C++ CStopWatch::Stop方法代码示例

void CBathymetryRasterizer::RasterizeImage()
{
	CStopWatch sw;
	sw.Start();

	int LowPixel = 255;
	int HighPixel = 0;

	byte * ImageData = new byte[ImageSize * ImageSize * 3];
	for (int i = 0; i < ImageSize; ++ i)
	{
		for (int j = 0; j < ImageSize; ++ j)
		{
			int const Index = ImageSize * i + j;

			if (Buckets[Index].Count > 0)
			{
				double const Value = Buckets[Index].Sum / Buckets[Index].Count;
				double const Intensity = 2.5f;
				double const Bottom = 0;
				int const Pixel = 255 - Clamp<int>((int) (Value * Intensity - Bottom), 0, 255);

				LowPixel = Min(LowPixel, Pixel);
				HighPixel = Max(HighPixel, Pixel);

				ImageData[Index * 3 + 0] = Pixel;
				ImageData[Index * 3 + 1] = 0;
				ImageData[Index * 3 + 2] = 0;
			}
			else
			{
				ImageData[Index * 3 + 0] = 0;
				ImageData[Index * 3 + 1] = 0;
				ImageData[Index * 3 + 2] = 255;
			}

			if (Buckets[Index].Tag == -1)
			{
				ImageData[Index * 3 + 1] = 255;
			}
			//else if (Buckets[Index].Tag > 0)
			//{
			//	if (TagGroups[Buckets[Index].Tag].IsBridge)
			//	{
			//		ImageData[Index * 3 + 1] = ImageData[Index * 3 + 0];
			//		ImageData[Index * 3 + 0] = 0;
			//		ImageData[Index * 3 + 2] = 128;
			//	}
			//}
		}
	}

	Log::Info("Low value: %d High Value: %d", LowPixel, HighPixel);

	CImage * Image = new CImage(ImageData, vec2u(ImageSize), 3);
	Image->FlipY();
	Image->Write(OutputName);

	Log::Info("Rasterize to image took %.3f", sw.Stop());
}

void
CSeqDBPerfApp::x_InitApplicationData()
{
    CStopWatch sw;
    sw.Start();
    const CArgs& args = GetArgs();
    const CSeqDB::ESeqType kSeqType = ParseMoleculeTypeString(args["dbtype"].AsString());
    const string& kDbName(args["db"].AsString());
    m_BlastDb.Reset(new CSeqDBExpert(kDbName, kSeqType));
    m_DbIsProtein = static_cast<bool>(m_BlastDb->GetSequenceType() == CSeqDB::eProtein);

    int kNumThreads = 1;
#if (defined(_OPENMP) && defined(NCBI_THREADS))
    kNumThreads = args["num_threads"].AsInteger();
#endif
    m_DbHandles.reserve(kNumThreads);
    m_DbHandles.push_back(m_BlastDb);
    if (kNumThreads > 1) {
        for (int i = 1; i < kNumThreads; i++) {
            m_BlastDb.Reset(new CSeqDBExpert(kDbName, kSeqType));
            m_DbHandles.push_back(m_BlastDb);
        }
    }
    m_MemoryUsage.assign(kNumThreads, SMemUsage());

    sw.Stop();
    cout << "Initialization time: " << sw.AsSmartString() << endl;
}

void CTopographyRasterizer::FillInteriorPoints()
{
	CStopWatch sw;
	sw.Start();

	Buckets = new SPixelBucket[ImageSize * ImageSize];

	vector<STriangle2D<double>> Triangles;
	AddAtEnd(Triangles, TriangulateEarClipping(CatalinaOutline));

	double ActualMax = 0;

	for (int i = 0; i < ImageSize; ++ i)
	{
		for (int j = 0; j < ImageSize; ++ j)
		{
			bool InsideTriangle = false;
			vec2d const Point = vec2d(
				RegionXCorner + ((double) i / (double) (ImageSize - 1)) * RegionXSize,
				RegionYCorner + ((double) j / (double) (ImageSize - 1)) * RegionYSize
			);

			for (auto const & Triangle : Triangles)
			{
				if (ion::IsPointInOrOnTriangle(Triangle.A, Triangle.C, Triangle.B, Point))
				{
					InsideTriangle = true;
					break;
				}
			}

			if (InsideTriangle)
			{
				auto Bucket = Helper_GetBucket(i, j);
				Bucket->Interior = true;
				Bucket->Value = Helper_ClosestEdgeDistance(Point);

