A new repository for MitoGen framework has just been created ;-)

#######################################################################

#

# Cross platform CMake configure script

#

# This file is part of MitoGen

# 

# Copyright (C) 2013-2016 -- Centre for Biomedical Image Analysis (CBIA)

# http://cbia.fi.muni.cz/

# 

# MitoGen is free software: you can redistribute it and/or modify

# it under the terms of the GNU General Public License as published by

# the Free Software Foundation, either version 3 of the License, or

# (at your option) any later version.

# 

# MitoGen is distributed in the hope that it will be useful,

# but WITHOUT ANY WARRANTY; without even the implied warranty of

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

# GNU General Public License for more details.

# 

# You should have received a copy of the GNU General Public License

# along with MitoGen. If not, see <http://www.gnu.org/licenses/>.

# 

# Author: David Svoboda and Vladimir Ulman

# 

# Description: main configuration file 

#

#######################################################################

cmake_minimum_required(VERSION 2.8)

#

# set the compilation way

#

set(CMAKE_VERBOSE_MAKEFILE ON CACHE STRING

		  "Tracing the compilation process" FORCE)

#

# set the debug/release version

#

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

if (DEBUG_VERSION)

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

	add_definitions(-DMITOGEN_DEBUG -Wall)

else (DEBUG_VERSION)

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

	add_definitions(-Wall)

endif (DEBUG_VERSION)

#

# options

#

option (BUILD_STATIC "Shall I prepare the MitoPacq as a static executable?" OFF)

option (SHOW_TERRITORIES "Shall I also output images with labelled territories?" OFF)

option (SHOW_CENTRES "Shall I also incorporate chromocentres into output phantom images?" OFF)

option (SAVE_NUCLEI "Shall I also output images with nuclei masks?" OFF)

option (SAVE_ANISOTROPIC_GT "Shall I provide also resampled phantom and mask images (often of anisotropic resolution)?" OFF)

option (SAVE_FINAL "Shall I also generate final images from phantom images?" ON)

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 (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)

option (DO_EVENTS_SYNCHRONIZED "Shall I force more-or-less strong synchronization of cell mitoses?" OFF)

option (DO_PHOTOBLEACHING "Shall I imitate photobleaching of fluorochrome" ON)

option (DO_MULTITHREADING "Shall I do parallel computing (based on threads) if available?" ON)

option (ENABLE_NUCLEOLI "Shall I generate also the nucleoli?" ON)

option (SOFA_CONNECTOR "Shall I produce/consume data for/from the SOFA framework?" OFF)

if (SHOW_TERRITORIES)

    add_definitions(-DGTGEN_WITH_TERRITORIES)

endif (SHOW_TERRITORIES)

if (SHOW_CENTRES)

    add_definitions(-DGTGEN_WITH_CHRCENTRESINPHANTHOMS)

endif (SHOW_CENTRES)

if (SAVE_NUCLEI)

    add_definitions(-DGTGEN_WITH_NUCLEIMASKS)

endif (SAVE_NUCLEI)

if (SAVE_ANISOTROPIC_GT)

    add_definitions(-DGTGEN_WITH_ANISOTROPIC_GT)

endif (SAVE_ANISOTROPIC_GT)

if (SAVE_FINAL)

    add_definitions(-DGTGEN_WITH_FINALIMAGES)

endif (SAVE_FINAL)

if (USE_REAL_PSF)

    add_definitions(-DGTGEN_WITH_REAL_PSF)

endif (USE_REAL_PSF)	

if (HIGH_SNR)

    add_definitions(-DGTGEN_WITH_HIGHSNR)

endif (HIGH_SNR)

if (SAVE_TifFS)

    add_definitions(-DGTGEN_WITH_TifFS)

endif (SAVE_TifFS)

if (SAVE_FLOWFIELDS)

    add_definitions(-DGTGEN_WITH_FLOWFIELDS)

endif (SAVE_FLOWFIELDS)

if (DO_RIGID_MOTION)

    add_definitions(-DGTGEN_WITH_RIGIDMOTION)

endif (DO_RIGID_MOTION)

if (DO_NONRIGID_MOTION)

    add_definitions(-DGTGEN_WITH_NONRIGIDMOTION)

endif (DO_NONRIGID_MOTION)

if (DO_FLAT_2DMOTION)

    add_definitions(-DGTGEN_WITH_JUST2DTRANSLATIONS)

endif (DO_FLAT_2DMOTION)

if (DO_EVENTS_SYNCHRONIZED)

    add_definitions(-DGTGEN_WITH_STRONGSYNCHRONIZATION)

endif (DO_EVENTS_SYNCHRONIZED)

if (DO_PHOTOBLEACHING)

		  add_definitions(-DGTGEN_WITH_PHOTOBLEACHING)

endif (DO_PHOTOBLEACHING)

if (DO_MULTITHREADING)

    add_definitions(-DGTGEN_WITH_MULTITHREADING)

endif (DO_MULTITHREADING)

if (ENABLE_NUCLEOLI)

	add_definitions(-DENABLE_NUCLEOLI)

endif (ENABLE_NUCLEOLI)

if (SOFA_CONNECTOR)

	add_definitions(-DGTGEN_WITH_SOFA)

endif (SOFA_CONNECTOR)

#

# documentation stuff

#

option (DOCUMENTATION "Shall I generate documentation (requires Doxygen)?" OFF)

if (DOCUMENTATION)

	find_program(DOXYGEN_PROGRAM doxygen PATHS ${BIN_DIRS}

			  DOC "Path to the Doxygen documentation program.")

	add_custom_target(docs

			  ${CMAKE_COMMAND} -E chdir ${CMAKE_SOURCE_DIR}

			  ${DOXYGEN_PROGRAM} Doxyfile)

endif (DOCUMENTATION)

