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Commit eccf6c88 by maarten
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refactored MapMaker 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@240 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 2a2fefa8
Showing with 274 additions and 99 deletions
include/cif++/MapMaker.h
...@@ -7,13 +7,45 @@ ...@@ -7,13 +7,45 @@
namespace libcif namespace libcif
{ {
template<typename FTYPE> template<typename FTYPE>
class MapMaker class Map
{ {
public: public:
typedef FTYPE ftype; typedef FTYPE ftype;
typedef typename clipper::Xmap<ftype> Xmap; typedef typename clipper::Xmap<ftype> Xmap;
Map();
~Map();
void calculateStats();
double rmsDensity() const { return mRMSDensity; }
double meanDensity() const { return mMeanDensity; }
operator Xmap& () { return mMap; }
operator const Xmap& () const { return mMap; }
// These routines work with CCP4 map files
void read(const boost::filesystem::path& f);
void write(const boost::filesystem::path& f);
clipper::Spacegroup spacegroup() const { return mMap.spacegroup(); }
clipper::Cell cell() const { return mMap.cell(); }
private:
Xmap mMap;
double mRMSDensity, mMeanDensity;
};
template<typename FTYPE>
class MapMaker
{
public:
typedef Map<FTYPE> MapType;
typedef typename MapType::Xmap Xmap;
typedef clipper::HKL_data<clipper::data32::F_phi> FPdata; typedef clipper::HKL_data<clipper::data32::F_phi> FPdata;
typedef clipper::HKL_data<clipper::data32::F_sigF> FOdata; typedef clipper::HKL_data<clipper::data32::F_sigF> FOdata;
typedef clipper::HKL_data<clipper::data32::Phi_fom> WData; typedef clipper::HKL_data<clipper::data32::Phi_fom> WData;
...@@ -27,7 +59,7 @@ class MapMaker ...@@ -27,7 +59,7 @@ class MapMaker
as_None, as_Observed, as_Calculated as_None, as_Observed, as_Calculated
}; };
MapMaker(Xmap& fb, Xmap& fd); MapMaker();
~MapMaker(); ~MapMaker();
void loadFromMTZ(const boost::filesystem::path& mtzFile, void loadFromMTZ(const boost::filesystem::path& mtzFile,
...@@ -36,22 +68,27 @@ class MapMaker ...@@ -36,22 +68,27 @@ class MapMaker
std::initializer_list<std::string> fdLabels = { "DELFWT", "PHDELWT" }, std::initializer_list<std::string> fdLabels = { "DELFWT", "PHDELWT" },
std::initializer_list<std::string> foLabels = { "FP", "SIGFP" }, std::initializer_list<std::string> foLabels = { "FP", "SIGFP" },
std::initializer_list<std::string> fcLabels = { "FC_ALL", "PHIC_ALL" }); std::initializer_list<std::string> fcLabels = { "FC_ALL", "PHIC_ALL" });
void recalculateFromMTZ(const boost::filesystem::path& mtzFile, void recalculateFromMTZ(const boost::filesystem::path& mtzFile,
const Structure& structure, const Structure& structure,
bool noBulk, AnisoScalingFlag anisoScaling, bool noBulk, AnisoScalingFlag anisoScaling,
float samplingRate = 4.5, bool electronScattering = false, float samplingRate = 4.5, bool electronScattering = false,
std::initializer_list<std::string> foLabels = { "FP", "SIGFP" }, std::initializer_list<std::string> foLabels = { "FP", "SIGFP" },
std::initializer_list<std::string> freeLabels = { "FREE" }); std::initializer_list<std::string> freeLabels = { "FREE" });
void loadFromMapFiles(const boost::filesystem::path& fbMapFile,
const boost::filesystem::path& fdMapFile);
