/** Return the maximum value in the dataset. */
double DS_Math::Max(DataSet& ds) {
// Check # values
if ( ds.Size() == 0 ) return 0;
double max = 0;
// Check if this set is a good type
if ( GoodCalcType(ds) ) {
max = ds.Dval( 0 );
for (int i = 1; i < ds.Size(); ++i) {
double val = ds.Dval( i );
if (val > max) max = val;
}
}
return max;
}
/** Return the minimum value in the dataset. */
double DS_Math::Min(DataSet& ds) {
// Check # values
if (ds.Size()==0) return 0;
double min = 0;
// Check if this set is a good type
if ( GoodCalcType(ds) ) {
min = ds.Dval( 0 );
for (int i = 1; i < ds.Size(); ++i) {
double val = ds.Dval( i );
if (val < min) min = val;
}
}
return min;
}
/** Calculate Pearson product-moment correlation between DataSets.
* \D1 DataSet to caclculate correlation for.
* \D2 DataSet to caclulate correlation to.
* \return Pearson product-moment correlation coefficient.
*/
double DS_Math::CorrCoeff( DataSet& D1, DataSet& D2 ) {
// Check if D1 and D2 are valid types
if ( !GoodCalcType(D1) ) return 0;
if ( !GoodCalcType(D2) ) return 0;
// Check that D1 and D2 have same # data points.
int Nelements = D1.Size();
if (Nelements != D2.Size()) {
mprinterr("Error: Corr: # elements in dataset %s (%i) not equal to\n",
D1.Legend().c_str(), Nelements);
mprinterr("Error: # elements in dataset %s (%i)\n",
D2.Legend().c_str(), D2.Size());
return 0;
}
// Calculate averages
double avg1 = Avg(D1);
double avg2 = Avg(D2);
// Calculate average deviations.
double sumdiff1_2 = 0.0;
double sumdiff2_2 = 0.0;
double corr_coeff = 0.0;
//mprinterr("DATASETS %s and %s\n", c_str(), D2.c_str());
for (int i = 0; i < Nelements; i++) {
double diff1 = D1.Dval(i) - avg1;
double diff2 = D2.Dval(i) - avg2;
sumdiff1_2 += (diff1 * diff1);
sumdiff2_2 += (diff2 * diff2);
corr_coeff += (diff1 * diff2);
}
if (sumdiff1_2 == 0.0 || sumdiff2_2 == 0.0) {
mprintf("Warning: Corr: %s to %s, Normalization is 0\n",
D1.Legend().c_str(), D2.Legend().c_str());
return 0;
}
// Correlation coefficient
corr_coeff /= ( sqrt( sumdiff1_2 ) * sqrt( sumdiff2_2 ) );
//mprintf(" CORRELATION COEFFICIENT %6s to %6s IS %10.4f\n",
// D1_->c_str(), D2_->c_str(), corr_coeff );
return corr_coeff;
}
/** Calculate the average over values in this set (and optionally the
* standard deviation).
