int Action_Esander::AddSet(Energy_Sander::Etype typeIn, DataSetList& DslIn, DataFile* outfile,
std::string const& setname)
{
Esets_[typeIn] = DslIn.AddSet(DataSet::DOUBLE, MetaData(setname, Energy_Sander::Easpect(typeIn)));
if (Esets_[typeIn] == 0) return 1;
if (outfile != 0) outfile->AddDataSet( Esets_[typeIn] );
return 0;
}
int Action_Energy::AddSet(Etype typeIn, DataSetList& DslIn, DataFile* outfile,
std::string const& setname)
{
Energy_[typeIn] = DslIn.AddSet(DataSet::DOUBLE, MetaData(setname, Estring[typeIn]));
if (Energy_[typeIn] == 0) return 1;
if (outfile != 0) outfile->AddDataSet( Energy_[typeIn] );
return 0;
}
// DataIO_OpenDx::ReadData()
int DataIO_OpenDx::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
// Add grid data set. Default to float for now.
DataSet* ds = datasetlist.AddSet( DataSet::GRID_FLT, dsname, "GRID" );
if (ds==0) return 1;
if (LoadGrid(fname.full(), *ds)) {
// Load failed. Erase grid data set.
datasetlist.RemoveSet( ds );
return 1;
}
return 0;
}
// Analysis_Hist::Setup()
Analysis::RetType Analysis_Hist::ExternalSetup(DataSet_1D* dsIn, std::string const& histname,
int setidx, std::string const& outfilenameIn,
bool minArgSetIn, double minIn,
bool maxArgSetIn, double maxIn,
double stepIn, int binsIn, double tempIn,
NormMode normIn,
DataSetList& datasetlist, DataFileList& DFLin)
{
debug_ = 0;
if (dsIn == 0) return Analysis::ERR;
outfilename_ = outfilenameIn;
outfile_ = DFLin.AddDataFile(outfilename_);
Temp_ = tempIn;
if (Temp_ != -1.0)
calcFreeE_ = true;
else
calcFreeE_ = false;
gnuplot_ = false;
normalize_ = normIn;
circular_ = false;
nativeOut_ = false;
minArgSet_ = minArgSetIn;
if (minArgSet_)
default_min_ = minIn;
maxArgSet_ = maxArgSetIn;
if (maxArgSet_)
default_max_ = maxIn;
default_step_ = stepIn;
default_bins_ = binsIn;
calcAMD_ = false;
amddata_ = 0;
dimensionArgs_.push_back( ArgList(dsIn->Meta().Legend()) ); // Needed for dim label
histdata_.push_back( dsIn );
N_dimensions_ = 1;
std::string setname = histname;
std::string htype;
if (calcFreeE_)
htype = "FreeE_";
else
htype = "Hist_";
if (setname.empty())
setname = datasetlist.GenerateDefaultName(htype + dsIn->Meta().Name());
hist_ = datasetlist.AddSet( DataSet::DOUBLE, MetaData(setname, dsIn->Meta().Aspect(), setidx) );
if (hist_ == 0) return Analysis::ERR;
hist_->SetLegend(htype + dsIn->Meta().Legend());
if (outfile_ != 0) outfile_->AddDataSet( hist_ );
return Analysis::OK;
}
Analysis::RetType Analysis_KDE::ExternalSetup(DataSet_1D* dsIn, std::string const& histname,
int setidx, std::string const& outfilenameIn,
bool minArgSetIn, double minIn,
bool maxArgSetIn, double maxIn,
double stepIn, int binsIn, double tempIn,
DataSetList& datasetlist, DataFileList& DFLin)
{
if (dsIn == 0) return Analysis::ERR;
data_ = dsIn;
q_data_ = 0;
kldiv_ = 0;
amddata_ = 0;
bandwidth_ = -1.0;
minArgSet_ = minArgSetIn;
if (minArgSet_)
default_min_ = minIn;
maxArgSet_ = maxArgSetIn;
if (maxArgSet_)
default_max_ = maxIn;
default_step_ = stepIn;
default_bins_ = binsIn;
Temp_ = tempIn;
if (Temp_ != -1.0)
calcFreeE_ = true;
else
calcFreeE_ = false;
std::string setname = histname;
std::string htype;
if (calcFreeE_)
htype = "FreeE_";
else
htype = "KDE_";
if (setname.empty())
setname = datasetlist.GenerateDefaultName(htype + dsIn->Meta().Name());
DataFile* outfile = DFLin.AddDataFile( outfilenameIn );
output_ = datasetlist.AddSet(DataSet::DOUBLE, MetaData(setname, dsIn->Meta().Aspect(), setidx));
if (output_ == 0) return Analysis::ERR;
