diff -r -u 20110921/ccp4-6.2.0/src/pointless/ChangeLog 20110923/ccp4-6.2.0/src/pointless/ChangeLog --- 20110921/ccp4-6.2.0/src/pointless/ChangeLog 2011-09-06 17:49:04.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/ChangeLog 2011-09-20 17:41:24.000000000 +0100 @@ -1,5 +1,11 @@ Release notes +1.6.5 + - Fixed a nasty bug in accessing a potentially deleted +object in probability calculation (thanks to Charles Ballard) which +crashed in Windows, also some "uninitialised variable" errors +found by Clemens Vonrhein + 1.6.4 - Reindexing merged files now deals properly with phase and ABCD columns, eg for I2<->C2 or P2 21 21 <-> P21 21 2 conversions diff -r -u 20110921/ccp4-6.2.0/src/pointless/datatypes.cpp 20110923/ccp4-6.2.0/src/pointless/datatypes.cpp --- 20110921/ccp4-6.2.0/src/pointless/datatypes.cpp 2010-08-25 17:14:06.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/datatypes.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -12,6 +12,16 @@ const double SDcorrection::MINSDFRAC = 0.2; // minimum SDfac //-------------------------------------------------------------- + SDcorrection::SDcorrection() : sdfac(1.0), sdadd(0.0) {ResetRange();} + // Reset minimum & maximum + //-------------------------------------------------------------- + SDcorrection::SDcorrection(const double& SDfac, + const double& SDb, const double& SDadd, + const bool& fixSDb) + : sdfac(SDfac), sdb(SDb), sdadd(SDadd), fixsdb(fixSDb) {ResetRange();} + //-------------------------------------------------------------- + void SDcorrection::ResetRange() {mincorr = +1.0e10; maxcorr = -mincorr;} + //-------------------------------------------------------------- void SDcorrection::Correct(observation& Observation, const float& Iav) const // in-place correction, using Iav as intensity { diff -r -u 20110921/ccp4-6.2.0/src/pointless/datatypes.hh 20110923/ccp4-6.2.0/src/pointless/datatypes.hh --- 20110921/ccp4-6.2.0/src/pointless/datatypes.hh 2010-08-25 17:14:07.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/datatypes.hh 2011-09-20 17:41:24.000000000 +0100 @@ -12,16 +12,15 @@ // sd' = SDfac * Sqrt(sd^2 + SdB * I + (SDadd * I)^2) { public: - SDcorrection() : sdfac(1.0), sdadd(0.0) {} + SDcorrection(); SDcorrection(const double& SDfac, const double& SDb, const double& SDadd, - const bool& fixSDb=false) - : sdfac(SDfac), sdb(SDb), sdadd(SDadd), fixsdb(fixSDb) {} + const bool& fixSDb=false); void FixSDb() {fixsdb = true;} void UnFixSDb() {fixsdb = false;} // Reset minimum & maximum - void ResetRange() {mincorr = +1.0e10; maxcorr = -mincorr;} + void ResetRange(); // Multiply SDfac by update void UpdateFactor(const double& update) {sdfac *= update;} diff -r -u 20110921/ccp4-6.2.0/src/pointless/hkl_controls.cpp 20110923/ccp4-6.2.0/src/pointless/hkl_controls.cpp --- 20110921/ccp4-6.2.0/src/pointless/hkl_controls.cpp 2011-09-06 17:49:04.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/hkl_controls.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -37,6 +37,10 @@ nrej_reso = 0; nrej_mflag = 0; inputscale = 1.0; + // fraction of maximum resolution to use in test for blank batches + nullResolutionfraction = -1.0; + // Threshold on proportion of negative reflections + nullNegativeReject = -1.0; } //-------------------------------------------------------------- void file_select::set_reslimits(const ResoRange& resrange) diff -r -u 20110921/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp 20110923/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp --- 20110921/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp 2011-09-06 17:49:04.