/*
* Helper for element and docuemnt constructors to insert sequence
* of atomic values. Returns true if node was actually inserted.
* In this case left pointer is changed to the last inserted indirection.
* In any case at_vals sequence is cleared.
*/
static inline bool
process_atomic_values(xptr& left, const xptr& parent, sequence& at_vals) {
if (at_vals.size() > 0)
{
executor_globals::tmp_op_str_buf.clear();
tuple_cell tcc;
sequence::iterator it = at_vals.begin();
do {
tcc = tuple_cell::make_sure_light_atomic((*it).cells[0]);
tcc = cast(tcc, xs_string);
executor_globals::tmp_op_str_buf.append(tcc);
it++;
}
while (it != at_vals.end());
at_vals.clear();
if(executor_globals::tmp_op_str_buf.get_size() > 0) {
insert_text(indirectionDereferenceCP(left),
XNULL,
indirectionDereferenceCP(parent),
text_source_strbuf(&(executor_globals::tmp_op_str_buf)));
left = get_last_mo_inderection();
return true;
}
}
return false;
}
SequenceStatus GestureSeqRecorder::registerSequence(midasMode mode, sequence seq, CommandData seqResponse, std::string name)
{
sequenceInfo seqInfo;
seqInfo.seq = seq;
seqInfo.sequenceResponse = seqResponse;
seqInfo.sequenceName = name;
SequenceStatus status = checkLegalRegister(mode, seqInfo);
if (status != SequenceStatus::SUCCESS)
{
return status;
}
sequenceList *seqList = (*seqMapPerMode)[mode];
seqList->push_back(seqInfo);
seqList = NULL;
std::vector<int> ids;
std::vector<PoseLength> lengths;
sequence::iterator it;
for (it = seq.begin(); it != seq.end(); ++it)
{
ids.push_back(it->type);
lengths.push_back(it->poseLen);
}
std::vector<sequenceImageSet> images = imageManager.formSequenceSetFromIds(ids, lengths);
gestureSignaller.emitRegisterSequence(seqInfo.id, QString(seqInfo.sequenceName.c_str()), images);
return SequenceStatus::SUCCESS;
}
bool
operator > (const sequence<Iter2, Comp2>& seq) const
{
return std::lexicographical_compare (seq.begin(), seq.end(),
begin(), end(),
compare);
}
viterbi_trellis crf::viterbi_scorer::viterbi(const sequence& seq)
{
// we only need the scores for the states as the transition scores, set
// up during construction, will never change between sequences
scorer_.state_scores(*model_, seq);
viterbi_trellis table{seq.size(), model_->num_labels()};
// initialize first column of trellis. We use the original state() and
// trans() matrices because we are working in the log domain.
for (label_id lbl{0}; lbl < model_->num_labels(); ++lbl)
table.probability(0, lbl, scorer_.state(0, lbl));
// compute remaining columns of trellis using recursive formulation
for (uint64_t t = 1; t < seq.size(); ++t)
{
for (label_id lbl{0}; lbl < model_->num_labels(); ++lbl)
{
double max_score = std::numeric_limits<double>::lowest();
for (label_id in{0}; in < model_->num_labels(); ++in)
{
auto score = table.probability(t - 1, in)
+ scorer_.trans(in, lbl);
if (score > max_score)
{
max_score = score;
table.previous_tag(t, lbl, in);
}
}
table.probability(t, lbl, max_score + scorer_.state(t, lbl));
}
}
return table;
}
string decode(const sequence& s)
{
string result(s.length(), 0);
for (unsigned int i = 0; i < s.length(); ++i)
result[i] = s[i] >= 23 ? '.' : kResidues[s[i]];
return result;
}
// is end of a chunk (IOB1)?
int evaluation::is_end_of_chunk_iob1(int human_model, int i, sequence & seq,
string b_tag, string i_tag) {
if (human_model == 1) {
if (seq[i].label == atoi(b_tag.c_str())) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1].label != atoi(i_tag.c_str())) {
return 1;
} else {
return 0;
}
}
} else if (seq[i].label == atoi(i_tag.c_str())) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1].label != atoi(i_tag.c_str())) {
return 1;
} else {
return 0;
}
}
} else {
return 0;
}
} else if (human_model == 2) {
if (seq[i].model_label == atoi(b_tag.c_str())) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1].model_label != atoi(i_tag.c_str())) {
return 1;
} else {
return 0;
}
}
} else if (seq[i].model_label == atoi(i_tag.c_str())) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1].model_label != atoi(i_tag.c_str())) {
return 1;
} else {
return 0;
}
}
} else {
return 0;
}
} else {
return 0;
}
}
// is end of a chunk (IOB1)?
