bool ns_machine_analysis_region_data::recalculate_from_saved_movement_quantification(const unsigned long region_id,ns_sql & sql){
death_time_annotation_set.clear();
metadata.region_id = region_id;
//load 3d point cloud
const ns_time_path_solver_parameters solver_parameters(ns_time_path_solver_parameters::default_parameters(region_id,sql));
const ns_time_series_denoising_parameters time_series_denoising_parameters(ns_time_series_denoising_parameters::load_from_db(region_id,sql));
ns_time_path_solver solver;
solver.load(region_id,sql);
solver.solve(solver_parameters,time_path_solution);
time_path_solution.save_to_db(region_id,sql);
//time_path_solution.load_from_db(region_id,sql);
//load cached movement quantification
ns_acquire_for_scope<ns_analyzed_image_time_path_death_time_estimator> death_time_estimator(
ns_get_death_time_estimator_from_posture_analysis_model(
image_server.get_posture_analysis_model_for_region(region_id,sql)));
time_path_image_analyzer.load_completed_analysis(region_id,time_path_solution,time_series_denoising_parameters, &death_time_estimator(),sql);
death_time_estimator.release();
//generate annotations from quantification
time_path_image_analyzer.produce_death_time_annotations(death_time_annotation_set);
time_path_image_analyzer.clear_annotations();
//save annotations
ns_image_server_results_subject results_subject;
results_subject.region_id = region_id;
ns_image_server_results_file censoring_results(image_server.results_storage.machine_death_times(results_subject,ns_image_server_results_storage::ns_censoring_and_movement_transitions,
"time_path_image_analysis",sql));
ns_image_server_results_file state_results(image_server.results_storage.machine_death_times(results_subject,ns_image_server_results_storage::ns_worm_position_annotations,
"time_path_image_analysis",sql));
ns_acquire_for_scope<std::ostream> censoring_out(censoring_results.output());
ns_acquire_for_scope<std::ostream> state_out(state_results.output());
death_time_annotation_set.write_split_file_column_format(censoring_out(),state_out());
censoring_out.release();
state_out.release();
return true;
}
void Process(StrLen file_name)
{
SplitPath dev_name(file_name);
SplitName path_name(dev_name.path);
SplitExt name_ext(path_name.name);
String in_name;
if( !name_ext )
{
in_name=StringCat(dev_name.dev,path_name.path,name_ext.name,".lang");
}
else
{
in_name=file_name;
}
TrackStage("Load file #.q;",StrLen(Range(in_name)));
CondLang clang(Range(in_name));
TrackStage("Build top lang");
TopLang top(clang);
TrackStage("Run good test on top lang");
if( !RunGoodTest(top) ) return;
TrackStage("Build bottom lang");
BottomLang bottom(clang);
TrackStage("Extend bottom lang");
ExtLang ext_bottom(bottom);
TrackStage("Process top lang");
ExtLang ext_top(top);
LangDiagram diagram(ext_top);
LangStateMachine<LR1Estimate,LR1MapContext> machine(ext_top,diagram,ext_bottom);
StateCompress<LR1Estimate> compress(machine);
TrackStage("LR1) #;",PrintCompressCounts(compress));
{
ulen conflicts=0;
for(auto &est : compress.getProps() ) conflicts+=est.hasConflict();
if( conflicts )
{
String out_name=StringCat(dev_name.dev,path_name.path,name_ext.name,".bad.txt");
PrintFile out(Range(out_name));
