static inline bool IsAtomLine(ArgList& lineIn) {
for (int i = 0; i < lineIn.Nargs(); i++) {
std::string item = lineIn.GetStringNext();
if (i == 0 || i >= 5) {
try {
convertToInteger( item );
}
catch (std::runtime_error e) {
return false;
}
} else if (i >= 2 && i < 5) {
try {
convertToDouble( item );
}
catch (std::runtime_error e) {
return false;
}
}
}
return true;
}
/**
* @brief OptionDefinition::convertValue
* @param stringValue
* @return
*/
QVariant OptionDefinition::convertValue(const QString &stringValue) const
{
QVariant value(QVariant::Invalid);
switch (d->m_dataType) {
case QVariant::Bool:
value.setValue(convertToBool(stringValue));
break;
case QVariant::Date:
value.setValue(convertToDate(stringValue));
break;
case QVariant::DateTime:
value.setValue(convertToDateTime(stringValue));
break;
case QVariant::Double:
value.setValue(convertToDouble(stringValue));
break;
case QVariant::Int:
value.setValue(convertToInt(stringValue));
break;
case QVariant::LongLong:
value.setValue(convertToLongLong(stringValue));
break;
case QVariant::String:
value.setValue(stringValue);
break;
case QVariant::Time:
value.setValue(convertToTime(stringValue));
break;
case QVariant::UInt:
value.setValue(convertToUInt(stringValue));
break;
case QVariant::ULongLong:
value.setValue(convertToULongLong(stringValue));
break;
default:
break;
}
return value;
}
bool TinkerFile::ID_Tinker(CpptrajFile& fileIn) {
// NOTE: ASSUME FILE SET UP FOR READ
if (fileIn.OpenFile()) return false;
ArgList firstLine( fileIn.NextLine() );
ArgList secondLine( fileIn.NextLine() );
ArgList thirdLine( fileIn.NextLine() );
fileIn.CloseFile();
// First line should have <natom> <title> only
int natom = 0;
std::string title;
if ( SetNatomAndTitle(firstLine, natom, title) != 0 )
return false;
//mprinterr("Past SetNatomAndTitle\n");
if (secondLine.Nargs() == 6) {
bool isBoxLine = true;
for (int i = 0; i < 6; i++) {
// It is a box line if all 6 tokens are doubles
try {
convertToDouble( secondLine.GetStringNext() );
}
catch (std::runtime_error e) {
if (i != 1) return false;
// We found a non-double on the second character -- it could be an atom
// name. Check that the rest of the line matches an atom record
isBoxLine = false;
break;
}
}
// If we are here it is not a box line, so make sure
if (!isBoxLine) {
return IsAtomLine(secondLine);
} else { // our second line WAS a box, now check the 3rd line
return IsAtomLine(thirdLine);
}
}
// There is no box, check that the second line is an atom line
return IsAtomLine(secondLine);
}
void PDI::gaussianConvolution(int sigma, cv::Mat &image, bool separated_kernel){
// Get the image range (to re-convert)
int min, max;
getImageRange(image, min, max);
// Create a copy of the values (as double)
cv::Mat g = convertToDouble(image);
// Image double of zeros
cv::Mat f = cv::Mat::zeros(g.rows, g.cols, CV_64F);
if(separated_kernel){ // Kernel separated routine
// Generating Kernel
double h0[6*sigma];
double h1[6*sigma];
gaussianArrays(sigma, h0, h1);
f = convolutionSeparatedKernel(g, h0, 6*sigma, h1, 6*sigma);
}
else{ // Unique Kernel routine
// Generating Kernel
cv::Mat h = gaussianImage(sigma);
cv::namedWindow("Kernel",CV_WINDOW_NORMAL);
cv::imshow("Kernel", convertToInterger(h));
f = convolution(g, h);
}
// Image double converted into integer
normalizateMatrix(f, min, max);
cv::Mat img = convertToInterger(f);
cv::namedWindow("Initial Image");
cv::imshow("Initial Image", image);
cv::namedWindow("Final Image");
cv::imshow("Final Image", img);
}
/** Given an ArgList containing name,[min,max,step,bins,col,N], set up a
* coordinate with that name and parameters min, max, step, bins.
* If '*' or not specified, a default value will be set.
* \return 1 if error occurs, 0 otherwise.
*/
int Analysis_Hist::setupDimension(ArgList &arglist, DataSet_1D const& dset, size_t& offset) {
bool minArg = false;
bool maxArg = false;
bool stepArg = false;
bool binsArg = false;
if (debug_>1)
arglist.PrintList();
// Set up dimension name
// NOTE: arglist[0] should be same as dset name from CheckDimension
std::string const& dLabel = arglist[0];
// Cycle through coordinate arguments. Any argument left blank will be
// assigned a default value later.
double dMin = 0.0;
double dMax = 0.0;
double dStep = 0.0;
int dBins = -1;
for (int i = 1; i < arglist.Nargs(); i++) {
if (debug_>1) mprintf("DEBUG: setupCoord: Token %i (%s)\n", i, arglist[i].c_str());
// '*' means default explicitly requested
if (arglist[i] == "*") continue;
switch (i) {
case 1 : dMin = convertToDouble( arglist[i]); minArg = true; break;
case 2 : dMax = convertToDouble( arglist[i]); maxArg = true; break;
case 3 : dStep = convertToDouble( arglist[i]); stepArg = true; break;
case 4 : dBins = convertToInteger(arglist[i]); binsArg = true; break;
}
}
// If no min arg and no default min arg, get min from dataset
if (!minArg) {
if (!minArgSet_)
dMin = dset.Min();
else
dMin = default_min_;
}
// If no max arg and no default max arg, get max from dataset
if (!maxArg) {
if (!maxArgSet_)
dMax = dset.Max();
else
dMax = default_max_;
}
// If bins/step not specified, use default
if (!binsArg)
dBins = default_bins_;
if (!stepArg)
dStep = default_step_;
// Calculate dimension from given args.
