Improve performance and disable clock timing

Former-commit-id: 085b8cd561cfa66c78dfc7bd7147d67b96d95af8
PNNL-Comp-Mass-Spec · Aug 2, 2013 · 758b548 · 758b548
1 parent 65ca656
commit 758b548
Show file tree

Hide file tree

Showing 10 changed files with 145 additions and 88 deletions.
diff --git a/ChargeDetermination/AutoCorrelationChargeDetermination.cpp b/ChargeDetermination/AutoCorrelationChargeDetermination.cpp
@@ -35,26 +35,27 @@ namespace Engine
 
 		void AutoCorrelationChargeDetermine::ACss(std::vector<double> &Iv, std::vector<double> &Ov)
 		{
-			int     i,j;
-			float   sum,ave;
+			int     i,j,topIndex;
+			double  sum,ave;
 
 			int IvN = (int)Iv.size() ; 
 
 			ave=0.0;
 			for(j=0;j<IvN;j++) 
-				ave += (float) Iv[j];
+				ave += Iv[j];
 			ave = ave/IvN;
 			//	for(i=0;i<IvN/2;i++)  GAA 09/27/03
 			for(i=0;i<IvN;i++)
 			{
 				sum = 0.0;
-				for(j=0;j<IvN-i-1;j++)
-					sum += (float)((Iv[j]-ave) * (Iv[j+i]-ave));
+				topIndex = IvN-i-1;
+				for(j=0;j<topIndex;j++)
+					sum += ((Iv[j]-ave) * (Iv[j+i]-ave));
 
 				if(j > 0)
 				{
 					// too much weight given to high charges this way. DJ Jan 07 2007
-					Ov.push_back(sum/IvN) ;
+					Ov.push_back((float)(sum/IvN)) ;
 					//Ov.push_back(sum/j) ;
 				}
 				else
@@ -64,7 +65,8 @@ namespace Engine
 
 		short AutoCorrelationChargeDetermine::GetChargeState(PeakProcessing::Peak &pk, PeakProcessing::PeakData &peak_data, bool debug)
 		{
-			clock_t auto_start_t = clock() ;
+			// Disable timing (MEM 2013)
+			// clock_t auto_start_t = clock() ;
 			debug = false ; 
 
 			double minMZ, maxMZ ; 
@@ -102,7 +104,8 @@ namespace Engine
 				mvect_Y.push_back(intensity) ; 
 			}
 
-			clock_t start_t = clock() ;
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ;
 			mobj_interpolation.Spline(mvect_X, mvect_Y, 0, 0) ; 
 
 			minMZ = mvect_X[0];
@@ -118,8 +121,9 @@ namespace Engine
 				fVal = mobj_interpolation.Splint(mvect_X, mvect_Y, xVal);
 				mvect_Iv.push_back(fVal) ;
 			}
-			clock_t stop_t = clock() ; 
-			mint_spline_time += (stop_t - start_t) ; 
+			// Disable timing (MEM 2013)
+			// clock_t stop_t = clock() ; 
+			// mint_spline_time += (stop_t - start_t) ; 
 
 			if (debug)
 			{
@@ -132,7 +136,9 @@ namespace Engine
 				}
 			}
 
-			start_t = clock() ;
+			// Disable timing (MEM 2013)
+			// start_t = clock() ;
+
 			ACss(mvect_Iv, mvect_autocorrelation_scores);
 			if (debug)
 			{
@@ -145,8 +151,9 @@ namespace Engine
 				}
 			}
 
-			stop_t = clock() ; 
-			mint_autocorrelation_time += (stop_t - start_t) ; 
+			// Disable timing (MEM 2013)
+			// stop_t = clock() ; 
+			// mint_autocorrelation_time += (stop_t - start_t) ; 
 
 			int j=0;
 			int minN ; 
@@ -209,7 +216,8 @@ namespace Engine
 						found = peak_data.GetPeakFromAllOriginalIntensity(peakA - FWHM, peakA + FWHM, iso_peak) ;
 						if (found)
 						{
-							mint_total_cs_time += (clock() - auto_start_t) ; 
+							// Disable timing (MEM 2013)
+							// mint_total_cs_time += (clock() - auto_start_t) ; 
 							return tmp ; 
 						}
 					}
@@ -219,14 +227,16 @@ namespace Engine
 						found = peak_data.GetPeakFromAllOriginalIntensity(peakA - FWHM, peakA + FWHM, iso_peak) ; 
 						if (found && iso_peak.mdbl_mz * tmp < 3000)
 						{
-							mint_total_cs_time += (clock() - auto_start_t) ; 
+							// Disable timing (MEM 2013)
+							// mint_total_cs_time += (clock() - auto_start_t) ; 
 							return tmp ; 
 						}
 					}
 				}
 			}
 