output_->SetLegend(htype + dsIn->Meta().Legend());
if (outfile != 0) outfile->AddDataSet( output_ );
return Analysis::OK;
}
// Exec_SortEnsembleData::Sort_pH_Data()
int Exec_SortEnsembleData::Sort_pH_Data(DataSetList const& setsToSort, DataSetList& OutputSets,
unsigned int maxFrames)
const
{
// Cast sets back to DataSet_PHREMD
typedef std::vector<DataSet_PHREMD*> Parray;
Parray PHsets;
for (DataSetList::const_iterator ds = setsToSort.begin(); ds != setsToSort.end(); ++ds)
PHsets.push_back( (DataSet_PHREMD*)*ds );
// Gather initial pH data values, ensure no duplicates
typedef std::vector<double> Darray;
Darray pHvalues;
# ifdef MPI
pHvalues.resize( Parallel::Ensemble_Size() );
Darray phtmp;
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
phtmp.push_back( (*ds)->Initial_pH() );
if (comm_.AllGather(&phtmp[0], phtmp.size(), MPI_DOUBLE, &pHvalues[0])) {
rprinterr("Error: Gathering pH values.\n");
return 1;
}
# else
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
pHvalues.push_back( (*ds)->Initial_pH() );
# endif
ReplicaInfo::Map<double> pH_map;
if (pH_map.CreateMap( pHvalues )) {
rprinterr("Error: Duplicate pH value detected (%.2f) in ensemble.\n", pH_map.Duplicate());
return 1;
}
Darray sortedPH;
mprintf("\tInitial pH values:");
for (ReplicaInfo::Map<double>::const_iterator ph = pH_map.begin(); ph != pH_map.end(); ++ph)
{
mprintf(" %6.2f", ph->first);
sortedPH.push_back( ph->first );
}
mprintf("\n");
// Create sets to hold sorted pH values. Create a set for each pH value
// and each residue. Final output sets will be PH0R0, PH0R1, PH1R0, ...
// TODO check that residue info all the same
DataSet_PHREMD::Rarray const& Residues = PHsets[0]->Residues();
int defaultState = 0;
# ifdef MPI
if ( PHsets[0]->Type() == DataSet::PH_IMPL)
defaultState = -1;
# endif
if (debug_ > 0)
rprintf("DEBUG: Sorting %u frames for %zu sets, %zu pH values.\n",
maxFrames, PHsets.size(), sortedPH.size());
for (unsigned int idx = 0; idx != sortedPH.size(); idx++) {
OutputSets.SetEnsembleNum( idx );
for (unsigned int res = 0; res != Residues.size(); ++res) {
MetaData md(PHsets[0]->Meta().Name(), Residues[res].Name().Truncated(), Residues[res].Num());
DataSet_pH* out = (DataSet_pH*)OutputSets.AddSet( DataSet::PH, md );
if (out==0) return 1;
//out->SetLegend( "pH " + doubleToString( sortedPH[idx] ) );
out->Set_Solvent_pH( sortedPH[idx] );
out->SetResidueInfo( Residues[res] );
out->SetTimeValues(PHsets[0]->Time());
out->Resize( maxFrames, defaultState );
}
}
// ---------------------------------------------
if ( PHsets[0]->Type() == DataSet::PH_EXPL) {
// Loop over unsorted sets
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
{
DataSet_PHREMD_Explicit* in = (DataSet_PHREMD_Explicit*)*ds;
unsigned int phidx = 0;
for (unsigned int n = 0; n < maxFrames; n++)
{
float phval = in->pH_Values()[n];
int setidx = pH_map.FindIndex( phval ) * Residues.size();
//rprintf("DEBUG: %6u Set %10s pH= %6.2f going to %2i\n", n+1, in->legend(), phval, idx);
//mflush();
for (unsigned int res = 0; res < in->Residues().size(); res++, setidx++, phidx++)
{
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx];
//if (res == 0 && idx == 0) {
// rprintf("DEBUG: Frame %3u res %2u State %2i pH %6.2f\n",
// n, res, in->Res(res).State(n), phval);
// mflush();
//}
out->SetState(n, in->ResStates()[phidx], in->RecordType(n));
}
}
} // END loop over unsorted sets
# ifdef MPI
// Now we need to reduce down each set onto the thread where it belongs.