HistBin dim;
if (dim.CalcBinsOrStep( dMin, dMax, dStep, dBins, dLabel )) {
mprinterr("Error: Could not set up histogram dimension '%s'\n", dLabel.c_str());
return 1;
}
dim.PrintHistBin();
dimensions_.push_back( dim );
// Recalculate offsets for all dimensions starting at farthest coord. This
// follows row major ordering.
size_t last_offset = 1UL; // For checking overflow.
offset = 1UL;
binOffsets_.resize( dimensions_.size() );
OffType::iterator bOff = binOffsets_.begin();
for (HdimType::const_iterator rd = dimensions_.begin();
rd != dimensions_.end(); ++rd, ++bOff)
{
if (debug_>0) mprintf("\tHistogram: %s offset is %zu\n", rd->label(), offset);
*bOff = (long int)offset;
offset *= rd->Bins();
// Check for overflow.
if ( offset < last_offset ) {
mprinterr("Error: Too many bins for histogram. Try reducing the number of bins and/or\n"
"Error: the number of dimensions.\n");
return 1;
}
last_offset = offset;
}
// offset should now be equal to the total number of bins across all dimensions
if (debug_>0) mprintf("\tHistogram: Total Bins = %zu\n",offset);
return 0;
}
// Parm_CIF::ReadParm()
int Parm_CIF::ReadParm(FileName const& fname, Topology &TopIn) {
CIFfile infile;
CIFfile::DataBlock::data_it line;
if (infile.Read( fname, debug_ )) return 1;
CIFfile::DataBlock const& block = infile.GetDataBlock("_atom_site");
if (block.empty()) {
mprinterr("Error: CIF data block '_atom_site' not found.\n");
return 1;
}
// Does this CIF contain multiple models?
int Nmodels = 0;
int model_col = block.ColumnIndex("pdbx_PDB_model_num");
if (model_col != -1) {
line = block.end();
--line;
Nmodels = convertToInteger( (*line)[model_col] );
if (Nmodels > 1)
mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n",
fname.full(), Nmodels);
}
// Get essential columns
int COL[NENTRY];
for (int i = 0; i < (int)NENTRY; i++) {
COL[i] = block.ColumnIndex(Entries[i]);
if (COL[i] == -1) {
mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n",
fname.full(), Entries[i], block.Header().c_str());
return 1;
}
if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]);
}
// Get optional columns
int occ_col = block.ColumnIndex("occupancy");
int bfac_col = block.ColumnIndex("B_iso_or_equiv");
int icode_col = block.ColumnIndex("pdbx_PDB_ins_code");
int altloc_col = block.ColumnIndex("label_alt_id");
std::vector<AtomExtra> extra;
// Loop over all atom sites
int current_res = 0;
double XYZ[3];
double occupancy = 1.0;
double bfactor = 0.0;
char altloc = ' ';
char icode;
icode = ' ';
Frame Coords;
for (line = block.begin(); line != block.end(); ++line) {
// If more than 1 model check if we are done.
if (Nmodels > 1) {
if ( convertToInteger( (*line)[model_col] ) > 1 )
break;
}
if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] );
if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] );
if (altloc_col != -1) altloc = (*line)[ altloc_col ][0];
// '.' altloc means blank?
if (altloc == '.') altloc = ' ';
extra.push_back( AtomExtra(occupancy, bfactor, altloc) );
if (icode_col != -1) {
icode = (*line)[ icode_col ][0];
// '?' icode means blank
if (icode == '?') icode = ' ';
}
XYZ[0] = convertToDouble( (*line)[ COL[X] ] );
XYZ[1] = convertToDouble( (*line)[ COL[Y] ] );
XYZ[2] = convertToDouble( (*line)[ COL[Z] ] );
NameType currentResName( (*line)[ COL[RNAME] ] );
// It seems that in some CIF files, there doesnt have to be a residue
// number. Check if residue name has changed.
if ( (*line)[ COL[RNUM] ][0] == '.' ) {
Topology::res_iterator lastResidue = TopIn.ResEnd();
--lastResidue;
if ( currentResName != (*lastResidue).Name() )
current_res = TopIn.Nres() + 1;
} else
current_res = convertToInteger( (*line)[ COL[RNUM] ] );
TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], " "),
Residue(currentResName, current_res, icode,
(*line)[ COL[CHAINID] ][0]) );
Coords.AddXYZ( XYZ );
}
if (TopIn.SetExtraAtomInfo( 0, extra )) return 1;
// Search for bonds // FIXME nobondsearch?
BondSearch( TopIn, Coords, Offset_, debug_ );
// Get title.
CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry");
std::string ciftitle;
if (!entryblock.empty())
ciftitle = entryblock.Data("id");
TopIn.SetParmName( ciftitle, infile.CIFname() );
// Get unit cell parameters if present.
CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell");
if (!cellblock.empty()) {
double cif_box[6];
cif_box[0] = convertToDouble( cellblock.Data("length_a") );
cif_box[1] = convertToDouble( cellblock.Data("length_b") );
cif_box[2] = convertToDouble( cellblock.Data("length_c") );
cif_box[3] = convertToDouble( cellblock.Data("angle_alpha") );
cif_box[4] = convertToDouble( cellblock.Data("angle_beta" ) );
cif_box[5] = convertToDouble( cellblock.Data("angle_gamma") );
mprintf("\tRead cell info from CIF: a=%g b=%g c=%g alpha=%g beta=%g gamma=%g\n",
cif_box[0], cif_box[1], cif_box[2], cif_box[3], cif_box[4], cif_box[5]);
TopIn.SetParmBox( Box(cif_box) );
}
return 0;
}
// DataIO_Mdout::ReadData()
int DataIO_Mdout::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
mprintf("\tReading from mdout file: %s\n", fname.full());
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
const char* ptr = buffer.Line();
if (ptr == 0) {
mprinterr("Error: Nothing in MDOUT file: %s\n", fname.full());
return 1;
}
// ----- PARSE THE INPUT SECTION -----
int imin = -1; // imin for this file
const char* Trigger = 0; // Trigger for storing energies, must be 8 chars long.
int frame = 0; // Frame counter for this file
double dt = 1.0; // Timestep for this file (MD)
double t0 = 0.0; // Initial time for this file (MD)
int ntpr = 1; // Value of ntpr
int irest = 0; // Value of irest
while ( ptr != 0 && strncmp(ptr, " 2. CONTROL DATA", 20) != 0 )
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
// Determine whether this is dynamics or minimization, get dt
ptr = buffer.Line(); // Dashes
ptr = buffer.Line(); // Blank
ptr = buffer.Line(); // title line
while ( strncmp(ptr, " 3. ATOMIC", 13) != 0 )
{
ArgList mdin_args( ptr, " ,=" ); // Remove commas, equal signs
// Scan for stuff we want
//mprintf("DEBUG:\tInput[%i] %s", mdin_args.Nargs(), mdin_args.ArgLine());
for (int col=0; col < mdin_args.Nargs(); col += 2) {
int col1 = col + 1;
if (mdin_args[col] == "imin") {
imin = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: imin is %i\n", imin);
// Set a trigger for printing. For imin5 this is the word minimization.
// For imin0 or imin1 this is NSTEP.
if (imin==0) Trigger = " NSTEP =";
else if (imin==1) Trigger = " NSTEP";
else if (imin==5) Trigger = "minimiza";
// Since imin0 and imin1 first trigger has no data, set frame 1 lower.
if (imin==1 || imin==0) frame = -1;
} else if (mdin_args[col] == "dt") {
dt = convertToDouble( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: dt is %f\n", dt);
} else if (mdin_args[col] == "t") {
t0 = convertToDouble( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: t is %f\n", t0);
} else if (mdin_args[col] == "ntpr") {
ntpr = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: ntpr is %i\n", ntpr);
} else if (mdin_args[col] == "irest") {
irest = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: irest is %i\n", irest);
}
}
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
}
if (Trigger == 0) {
mprinterr("Error: Could not determine whether MDOUT is md, min, or post-process.\n");
return 1;
}
// ----- PARSE THE ATOMIC ... SECTION -----
while ( ptr != 0 && strncmp(ptr, " 4. RESULTS", 14) != 0 )
{
ptr = buffer.Line();
// If run is a restart, set the initial time value.
if (irest == 1) {
if (strncmp(ptr, " begin time", 11) == 0) {
sscanf(ptr, " begin time read from input coords = %lf", &t0);
if (debug_ > 0) mprintf("\t\tMD restart initial time= %f\n", t0);
}
}
}
if (ptr == 0) return EOF_ERROR();
// ----- PARSE THE RESULTS SECTION -----
bool finalE = false;
int nstep;
int minStep = 0; // For imin=1 only
if (irest == 0)
nstep = 0;
else
nstep = ntpr;
double Energy[N_FIELDTYPES];
std::fill( Energy, Energy+N_FIELDTYPES, 0.0 );
std::vector<bool> EnergyExists(N_FIELDTYPES, false);
DataSetList::Darray TimeVals;
DataSetList::DataListType inputSets(N_FIELDTYPES, 0);
Sarray Name(2);
double time = 0.0;
while (ptr != 0) {
// Check for end of imin 0 or 1 run; do not record Average and Stdevs
if ( (imin == 1 && (strncmp(ptr, " FINAL", 25) == 0 ||
strncmp(ptr, " 5. TIMINGS", 14) == 0 )) ||
(imin == 0 && strncmp(ptr, " A V", 9) == 0))
finalE = true;
// Check for '| TI region 2' to prevent reading duplicate energies
if ( strncmp(ptr, "| TI region 2", 14) == 0 ) {
while (ptr != 0 && !(ptr[0] == ' ' && ptr[1] == '-'))
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
}
// Record set for energy post-processing
if (imin == 5 && strncmp(ptr, "minimizing", 10) == 0)
nstep = atoi( ptr + 22 );
// MAIN OUTPUT ROUTINE
// If the trigger has been reached print output.
