Commit 6d550efc authored by Vladimír Ulman's avatar Vladimír Ulman
Browse files

Added rigid movement of cells with SOFA. 

Since routines from Cell::SOFA_MoveImportedToReferencePosition() and
Cell::SOFA_MoveInitialToReferencePosition() could have been reused for
the rigid movements, their become wrappers to some new helper BPs
moving functions.

M    src/cell_08_G2Phase.cpp		- added support for cell movement with SOFA
M    src/cell.h						- added docs to the new functions
M    src/cellSOFA.cpp				- guess what :-)
M    ISBI2015/config-smallVOI-lowSNR.ini		- introduced new testing parameter: "disable rigid movement"
parent e4916ceb

ISBI2015/config-smallVOI-lowSNR.ini

+18 −8
Original line number Diff line number Diff line
@@ -223,10 +223,10 @@ export mask grid stepping = 7 
; One can disable certain import by disabling/commenting respective parameter.

;

; The syntax follows that of the standard C library printf() function.

import name nucleus BP          = ../deformationsID01-05/all/ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

import name nucleoli1 BP        = ../deformationsID01-05/all/ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

import name nucleoli2 BP        = ../deformationsID01-05/all/ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

import name chromatin molecules = ../deformationsID01-05/all/ID%02u_T%03lu_chromatinPoints.txt

import name nucleus BP          = ../deformationsID01-10/ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

import name nucleoli1 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

import name nucleoli2 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

import name chromatin molecules = ../deformationsID01-10/ID%02u_T%03lu_chromatinPoints.txt



; import name nucleus BP          = ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

; import name nucleoli1 BP        = ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt
@@ -242,10 +242,12 @@ import name chromatin molecules = ../deformationsID01-05/all/ID%02u_T%03lu_chrom 
; The centre position is given in microns relative to the scene [0,0,0],

; as three (positive) real numbers separated with white space.

; The angle is given, for user convenience, in degrees.

ID01 initial position = 40.6   43		4.5

ID01 initial rotation = 45

;ID01 initial position = 40.6   43		4.5

;ID01 initial rotation = 45

ID03 initial position = 20.6 48.8 4.5

ID03 initial rotation = -90

ID04 initial position = 10.8 35.4 4.5

ID02 initial rotation = 30





;
@@ -350,7 +352,7 @@ level = 1 
;

; Used in the Scheduler constructor. Should be positive natural numbers.

;init mask min label = 1

;init mask max label = 1

init mask max label = 2



;

; For non-rigid deformations, the simulator uses a coherent deformation pool
@@ -391,5 +393,13 @@ single run length = 1 
; cells the same.

;

; Used in both Scheduler constructors. Should be positive natural number.

cell initial G2 life = 50

cell initial G2 life = 20



;

; If rigid movement of cells is enabled in the CMake, this parameter can

; disable it. It cannot, however, enable it if the rigid movement is disabled

; in the CMake (as the code is simply missing in the simulator binary then).

;

; Presence of the parameter with any value disables the movements,

; and vice versa.

disable rigid movement = 1

src/cell.h

+32 −0
Original line number Diff line number Diff line
@@ -909,6 +909,38 @@ template <class MV, class PV> class Cell 
			  * relative to the position found in the SOFA import files.

			  */

			 void SOFA_InitReferencePosition(void);



			 /**

			  * Helper functions, but actually these are the workhorses for

			  * rigid movements of cells under SOFA enabled in the CMake.

			  *

			  * This one works with cell boundary points.

			  *

			  * Performs rotation by \e rotAngle (in radians) around the centre

			  * at \e preRotTrans and then shifts the cell by \e postRotTrans - \e preRotTrans

			  * (both in microns).

			  *

			  * \param[in] preRotTrans

			  * \param[in] rotAngle

			  * \param[in] postRotTrans

			  */

			 void SOFA_TransformCellBPs(const i3d::Vector3d<float> preRotTrans,

										 const float rotAngle,

										 const i3d::Vector3d<float> postRotTrans);

			 /**

			  * Same as Cell::SOFA_TransformCellBPs() except that this one

			  * deals with nucleus and nuclei boundary points.

			  */

			 void SOFA_TransformNuclStarBPs(const i3d::Vector3d<float> preRotTrans,

										 const float rotAngle,

										 const i3d::Vector3d<float> postRotTrans);

			 /**

			  * Same as Cell::SOFA_TransformCellBPs() except that this one

			  * deals with chromatin points.

