aboutsummaryrefslogtreecommitdiff
path: root/src/indexamajig.c
diff options
context:
space:
mode:
authorYaroslav Gevorkov <yaroslav.gevorkov@desy.de>2018-05-24 15:47:34 +0200
committerThomas White <taw@physics.org>2018-05-25 17:32:20 +0200
commit21e6b3e38e9df7e0fa3cf647a8eb8041ea019199 (patch)
treead22b7d963d9b242484ed9a106f0bc6cf222f17c /src/indexamajig.c
parent998e9126b3454a9b8a47b20efefe7263e24571e2 (diff)
Change getopt numbers to avoid overlap with chars
Diffstat (limited to 'src/indexamajig.c')
-rw-r--r--src/indexamajig.c206
1 files changed, 103 insertions, 103 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 714af5cd..cab727a5 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -374,60 +374,60 @@ int main(int argc, char *argv[])
{"use-saturated", 0, &iargs.use_saturated, 1},
/* Long-only options with arguments */
- {"peaks", 1, NULL, 2},
- {"cell-reduction", 1, NULL, 3},
- {"min-gradient", 1, NULL, 4},
- {"record", 1, NULL, 5},
- {"cpus", 1, NULL, 6},
- {"cpugroup", 1, NULL, 7},
- {"cpuoffset", 1, NULL, 8},
- {"hdf5-peaks", 1, NULL, 9},
- {"copy-hdf5-field", 1, NULL, 10},
- {"min-snr", 1, NULL, 11},
- {"tolerance", 1, NULL, 13},
- {"int-radius", 1, NULL, 14},
- {"median-filter", 1, NULL, 15},
- {"integration", 1, NULL, 16},
- {"temp-dir", 1, NULL, 17},
- {"int-diag", 1, NULL, 18},
- {"push-res", 1, NULL, 19},
- {"res-push", 1, NULL, 19}, /* compat */
- {"peak-radius", 1, NULL, 20},
- {"highres", 1, NULL, 21},
- {"fix-profile-radius", 1, NULL, 22},
- {"fix-bandwidth", 1, NULL, 23},
- {"fix-divergence", 1, NULL, 24},
- {"felix-options", 1, NULL, 25},
- {"min-pix-count", 1, NULL, 26},
- {"max-pix-count", 1, NULL, 27},
- {"local-bg-radius", 1, NULL, 28},
- {"min-res", 1, NULL, 29},
- {"max-res", 1, NULL, 30},
- {"min-peaks", 1, NULL, 31},
- {"taketwo-member-threshold", 1, NULL, 32},
- {"taketwo-member-thresh", 1, NULL, 32}, /* compat */
- {"taketwo-len-tolerance", 1, NULL, 33},
- {"taketwo-len-tol", 1, NULL, 33}, /* compat */
- {"taketwo-angle-tolerance", 1, NULL, 34},
- {"taketwo-angle-tol", 1, NULL, 34}, /* compat */
- {"taketwo-trace-tolerance", 1, NULL, 35},
- {"taketwo-trace-tol", 1, NULL, 35}, /* compat */
- {"felix-tthrange-min", 1, NULL, 36},
- {"felix-tthrange-max", 1, NULL, 37},
- {"felix-min-visits", 1, NULL, 38},
- {"felix-min-completeness", 1, NULL, 39},
- {"felix-max-uniqueness", 1, NULL, 40},
- {"felix-num-voxels", 1, NULL, 41},
- {"felix-fraction-max-visits",1, NULL, 42},
- {"felix-sigma", 1, NULL, 43},
- {"serial-start", 1, NULL, 44},
- {"felix-domega", 1, NULL, 45},
- {"felix-max-internal-angle", 1, NULL, 46},
- {"sig-fac-biggest-pix" ,1, NULL, 47},
- {"sig-fac-peak-pix" ,1, NULL, 48},
- {"min-sig" ,1, NULL, 49},
- {"min-peak-over-neighbour" ,1, NULL, 50},
- {"window-radius" ,1, NULL, 51},
+ {"peaks", 1, NULL, 302},
+ {"cell-reduction", 1, NULL, 303},
+ {"min-gradient", 1, NULL, 304},
+ {"record", 1, NULL, 305},
