Commit 7f3e2abb authored by David Wiesner's avatar David Wiesner
Browse files

ADD: Options MITOGEN_DEBUG_MULTITHREADING, GTGEN_WITH_LOCKVISUALIZATION. 

ADD: New REPORT macro DEBUG_THR_REPORT.
ADD: Cell ID into filename of visualization.
ADD: i3d::Resample when saving visualization.
BUG_FIX: Visualization of sphere-locks wasn't correct.
parent 8f94e9e9

CMakeLists.txt

+9 −1
Original line number Diff line number Diff line
@@ -38,7 +38,6 @@ set(CMAKE_VERBOSE_MAKEFILE ON CACHE STRING 
# set the debug/release version

#

option(DEBUG_VERSION "Shall I add debug information?" OFF)



if (DEBUG_VERSION)

	set(CMAKE_BUILD_TYPE "RELEASE" CACHE STATIC "" FORCE)

	add_definitions(-DMITOGEN_DEBUG -std=c++11 -Wall)
@@ -47,6 +46,11 @@ else (DEBUG_VERSION) 
	add_definitions(-std=c++11 -Wall)

endif (DEBUG_VERSION)



option(DEBUG_MULTITHREADING "Shall I add multi-threading debug information?" OFF)

if (DEBUG_MULTITHREADING)

    add_definitions(-DMITOGEN_DEBUG_MULTITHREADING)

endif (DEBUG_MULTITHREADING)



#

# options

#
@@ -60,6 +64,7 @@ option (USE_REAL_PSF "Shall I use real PSF for final images (slower!!!)?" OFF) 
option (HIGH_SNR "Shall I generate final images of higher SNR (not applied if real PSF is used)?" ON)

option (SAVE_TIFFS "Shall I save 3D TIFF images rather than ICS images?" OFF)

option (SAVE_FLOWFIELDS "Shall I also output flow field images?" OFF)

option (SAVE_LOCK_VISUALIZATION "Shall I save visualization of custom-shaped locks? (Only when DO_MULTITHREADING is turned ON.)" OFF)

option (DO_RIGID_MOTION "Shall I include rigid movement (translation plus rotation) of cells into the simulation?" ON)

option (DO_NONRIGID_MOTION "Shall I include non-rigid movement (smooth shape deformation) of cells into the simulation?" ON)

option (DO_FLAT_2DMOTION "Shall I prevent cells from movement along z-axis?" OFF)
@@ -96,6 +101,9 @@ endif (SAVE_TIFFS) 
if (SAVE_FLOWFIELDS)

    add_definitions(-DGTGEN_WITH_FLOWFIELDS)

endif (SAVE_FLOWFIELDS)

if (SAVE_LOCK_VISUALIZATION)

    add_definitions(-DGTGEN_WITH_LOCKVISUALIZATION)

endif (SAVE_LOCK_VISUALIZATION)

if (DO_RIGID_MOTION)

    add_definitions(-DGTGEN_WITH_RIGIDMOTION)

endif (DO_RIGID_MOTION)

src/cell.h

+1 −0
Original line number Diff line number Diff line
@@ -95,6 +95,7 @@ template <class MV, class PV> class Cell 
					isRunning_st(false),

#endif

					configIni(_configIni),

					// needed to be initialized here for the visualization

					ID(GetNewCellID<MV>()),

					parentID(parenttID),

					centrosomeA(NULL),

src/macros.h

+6 −0
Original line number Diff line number Diff line
@@ -88,6 +88,12 @@ 
   #define DEBUG_REPORT(x)

#endif



#ifdef MITOGEN_DEBUG_MULTITHREADING

   #define DEBUG_THR_REPORT(x) REPORT(x)

#else

   #define DEBUG_THR_REPORT(x)

#endif



/// helper macro to unify error reports

#define ERROR_REPORT(x) std::string(_SHORT_FILE_)+"::"+__FUNCTION__+"(): "+x

src/scheduler.cpp

+9 −5
Original line number Diff line number Diff line
@@ -257,9 +257,11 @@ Scheduler<MV, PV>::Scheduler(const IniHandler _configIni, 
	 else

	   close(file);

	 

	 // set visualization parameters ///////////////////////////////////////////

#ifdef GTGEN_WITH_LOCKVISUALIZATION	   

	 // set visualization parameters

	 sceneLocks_st->setImgRes(this->GetSceneRes());

	 sceneLocks_st->setImgSize(this->GetSceneSizePX());

#endif

}



//-----------------------------------------------------------------------------
@@ -397,9 +399,11 @@ Scheduler<MV, PV>::Scheduler(const IniHandler _configIni) : 
	 else

	   close(file);

	 

	 // set visualization parameters ///////////////////////////////////////////

#ifdef GTGEN_WITH_LOCKVISUALIZATION  

	 // set visualization parameters

	 sceneLocks_st->setImgRes(this->GetSceneRes());

	 sceneLocks_st->setImgSize(this->GetSceneSizePX());

#endif

}



//-----------------------------------------------------------------------------
@@ -847,7 +851,7 @@ void Scheduler<MV, PV>::Run_st(const size_t noFrames) 
	// detect available hardware threads