				ActualMax = Max(ActualMax, Bucket->Value);
			}
		}
	}

	double const ApexPoint = 0.06;
	double const ScaleUp = 255.0 / 0.05;

	for (int i = 0; i < ImageSize; ++ i)
	{
		for (int j = 0; j < ImageSize; ++ j)
		{
			auto Bucket = Helper_GetBucket(i, j);
			Bucket->Value /= ApexPoint;
			Bucket->Value = pow(Bucket->Value, 0.65f);
			Bucket->Value *= ApexPoint * ScaleUp;
		}
	}

	Log::Info("Max: %f Scaled Max: %f", ActualMax, ActualMax * ScaleUp);
	Log::Info("Topography fill interior took %.3f", sw.Stop());
}

void CBathymetryRasterizer::FillBridgeGroups()
{
	CStopWatch sw;
	sw.Start();

	static vector<vec2i> const Neighbors =
	{
		vec2i(-1, 0),
		vec2i(1, 0),
		vec2i(0, -1),
		vec2i(0, 1),
	};

	int Tag = 1;
	while (TagGroups[Tag].count)
	{
		if (TagGroups[Tag].IsBridge)
		{
			vector<vec2i> Queue = Helper_GetAllMatchingGroup(Tag);

			int KernelSize = 4;
			int MinSamples = 2;

			while (Queue.size() && KernelSize <= 512)
			{
				for (auto const & Spot : Queue)
				{
					Helper_EstimatePixelValueBridge(Spot, KernelSize, MinSamples);
				}

				for (auto it = Queue.begin(); it != Queue.end(); )
				{
					if (Helper_GetBucket(*it)->Count > 0)
					{
						it = Queue.erase(it);
					}
					else
					{
						it ++;
					}
				}
				
				KernelSize += 2;
				MinSamples = 4;
			}
		}

		Tag ++;
	}

	Log::Info("Fill bridge groups took %.3f", sw.Stop());
}

void CBathymetryRasterizer::FillGroups()
{
	CStopWatch sw;
	sw.Start();

	int tag = 1;
	while (TagGroups[tag].count)
	{
		if (TagGroups[tag].count < 96 && ! TagGroups[tag].IsBridge)
		{
			Helper_ReconstructTagGroup(TagGroups[tag], tag);
		}
		tag ++;
	}

	Log::Info("Fill groups took %.3f", sw.Stop());
}

void CBathymetryRasterizer::CopySourcePointsToBuckets()
{
	CStopWatch sw;
	sw.Start();

	for (auto const & Point : SourceElevationPostings)
	{
		int const IndexX = (int) (((Point.X - RegionXCorner) / RegionXSize) * ImageSize);
		int const IndexY = (int) (((Point.Y - RegionYCorner) / RegionYSize) * ImageSize);

		if (IndexX >= 0 && IndexX < ImageSize &&
			IndexY >= 0 && IndexY < ImageSize)
		{
			Buckets[ImageSize * IndexX + IndexY].Sum += Point.Z;
			Buckets[ImageSize * IndexX + IndexY].Count ++;
		}
	}

	Log::Info("Copy to buckets took %.3f", sw.Stop());
}

TEST(TestStopWatch, Stop)
{
  CStopWatch a;
  CTestStopWatchThread thread;

