c_cpp/salusFstReCoord/src1/worker.c

   1 #include <float.h>  // DBL_MAX
   2 #include <math.h>   // floor, nextafter, INFINITY
   3
   4 #include "common.h"
   5
   6 FORCE_INLINE void transCorrd(double *restrict ChipXY, const double *restrict FovXY, const int_least16_t *restrict FovRowCol) {
   7         double new_x = (FovRowCol[1] - (CenterFOV_COL - 1)) * FOV_USED_WIDTH - FovXY[1] - 1;
   8         double new_y = FovXY[0] + (FovRowCol[0] - (CenterFOV_ROW - 1) - 1) * FOV_USED_HEIGHT;
   9         ChipXY[0] = floor(nextafter(new_x * RECIPROCALPRECISION, copysign(INFINITY, new_x))) * OUTPUTPRECISION;
  10         ChipXY[1] = floor(nextafter(new_y * RECIPROCALPRECISION, copysign(INFINITY, new_y))) * OUTPUTPRECISION;
  11         // ChipXY[0] = floor(new_x * RECIPROCALPRECISION) * OUTPUTPRECISION;
  12         // ChipXY[1] = floor(new_y * RECIPROCALPRECISION) * OUTPUTPRECISION;
  13 }
  14
  15 FORCE_INLINE char *strncpy_no_colon(char *restrict dest, const char *restrict src, size_t n) {
  16         size_t j = 0;  // destination index
  17         for (size_t i = 0; i < n && src[i] != '\0'; i++) {
  18                 if (src[i] != ':') dest[j++] = src[i];
  19         }
  20         // for ( ; j < n; j++) dest[j] = '\0';
  21         if (j < n) dest[j] = '\0';
  22         return dest;
  23 }
  24
  25 void worker(int_least16_t worker_id) {
  26         workerArray_t *worker = &Parameters.worksQuene[worker_id];
  27         regmatch_t matches[2];
  28         char **splitSets = worker->tokens;
  29         // char* readName = malloc(91);          // for testing CHARsCPYSTR
  30         char readName[MAXFQIDLEN + 1] = {0};  // 81 => [0,80]
  31         char fovRC[9] = {0};                  // R123C567
  32         double GIVENunZoomRatio = (double)Parameters.unZoomRatio;
  33         double unZoomRatio = 0;
  34         for (uint64_t index = 0; index < JOBITEMSIZE; index++) {
  35                 fstBCdata_t *fstBCdata_p = &worker->jobDatArray[index];
  36                 if (fstBCdata_p->name[0] == 0) {
  37                         break;
  38                 }
  39                 // fstBCoutput_t *fstBCoutput_p = &worker->output_array[index];
  40                 ARRAYcpySTR(readName, fstBCdata_p->name);
  41                 assert(readName[sizeof(fstBCdata_p->name)] == '\0');
  42 #ifndef RELEASE
  43                 fprintf(stderr, "###### %llu\t[%s] %d <--\n", index, readName, readName[sizeof(fstBCdata_p->name)]);
  44 #endif
  45                 int_least16_t RowCol[2] = {0};
  46                 double oldXY[2] = {0.0};
  47                 double newXY[2] = {0.0};
  48                 char *delim = ":";
  49                 if (regexec(&Parameters.regex, readName, 2, matches, 0) != 0) {
  50                         fstBCdata_p->name[0] = 0;
  51                         continue;
  52                 }
  53                 //__builtin_dump_struct(&matches[0], &printf);
  54                 //__builtin_dump_struct(&matches[1], &printf);
  55                 size_t relen = matches[0].rm_eo - matches[0].rm_so;
  56                 strncpy_no_colon(fovRC, readName + matches[0].rm_so, relen);
  57                 // fovRC[relen-1] = '\0';
  58                 assert(fovRC[sizeof(fovRC) - 1] == '\0');
  59                 // memcpy(fstBCdata_p->RowCol, fovRC, relen-1);
  60                 fstBCdata_p->fov_row = (uint8_t)(RowCol[0] = atoi(fovRC + 1));
  61                 fstBCdata_p->fov_column = (uint8_t)(RowCol[1] = atoi(fovRC + 5));
  62                 if (unlikely(matches[1].rm_so == -1)) {
  63                         delim = "_";
  64                         unZoomRatio = 1.0;
  65                 } else {
  66                         delim = ":";
  67                         unZoomRatio = GIVENunZoomRatio;
  68                 }
  69                 assert(relen == (delim[0] == ':' ? sizeof(fovRC) : sizeof(fovRC) - 1));
  70                 // printf("%llu\t[%s], delim:[%s], fov[%s]\n", index, readName, delim, fovRC);
  71                 const char *theDelim = delim;
  72                 char *saveptr = NULL;
  73                 char *token = strtok_r(readName, theDelim, &saveptr);
  74                 // printf("-f- [%zu] [%zu] [%s]\n", readName, token, token);
  75                 if (unlikely(token == NULL)) {
  76                         // printf("-b->\t[%s], delim:[%s]\n", readName, theDelim);
  77                         fstBCdata_p->name[0] = 0;
  78                         break;
  79                 } else {
  80                         int_least16_t idx = 0;
  81                         for (idx = 0; likely(token != NULL); token = strtok_r(NULL, theDelim, &saveptr), idx++) {
  82                                 splitSets[idx] = token;
  83                                 // printf("-s- %d:[%zu] [%s]\n", idx, splitSets[idx], token);
  84                         }
  85                         oldXY[1] = atof(splitSets[idx - 1]);
  86                         oldXY[0] = atof(splitSets[idx - 2]);
  87 #ifdef DEBUG
  88                         fprintf(stderr, "oldXY: [%s],[%s] as [%.2f %.2f]\n", splitSets[idx - 2], splitSets[idx - 1], oldXY[0], oldXY[1]);
  89                         /* for (idx = 0; idx < MAXDELIMITEMS; idx++) {
  90                             printf("-t- %d:[%zu] [%s]\n", idx, (void *)splitSets[idx], splitSets[idx]);
  91                         } */
  92 #endif
  93                 }
  94                 if (unlikely(unZoomRatio != 1.0f)) {
  95                         oldXY[0] /= unZoomRatio;
  96                         oldXY[1] /= unZoomRatio;
  97                 }
  98 #ifdef DEBUG
  99                 fprintf(stderr, "[%s]->[%s]=RC(%d,%d), X:%f Y:%f\n", readName, fovRC, RowCol[0], RowCol[1], oldXY[0], oldXY[1]);
 100 #endif
 101                 if ((FOV_X_MIN < oldXY[0] && oldXY[0] <= FOV_X_MAX) && (FOV_Y_MIN < oldXY[1] && oldXY[1] <= FOV_Y_MAX)) {
 102                         oldXY[0] -= FOV_X_MIN;
 103                         oldXY[1] -= FOV_Y_MIN;
 104                         transCorrd(newXY, oldXY, RowCol);
 105                         // printf("-->gX:%.2f gY:%.2f\n", newXY[0], newXY[1]);
 106                         memcpy(fstBCdata_p->newXY, newXY, sizeof(newXY));
 107 #ifdef DEBUG
 108                         char readSeq[BARCODELEN + 1];
 109                         ARRAYcpySTR(readSeq, fstBCdata_p->seq);
 110                         fprintf(stderr, "->SpatiaStr:[%s %.2f %.2f]\n", readSeq, fstBCdata_p->newXY[0], fstBCdata_p->newXY[1]);
 111 #endif
 112                 } else {
 113                         fstBCdata_p->name[0] = 0;
 114                 }
 115         }
 116 }