*/
double DS_Math::Avg(DataSet& ds, double* stdev) {
// Check # values
int numvalues = ds.Size();
if ( numvalues < 1 ) {
if (stdev != 0) *stdev = 0.0;
return 0.0;
}
double avg = 0;
// Check if this set is a good type
if ( GoodCalcType(ds) ) {
if (IsTorsionArray(ds)) {
// Cyclic torsion average
double sumy = 0.0;
double sumx = 0.0;
for ( int i = 0; i < numvalues; ++i ) {
double theta = ds.Dval( i ) * DEGRAD;
sumy += sin( theta );
sumx += cos( theta );
}
avg = atan2(sumy, sumx) * RADDEG;
// Torsion Stdev
sumy = 0;
for ( int i = 0; i < numvalues; ++i) {
double diff = fabs(avg - ds.Dval( i ));
if (diff > 180.0)
diff = 360.0 - diff;
diff *= diff;
sumy += diff;
}
sumy /= (double)numvalues;
*stdev = sqrt(sumy);
} else {
// Non-cyclic, normal average
double sum = 0;
for ( int i = 0; i < numvalues; ++i )
sum += ds.Dval( i );
avg = sum / (double)numvalues;
if (stdev==0) return avg;
// Stdev
sum = 0;
for ( int i = 0; i < numvalues; ++i ) {
double diff = avg - ds.Dval( i );
diff *= diff;
sum += diff;
}
sum /= (double)numvalues;
*stdev = sqrt(sum);
}
}
return avg;
}
/** Replace all variables in given ArgList with their values. */
ArgList VariableArray::ReplaceVariables(ArgList const& argIn, DataSetList const& DSL, int debug)
{
if (debug > 0) mprintf("DEBUG: Before variable replacement: [%s]\n", argIn.ArgLine());
ArgList modCmd = argIn;
for (int n = 0; n < modCmd.Nargs(); n++) {
size_t pos = modCmd[n].find("$");
while (pos != std::string::npos) {
// Argument is/contains a variable. Find first non-alphanumeric char
size_t len = 1;
for (size_t pos1 = pos+1; pos1 < modCmd[n].size(); pos1++, len++)
if (!isalnum(modCmd[n][pos1])) break;
std::string var_in_arg = modCmd[n].substr(pos, len);
// See if variable occurs in CurrentVars_
Varray::const_iterator vp = CurrentVars_.begin();
for (; vp != CurrentVars_.end(); ++vp)
if (vp->first == var_in_arg) break;
// If found replace with value from CurrentVars_
if (vp != CurrentVars_.end()) {
if (debug > 0)
mprintf("DEBUG: Replaced variable '%s' with value '%s'\n",
var_in_arg.c_str(), vp->second.c_str());
std::string arg = modCmd[n];
arg.replace(pos, vp->first.size(), vp->second);
modCmd.ChangeArg(n, arg);
} else {
// Not found in CurrentVars_; see if this is a DataSet.
for (size_t pos1 = pos+len; pos1 < modCmd[n].size(); pos1++, len++)
if (!isalnum(modCmd[n][pos1]) &&
modCmd[n][pos1] != '[' &&
modCmd[n][pos1] != ':' &&
modCmd[n][pos1] != ']' &&
modCmd[n][pos1] != '_' &&
modCmd[n][pos1] != '-' &&
modCmd[n][pos1] != '%')
break;
var_in_arg = modCmd[n].substr(pos+1, len-1);
DataSet* ds = DSL.GetDataSet( var_in_arg );
if (ds == 0) {
mprinterr("Error: Unrecognized variable in command: %s\n", var_in_arg.c_str());
return ArgList();
} else {
if (ds->Type() != DataSet::STRING && ds->Group() != DataSet::SCALAR_1D) {
mprinterr("Error: Only 1D data sets supported.\n");
return ArgList();
}
if (ds->Size() < 1) {
mprinterr("Error: Set is empty.\n");
return ArgList();
}
if (ds->Size() > 1)
mprintf("Warning: Only using first value.\n");
std::string value;
if (ds->Type() == DataSet::STRING)
value = (*((DataSet_string*)ds))[0];
else
value = doubleToString(((DataSet_1D*)ds)->Dval(0));
if (debug > 0)
mprintf("DEBUG: Replaced variable '$%s' with value '%s' from DataSet '%s'\n",
var_in_arg.c_str(), value.c_str(), ds->legend());
std::string arg = modCmd[n];
arg.replace(pos, var_in_arg.size()+1, value);
modCmd.ChangeArg(n, arg);
}
}
pos = modCmd[n].find("$");
} // END loop over this argument
}
return modCmd;
}
/** Calculate time correlation between two DataSets.
* \D1 DataSet to calculate correlation for.
* \D2 DataSet to calculate correlation to.