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -74,7 +74,7 @@ lattype = HorR; } if (!scala::AllowedLatticeType(lattype)) { - Message::message(Message_fatal("Illegal lattice type "+lattype)); + Message::message(Message_fatal(clipper::String("Illegal lattice type ")+lattype)); } sname = StringUtil::Trim(sname.substr(1)); std::string lt = std::string(1,lattype); @@ -1026,7 +1026,8 @@ return ((-hkl.h()+hkl.k()+hkl.l())%3 == 0); } else { Message::message - (Message_fatal("hkl_symmetry::LatticePresent: unrecognised lattice "+LatType)); + (Message_fatal(clipper::String("hkl_symmetry::LatticePresent: unrecognised lattice ") + +LatType)); } return false; // dummy, never gets here } diff -r -u 20110921/ccp4-6.2.0/src/pointless/intensitystatistics.cpp 20110923/ccp4-6.2.0/src/pointless/intensitystatistics.cpp --- 20110921/ccp4-6.2.0/src/pointless/intensitystatistics.cpp 2011-09-06 17:50:02.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/intensitystatistics.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -89,8 +89,8 @@ // Probability double mcent = 0.968; double macen = 0.736; - DM_2sqrt *DMcentric = new DM_2sqrt(macen, mcent); - double pcentro = ProbBiassed(TotE2minus1, SD_E2m1, mcent, *DMcentric); + DM_2sqrt DMcentric(macen, mcent); + double pcentro = ProbBiassed(TotE2minus1, SD_E2m1, mcent, DMcentric); // double dc = Max(mcent - TotE2minus1, 0.0)/SD_E2m1; diff -r -u 20110921/ccp4-6.2.0/src/pointless/normalise.cpp 20110923/ccp4-6.2.0/src/pointless/normalise.cpp --- 20110921/ccp4-6.2.0/src/pointless/normalise.cpp 2011-05-09 10:25:11.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/normalise.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -46,6 +46,15 @@ return sum_time/double(N); } //-------------------------------------------------------------- + BfactorModel::BfactorModel() + : valid(false), lnC0(0.0), B0(0.0), B(0.0), + time0(0.0), dtime(0.0), nparam(3) {} + //-------------------------------------------------------------- + // Constant = true for B constant with time + BfactorModel::BfactorModel(const bool& Constant) + : valid(false), lnC0(0.0), B0(0.0), B(0.0), + time0(0.0), dtime(0.0) { + Setup(Constant);} //-------------------------------------------------------------- void BfactorModel::Setup(const bool& Constant, const double& Time0) { @@ -159,7 +168,11 @@ double mnI = sums_st[ir](is,ib).MeanI(); double mnSSqr = sums_st[ir](is,ib).MeanSSqr(); double mnTime = sums_st[ir](is,ib).MeanTime(); // from start - DTime = Max(DTime, sums_st[ir](is,ib).MaxTime());// maximum time from start of run + //^ + // std::cout << "Maxtime " << ir <<" "< 0.001) { // Measurement vector = (1 s2 [s2*t]) mv = Bfactors[ir].MeasurementVector(mnSSqr, mnTime); @@ -174,12 +187,12 @@ } else { Bfactors[ir].Invalid(); } - DTime -= Time0; + DTime -= Time0; // maximum time from start of run avgtime[ir] = 0.5*DTime; // average time for run (relative) Bfactors[ir].DTime() = DTime; // store maximum time for run //^ // std::cout << "run, time0, dtime " << ir << " " - // << Time0 << " " << DTime << "\n"; + // << Time0 << " " << DTime << "\n"; } // end loop runs // + + + + + + + + + + + + @@ -526,7 +539,8 @@ sums_st[irun](rbin,ib).add(this_obs.kI(), sSqr, this_obs.time()); numobs++; //^ - // std::cout << "sums_st[irun](rbin,ib) " << irun <<" "<< rbin <<" "<< ib <<" " + // std::cout << "sums_st[irun](rbin,ib) " << irun <<" "<< rbin <<" "<< ib + // <<" time " << this_obs.time() <<" " // << this_obs.kI() <<"\n"; //^- } } diff -r -u 20110921/ccp4-6.2.0/src/pointless/normalise.hh 20110923/ccp4-6.2.0/src/pointless/normalise.hh --- 20110921/ccp4-6.2.0/src/pointless/normalise.hh 2011-05-09 10:25:12.