  EXPECT_FALSE(a.IsRunning());
  EXPECT_EQ(0.0f, a.GetElapsedSeconds());
  EXPECT_EQ(0.0f, a.GetElapsedMilliseconds());

  std::cout << "Calling Start()" << std::endl;
  a.Start();
  thread.Sleep(1000);
  EXPECT_TRUE(a.IsRunning());
  std::cout << "Elapsed Seconds: " << a.GetElapsedSeconds() << std::endl;
  std::cout << "Elapsed Milliseconds: " << a.GetElapsedMilliseconds() << std::endl;

  a.Stop();
  EXPECT_FALSE(a.IsRunning());
  EXPECT_EQ(0.0f, a.GetElapsedSeconds());
  EXPECT_EQ(0.0f, a.GetElapsedMilliseconds());
}

//.........这里部分代码省略.........
	if(iMinMergeLength < 0 || iMinMergeLength > cMaxLengthRange)
		{
		printf("Error: Minimum output merged element length '-m%d' is not in range 0..%d",iMinMergeLength,cMaxLengthRange);
		exit(1);
		}

	iMaxMergeLength = MaxMergeLength->count ? MaxMergeLength->ival[0] : cDfltMaxLength;
	if(iMaxMergeLength < iMinMergeLength || iMaxMergeLength > cMaxLengthRange)
		{
		printf("Error: Maximum element length '-M%d' is not in range %d..%d",iMaxMergeLength,iMinMergeLength,cMaxLengthRange);
		exit(1);
		}

	iJoinDistance = JoinDistance->count ? JoinDistance->ival[0] : cDfltJoinOverlap;
	if(iJoinDistance < 0 || iJoinDistance > cMaxJoinOverlap)
		{
		printf("Error: Join separation length '-j%d' is not in range %d..%d",iJoinDistance,0,cMaxJoinOverlap);
		exit(1);
		}

	iRefExtend = RefExtend->count ? RefExtend->ival[0] : 0;
	if(iRefExtend < (-1 * cMaxExtendLength) || iRefExtend > cMaxExtendLength)
		{
		printf("Error: Ref Extension length '-e%d' is not in range %d..%d",iRefExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
		exit(1);
		}

	iRelExtend = RelExtend->count ? RelExtend->ival[0] : 0;
	if(iRelExtend < (-1 * cMaxExtendLength) || iRelExtend > cMaxExtendLength)
		{
		printf("Error: Rel Extension length '-E%d' is not in range %d..%d",iRelExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
		exit(1);
		}


	strncpy(szRefFile,RefFile->filename[0],_MAX_PATH);
	szRefFile[_MAX_PATH-1] = '\0';

	if(RelFile->count)
		{
		strncpy(szRelFile,RelFile->filename[0],_MAX_PATH);
		szRelFile[_MAX_PATH-1] = '\0';
		}
	else
		{
		if(iProcMode == ePMElRefExclusive || iProcMode == ePMElRefRelUnion)
			szRelFile[0] = '\0';
		else
			{
			printf("Error: Rel loci file must be specified in processing mode '-p%d' (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
			exit(1);
			}
		}

		// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference CSV file: '%s'",szRefFile);
	if(szRelFile[0] != '\0')
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Relative CSV file: '%s'",szRelFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output processed loci into CSV file: '%s'",szOutLociFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file ref species: '%s'",szRefSpecies);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file rel species: '%s'",szRelSpecies);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file element type: '%s'",szElType);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum input element length: %d",iMinLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum input element length: %d",iMaxLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Ref element flank extension length: %d",iRefExtend);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Rel element flank extension length: %d",iRelExtend);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Merge output elements separated by at most this many bases: %d",iJoinDistance);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum output merged element length: %d",iMinMergeLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum output merged element length: %d",iMaxMergeLength);


	// processing here...
	gStopWatch.Start();
#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif	
	Rslt = Process((etProcMode)iProcMode,iMinLength,iMaxLength,iRefExtend,iRelExtend,iJoinDistance,iMinMergeLength,iMaxMergeLength,szRefFile,szRelFile,szOutLociFile,
		szRefSpecies,szRelSpecies,szElType);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s CSV Merge Elements, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
}