Putobj(out,clang);
PrintBad(out,ext_top,compress);
Printf(Exception,"#; CONFLICTs detected. Not LR1 language.",conflicts);
}
else
{
TrackStage("No conflicts. LR1 language.");
}
}
StateCompress<LR1Estimate,LR1PropNonEmpty> compress_ne(machine);
TrackStage("NonEmpty) #;",PrintCompressCounts(compress_ne));
#if 0
StateCompress<LR1Estimate,LR1PropShiftSet> compress_shift(machine);
TrackStage("Shift) #;",PrintCompressCounts(compress_shift));
StateCompress<LR1Estimate,LR1PropValidSet> compress_valid(machine);
TrackStage("Valid) #;",PrintCompressCounts(compress_valid));
StateCompress<LR1Estimate,LR1PropRuleSet> compress_rules(machine);
TrackStage("Rules) #;",PrintCompressCounts(compress_rules));
StateMap map(compress,compress_ne);
String out_name=StringCat(dev_name.dev,path_name.path,"Result.txt");
PrintFile out(Range(out_name));
PrintFibres(out,compress,compress_ne,map);
Putobj(out,BindOpt(ext_top,compress_ne));
#endif
{
String out_name=StringCat(dev_name.dev,path_name.path,name_ext.name,".txt");
PrintFile out(Range(out_name));
Putobj(out,clang);
Putobj(out,BindOpt(ext_top,compress));
}
{
String out_name=StringCat(dev_name.dev,path_name.path,name_ext.name,".ddl");
PosPrint<PrintFile> out(Range(out_name));
Printf(out,"/* #;.ddl */\n\n",name_ext.name);
Putobj(out,"//include <LangTypes.ddl>\n\n");
Putobj(out,"Lang lang=\n");
// lang
{
ListPrint<decltype(out)> lang_out(out);
// atoms
{
ListPrint<decltype(lang_out)> atom_out(lang_out);
for(auto &atom : clang.getAtoms() )
Printf(atom_out,"{ #; , #; , lang.elements+#; }#;",atom.index,StrLen(atom.name.inner(2,1)),atom.index,EndItem());
Putobj(atom_out,EndList());
}
Putobj(lang_out,EndItem());
// synts
{
ListPrint<decltype(lang_out)> synt_out(lang_out);
ulen element=clang.getAtomCount();
ulen top_index=0;
for(auto &synt : clang.getSynts() )
{
Printf(synt_out,"{ #; , #.q; ,",synt.index,synt.name);
auto kinds=synt.kinds;
if( !kinds )
{
Indent indent(synt_out.getCol());
Printf(synt_out," { { #; , 0 , \"\" , lang.synts+#; , lang.elements+#; ,#;",top_index,synt.index,element++,AutoIndent());
auto &top_synt=top.getSynts()[top_index++];
ListPrint<decltype(synt_out)> rule_out(synt_out);
for(auto &top_rule : top_synt.rules )
Printf(rule_out,"lang.top_rules+#;#;",top_rule.index,EndItem());
Putobj(rule_out,EndList());
Printf(synt_out,"#; }#; } ,#;",indent,indent,indent);
}
else
{
Indent indent(synt_out.getCol());
Putobj(synt_out,indent);
ListPrint<decltype(synt_out)> kind_out(synt_out);
for(auto &kind : kinds )
{
Printf(kind_out,"{ #; , #; , #.q; , lang.synts+#; , lang.elements+#; ,#;",top_index,kind.index,kind.name,synt.index,element++,AutoIndent());
auto &top_synt=top.getSynts()[top_index++];
ListPrint<decltype(kind_out)> rule_out(kind_out);
for(auto &top_rule : top_synt.rules )
Printf(rule_out,"lang.top_rules+#;#;",top_rule.index,EndItem());
Putobj(rule_out,EndList());
Printf(kind_out,"\n}#;",EndItem());
}
Putobj(kind_out,EndList());
Putobj(synt_out," ,",indent);
}
ListPrint<decltype(synt_out)> rule_out(synt_out);
for(auto &rule : synt.rules )
Printf(rule_out,"lang.rules+#;#;",rule.index,EndItem());
Putobj(rule_out,EndList());
Putobj(synt_out,"\n}",EndItem());
}
Putobj(synt_out,EndList());
}
Putobj(lang_out,EndItem());
// lang