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/normalise.hh 2011-09-20 17:41:24.000000000 +0100 @@ -19,13 +19,12 @@ class BinSums { public: BinSums(const Rtype& Time0=0.0) - : sum_I(0.0), sum_sSqr(0.0), N(0), sum_time(0.0), - max_time(0.0) - {time0=Time0;} // construct & zero + : sum_I(0.0), sum_sSqr(0.0), N(0), sum_time(0.0) + {time0=Time0;max_time=Time0;} // construct & zero void clear(const Rtype& Time0=0.0) {sum_I=0.0;sum_sSqr=0.0;N=0;sum_time=0.0; - time0=Time0;max_time=0.0;} + time0=Time0;max_time=Time0;} // Add in I, s^2, time void add(const Rtype& I, const Rtype& sSqr, const Rtype& Time=0.0); @@ -77,11 +76,9 @@ // // Three parameters: c0 (determinated as ln(c0)); B0; B public: - BfactorModel() - : valid(false), time0(0.0), dtime(0.0), nparam(3) {} + BfactorModel(); // Constant = true for B constant with time - BfactorModel(const bool& Constant) : valid(false), dtime(0.0) { - Setup(Constant);} + BfactorModel(const bool& Constant); // Constant = true for B constant with time void Setup(const bool& Constant, const double& Time0=0.0); diff -r -u 20110921/ccp4-6.2.0/src/pointless/pgscore.cpp 20110923/ccp4-6.2.0/src/pointless/pgscore.cpp --- 20110921/ccp4-6.2.0/src/pointless/pgscore.cpp 2011-09-06 17:50:02.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/pgscore.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -112,19 +112,23 @@ if (NAveragedZCCfor == 0 && NAveragedZCCagainst == 0) return; IntgrtProb IP1; - if (Close(exponent, 2.0)) { - DM_2sqrt *DM = new DM_2sqrt(0.0,CCTrueScore); // Model for CC- if true, most likely 0.0 + MeanModelBase* pDM = NULL; // pointer to base function + + if (Close(exponent, 2.0)) { + // Model for CC- if true, most likely 0.0 + pDM = new DM_2sqrt(0.0,CCTrueScore); + //DM_2sqrt DM(0.0,1.0); // Model for CC- if true, most likely 0.0 // DM_lin DM(0.0,CCTrueScore); // DM_cubic DM(0.0,CCTrueScore); // DM_cubicsu DM(0.0,CCTrueScore); // DM_1minusmSq DM(0.0,CCTrueScore); // DM_1minusmCu DM(0.0,CCTrueScore); - IP1.init(*DM); + IP1.init(*pDM); } else { - DM_power *DM = new DM_power(0.0,CCTrueScore); - DM->SetPower(exponent); - IP1.init(*DM); + pDM = new DM_power(0.0,CCTrueScore); + pDM->SetPower(exponent); + IP1.init(*pDM); } const bool DEBUG = false; @@ -176,6 +180,8 @@ } } + if(pDM != NULL) {delete pDM;} // clean up + likelihood = exp(PLfor+PLagainst); //^ if (DEBUG) { diff -r -u 20110921/ccp4-6.2.0/src/pointless/pointless.cpp 20110923/ccp4-6.2.0/src/pointless/pointless.cpp --- 20110921/ccp4-6.2.0/src/pointless/pointless.cpp 2011-09-06 17:49:04.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/pointless.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -2380,7 +2380,7 @@ CCP4::ccp4fyp(argc, argv); CCP4::ccp4ProgramName (PROGRAM_NAME.c_str()); - std::string rcsdate = "$Date: 2011/09/06 16:49:04 $"; + std::string rcsdate = "$Date: 2011/09/20 16:41:24 $"; CCP4::ccp4RCSDate (rcsdate.c_str()); CCP4::ccp4_prog_vers(PROGRAM_VERSION); CCP4::ccp4_banner(); diff -r -u 20110921/ccp4-6.2.0/src/pointless/pointless.html 20110923/ccp4-6.2.0/src/pointless/pointless.html --- 20110921/ccp4-6.2.0/src/pointless/pointless.html 2011-09-06 17:49:04.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/pointless.html 2011-09-20 17:41:24.000000000 +0100 @@ -24,6 +24,7 @@ + CCP4 Program Suite: pointless @@ -956,7 +957,12 @@


Release notes

+

1.6.5

Fixed a nasty bug in accessing a potentially deleted +object in probability calculation (thanks to Charles Ballard) which +crashed in Windows, also some  "uninitialised variable" errors +found by Clemens Vonrhein

1.6.4

