ist4D.com -help
Output:
ist4D.com 2020.023.18.46
Perform IST Recontruction of 4D Non-Uniformly Sampled (NUS) Data:
-in inName [Auto] Expanded Time-Domain Input.
-mask maskName [mask/mask%04d.fid] Corresponding Time-Domain Mask Input.
-out outName [ist/test%04d.ft4] IST Spectrum Output.
-ft1 ft1Name [None] IST Interferogram Output (Sets -noapod).
-nus Input is NUS (Default).
-us Input is Uniformly Sampled (US).
-yz Exchange Y-Axis and Z-Axis of Result.
-ya Exchange Y-Axis and A-Axis of Result.
IST Parameters:
-istMaxRes r [Auto] Target Max in Residual, as % of Original Max (Or Auto).
-istTMult t [0.70] Fraction for Threshold at Each Iteration
-istCMult c [0.30] Fraction for Reducing Data Above Threshold.
-istIter n [2048] Maximum Allowed Iterations.
-mult m [1.0] Multiplication Factor for -istMaxRes Auto.
-retain Retain Original Time-Domain Data Points (Sets -noapod).
-noretain Replace Original Time-Domain Data Points (Default).
-rist Same as -retain Option.
-pos Use All-Positive IST (No Negative Signals).
Noise Estimate (Used Only for Statistic Reports):
-noise s [None] Estimate of Noise in Spectrum.
Processing Parameters (Use -x... -y... -z... -a...):
-xSOL sName [NULL] Solvent Function Name and Options (X-Axis Only).
-xAPOD aName [SP] Window Function Name.
-xQ1 q1 [0.50] Window Parameter Q1.
-xQ2 q2 [0.95] Window Parameter Q2.
-xQ3 q3 [2] Window Parameter Q3 (Default for -yQ3/-zQ3 is 1).
-xELB elb [0.0] Exponential Line Broaden, Hz.
-xGLB glb [0.0] Gaussian Line Broaden, Hz.
-xGOFF goff [0.0] Gaussian Center, 0.0 to 1.0.
-xC1 c [Auto] First-Point Time-Domain Scale (0.5 1.0 Auto).
-xP0 p0 [0.0] Zero-Order Phase Correction.
-xP1 p1 [0.0] First Order Phase Correction.
-xZFARG zfArgs [zf=1,auto] ZF (Zero Fill) Option.
-xFTARG ftArg [None] FT (Fourier Transform) Options (None neg alt).
-xEXTX1 x1 [0%] Extract Range Start (X-Axis Only) (% Hz ppm pts).
-xEXTXN xn [100%] Extract Range End (X-Axis Only) (% Hz ppm pts).
-apodDF Adjust Window Function for Digital Oversampling.
-noapod No Apodization for Indirect Dimensions.
-ssNMR Set Defaults for Solid-State NMR Data.
Processing Parameters for X-Axis Only:
-xBASEARG_INIT bArgs [NULL] Baseline Correction Before Region Extraction.
-xP0EXT p0Ext [0.0] Zero-Order Phase After Region Extraction.
-xP1EXT p1Ext [0.0] First Order Phase After Region Extraction.
NUS Zero-Fill Mode (Time-Domain Extrapolation by IST):
-nusZF NUS Zero-Fill Extrapolation ON (Default).
-nonusZF NUS Zero-Fill Extrapolation OFF.
-yNUSZF zfArgs [zf=1] Amount of Y-Axis NUS Zero-Fill Extrapolation.
-zNUSZF zfArgs [zf=1] Amount of Z-Axis NUS Zero-Fill Extrapolation.
-aNUSZF zfArgs [zf=1] Amount of A-Axis NUS Zero-Fill Extrapolation.
-istName outName [ist/test%04d.ft4] Overrides -out Setting.
Baseline Correction Function Name and Options (Use -x... -y... -z...):
-xBASEARG_FT1 [NULL] Interferogram Baseline Correction (X-Axis Only).
-xBASEARG [NULL] Spectrum Baseline Correction.
-xBASEARG_FINAL [NULL] Baseline Correction for Final IST Result.
Baseline Correction Applied to Final Residual:
-rBASEARG [POLY,auto,ord=0] Residual Baseline Correction.
Other Options:
-clean Delete Intermediate Results (Default).
-noclean Retain Intermediate Results.
echi: Command not found.
-progress Display Progress Bar Graphic.
-yz Move Z-Axis to Y-Axis of Result.
-ya Move A-Axis to Y-Axis of Result.
Notes:
1. Options -xSOL -xBASEARG_FT1 -xBASEARG and -xBASEARG_FINAL are expanded
into NMRPipe processing function names and command line arguments.
Options should contain no spaces. Flags are separated by commas, and
values are given using = signs. For example, solvent filter:
-xSOL NULL Becomes: nmrPipe -fn NULL (No Solvent Filter)
-xSOL SOL Becomes: nmrPipe -fn SOL
-xSOL POLY,time Becomes: nmrPipe -fn POLY -time
For baseline correction:
-xBASEARG NULL Becomes: nmrPipe -fn NULL (No Correction)
-xBASEARG POLY,auto,ord=0 Becomes: nmrPipe -fn POLY -auto -ord 0
2. Options -xZFARG -xFTARG are expanded to command line arguments for ZF
and FT, for example:
-xZFARG zf=2,auto Becomes: nmrPipe -fn ZF -zf 2 -auto
-xFTARG neg Becomes: nmrPipe -fn FT -neg
-xFTARG neg,alt Becomes: nmrPipe -fn FT -neg -alt
3. When first-point time-domain scaling is set to Auto (-xC1 Auto etc),
the scaling value will be set to 0.5 if the first-order phase correction
for that dimension is 0+/-10 degrees, or to 1.0 otherwise.
4. For applying NUS Zero Fill to conventional data, use -nusZF -mask Auto to
automatically create mask data via the nusZF.com script.
5. If the X-Axis label of the input spectrum starts with 'HN', default
parameters will be adjusted as follows:
-xSOL SOL -xBASEARG_FINAL POLY,auto -xEXTX1 3% -xEXTXN 47%
Or when -nusZF -mask Auto is used for conventional data:
-xSOL SOL -xBASEARG POLY,auto -xEXTX1 3% -xEXTXN 47%
6. If the -ssNMR flag is used, default parameters will be:
-xSOL NULL -xBASEARG NULL -xBASEARG_FINAL NULL
7. Commonly, only region of interest, FT, and phase correction options need
to be provided, and the convergence parameter can be set automatically.
Include -nusZF if extrapolation during reconstruction is desired. Example:
ist4D.com -xP0 -75 -xP1 0 -xEXTX1 10.4ppm -xEXTXN 5.4ppm \
-yP0 -90 -yP1 180 -zFTARG alt -aFTARG alt -nusZF
8. To stop an IST calculation in progress:
touch ist.stop
9. See utility nusExpand.tcl for expanding time-domain NUS data and
creating time-domain NUS schedule mask.