	// (equals to 0 if function can't determine the number of available threads)

	const size_t hwThreads_st = std::thread::hardware_concurrency();

	DEBUG_REPORT("Available hardware threads: " << hwThreads_st);

	DEBUG_THR_REPORT("Detected available hardware threads: " << hwThreads_st);

	

	// in current implementation, using more than 8 threads doesn't offer

	// any performance improvements (only increases scheduling overhead)

src/toolbox/regionlock.cpp

+76 −63
Original line number Diff line number Diff line
@@ -27,6 +27,9 @@ 
*

***********************************************************************/



#ifdef GTGEN_WITH_LOCKVISUALIZATION

	#include <i3d/transform.h> // i3d::Resample

#endif



#include "regionlock.h"
@@ -122,17 +125,13 @@ lock_handle SceneLocks::checkAndLock(CustomLock* newLock) 
			// *** Lock acquired ***

			listOfCustomLocks.push_back(newLock);

			lockAcquired = true;

#ifdef MITOGEN_DEBUG

#ifdef MITOGEN_DEBUG_MULTITHREADING

			newLock->printLockInfo();

#endif

		

			// save visualization //////////////////////////////////////////////

			if (newLock->getLockType() == sphere_lock)

#ifdef GTGEN_WITH_LOCKVISUALIZATION

			// save visualization

			saveVisualization(newLock, true);

			

			/*DEBUG_REPORT("*** Lock acquired - timePoint: "

				<< newLockHandle->getFromTimePoint() << " to "

				<< newLockHandle->getToTimePoint());*/

#endif

		}

		else

		{
@@ -200,13 +199,16 @@ bool SceneLocks::ableToLockSphere(CustomLock* curLock, CustomLock* newLock) 
	return true;

}





// visualization ///////////////////////////////////////////////////////////////

// (currently only for sphere-locks on sceneMasks)

#ifdef GTGEN_WITH_LOCKVISUALIZATION

void SceneLocks::saveVisualization(CustomLock* newLock, bool addedLock)

{

	using namespace std;

	

	// TODO: currently implemented only for sphere-locks on sceneMasks

	if (newLock->getLockType() != sphere_lock

		|| newLock->getSceneType() != masks)

		return;

	

	// draw only timePoints influenced by the current lock

	const size_t drawFromTimePoint = newLock->getFromTimePoint();

	const size_t drawToTimePoint = newLock->getToTimePoint();
@@ -265,6 +267,7 @@ void SceneLocks::saveVisualization(CustomLock* newLock, bool addedLock) 
					int z = lockImg->GetZ(i);

		

					// write cellID if voxel is in the sphere

					// (cell IDs start from 1)

					if (pow((x-x0), 2) + pow((y-y0), 2) + pow((z-z0), 2) <= pow(r, 2))

						*m=cellID;

				}
@@ -273,8 +276,6 @@ void SceneLocks::saveVisualization(CustomLock* newLock, bool addedLock) 
			++iter;

		}

		

		if (sphereCount > 0)

		{

		// get time stamp

		const report_clock::time_point currentTime_st = report_clock::now();

		const report_clock::duration runTime_st = currentTime_st - this->startTime;
@@ -290,7 +291,7 @@ void SceneLocks::saveVisualization(CustomLock* newLock, bool addedLock) 
		const chrono::milliseconds msec =

			chrono::duration_cast<chrono::milliseconds> (runTime_msec_st % chrono::seconds(1));

			

			// get date

		// get date & time

		time_t rawtime;

		struct tm* timeinfo;

		time (&rawtime);
@@ -310,6 +311,7 @@ void SceneLocks::saveVisualization(CustomLock* newLock, bool addedLock) 
			addedOrRemoved = "afterLockRemoved";				

			

		// generate file name

		SphereLock* _newLock = dynamic_cast<SphereLock*>(newLock);

		stringstream fileName;

		fileName << "lockImg_masks_tp" << setfill('0')

			<< setw(4) << tP << "_"
@@ -321,15 +323,26 @@ void SceneLocks::saveVisualization(CustomLock* newLock, bool addedLock) 
   			<< "time" << hour << "h" << min << "m" << sec << "s_" 

   			<< "date" << year << "-" << month << "-" << day << "_"

   			<< sphereCount << "locks_"

   			<< "cellId" << _newLock->getCellID() << "_"

   			<< addedOrRemoved << "." << SUFFIX;

   		

   		// resample image to custom resolution

   		i3d::Image3d<i3d::GRAY8>* resampledLockImg = new i3d::Image3d<i3d::GRAY8>();

   		i3d::Resample(*lockImg, *resampledLockImg,

   			this->imgSize.x/4,

   			this->imgSize.y/4,

   			this->imgSize.z/4);



   		// save image to HDD

	   		lockImg->SaveImage(fileName.str().c_str());   		

		}

   		resampledLockImg->SaveImage(fileName.str().c_str());

   		

   		// free memory

   		delete resampledLockImg;   		

	}



	// free memory

	delete lockImg;

}

#endif