{
ListPrint<decltype(lang_out)> synt_out(lang_out);
for(auto &synt : clang.getSynts() )
if( synt.is_lang )
{
Printf(synt_out,"lang.synts+#;",synt.index);
}
Putobj(synt_out,EndList());
}
Putobj(lang_out,EndItem());
// elements
{
ListPrint<decltype(lang_out)> elem_out(lang_out);
ulen element=0;
for(auto &atom : clang.getAtoms() )
Printf(elem_out,"{ #; , lang.atoms+#; }#;",element++,atom.index,EndItem());
for(auto &synt : clang.getSynts() )
{
auto len=synt.kinds.len;
if( !len ) len=1;
for(ulen i=0; i<len ;i++)
{
Printf(elem_out,"{ #; , lang.synts[#;].kinds+#; }#;",element++,synt.index,i,EndItem());
}
}
Putobj(elem_out,EndList());
}
Putobj(lang_out,EndItem());
// rules
{
ListPrint<decltype(lang_out)> rule_out(lang_out);
for(auto &rule : clang.getRules() )
{
Printf(rule_out,"{ #; , #.q; , lang.synts[#;].kinds+#; ,#;",rule.index,rule.name,rule.ret->index,rule.getKindIndex(),AutoIndent());
ListPrint<decltype(rule_out)> arg_out(rule_out);
for(auto &element : rule.args )
element.apply( [&] (const CondLangBase::AtomDesc *desc)
{
Printf(arg_out,"lang.atoms+#;#;",desc->index,EndItem());
} ,
[&] (const CondLangBase::SyntDesc *desc)
{
Printf(arg_out,"lang.synts+#;#;",desc->index,EndItem());
}
);
Putobj(arg_out,EndList());
Putobj(rule_out,"\n}",EndItem());
}
Putobj(rule_out,EndList());
}
Putobj(lang_out,EndItem());
// top rules
{
ListPrint<decltype(lang_out)> rule_out(lang_out);
for(auto &rule : top.getRules() )
{
Printf(rule_out,"{ #; , #.q; , lang.rules+#; , lang.synts[#;].kinds+#; ,#;",
rule.index,rule.name,rule.map_index,rule.ret->map_index,rule.ret->kind_index,AutoIndent());
ListPrint<decltype(rule_out)> arg_out(rule_out);
for(auto &element : rule.args )
element.apply( [&] (const LangBase::AtomDesc *desc)
{
Printf(arg_out,"lang.atoms+#;#;",desc->index,EndItem());
} ,
[&] (const LangBase::SyntDesc *desc)
{
Printf(arg_out,"lang.synts[#;].kinds+#;#;",desc->map_index,desc->kind_index,EndItem());
}
);
Putobj(arg_out,EndList());
Putobj(rule_out,"\n}",EndItem());
}
Putobj(rule_out,EndList());
}
Putobj(lang_out,EndItem());
// states
{
ListPrint<decltype(lang_out)> state_out(lang_out);
for(auto &state : compress.getStateTable() )
{
Printf(state_out,"{ #; , lang.finals+#; ,#;",state.index,state.prop_index,AutoIndent());
ListPrint<decltype(state_out)> trans_out(state_out);
for(auto &trans : state.transitions )
Printf(trans_out,"{ lang.elements+#; , lang.states+#; }#;",trans.element,trans.dst->index,EndItem());
Putobj(trans_out,EndList());
Putobj(state_out,"\n}",EndItem());
}
Putobj(state_out,EndList());
}
Putobj(lang_out,EndItem());
// finals
{
ListPrint<decltype(lang_out)> final_out(lang_out);
ulen atom_count=clang.getAtomCount();
ulen index=0;
for(auto &final : compress.getProps() )
{
Printf(final_out,"{ #; ,#;",index++,AutoIndent());
ListPrint<decltype(final_out)> action_out(final_out);
if( final.hasNull() )
{
Printf(action_out,"{ null , null }#;",EndItem());
}
else
{
auto &alpha=final.getAlpha();
if( alpha.nonEmpty() )
{
Printf(action_out,"{ null , lang.rules+#; }#;",alpha.getPtr()->getIndex()-atom_count,EndItem());
}
}
for(auto &rec : Range(final.getBeta()) )
{
if( rec.object.shift )
{
Printf(action_out,"{ lang.atoms+#; , null }#;",rec.index.getIndex(),EndItem());