int is_end_of_chunk_iob1(int human_model, int i, sequence & seq,
string b_tag, string i_tag) {
if (human_model == 1) {
if (seq[i][seq[i].size() - 2] == b_tag) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1][seq[i + 1].size() - 2] != i_tag) {
return 1;
} else {
return 0;
}
}
} else if (seq[i][seq[i].size() - 2] == i_tag) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1][seq[i + 1].size() - 2] != i_tag) {
return 1;
} else {
return 0;
}
}
} else {
return 0;
}
} else if (human_model == 2) {
if (seq[i][seq[i].size() - 1] == b_tag) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1][seq[i + 1].size() - 1] != i_tag) {
return 1;
} else {
return 0;
}
}
} else if (seq[i][seq[i].size() - 1] == i_tag) {
if (i >= seq.size() - 1) {
return 1;
} else {
if (seq[i + 1][seq[i + 1].size() - 1] != i_tag) {
return 1;
} else {
return 0;
}
}
} else {
return 0;
}
} else {
return 0;
}
}
void show_list(sequence<T> src)
// Pre: (none)
// Post: The items of src are printed to cout (one per line).
{
for ( src.start(); src.is_item(); src.advance() )
cout << src.current() << " ";
}
sequence<T> adjoint( sequence<T> X )
{
int t1 = X.t1();
int t2 = X.t2();
for( int t = t1; t <= t2; t++ )
X(t) = adjoint(X(t));
return X.timereverse();
}
RObject
AORB::object_key_to_object(sequence<octet>& object_key)
{
RString str = new String((const char*)object_key.data(), object_key.size(), NormalSST | CCAscii);
ObjectKey objkey(str);
if (objkey.isLocal() == true)
return objkey.getLocalObject();
// return Skelleton here
return Nil;
}
sequence sequence::breed(sequence const &a, sequence const &b) {
sequence child;
for (unsigned int i=0; i < sequence::solution.size(); i++) {
if (random::probability(0.5)) {
child.set_gene(i, a.get_gene(i));
} else {
child.set_gene(i, b.get_gene(i));
}
}
return child;
}
void generate_vietoris_sequence(sequence& a) {
if (a.empty())
return;
a[0] = rdm(0, MAX_VAL);
if (a.size() < 2)
return;
a[1] = rdm(0, a[0]);
for (int k = 2; k < a.size(); k++) {
a[k] = rdm(0, (1.0 * k - 1) / k) * a[k - 1];
}
}
void generate_vietoris_sequence(sequence& a) {
if (a.empty())
return;
a[0] = 1;
if (a.size() < 2)
return;
a[1] = .5;
for (int k = 2; k < a.size(); k++) {
a[k] = a[k - 1] * (k - 1) / k;
}
}
editable_events::editable_events (sequence & seq, int bpm)
:
m_events (),
m_current_event (m_events.end()),
m_sequence (seq),
m_midi_parameters
(
bpm, seq.get_beats_per_bar(), seq.get_beat_width(), seq.get_ppqn()
)
{
// Empty body
}
// compares the given two instances of ss
double cm_assembly_ssq3::compare(ss const &__first, ss const &__second) const {
sequence<cchb_dssp> const seq1(__first.get_sequence()), seq2(__second.get_sequence());
if(seq1.size() != seq2.size()) {
throw math::compare_error(get_identifier() + ": Sequence length differ, sequence1.length=" +
std::to_string(seq1.size()) + ", sequence2.length=" + std::to_string(seq2.size()));
} // if
size_t c_correct(0), h_correct(0), e_correct(0); // initialize
for(size_t pos(0); pos < seq1.size(); ++pos) { // works for both sequences b/c of same length
char const sequence1_ss(seq1[pos].get_identifier_char());
char const sequence2_ss(seq2[pos].get_identifier_char());
if(sequence1_ss == sequence2_ss) { // actually it's only important that they are the same, not which one
if(sequence1_ss == 'C') {
++c_correct;
} // if
else if(sequence1_ss == 'H') {
++h_correct;
} // else if
else if(sequence1_ss == 'E') {
++e_correct;
} // else if
} // if
} // for
DEBUG << get_identifier() << ": c_correct=" << c_correct << " h_correct=" << h_correct
<< " e_correct=" << e_correct << " seq_len=" << seq1.size();
return ((double)c_correct + h_correct + e_correct) / seq1.size();
} // compare()
// **************************************************************************
// bool correct(sequence& test, size_t s, size_t cursor_spot, double items[])
// This function determines if the sequence (test) is "correct" according to
// these requirements:
// a. it has exactly s items.
// b. the items (starting at the front) are equal to
// items[0] ... items[s-1]
// c. if cursor_spot < s, then test's cursor must be at
// the location given by cursor_spot.