if (Parallel::World().Size() > 1) {
for (int idx = 0; idx != (int)OutputSets.size(); idx++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[idx];
int ensembleRank = Parallel::MemberEnsCommRank( out->Meta().EnsembleNum() );
//rprintf("DEBUG: Reduce set %s to rank %i\n", out->legend(), ensembleRank);
out->Reduce( comm_, ensembleRank );
}
// Remove sets that do not belong on this rank
for (int idx = (int)OutputSets.size() - 1; idx > -1; idx--) {
DataSet* out = OutputSets[idx];
int ensembleRank = Parallel::MemberEnsCommRank( out->Meta().EnsembleNum() );
if (ensembleRank != comm_.Rank()) {
//rprintf("DEBUG: Remove set %s (%i) from rank %i\n", out->legend(),
// idx, comm_.Rank());
OutputSets.RemoveSet( out );
}
}
}
# endif
// ---------------------------------------------
} else if ( PHsets[0]->Type() == DataSet::PH_IMPL) {
# ifdef MPI
typedef std::vector<int> Iarray;
typedef std::vector<Iarray> Iarray2;
typedef std::vector<bool> Barray;
// True if I have this pH value
Barray isMyPh( sortedPH.size(), false );
// Which rank in ensemble has which pH
Iarray pHrank( sortedPH.size(), 0 );
for (int phidx = 0; phidx != (int)sortedPH.size(); phidx++)
{
int ensembleRank = Parallel::MemberEnsCommRank( phidx );
pHrank[phidx] = ensembleRank;
isMyPh[phidx] = (ensembleRank == comm_.Rank());
}
// DEBUG
for (unsigned int idx = 0; idx != pHrank.size(); idx++)
mprintf("\tpH %6.2f on rank %i\n", sortedPH[idx], pHrank[idx]);
// Hold frame-residue-state for each pH not on this rank.
Iarray2 FrmResState( sortedPH.size() );
// Loop over unsorted sets
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
{
DataSet_PHREMD_Implicit* in = (DataSet_PHREMD_Implicit*)*ds;
// Loop over frames
for (unsigned int n = 0; n < maxFrames; n++)
{
DataSet_PHREMD_Implicit::Record const& Rec = in->Records()[n];
float phval = Rec.pH();
int phidx = pH_map.FindIndex( phval );
if (isMyPh[phidx]) {
// This pH belongs to me. Set value.
int setidx = phidx * Residues.size();
if (Rec.RecType() == Cph::FULL_RECORD) {
// Info for all residues
for (unsigned int res = 0; res < in->Residues().size(); res++, setidx++)
((DataSet_pH*)OutputSets[setidx])->SetState(n, Rec.ResStates()[res], Rec.RecType());
} else if (Rec.RecType() > -1) {
// Info for single residue, record type for all residues
//rprintf("\tSetting my pH %6.2f frame %8i state %2i idx %6i res %6i '%s'\n", sortedPH[phidx], n, Rec.ResStates()[0], setidx, Rec.RecType(), OutputSets[setidx+Rec.RecType()]->legend());
for (int res = 0; res < (int)in->Residues().size(); res++, setidx++)
if (res == Rec.RecType())
((DataSet_pH*)OutputSets[setidx])->SetState(n, Rec.ResStates()[0], Rec.RecType());
else
((DataSet_pH*)OutputSets[setidx])->SetRecType(n, Rec.RecType());
}
} else {
// This pH belongs to another rank. Save it.
if (Rec.RecType() > -1) {
// Info for a single residue present
FrmResState[phidx].push_back( n );
FrmResState[phidx].push_back( Rec.RecType() );
FrmResState[phidx].push_back( Rec.ResStates()[0] );
} else {
// Info for all residues present
FrmResState[phidx].push_back( n );
FrmResState[phidx].push_back( Rec.RecType() );
for (unsigned int res = 0; res < in->Residues().size(); res++)
FrmResState[phidx].push_back( Rec.ResStates()[res] );
}
}
} // END loop over frames
} // END loop over sets
// DEBUG
/*
comm_.Barrier();
for (int rank = 0; rank < comm_.Size(); rank++)
{
if (rank == comm_.Rank())
{
for (unsigned int phidx = 0; phidx != sortedPH.size(); phidx++) {
rprintf("DEBUG: pH %6.2f: %8s %6s %2s\n", sortedPH[phidx], "Frm", "Res", "St");
Iarray const& FRS = FrmResState[phidx];
unsigned int idx = 0;
while (idx < FRS.size()) {
int rec = FRS[idx+1];
if (rec > -1) {
rprintf(" %8i %6i %2i\n", FRS[idx], rec, FRS[idx+2]);
idx += 3;
} else {
rprintf(" %8i %6i All Residues\n", FRS[idx], rec);
idx += (2 + Residues.size());
}
}
}
}
comm_.Barrier();
}
*/
// Communicate states to other ranks
typedef std::vector<unsigned int> Uarray;
Uarray sizeOnRank( comm_.Size() );
for (unsigned int phidx = 0; phidx != sortedPH.size(); phidx++)
{
// Each rank says how many frames of this pH they have collected and
// send to rank the pH belongs to.
