void can_project_micropolygon() {
MeshPoint mp1(-10, -10, 100);
MeshPoint mp2(10, -10, 100);
MeshPoint mp3(-10, 10, 100);
MeshPoint mp4(10, 10, 100);
MicroPolygon poly;
poly.a = mp1;
poly.b = mp2;
poly.c = mp3;
poly.d = mp4;
FrameBuffer fb(500, 500);
fb.projectMicroPolygon(poly);
ASSERT_EQUAL_FLOAT(poly.a.getX(), 206.699, 0.1);
ASSERT_EQUAL_FLOAT(poly.a.getY(), 206.699, 0.1);
ASSERT_EQUAL_FLOAT(poly.b.getX(), 293.301, 0.1);
ASSERT_EQUAL_FLOAT(poly.b.getY(), 206.699, 0.1);
ASSERT_EQUAL_FLOAT(poly.c.getX(), 206.699, 0.1);
ASSERT_EQUAL_FLOAT(poly.c.getY(), 293.301, 0.1);
ASSERT_EQUAL_FLOAT(poly.d.getX(), 293.301, 0.1);
ASSERT_EQUAL_FLOAT(poly.d.getY(), 293.301, 0.1);
}
void can_project_mesh_point() {
FrameBuffer fb(500, 500);
MeshPoint mp(0, 0, 100);
fb.projectAndScalePoint(mp);
ASSERT_EQUAL_FLOAT(mp.getX(), 250, 0.1);
ASSERT_EQUAL_FLOAT(mp.getY(), 250, 0.1);
MeshPoint mp2(-10, -10, 100);
fb.projectAndScalePoint(mp2);
ASSERT_EQUAL_FLOAT(mp2.getX(), 206.699, 0.1);
ASSERT_EQUAL_FLOAT(mp2.getY(), 206.699, 0.1);
}
void serializeMultipartToEntity()
{
cxxtools::MimeMultipart mp;
mp.addObject();
mp.addObject();
cxxtools::SerializationInfo si;
si <<= mp;
cxxtools::MimeEntity me;
si >>= me;
CXXTOOLS_UNIT_ASSERT(me.isMultipart());
cxxtools::MimeMultipart mp2(me);
CXXTOOLS_UNIT_ASSERT_EQUALS(mp2.size(), 2);
}
capd::map::CnCoeff<MatrixType> linearSubstitution(
const MatrixType& N,
const capd::map::CnCoeff<MatrixType>& s,
const MatrixType& M
)
{
typedef capd::vectalg::Multiindex::MultiindexVector MultiindexVector;
typedef typename MatrixType::ScalarType ScalarType;
int dimension = s.dimension();
int rank = s.rank();
capd::vectalg::Multiindex::IndicesSet indices;
capd::vectalg::Multiindex::generateList(dimension,rank,indices);
if(dimension!=M.numberOfRows() || dimension!=M.numberOfColumns() || dimension!=N.numberOfRows() || dimension!=N.numberOfColumns() )
{
throw std::runtime_error("normalForms::linearSubstitution - incompatible dimensions");
}
capd::map::CnCoeff<MatrixType> result (dimension,rank);
for(int r=1;r<=rank;++r)
{
capd::vectalg::Multipointer mp = s.first(r);
do{
typename capd::map::CnCoeff<MatrixType>::VectorType temp(dimension);
MultiindexVector::iterator b=indices[r-1].begin(), e=indices[r-1].end();
while(b!=e)
{
ScalarType product = M((*b)[0]+1,mp[0]+1);
for(int j=1;j<r;++j)
product *= M((*b)[j]+1,mp[j]+1);
capd::vectalg::Multipointer mp2(b->dimension(),b->begin());
std::sort(mp2.begin(),mp2.end());
temp += s(mp2)*product;
++b;
}
result(mp) = N*temp;
}while(s.next(mp));
}
return result;
}
void bounding_box_for_microPolygon_has_right_coords() {
MeshPoint mp1(-10, -10, 100);
MeshPoint mp2(10, -10, 100);
MeshPoint mp3(-10, 10, 100);
MeshPoint mp4(10, 10, 100);
MicroPolygon poly;
poly.a = mp1;
poly.b = mp2;
poly.c = mp3;
poly.d = mp4;
FrameBuffer fb(500, 500);
fb.projectMicroPolygon(poly);
BoundingBox box = poly.getBoundingBox();
ASSERT_EQUAL_INT(box.X_start, 206);
ASSERT_EQUAL_INT(box.Y_start, 206);
ASSERT_EQUAL_INT(box.X_stop, 294);
ASSERT_EQUAL_INT(box.Y_stop, 294);
}
int main(int argc, char** argv) {
BinarySerializer bs;
Point<double> p(2);
p.mX[0] = 1;
p.mX[1] = 2;
bs << p;
MultiPoint<double> mp(2,2);
mp.mParam.mX[0] = 1;
mp.mParam.mX[1] = 2;
mp.mCrit.mX[0] = 3;
mp.mCrit.mX[1] = 4;
bs << mp;
Point<double> q(2);
bs.reset();
bs >> q;
//rintf("%s\n", q.toString().c_str());
