mrTools - matlab based tools for fMRI.zip

#ifdef documentation ========================================================================= program: getfidkmex.c by: justin gardner purpose: reads fid data from VNMR system date: 05/06/03 compile: mex getfidk.c history: 2008/12/01, Pei, add endian detect and byte swap part. Default format of fid is big endian, as we acquaire data on VNMR Sun Solaris, also epirri5 keep the same endian. Note: SWAP data firstly and then DO typecast. This is an obsolete function that has been replaced by getfidkraw.c and getfidk.m ========================================================================= #endif //////////////////// // include section //////////////////// #include <stdio.h> #include <stdlib.h> #include <math.h> #include <memory.h> #include <unistd.h> #include <ctype.h> #include "mex.h" #include "vnmrdata.h" /////////////////// // define section /////////////////// #define STRSIZE 2048 #define LINESIZE 4096 #define FALSE 0 #define TRUE 1 #define INT16 int16 #define INT32 int32 #define FLOAT float //////////////////// // data structures //////////////////// typedef struct { int numslices; // number of slices int numvolumes; // number of volumes int numlines; // number of k-space lines in each image int numreceivers; // number of receivers int numshots; // number of shots int linelen; // number of voxels in each line int navechoes; // number of naviagtor echoes int accFactor; // acceleration factor int ndim; // number of dimensions mwSize dims[5]; // size of those dimensions int numimages; // number of images = slices*volumes*receivers int imagesize; // number of voxels in each image mxClassID datatype; // matlab type of data int totalsize; // total size of array } datainfo; /////////////////// // function decls /////////////////// void usageError(); void fileNotFound(char *); int fileLength(char *,FILE *); void errorExit(mxArray *[]); // functions of bytes swap void swap_bytes(void * p, size_t s); //////////////////// // global variables //////////////////// int verbose; FILE *ffid = NULL,*fprocpar = NULL; // declared global so we can close files on error ///////////////////////// // for output structure ///////////////////////// const char *fieldNames[] = {"name","filepath","data"}; #define NUMFIELDS 3 const char *originalFormatFieldNames[] = {"name","filepath","real","imag"}; #define ORIGINAL_FORMAT_NUMFIELDS 4 const mwSize dims[2] = {1, 1}; ////////////////////////////////////////// // function mexFunction called by matlab ////////////////////////////////////////// void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) { char filename[STRSIZE],inputname[STRSIZE], pathname[STRSIZE],procparname[STRSIZE], fullpath[STRSIZE],line[LINESIZE],*token; struct datafilehead header; struct datablockhead blockheader; datainfo info; INT16 *data_int16,*datai_int16,*raw_int16, tokenint16; INT32 *data_int32,*datai_int32,*raw_int32, tokenint32; FLOAT *data_float,*datai_float,*raw_float, tokenfloat; double *data,*datai; INT16 *block; mxArray *mxdata,*mxdatar,*mxdatai; int originalformat; int i,j,k,n; int isLittleEndianPlatform, swapFlag, gotNavechoes; // check input arguments if ((nrhs < 1) || (nrhs > 3)){ usageError(); return; } // check output arguments else if (nlhs > 1) { usageError(); return; } // set whether to verbosely report errors if (nrhs >= 2) { verbose = (int)*mxGetPr(prhs[1]); } else { verbose = FALSE; } // set whether to return data in original format or not if (nrhs >= 3) { originalformat = (int)*mxGetPr(prhs[2]); } else { originalformat = FALSE; } // get filename mxGetString(prhs[0], inputname, mxGetN(prhs[0])+1); // create the output structure if (originalformat) plhs[0] = mxCreateStructArray(2, dims, ORIGINAL_FORMAT_NUMFIELDS, originalFormatFieldNames); else plhs[0] = mxCreateStructArray(2, dims, NUMFIELDS, fieldNames); // put filename in output structure mxSetField(plhs[0],0,"name",mxCreateString(inputname)); // figure out where the fid file is // did the user input the full directory? sprintf(pathname,"%s",inputname); sprintf(filename,"%s/fid",pathname); if (verbose) mexPrintf("(getfidkmex) Trying filename %s\n",filename); if ((ffid = fopen(filename,"r")) == NULL) { // maybe the user gave the directory without .fid sprintf(pathname,"%s.fid",inputname); sprintf(filename,"%s/fid",pathname); if (verbose) mexPrintf("(getfidkmex) Trying filename %s\n",filename); if ((ffid = fopen(filename,"r")) == NULL) { // nope, maybe it is simply the filename sprintf(pathname,"."); sprintf(filename,"%s/%s",pathname,inputname); if (verbose) mexPrintf("(getfidkmex) Trying filename %s\n",filename); if ((ffid = fopen(filename,"r")) == NULL) { // nothing found, give up. fileNotFound(inputname); errorExit(plhs); return; } } } if (verbose) mexPrintf("(getfidkmex) Opened %s\n", filename); // get the full path getcwd(fullpath,STRSIZE); strcat(fullpath,"/"); if (!strcmp(pathname,".")) { if (!strcmp(inputname,".")) strcat(fullpath,"fid"); else strcat(fullpath,inputname); } else strcat(fullpath,filename); // save the full qualified path in the output structure mxSetField(plhs[0],0,"filepath",mxCreateString(fullpath)); // open the procpar sprintf(procparname,"%s/procpar",pathname); if ((fprocpar = fopen(procparname,"r")) == NULL) { // no procpar fileNotFound(filename); errorExit(plhs); return; } info.navechoes = 0; gotNavechoes = 0; info.numshots = 1; info.accFactor = 1; info.numvolumes = 1; info.numreceivers = 1; // scan through procpar looking for parameters needed for parsing while (fgets(line,LINESIZE,fprocpar)) { // get the first token of the line token = (char*)strtok(line," "); // get number of slices if (!strcmp(token,"pss")) { info.numslices = atoi(fgets(line,LINESIZE,fprocpar)); if (verbose) mexPrintf("(getfidkmex) numslices = %i\n",info.numslices); } // get number of volumes if (!strcmp(token,"cntr")) { info.numvolumes = atoi(fgets(line,LINESIZE,fprocpar)); if (verbose) mexPrintf("(getfidkmex) numvolumes = %i\n",info.numvolumes); } // get number of voxels per line if (!strcmp(token,"np")) { fgets(line,LINESIZE,fprocpar); token = (char*)strtok(line," "); token = (char*)strtok(NULL," "); // that should be number of slices info.linelen = atoi(token)/2; if (verbose) mexPrintf("(getfidkmex) linelen = %i\n",info.linelen); } // get the number of receivers if (!strcmp(token,"rcvrs")) { fgets(line,LINESIZE,fprocpar); token = (char*)strtok(line," "); token = (char*)strtok(NULL," "); info.numreceivers = 0; // Count the number of 'y's that is the number of receivers for (i = 0;i < strlen(token);i++) if (token[i] == 'y') info.numreceivers++; // make sure we have atleast 1 receiver if (info.numreceivers <= 0) info.numreceivers = 1; if (verbose) mexPrintf("(getfidkmex) Number of receivers = %i\n",info.numreceivers); } // get number of lines per image if (!strcmp(token,"ni")) { fgets(line,LINESIZE,fprocpar); token = (char*)strtok(line," "); token = (char*)strtok(NULL," "); info.numlines = atoi(token); if (verbose) mexPrintf("(getfidkmex) numlines = %i\n",info.numlines); } // get number of navechoes if (!strcmp(token,"nv")) { fgets(line,LINESIZE,fprocpar); token = (char*)strto