unsigned int nph = FrmResState[phidx].size();
comm_.Gather(&nph, 1, MPI_UNSIGNED, &sizeOnRank[0], pHrank[phidx]);
if (pHrank[phidx] == comm_.Rank())
{
// This pH belongs to me. I should have no frames at this pH.
if (sizeOnRank[comm_.Rank()] > 0) {
rprinterr("Internal Error: Rank has frames to communicate at its pH\n");
Parallel::Abort(1);
}
unsigned int totalSize = 0;
for (unsigned int idx = 0; idx != sizeOnRank.size(); idx++) {
totalSize += sizeOnRank[idx];
//rprintf("DEBUG: Rank %4u has %8u frames of pH %6.2f\n",
// idx, sizeOnRank[idx], sortedPH[phidx]);
}
//rprintf("DEBUG: Total incoming size: %u\n", totalSize);
FrmResState[phidx].resize( totalSize );
// Receive state info for this pH from other ranks
int* frsArray = &(FrmResState[phidx][0]);
for (int rank = 0; rank != comm_.Size(); rank++) {
if (rank != comm_.Rank()) {
comm_.Recv(frsArray, sizeOnRank[rank], MPI_INT, rank, 1600+rank);
frsArray += sizeOnRank[rank];
}
}
} else {
// This pH belongs to another rank. Send my info there.
int* frsArray = &(FrmResState[phidx][0]);
comm_.Send(frsArray, nph, MPI_INT, pHrank[phidx], 1600+comm_.Rank());
}
comm_.Barrier();
}
// Fill in state info
std::vector<DataSet*> ToRemove;
for (unsigned int phidx = 0; phidx != sortedPH.size(); phidx++)
{
int setidx = phidx * Residues.size();
if (pHrank[phidx] == comm_.Rank())
{
Iarray const& FRS = FrmResState[phidx];
// This pH belongs to me. Fill in the information received from
// other ranks.
unsigned int idx = 0;
while (idx < FRS.size()) {
int rec = FRS[idx+1];
if (rec > -1) {
// Info for single residue, record type for all residues
//rprintf("\tSetting pH %6.2f frame %8i state %2i idx %6i res %6i '%s'\n", sortedPH[phidx], FRS[idx], FRS[idx+2], setidx, rec, OutputSets[setidx+rec]->legend());
for (int res = 0; res != (int)Residues.size(); res++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx + res];
if (rec == res)
out->SetState( FRS[idx], FRS[idx+2], rec );
else
out->SetRecType( FRS[idx], rec );
}
idx += 3;
} else {
//rprintf(" %8i %6i All Residues\n", FRS[idx], rec);
int frm = FRS[idx];
idx += 2;
for (unsigned int res = 0; res != Residues.size(); res++, idx++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx + res];
out->SetState( frm, FRS[idx], rec );
}
}
}
// Fill in any remaining data. FIXME safe to assume first frame is set?
for (unsigned int res = 0; res != Residues.size(); res++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx + res];
for (unsigned int n = 1; n < maxFrames; n++)
if (out->State(n) == -1)
out->SetState(n, out->State(n-1), out->RecordType(n));
}
} else {
// This pH does not belong to me. Mark associated data sets to be removed.
for (unsigned int res = 0; res != Residues.size(); res++)
ToRemove.push_back( OutputSets[setidx + res] );
}
}
// Remove data sets that do not belong to me.
for (std::vector<DataSet*>::reverse_iterator it = ToRemove.rbegin();
it != ToRemove.rend(); ++it)
{
//rprintf("DEBUG: '%s' does not belong to me.\n", (*it)->legend());
OutputSets.RemoveSet( *it );
}
# else /* if not MPI */
// Loop over frames
for (unsigned int n = 0; n < maxFrames; n++)
{
// Loop over unsorted sets
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
{
DataSet_PHREMD_Implicit* in = (DataSet_PHREMD_Implicit*)*ds;
DataSet_PHREMD_Implicit::Record const& Rec = in->Records()[n];
float phval = Rec.pH();
int setidx = pH_map.FindIndex( phval ) * Residues.size();
if (Rec.RecType() == Cph::FULL_RECORD) {
for (unsigned int res = 0; res < in->Residues().size(); res++, setidx++)
{
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx];
//if (res == 0 && idx == 0) {
// rprintf("DEBUG: Frame %3u res %2u State %2i pH %6.2f\n",
// n, res, in->Res(res).State(n), phval);
// mflush();
//}
out->SetState(n, Rec.ResStates()[res], Rec.RecType());
}
} else {
for (int res = 0; res < (int)in->Residues().size(); res++, setidx++)
{
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx];
if (res == Rec.RecType())
out->SetState(n, Rec.ResStates()[0], Rec.RecType());
else
// State for this residue not recorded - use previous state.