// d. if cursor_spot >= s, then test must not have a cursor.
// NOTE: The function also moves the cursor off the sequence.
// **************************************************************************
bool correct(sequence& test, size_t size, size_t cursor_spot, double items[])
{
bool has_cursor = (cursor_spot < size);
// Check the sequence's size and whether it has a cursor.
if (!test_basic(test, size, has_cursor))
{
cout << "Basic test of size() or is_item() failed." << endl << endl;
return false;
}
// If there is a cursor, check the items from cursor to end of the sequence.
if (has_cursor && !test_items(test, size, cursor_spot, items))
{
cout << "Test of the sequence's items failed." << endl << endl;
return false;
}
// Restart the cursor at the front of the sequence and test items again.
cout << "I'll call start() and look at the items one more time..." << endl;
test.start( );
if (has_cursor && !test_items(test, size, 0, items))
{
cout << "Test of the sequence's items failed." << endl << endl;
return false;
}
// If the code reaches here, then all tests have been passed.
cout << "All tests passed for this sequence." << endl << endl;
return true;
}
// is matching chunk (IOE2)?
int evaluation::is_matching_chunk_ioe2(int i, sequence & seq, string i_tag, string e_tag) {
if (!is_start_of_chunk_ioe2(1, i, seq, i_tag, e_tag) ||
!is_start_of_chunk_ioe2(2, i, seq, i_tag, e_tag)) {
return 0;
}
int len = seq.size();
int j = i, k = i;
while (j < len) {
if (is_end_of_chunk_ioe2(1, j, seq, i_tag, e_tag)) {
break;
} else {
j++;
}
}
while (k < len) {
if (is_end_of_chunk_ioe2(2, k, seq, i_tag, e_tag)) {
break;
} else {
k++;
}
}
return (j == k);
}
orthonomial(const sequence &a, const sequence &b, const sequence &c) : n(c.size() - 1), a(a), b(b), c(c) {
/* Ze względów bezpieczeństwa. */
this->a.push_back(0);
this->b.push_back(0);
this->c.push_back(0);
this->c.push_back(0);
}
void crf::tagger::tag(sequence& seq)
{
auto trellis = scorer_.viterbi(seq);
auto lbls = util::range(label_id{0},
label_id(static_cast<uint32_t>(num_labels_ - 1)));
auto last_lbl = functional::argmax(
lbls.begin(), lbls.end(), [&](label_id lbl)
{
return trellis.probability(seq.size() - 1, lbl);
});
seq[seq.size() - 1].label(*last_lbl);
for (uint64_t t = seq.size() - 1; t > 0; t--)
seq[t - 1].label(trellis.previous_tag(t, seq[t].label()));
}
double emissionFuncParam::evaluate(sequence& seq , size_t pos) {
double val = (*emissionFunction)(seq.getUndigitized(),pos);
if (emissionFuncScaling!=NULL) {
val = emissionFuncScaling->getWeightedScore(val);
}
return val;
}
void perceptron::tag(sequence& seq) const
{
for (uint64_t t = 0; t < seq.size(); ++t)
{
analyzer_.analyze(seq, t);
seq[t].label(model_.best_class(seq[t].features()));
seq[t].tag(analyzer_.tag(seq[t].label()));
}
}
sequence::sequence(const sequence& seq){
capacity=seq.capacity;
used=seq.used;
data=new int[capacity];
seq.shift(data);
missing=new int[capacity];
for (size_t i = 0; i < capacity; i++)
missing[i]=0;
numMissing=0;
}
// **************************************************************************
// bool test_basic(const sequence& test, size_t s, bool has_cursor)
// Postcondition: A return value of true indicates:
// a. test.size() is s, and
// b. test.is_item() is has_cursor.
// Otherwise the return value is false.
// In either case, a description of the test result is printed to cout.
// **************************************************************************
bool test_basic(const sequence& test, size_t s, bool has_cursor)
{
bool answer;
cout << "Testing that size() returns " << s << " ... ";
cout.flush( );
answer = (test.size( ) == s);
cout << (answer ? "Passed." : "Failed.") << endl;
if (answer)
{
cout << "Testing that is_item() returns ";
cout << (has_cursor ? "true" : "false") << " ... ";
cout.flush( );
answer = (test.is_item( ) == has_cursor);
cout << (answer ? "Passed." : "Failed.") << endl;
}
return answer;
}
bool sequence::operator==(const sequence& seq){
if(capacity!=seq.capacity) return false;
if(used!=seq.used) return false;
int* temp1=new int[capacity];
shift(temp1);
int* temp2=new int[capacity];
seq.shift(temp2);
for (size_t i = 0; i < used; i++) {
if(temp1[i]!=temp2[i]) return false;
}
return true;
}
// **************************************************************************
// bool test_items(sequence& test, size_t s, size_t i, double items[])
// The function determines if the test sequence has the correct items
// Precondition: The size of the items array is at least s.