+ {"cpus", 1, NULL, 306},
+ {"cpugroup", 1, NULL, 307},
+ {"cpuoffset", 1, NULL, 308},
+ {"hdf5-peaks", 1, NULL, 309},
+ {"copy-hdf5-field", 1, NULL, 310},
+ {"min-snr", 1, NULL, 311},
+ {"tolerance", 1, NULL, 313},
+ {"int-radius", 1, NULL, 314},
+ {"median-filter", 1, NULL, 315},
+ {"integration", 1, NULL, 316},
+ {"temp-dir", 1, NULL, 317},
+ {"int-diag", 1, NULL, 318},
+ {"push-res", 1, NULL, 319},
+ {"res-push", 1, NULL, 319}, /* compat */
+ {"peak-radius", 1, NULL, 320},
+ {"highres", 1, NULL, 321},
+ {"fix-profile-radius", 1, NULL, 322},
+ {"fix-bandwidth", 1, NULL, 323},
+ {"fix-divergence", 1, NULL, 324},
+ {"felix-options", 1, NULL, 325},
+ {"min-pix-count", 1, NULL, 326},
+ {"max-pix-count", 1, NULL, 327},
+ {"local-bg-radius", 1, NULL, 328},
+ {"min-res", 1, NULL, 329},
+ {"max-res", 1, NULL, 330},
+ {"min-peaks", 1, NULL, 331},
+ {"taketwo-member-threshold", 1, NULL, 332},
+ {"taketwo-member-thresh", 1, NULL, 332}, /* compat */
+ {"taketwo-len-tolerance", 1, NULL, 333},
+ {"taketwo-len-tol", 1, NULL, 333}, /* compat */
+ {"taketwo-angle-tolerance", 1, NULL, 334},
+ {"taketwo-angle-tol", 1, NULL, 334}, /* compat */
+ {"taketwo-trace-tolerance", 1, NULL, 335},
+ {"taketwo-trace-tol", 1, NULL, 335}, /* compat */
+ {"felix-tthrange-min", 1, NULL, 336},
+ {"felix-tthrange-max", 1, NULL, 337},
+ {"felix-min-visits", 1, NULL, 338},
+ {"felix-min-completeness", 1, NULL, 339},
+ {"felix-max-uniqueness", 1, NULL, 340},
+ {"felix-num-voxels", 1, NULL, 341},
+ {"felix-fraction-max-visits",1, NULL, 342},
+ {"felix-sigma", 1, NULL, 343},
+ {"serial-start", 1, NULL, 344},
+ {"felix-domega", 1, NULL, 345},
+ {"felix-max-internal-angle", 1, NULL, 346},
+ {"sig-fac-biggest-pix" ,1, NULL,347},
+ {"sig-fac-peak-pix" ,1, NULL,348},
+ {"min-sig" ,1, NULL,349},
+ {"min-peak-over-neighbour" ,1, NULL,350},
+ {"window-radius" ,1, NULL,351},
{0, 0, NULL, 0}
};
@@ -485,11 +485,11 @@ int main(int argc, char *argv[])
iargs.threshold = strtof(optarg, NULL);
break;
- case 2 :
+ case 302 :
speaks = strdup(optarg);
break;
- case 3 :
+ case 303 :
ERROR("The option '--cell-reduction' is no longer "
"used.\n"
"The complete indexing behaviour is now "
@@ -498,63 +498,63 @@ int main(int argc, char *argv[])
"available methods.\n");
return 1;
- case 4 :
+ case 304 :
iargs.min_gradient = strtof(optarg, NULL);
break;
- case 5 :
+ case 305 :
ERROR("The option '--record' is no longer used.\n"
"Use '--no-peaks-in-stream' and"
"'--no-refls-in-stream' if you need to control"
"the contents of the stream.\n");
return 1;
- case 6 :
- case 7 :
- case 8 :
+ case 306 :
+ case 307 :
+ case 308 :
ERROR("The options --cpus, --cpugroup and --cpuoffset"
" are no longer used by indexamajig.\n");
break;
- case 9 :
+ case 309 :
free(command_line_peak_path);
command_line_peak_path = strdup(optarg);
break;
- case 10 :
+ case 310 :
add_imagefile_field(iargs.copyme, optarg);