// Should be fine since first state always has all residues.
out->SetState(n, out->State(n-1), Rec.RecType());
}
}
} // END loop over unsorted sets
} // END loop over frames
# endif /* MPI */
// ---------------------------------------------
} else {
return 1; // Sanity check
}
return 0;
}
/** Header is 256 4-byte words. Integer unless otherwise noted. First 56 words are:
* 0-2: columns, rows, sections (fastest changing to slowest)
* 3: mode: 0 = envelope stored as signed bytes (from -128 lowest to 127 highest)
* 1 = Image stored as Integer*2
* 2 = Image stored as Reals
* 3 = Transform stored as Complex Integer*2
* 4 = Transform stored as Complex Reals
* 5 == 0
* 4-6: Column, row, and section offsets
* 7-9: Intervals along X, Y, Z
* 10-15: float; 3x cell lengths (Ang) and 3x cell angles (deg)
* 16-18: Map of which axes correspond to cols, rows, sections (1,2,3 = x,y,z)
* 19-21: float; Min, max, and mean density
* 22-24: Space group, bytes used for storing symm ops, flag for skew transform
* If skew flag != 0, skew transformation is from standard orthogonal
* coordinate frame (as used for atoms) to orthogonal map frame, as:
* Xo(map) = S * (Xo(atoms) - t)
* 25-33: Skew matrix 'S' (in order S11, S12, S13, S21 etc)
* 34-36: Skew translation 't'
* 37-51: For future use and can be skipped.
* 52: char; 'MAP '
* 53: char; machine stamp for determining endianness
* 54: float; RMS deviation of map from mean
* 55: Number of labels
*/
int DataIO_CCP4::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
CpptrajFile infile;
if (infile.OpenRead( fname )) return 1;
// Read first 56 words of the header into a buffer.
headerbyte buffer;
if (infile.Read(buffer.i, 224*sizeof(unsigned char)) < 1) {
mprinterr("Error: Could not buffer CCP4 header.\n");
return 1;
}
if (debug_ > 0)
mprintf("DEBUG: MAP= '%c %c %c %c' MACHST= '%x %x %x %x'\n",
buffer.c[208], buffer.c[209], buffer.c[210], buffer.c[211],
buffer.c[212], buffer.c[213], buffer.c[214], buffer.c[215]);
// SANITY CHECK
if (!MapCharsValid(buffer.c + 208)) {
mprinterr("Error: CCP4 file missing 'MAP ' string at word 53\n");
return 1;
}
// Check endianess
bool isBigEndian = (buffer.c[212] == 0x11 && buffer.c[213] == 0x11 &&
buffer.c[214] == 0x00 && buffer.c[215] == 0x00);
if (!isBigEndian) {
if (debug_ > 0) mprintf("DEBUG: Little endian.\n");
// SANITY CHECK
if ( !(buffer.c[212] == 0x44 && buffer.c[213] == 0x41 &&
buffer.c[214] == 0x00 && buffer.c[215] == 0x00) )
mprintf("Warning: Invalid machine stamp: %x %x %x %x : assuming little endian.\n",
buffer.c[212], buffer.c[213], buffer.c[214], buffer.c[215]);
} else {
if (debug_ > 0) mprintf("DEBUG: Big endian.\n");
// Perform endian swapping on header if necessary
endian_swap(buffer.i, 56);
}
// Print DEBUG info
if (debug_ > 0) {
mprintf("DEBUG: Columns=%i Rows=%i Sections=%i\n", buffer.i[0], buffer.i[1], buffer.i[2]);
mprintf("DEBUG: Mode=%i\n", buffer.i[3]);
mprintf("DEBUG: Offsets: C=%i R=%i S=%i\n", buffer.i[4], buffer.i[5], buffer.i[6]);
mprintf("DEBUG: NXYZ={ %i %i %i }\n", buffer.i[7], buffer.i[8], buffer.i[9]);
mprintf("DEBUG: Box XYZ={ %f %f %f } ABG={ %f %f %f }\n",
buffer.f[10], buffer.f[11], buffer.f[12],
buffer.f[13], buffer.f[14], buffer.f[15]);
mprintf("DEBUG: Map: ColAxis=%i RowAxis=%i SecAxis=%i\n",
buffer.i[16], buffer.i[17], buffer.i[18]);
mprintf("DEBUG: SpaceGroup#=%i SymmOpBytes=%i SkewFlag=%i\n",
buffer.i[22], buffer.i[23], buffer.i[24]);
const int* MSKEW = buffer.i + 25;
mprintf("DEBUG: Skew matrix: %i %i %i\n"
" %i %i %i\n"
" %i %i %i\n", MSKEW[0], MSKEW[1], MSKEW[2], MSKEW[3],
MSKEW[4], MSKEW[5], MSKEW[6], MSKEW[7], MSKEW[8]);
const int* TSKEW = buffer.i + 34;
mprintf("DEBUG: Skew translation: %i %i %i\n", TSKEW[0], TSKEW[1], TSKEW[2]);
mprintf("DEBUG: Nlabels=%i\n", buffer.i[55]);
}
// Check input data. Only support mode 2 for now.
