero Fill Options (Use Only One; Use -x... -y...):
-xzf zfCount [2] Number of Times to Double Size.
-xzfSize zfSize [0] Size After Zero Fill.
Fourier Transform Modes (Use -x... -y...):
-xAlt Use Sign Alternation Before FT.
-xNeg Negate Imaginaries Before FT.
Options for CT Evolution and Acq Time Extension (Use -x... -y...):
-xCT xCT [0] Number of Data Points Collected in CT.
-xT xT [0] Size extended (0 for 50% Extension).
Apodization Parameters (Use -x... -y...):
-xApod xApodFunc [SP] Window Function: EM GM SP.
-xQ1 xQ1 [0.50] Window Function Parameter Q1.
-xQ2 xQ2 [0.98] Window Function Parameter Q2.
-xQ3 xQ3 [1.00] Window Function Parameter Q3.
Composite Window Options, for SP Only (Use -x... -y...):
-xELB xElbHz [0.0] Exponential, Hz.
-xGLB xGlbHz [0.0] Gaussian, Hz.
-xGOFF xGOff [0.0] Gauss Offset, 0 to 1.
Lineshape Simulation Parameters for Obtaining Linewidth-R2 Relationship:
-minTDL minTDL [0.25] Min TD Length (Tacq/max(T2)) for LW sim.
-maxTDL maxTDL [4.00] Max TD Length (Tacq/min(T2)) for LW sim.
Options for unresolved scalar couplings (Use -x... -y...):
-xJ [0.0] Size of the unresolved J coupling;
Options for Signal Detection, Reconstruction, and SMILE Termination:
-sigma sigma [0.0] Noise in the Data (0 for Auto Estimate).
-nSigma nSigma [5.0] Noise Factor for the Signal Cutoff.
-thresh thresh [0.80] Threshold for Signal Detection.
-maxNPks maxNPks [0] Max Number of Peaks (0 for Auto).
-fraction fraction [1.00] Fraction of Signals to be Reconstructed.
-maxIter maxIter [800] Max Number of Iterations.
-maxTime maxTime [0.0] Max Wall Time (hours) for the SMILE job.
Options for Output Control:
-scaling scaling [0.0] Signal Downscaling Factor (0 for Auto).
-log logName [smile.log] Log File Name
-report verbose [0] Report Level:
0=No Report
1=Output SMILE info (stderr & smile.log)
2=More SMILE info on stderr
Notes:
1. Important options are -sample -xP0... -xP1...
2. Auto setting for -nThread is Max(1, Number_of_Logical_Cores/2).
3. Auto setting for -maxMem is 80% of the physical memory.
4. When -xzf ... is used, zero fill size is rounded to a power of two.
if a specific size is required, use -xzfSize ... instead.
5. Use -xAlt ... if sign alternation is needed for FT of the given dimension.
6. Use -xNeg ... if negation of imaginaries is needed for FT of the given dimension.
7. Options -xAlt and -xNeg can be used together if needed.
8. When setting an explicit value for -xT to perform extrapolation, use a value
which is larger than the original time-domain size of the given dimension.
9. Use the same -scaling value for spectra in a series, such as relaxation data.