// For imin0 and imin1 the first trigger will have no data.
// If the end of the file has been reached print then exit.
if ( strncmp(ptr, Trigger, 8) == 0 || finalE ) {
if (frame > -1) {
// Store all energies present.
for (int i = 0; i < (int)N_FIELDTYPES; i++) {
if (EnergyExists[i]) {
if (inputSets[i] == 0) {
MetaData md( dsname, Enames[i] );
md.SetLegend( dsname + "_" + Enames[i] );
inputSets[i] = new DataSet_double();
inputSets[i]->SetMeta( md );
}
// Since energy terms can appear and vanish over the course of the
// mdout file, resize if necessary.
if (frame > (int)inputSets[i]->Size())
((DataSet_double*)inputSets[i])->Resize( frame );
((DataSet_double*)inputSets[i])->AddElement( Energy[i] );
}
}
TimeVals.push_back( time );
nstep += ntpr;
}
frame++;
if (finalE) break;
}
// Check for NSTEP in minimization or post-processing. Values will be
// on the next line. NOTE: NSTEP means something different for imin=5.
if ((imin == 1 || imin == 5) && strncmp(ptr, " NSTEP", 8) == 0) {
ptr = buffer.Line(); // Get next line
//sscanf(ptr, " %6lf %13lE %13lE %13lE", Energy+NSTEP, Energy+EPtot, Energy+RMS, Energy+GMAX);
sscanf(ptr, " %i %lE %lE %lE", &minStep, Energy+EPtot, Energy+RMS, Energy+GMAX);
EnergyExists[EPtot] = true;
EnergyExists[RMS] = true;
EnergyExists[GMAX] = true;
ptr = buffer.Line();
}
// Tokenize line, scan through until '=' is reached; value after is target.
int ntokens = buffer.TokenizeLine(" ");
if (ntokens > 0) {
int nidx = 0;
Name[0].clear();
Name[1].clear();
for (int tidx = 0; tidx < ntokens; tidx++) {
const char* tkn = buffer.NextToken();
if (tkn[0] == '=') {
FieldType Eindex = getEindex(Name);
tkn = buffer.NextToken();
++tidx;
if (tkn == 0)
mprintf("Warning: No numerical value, line %i column %i. Skipping.\n",
buffer.LineNumber(), tidx+1);
else if (tkn[0] == '*' || tkn[0] == 'N') // Assume if number begins with N it is NaN
mprintf("Warning: Numerical overflow detected, line %i column %i. Skipping.\n",
buffer.LineNumber(), tidx+1);
else {
if (Eindex != N_FIELDTYPES) {
Energy[Eindex] = atof( tkn );
EnergyExists[Eindex] = true;
}
}
nidx = 0;
Name[0].clear();
Name[1].clear();
} else {
if (nidx > 1) break; // Two tokens, no '=' found. Not an E line.
Name[nidx++].assign( tkn );
}
}
}
// Set time
switch (imin) {
case 5: time = (double)nstep + t0; break;
case 1: time = (double)minStep + t0; break;
case 0: time = ((double)nstep * dt) + t0; break;
}
// Read in next line
ptr = buffer.Line();
}
mprintf("\t%i frames\n", frame);
buffer.CloseFile();
std::string Xlabel;
if (imin == 5) Xlabel.assign("Set");
else if (imin == 1) Xlabel.assign("Nstep");
else Xlabel.assign("Time"); // imin == 0
if (datasetlist.AddOrAppendSets( Xlabel, TimeVals, inputSets )) return 1;
return 0;
}
double moProperty::asDouble() {
return convertToDouble(this->type, this->val);
}
void summariseEigensoft() {
std::ifstream* eigenFile = new std::ifstream(opt::eigensoftFile.c_str());
string fileRoot = stripExtension(opt::eigensoftFile);
string FstResultsFileName = fileRoot + "_" + opt::runName + "_fst_matrix.forR";
std::ofstream* pFst = new std::ofstream(FstResultsFileName.c_str());
std::vector<std::vector<std::string> > fst_matrix;
string line;
getline(*eigenFile, line); // Get the first description line
short type;
if (line == "##") {
type = 1;
} else {
type = 2;
}
std::cerr << "It is type: " << type << std::endl;
if (type == 1) {
getline(*eigenFile, line);
std::vector<std::string> fields = split(line, '\t');
std::vector<std::string> this_indiv_fst;
std::vector<std::string> all_indiv;
string this_indiv = fields[0];
this_indiv_fst.push_back(fields[2]);
while (getline(*eigenFile, line)) {
fields = split(line, '\t');
std::cerr << "Indiv: " << fields[0] << std::endl;
if (this_indiv == fields[0]) {
this_indiv_fst.push_back(fields[2]);
} else {
fst_matrix.push_back(this_indiv_fst);
all_indiv.push_back(this_indiv);
this_indiv = fields[0];
this_indiv_fst.clear();
this_indiv_fst.push_back(fields[2]);
}