if (buffer.i[3] != 2) {
mprinterr("Error: Mode %i; currently only mode 2 for CCP4 files is supported.\n", buffer.i[3]);
return 1;
}
// Check offsets.
if (buffer.i[4] != 0 || buffer.i[5] != 0 || buffer.i[6] != 0)
mprintf("Warning: Non-zero offsets present. This is not yet supported and will be ignored.\n");
// Check that mapping is col=x row=y section=z
if (buffer.i[16] != 1 || buffer.i[17] != 2 || buffer.i[18] != 3) {
mprinterr("Error: Currently only support cols=X, rows=Y, sections=Z\n");
return 1;
}
if (buffer.i[24] != 0) {
mprintf("Warning: Skew information present but not yet supported and will be ignored.\n");
return 1;
}
// Read 10 80 character text labels
char Labels[801];
Labels[800] = '\0';
infile.Read( Labels, 200*wSize );
mprintf("\t%s\n", Labels);
// Symmetry records: operators separated by * and grouped into 'lines' of 80 characters
int NsymmRecords = buffer.i[23] / 80;
if (NsymmRecords > 0) {
char symBuffer[81];
mprintf("\t%i symmetry records.\n", NsymmRecords);
for (int ib = 0; ib != NsymmRecords; ib++) {
infile.Gets( symBuffer, 80 );
mprintf("\t%s\n", symBuffer);
}
}
// Add grid data set. Default to float for now.
DataSet* gridDS = datasetlist.AddSet( DataSet::GRID_FLT, dsname, "GRID" );
if (gridDS == 0) return 1;
DataSet_GridFlt& grid = static_cast<DataSet_GridFlt&>( *gridDS );
// Allocate grid from dims and spacing. FIXME OK to assume zero origin?
if (grid.Allocate_N_O_Box( buffer.i[7], buffer.i[8], buffer.i[9],
Vec3(0.0), Box(buffer.f + 10) ) != 0)
{
mprinterr("Error: Could not allocate grid.\n");
return 1;
}
// FIXME: Grids are currently indexed so Z is fastest changing.
// Should be able to change indexing in grid DataSet.
size_t mapSize = buffer.i[7] * buffer.i[8] * buffer.i[9];
mprintf("\tCCP4 map has %zu elements\n", mapSize);
mprintf("\tDensity: Min=%f Max=%f Mean=%f RMS=%f\n",
buffer.f[19], buffer.f[20], buffer.f[21], buffer.f[54]);
std::vector<float> mapbuffer( mapSize );
int mapBytes = mapSize * wSize;
int numRead = infile.Read( &mapbuffer[0], mapBytes );
if (numRead < 1) {
mprinterr("Error: Could not read CCP4 map data.\n");
return 1;
} else if (numRead < mapBytes)
mprintf("Warning: Expected %i bytes, read only %i bytes\n", mapBytes, numRead);
if (isBigEndian) endian_swap(&mapbuffer[0], mapSize);
// FIXME: Place data into grid DataSet with correct ordering.