//.........这里部分代码省略.........
		exit(1);
		}

	strncpy(szRsltsFile,rsltsfile->filename[0],_MAX_PATH);
	szRsltsFile[_MAX_PATH-1] = '\0';
	CUtility::TrimQuotedWhitespcExtd(szRsltsFile);
	if(szRsltsFile[0] == '\0')
		{
		printf("\nError: No results file ('-o<file> option') specified after removal of leading/trailing quotes and whitespace");
		exit(1);
		}

	NumIncludeChroms = IncludeChroms->count;
	for(Idx=0;Idx < IncludeChroms->count; Idx++)
		{
		LenChromList = (int)strlen(IncludeChroms->sval[Idx]);
		pszIncludeChroms[Idx] = new char [LenChromList+1];
		strcpy(pszIncludeChroms[Idx],IncludeChroms->sval[Idx]);
		CUtility::TrimQuotes(pszIncludeChroms[Idx]);
		}

	NumExcludeChroms = ExcludeChroms->count;
	for(Idx=0;Idx < ExcludeChroms->count; Idx++)
		{
		LenChromList = (int)strlen(ExcludeChroms->sval[Idx]);
		pszExcludeChroms[Idx] = new char [LenChromList+1];
		strcpy(pszExcludeChroms[Idx],ExcludeChroms->sval[Idx]);
		CUtility::TrimQuotes(pszExcludeChroms[Idx]);
		}

			// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
	const char *pszProcMode;
	switch(PMode) {
		case ePMNDyadRegionDist:
			pszProcMode = "background dyad regional distribution";
			break;

		case ePMNDyadOverlap:
			pszProcMode = "sample dyads overlap onto background dyads";
			break;

		};
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: '%s'",pszProcMode);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"offset background loci by: %d",BkgDyadOfs);
	if(PMode == ePMNDyadOverlap)
		{
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"offset sample loci by: %d",SmplDyadOfs);
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"window flanking: %d",WindDyad);
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"input background loci file: '%s'",szDyadFile);

	if(PMode == ePMNDyadOverlap)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"input sample loci file: '%s'",szSampleFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"results file: '%s'",szRsltsFile);

	for(Idx = 0; Idx < NumIncludeChroms; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to include: '%s'",pszIncludeChroms[Idx]);
	for(Idx = 0; Idx < NumExcludeChroms; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to exclude: '%s'",pszExcludeChroms[Idx]); 

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();
	Rslt = Process(PMode,					// processing mode
					BkgDyadOfs,				// offset background loci by this many bases to derive dyad loci
					SmplDyadOfs,			// offset sample loci by this many bases to derive dyad loci
					WindDyad,				// accept sample dyad as matching background loci if within +/- this many bases
					NumIncludeChroms,
					pszIncludeChroms,
					NumExcludeChroms,
					pszExcludeChroms,
					szDyadFile,				// CSV file containing background dyad loci
					szSampleFile,			// CSV file containing sample dyad loci
					szRsltsFile);			// output results to this file
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nend of help\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No input alignment file(s) specified with with '-I<filespec>' option)");
		exit(1);
		}

	for(NumAlignFiles=Idx=0;NumAlignFiles < cRRMaxInFileSpecs && Idx < alignfiles->count; Idx++)
		{
		pszAlignFiles[Idx] = NULL;
		if(pszAlignFiles[NumAlignFiles] == NULL)
			pszAlignFiles[NumAlignFiles] = new char [_MAX_PATH];
		strncpy(pszAlignFiles[NumAlignFiles],alignfiles->filename[Idx],_MAX_PATH);
		pszAlignFiles[NumAlignFiles][_MAX_PATH-1] = '\0';
		CUtility::TrimQuotedWhitespcExtd(pszAlignFiles[NumAlignFiles]);
		if(pszAlignFiles[NumAlignFiles][0] != '\0')
			NumAlignFiles++;
		}

	if(!NumAlignFiles)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input alignment file(s) specified with '-I<filespec>' option");
		exit(1);
		}