}
all_indiv.push_back(this_indiv);
fst_matrix.push_back(this_indiv_fst);
this_indiv_fst.clear(); this_indiv_fst.push_back("0"); all_indiv.push_back(fields[1]);
fst_matrix.push_back(this_indiv_fst);
for (std::vector<std::vector<std::string> >::size_type i = 0; i != fst_matrix.size(); i++) {
std::reverse(fst_matrix[i].begin(), fst_matrix[i].end());
fst_matrix[i].insert(fst_matrix[i].end(), "0");
while (fst_matrix[i].size() != fst_matrix[0].size()) {
fst_matrix[i].insert(fst_matrix[i].end(), "0");
}
}
std::reverse(fst_matrix.begin(), fst_matrix.end());
std::reverse(all_indiv.begin(), all_indiv.end());
print_vector(all_indiv, *pFst);
print_matrix(fst_matrix, *pFst);
} else if (type == 2) {
std::cerr << "type2" << std::endl;
std::vector<std::string> fields = split(line, '\t');
std::vector<std::string> all_indiv(fields.begin()+1,fields.end());
getline(*eigenFile, line); getline(*eigenFile, line);
std::vector<std::string> this_indiv_fst;
while (getline(*eigenFile, line)) {
fields = split(line, '\t');
std::copy(fields.begin()+1,fields.end(),std::back_inserter(this_indiv_fst));
for (std::vector<std::string>::size_type i = 0; i != this_indiv_fst.size(); i++) {
double fst = convertToDouble(this_indiv_fst[i]) / 1000;
this_indiv_fst[i] = numToString(fst);
}
fst_matrix.push_back(this_indiv_fst);
this_indiv_fst.clear();
}
print_vector(all_indiv, *pFst);
print_matrix(fst_matrix, *pFst);
}
}
// Exec_DataSetCmd::Remove()
Exec::RetType Exec_DataSetCmd::Remove(CpptrajState& State, ArgList& argIn) {
std::string status;
// Get criterion type
CriterionType criterion = UNKNOWN_C;
for (int i = 1; i < (int)N_C; i++)
if (argIn.hasKey( CriterionKeys[i] )) {
criterion = (CriterionType)i;
status.assign( CriterionKeys[i] );
break;
}
if (criterion == UNKNOWN_C) {
mprinterr("Error: No criterion specified for 'remove'.\n");
return CpptrajState::ERR;
}
// Get select type
SelectType select = UNKNOWN_S;
std::string val1, val2;
for (const SelectPairType* ptr = SelectKeys; ptr->key_ != 0; ptr++)
if (argIn.Contains( ptr->key_ )) {
select = ptr->type_;
val1 = argIn.GetStringKey( ptr->key_ );
status.append( " " + std::string(ptr->key_) + " " + val1 );
// Get 'and' value for between/outside. TODO put nargs in SelectPairType?
if (select == BETWEEN || select == OUTSIDE) {
val2 = argIn.GetStringKey("and");
if (val2.empty()) {
mprinterr("Error: Missing 'and' value for selection '%s'\n", ptr->key_);
return CpptrajState::ERR;
}
status.append(" and " + val2);
}
break;
}
if (select == UNKNOWN_S || val1.empty()) {
mprinterr("Error: No selection specified for 'remove'.\n");
return CpptrajState::ERR;
}
if ( (criterion == SMODE || criterion == STYPE) &&
(select != EQUAL && select != NOT_EQUAL) )
{
mprinterr("Error: Specified select not valid for criterion '%s'\n", CriterionKeys[criterion]);
return CpptrajState::ERR;
}
mprintf("\tRemoving data sets");
std::string setSelectArg = argIn.GetStringNext();
if (setSelectArg.empty())
setSelectArg.assign("*");
else
mprintf(" within selection '%s'", setSelectArg.c_str());
mprintf(" %s\n", status.c_str());
DataSetList tempDSL = State.DSL().GetMultipleSets( setSelectArg );
if (tempDSL.empty()) {
mprinterr("Error: No data sets selected.\n");
return CpptrajState::ERR;
}
// Remove sets
unsigned int Nremoved = 0;
if ( criterion == AVERAGE ) {
if (!validDouble( val1 )) {
mprinterr("Error: '%s' is not a valid number\n", val1.c_str());
return CpptrajState::ERR;
}
double d_val1 = convertToDouble( val1 );
double d_val2 = d_val1;
if (!val2.empty()) {
if (!validDouble( val2 )) {
mprinterr("Error: '%s' is not a valid number\n", val2.c_str());
return CpptrajState::ERR;
}
d_val2 = convertToDouble( val2 );
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D )
mprintf("Warning: '%s' is not a valid data set for 'average' criterion.\n", (*ds)->legend());
else {
DataSet_1D const& ds1 = static_cast<DataSet_1D const&>( *(*ds) );
double avg = ds1.Avg();
bool remove = false;
switch (select) {
