Vylepšená dokumentace ve stylu Doxygen. (bc3e1c0a) · Commits · Vladimír Ulman / ofTools

CMakeLists.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -143,6 +143,7 @@ set (SRCS
		src/molecule.cpp
		src/scheduler.cpp
		src/cell.cpp
		src/cell_00_Samplephase.cpp
		src/cell_01_Prophase.cpp
		src/cell_02_Metaphase.cpp
		src/cell_03_Anaphase.cpp

Doxyfile

+4 −4

Original line number	Diff line number	Diff line
		@@ -32,7 +32,7 @@ PROJECT_NAME = MitoGen
		# This could be handy for archiving the generated documentation or
		# if some version control system is used.

		PROJECT_NUMBER = "release 6.2016"
		PROJECT_NUMBER = "release 2016.7"

		# Using the PROJECT_BRIEF tag one can provide an optional one line description
		# for a project that appears at the top of each page and should give viewer
		@@ -44,9 +44,9 @@ PROJECT_BRIEF = "Generator of simulated 3D time-lapse biomedical datase
		# included in the documentation. The maximum height of the logo should not
		# exceed 55 pixels and the maximum width should not exceed 200 pixels.
		# Doxygen will copy the logo to the output directory.

		PROJECT_LOGO = doc/cbia_logo.png

		#
		# PROJECT_LOGO = doc/cbia_logo.png
		#
		# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
		# base path where the generated documentation will be put.
		# If a relative path is entered, it will be relative to the location

src/cell.cpp

+3 −0

Original line number	Diff line number	Diff line
		@@ -655,6 +655,9 @@ ListOfPhases Cell<MV, PV>::GetNextPhase() const
		return nextPhase;
		}

		/**
		* \ingroup edit
		*/
		//------------------------------------------------------------------
		template <class MV, class PV>
		void Cell<MV, PV>::DoNextPhase(void)

src/cell.h

+35 −4

Original line number	Diff line number	Diff line
		@@ -42,18 +42,30 @@
		#include "toolbox/randWalk.h"

		/**
		* \ingroup cell
		*
		* A helper function to provide IDs for objects which guarantees their uniqueness
		* within the whole scene throughout the whole simulation.
		*/
		template <class ID_TYPE> ID_TYPE GetNewCellID(void);

		/// prototype of a class defined in file 'scheduler.h'
		/**
		* \ingroup scheduler
		*
		* prototype of a class defined in file 'scheduler.h'
		*/
		template <class MV, class PV> class Scheduler;

		/// prototype of a struct defined in file 'scheduler.h'
		/**
		* \ingroup scheduler
		*
		* prototype of a struct defined in file 'scheduler.h'
		*/
		template <class TYPE> struct TrackRecord;

		/**
		* \ingroup cell
		*
		* Basic class defining live 'cell'
		* MV ... mask voxel datatype
		* PV ... phantom voxel datatype
		@@ -268,6 +280,9 @@ template <class MV, class PV> class Cell
		/// perform one atomic phase of cell cycle
		void DoNextPhase(void);

		/// perform nothing (specimen empty method)
		void DoSamplePhase(const size_t noFrames);

		/// perform one atomic phase of cell cycle
		void DoProphase(const size_t noFrames);

		@@ -1405,6 +1420,8 @@ template <class MV, class PV> class Cell

		//---------------------------------------------------------------
		/**
		* \ingroup cell
		*
		* Calculates SVD from the true-valued voxels in the \e cellMask
		* and returns the eigen vector associated with the largest eigen value.
		* The output vector \e polVec should then (hopefully) tell the major
		@@ -1420,6 +1437,8 @@ void GetCellPolarityAndCentreVector(const i3d::Image3d<bool> &cellMask,

		//---------------------------------------------------------------
		/**
		* \ingroup cell
		*
		* A function generating two independent centrosomes in the given
		* cell mask.
		*
		@@ -1433,6 +1452,8 @@ void GenerateCentrosomes(const i3d::Image3d<bool> &cellMask,

		//-------------------------------------------------------------------
		/**
		* \ingroup cell
		*
		* A function expectes two lists of Dots understood as input list
		* and output list. The function solves the min assignment problem
		* between these to lists. Finall the sequence of moving Dots from
		@@ -1452,7 +1473,10 @@ void GenerateMovementOfChromocenters
		std::vector < std::vector<Dot> > &movementOfChromocenters);