	// number of alignment files must be same as the number of SNP files and genome names!
	if(NumAlignFiles != NumSNPFiles && NumAlignFiles != NumRelGenomes)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected same number of genome names, alignment files and SNP files, %d genome names, %d alignment files, %d SNP files",NumRelGenomes,NumAlignFiles,NumSNPFiles);
		exit(1);
		}
	
	MinSpeciesTotCntThres = mincovspecies->count ? mincovspecies->ival[0] : 1;
	if(MinSpeciesTotCntThres < 1 || MinSpeciesTotCntThres > 10000)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum species total bases '-z%d' must be in range 1..10000",MinSpeciesTotCntThres);
		exit(1);
		}

	MinSpeciesWithCnts = mincovspecies->count ? mincovspecies->ival[0] : 1;
	if(MinSpeciesWithCnts < 1 || MinSpeciesWithCnts > NumAlignFiles)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum species to call marker '-Z%d' must be in range 1..%d",NumAlignFiles);
		exit(1);
		}

// show user current resource limits
#ifndef _WIN32
	gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
	const char *pszDescr;

	switch(PMode) {
		case ePMdefault:
			pszDescr = "Default marker processing";
			break;
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum coverage : %d",MinCovBases);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum P-Value : %1.4f'",MaxPValue);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference genome assembly name : '%s'",szRefGenome);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum total bases for species at SNP call loci : %d",MinSpeciesTotCntThres);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum alternative species coverage at SNP call loci : %d",AltSpeciesMaxCnt);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum number of species with SNP call at same loci : %d",MinSpeciesWithCnts);

	for(Idx=0; Idx < NumRelGenomes; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Alignments and SNPs from this genome (%d) : '%s'",Idx+1,pszRelGenomes[Idx]);

	for(Idx=0; Idx < NumSNPFiles; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input SNP file (%d) : '%s'",Idx+1,pszSNPFiles[Idx]);

	for(Idx=0; Idx < NumAlignFiles; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input alignment file (%d) : '%s'",Idx+1,pszAlignFiles[Idx]);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output markers to file : '%s'",szMarkerFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"number of threads : %d",NumThreads);

	#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();
	Rslt = Process(PMode,MinCovBases,MaxPValue,MinSpeciesTotCntThres,MinSpeciesWithCnts,AltSpeciesMaxCnt,szRefGenome,NumRelGenomes,pszRelGenomes,NumThreads,NumSNPFiles,pszSNPFiles,NumAlignFiles,pszAlignFiles,szMarkerFile);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s Generate Markers, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........

	iMode = Mode->count ? Mode->ival[0] : eProcModeStandard;
	if(iMode < eProcModeStandard || iMode > eProcModeStandard)
		{
		printf("\nError: Requested processing mode '-x%d' not supported",iMode);
		exit(1);
		}

	if(RegionsIn->count)
		{
		strcpy(szRegionsIn,RegionsIn->sval[0]);
		TrimQuotes(szRegionsIn);
		if((iRegionsIn = ParseRegions(szRegionsIn)) < 0)
			{
			printf("Error: unable to parse '-r%s' into regions to retain",szRegionsIn);
			exit(1);
			}
		}
	else
		{
		szRegionsIn[0] = '\0';
		iRegionsIn = (cFeatBitIG | cFeatBitUpstream | cFeatBit5UTR | cFeatBitCDS | cFeatBitIntrons | cFeatBit3UTR | cFeatBitDnstream);
		}

	if(RegionsOut->count)
		{
		strcpy(szRegionsOut,RegionsOut->sval[0]);
		TrimQuotes(szRegionsOut);
		if((iRegionsOut = ParseRegions(szRegionsOut)) < 0)
			{
			printf("Error: unable to parse '-R%s' into regions to remove",szRegionsOut);
			exit(1);
			}
		}
	else
		{
		szRegionsOut[0] = '\0';
		iRegionsOut = 0;
		}
	iRegionsIn &= ~iRegionsOut;
	if(!iRegionsIn)
		{
		printf("Error: no regions to retain");
		exit(1);
		}