			  */

			 void SOFA_TransformChromatinPs(const i3d::Vector3d<float> preRotTrans,

										 const float rotAngle,

										 const i3d::Vector3d<float> postRotTrans);

			 //-------- SOFA -------- 



			 ///if the cell is comet, this represents its state

src/cellSOFA.cpp

+65 −39
Original line number Diff line number Diff line
@@ -222,22 +222,45 @@ void Cell<MV, PV>::SOFA_NextImport(const size_t T) 


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

template <class MV, class PV>

void Cell<MV, PV>::SOFA_MoveImportedToReferencePosition(void)

void Cell<MV, PV>::SOFA_TransformCellBPs(const i3d::Vector3d<float> preRotTrans,

										 const float rotAngle,

										 const i3d::Vector3d<float> postRotTrans)

{

	//cached results of "expensive" functions...

	const float ccooss=cos(rotAngle);

	const float ssiinn=sin(rotAngle);



	//iterators to sweep the lists...

	std::vector< i3d::Vector3d<float> >::iterator Fiter;

	

	//process cell BPs

	Fiter=scmCellBPList.begin();

	while (Fiter != scmCellBPList.end())

	{

	//time-savers...

	const i3d::Vector3d<float>

			preRotTrans( scmNucleusBPCentre );

		*Fiter -= preRotTrans;

		float nx=ccooss*Fiter->x - ssiinn*Fiter->y;

		float ny=ssiinn*Fiter->x + ccooss*Fiter->y;

		Fiter->x = nx + postRotTrans.x;

		Fiter->y = ny + postRotTrans.y;

		Fiter->z +=     postRotTrans.z;



	const i3d::Vector3d<float>

			postRotTrans ( SOFA_InitialPosition );

		++Fiter;

	}

	scmCellBPCentre=postRotTrans;

}



	//and cached results of "expensive" functions...

	const float ccooss=cos(SOFA_InitialRotation);

	const float ssiinn=sin(SOFA_InitialRotation);

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

template <class MV, class PV>

void Cell<MV, PV>::SOFA_TransformNuclStarBPs(const i3d::Vector3d<float> preRotTrans,

										 const float rotAngle,

										 const i3d::Vector3d<float> postRotTrans)

{

	//cached results of "expensive" functions...

	const float ccooss=cos(rotAngle);

	const float ssiinn=sin(rotAngle);



	//iterators to sweep the lists...

	std::vector< i3d::Vector3d<float> >::iterator Fiter;

	std::vector< Molecule >::iterator Miter;

	

	//process nucleus:

	Fiter=scmNucleusBPList.begin();
@@ -295,6 +318,20 @@ void Cell<MV, PV>::SOFA_MoveImportedToReferencePosition(void) 
	scmNucleoli2BPCentre.y = ny + postRotTrans.y;

	scmNucleoli2BPCentre.z +=     postRotTrans.z;

#endif

}



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

template <class MV, class PV>

void Cell<MV, PV>::SOFA_TransformChromatinPs(const i3d::Vector3d<float> preRotTrans,

										 const float rotAngle,

										 const i3d::Vector3d<float> postRotTrans)

{

	//cached results of "expensive" functions...

	const float ccooss=cos(rotAngle);

	const float ssiinn=sin(rotAngle);



	//iterator...

	std::vector< Molecule >::iterator Miter;



	//process chromatin:

	Miter=chrDotList.begin();
@@ -313,37 +350,26 @@ void Cell<MV, PV>::SOFA_MoveImportedToReferencePosition(void) 


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

template <class MV, class PV>

void Cell<MV, PV>::SOFA_MoveInitialToReferencePosition(void)

{

	//time-savers...

	const i3d::Vector3d<float>

			preRotTrans( scmCellBPCentre );



	const i3d::Vector3d<float>

			postRotTrans ( SOFA_InitialPosition );



	//and cached results of "expensive" functions...

	const float ccooss=cos(SOFA_InitialRotation);

	const float ssiinn=sin(SOFA_InitialRotation);



	//iterators to sweep the lists...

	std::vector< i3d::Vector3d<float> >::iterator Fiter;

	

	//process cell BPs

	Fiter=scmCellBPList.begin();

	while (Fiter != scmCellBPList.end())

void Cell<MV, PV>::SOFA_MoveImportedToReferencePosition(void)

{

		*Fiter -= preRotTrans;

		float nx=ccooss*Fiter->x - ssiinn*Fiter->y;

		float ny=ssiinn*Fiter->x + ccooss*Fiter->y;

		Fiter->x = nx + postRotTrans.x;

		Fiter->y = ny + postRotTrans.y;

		Fiter->z +=     postRotTrans.z;



		++Fiter;

	SOFA_TransformChromatinPs(scmNucleusBPCentre,

				SOFA_InitialRotation,SOFA_InitialPosition);



	SOFA_TransformNuclStarBPs(scmNucleusBPCentre,

				SOFA_InitialRotation,SOFA_InitialPosition);

	//

	//note1: Chromatin must be transformed first as transforming Nucl* points also modifies

	//their centre scmNucleusBPCentre...