break;
- case 11 :
+ case 311 :
iargs.min_snr = strtof(optarg, NULL);
iargs.sig_fac_whole_peak = iargs.min_snr;
break;
- case 13 :
+ case 313 :
toler = strdup(optarg);
break;
- case 14 :
+ case 314 :
intrad = strdup(optarg);
break;
- case 15 :
+ case 315 :
iargs.median_filter = atoi(optarg);
break;
- case 16 :
+ case 316 :
int_str = strdup(optarg);
break;
- case 17 :
+ case 317 :
tempdir = strdup(optarg);
break;
- case 18 :
+ case 318 :
int_diag = strdup(optarg);
break;
- case 19 :
+ case 319 :
if ( sscanf(optarg, "%f", &iargs.push_res) != 1 ) {
ERROR("Invalid value for --push-res\n");
return 1;
@@ -563,11 +563,11 @@ int main(int argc, char *argv[])
have_push_res = 1;
break;
- case 20 :
+ case 320 :
pkrad = strdup(optarg);
break;
- case 21 :
+ case 321 :
if ( sscanf(optarg, "%f", &iargs.highres) != 1 ) {
ERROR("Invalid value for --highres\n");
return 1;
@@ -576,7 +576,7 @@ int main(int argc, char *argv[])
iargs.highres = 1.0 / (iargs.highres/1e10);
break;
- case 22 :
+ case 322 :
if ( sscanf(optarg, "%f", &iargs.fix_profile_r) != 1 ) {
ERROR("Invalid value for "
"--fix-profile-radius\n");
@@ -584,50 +584,50 @@ int main(int argc, char *argv[])
}
break;
- case 23 :
+ case 323 :
if ( sscanf(optarg, "%f", &iargs.fix_bandwidth) != 1 ) {
ERROR("Invalid value for --fix-bandwidth\n");
return 1;
}
break;
- case 24 :
+ case 324 :
if ( sscanf(optarg, "%f", &iargs.fix_divergence) != 1 ) {
ERROR("Invalid value for --fix-divergence\n");
return 1;
}
break;
- case 25 :
+ case 325 :
ERROR("--felix-options is no longer used.\n");
ERROR("See --help for the new Felix options.\n");
return 1;
- case 26:
+ case 326:
iargs.min_pix_count = atoi(optarg);
break;
- case 27:
+ case 327:
iargs.max_pix_count = atoi(optarg);
break;
- case 28:
+ case 328:
iargs.local_bg_radius = atoi(optarg);
break;
- case 29:
+ case 329:
iargs.min_res = atoi(optarg);
break;
- case 30:
+ case 330:
iargs.max_res = atoi(optarg);
break;
- case 31:
+ case 331:
iargs.min_peaks = atoi(optarg);
break;
- case 32:
+ case 332:
if ( sscanf(optarg, "%i", &iargs.taketwo_opts.member_thresh) != 1 )
{
ERROR("Invalid value for --taketwo-member-threshold\n");
@@ -635,7 +635,7 @@ int main(int argc, char *argv[])
}
break;
- case 33:
+ case 333:
if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.len_tol) != 1 )
{
ERROR("Invalid value for --taketwo-len-tolerance\n");
@@ -645,7 +645,7 @@ int main(int argc, char *argv[])
iargs.taketwo_opts.len_tol *= 1e10;
break;
- case 34:
+ case 334:
if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.angle_tol) != 1 )
{
ERROR("Invalid value for --taketwo-angle-tolerance\n");
@@ -655,7 +655,7 @@ int main(int argc, char *argv[])
iargs.taketwo_opts.angle_tol = deg2rad(iargs.taketwo_opts.angle_tol);
break;
- case 35:
+ case 335:
if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.trace_tol) != 1 )
{
ERROR("Invalid value for --taketwo-trace-tolerance\n");
