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.

Frank Delaglio, Ph.D.