// DataIO_CCP4::ID_DataFormat()
bool DataIO_CCP4::ID_DataFormat( CpptrajFile& infile ) {
bool isCCP4 = false;
if (!infile.OpenFile()) {
unsigned char MAP[4];
if (infile.Seek(52 * wSize) == 0) {
infile.Read( MAP, wSize );
isCCP4 = MapCharsValid( MAP );
}
infile.CloseFile();
}
return isCCP4;
}
/** \return true if TRR/TRJ file. Determine endianness. */
bool Traj_GmxTrX::IsTRX(CpptrajFile& infile) {
int magic;
if ( infile.Read( &magic, 4 ) != 4 ) return 1;
if (magic != Magic_) {
// See if this is big endian
endian_swap( &magic, 1 );
if (magic != Magic_)
return false;
else
isBigEndian_ = true;
} else
isBigEndian_ = false;
// TODO: At this point file is trX, but not sure how best to differentiate
// between TRR and TRJ. For now do it based on extension. Default TRR.
if (infile.Filename().Ext() == ".trr") format_ = TRR;
else if (infile.Filename().Ext() == ".trj") format_ = TRJ;
else format_ = TRR;
return true;
}
/** 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;
}