Programs of the NMRPipe System
bin2pipe: General-Purpose Four-Byte Binary Data to NMRPipe-Format Conversion.

bin2pipe hdrFlags < binData > pipeFile
General Flags:

Flag	Argument	Default	Description
`-in`	`inName`		Four-Byte Binary Input.
`-in`	`inNameR inNameI`		Four-Byte Binary Input Pair.
`-out`	`outTemplate`		NMRPipe Output.
`-ov`			Force Overwrite.
`-nodir`			Suppress Directory Creation.
`-nofs`			Suppress File Size Check.
`-verb`			Verbose Mode On.

General Format Flags:

`-bo`	`bytOff`	`0`	Byte Offset at Start of Input.
`-bp`	`bytPad`	`0`	Bytes Between 1D Slices in Input.
`-pad`			Pad missing data by zeros.
`-nopad`			Suppress padding by zeros (Default).
`-il`			Interleave Pairs of Input Planes (Default if two inputs are given).
`-noil`			No Interleave of Input Planes (Default if one input is given).
`-i2r`			Do Int-to-Real Conversion.
`-neg`			Do Negation of Imaginary Data.
`-ri`			Do Separation of Real/Imag.
`-bad`	`bPt`	`0.0`	Bad Point Threshold (Use 0.0 for No Bad Point Adjust).

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)

Specific Format Flags:

`-alpha`			Same As: -bo 8704 -i2r -ri -neg -aswap
`-alpha2`			Same As: -bo 16384 -i2r -ri -neg -aswap
`-lambda`			Same As: -bo -1 -ri -neg -aswap
`-gsx`			Same As: -ri -i2r -aswap
`-ex`			Same As: -ri -i2r -aswap
`-chem`			Same As: -i2r -aswap
`-ge`			Same As: -ri -noaswap
`-ftOLD`			Same As: -bo 8 -bp 12 -ri -pad -noaswap (Required byte offset may vary)
`-ftNEW`			Same As: -bo 1036 -bp 4 -ri -pad -noaswap (Required byte offset may vary)

Null Data Flags:

`-noIn`			No Input Data (Use Zeros).
`-noOut`			No Output Data (Header Only).

Parallel Processing: (Not yet 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`	`u1`	`0.0`	User Parameter 1.
`-u2`	`u2`	`0.0`	User Parameter 2.
`-u3`	`u3`	`0.0`	User Parameter 3.
`-u4`	`u4`	`0.0`	User Parameter 4.
`-u5`	`u5`	`0.0`	User Parameter 5.
`-ndim`	`ndim`	`0`	Number of Dimensions.
`-tau`	`tau`	`0`	Tau Value.
`-day`	`day`	`0`	Day.
`-month`	`month`	`0`	Month (1-12).
`-year`	`year`	`0`	Year.
`-hours`	`h`	`0`	Hours (0-23)
`-mins`	`m`	`0`	Minutes (0-59)
`-secs`	`s`	`0`	Seconds (0-59)
`-temp`	`t`	`0.0`	Temperature, Degrees C.
`-aq2D`	`aq2D`	`0`	2D Acquisition Code or Keyword: 0=Magnitude. 1=TPPI. 2=States. 3=Image.
`-pipeFlag`	`pipeFlag`	`0`	0=Multi-File Data. 1=Pipeline Stream or Single File.
`-tpFlag`	`tpFlag`	`0`	0=Not Transposed. 1=Transposed.

Header Labels:

`-srcName`	`src`	Source File Name (16 Characters Max).
`-operName`	`oper`	Operator Name (32 Characters Max).
`-userName`	`user`	User Name (16 Characters Max).
`-comment`	`comment`	Comment (160 Characters Max).
`-title`	`title`	Title (60 Characters Max).

Axis-Specific Header Flags -x.. -y.. etc:

`-xN`	`xN`	`0`	Actual Size in File Pts Real + Imag.
`-xT`	`xT`	`0`	Current Time Domain Size Pts Real or Imag.
`-xSW`	`xSW`	`0.0`	Full Spectral Width Hz.
`-xOBS`	`xOBS`	`0.0`	Observe Frequency MHz.
`-xCAR`	`xCAR`	`0.0`	Carrier Position ppm.
`-xLAB`	`xLAB`	`None`	Axis Label 8 Chars, No Spaces.
`-xMODE`	`xMODE`	`0`	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`	`xALT`	`0`	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.

Axis-Specific Header Flags -xQ -yQ etc. Not required for conversion. Used to adjust header:

`-xTD`	`xTD`	Original Time Domain Size. Pts.
`-xFD`	`xFD`	Final Max Freq Domain Size. Pts.
`-xZFP`	`xZFP`	Zero Fill Parameter. Pts (Negative).
`-xMID`	`xMID`	Carrier Virtual Loc. Pts.
`-xORIG`	`xORIG`	Last Point Coord. Hz.
`-xDIM`	`xDIM`	Dimension Order. 2=Original X-Axis 1=Original Y-Axis 3=Original Z-Axis 4=Original A-Axis
`-xFT`	`xFT`	Fourier Flag Code or Keyword: 0=Time Time-Domain Data. 1=Freq Frequency-Domain Data.

Special Acquisition-Axis Flags (no longer required):

`-aqN`	`aqN`		Actual Size. Pts Real or Imag.
`-aqMODE`	`aqMODE`		Acquisition Mode. 0=Complex. 1=Real. 2=Sequential.

Axis-Specific Processing Values -xQ -yQ etc:

`-xAPOD`	`xAPOD`	Apodize Function SP EM GM TM TRI or NONE.
`-xQ1`	`xQ1`	Apodize Parameter 1. Depends on Function.
`-xQ2`	`xQ2`	Apodize Parameter 2. Depends on Function.
`-xQ3`	`xQ3`	Apodize Parameter 3. Depends on Function.
`-xC1`	`xC1`	First Point Scale. Default is 1.0.
`-xP0`	`xP0`	Zero Order Phase. Degrees.
`-xP1`	`xP1`	First Order Phase. Degrees.

Notes:
1. JEOL GSX Phase-Sensitive input is specified as a pair of file names.
2. JEOL LAMBDA mode (-lambda) will attempt to find the byte offset from the JEOL header.
3. By default, byte-swap is ON for Pentium systems, and OFF for other platforms.

Frank Delaglio, Ph.D.