-			mint_total_cs_time += (clock() - auto_start_t) ; 
+			// Disable timing (MEM 2013)
+			// mint_total_cs_time += (clock() - auto_start_t) ; 
 			return returnCSVal;
 		}
 

diff --git a/DeconEngine.sdf.REMOVED.git-id b/DeconEngine.sdf.REMOVED.git-id
@@ -1 +1 @@
-1cbead774513b91da7785109ff6d94f1a7c1bd3a
+c4ea9077030eabdeb273d15369f98081f813e204
diff --git a/DeconEngine.sln b/DeconEngine.sln
@@ -5,8 +5,6 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "DeconEngineV2", "DeconEngin
 EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "UnitTests", "UnitTests\UnitTests\UnitTests.csproj", "{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "ConsoleBasedTesting", "..\ConsoleBasedTesting\ConsoleBasedTesting.csproj", "{9E48169B-1AE5-442F-AC76-F0B543906886}"
-EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -35,29 +33,15 @@ Global
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Any CPU.ActiveCfg = Debug|x86
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Any CPU.Build.0 = Debug|x86
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Mixed Platforms.ActiveCfg = Debug|x86
-		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Mixed Platforms.Build.0 = Debug|x86
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Win32.ActiveCfg = Debug|Any CPU
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|x86.ActiveCfg = Debug|x86
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|x86.Build.0 = Debug|x86
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Any CPU.Build.0 = Release|Any CPU
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Mixed Platforms.ActiveCfg = Release|Any CPU
-		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Mixed Platforms.Build.0 = Release|Any CPU
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Win32.ActiveCfg = Release|Any CPU
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|x86.ActiveCfg = Release|x86
 		{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|x86.Build.0 = Release|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Any CPU.ActiveCfg = Debug|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Mixed Platforms.ActiveCfg = Debug|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Mixed Platforms.Build.0 = Debug|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Win32.ActiveCfg = Debug|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|x86.ActiveCfg = Debug|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|x86.Build.0 = Debug|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Any CPU.ActiveCfg = Release|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Mixed Platforms.ActiveCfg = Release|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Mixed Platforms.Build.0 = Release|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Win32.ActiveCfg = Release|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Release|x86.ActiveCfg = Release|x86
-		{9E48169B-1AE5-442F-AC76-F0B543906886}.Release|x86.Build.0 = Release|x86
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

diff --git a/DeconEngine.vcxproj b/DeconEngine.vcxproj
@@ -68,7 +68,7 @@
     <Link>
       <AdditionalDependencies>mscoree.lib;msvcrtd.lib;Ws2_32.lib;xerces-c_2.lib;msvcrt.lib;xerces-c_2D.lib;%(AdditionalDependencies)</AdditionalDependencies>
       <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
-      <AdditionalLibraryDirectories>C:\xerces\xerces-c-windows_2000-msvc_60\lib;C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
+      <AdditionalLibraryDirectories>C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\lib;C:\xerces\xerces-c-windows_2000-msvc_60\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <ForceSymbolReferences>__DllMainCRTStartup%4012;%(ForceSymbolReferences)</ForceSymbolReferences>
       <GenerateDebugInformation>true</GenerateDebugInformation>
       <AssemblyDebug>true</AssemblyDebug>
@@ -79,7 +79,7 @@
   </ItemDefinitionGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
     <ClCompile>
-      <AdditionalIncludeDirectories>C:\xerces\xerces-c-windows_2000-msvc_60\include\;C:\PNL\LTE\Proteomics\xerces-c-windows_2000-msvc_60\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <AdditionalIncludeDirectories>C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\include\;C:\xerces\xerces-c-windows_2000-msvc_60\include\;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
       <PreprocessorDefinitions>WIN32;NDEBUG;MASSLYNX_4_INSTALLED;ANALYST_INSTALLED;XCALIBUR_INSTALLED;%(PreprocessorDefinitions)</PreprocessorDefinitions>
       <MinimalRebuild>false</MinimalRebuild>
       <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
@@ -93,7 +93,7 @@
     <Link>
       <AdditionalDependencies>mscoree.lib;msvcrt.lib;Ws2_32.lib;xerces-c_2.lib;%(AdditionalDependencies)</AdditionalDependencies>
       <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
-      <AdditionalLibraryDirectories>C:\xerces\xerces-c-windows_2000-msvc_60\lib;C:\PNL\LTE\Proteomics\xerces-c-windows_2000-msvc_60\lib;C:\Projects\Decon2LS\DeconEngine\bin;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
+      <AdditionalLibraryDirectories>C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\lib;C:\xerces\xerces-c-windows_2000-msvc_60\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <ForceSymbolReferences>__DllMainCRTStartup%4012;%(ForceSymbolReferences)</ForceSymbolReferences>
       <GenerateDebugInformation>true</GenerateDebugInformation>
       <RandomizedBaseAddress>false</RandomizedBaseAddress>

