BWA::BWA(const char* ann_filename,
const char* amb_filename,
const char* pac_filename,
const char* forward_bwt_filename,
const char* forward_sa_filename,
const char* reverse_bwt_filename,
const char* reverse_sa_filename)
{
// Load the bns (?) and reference
bns = bns_restore_core(ann_filename,amb_filename,pac_filename);
reference = new ubyte_t[bns->l_pac/4+1];
rewind(bns->fp_pac);
fread(reference, 1, bns->l_pac/4+1, bns->fp_pac);
fclose(bns->fp_pac);
bns->fp_pac = NULL;
// Load the BWTs (both directions) and suffix arrays (both directions)
bwts[0] = bwt_restore_bwt(forward_bwt_filename);
bwt_restore_sa(forward_sa_filename, bwts[0]);
bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
bwt_restore_sa(reverse_sa_filename, bwts[1]);
load_default_options();
// Always reinitialize the random seed whenever a new set of files are loaded.
initialize_random_seed();
// initialize the bwase subsystem
bwase_initialize();
}
Location_options parse_options_pf (Pf *pf)
{
Location_options o;
char *s; /* string buffer */
int i;
int recenter=0; /* recenter flag */
o = load_default_options();
s = pfget_string(pf,"arrival_residual_weight_method");
/* Note this implicitly accepts the default if the keyword is missing */
if(s != NULL)
{
if(!strcasecmp(s,"bisquare")) o.atime_residual_weight = BISQUARE;
if(!strcasecmp(s,"thomson")) o.atime_residual_weight = THOMSON;
if(!strcasecmp(s,"huber")) o.atime_residual_weight = HUBER;
if(!strcasecmp(s,"none")) o.atime_residual_weight = NONE;
}
/* Do the same for slowness */
s = pfget_string(pf,"slowness_residual_weight_method");
if(s != NULL)
{
if(!strcasecmp(s,"bisquare")) o.slow_residual_weight = BISQUARE;
if(!strcasecmp(s,"thomson")) o.slow_residual_weight = THOMSON;
if(!strcasecmp(s,"huber")) o.slow_residual_weight = HUBER;
if(!strcasecmp(s,"none")) o.slow_residual_weight = NONE;
}
o.atime_distance_weight = pfget_boolean_wdef(pf,
"time_distance_weighting",o.atime_distance_weight);
o.slow_distance_weight = pfget_boolean_wdef(pf,
"slowness_distance_weighting",o.slow_distance_weight);
o.slowness_weight_scale_factor = (float) pfget_double_wdef(pf,
"slowness_weight_scale_factor",
o.slowness_weight_scale_factor);
o.min_error_scale = (float) pfget_double_wdef(pf,
"min_error_scale",o.min_error_scale);
o.max_error_scale = (float) pfget_double_wdef(pf,
"max_error_scale",o.max_error_scale);
for(i=0;i<4;++i) o.fix[i] = 0;
if(pfget_boolean_wdef(pf,"fix_longitude",0)) o.fix[0] = 1;
if(pfget_boolean_wdef(pf,"fix_latitude",0)) o.fix[1] = 1;
if(pfget_boolean_wdef(pf,"fix_depth",0)) o.fix[2] = 1;
if(pfget_boolean_wdef(pf,"fix_origin_time",0)) o.fix[3] = 1;
if(pfget_boolean_wdef(pf,"recenter",0)) recenter = 1;
s = pfget_string(pf,"generalized_inverse");
if(s != NULL)
{
if(!strcasecmp(s,"marquardt"))
{
o.min_relative_damp = (float) pfget_double_wdef(pf,
"min_relative_damp",o.min_relative_damp);
if(o.min_relative_damp < FLT_EPSILON)
{
elog_log(0,"Warning: minimum relative damping must be at least single precision epsilon.\nParameter file wanted %f\nReset to %f\n",
o.min_relative_damp, FLT_EPSILON);
o.min_relative_damp = FLT_EPSILON;
}
o.max_relative_damp = (float) pfget_double_wdef(pf,
"max_relative_damp",o.max_relative_damp);
o.damp_adjust_factor = (float) pfget_double_wdef(pf,
"damp_adjust_factor",o.damp_adjust_factor);
if(recenter)
o.generalized_inverse = DAMPED_RECENTERED;
else
o.generalized_inverse = DAMPED_INVERSE;
}
if(!strcasecmp(s,"pseudoinverse"))
{
o.sv_relative_cutoff = (float) pfget_double_wdef(pf,
"singular_value_cutoff",o.sv_relative_cutoff);
if(recenter)
o.generalized_inverse = PSEUDO_RECENTERED;
else
o.generalized_inverse = PSEUDOINVERSE;
}
}
o.depth_ceiling = (float) pfget_double_wdef(pf,
"depth_ceiling",o.depth_ceiling);
o.depth_floor = (float) pfget_double_wdef(pf,
"depth_floor",o.depth_floor);
o.step_length_scale_factor = (float) pfget_double_wdef(pf,
"step_length_scale_factor",o.step_length_scale_factor);
o.min_step_length_scale = (float) pfget_double_wdef(pf,
"min_step_length_scale",o.min_step_length_scale);
if(o.step_length_scale_factor >= 1.0)
{
elog_log(0,"Step length damping factors reset\nScale factors must be less than 1.0\nResetting to default of %f\n",DEFAULT_SLSF);
o.step_length_scale_factor = DEFAULT_SLSF;
if(o.min_step_length_scale >= o.step_length_scale_factor)
{
o.min_step_length_scale = (float)pow(DEFAULT_SLSF,SLSF_POW_MIN);
elog_log(0,"Min step length scale also reset to %f\n",
o.min_step_length_scale);
}
}
if(o.min_step_length_scale >= o.step_length_scale_factor)
{
o.min_step_length_scale = (float)pow(o.step_length_scale_factor,
SLSF_POW_MIN);
elog_log(0,"Min step length scale is not consistent with step length scale factor parameter\nReset to %f\n",
o.min_step_length_scale);
}
o.max_hypo_adjustments = pfget_int_wdef(pf,
"maximum_hypocenter_adjustments",o.max_hypo_adjustments);
o.dx_convergence = (float) pfget_double_wdef(pf,
"deltax_convergence_size",o.dx_convergence);
o.relative_rms_convergence = (float) pfget_double_wdef(pf,
"relative_rms_convergence_value",o.relative_rms_convergence);
return(o);
}