* \Ct DataSet to store time correlation fn, must be DOUBLE.
* \lagmaxIn Max lag to calculate corr. -1 means use size of dataset.
* \calccovar If true calculate covariance (devation from avg).
* \return 0 on success, 1 on error.
*/
int DS_Math::CrossCorr( DataSet& D1, DataSet& D2, DataSet& Ct, int lagmaxIn,
bool calccovar, bool usefft )
{
int lagmax;
double ct;
// Check if D1 and D2 are valid types
if ( !GoodCalcType(D1) ) return 1;
if ( !GoodCalcType(D2) ) return 1;
// Check that D1 and D2 have same # data points.
int Nelements = D1.Size();
if (Nelements != D2.Size()) {
mprinterr("Error: CrossCorr: # elements in dataset %s (%i) not equal to\n",
D1.Legend().c_str(), Nelements);
mprinterr("Error: # elements in dataset %s (%i)\n",
D2.Legend().c_str(), D2.Size());
return 1;
}
if (Nelements < 2) {
mprinterr("Error: CrossCorr: # elements is less than 2 (%i)\n", Nelements);
return 1;
}
// Check return dataset type
if ( Ct.Type() != DataSet::DOUBLE ) {
mprinterr("Internal Error: CrossCorr: Ct must be of type DataSet::DOUBLE.\n");
return 1;
}
// Check if lagmaxIn makes sense. Set default lag to be Nelements
// if not specified.
if (lagmaxIn == -1)
lagmax = Nelements;
else if (lagmaxIn > Nelements) {
mprintf("Warning: CrossCorr [%s][%s]: max lag (%i) > Nelements (%i), setting to Nelements.\n",
D1.Legend().c_str(), D2.Legend().c_str(), lagmaxIn, Nelements);
lagmax = Nelements;
} else
lagmax = lagmaxIn;
// If calculating covariance calculate averages
double avg1 = 0;
double avg2 = 0;
if ( calccovar ) {
avg1 = Avg(D1);
avg2 = Avg(D2);
}
// Calculate correlation
double norm = 1.0;
if ( usefft ) {
// Calc using FFT
CorrF_FFT pubfft1(Nelements);
ComplexArray data1 = pubfft1.Array();
data1.PadWithZero(Nelements);
for (int i = 0; i < Nelements; ++i)
data1[i*2] = D1.Dval(i) - avg1;
if (&D2 == &D1)
pubfft1.AutoCorr(data1);
else {
// Populate second dataset if different
ComplexArray data2 = pubfft1.Array();
data2.PadWithZero(Nelements);
for (int i = 0; i < Nelements; ++i)
data2[i*2] = D2.Dval(i) - avg2;
pubfft1.CrossCorr(data1, data2);
}
// Put real components of data1 in output DataSet
norm = 1.0 / fabs( data1[0] );
for (int i = 0; i < lagmax; ++i) {
ct = data1[i*2] * norm;
Ct.Add(i, &ct);
}
} else {
// Direct calc
for (int lag = 0; lag < lagmax; ++lag) {
ct = 0;
int jmax = Nelements - lag;
for (int j = 0; j < jmax; ++j)
ct += ((D1.Dval(j) - avg1) * (D2.Dval(j+lag) - avg2));
if (lag == 0) {
if (ct != 0)
norm = fabs( ct );
}
ct /= norm;
Ct.Add(lag, &ct);
}
}
return 0;
}
/** Syntax: dataset invert <set arg0> ... name <new name> */
Exec::RetType Exec_DataSetCmd::InvertSets(CpptrajState& State, ArgList& argIn) {
DataSetList& DSL = State.DSL();
// Get keywords
DataSet* inputNames = 0;
std::string dsname = argIn.GetStringKey("legendset");
if (!dsname.empty()) {
inputNames = DSL.GetDataSet( dsname );
if (inputNames == 0) {
mprinterr("Error: Name set '%s' not found.\n", dsname.c_str());
return CpptrajState::ERR;
}
if (inputNames->Type() != DataSet::STRING) {
mprinterr("Error: Set '%s' does not contain strings.\n", inputNames->legend());