diff --git a/HornTransform/AreaFit.cpp b/HornTransform/AreaFit.cpp
@@ -30,7 +30,8 @@ namespace Engine
 			bool debug)
 		{
 
-			clock_t start_t = clock() ; 
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ; 
 			int num_points = (int)mvect_distribution_mzs.size() ; 
 			if (num_points < 3)
 				return 1 ; 
@@ -63,8 +64,9 @@ namespace Engine
 				}
 			}
 
-			clock_t stop_t = clock() ; 
-			mint_fit_processing_time += (stop_t - start_t) ; 
+			// Disable timing (MEM 2013)
+			// clock_t stop_t = clock() ; 
+			// mint_fit_processing_time += (stop_t - start_t) ; 
 
 			return fit/(sum + 0.001) ; 
 		}
@@ -73,7 +75,8 @@ namespace Engine
 			double intensity_normalizer, double mz_delta, double min_intensity_for_score,
 			bool debug )
 		{
-			clock_t start_t = clock() ; 
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ; 
 			int num_points = (int)mvect_distribution_mzs.size() ; 
 			if (num_points < 3)
 				return 1 ; 
@@ -95,8 +98,10 @@ namespace Engine
 					sum += theoretical_intensity * theoretical_intensity ; 
 				}
 			}
-			clock_t stop_t = clock() ; 
-			mint_fit_processing_time += (stop_t - start_t) ; 
+
+			// Disable timing (MEM 2013)
+			// clock_t stop_t = clock() ; 
+			// mint_fit_processing_time += (stop_t - start_t) ; 
 
 			return fit/(sum + 0.001) ; 
 		}

diff --git a/HornTransform/ChiSqFit.cpp b/HornTransform/ChiSqFit.cpp
@@ -26,7 +26,8 @@ namespace Engine
 		double ChiSqFit::FitScore(PeakProcessing::PeakData &pk_data, short cs, PeakProcessing::Peak &pk, double mz_delta, 
 			double min_intensity_for_score, bool debug)
 		{
-			clock_t start_t = clock() ; 
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ; 
 			int num_points = (int)mvect_distribution_mzs.size() ; 
 			if (num_points < 3)
 				return 1 ; 
@@ -50,15 +51,17 @@ namespace Engine
 				}
 			}
 
-			clock_t stop_t = clock() ; 
-			mint_fit_processing_time += (stop_t - start_t) ; 
+			// Disable timing (MEM 2013)
+			// clock_t stop_t = clock() ; 
+			// mint_fit_processing_time += (stop_t - start_t) ; 
 			return fit/(sum + 0.001) ; 
 		}
 
 		double ChiSqFit::FitScore(PeakProcessing::PeakData &pk_data, short cs, double intensity_normalizer, double mz_delta, 
 			double min_intensity_for_score, bool debug)
 		{
-			clock_t start_t = clock() ; 
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ; 
 
 			int num_points = (int)mvect_distribution_mzs.size() ; 
 			if (num_points < 3)
@@ -82,8 +85,9 @@ namespace Engine
 					sum += theoretical_intensity * observed_intensity ; 
 				}
 			}
-			clock_t stop_t = clock() ; 
-			mint_fit_processing_time += (stop_t - start_t) ; 
+			// Disable timing (MEM 2013)
+			// clock_t stop_t = clock() ; 
+			// mint_fit_processing_time += (stop_t - start_t) ; 
 
 			return fit/(sum + 0.001) ; 
 		}

diff --git a/HornTransform/IsotopeFit.cpp b/HornTransform/IsotopeFit.cpp
@@ -54,11 +54,13 @@ namespace Engine
 
 		bool IsotopeFit::FindPeak(double min_mz, double max_mz, double &mz_value, double &intensity, bool debug)
 		{
-			clock_t start_t = clock() ; 
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ; 
 			if (!mbln_last_value_was_cached)
 			{
 				bool found = mobj_isotope_dist.FindPeak(min_mz, max_mz, mz_value, intensity) ; 
-				mint_find_peak_calc += (clock() - start_t) ; 
+				// Disable timing (MEM 2013)
+				// mint_find_peak_calc += (clock() - start_t) ; 
 				return found ; 
 			}
 
