Programs of the NMRPipe System
Var2Pipe: Varian to NMRPipe-Format Conversion
Usage:
var2pipe hdrFlags < varData > pipeFile
General Flags:
| Flag |
Argument |
Default |
Description |
-in |
inName |
|
Varian Input. |
-out |
outTemplate |
|
NMRPipe Output. |
-ov |
|
|
Force Overwrite. |
-nofs |
|
|
No File Size Check. |
-nodir |
|
|
Suppress Creation of Directory. |
-verb |
|
|
Verbose Mode On. |
Byte-Swap Options:
-swap |
|
|
Do Four-Byte Swap (Default). |
-noswap |
|
|
Suppress Four-Byte Swap. |
-aswap |
|
|
Suppress Four-Byte Swap. (Meaning is System-dependant) |
-noaswap |
|
|
Do Four-Byte Swap. (Meaning is System-dependant) |
Varian Header Flags:
-hdr |
|
|
Use Varian Header Data (Default). |
-nohdr |
|
|
Don't Use Varian Header. |
-hw |
hSize |
8 |
Header Size in Four-Byte Words. |
-pw |
pSize |
7 |
Pad Size in Four-Byte Words. |
-info |
|
|
Show Header Info on stdout, Don't Convert Data. |
Options Set Via Varian Header:
-i2r |
|
|
Convert Integer to Real. |
-noi2r |
|
|
No Integer to Real Conversion. |
-short |
|
|
Input is Two-Byte Data. |
-long |
|
|
Input is Four-Byte Data. |
-dsp |
|
|
Input is floating-point DSP data (Same as -noi2r). |
Parallel Processing (Not Implemented):
-par |
|
|
sListName Server List File Name. |
-first |
|
|
firstPlane First Plane to process. |
-last |
|
|
lastPlane Last Plane to process. |
General Header Arguments:
-fdata |
|
|
loc val... Adjust File Header. |
-u1 |
|
|
-u2...-u5 User Parameters. |
-ndim |
|
|
Number of Dimensions. |
-tau |
|
|
Tau Value. |
-day |
|
|
Day. |
-month |
|
|
Month (1-12). |
-year |
|
|
Year. |
-hours |
|
|
Hours (0-23). |
-mins |
|
|
Minutes (0-59). |
-secs |
|
|
Seconds (0-59). |
-temp |
|
|
Temperature, Degrees C. |
-aq2D |
|
|
2D Acquisition Code or Keyword: |
0=Magnitude.
1=TPPI.
2=States.
3=Image.
-pipeFlag |
|
|
0=Multi-File Data. |
1=Pipeline Stream or Single File.
-tpFlag |
|
|
0=Not Transposed. |
1=Transposed.
Header Labels:
-srcName |
|
|
Source File Name. |
-operName |
|
|
Operator Name. |
-userName |
|
|
User Name. |
-comment |
|
|
Comment. |
-title |
|
|
Title. |
Axis-Specific Header Flags -x.. -y.. etc:
Default Values are zero:
-xN |
|
|
Actual Size in File Pts Real + Imag. |
-xT |
|
|
Current Time Domain Size Pts Real or Imag. |
-xSW |
|
|
Full Spectral Width Hz. |
-xOBS |
|
|
Observe Frequency MHz. |
-xCAR |
|
|
Carrier Position ppm. |
-xLAB |
|
|
Axis Label 8 Chars, No Spaces. |
-xMODE |
|
|
Acquisition Mode Code or Keyword: |
0=Complex,States,Complex-N,States-N.
0=States-TPPI,States-TPPI-N.
1=Real,TPPI.
2=Sequential,Bruker.
-xALT |
|
|
Sign Adjustment Code or Keyword: |
0=Complex,States No Alternation Needed.
0=Real,TPPI No Alternation Needed.
1=Sequential,Bruker Real Alternation.
2=States-TPPI Complex Alternation.
With Negation of Imaginaries:
16=Complex-N No Alternation Needed.
16=States-N No Alternation Needed.
18=States-TPPI-N Complex Alternation.
Note: Default Sign Adjustment Mode is Automatically
Set by the Corresponding Acquisition Mode Keyword.
Axis-Specific Header Flags -xQ -yQ etc. Not required for conversion. Used to adjust header:
-xTD |
|
|
Original Time Domain Size. Pts. |
-xFD |
|
|
Final Max Freq Domain Size. Pts. |
-xZFP |
|
|
Zero Fill Parameter. Pts (Negative). |
-xMID |
|
|
Carrier Virtual Loc. Pts. |
-xORIG |
|
|
Last Point Coord. Hz. |
-xDIM |
|
|
Dimension Order. |
2=Original X-Axis
1=Original Y-Axis
3=Original Z-Axis
4=Original A-Axis
-xFT |
|
|
Fourier Flag Code or Keyword: |
0=Time Time-Domain Data.
1=Freq Frequency-Domain Data.
Special Acquisition-Axis Flags (no longer required):
-aqN |
|
|
Actual Size. Pts Real or Imag. |
-aqMODE |
|
|
Acquisition Mode. 0=Complex. |
1=Real.
2=Sequential.
Axis-Specific Processing Values -xQ -yQ etc:
-xAPOD |
|
|
Apodize Function SP EM GM TM TRI or NONE. |
-xQ1 |
|
|
Apodize Parameter 1. Depends on Function. |
-xQ2 |
|
|
Apodize Parameter 2. Depends on Function. |
-xQ3 |
|
|
Apodize Parameter 3. Depends on Function. |
-xC1 |
|
|
First Point Scale. Default is 1.0. |
-xP0 |
|
|
Zero Order Phase. Degrees. |
-xP1 |
|
|
First Order Phase. Degrees. |
Special Varian Format Flags:
-sign |
|
|
Use Sign Adjustment (Default). |
-nosign |
|
|
Suppress Sign Adjustment. |
-aqORD |
aqOrd |
0 |
Acquisition Order Code. |
0 = 2D d2,phase
0 = 3D d3,d2,phase2,phase
0 = 4D d4,d3,d2,phase3,phase2,phase
1 = 3D d3,d2,phase,phase2
1 = 4D d4,d3,d2,phase,phase2,phase3
2 = 4D d3,d2,d4,phase3,phase2,phase
Notes:
1. 4D Conversion requires explicit input file
as specified by the -in argument.
2. By default, byte-swap is ON for Pentium systems,
and OFF for other platforms.
|
Under Construction
|