case EQUAL : remove = (avg == d_val1); break;
case NOT_EQUAL : remove = (avg != d_val1); break;
case LESS_THAN : remove = (avg < d_val1); break;
case GREATER_THAN : remove = (avg > d_val1); break;
case BETWEEN : remove = (avg > d_val1 && avg < d_val2); break;
case OUTSIDE : remove = (avg < d_val1 || avg > d_val2); break;
case UNKNOWN_S:
case N_S : return CpptrajState::ERR; // Sanity check
}
if (remove) {
mprintf("\t Removing set '%s' (avg is %g)\n", (*ds)->legend(), avg);
State.RemoveDataSet( *ds );
++Nremoved;
}
}
}
} else if ( criterion == SIZE ) {
if (!validInteger( val1 )) {
mprinterr("Error: '%s' is not a valid number\n", val1.c_str());
return CpptrajState::ERR;
}
unsigned int i_val1 = (unsigned int)convertToInteger( val1 );
unsigned int i_val2 = i_val1;
if (!val2.empty()) {
if (!validInteger( val2 )) {
mprinterr("Error: '%s' is not a valid number\n", val2.c_str());
return CpptrajState::ERR;
}
i_val2 = convertToInteger( val2 );
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
unsigned int size = (*ds)->Size();
bool remove = false;
switch ( select ) {
case EQUAL : remove = (size == i_val1); break;
case NOT_EQUAL : remove = (size != i_val1); break;
case LESS_THAN : remove = (size < i_val1); break;
case GREATER_THAN : remove = (size > i_val1); break;
case BETWEEN : remove = (size > i_val1 && size < i_val2); break;
case OUTSIDE : remove = (size < i_val1 || size > i_val2); break;
case UNKNOWN_S:
case N_S : return CpptrajState::ERR; // Sanity check
}
if (remove) {
mprintf("\t Removing set '%s' (size is %u)\n", (*ds)->legend(), size);
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else if ( criterion == SMODE ) {
MetaData::scalarMode mode_val = MetaData::ModeFromKeyword( val1 );
if (mode_val == MetaData::UNKNOWN_MODE) {
mprinterr("Error: '%s' is not a valid mode.\n", val1.c_str());
return CpptrajState::ERR;
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
bool remove = false;
MetaData::scalarMode mode = (*ds)->Meta().ScalarMode();
if (select == EQUAL ) remove = ( mode == mode_val );
else if (select == NOT_EQUAL) remove = ( mode != mode_val );
else return CpptrajState::ERR; // Sanity check
if (remove) {
mprintf("\t Removing set '%s' (mode is '%s')\n", (*ds)->legend(), MetaData::ModeString(mode));
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else if ( criterion == STYPE ) {
MetaData::scalarType type_val = MetaData::TypeFromKeyword( val1, MetaData::UNKNOWN_MODE );
if (type_val == MetaData::UNDEFINED) {
mprinterr("Error: '%s' is not a valid type.\n", val1.c_str());
return CpptrajState::ERR;
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
bool remove = false;
MetaData::scalarType type = (*ds)->Meta().ScalarType();
if (select == EQUAL ) remove = ( type == type_val );
else if (select == NOT_EQUAL) remove = ( type != type_val );
else return CpptrajState::ERR; // Sanity check
if (remove) {
mprintf("\t Removing set '%s' (typeis '%s')\n", (*ds)->legend(), MetaData::TypeString(type));
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else {
mprinterr("Internal Error: Criterion not yet implemented.\n");
return CpptrajState::ERR;
}
mprintf("\tRemoved %u of %zu sets.\n", Nremoved, tempDSL.size());
return CpptrajState::OK;
}
void PDI::mosaicEcualization(cv::Mat &img, int pixels, bool interpolate){
cv::Mat temp;
imageRGB(img);
// Slices (pixels * pixels)
int hor = int(img.cols/pixels);
int ver = int(img.rows/pixels);
int rHor = int(img.cols%pixels);
int rVer = int(img.rows%pixels);
int x, y;
for(int i=0; i<ver; i++){ // Moving in rows
y = i*pixels;
for(int j=0; j<hor; j++){
x = j*pixels;
temp = cv::Mat(img, cvRect(x, y, pixels, pixels));
// Ecualizing subimage
ecualizeImage(temp);
if(rHor>0 && j==hor-1){
temp = cv::Mat(img, cvRect(x+pixels, y, rHor, pixels));
// Ecualizing subimage
ecualizeImage(temp);
}
}
if(rVer>0 && i==ver-1){
for(int j=0; j<hor; j++){
x = j*pixels;
temp = cv::Mat(img, cvRect(x, y+pixels, pixels, rVer));
// Ecualizing subimage