	iRegLen = RegLen->count ? RegLen->ival[0] : cDfltRegLen;
	if(iRegLen < cMinRegLen)
		{
		printf("\nRegulatory region length '-L%d' less than minimum %d, assuming you meant to use '-L%d'",iRegLen,cMinRegLen,cMinRegLen);
		iRegLen = cMinRegLen;
		}
	else
		{
		if(iRegLen > cMaxRegLen)
			{
			printf("\nRegulatory region length '-L%d' more than maximum %d, assuming you meant to use '-L%d'",iRegLen,cMaxRegLen,cMaxRegLen);
			iRegLen = cMaxRegLen;
			}
		}

	strcpy(szInputFile,InFile->filename[0]);
	strcpy(szOutputFile,OutFile->filename[0]);
	strcpy(szInputBiobedFile,InBedFile->filename[0]);
	strcpy(szInSeqFile,InSeqFile->filename[0]);

		// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Loci file (.csv) file to process: '%s'",szInputFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"bio assembly (.seq) file to process: '%s'",szInSeqFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"where to write out fasta with random sequences: '%s'",szOutputFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"biobed file containing regional features: '%s'",szInputBiobedFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: %s",iMode == eProcModeStandard ? "standard" : iMode == eProcModeStandard ? "extended" : "summary");
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Accept random samples in any of these regions: '%s'",Regions2Txt(iRegionsIn));

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif

	Rslt = Process(iMode,iRegionsIn,iRegLen,szInputFile,szInputBiobedFile,szInSeqFile,szOutputFile);
	gStopWatch.Stop();
	Rslt = Rslt < 0 ? 1 : 0;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit Code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nend of help\n");
	exit(1);
	}
}

void CBathymetryRasterizer::DetectBridgeGroups()
{
	CStopWatch sw;
	sw.Start();

	static vector<vec2i> const Neighbors =
	{
		vec2i(-1, 0),
		vec2i(1, 0),
		vec2i(0, -1),
		vec2i(0, 1),
	};

	int Tag = 1;
	while (TagGroups[Tag].count)
	{
		vector<vec2i> const Group = Helper_GetAllMatchingGroup(Tag);

		bool NextToData = false;
		bool NextToLand = false;
		vec2i LandPt, DataPt;

		for (auto Tile : Group)
		{
			for (auto Neighbor : Neighbors)
			{
				auto Bucket = Helper_GetBucket(Tile + Neighbor);

				if (Bucket)
				{
					if (Bucket->Count > 0)
					{
						NextToData = true;
						DataPt = Tile;
						if (NextToLand)
						{
							break;
						}
					}

					if (Bucket->Tag == -1)
					{
						NextToLand = true;
						LandPt = Tile;
						if (NextToData)
						{
							break;
						}
					}
				}
			}

			if (NextToData && NextToLand)
			{
				break;
			}
		}

		if (NextToData && NextToLand)
		{
			TagGroups[Tag].IsBridge = true;
			Log::Info("      Tag group %d is bridge because {%d, %d} next to Data and {%d, %d} next to Land", Tag, DataPt.X, DataPt.Y, LandPt.X, LandPt.Y);
		}

		Tag ++;
	}

	Log::Info("Detect bridge groups took %.3f", sw.Stop());
}

//.........这里部分代码省略.........
			{
			gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment name specified with '-w<str>' option");
			return(1);
			}
		if(experimentdescr->count)
			{
			strncpy(szExperimentDescr,experimentdescr->sval[0],sizeof(szExperimentDescr)-1);
			szExperimentDescr[sizeof(szExperimentDescr)-1] = '\0';
			CUtility::TrimQuotedWhitespcExtd(szExperimentDescr);
			}
		if(strlen(szExperimentDescr) < 1)
			{
			gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment description specified with '-W<str>' option");
			return(1);
			}