}
else
{
auto &rules=rec.object.rules;
if( rules.nonEmpty() )
{
Printf(action_out,"{ lang.atoms+#; , lang.rules+#; }#;",rec.index.getIndex(),rules.getPtr()->getIndex()-atom_count,EndItem());
}
}
}
Putobj(action_out,EndList());
Putobj(final_out,"\n}",EndItem());
}
Putobj(final_out,EndList());
}
Putobj(lang_out,EndItem(),EndList());
}
Putobj(out,";\n\n");
}
aes_rval aes_dec_blk(const unsigned char in_blk[], unsigned char out_blk[], const aes_ctx cx[1])
{ uint32_t locals(b0, b1);
const uint32_t *kp = cx->k_sch + nc * cx->n_rnd;
dec_imvars /* declare variables for inv_mcol() if needed */
if(!(cx->n_blk & 2)) return aes_bad;
#if (DEC_UNROLL == FULL)
state_in((cx->n_rnd & 1 ? b1 : b0), in_blk, kp);
kp = cx->k_sch + 9 * nc;
switch(cx->n_rnd)
{
case 14: round(inv_rnd, b1, b0, kp + 4 * nc);
case 13: round(inv_rnd, b0, b1, kp + 3 * nc);
case 12: round(inv_rnd, b1, b0, kp + 2 * nc);
case 11: round(inv_rnd, b0, b1, kp + nc);
case 10: round(inv_rnd, b1, b0, kp );
round(inv_rnd, b0, b1, kp - nc);
round(inv_rnd, b1, b0, kp - 2 * nc);
round(inv_rnd, b0, b1, kp - 3 * nc);
round(inv_rnd, b1, b0, kp - 4 * nc);
round(inv_rnd, b0, b1, kp - 5 * nc);
round(inv_rnd, b1, b0, kp - 6 * nc);
round(inv_rnd, b0, b1, kp - 7 * nc);
round(inv_rnd, b1, b0, kp - 8 * nc);
round(inv_lrnd, b0, b1, kp - 9 * nc);
}
#else
{ uint32_t rnd;
state_in(b0, in_blk, kp);
#if (DEC_UNROLL == PARTIAL)
for(rnd = 0; rnd < (cx->n_rnd - 1) >> 1; ++rnd)
{
kp -= nc;
round(inv_rnd, b1, b0, kp);
kp -= nc;
round(inv_rnd, b0, b1, kp);
}
if(cx->n_rnd & 1)
{
l_copy(b1, b0);
}
else
{
kp -= nc;
round(inv_rnd, b1, b0, kp);
}
#else
for(rnd = 0; rnd < cx->n_rnd - 1; ++rnd)
{
kp -= nc;
round(inv_rnd, b1, b0, kp);
l_copy(b0, b1);
}
#endif
kp -= nc;
round(inv_lrnd, b0, b1, kp);
}
#endif
state_out(out_blk, b0);
return aes_good;
}
aes_rval aes_enc_blk(const unsigned char in_blk[], unsigned char out_blk[], const aes_ctx cx[1])
{ aes_32t locals(b0, b1);
const aes_32t *kp = cx->k_sch;
dec_fmvars /* declare variables for fwd_mcol() if needed */
if(!(cx->n_blk & 1)) return aes_bad;
#if (ENC_UNROLL == FULL)
state_in((cx->n_rnd & 1 ? b1 : b0), in_blk, kp);
kp += (cx->n_rnd - 9) * nc;
switch(cx->n_rnd)
{
case 14: round(fwd_rnd, b1, b0, kp - 4 * nc);
case 13: round(fwd_rnd, b0, b1, kp - 3 * nc);
case 12: round(fwd_rnd, b1, b0, kp - 2 * nc);
case 11: round(fwd_rnd, b0, b1, kp - nc);
case 10: round(fwd_rnd, b1, b0, kp );
round(fwd_rnd, b0, b1, kp + nc);
round(fwd_rnd, b1, b0, kp + 2 * nc);
round(fwd_rnd, b0, b1, kp + 3 * nc);
round(fwd_rnd, b1, b0, kp + 4 * nc);
round(fwd_rnd, b0, b1, kp + 5 * nc);
round(fwd_rnd, b1, b0, kp + 6 * nc);
round(fwd_rnd, b0, b1, kp + 7 * nc);
round(fwd_rnd, b1, b0, kp + 8 * nc);
round(fwd_lrnd, b0, b1, kp + 9 * nc);
}
#else
{ aes_32t rnd;
state_in(b0, in_blk, kp);
#if (ENC_UNROLL == PARTIAL)
for(rnd = 0; rnd < (cx->n_rnd - 1) >> 1; ++rnd)
{
kp += nc;
round(fwd_rnd, b1, b0, kp);
kp += nc;
round(fwd_rnd, b0, b1, kp);
}
if(cx->n_rnd & 1)
{
l_copy(b1, b0);
}
else
{
kp += nc;
round(fwd_rnd, b1, b0, kp);
}
#else
for(rnd = 0; rnd < cx->n_rnd - 1; ++rnd)
{
kp += nc;
round(fwd_rnd, b1, b0, kp);
l_copy(b0, b1);
}
#endif
kp += nc;
round(fwd_lrnd, b0, b1, kp);
}
#endif
state_out(out_blk, b0);
return aes_good;
}