ecualizeImage(temp);
if(rHor>0 && j==hor-1){
temp = cv::Mat(img, cvRect(x+pixels, y+pixels, rHor, rVer));
// Ecualizing subimage
ecualizeImage(temp);
}
}
}
}
if(interpolate){
if(img.cols < 2*pixels || img.rows < 2*pixels ){
std::cout << "ERROR: It's not possible to equalize, try again changing the dimensions of the sub-images." << std::endl;
std::cout << "Image Dimensions: " << img.rows << ", " << img.cols << std::endl;
std::cout << "Sub-image Dimensions: " << pixels << ", " << pixels << std::endl;
}
else{
// Get the image range (to re-convert)
int min, max;
getImageRange(img, min, max);
int subimg = 0;
int f00, f01, f10, f11;
cv::Mat im = convertToDouble(img);
// img: imagen de entrada (en cuadritos)
// pixels: dimensiones del cuadrito
// hor: num de cuadros horizontales
// ver: num de cuadros verticales
// rHor: pixeles horizontales sobrantes
// rVer: pixeles verticales sobrantes
// y: fila inicial para la sub imagen
// x: columna inicial para la sub imagen
std::cout << "Image dims: " << img.rows << " x " << img.cols << std::endl;
for(int v=0; v<ver; v++){ // Moving in rows (Vertical)
y = v*pixels + pixels/2;
for(int h=0; h<hor; h++){ // Moving in colums (Horizontal)
x = h*pixels + pixels/2;
std::cout << "(" << v << ", " << h << "): " << y << ", " << x << std::endl;
if( y+pixels < img.rows && x+pixels < img.cols ){
temp = cv::Mat(img, cvRect(x, y, pixels, pixels));
for(int i=0; i<temp.rows; i++){
for(int j=0; j<temp.cols; j++){
int s = j + 1;
int t = i + 1;
f00 = vHistograms[subimg].HistA[temp.at<uchar>(i, j)];
f01 = vHistograms[subimg+1].HistA[temp.at<uchar>(i, j)];
f10 = vHistograms[subimg+ver].HistA[temp.at<uchar>(i, j)];
f11 = vHistograms[subimg+ver+1].HistA[temp.at<uchar>(i, j)];
temp.at<uchar>(i,j) = (1-s) * (1-t) * f00 + s * (1-t) * f10
+ (1-s) * t+1 * f01 + s * t * f11;
}
}
}
subimg++;
}
}
/*
for(int v=0; v<ver; v++){ // Moving in rows
y = v*pixels;
for(int h=0; h<hor; h++){
x = h*pixels;
// Ecualizing subimage
std::cout << subimg << std::endl;
Hists = vHistograms[subimg];
for(int s=0; s<pixels; s++){
for(int t=0; t<pixels; t++){
int ss = s + v * pixels;
int tt = t + h * pixels;
f00 = vHistograms[subimg].HistA[img.at<uchar>(s, t)];
f01 = vHistograms[subimg+1].HistA[img.at<uchar>(s, t)];
f10 = vHistograms[subimg+ver].HistA[img.at<uchar>(s, t)];
f11 = vHistograms[subimg+ver+1].HistA[img.at<uchar>(s, t)]; // std::cout << "s: " << s << " ss: " << ss << " t: " << t << " tt: " << tt << " => ";
// std::cout << "f00(" << 0+v*pixels << ", " << 0+h*pixels << ") - "
// << "f10(" << 0+v*pixels << ", " << pixels-1+h*pixels << ") - "
// << "f01(" << pixels-1+v*pixels << ", " << 0+h*pixels << ") - "
// << "f11(" << pixels-1+v*pixels << ", " << pixels-1+h*pixels << ")" << std::endl;
im.at<double>(ss,tt) = (1-s) * (1-t) * f00 + s * (1-t) * f10
+ (1-s) * t+1 * f01 + s * t * f11;
}
}
subimg++;
if(rHor>0 && h==hor-1){
std::cout << subimg << std::endl;
Hists = vHistograms[subimg];
// Ecualizing subimage
subimg++;
}
}
if(rVer>0 && v==ver-1){
for(int h=0; h<hor; h++){
x = h*pixels;
std::cout << subimg << std::endl;
Hists = vHistograms[subimg];
// Ecualizing subimage
subimg++;
if(rHor>0 && h==hor-1){
std::cout << subimg << std::endl;
Hists = vHistograms[subimg];
// Ecualizing subimage
subimg++;
}
}
}
}
*/
// Image double converted into integer
// normalizateMatrix(im, min, max);
// cv::Mat im2 = convertToInterger(im);
// im2.copyTo(img);
}
}
}
double TDataToDouble(const TData *context)
{
if (context) return convertToDouble(context->data, context->type);
return 0;
}
// Action_MakeStructure::Init()
Action::RetType Action_MakeStructure::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
debug_ = debugIn;
secstruct_.clear();
// Get all arguments
std::string ss_expr = actionArgs.GetStringNext();
while ( !ss_expr.empty() ) {
ArgList ss_arg(ss_expr, ":");
if (ss_arg.Nargs() < 2) {
mprinterr("Error: Malformed SS arg.\n");
Help();
return Action::ERR;
}
// Type is 1st arg, range is 2nd arg.