		gExperimentID = gSQLiteSummaries.StartExperiment(szSQLiteDatabase,false,true,szExperimentName,szExperimentName,szExperimentDescr);
		if(gExperimentID < 1)
			return(1);
		gProcessID = gSQLiteSummaries.AddProcess((char *)gszProcName,(char *)gszProcName,(char *)szExperimentDescr);
		if(gProcessID < 1)
			return(1);
		gProcessingID = gSQLiteSummaries.StartProcessing(gExperimentID,gProcessID,(char *)cpszProgVer);
		if(gProcessingID < 1)
			return(1);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"Initialised SQLite database '%s' for results summary collection",szSQLiteDatabase);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database experiment identifier for '%s' is %d",szExperimentName,gExperimentID);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database process identifier for '%s' is %d",(char *)gszProcName,gProcessID);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database processing instance identifier is %d",gProcessingID);
		}
	else
		{
		szSQLiteDatabase[0] = '\0';
		szExperimentDescr[0] = '\0';
		}

	PMode = mode->count ? mode->ival[0] : 0;
	if(PMode < 0 || PMode > 1)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' must be in range 0..0",PMode);
		return(1);
		}

	strcpy(szInPE1File,inpe1file->filename[0]);
	CUtility::TrimQuotedWhitespcExtd(szInPE1File);

	strcpy(szInPE2File,inpe2file->filename[0]);
	CUtility::TrimQuotedWhitespcExtd(szInPE2File);

	strcpy(szOutFile,outfile->filename[0]);
	CUtility::TrimQuotedWhitespcExtd(szOutFile);

// show user current resource limits
#ifndef _WIN32
	gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
	const char *pszDescr;
	switch(PMode) {
		case 0:
			pszDescr = "Corelate PE1 and PE2 alignments";
			break;
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Experiment name : '%s'",szExperimentName);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Experiment description : '%s'",szExperimentDescr);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"SQLite database file: '%s'",szOutFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"PE1 SAM file: '%s'",szInPE1File);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"PE2 SAM file: '%s'",szInPE2File);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Corelations to file: '%s'",szOutFile);

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();

	Rslt = Process(PMode,szInPE1File,szInPE2File,szOutFile);
	Rslt = Rslt >=0 ? 0 : 1;
	if(gExperimentID > 0)
		{
		if(gProcessingID)
			gSQLiteSummaries.EndProcessing(gProcessingID,Rslt);
		gSQLiteSummaries.EndExperiment(gExperimentID);
		}
	gStopWatch.Stop();
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
    printf("\n%s, Version %s\n", gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
return 0;
}

void CBathymetryRasterizer::ClassifyGroups()
{
	CStopWatch sw;
	sw.Start();

	vector<STriangle2D<double>> Triangles;
	AddAtEnd(Triangles, TriangulateEarClipping(CatalinaOutline));
	AddAtEnd(Triangles, TriangulateEarClipping(BirdRock));

	for (int i = 0; i < ImageSize; ++ i)
	{
		for (int j = 0; j < ImageSize; ++ j)
		{
			bool InsideTriangle = false;
			vec2d const Point = vec2d(
				RegionXCorner + ((double) i / (double) (ImageSize - 1)) * RegionXSize,
				RegionYCorner + ((double) j / (double) (ImageSize - 1)) * RegionYSize
			);

			for (auto const & Triangle : Triangles)
			{
				if (ion::IsPointInOrOnTriangle(Triangle.A, Triangle.C, Triangle.B, Point))
				{
					InsideTriangle = true;
					break;
				}
			}

			if (InsideTriangle)
			{
				auto Bucket = Helper_GetBucket(i, j);
				Bucket->Tag = -1;
				Bucket->Count = 1;
				Bucket->Sum = 0;
			}
		}
	}

	int tag = 1;
	TagGroups = new STagInfo[ImageSize * ImageSize]();
	for (int i = 0; i < ImageSize; ++ i)
	{
		for (int j = 0; j < ImageSize; ++ j)
		{
			TagGroups[tag].count = Helper_FillBucketTags(i, j, tag);
			if (TagGroups[tag].count)
			{
				TagGroups[tag].start_x = i;
				TagGroups[tag].start_y = j;
				tag ++;
			}
		}
	}
	tag = 1;
	while (TagGroups[tag].count)
	{
		Log::Info("    Group %d has %d members", tag, TagGroups[tag].count);
		tag ++;
	}