	//

	//note2: parameters are handed intentionally by value (copies are made)

}



	scmCellBPCentre=postRotTrans;

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

template <class MV, class PV>

void Cell<MV, PV>::SOFA_MoveInitialToReferencePosition(void)

{

	SOFA_TransformCellBPs(scmCellBPCentre,

				SOFA_InitialRotation,SOFA_InitialPosition);

}



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

src/cell_08_G2Phase.cpp

+67 −1
Original line number Diff line number Diff line
@@ -47,6 +47,12 @@ void Cell<MV, PV>::DoG2Phase(const size_t noFrames) 


	// ---------- actions a phase needs to do before the frame generating cycle ----------

	//prepare the activity plan to spread the phase duties over the given number of frames



#else //after SOFA



	//accumulated translation and rotation

	i3d::Vector3d<float> slsTranslation(0.f);

	float slsRotation=0.f;

#endif //after SOFA



	//the main cycle
@@ -100,11 +106,71 @@ void Cell<MV, PV>::DoG2Phase(const size_t noFrames) 
		MoveBPListAndCentre(scmNucleoli2BPList,scmNucleoli2BPCentre,FF);

#endif

#else //after SOFA

		//read the current cell shape, driven now by the SOFA:

		//read the comming cell shape, driven now by the SOFA:

		SOFA_NextImport(timePoint+1);

		scmCellBPList=scmNucleusBPList;

		scmCellOuterBPNumber=scmNucleusOuterBPNumber;

		scmCellBPCentre=scmNucleusBPCentre;



#ifdef GTGEN_WITH_RIGIDMOTION

		if ( !configIni["testing"].present("disable rigid movement") )

		{

			//try to move the cell...

			i3d::Vector3d<float> sugTranslation;	//suggested transl.

			float sugRotation;							//suggested rotation



			int tries=0;									//attempts counter

			bool collision=true;							//suggested configuration flag



			//while not many unsuccessful attempts...

			while ((collision) && (tries < 500))

			{

				SuggestBrownianVector(sugTranslation,

						i3d::Vector3d<float>(cellMagnitudeOfMovementPerFrame,

													cellMagnitudeOfMovementPerFrame,

													0.f) //cellMagnitudeOfMovementPerFrame/3.f)

											);

				//sugRotation=GetRandomGauss(0.f,0.23f);

				sugRotation=GetRandomGauss(0.3*scmLastRotationAngle,0.23f * (1.f + float(tries)/500.0));

				++tries;



				//check the new suggestion...

				collision=ScmNewCellPositionCollide(SOFA_InitialPosition,

																slsRotation+sugRotation,

																slsTranslation+sugTranslation);

			}

			if (!collision)

			{

				//accept the new position

				REPORT("translating by " << sugTranslation

							<< " microns and rotating by "

							<< sugRotation*180.f/3.14159f

							<< " degrees after " << tries << " tries");



				//remember the linking transformation

				slsRotation+=sugRotation;

				slsTranslation+=sugTranslation;



				//remember the last movement

				scmLastTranslationVector=sugTranslation;

				scmLastRotationAngle=sugRotation;



				//and commit it to the cell representation

				SOFA_TransformCellBPs(SOFA_InitialPosition,

								slsRotation,SOFA_InitialPosition+slsTranslation);

				SOFA_TransformNuclStarBPs(SOFA_InitialPosition,

								slsRotation,SOFA_InitialPosition+slsTranslation);

				SOFA_TransformChromatinPs(SOFA_InitialPosition,

								slsRotation,SOFA_InitialPosition+slsTranslation);

			}

			else

				//if unsuccessful in suggesting, try also the current position

				if (ScmNewCellPositionCollide(i3d::Vector3d<float>(0.f)))

					throw ERROR_REPORT("Unable to find non-colliding movement.");

		}

		else

		REPORT("TESTING MODE: rigid cell movement is disabled");

#endif

#endif //after SOFA