BNB_ASSERT((p.mX[0] == q.mX[0]) && (p.mX[1] == q.mX[1]));
MultiPoint<double> mq(2,2);
bs >> mq;
//printf("%s\n", mq.toString().c_str());
BNB_ASSERT((mp.mParam.mX[0] == mq.mParam.mX[0]) && (mp.mParam.mX[1] == mq.mParam.mX[1]));
BNB_ASSERT((mp.mCrit.mX[0] == mq.mCrit.mX[0]) && (mp.mCrit.mX[1] == mq.mCrit.mX[1]));
MultiPoint<double> mp1(2,3);
mp1.mParam.mX[0] = 0;
mp1.mParam.mX[1] = 1;
mp1.mCrit.mX[0] = 3;
mp1.mCrit.mX[1] = 4;
mp1.mCrit.mX[2] = 5;
MultiPoint<double> mp2(2,3);
mp2.mParam.mX[0] = 10;
mp2.mParam.mX[1] = 11;
mp2.mCrit.mX[0] = 5;
mp2.mCrit.mX[1] = 4;
mp2.mCrit.mX[2] = 3;
MPSimpBag<double> mpsbag;
mpsbag.put(mp1);
mpsbag.put(mp2);
bs.reset();
bs << mpsbag;
bs.reset();
MPSimpBag<double> mpsbagn;
bs >> mpsbagn;
//printf("%s\n", mpsbagn.toString().c_str());
BNB_ASSERT(mpsbagn.size() == 2);
bs.reset();
Box<double> bx1(2);
bx1.mA[0] = 1;
bx1.mA[1] = 2;
bx1.mB[0] = 3;
bx1.mB[1] = 4;
bs << bx1;
Box<double> bx2(2);
bs.reset();
bs >> bx2;
//printf("%s\n", BoxUtils::toString(bx2).c_str());
BNB_ASSERT(bx1.mA[0] == bx2.mA[0]);
BNB_ASSERT(bx1.mA[1] == bx2.mA[1]);
BNB_ASSERT(bx1.mB[0] == bx2.mB[0]);
BNB_ASSERT(bx1.mB[1] == bx2.mB[1]);
SimpBoxBag<double> sb;
sb.put(bx1);
sb.put(bx2);
bs.reset();
bs << sb;
bs.reset();
SimpBoxBag<double> sb1;
bs >> sb1;
//printf("sb1: %s\n", sb1.toString().c_str());
BNB_ASSERT(sb1.size() == 2);
return 0;
}
int main()
{
write(mp2(10000));
return 0;
}
int main(int argc, char *argv[])
{
b_po::variables_map vmgeneral;
parsecommandlineExtract(argc, argv, vmgeneral);
ralab::findmf::apps::Params aparam;
analysisParameters(aparam,vmgeneral);
int res = 0;
boost::filesystem::path p1,p2;
{
// LOG(INFO) << "i::::" << i << std::endl;
p1 = ralab::findmf::createOutputs(aparam.infile,"");
p2 = ralab::findmf::createOutputs(aparam.infile,"filtered");
if( !boost::filesystem::exists(aparam.infile) )
{
return -1;
}
ralab::findmf::datastruct::MSFileInfoPtr sip;
try{
ralab::findmf::SwathPropertiesReader swathPropReader(aparam.infile);
sip = swathPropReader.getSwathInfo();
} catch(std::exception & e){
std::cerr << "infile : " << aparam.infile << std::endl;
std::cerr << "can't open file: " << e.what() << std::endl;
return 0;
}
double ppm = aparam.ppm;
pwiz::msdata::MSDataPtr msdataptr = pwiz::msdata::MSDataPtr(new pwiz::msdata::MSDataFile(aparam.infile));
ralab::findmf::LCMSImageReader sm(msdataptr, sip, ppm, aparam.rt2sum_ );
ralab::findmf::datastruct::LCMSImage mp;
sm.getMap( 0 , aparam.minmass, aparam.maxmass, mp);
// LOG(INFO) << " " << mp.getMZsize() << " " << mp.getRTsize();
ralab::findmf::datastruct::LCMSImage mp2( mp );
{
ralab::findmf::LCMSImageFilterGauss imgf;
// imgf.filterMap( mp2.getImageMap().getMap() , aparam.mzpixelwidth , aparam.rtpixelwidth, aparam.mzscale, aparam.rtscale);
imgf.filter( mp2.getImageMap().getMap() , aparam.mzpixelwidth , aparam.rtpixelwidth, aparam.mzscale, aparam.rtscale);
mp2.getImageMap().updateImageRange();
std::cout << mp2.getImageMap().getImageMin() << std::endl;
//imgf.filterMap();
}
// feature finding
ralab::findmf::FeatureFinderLocalMax ff;
ff.findFeature( mp2.getImageMap().getMap() , aparam.minintensity );
ralab::findmf::datastruct::FeaturesMap map;
map.setMapDescription(mp2.getMapDescription());
ralab::findmf::ComputeFeatureStatistics cfs;
cfs.extractFeatures(map,mp2.getImageMap().getMap(),ff.getLabels());
//this writes the accessor....
