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leiferlab · Jul 15, 2022 · 87ec931 · 87ec931
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commit 87ec931
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Showing 233 changed files with 92 additions and 16 deletions.
diff --git a/...160620 Optotune Lens Driver 4 Labview package/Lens Driver (20.06.2016)/Lens Driver.lvproj b/...160620 Optotune Lens Driver 4 Labview package/Lens Driver (20.06.2016)/Lens Driver.lvproj
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<Project Type="Project" LVVersion="15008000">
+<Project Type="Project" LVVersion="17008000">
 	<Item Name="My Computer" Type="My Computer">
 		<Property Name="IOScan.Faults" Type="Str"></Property>
 		<Property Name="IOScan.NetVarPeriod" Type="UInt">100</Property>

diff --git a/acquisitionFindFrameInBuffer.vi b/acquisitionFindFrameInBuffer.vi
diff --git a/acquisitionGetChannelsFromFrame.vi b/acquisitionGetChannelsFromFrame.vi
diff --git a/acquisitionGetFrame.vi b/acquisitionGetFrame.vi
diff --git a/acquisitionGetVolume.vi b/acquisitionGetVolume.vi
diff --git a/acquisitionGetZLatestVolume.vi b/acquisitionGetZLatestVolume.vi
diff --git a/acquisitionReorderFrames.vi b/acquisitionReorderFrames.vi
diff --git a/acquisitionSaveFrames.vi b/acquisitionSaveFrames.vi
diff --git a/acquisitionStepByStep.vi b/acquisitionStepByStep.vi
diff --git a/computeDisplayImages.vi b/computeDisplayImages.vi
diff --git a/configurePorts.vi b/configurePorts.vi
diff --git a/csu.vi b/csu.vi
diff --git a/csuClose.vi b/csuClose.vi
diff --git a/csuCloseShutter.vi b/csuCloseShutter.vi
diff --git a/csuOpen.vi b/csuOpen.vi
diff --git a/csuOpenShutter.vi b/csuOpenShutter.vi
diff --git a/cwlaserClose.vi b/cwlaserClose.vi
diff --git a/cwlaserOpen.vi b/cwlaserOpen.vi
diff --git a/cwlaserSetPower.vi b/cwlaserSetPower.vi
diff --git a/cwlaserShutterFromWavelength.vi b/cwlaserShutterFromWavelength.vi
diff --git a/cwlaserShutterOpenOneCloseOthers.vi b/cwlaserShutterOpenOneCloseOthers.vi
diff --git a/daqCreateFile.vi b/daqCreateFile.vi
diff --git a/daqRead.vi b/daqRead.vi
diff --git a/daqReadEtl.vi b/daqReadEtl.vi
diff --git a/daqReadEtlSegment.vi b/daqReadEtlSegment.vi
diff --git a/displayVolume.vi b/displayVolume.vi
diff --git a/dll/wormUtilities/.vs/wormUtilities/v15/.suo b/dll/wormUtilities/.vs/wormUtilities/v15/.suo
diff --git a/dll/wormUtilities/.vs/wormUtilities/v15/Browse.VC.db b/dll/wormUtilities/.vs/wormUtilities/v15/Browse.VC.db
diff --git a/dll/wormUtilities/.vs/wormUtilities/v15/ipch/abf42a6bdbb9438f.ipch b/dll/wormUtilities/.vs/wormUtilities/v15/ipch/abf42a6bdbb9438f.ipch
diff --git a/dll/wormUtilities/wormUtilities/Header.h b/dll/wormUtilities/wormUtilities/Header.h
@@ -16,6 +16,8 @@ extern "C" WORMUTILITIES_API void segment_singleframe(
 	double &maxX, double &maxY, double maxXInStack, double maxYInStack,
 	float threshold, bool resize);
 
+float kthlargest(float array[], int size, int k);
+
 extern "C" WORMUTILITIES_API void segment_check2dcandidates_5planes(
 	float ArrB0[], float ArrB1[], float ArrB2[],
 	float ArrB3[], float ArrB4[], signed __int32 sizeBx, signed __int32 sizeBy,
@@ -44,11 +46,25 @@ extern "C" WORMUTILITIES_API void gmmreg_registration(
 
 extern "C" WORMUTILITIES_API void dsmm_registration(double *X, double *Y, int M, int N, int D,
 	double beta, double lambda, double neighbor_cutoff,