int gidx = 0;
int NXY = buffer.i[7] * buffer.i[8];
for (int ix = 0; ix != buffer.i[7]; ix++)
for (int iy = 0; iy != buffer.i[8]; iy++)
for (int iz = 0; iz != buffer.i[9]; iz++) {
int midx = (iz * NXY) + (iy * buffer.i[7]) + ix;
grid[gidx++] = mapbuffer[midx];
}
infile.CloseFile();
return 0;
}
// DataIO_Std::Read_3D()
int DataIO_Std::Read_3D(std::string const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
mprintf("\tData will be read as 3D grid: X Y Z Value\n");
if (binCorners_)
mprintf("\tAssuming X Y Z are bin corners\n");
else
mprintf("\tAssuming X Y Z are bin centers\n");
const char* ptr = buffer.Line();
// Check if #counts is present
if (strncmp(ptr,"#counts",7)==0) {
mprintf("\tReading grid dimensions.\n");
unsigned int counts[3];
sscanf(ptr+7,"%u %u %u", counts, counts+1, counts+2);
for (int i = 0; i < 3; i++) {
if (dims_[i] == 0)
dims_[i] = counts[i];
else if (dims_[i] != (size_t)counts[i])
mprintf("Warning: Specified size for dim %i (%zu) differs from size in file (%u)\n",
i, dims_[i], counts[i]);
}
ptr = buffer.Line();
}
if (dims_[0] == 0 || dims_[1] == 0 || dims_[2] == 0) {
mprinterr("Error: 'dims' not specified for 'read3d' and no dims in file\n");
return 1;
}
// Check if #origin is present
if (strncmp(ptr,"#origin",7)==0) {
mprintf("\tReading grid origin.\n");
double oxyz[3];
sscanf(ptr+7,"%lf %lf %lf", oxyz, oxyz+1, oxyz+2);
for (int i = 0; i < 3; i++) {
if (!originSpecified_)
origin_[i] = oxyz[i];
else if (origin_[i] != oxyz[i])
mprintf("Warning: Specified origin for dim %i (%g) differs from origin in file (%g)\n",
i, origin_[i], oxyz[i]);
}
ptr = buffer.Line();
}
// Check if #delta is present
bool nonortho = false;
Box gridBox;
if (strncmp(ptr,"#delta",6)==0) {
mprintf("\tReading grid deltas.\n");
double dvals[9];
int ndvals = sscanf(ptr+6,"%lf %lf %lf %lf %lf %lf %lf %lf %lf", dvals,
dvals+1, dvals+2, dvals+3, dvals+4, dvals+5,
dvals+6, dvals+7, dvals+8);
if (ndvals == 3) {
for (int i = 0; i < 3; i++) {
if (!deltaSpecified_)
delta_[i] = dvals[i];
else if (delta_[i] != dvals[i])
mprintf("Warning: Specified delta for dim %i (%g) differs from delta in file (%g)\n",
i, delta_[i], dvals[i]);
}
} else {
nonortho = true;
dvals[0] *= (double)dims_[0]; dvals[1] *= (double)dims_[0]; dvals[2] *= (double)dims_[0];
dvals[3] *= (double)dims_[1]; dvals[4] *= (double)dims_[1]; dvals[5] *= (double)dims_[1];
dvals[6] *= (double)dims_[2]; dvals[7] *= (double)dims_[2]; dvals[8] *= (double)dims_[2];
gridBox = Box(Matrix_3x3(dvals));
}
ptr = buffer.Line();
}
// Get or allocate data set
DataSet::DataType dtype;
if (prec_ == DOUBLE) {
dtype = DataSet::GRID_DBL;
mprintf("\tGrid is double precision.\n");
} else {
dtype = DataSet::GRID_FLT;
mprintf("\tGrid is single precision.\n");
}
MetaData md( dsname );
DataSet_3D* ds = 0;
DataSet* set = datasetlist.CheckForSet( md );
if (set == 0) {
ds = (DataSet_3D*)datasetlist.AddSet(dtype, dsname);
if (ds == 0) return 1;
int err = 0;
if (nonortho)
err = ds->Allocate_N_O_Box(dims_[0], dims_[1], dims_[2], origin_, gridBox);
else
err = ds->Allocate_N_O_D(dims_[0], dims_[1], dims_[2], origin_, delta_);
if (err != 0) return 1;
} else {
mprintf("\tAppending to existing set '%s'\n", set->legend());
if (set->Group() != DataSet::GRID_3D) {
mprinterr("Error: Set '%s' is not a grid set, cannot append.\n", set->legend());
return 1;
}
ds = (DataSet_3D*)set;
// Check that dimensions line up. TODO check origin etc too?
if (dims_[0] != ds->NX() ||
dims_[1] != ds->NY() ||
dims_[2] != ds->NZ())
{
mprintf("Warning: Specified grid dimensions (%zu %zu %zu) do not match\n"
"Warning: '%s' dimensions (%zu %zu %zu)\n", dims_[0], dims_[1], dims_[2],
ds->legend(), dims_[0], dims_[1], dims_[2]);
}
}
ds->GridInfo();
// Determine if an offset is needed
Vec3 offset(0.0);
if (binCorners_) {
// Assume XYZ coords are of bin corners. Need to offset coords by half
// the voxel size.