	Log::Info("Classify groups took %.3f", sw.Stop());
}

//.........这里部分代码省略.........
    });
    loader.OnParsed([](const InfoTextLoader::LinedataType& data)
    {
        cout << "[" << std::setfill('0') << std::setw(3) << 0 << "]Data   : (" << data.data.size() << ") " << data.line << endl;
    });
    instreamCText >> loader;
    cout << "Version of CText data stream was: " << loader.Version() << " " << endl;
    cout << endl;

    //gui::components::CPoint p1(0, 0);
    CRectangle r1(10, 20, 33, 55);
    cout << "Simulate running" << endl;
    cout << r1 << endl;
    std::ostringstream outstring;
    outstring << r1;
    std::string outFromr1 = outstring.str();

    std::istringstream instream;
    instream.str(outFromr1);
    CRectangle r2;
    //std::cin >> r2;
    instream >> r2;
    cout << r2 << endl;

    {
        std::istringstream instream2;
        instream2.str("\"Older Depp, Du.\"");
        std::locale x(std::locale::classic(), new my_ctypeComma);
        instream2.imbue(x);

        std::string tmp1, tmp2, tmp3, tmp4, tmp5, tmp6, tmp7;
        instream2 >> tmp1;
        instream2 >> tmp2;
        instream2 >> tmp3;
        instream2 >> tmp4;
        instream2 >> tmp5;
    }

    //std::string newstr = "CText Arial, \"Use the up and down arrow or[w] and[s] to move the menu
    // cursor up and down.\", DarkRed;";
    std::string newstr = "CText Arial, 34, \"Use the up and down arrow, or[w] and[s] to move the menu cursor up and down.\", DarkRed;";
    {
        std::string delimiters("\",;");
        std::vector<std::string> parts;
        split(parts, newstr, boost::is_any_of(delimiters));
    }

    {
        std::istringstream instream4;
        instream4.str(newstr);
        std::string sin((std::istreambuf_iterator<char>(instream4)),
                std::istreambuf_iterator<char>());

        //std::regex
        // word_regex(",(?!(?<=(?:^|,)\s*\"(?:[^\"]|\"\"|\\\")*,)(?:[^\"]|\"\"|\\\")*\"\s*(?:,|$))");
        std::regex word_regex(",(?=([^\"]*\"[^\"]*\")*[^\"]*$)");
        auto what =
            std::sregex_iterator(sin.begin(), sin.end(), word_regex);
        auto wend = std::sregex_iterator();

        std::vector<std::string> v;

        for(; what != wend; ++what) {
            std::smatch match = *what;
            v.push_back(match.str());
        }
    }

    cout << endl;
    cout << endl;
    const int iMax = 1000;
    const char* versionString = "Version 1.2.3.4";
    stdcOut(iMax << " * Version parse of '" << versionString << "'.");

    CStopWatch sw;
    sw.Start();
    //std::time()
    VersionToken vtok1;

    for(int i = 0; i < iMax; ++i)
    {
        std::istringstream instream3;
        instream3.str(versionString);
        instream3 >> vtok1;

        /*std::istringstream instreamCText2;
           instreamCText2.str(str);
           //instreamCText2.seekg(std::ios_base::beg);
           InfoTextLoader loader2;
           instreamCText2 >> loader2;*/
    }
    sw.Stop();
    cout << "Time: " << sw.GetDuration() << endl;
    cout << "VersionToken: " << vtok1 << endl;
    cout << endl;
    cout << endl;

    // Todo: create a version class derived from a token class in the serializer lib
    //       that reads in versioned stuff from iostream.
} // SimulateInOut