6 NMRi I/O
Contents
1. BLKB 127 i BLK1 NMRi fp BLKB 0 1 Last 1 needed as previous NMRi files used for i 1 i lt 128 i Output 128 1D blocks to NMRi file only the reals are output here BLKB i BLKA 127 i BLK1 Copyright Scott A Smith May 22 1998 GAMMA NMRi I O 108 User Documenation Routines 6 3 NMRi fp BLKB 0 fp close Close file NMURND tst The last NMRi file produced NMURND tst was made by first opening a file successively writing 1D spectra to it then closing the file Since this program accessed NMRi files previously during the creation of NMRID tst and NMR2D tst the first spectrum was independently written outside the loop with the zero flag set when calling NMRi This sets the internal counter to zero something unnecessary had NMRi files not been previously created in the program 6 3 2 NMRi_1D Usage include lt NMRi h gt block_1D NMRi_1D const char filename int spectrum 1 Description The function NMRi_1D is used to read a 1D spectrum from an NMRi file that is a file in the standard NMRi format The NMRi file name is filename Returned is an 1D data block containing the parameters in the NMRi file along with the spectrum chosen with spectrum The default spectrum will be the initial one Return Value A one dimensional data block Example 6 3 3 NMRi_2D Usage include lt NMRi h gt block_2D NMRi_2D const char filename Description The functi2. NMRi 1D spectrum Again for consistency with the program description found in the supplied manuals the file struc ture will be discussed in terms of blocks of length 64 The data begins at block number 4 and the length of each 1D spectrum will be LENGTH SIZE 64 for a complex data set where LENGTH is given in blocks For a real data set this number will be halved GAMMA When creating NMRi files GAMMA will initially write an empty header 512 prior to any spectral data After each 1D spectrum is written the header will be updated to reflect how many lines of 1D data are present That would be the variable SPECNUM shown in Figure 25 1 1 The block length of 64 is intrinsic to the file structure as utilized in the FORTRAN code for file I O supplied with the NMRi programs GAMMA uses C code to perform I O withe NMRi making this conceptual divi sion nearly unnecessary 2 See the previous footnote This information is only useful in clarification of the manual description Copyright Scott A Smith May 22 1998
3. lt n n Output line feed so screen is nice NMRi_header filename verbose Output the header info in filename In this example the user is queried for the file and the amount of information should be returned The default value of 0 returns the minimal amount of information the amount increases as verbose increases up to 10 The header information is returned to the standard output stream Copyright Scott A Smith May 22 1998 GAMMA NMRi I O 110 User Documenation Routines 6 3 6 4 Description NMRi File Structure NMRi files begin with a header which contains 512 parameters describ ing the spectral data A 1D spectrum of length SIZE is written immediately after the header all real values followed by all imaginary values If the data is not complex the imaginary values are absent from the file A two or multi dimensional spectrum is successive 1D spectra sharing the same header information as depicted in the figure below NMRi File Structure Spectrum 2 SIZE Reals Spectrum 2 SIZE Imaginaries Spectrum SPECNUM SIZE Reals Spectrum SPECNUM SIZE Imaginaries Figure 25 1 Overall file structure of a NMRi file containing SPECNUM 1D complex spectra each of length SIZE This file structure is described in the NMRi manual LAB ONE NMR2 USER MANUAL Release 3 5 on page 29 NMRi Header Structure A full listing of the parameters contained in the header is given in the NMRi manual LAB ONE NMR1 USER MANU
4. AL Release 3 8 on page 1 37 Of the 512 pa rameters it contains few are useful outside of the NMRi programs Those absolutely required are given in the NMR2 manual cited previously on page 28 and listed here e 100 First dimension size This is SIZE in Figure 25 1 e 101 First dimension spectral width e 107 Data type 0 0 quadrature 1 0 singulature 2 0 singulature sorted e 220 Second dimension size This is SPECNUM in Figure 25 1 e 230 Second dimension spectral width Copyright Scott A Smith May 22 1998 GAMMA NMRi I O 111 User Documenation Routines 6 3 For consistency with the program description found in the supplied manuals the file structure will be briefly discussed in terms of blocks each block being of length 64 Thus the header takes up 4 blocks NMRi Header Structure a ee ee ee ee Figure 25 2 Header Structure of a NMRi file The header is conceptually divided into 4 blocks each containing 64 param eters NMRi Data Structure The actual data starts immediately after the header In a file containing mul tiple spectra i e a 1D spectrum each spectrum must be of the same size and this size must be a power of 2 64 128 256 If the any spectrum does not meet this latter requirement it will be padded with zeros until the size is a power of 2 Furthermore they must all be real or all be com plex NMRi Data Structure SIZE Reals SIZE Imaginaries Optional Figure 25 3 Structure of