if (!ds->Bin().IsOrthoGrid()) {
GridBin_Nonortho const& b = static_cast<GridBin_Nonortho const&>( ds->Bin() );
offset = b.Ucell().TransposeMult(Vec3( 1/(2*(double)ds->NX()),
1/(2*(double)ds->NY()),
1/(2*(double)ds->NZ()) ));
} else {
GridBin_Ortho const& b = static_cast<GridBin_Ortho const&>( ds->Bin() );
offset = Vec3(b.DX()/2, b.DY()/2, b.DZ()/2);
}
}
if (debug_ > 0)
mprintf("DEBUG: Offset: %E %E %E\n", offset[0], offset[1], offset[2]);
// Read file
unsigned int nvals = 0;
while (ptr != 0) {
if (ptr[0] != '#') {
int ntokens = buffer.TokenizeLine( SEPARATORS );
if (ntokens != 4) {
mprinterr("Error: Expected 4 columns (X, Y, Z, data), got %i\n", ntokens);
return 1;
}
nvals++;
double xyzv[4];
xyzv[0] = atof( buffer.NextToken() );
xyzv[1] = atof( buffer.NextToken() );
xyzv[2] = atof( buffer.NextToken() );
xyzv[3] = atof( buffer.NextToken() );
size_t ix, iy, iz;
if ( ds->Bin().Calc(xyzv[0]+offset[0],
xyzv[1]+offset[1],
xyzv[2]+offset[2], ix, iy, iz ) )
ds->UpdateVoxel(ds->CalcIndex(ix, iy, iz), xyzv[3]);
else
mprintf("Warning: Coordinate out of bounds (%g %g %g, ), line %i\n",
xyzv[0], xyzv[1], xyzv[2], buffer.LineNumber());
}
ptr = buffer.Line();
}
mprintf("\tRead %u values.\n", nvals);
return 0;
}
/** Read cluster matrix file. Can only get here if file has already been
* determined to be in the proper format, so do no further error checking.
* Expected format:
* <int> <int> <name>
*/
int DataIO_Std::ReadCmatrix(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
// Allocate output data set
DataSet* ds = datasetlist.AddSet( DataSet::CMATRIX, dsname );
if (ds == 0) return 1;
DataSet_Cmatrix_MEM& Mat = static_cast<DataSet_Cmatrix_MEM&>( *ds );
// Buffer file
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
// Read past title. See if optional 'nframes' key is there.
const char* ptr = buffer.Line();
ArgList header;
header.SetList(ptr+1, SEPARATORS );
int nframes = header.getKeyInt("nframes", -1);
// Need to keep track of frame indices so we can check for sieving.
std::vector<char> sieveStatus;
if (nframes > 0)
sieveStatus.assign(nframes, 'T');
// Keep track of matrix values.
std::vector<float> Vals;
// Read file
bool checkSieve = true;
int f1 = -1, f2 = -1, firstf1 = -1;
float val = 0;
while ( (ptr = buffer.Line()) != 0 )
{
if (checkSieve) {
sscanf(ptr, "%i %i %f", &f1, &f2, &val);
if (f2 > (int)sieveStatus.size())
sieveStatus.resize(f2, 'T');
if (firstf1 == -1) {
// First values.
sieveStatus[f1-1] = 'F';
sieveStatus[f2-1] = 'F';
firstf1 = f1;
} else if (f1 > firstf1) {
checkSieve = false;
} else {
sieveStatus[f2-1] = 'F';
}
} else {
sscanf(ptr, "%*i %*i %f", &val);
}
Vals.push_back( val );
}
// DEBUG
//mprintf("Sieved array:\n");
//for (unsigned int i = 0; i < sieveStatus.size(); i++)
// mprintf("\t%6u %c\n", i+1, sieveStatus[i]);
// Try to determine if sieve is random or not.
int sieveDelta = 1;
f1 = -1;
f2 = -1;
int actual_nrows = 0;
for (int i = 0; i < (int)sieveStatus.size(); i++) {
if (sieveStatus[i] == 'F') {
actual_nrows++;
if (sieveDelta != -2) {
if (f1 == -1) {
f1 = i;
} else if (f2 == -1) {
sieveDelta = i - f1;
f1 = i;
f2 = i;
} else {
int newDelta = i - f1;
if (newDelta != sieveDelta) {
// Random. No need to calculate sieveDelta anymore.
sieveDelta = -2;
}
f1 = i;
}
}
}
}
if (sieveDelta == -2) {
// Random sieve. Try to figure out original sieve value.
int o_frames = (int)sieveStatus.size();
int o_sieve_value = o_frames / actual_nrows;
if ( (o_frames % actual_nrows) != 0 )
o_sieve_value++;
sieveDelta = -o_sieve_value;
}
if (debug_ > 0)
mprintf("DEBUG: sieve %i, actual_nrows= %i\n", sieveDelta, actual_nrows);
if (sieveDelta != 1 && nframes == -1)
mprintf("Warning: Pairwise distance matrix file contains sieved frames but\n"
"Warning: number of original frames is not present in file - this\n"
"Warning: may lead to ignored frames in cluster output. Please add\n"
"Warning: 'nframes <# original frames>' to the pairwise distance\n"
"Warning: matrix file header, e.g. '#F1 F2 pw.dat nframes 1000'.\n");
// Save cluster matrix
if (Mat.Allocate( DataSet::SizeArray(1, actual_nrows) )) return 1;
std::copy( Vals.begin(), Vals.end(), Mat.Ptr() );
Mat.SetSieveFromArray(sieveStatus, sieveDelta);
return 0;
}