SecStructHolder ss_holder(ss_arg[1], FindSStype(ss_arg[0]));
if (ss_arg.Nargs() == 2) {
// Find SS type: <ss type>:<range>
if (ss_holder.sstype_idx == SS_EMPTY) {
mprinterr("Error: SS type %s not found.\n", ss_arg[0].c_str());
return Action::ERR;
}
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
secstruct_.push_back( ss_holder );
} else if (ss_arg[0] == "ref") {
// Use dihedrals from reference structure
if (ss_arg.Nargs() < 3) {
mprinterr("Error: Invalid 'ref' arg. Requires 'ref:<range>:<refname>[:<ref range>]'\n");
return Action::ERR;
}
ss_arg.MarkArg(0);
ss_arg.MarkArg(1);
// Sanity check: Currently only unique args of this type are allowed
if (ss_holder.sstype_idx != SS_EMPTY) {
mprinterr("Error: Ref backbone types must be unique [%s]\n", ss_arg[0].c_str());
return Action::ERR;
}
// Use backbone phi/psi from reference structure
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
// Get reference structure
DataSet_Coords_REF* REF = (DataSet_Coords_REF*)
DSL->FindSetOfType(ss_arg.GetStringNext(),
DataSet::REF_FRAME); // ss_arg[2]
if (REF == 0) {
mprinterr("Error: Could not get reference structure [%s]\n", ss_arg[2].c_str());
return Action::ERR;
}
// Get reference residue range, or use resRange
Range refRange(ss_arg.GetStringNext(), -1); // ss_arg[3]
if (!refRange.Empty()) {
if (ss_holder.resRange.Size() != refRange.Size()) {
mprinterr("Error: Reference range [%s] must match residue range [%s]\n",
refRange.RangeArg(), ss_holder.resRange.RangeArg());
return Action::ERR;
}
} else
refRange = ss_holder.resRange;
// Look for phi/psi only in reference
DihedralSearch refSearch;
refSearch.SearchFor(MetaData::PHI);
refSearch.SearchFor(MetaData::PSI);
if (refSearch.FindDihedrals( REF->Top(), refRange )) return Action::ERR;
// For each found dihedral, set theta
for (DihedralSearch::mask_it dih = refSearch.begin(); dih != refSearch.end(); ++dih)
{
double torsion = Torsion( REF->RefFrame().XYZ(dih->A0()),
REF->RefFrame().XYZ(dih->A1()),
REF->RefFrame().XYZ(dih->A2()),
REF->RefFrame().XYZ(dih->A3()) );
ss_holder.thetas_.push_back( (float)torsion );
}
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 4 && isalpha(ss_arg[2][0])) {
// Single dihedral type: <name>:<range>:<dih type>:<angle>
DihedralSearch::DihedralType dtype = DihedralSearch::GetType(ss_arg[2]);
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (dtype == MetaData::UNDEFINED) {
mprinterr("Error: Dihedral type %s not found.\n", ss_arg[2].c_str());
return Action::ERR;
}
if (!validDouble(ss_arg[3])) {
mprinterr("Error: 4th arg (angle) is not a valid number.\n");
return Action::ERR;
}
SS.push_back( SS_TYPE(convertToDouble(ss_arg[3]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
ss_holder.dihSearch_.SearchFor( dtype );
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 7 || ss_arg.Nargs() == 8) {
// Single custom dihedral type: <name>:<range>:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (!validDouble(ss_arg[6])) {
mprinterr("Error: 7th arg (angle) is not a valid number.\n");
return Action::ERR;
}
SS.push_back( SS_TYPE(convertToDouble(ss_arg[6]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
int offset = 0;
if (ss_arg.Nargs() == 8) {
if (!validInteger(ss_arg[7])) {
mprinterr("Error: 8th arg (offset) is not a valid number.\n");
return Action::ERR;
}
offset = convertToInteger(ss_arg[7]);
}
ss_holder.dihSearch_.SearchForNewType(offset,ss_arg[2],ss_arg[3],ss_arg[4],ss_arg[5],
ss_arg[0]);
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 4 || ss_arg.Nargs() == 6) {
// Custom SS/turn type: <name>:<range>:<phi1>:<psi1>[:<phi2>:<psi2>]
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (!validDouble(ss_arg[2]) || !validDouble(ss_arg[3])) {
mprinterr("Error: 3rd or 4th arg (phi1/psi1) is not a valid number.\n");
return Action::ERR;
}
double phi1 = convertToDouble(ss_arg[2]);
double psi1 = convertToDouble(ss_arg[3]);
int isTurn = 0;
double phi2 = 0.0;
double psi2 = 0.0;
if (ss_arg.Nargs() == 6) {
isTurn = 1;
if (!validDouble(ss_arg[4]) || !validDouble(ss_arg[5])) {
mprinterr("Error: 5th or 6th arg (phi2/psi2) is not a valid number.\n");
return Action::ERR;
}
phi2 = convertToDouble(ss_arg[4]);
psi2 = convertToDouble(ss_arg[5]);
}
SS.push_back(SS_TYPE(phi1, psi1, phi2, psi2, isTurn, ss_arg[0] ));
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
secstruct_.push_back( ss_holder );
} else {
mprinterr("Error: SS arg type [%s] not recognized.\n", ss_arg[0].c_str());
return Action::ERR;
}
ss_expr = actionArgs.GetStringNext();
} // End loop over args
if (secstruct_.empty()) {
mprinterr("Error: No SS types defined.\n");
return Action::ERR;
}
mprintf(" MAKESTRUCTURE:\n");
for (std::vector<SecStructHolder>::iterator ss = secstruct_.begin();
ss != secstruct_.end(); ++ss)
{
if (ss->sstype_idx != SS_EMPTY) {
const SS_TYPE& myType = SS[ss->sstype_idx];
switch ( myType.isTurn ) {
case 0:
mprintf("\tSS type %s will be applied to residue(s) %s\n",
myType.type_arg.c_str(), ss->resRange.RangeArg());
break;
case 1:
mprintf("\tTurn type %s will be applied to residue(s) %s\n",
myType.type_arg.c_str(), ss->resRange.RangeArg());
break;
case 2:
mprintf("\tDihedral value of %.2f will be applied to %s dihedrals in residue(s) %s\n",
myType.phi, myType.type_arg.c_str(), ss->resRange.RangeArg());
}
} else
mprintf("\tBackbone angles from reference will be applied to residue(s) %s\n",
ss->resRange.RangeArg());
}
return Action::OK;
}