return CpptrajState::ERR;
}
mprintf("\tUsing names from set '%s' as legends for inverted sets.\n", inputNames->legend());
}
dsname = argIn.GetStringKey("name");
if (dsname.empty()) {
mprinterr("Error: 'invert' requires that 'name <new set name>' be specified.\n");
return CpptrajState::ERR;
}
mprintf("\tNew sets will be named '%s'\n", dsname.c_str());
DataFile* outfile = State.DFL().AddDataFile( argIn.GetStringKey("out"), argIn );
if (outfile != 0)
mprintf("\tNew sets will be output to '%s'\n", outfile->DataFilename().full());
// TODO determine type some other way
DataSet::DataType outtype = DataSet::DOUBLE;
// Get input DataSets
std::vector<DataSet_1D*> input_sets;
std::string dsarg = argIn.GetStringNext();
while (!dsarg.empty()) {
DataSetList sets = DSL.GetMultipleSets( dsarg );
for (DataSetList::const_iterator ds = sets.begin(); ds != sets.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D ) {
mprintf("Warning: '%s': Inversion only supported for 1D scalar data sets.\n",
(*ds)->legend());
} else {
if (!input_sets.empty()) {
if ( (*ds)->Size() != input_sets.back()->Size() ) {
mprinterr("Error: Set '%s' has different size (%zu) than previous set (%zu)\n",
(*ds)->legend(), (*ds)->Size(), input_sets.back()->Size());
return CpptrajState::ERR;
}
}
input_sets.push_back( (DataSet_1D*)*ds );
}
}
dsarg = argIn.GetStringNext();
}
if (input_sets.empty()) {
mprinterr("Error: No sets selected.\n");
return CpptrajState::ERR;
}
if (inputNames != 0 && inputNames->Size() != input_sets.front()->Size()) {
mprinterr("Error: Name set '%s' size (%zu) differs from # data points (%zu).\n",
inputNames->legend(), inputNames->Size(), input_sets.front()->Size());
return CpptrajState::ERR;
}
mprintf("\t%zu input sets; creating %zu output sets.\n",
input_sets.size(), input_sets.front()->Size());
// Need an output data set for each point in input sets
std::vector<DataSet*> output_sets;
int column = 1;
for (int idx = 0; idx != (int)input_sets[0]->Size(); idx++, column++) {
DataSet* ds = 0;
ds = DSL.AddSet(outtype, MetaData(dsname, column));
if (ds == 0) return CpptrajState::ERR;
if (inputNames != 0)
ds->SetLegend( (*((DataSet_string*)inputNames))[idx] );
output_sets.push_back( ds );
if (outfile != 0) outfile->AddDataSet( ds );
}
// Create a data set containing names of each input data set
DataSet* nameset = DSL.AddSet(DataSet::STRING, MetaData(dsname, column));
if (nameset == 0) return CpptrajState::ERR;
if (inputNames != 0)
nameset->SetLegend("Names");
if (outfile != 0) outfile->AddDataSet( nameset );
// Populate output data sets
for (int jdx = 0; jdx != (int)input_sets.size(); jdx++)
{
DataSet_1D const& INP = static_cast<DataSet_1D const&>( *(input_sets[jdx]) );
nameset->Add( jdx, INP.legend() );
for (unsigned int idx = 0; idx != INP.Size(); idx++)
{
double dval = INP.Dval( idx );
output_sets[idx]->Add( jdx, &dval );
}
}
return CpptrajState::OK;
}
// Exec_DataSetCmd::ModifyPoints()
Exec::RetType Exec_DataSetCmd::ModifyPoints(CpptrajState& State, ArgList& argIn, bool drop) {
const char* mode;
if (drop)
mode = "Drop";
else
mode = "Kee";
// Keywords