@@ -665,7 +665,7 @@ int main(int argc, char *argv[])
iargs.taketwo_opts.trace_tol = deg2rad(iargs.taketwo_opts.trace_tol);
break;
- case 36:
+ case 336:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.ttmin) != 1 )
{
ERROR("Invalid value for --felix-tthrange-min\n");
@@ -674,7 +674,7 @@ int main(int argc, char *argv[])
iargs.felix_opts.ttmin = deg2rad(iargs.felix_opts.ttmin);
break;
- case 37:
+ case 337:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.ttmax) != 1 )
{
ERROR("Invalid value for --felix-tthrange-max\n");
@@ -683,7 +683,7 @@ int main(int argc, char *argv[])
iargs.felix_opts.ttmax = deg2rad(iargs.felix_opts.ttmax);
break;
- case 38:
+ case 338:
if ( sscanf(optarg, "%i", &iargs.felix_opts.min_visits) != 1 )
{
ERROR("Invalid value for --felix-min-visits\n");
@@ -691,7 +691,7 @@ int main(int argc, char *argv[])
}
break;
- case 39:
+ case 339:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.min_completeness) != 1 )
{
ERROR("Invalid value for --felix-min-completeness\n");
@@ -699,7 +699,7 @@ int main(int argc, char *argv[])
}
break;
- case 40:
+ case 340:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.max_uniqueness) != 1 )
{
ERROR("Invalid value for --felix-max-uniqueness\n");
@@ -707,7 +707,7 @@ int main(int argc, char *argv[])
}
break;
- case 41:
+ case 341:
if ( sscanf(optarg, "%i", &iargs.felix_opts.n_voxels) != 1 )
{
ERROR("Invalid value for --felix-num-voxels\n");
@@ -715,7 +715,7 @@ int main(int argc, char *argv[])
}
break;
- case 42:
+ case 342:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.fraction_max_visits) != 1 )
{
ERROR("Invalid value for --felix-fraction-max-visits\n");
@@ -723,7 +723,7 @@ int main(int argc, char *argv[])
}
break;
- case 43:
+ case 343:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.sigma) != 1 )
{
ERROR("Invalid value for --felix-sigma\n");
@@ -731,7 +731,7 @@ int main(int argc, char *argv[])
}
break;
- case 44:
+ case 344:
if ( sscanf(optarg, "%i", &serial_start) != 1 )
{
ERROR("Invalid value for --serial-start\n");
@@ -739,7 +739,7 @@ int main(int argc, char *argv[])
}
break;
- case 45:
+ case 345:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.domega) != 1 )
{
ERROR("Invalid value for --felix-domega\n");
@@ -747,7 +747,7 @@ int main(int argc, char *argv[])
}
break;
- case 46:
+ case 346:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.max_internal_angle) != 1 )
{
ERROR("Invalid value for --felix-max-internal-angle\n");
@@ -755,23 +755,23 @@ int main(int argc, char *argv[])
}
break;
- case 47:
+ case 347:
iargs.sig_fac_biggest_pix = strtof(optarg, NULL);
break;
- case 48:
+ case 348:
iargs.sig_fac_peak_pix = strtof(optarg, NULL);
break;
- case 49:
+ case 349:
iargs.min_sig = strtof(optarg, NULL);
break;
- case 50:
+ case 350:
iargs.min_peak_over_neighbour = strtof(optarg, NULL);
break;
- case 51:
+ case 351:
iargs.window_radius = atoi(optarg);
case 0 :