-	double alpha, double conv_epsilon,
+	double alpha, double gamma0,
+	double conv_epsilon, double eq_tol,
 	double *pwise_dist, double *pwise_distYY,
 	double *Gamma, double *CDE_term,
 	double *w, double *F_t, double *wF_t, double *wF_t_sum,
-	double *p, double *u,
+	double *p, double *u, int *Match,
 	double *hatP, double *hatPI_diag, double *hatPIG, double *hatPX, double *hatPIY,
 	double *G, double *W, double *GW,
-	double *sumPoverN, double *expAlphaSumPoverN);
+	double *sumPoverN, double *expAlphaSumPoverN);
+
+extern "C" WORMUTILITIES_API void displayImg(uint16_t* ArrA, int sizex, int sizey, int refresh_time, float* stop);
+
+extern "C" WORMUTILITIES_API uint16_t* stealPointer_uint16(uint16_t* A);
+extern "C" WORMUTILITIES_API float* stealPointer_float(float* A);
+extern "C" WORMUTILITIES_API float* stealPointer_float(float* A);
+extern "C" WORMUTILITIES_API uint16_t* allocateArray_uint16(int size);
+extern "C" WORMUTILITIES_API void deallocateArray_uint16(uint16_t* ptr);
+extern "C" WORMUTILITIES_API void writeInArray_uint16(uint16_t* src, uint16_t* dst, int size);
+
+extern "C" WORMUTILITIES_API double displayImg_py(uint16_t* ArrA, int sizex, int sizey, int refresh_time, float* stop);
+extern "C" WORMUTILITIES_API double hyperstack(uint16_t* ArrA, int shape0, int shape1, int shape2, int shape3, float* stop, float* out, int out_n, double refresh_time);
+extern "C" WORMUTILITIES_API double python_emb();
diff --git a/dll/wormUtilities/wormUtilities/wormUtilities.cpp b/dll/wormUtilities/wormUtilities/wormUtilities.cpp
diff --git a/dll/wormUtilities/wormUtilities/wormUtilities.vcxproj b/dll/wormUtilities/wormUtilities/wormUtilities.vcxproj
@@ -81,6 +81,7 @@
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
     <LinkIncremental>false</LinkIncremental>
+    <LibraryPath>$(VC_LibraryPath_x64);$(WindowsSDK_LibraryPath_x64);$(NETFXKitsDir)Lib\um\x64;</LibraryPath>
   </PropertyGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
     <ClCompile>
@@ -141,7 +142,7 @@
       <SDLCheck>true</SDLCheck>
       <PreprocessorDefinitions>NDEBUG;WORMUTILITIES_EXPORTS;_WINDOWS;_USRDLL;%(PreprocessorDefinitions)</PreprocessorDefinitions>
       <ConformanceMode>true</ConformanceMode>
-      <AdditionalIncludeDirectories>$(OPENCV_DIR)\..\..\include;C:\Users\francesco\dev\vxl\build\include\vxl\core;C:\Users\francesco\dev\vxl\build\include\vxl\vcl;C:\Users\francesco\dev\gmmreg-lw\gmmreg_lw;;C:\Users\francesco\dev\wormbrain\dsmm;;C:\Users\francesco\dev\eigen;;C:\Users\francesco\dev\boost;</AdditionalIncludeDirectories>
+      <AdditionalIncludeDirectories>$(OPENCV_DIR)\..\..\include;C:\Users\francesco\dev\vxl\build\include\vxl\core;C:\Users\francesco\dev\vxl\build\include\vxl\vcl;C:\Users\francesco\dev\gmmreg-lw\gmmreg_lw;C:\Users\francesco\dev\wormbrain\dsmm;C:\Users\francesco\dev\include;C:\Users\francesco\dev\include\eigen\;C:\Users\francesco\dev\include\eigen\Eigen\;C:\Users\francesco\Anaconda3\include\;C:\Users\francesco\Anaconda3\Lib\site-packages\numpy\core\include\numpy</AdditionalIncludeDirectories>
       <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
       <OmitFramePointers>
       </OmitFramePointers>
@@ -151,14 +152,16 @@
       <MultiProcessorCompilation>false</MultiProcessorCompilation>
       <EnableFiberSafeOptimizations>true</EnableFiberSafeOptimizations>