		//----------------------------------------------------------------------
		/** A function that generates required number of points into
		/**
		* \ingroup cell
		*
		* A function that generates required number of points into
		* given mask.
		*
		* \param[in] mask given mask
		@@ -1467,7 +1491,10 @@ void GenerateRandomPositions(const i3d::Image3d<T> &mask,
		const T label = T(1));

		//---------------------------------------------------------------
		/** A function that take tow 3d points (centrosomes), generates
		/**
		* \ingroup cell
		*
		* A function that take tow 3d points (centrosomes), generates
		* corresponding metaphase plate a splits the image according
		* to this plate.
		*
		@@ -1486,6 +1513,8 @@ void SplitMaskIntoTwoHalves(const i3d::Image3d<bool> &cellMask,

		//-------------------------------------------------------------------
		/**
		* \ingroup cell
		*
		* Resample array with nearest neighbour strategy with right alignment!
		* We need right alignment as the array contains time sequence and we are
		* interested in the most recent (the right most) states of the objects.
		@@ -1502,6 +1531,8 @@ void ResampleArrayNN(std::vector<T> &array, size_t samples);

		//-------------------------------------------------------------------
		/**
		* \ingroup cell
		*
		* This function sorts the second array of Dots in a way that the
		* dots in both arrays (oldDots, newDots) in corresponding
		* positions have globaly the shortest distance one to each other.

src/cell_00_Samplephase.cpp

+16 −5

Original line number	Diff line number	Diff line
		@@ -37,10 +37,13 @@
		// INSTANCE, SKIP THE NUCLEOLUS PARTS IF NO NUCLEOLUS SHOULD EXIST IN THE PHASE
		//

		/**
		* \ingroup edit
		*/
		template <class MV, class PV>
		void Cell<MV, PV>::DoSPhase(const size_t noFrames)
		void Cell<MV, PV>::DoSamplePhase(const size_t noFrames)
		{
		REPORT("\n *** *** cell ID=" << ID << ", STARTING S-phase at timePoint=" << timePoint);
		REPORT("\n *** *** cell ID=" << ID << ", STARTING Ssample-phase at timePoint=" << timePoint);

		//helper information flags:
		//whether to keep local images updated (=synchronized) with the Scheduler::scene images
		@@ -91,6 +94,8 @@ void Cell<MV, PV>::DoSPhase(const size_t noFrames)
		FlowField<float> FF;
		InitFlowField(maskCell,FF);

		i3d::Image3d<float> *distanceMap = NULL;

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

		@@ -152,7 +157,7 @@ void Cell<MV, PV>::DoSPhase(const size_t noFrames)
		//do "significant" Brownian motion within the mask
		ChrMoveWithBrown(i,0.25f,maskNucleus,1);
		//do "very little" Gravity-induced motion within the mask
		ChrMoveWithGravity(i,0.25f,maskNucleus,1);
		ChrMoveWithGravity(i,0.25f,maskNucleus,distanceMap, 1);
		}


		@@ -276,6 +281,12 @@ void Cell<MV, PV>::DoSPhase(const size_t noFrames)
		RenderBPListIntoMask(maskNucleus,(MV)3,
		scmNucleoli2BPList,scmNucleoli2BPCentre,scmNucleoli2OuterBPNumber);

		if (distanceMap)
		{
		delete distanceMap;
		distanceMap = NULL; // force recomputing distance map
		}

		//masks are done, move on to the phantom image:
		//synchronize chrDotList to the new situation
		ChrMoveByFlow(FF,*scheduler.sceneMasks[timePoint+1],this->ID);
		@@ -283,8 +294,8 @@ void Cell<MV, PV>::DoSPhase(const size_t noFrames)
		//will not appear outside the ground-truth mask, that's good ;-)
		//
		//alternatively, may be a bit faster (as smaller image is considered)
		ChrMoveByFlowBM(FF,maskCell);
		ChrCentrosomesMoveByFlowBM(FF,maskCell);
		ChrMoveByFlowBM(FF,maskCell, distanceMap);
		ChrCentrosomesMoveByFlowBM(FF,maskCell, distanceMap);

		//draw the phantom image
		ChrRenderIntoPhantoms(*scheduler.scenePhantoms[timePoint+1]);