@@ -106,7 +108,8 @@ namespace Engine
 			}
 			if (max_index == -1)
 			{
-				mint_find_peak_cached += (clock() - start_t) ; 
+				// Disable timing (MEM 2013)
+				// mint_find_peak_cached += (clock() - start_t) ; 
 				return false ; 
 			}
 
@@ -141,13 +144,16 @@ namespace Engine
 					mz_value = X2 ; 
 					intensity = mvect_distribution_intensities[max_index] ; 
 				}
-				mint_find_peak_cached += (clock() - start_t) ; 
+				// Disable timing (MEM 2013)
+				// mint_find_peak_cached += (clock() - start_t) ; 
 				return true ; 
 			}
 
 			mz_value = X2 ; 
 			intensity = mvect_distribution_intensities[max_index] ; 
-			mint_find_peak_cached += (clock() - start_t) ; 
+
+			// Disable timing (MEM 2013)
+			// mint_find_peak_cached += (clock() - start_t) ; 
 			return true ; 
 		}
 
@@ -687,9 +693,9 @@ namespace Engine
 		{
 			double current_mz = most_abundant_mass/charge + mdbl_cc_mass ;
 			double FWHM = current_mz / resolution ; 
-			clock_t start_t = clock() ;
-
-
+
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ;
 
 			//first check the UseCaching option; then check if it is in the cache or not. 
 			//if it is in the cache, the data is retrieved and the method returns true
@@ -733,8 +739,10 @@ namespace Engine
 				mobj_isotope_dist.mdbl_most_intense_mw = mobj_mercury_cache.mdbl_most_intense_mw ; 
 				mobj_isotope_dist.mdbl_max_peak_mz =  mobj_mercury_cache.mdbl_most_intense_mw/charge + mdbl_cc_mass - ELECTRON_MASS ; 
 			}
-			clock_t stop_t = clock() ; 
-			mint_distribution_processing_time  += (stop_t - start_t) ; 
+
+			// Disable timing (MEM 2013)
+			// clock_t stop_t = clock() ; 
+			// mint_distribution_processing_time  += (stop_t - start_t) ; 
 
 			return ; 
 		}

diff --git a/HornTransform/MassTransform.cpp b/HornTransform/MassTransform.cpp
@@ -214,8 +214,9 @@ namespace Engine
 				}
 			}
 			double best_fit = 0 ; 
-			clock_t start_t = clock() ; 
-
+
+			// Disable timing (MEM 2013)
+			// clock_t start_t = clock() ; 
 
 			PeakProcessing::Peak pkCharge1 = pk ;
 
@@ -255,7 +256,8 @@ namespace Engine
 				}
 			}
 
-			mint_get_fit_score_time += (clock() - start_t) ; 
+			// Disable timing (MEM 2013)
+			// mint_get_fit_score_time += (clock() - start_t) ; 
 
 			if (best_fit > mdbl_max_fit)       // check if fit is good enough
 				return false ; 
@@ -273,11 +275,14 @@ namespace Engine
 			PeakProcessing::Peak m3_peak ; 
 			double mono_pls_two_mz = record.mdbl_mono_mw / record.mshort_cs + 2.0/record.mshort_cs  + mdbl_cc_mass ; 
 
-			start_t = clock() ; 
+			// Disable timing (MEM 2013)
+			// start_t = clock() ; 
 			pk_data.FindPeak(mono_mz - pk.mdbl_FWHM, mono_mz + pk.mdbl_FWHM, mono_peak) ; 
 
 			pk_data.FindPeak(mono_pls_two_mz - pk.mdbl_FWHM, mono_pls_two_mz + pk.mdbl_FWHM, m3_peak) ; 
-			mint_remaining_time += (clock() - start_t) ; 
+
+			// Disable timing (MEM 2013)
+			// mint_remaining_time += (clock() - start_t) ; 
 
 			record.mint_mono_intensity = (int) mono_peak.mdbl_intensity ; 
 			record.mint_iplus2_intensity = (int) m3_peak.mdbl_intensity ;
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		1cbead774513b91da7785109ff6d94f1a7c1bd3a
		c4ea9077030eabdeb273d15369f98081f813e204