       <ForcedIncludeFiles>StdAfx.h;%(ForcedIncludeFiles)</ForcedIncludeFiles>
+      <OpenMPSupport>true</OpenMPSupport>
+      <FloatingPointModel>Fast</FloatingPointModel>
     </ClCompile>
     <Link>
       <SubSystem>Windows</SubSystem>
       <EnableCOMDATFolding>true</EnableCOMDATFolding>
       <OptimizeReferences>true</OptimizeReferences>
       <GenerateDebugInformation>true</GenerateDebugInformation>
-      <AdditionalLibraryDirectories>$(OPENCV_DIR)\lib;C:\Users\francesco\dev\vxl\build\lib</AdditionalLibraryDirectories>
-      <AdditionalDependencies>opencv_world341.lib;vnl_algo.lib;vnl.lib;v3p_netlib.lib;%(AdditionalDependencies)</AdditionalDependencies>
+      <AdditionalLibraryDirectories>$(OPENCV_DIR)\lib;C:\Users\francesco\dev\vxl\build\lib;C:\Users\francesco\Anaconda3\libs;</AdditionalLibraryDirectories>
+      <AdditionalDependencies>opencv_world341.lib;vnl_algo.lib;vnl.lib;v3p_netlib.lib;%(AdditionalDependencies);python36.lib</AdditionalDependencies>
     </Link>
   </ItemDefinitionGroup>
   <ItemGroup>

diff --git a/dll/wormUtilities/wormUtilities/x64/Release/dllmain.obj b/dll/wormUtilities/wormUtilities/x64/Release/dllmain.obj
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/dsmm.obj b/dll/wormUtilities/wormUtilities/x64/Release/dsmm.obj
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/dsmm_utils.obj b/dll/wormUtilities/wormUtilities/x64/Release/dsmm_utils.obj
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/gmmreg_lw.obj b/dll/wormUtilities/wormUtilities/x64/Release/gmmreg_lw.obj
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/gmmreg_lw_ext.obj b/dll/wormUtilities/wormUtilities/x64/Release/gmmreg_lw_ext.obj
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/stdafx.obj b/dll/wormUtilities/wormUtilities/x64/Release/stdafx.obj
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/vc141.pdb b/dll/wormUtilities/wormUtilities/x64/Release/vc141.pdb
diff --git a/dll/wormUtilities/wormUtilities/x64/Release/wormUtilities.log b/dll/wormUtilities/wormUtilities/x64/Release/wormUtilities.log
@@ -1,8 +1,12 @@
-  dsmm.cpp
+  wormUtilities.cpp
+c1xx : warning C4199: two-phase name lookup is not supported for C++/CLI, C++/CX, or OpenMP; use /Zc:twoPhase-
+c:\users\francesco\anaconda3\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(12): warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+c:\users\francesco\dev\pump-probe\dll\wormutilities\wormutilities\wormutilities.cpp(133): warning C4101: 'minY': unreferenced local variable
+c:\users\francesco\dev\pump-probe\dll\wormutilities\wormutilities\wormutilities.cpp(133): warning C4101: 'minX': unreferenced local variable
      Creating library C:\Users\francesco\dev\pump-probe\dll\wormUtilities\x64\Release\wormUtilities.lib and object C:\Users\francesco\dev\pump-probe\dll\wormUtilities\x64\Release\wormUtilities.exp
   Generating code
-  2 of 2313 functions (<0.1%) were compiled, the rest were copied from previous compilation.
+  2 of 2428 functions (<0.1%) were compiled, the rest were copied from previous compilation.
     0 functions were new in current compilation
-    2 functions had inline decision re-evaluated but remain unchanged
+    4 functions had inline decision re-evaluated but remain unchanged
   Finished generating code
   wormUtilities.vcxproj -> C:\Users\francesco\dev\pump-probe\dll\wormUtilities\x64\Release\wormUtilities.dll