Change getopt numbers to avoid overlap with chars

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 :