double rmsDensityFb() const { return mRMSDensityFb; } void loadFromMapFiles(
double meanDensityFb() const { return mMeanDensityFb; } const boost::filesystem::path& fbMapFile,
double rmsDensityFd() const { return mRMSDensityFd; } const boost::filesystem::path& fdMapFile,
double meanDensityFd() const { return mMeanDensityFd; } float reshi, float reslo);
MapType& fb() { return mFb; }
MapType& fd() { return mFd; }
const MapType& fb() const { return mFb; }
const MapType& fd() const { return mFd; }
double resLow() const { return mResLow; } double resLow() const { return mResLow; }
double resHigh() const { return mResHigh; } double resHigh() const { return mResHigh; }
const Spacegroup& spacegroup() const { return mSpacegroup; } const Spacegroup& spacegroup() const { return mSpacegroup; }
const Cell& cell() const { return mCell; } const Cell& cell() const { return mCell; }
...@@ -61,18 +98,12 @@ class MapMaker ...@@ -61,18 +98,12 @@ class MapMaker
void fixMTZ(FPdata& fb, FPdata& fd, FOdata& fo, FPdata& fc, WData& fom); void fixMTZ(FPdata& fb, FPdata& fd, FOdata& fo, FPdata& fc, WData& fom);
Xmap& mFb; MapType mFb, mFd;
Xmap& mFd; Spacegroup mSpacegroup;
Cell mCell;
Spacegroup mSpacegroup; Grid_sampling mGrid;
Cell mCell; float mSamplingRate;
Grid_sampling mGrid; double mResLow, mResHigh;
float mSamplingRate;
double mRMSDensityFb, mRMSDensityFd;
double mMeanDensityFb, mMeanDensityFd;
double mResLow, mResHigh;
}; };
} }
src/MapMaker.cpp
...@@ -3,7 +3,12 @@ ...@@ -3,7 +3,12 @@
#include <iomanip> #include <iomanip>
#include <boost/format.hpp> #include <boost/format.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/algorithm/string.hpp> #include <boost/algorithm/string.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/copy.hpp>
#include <clipper/clipper-contrib.h> #include <clipper/clipper-contrib.h>
#include <clipper/clipper-ccp4.h> #include <clipper/clipper-ccp4.h>
...@@ -13,6 +18,7 @@ ...@@ -13,6 +18,7 @@
using namespace std; using namespace std;
namespace fs = boost::filesystem; namespace fs = boost::filesystem;
namespace io = boost::iostreams;
namespace ba = boost::algorithm; namespace ba = boost::algorithm;
extern int VERBOSE; extern int VERBOSE;
...@@ -21,8 +27,110 @@ namespace libcif ...@@ -21,8 +27,110 @@ namespace libcif
{ {
template<typename FTYPE> template<typename FTYPE>
MapMaker<FTYPE>::MapMaker(Xmap& fb, Xmap& fd) Map<FTYPE>::Map()
: mFb(fb), mFd(fd) {
}
template<typename FTYPE>
Map<FTYPE>::~Map()
{
}
template<typename FTYPE>
void Map<FTYPE>::calculateStats()
{
double sum = 0, sum2 = 0;
int count = 0;
for (auto ix = mMap.first(); not ix.last(); ix.next())
{
auto v = mMap[ix];
if (isnan(v))
throw runtime_error("map contains NaN values");
++count;
sum += v;
sum2 += v * v;
}
mMeanDensity = sum / count;
mRMSDensity = sqrt((sum2 / count) - (mMeanDensity * mMeanDensity));
}
template<typename FTYPE>
void Map<FTYPE>::read(const fs::path& mapFile)
{
fs::path dataFile = mapFile;
if (VERBOSE)
cout << "Reading map from " << mapFile << endl;
if (mapFile.extension() == ".gz" or mapFile.extension() == ".bz2")
{
// file is compressed
fs::path p = mapFile.parent_path();
string s = mapFile.filename().string();
io::filtering_stream<io::input> in;
fs::ifstream fi(mapFile);