cfs.writeFeatures(aparam.outdir , p1.stem().string() );
ralab::FeaturesMapPrinter fp;
fp.writeFeatures(aparam.outdir , p1.stem().string(), map);
ralab::MultiArrayVisSegments<int> mavL( ff.getLabels() );
//write filtered data into mzML file
//TODO check why this isn't working
sm.write( p2.string() , mp2 );
if(1){
QApplication app(argc, argv);
ralab::TwoPaneledImageWidget tpi;
ralab::MultiArrayVisLog<float> adapt2( mp2.getImageMap().getMap() );
ralab::MultiArrayVisAsinh<float> adapt1( mp2.getImageMap().getMap() );
ralab::MultiArrayVisLog<float> adapt0( mp.getImageMap().getMap() );
tpi.setTopMap(&mavL);
//tpi.setBottomMap(&adapt0);
tpi.setBottomMap(&adapt0);
tpi.show();
res = app.exec();
}
}
return res;
}
CPatcher_EnableFSAA::CPatcher_EnableFSAA( void )
{
patchname = "Enable FSAA";
addrReadFSAA = CAddr::Addr(CGameOptionMgr_ReadFSAA);
addrReadFSAAQuality = CAddr::Addr(CGameOptionMgr_ReadFSAAQuality);
if (!addrReadFSAA ||
!addrReadFSAAQuality)
{
WriteLog("Patch initialization failed: %s.\n", patchname.c_str());
WriteLog(" Missing dependency.\n");
return;
}
vector<WORD> patch1;
vector<WORD> backup1;
backup1 +=
0x89, 0x7E, 0x10, // +3B: MOV [ESI+10h], EDI
0x89, 0x7E, 0x14, // +3E: MOV [ESI+14h], EDI
0xE8, -1, -1, -1, -1, // +41: CALL pleione::CGameOptionMgr::ReadDithering(void)
0x8B, 0xCE, // +46: MOV ECX, ESI
0x88, 0x46, 0x4C, // +48: MOV [ESI+4Ch], AL
0xE8, -1, -1, -1, -1, // +4B: CALL xxxxxxxx
0x8B, 0xCE, // +50: MOV ECX, ESI
0x88, 0x46, 0x4D; // +52: MOV [ESI+4Dh], AL
patch1 +=
0xE9, 0x01FF, 0x01FF, 0x01FF, 0x01FF, // +3B: JMP LONG patchFSAA
0x90, // NOP
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1;
MemoryPatch mp1( NULL, patch1, backup1 );
mp1.Search( L"Pleione.dll" );
mp1.PatchRelativeAddress( 0x01, (LPBYTE)patchFSAA );
addrTargetReturn = mp1.GetAddr() + 6; // Size of patch
vector<WORD> patch2;
vector<WORD> backup2;
backup2 +=
0x83, 0x4D, 0xFC, 0xFF, // +59E: OR [EBP-04h], 0xFFFFFFFF
0x8D, 0x4D, 0x08, // +5A2: LEA ECX, [EBP+08h]
0xFF, 0xD6, // +5A5: CALL ESI
0x8B, 0x8B, 0x1C, 0x01, 0x00, 0x00, // +5A7: MOV ECX, [EBX+11Ch]
0x8B, 0x01, // +5AD: MOV EAX, [ECX]
0x6A, 0x00, // +5AF: PUSH 0x00
0xFF, 0x50, 0x4C, // +5B1: CALL DWORD PTR [EAX+4Ch]
0x6A, 0x0B; // +5B4: PUSH 0x0B
patch2 +=
-1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1,
0x6A, 0x01, // +5AF: PUSH 0x00 => PUSH 0x01
-1, -1, -1, -1, -1;
MemoryPatch mp2( NULL, patch2, backup2 );
mp2.Search( L"Pleione.dll" );
patches += mp1;
patches += mp2;
if (CheckPatches())
WriteLog("Patch initialization successful: %s.\n", patchname.c_str());
else
WriteLog("Patch initialization failed: %s.\n", patchname.c_str());
}