+ Reindexing merged files now deals properly with phase and ABCD columns, eg for I2<->C2 or  P2 21 21 <-> P21 21 2 conversions
Improved/fixed detection of new space group after reindexing
diff -r -u 20110921/ccp4-6.2.0/src/pointless/probfunctions.cpp 20110923/ccp4-6.2.0/src/pointless/probfunctions.cpp --- 20110921/ccp4-6.2.0/src/pointless/probfunctions.cpp 2011-09-06 17:50:02.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/probfunctions.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -12,7 +12,6 @@ // Gaussian probability density function // returns p = (1/(sd*sqrt(twopi))) exp (-1/2 z^2) // where z = (val-mean)/sd - // { if (sd <= 0.0) clipper::Message::message(clipper::Message_fatal diff -r -u 20110921/ccp4-6.2.0/src/pointless/probfunctions.hh 20110923/ccp4-6.2.0/src/pointless/probfunctions.hh --- 20110921/ccp4-6.2.0/src/pointless/probfunctions.hh 2011-09-06 17:50:02.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/probfunctions.hh 2011-09-20 17:41:24.000000000 +0100 @@ -63,6 +63,8 @@ double HighProb() const {return High;} double LowProb() const {return Low;} + virtual void SetPower(const double& power) {} // dummy + protected: // Returns v mapped on to range 0->1 double nmap(const double& v) const @@ -153,7 +155,6 @@ { public: IntgrtProb() : nd(10000) {} - ~IntgrtProb() { delete DMeanModel; } // Note that this stores a pointer to the external function // which therefore must continue to exist while this class diff -r -u 20110921/ccp4-6.2.0/src/pointless/scsignificance.cpp 20110923/ccp4-6.2.0/src/pointless/scsignificance.cpp --- 20110921/ccp4-6.2.0/src/pointless/scsignificance.cpp 2011-09-06 17:50:02.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/scsignificance.cpp 2011-09-20 17:41:24.000000000 +0100 @@ -37,7 +37,7 @@ // P(S|score)/[P(S|score) + P(!S|score)] // E(score|S) = TrueScore (eg 1.0 for correlation coefficient) // E(score|!S) is in range 0.0 to TrueScore - + // // Returns = 0.0 if SDUnrelSC = 0.0 // = 1.0 if SDUnrelSC < 0 { @@ -45,20 +45,23 @@ if (SDUnrelSC <= 0.0) return 0.0; IntgrtProb IP; + MeanModelBase* pDM = NULL; // pointer to base function if (Close(exponent, 2.0)) { - DM_2sqrt *DM = new DM_2sqrt(0.0,truescore); // Model for CC- if true, most likely 0.0 + // Model for CC- if true, most likely 0.0 + pDM = new DM_2sqrt(0.0,truescore); + // DM_2sqrt DM(0.0,1.0); // Model for CC- if true, most likely 0.0 // DM_lin DM(0.0,1.0); // DM_cubic DM(0.0,1.0); // DM_cubicsu DM(0.0,1.0); // DM_1minusmSq DM(0.0,1.0); // DM_1minusmCu DM(0.0,1.0); - IP.init(*DM); + IP.init(*pDM); } else { - DM_power *DM = new DM_power(0.0,truescore); - DM->SetPower(exponent); - IP.init(*DM); + pDM = new DM_power(0.0,truescore); + pDM->SetPower(exponent); + IP.init(*pDM); } double PS, PnotS; @@ -76,6 +79,7 @@ // << SDrelSC << " " << truescore << " " << PS << " " << PnotS << " " // << PS/(PS+PnotS) << "\n"; //^- + if(pDM != NULL) {delete pDM;} // clean up return PS/(PS+PnotS); // Normalise } diff -r -u 20110921/ccp4-6.2.0/src/pointless/version.hh 20110923/ccp4-6.2.0/src/pointless/version.hh --- 20110921/ccp4-6.2.0/src/pointless/version.hh 2011-09-06 17:49:04.000000000 +0100 +++ 20110923/ccp4-6.2.0/src/pointless/version.hh 2011-09-20 17:41:24.000000000 +0100 @@ -4,9 +4,9 @@ #define PROGRAM_VERSION_HEADER #define PROGRAM_NAME std::string("POINTLESS") -#define PROGRAM_VERSION "1.6.4" -#define PROGRAM_DATE "17th August 2011" -#define PROGRAM_DATE2 "2011/08/17" +#define PROGRAM_VERSION "1.6.5" +#define PROGRAM_DATE "20th September 2011" +#define PROGRAM_DATE2 "2011/09/20" #define PROGRAM_EXPIRES bool(false) #define EXPIRE_DAY int(1) #define EXPIRE_MONTH int(1)