if (mapFile.extension() == ".gz")
in.push(io::gzip_decompressor());
else
in.push(io::bzip2_decompressor());
in.push(fi);
char tmpFileName[] = "/tmp/map-tmp-XXXXXX";
if (mkstemp(tmpFileName) < 0)
throw runtime_error(string("Could not create temp file for map: ") + strerror(errno));
dataFile = fs::path(tmpFileName);
fs::ofstream out(dataFile);
io::copy(in, out);
}
if (not fs::exists(dataFile))
throw runtime_error("Could not open map file " + mapFile.string());
using namespace clipper;
CCP4MAPfile mapin;
mapin.open_read(dataFile.string());
mapin.import_xmap(mMap);
mapin.close_read();
if (dataFile != mapFile)
fs::remove(dataFile);
calculateStats();
}
template<typename FTYPE>
void Map<FTYPE>::write(const fs::path& f)
{
assert(false);
}
template class Map<float>;
template class Map<double>;
// --------------------------------------------------------------------
// MapMaker mm(mFb, mFd);
//
// if (recalculateFc)
// mm.recalculateFromMTZ(dataFile, mStructure, noBulk, aniso);
// else
// mm.loadFromMTZ(dataFile);
template<typename FTYPE>
MapMaker<FTYPE>::MapMaker()
{ {
} }
...@@ -42,6 +150,38 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate, ...@@ -42,6 +150,38 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate,
<< " with labels: FD: " << ba::join(fdLabels, ",") << endl << " with labels: FD: " << ba::join(fdLabels, ",") << endl
<< " with labels: FO: " << ba::join(foLabels, ",") << endl << " with labels: FO: " << ba::join(foLabels, ",") << endl
<< " with labels: FC: " << ba::join(fcLabels, ",") << endl; << " with labels: FC: " << ba::join(fcLabels, ",") << endl;
fs::path dataFile = mtzFile;
if (mtzFile.extension() == ".gz" or mtzFile.extension() == ".bz2")
{
// file is compressed
fs::path p = mtzFile.parent_path();
string s = mtzFile.filename().string();
io::filtering_stream<io::input> in;
fs::ifstream fi(mtzFile);
if (mtzFile.extension() == ".gz")
in.push(io::gzip_decompressor());
else
in.push(io::bzip2_decompressor());
in.push(fi);
char tmpFileName[] = "/tmp/mtz-tmp-XXXXXX";
if (mkstemp(tmpFileName) < 0)
throw runtime_error(string("Could not create temp file for mtz: ") + strerror(errno));
dataFile = fs::path(tmpFileName);
fs::ofstream out(dataFile);
io::copy(in, out);
}
if (not fs::exists(dataFile))
throw runtime_error("Could not open mtz file " + mtzFile.string());
const string kBasePath("/%1%/%2%/[%3%]"); const string kBasePath("/%1%/%2%/[%3%]");
...@@ -53,7 +193,7 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate, ...@@ -53,7 +193,7 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate,
using clipper::data32::Phi_fom; using clipper::data32::Phi_fom;
CCP4MTZfile mtzin; CCP4MTZfile mtzin;
mtzin.open_read(mtzFile.string()); mtzin.open_read(dataFile.string());
HKL_info hklInfo; HKL_info hklInfo;
mtzin.import_hkl_info(hklInfo); mtzin.import_hkl_info(hklInfo);
...@@ -74,6 +214,9 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate, ...@@ -74,6 +214,9 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate,
(boost::format(kBasePath) % "*" % "*" % "PHWT,FOM").str()); (boost::format(kBasePath) % "*" % "*" % "PHWT,FOM").str());
mtzin.close_read(); mtzin.close_read();
if (dataFile != mtzFile)
fs::remove(dataFile);
mCell = hklInfo.cell(); mCell = hklInfo.cell();
