ADD: Visualization of Scheduling. (549a5b85) · Commits · Vladimír Ulman / ofTools

CMakeLists.txt

+7 −3

Original line number	Diff line number	Diff line
		@@ -64,7 +64,8 @@ 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 (SAVE_LOCK_VIS "Shall I save visualization of custom-shaped locks? (Only when DO_MULTITHREADING is turned ON.)" OFF)
		option (SAVE_SCHEDULING_VIS "Shall I save visualization of scheduling? (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)
		@@ -101,9 +102,12 @@ endif (SAVE_TIFFS)
		if (SAVE_FLOWFIELDS)
		add_definitions(-DGTGEN_WITH_FLOWFIELDS)
		endif (SAVE_FLOWFIELDS)
		if (SAVE_LOCK_VISUALIZATION)
		if (SAVE_LOCK_VIS)
		add_definitions(-DGTGEN_WITH_LOCKVISUALIZATION)
		endif (SAVE_LOCK_VISUALIZATION)
		endif (SAVE_LOCK_VIS)
		if (SAVE_SCHEDULING_VIS)
		add_definitions(-DGTGEN_WITH_SCHEDULINGVISUALIZATION)
		endif (SAVE_SCHEDULING_VIS)
		if (DO_RIGID_MOTION)
		add_definitions(-DGTGEN_WITH_RIGIDMOTION)
		endif (DO_RIGID_MOTION)

src/cell.cpp

+6 −0

Original line number	Diff line number	Diff line
		@@ -396,10 +396,12 @@ void Cell<MV,PV>::ReadMaskInG2Phase(const i3d::Image3d<MV> &cellMask,
		//to have all masks consistently generated, we must generate even this initial mask
		//with the ScmRenderCellIntoMask() function, which needs to know the CellBP vectors
		ScmRenderCellIntoMask(*scheduler.sceneMasks[this->timePoint],NULL,this->timePoint);
		#ifdef GTGEN_WITH_MULTITHREADING
		//also init the ScmRemoveCellFromMask()-related lock
		//(as it is just now when we learned the current position of the cell)
		scmReservationLock.setSphereRadius(1.25f * this->cellDiameter);
		scmReservationLock.updateSphereCentre(scmCellBPCentre);
		#endif

		//also init the cell polarity vector
		ScmResetCellPolarityVector();
		@@ -480,10 +482,12 @@ void Cell<MV,PV>::GenerateMaskInG2Phase()
		//to have all masks consistently generated, we must generate even this initial mask
		//with the ScmRenderCellIntoMask() function, which needs to know the CellBP vectors
		ScmRenderCellIntoMask(*scheduler.sceneMasks[this->timePoint],NULL,this->timePoint);
		#ifdef GTGEN_WITH_MULTITHREADING
		//also init the ScmRemoveCellFromMask()-related lock
		//(as it is just now when we learned the current position of the cell)
		scmReservationLock.setSphereRadius(1.25f * this->cellDiameter);
		scmReservationLock.updateSphereCentre(scmCellBPCentre);
		#endif

		//also init the cell polarity vector
		ScmResetCellPolarityVector();
		@@ -829,10 +833,12 @@ void Cell<MV, PV>::DoNextPhase(void)
		cellTP++;
		}

		#ifdef GTGEN_WITH_MULTITHREADING
		//update scmReservationLock
		//(only once/after the while-cycle
		// and only after outdated/old future reservations were wiped out)
		scmReservationLock.updateSphereCentre(scmCellBPCentre);
		#endif

		DEBUG_REPORT("changed reservations in "
		<< scheduler.newestScene - timePoint

src/cell.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -109,7 +109,9 @@ template <class MV, class PV> class Cell
		duplicatedCell1(NULL),
		duplicatedCell2(NULL),
		delay(0),
		#ifdef GTGEN_WITH_MULTITHREADING
		scmReservationLock(0,0,this,masks),
		#endif
		scmLastScmUsed(INT_MAX),
		SOFA_InitialPosition(0.f),
		SOFA_InitialRotation(0.f),
		@@ -1034,6 +1036,7 @@ template <class MV, class PV> class Cell
		*/
		void ScmRemoveCellFromMask(i3d::Image3d<MV> &mask);

		#ifdef GTGEN_WITH_MULTITHREADING
		/**
		* A SphereLock that represents the region (spatial extent) in which the cell
		* appeared when soft-reservation of future space was happening
		@@ -1045,6 +1048,7 @@ template <class MV, class PV> class Cell
		* The temporal extent of this structure is never updated.
		*/
		SphereLock scmReservationLock;
		#endif

		/**
		* Fills in the \e mask image using the list of boundary points Cell::scmCellBPList,

src/cellScm.cpp

+4 −3

Original line number	Diff line number	Diff line
		@@ -52,7 +52,8 @@ void Cell<MV, PV>::ScmRemoveCellFromMask(i3d::Image3d<MV> &mask)
		DEBUG_REPORT("removing ID=" << ID << " from source image at " << mask.GetOffset() << " of size " \
		<< i3d::PixelsToMicrons(mask.GetSize(),mask.GetResolution()) << " in microns");

		/* OLD code that was sweeping the whole image
		#ifndef GTGEN_WITH_MULTITHREADING
		// OLD code that was sweeping the whole image
		MV *m=mask.GetFirstVoxelAddr();
		#ifndef MITOGEN_DEBUG
		for (size_t i=0; i < mask.GetImageSize(); ++i, ++m)
		@@ -64,8 +65,7 @@ void Cell<MV, PV>::ScmRemoveCellFromMask(i3d::Image3d<MV> &mask)
		if (m == this->ID) { m=0; ++c; }
		REPORT(c << " dots were removed (ID " << ID << ")");
		#endif
		*/

		#else
		//NEW code that sweeps only the region given by this::scmReservationLock

		//time savers :-)
		@@ -113,6 +113,7 @@ void Cell<MV, PV>::ScmRemoveCellFromMask(i3d::Image3d<MV> &mask)
		}
		}
		DEBUG_REPORT(c << " dots were removed (ID " << ID << ")");
		#endif
		}

		//-----------------------------------------------------------------------------

src/cell_05_Cytokinesis.cpp

+2 −0

Original line number	Diff line number	Diff line
		@@ -849,11 +849,13 @@ void Cell<MV, PV>::DoCytokinesis(const size_t noFrames)
		#endif
		}

		#ifdef GTGEN_WITH_MULTITHREADING
		//init the scmReservationLocks for both daughters
		daughter1->scmReservationLock.setSphereRadius(1.25f * daughter1->cellDiameter);
		daughter1->scmReservationLock.updateSphereCentre(duplicatedCell1->scmCellBPCentre);
		daughter2->scmReservationLock.setSphereRadius(1.25f * daughter2->cellDiameter);
		daughter2->scmReservationLock.updateSphereCentre(duplicatedCell2->scmCellBPCentre);
		#endif

		// left cell - last finished phase and timepoint
		daughter1->currentPhase = Cytokinesis;