// Postcondition: A return value of true indicates that test.current()
// is equal to items[i], and after test.advance() the result of
// test.current() is items[i+1], and so on through items[s-1].
// At this point, one more advance takes the cursor off the sequence.
// If any of this fails, the return value is false.
// NOTE: The test sequence has been changed by advancing its cursor.
// **************************************************************************
bool test_items(sequence& test, size_t s, size_t i, double items[])
{
bool answer = true;
cout << "The cursor should be at item [" << i << "]" << " of the sequence\n";
cout << "(counting the first item as [0]). I will advance the cursor\n";
cout << "to the end of the sequence, checking that each item is correct...";
cout.flush( );
while ((i < s) && test.is_item( ) && (test.current( ) == items[i]))
{
i++;
test.advance( );
}
if ((i != s) && !test.is_item( ))
{ // The test.is_item( ) function returns false too soon.
cout << "\n Cursor fell off the sequence too soon." << endl;
answer = false;
}
else if (i != s)
{ // The test.current( ) function returned a wrong value.
cout << "\n The item [" << i << "] should be " << items[i] << ",\n";
cout << " but it was " << test.current( ) << " instead.\n";
answer = false;
}
else if (test.is_item( ))
{ // The test.is_item( ) function returns true after moving off the sequence.
cout << "\n The cursor was moved off the sequence,";
cout << " but is_item still returns true." << endl;
answer = false;
}
cout << (answer ? "Passed." : "Failed.") << endl;
return answer;
}
// counting matching chunks (IOE2)
int count_matching_chunks_ioe2(sequence & seq, string i_tag, string e_tag) {
int count = 0;
for (int i = 0; i < seq.size(); i++) {
if (is_start_of_chunk_ioe2(1, i, seq, i_tag, e_tag)) {
if (is_matching_chunk_ioe2(i, seq, i_tag, e_tag)) {
count++;
}
}
}
return count;
}
sequence<R> operator*( const sequence<T1> &X, const sequence<T2> &Y )
{
if( X.size()==0 || Y.size()==0 )
return sequence<R>();
vec<R> vec = conv( X.buffer(), Y.buffer() );
int t1 = X.t1() + Y.t1();
return sequence<R>( vec, t1 );
}
// counting number of chunks (IOE2)
int count_chunks_ioe2(int human_model, sequence & seq, string i_tag, string e_tag) {
int count = 0;
for (int i = 0; i < seq.size(); i++) {
if (human_model == 1 && is_start_of_chunk_ioe2(1, i, seq, i_tag, e_tag)) {
count++;
}
if (human_model == 2 && is_start_of_chunk_ioe2(2, i, seq, i_tag, e_tag)) {
count++;
}
}
return count;
}
void convert_IOB2_IOB1(int is_cap, int is_last, sequence & seq) {
map<int, int> fixedlabels;
map<int, int>::iterator obsrit;
char begin = is_cap ? 'B' : 'b';
char inside = is_cap ? 'I' : 'i';
string INSIDE = is_cap ? "I" : "i";
string str1, str2, istr, newlabel;
int i, len = seq.size();
for (i = 1; i < len; i++) {
int col1 = is_last ? seq[i - 1].size() - 1 : seq[i - 1].size() - 2;
int col2 = is_last ? seq[i].size() - 1 : seq[i].size() - 2;
str1 = seq[i - 1][col1];
str2 = seq[i][col2];
if (str2[0] != begin) {
continue;
}
istr = INSIDE;
istr += strtail(str2);
if (str1 == str2 || str1 == istr) {
fixedlabels.insert(pair<int, int>(i, i));
}
}
for (i = 0; i < len; i++) {
obsrit = fixedlabels.find(i);
if (obsrit != fixedlabels.end()) {
continue;
}
int col = is_last ? seq[i].size() - 1 : seq[i].size() - 2;
if (seq[i][col][0] == begin) {
// B- or b- => I- or i-
newlabel = INSIDE;
newlabel += strtail(seq[i][col]);
seq[i][col] = newlabel;
}
}
}
sequence<T> inv(const sequence<T>& X, int t1, int t2)
{
int YL = t2-t1+1;
// Convolution matrix
mat<T> CX = convmat(X,YL);
// Impulse function
int DL = CX.rows();
vec<T> D = zeros(DL);
int i = -t1-X.t1();
if(i > 0 && i < DL)
D(i) = 1;
// Inverse sequence
vec<T> Y = backslash( CX, D );
return sequence<T>( Y, t1 );
}