mSpacegroup = hklInfo.spacegroup(); mSpacegroup = hklInfo.spacegroup();
...@@ -100,11 +243,14 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate, ...@@ -100,11 +243,14 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate,
mGrid.init(mSpacegroup, mCell, mGrid.init(mSpacegroup, mCell,
hklInfo.resolution(), samplingRate); // define grid hklInfo.resolution(), samplingRate); // define grid
mFb.init(mSpacegroup, mCell, mGrid); // define map clipper::Xmap<FTYPE>& fbMap = mFb;
mFb.fft_from(fbData); // generate map clipper::Xmap<FTYPE>& fdMap = mFd;
fbMap.init(mSpacegroup, mCell, mGrid); // define map
fbMap.fft_from(fbData); // generate map
mFd.init(mSpacegroup, mCell, mGrid); // define map fdMap.init(mSpacegroup, mCell, mGrid); // define map
mFd.fft_from(fdData); // generate map fdMap.fft_from(fdData); // generate map
if (VERBOSE) if (VERBOSE)
cerr << "Read Xmaps with sampling rate: " << samplingRate << endl cerr << "Read Xmaps with sampling rate: " << samplingRate << endl
...@@ -112,31 +258,31 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate, ...@@ -112,31 +258,31 @@ void MapMaker<FTYPE>::loadFromMTZ(const fs::path& mtzFile, float samplingRate,
<< " calculated reshi = " << mResHigh << " reslo = " << mResLow << endl << " calculated reshi = " << mResHigh << " reslo = " << mResLow << endl
<< " spacegroup: " << mSpacegroup.symbol_hm() << endl << " spacegroup: " << mSpacegroup.symbol_hm() << endl
<< " cell: " << mCell.format() << endl; << " cell: " << mCell.format() << endl;
//
#if DEBUG //#if DEBUG
char tmpFoFileName[] = "/tmp/fo-XXXXXX.map"; // char tmpFoFileName[] = "/tmp/fo-XXXXXX.map";
if (mkstemps(tmpFoFileName, 4) < 0) // if (mkstemps(tmpFoFileName, 4) < 0)
throw runtime_error(string("Could not create temp file for map: ") + strerror(errno)); // throw runtime_error(string("Could not create temp file for map: ") + strerror(errno));
//
using clipper::CCP4MAPfile; // using clipper::CCP4MAPfile;
//
CCP4MAPfile foFile; // CCP4MAPfile foFile;
foFile.open_write(tmpFoFileName); // foFile.open_write(tmpFoFileName);
foFile.export_xmap(mFb); // foFile.export_xmap(mFb);
foFile.close_write(); // foFile.close_write();
//
char tmpFcFileName[] = "/tmp/df-XXXXXX.map"; // char tmpFcFileName[] = "/tmp/df-XXXXXX.map";
if (mkstemps(tmpFcFileName, 4) < 0) // if (mkstemps(tmpFcFileName, 4) < 0)
throw runtime_error(string("Could not create temp file for map: ") + strerror(errno)); // throw runtime_error(string("Could not create temp file for map: ") + strerror(errno));
//
CCP4MAPfile fcFile; // CCP4MAPfile fcFile;
fcFile.open_write(tmpFcFileName); // fcFile.open_write(tmpFcFileName);
fcFile.export_xmap(mFd); // fcFile.export_xmap(mFd);
fcFile.close_write(); // fcFile.close_write();
//
cout << "Wrote fo map to: " << tmpFoFileName << endl // cout << "Wrote fo map to: " << tmpFoFileName << endl
<< " and df map to: " << tmpFcFileName << endl; // << " and df map to: " << tmpFcFileName << endl;
#endif //#endif
} }
ostream& operator<<(ostream& os, const clipper::HKL& hkl) ostream& operator<<(ostream& os, const clipper::HKL& hkl)
...@@ -471,60 +617,58 @@ void MapMaker<FTYPE>::recalculateFromMTZ(const fs::path& mtzFile, ...@@ -471,60 +617,58 @@ void MapMaker<FTYPE>::recalculateFromMTZ(const fs::path& mtzFile,