5. GAMMA NMRi I O 106 User Documenation Overview 6 1 6 NMRiI O 6 1 Overview The NMRi I O routines are provided to allow the transfer of data between GAMMA and the pro grams NMR1 and NMR2 6 2 Available NMRi Functions NMRi Write an NMRi file page 106 NMRi_1D Read an NMRi file into a GAMMA vector page 108 NMRi_2D Read an NMRi file intoa GAMMA matrix page 108 NMRi_header Read the header of an NMRi file page 109 6 3 Routines 6 3 1 NMRi Usage include lt NMRi h gt void NMRi const char filename block_1D amp BLK int rc 1 void NMRi const char filename block_2D amp BLK int rc 1 void NMRi File amp file block_1D amp BLK int rc 1 int zero 0 Description The function NMRi is used to write files in the standard NMRi format The data is contained in the data block BLK The file is specified by either the name filename or by the file pointer file The parameter rc indicates whether to write real or complex default data If rc is 0 only the real data will be output If rc is negative only the imaginary data is written as reals and if rc gt 0 the complex data is written 1 NMRi const char filename block_1D amp BLK int re 1 When NMRi is invoked with this argument list it writes the data contained in the 1 dimensional data block BLK to a newly constructed file file name in the NMRi format If rc is 1 default the data is written as complex numbers If rc is se
6. on NMRi_2D is used to read a 2D spectrum from an NMRi file that is a file in the standard NMRi format The NMRi file name is filename Returned is an 2D data block containing the parameters in the NMRi file along with the entire 2D spectrum Return Value A two dimensional data block Example Copyright Scott A Smith May 22 1998 GAMMA NMRi I O 109 User Documenation Routines 6 3 6 3 4 NMRi_header Usage include lt NMRi h gt ostream amp NMRi_header const char filename int verbose 0 Description The function NMRi_header is used to quickly read the header information contained in an NMRi file The NMRi file name is filename The header contains 512 pieces of information only some of which is partic ularly useful outside of the NMRi programs themselves The integer verbose specifies how much of this in formation should be returned The default value of 0 returns the minimal amount of information the amount increases as verbose increases up to 10 The header is returned in an output stream Return Value None the function sends information to standard output Example include lt gamma h gt main String filename Declare a string cout lt lt Which Levy File Ask for filename cin gt gt filename Input filename int verbose Declear an integer cout lt lt nHow verbose Ask for verbose level cin gt gt verbose Input verbose level cout lt
7. t to zero only the real data of the block is output Any parameters in BLK compatible with the NMRi parameters will be automatically transferred into the NMRi file The file is closed upon the function return The func 1 NMR1 and NMR2 are a products of New Methods Research Inc 7 East Genesee Street Syracuse NY 13210 Phone 315 424 0329 FAX 315 424 0356 GAMMA was tested on Sun systems running the Sun views operating system NMRI release 3 8 and NMR2 release 3 5 were the manuals referred to during the programming Copyright Scott A Smith May 22 1998 GAMMA NMRi I O 107 User Documenation Routines 6 3 tion will overwrite any file filename previously in existence No other NMRi file should be open during the calling of this function 2 NMRi const char filename block_2D amp BLK int rc 1 This function is similar to the use above with 1D data blocks but writes the data contained in the 2 dimensional data block BLK This is done row wise i e first row 1 of BLK is written followed by row 2 and so on until the end of the data in BLK 3 NMRi File amp file block_1D amp BLK int re 1 When NMRi is invoked with this argument list it writes the data contained in the 1 dimensional data block BLK in the NMRi format to wherever the file point er file is at The file where file is pointing is assumed to be open opened explicitly sometime prior to the function call and will remain open with
8. the file pointer advanced to the file end at the function return The file should be closed externally as well The NMRi parameter block is updated with each function call An optional parameter in this function is zero which if non zero will set the count of 1D spectra present in the NMRi file to zero This is done automatically in most instances but should be used if multiple NMRi files are to be produced in a single program run it is necessary to re zero the count when writing the first spectrum of all NMRi files Note that NMRi can be called with a matrix instead of a block_2D or a row_ vector rather than a block_1D In these instances the parameter sets are not fully written into the NMRi file Return Value Nothing when producing a NMRi file Example include lt gamma hc gt main block_1D BLK1 128 Define a 1D data block BLK1 Gaussian 128 64 42 46 Set 1D block to Gaussian NMRi NMRID tst BLK1 Output 1D BLK to NMRi file block_2D BLK2 128 128 Define a 2D data block for int i 0 i lt 128 i Fill 2D block with 2D Gaussian for int j 0 j lt 128 j BLK2 ij BLK1 i BLK1 j NMRi NMR2D tst BLK2 Output 2D BLK to NMRi file File fp Specify a file pointer fp open NMRND tst io_writeonly a_create Open file NMRND tst block_1D BLKA 128 BLKB 128 Define two more 1D data blocks BLKA sinc 128 64 12 Set block to sinc function
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