std::string name = argIn.GetStringKey("name");
int start = argIn.getKeyInt("start", 0) - 1;
int stop = argIn.getKeyInt("stop", -1);
int offset = argIn.getKeyInt("offset", -1);
Range points;
if (start < 0 && stop < 0 && offset < 0) {
std::string rangearg = argIn.GetStringKey("range");
if (rangearg.empty()) {
mprinterr("Error: Must specify range or start/stop/offset.\n");
return CpptrajState::ERR;
}
points.SetRange( rangearg );
if (points.Empty()) {
mprinterr("Error: Range '%s' is empty.\n", rangearg.c_str());
return CpptrajState::ERR;
}
mprintf("\t%sping points in range %s\n", mode, rangearg.c_str());
// User args start from 1
points.ShiftBy(-1);
}
// Get data set to drop/keep points from
// Loop over all DataSet arguments
std::string ds_arg = argIn.GetStringNext();
while (!ds_arg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( ds_arg );
for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
{
DataSet* DS = *it;
if (DS->Size() < 1) {
mprinterr("Error: Set '%s' is empty.\n", DS->legend());
return CpptrajState::ERR;
}
// Restrict to 1D sets for now TODO more types
if (DS->Group() != DataSet::SCALAR_1D) {
mprinterr("Error: Currently only works for 1D scalar data sets.\n");
return CpptrajState::ERR;
}
DataSet_1D* ds1 = (DataSet_1D*)DS;
// Output data set
DataSet* out = 0;
if (name.empty()) {
// Modifying this set. Create new temporary set.
out = State.DSL().Allocate( ds1->Type() );
if (out == 0) return CpptrajState::ERR;
*out = *ds1;
mprintf("\tOverwriting set '%s'\n", ds1->legend());
} else {
// Write to new set
MetaData md = ds1->Meta();
md.SetName( name );
out = State.DSL().AddSet(ds1->Type(), md);
if (out == 0) return CpptrajState::ERR;
mprintf("\tNew set is '%s'\n", out->Meta().PrintName().c_str());
}
out->Allocate(DataSet::SizeArray(1, ds1->Size()));
if (points.Empty()) {
// Drop by start/stop/offset. Set defaults if needed
if (start < 0) start = 0;
if (stop < 0) stop = ds1->Size();
if (offset < 0) offset = 1;
mprintf("\t%sping points from %i to %i, step %i\n", mode, start+1, stop, offset);
for (int idx = start; idx < stop; idx += offset)
points.AddToRange( idx );
} // TODO check that range values are valid?
if (State.Debug() > 0) mprintf("DEBUG: Keeping points:");
Range::const_iterator pt = points.begin();
int idx = 0;
int odx = 0;
if (drop) {
// Drop points
for (; idx < (int)ds1->Size(); idx++) {
if (pt == points.end()) break;
if (*pt != idx) {
if (State.Debug() > 0) mprintf(" %i", idx + 1);
KeepPoint(ds1, out, idx, odx);
} else
++pt;
}
// Keep all remaining points
for (; idx < (int)ds1->Size(); idx++) {
if (State.Debug() > 0) mprintf(" %i", idx + 1);
KeepPoint(ds1, out, idx, odx);
}
} else {
// Keep points
for (; pt != points.end(); pt++) {
if (*pt >= (int)ds1->Size()) break;
if (State.Debug() > 0) mprintf(" %i", *pt + 1);
KeepPoint(ds1, out, *pt, odx);
}
}
if (State.Debug() > 0) mprintf("\n");
if (name.empty()) {
// Replace old set with new set
State.DSL().RemoveSet( ds1 );
State.DSL().AddSet( out );
}
} // END loop over sets
ds_arg = argIn.GetStringNext();
} // END loop over set args
return CpptrajState::OK;
}