mGrid.init(mSpacegroup, mCell, mGrid.init(mSpacegroup, mCell,
hklInfo.resolution(), samplingRate); // define grid hklInfo.resolution(), samplingRate); // define grid
mFb.init(mSpacegroup, mCell, mGrid); // define map clipper::Xmap<FTYPE>& fbMap = mFb;
mFb.fft_from(fb); // generate map clipper::Xmap<FTYPE>& fdMap = mFd;
fbMap.init(mSpacegroup, mCell, mGrid); // define map
fbMap.fft_from(fb); // generate map
mFd.init(mSpacegroup, mCell, mGrid); // define map fdMap.init(mSpacegroup, mCell, mGrid); // define map
mFd.fft_from(fd); // generate map fdMap.fft_from(fd); // generate map
if (VERBOSE) if (VERBOSE)
cerr << "Read Xmaps with sampling rate: " << samplingRate << endl cerr << "Read Xmaps with sampling rate: " << samplingRate << endl
<< " resolution: " << mResHigh << " resolution: " << mResHigh
<< endl; << endl;
//
#if DEBUG //#if DEBUG
char tmpFoFileName[] = "/tmp/fo-XXXXXX.map"; // char tmpFoFileName[] = "/tmp/fo-XXXXXX.map";
if (mkstemps(tmpFoFileName, 4) < 0) // if (mkstemps(tmpFoFileName, 4) < 0)
throw runtime_error(string("Could not create temp file for map: ") + strerror(errno)); // throw runtime_error(string("Could not create temp file for map: ") + strerror(errno));
//
using clipper::CCP4MAPfile; // using clipper::CCP4MAPfile;
//
CCP4MAPfile foFile; // CCP4MAPfile foFile;
foFile.open_write(tmpFoFileName); // foFile.open_write(tmpFoFileName);
foFile.export_xmap(mFb); // foFile.export_xmap(mFb);
foFile.close_write(); // foFile.close_write();
//
char tmpFcFileName[] = "/tmp/df-XXXXXX.map"; // char tmpFcFileName[] = "/tmp/df-XXXXXX.map";
if (mkstemps(tmpFcFileName, 4) < 0) // if (mkstemps(tmpFcFileName, 4) < 0)
throw runtime_error(string("Could not create temp file for map: ") + strerror(errno)); // throw runtime_error(string("Could not create temp file for map: ") + strerror(errno));
//
CCP4MAPfile fcFile; // CCP4MAPfile fcFile;
fcFile.open_write(tmpFcFileName); // fcFile.open_write(tmpFcFileName);
fcFile.export_xmap(mFd); // fcFile.export_xmap(mFd);
fcFile.close_write(); // fcFile.close_write();
//
cout << "Wrote fo map to: " << tmpFoFileName << endl // cout << "Wrote fo map to: " << tmpFoFileName << endl
<< " and df map to: " << tmpFcFileName << endl; // << " and df map to: " << tmpFcFileName << endl;
#endif //#endif
} }
template<typename FTYPE> template<typename FTYPE>
void MapMaker<FTYPE>::loadFromMapFiles(const fs::path& fbMapFile, const fs::path& fdMapFile) void MapMaker<FTYPE>::loadFromMapFiles(const fs::path& fbMapFile, const fs::path& fdMapFile,
float reshi, float reslo)
{ {
using clipper::CCP4MAPfile; mResHigh = reshi;
mResLow = reslo;
CCP4MAPfile fbFile;
fbFile.open_read(fbMapFile.string()); mFb.read(fbMapFile);
fbFile.import_xmap(mFb); mFd.read(fdMapFile);
mGrid = fbFile.grid_sampling();
mCell = fbFile.cell(); if (not mFb.cell().equals(mFd.cell()))
mSpacegroup = fbFile.spacegroup(); throw runtime_error("Fb and Fd map do not contain the same cell");
fbFile.close_read();
CCP4MAPfile fdFile;
fdFile.open_read(fdMapFile.string());
fdFile.import_xmap(mFd);
fdFile.close_read();
} }
template class MapMaker<float>; template class MapMaker<float>;
......
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