#

# collect all the source files

#

set (SRCS 

		  src/main.cpp

		  src/dots.cpp

		  src/molecule.cpp

		  src/scheduler.cpp 

		  src/cell.cpp 

		  src/cell_01_Prophase.cpp 

		  src/cell_02_Metaphase.cpp 

		  src/cell_03_Anaphase.cpp 

		  src/cell_04_Telophase.cpp 

		  src/cell_05_Cytokinesis.cpp 

		  src/cell_06_G1Phase.cpp

		  src/cell_07_SPhase.cpp

		  src/cell_08_G2Phase.cpp

		  src/cellChr.cpp

		  src/cellScm.cpp

		  src/cellSOFA.cpp

		  src/toolbox/rnd_generators.cpp 

		  src/toolbox/flowfields.cpp 

		  src/toolbox/collisions.cpp

		  src/toolbox/deformations.cpp

		  src/toolbox/perlin.cpp

		  src/toolbox/shape_rendering.cpp

		  src/toolbox/rnd_generators.cpp

		  src/toolbox/bp_lists.cpp 

		  src/toolbox/cell_movement.cpp

		  src/toolbox/finalpreview.cpp

		  src/toolbox/user_abort.cpp

		  src/toolbox/hungarian/Assignment.cpp

		  src/toolbox/hungarian/Hungarian.cpp

		  src/toolbox/hungarian/BipartiteGraph.cpp

		  src/toolbox/importexport.cpp

    )

# build the final target

ADD_EXECUTABLE(mitogen ${SRCS})

ADD_EXECUTABLE(getMax tools/getMax.cpp)

#

# dependencies...

#

include_directories(/usr/local/include)

if (BUILD_STATIC)

	set(CMAKE_find_library_SUFFIXES ".a")

   set(CMAKE_CXX_FLAGS "-static")

else (BUILD_STATIC)

	set(CMAKE_find_library_SUFFIXES ".so")

	# dynamic i3dalgo uses the f2c library for which

	# the following tweak must be here

	set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Xlinker -defsym -Xlinker MAIN__=main")

endif (BUILD_STATIC)

# GSL - gnu scientific library

find_path(INC_GSL "gsl/gsl_randist.h")

include_directories(${INC_GSL})

find_library(LIB_GSL "gsl")

set(LIBS ${LIBS} ${LIB_GSL})

# I3D - image 3D library

find_path(INC_I3D "i3d/image3d.h")

include_directories(${INC_I3D} ${INC_I3D}/i3d)

find_library(LIB_I3DCORE "i3dcore")

find_library(LIB_I3DALGO "i3dalgo")

set(LIBS ${LIBS} ${LIB_I3DALGO} ${LIB_I3DCORE})

# dynamic linker

# find_library(LIB_DL "dl")

# set(LIBS ${LIBS} ${LIB_DL})

# IniParser -- tool for parsing INI files (part of CytoPacq project)

find_path(INC_INIPARSER "ini/iniparser.h")

include_directories(${INC_INIPARSER})

find_library(LIB_INIPARSER "iniparser")

set(LIBS ${LIBS} ${LIB_INIPARSER})

# CytoPacq - static simulator & its features

find_path(INC_CYTOPACQ "cytopacq/cytogen.h")

include_directories(${INC_CYTOPACQ})

find_library(LIB_CYTOGEN "cytogen")

find_library(LIB_OPTIGEN "optigen")

find_library(LIB_ACQUIGEN "acquigen")

set(LIBS ${LIBS} ${LIB_CYTOGEN} ${LIB_OPTIGEN} ${LIB_ACQUIGEN})

if (BUILD_STATIC)

		  # add library required by I3Dlib

		  find_library(LIB_LAPACK lapack)

		  find_library(LIB_BLAS blas)

		  find_library(LIB_GFORTRAN gfortran PATHS /usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3)

		  set(LIBS ${LIBS} ${LIB_LAPACK} ${LIB_BLAS} ${LIB_GFORTRAN})

		  find_library(LIB_TIFF tiff)

		  find_library(LIB_JPEG jpeg)

		  find_library(LIB_ICS ics)

		  find_library(LIB_PNG png)

		  find_library(LIB_HDF5_HL hdf5_hl)

		  find_library(LIB_HDF5 hdf5) 

		  set(LIBS ${LIBS} ${LIB_TifF} ${LIB_JPEG} ${LIB_ICS}

		  					 ${LIB_PNG} ${LIB_HDF5} ${LIB_HDF5_HL})

		  find_library(LIB_LZMA lzma)

		  find_library(LIB_Z z)

		  set(LIBS ${LIBS} ${LIB_LZMA} ${LIB_Z})

		  find_library(LIB_FFTW_SINGLE_THREADS fftw3f_threads)

		  find_library(LIB_FFTW_SINGLE fftw3f)

		  find_library(LIB_FFTW_DOUBLE_THREADS fftw3_threads)

		  find_library(LIB_FFTW_DOUBLE fftw3)

		  find_library(LIB_FFTW_LDOUBLE_THREADS fftw3l_threads)

		  find_library(LIB_FFTW_LDOUBLE fftw3l)

		  set(LIBS ${LIBS} ${LIB_FFTW_SINGLE_THREADS}

					 ${LIB_FFTW_SINGLE}

					 ${LIB_FFTW_DOUBLE_THREADS}

					 ${LIB_FFTW_DOUBLE}

					 ${LIB_FFTW_LDOUBLE_THREADS}

					 ${LIB_FFTW_LDOUBLE})

		  find_library(LIB_GSL gsl)

		  find_library(LIB_GOMP gomp PATHS /usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3)

		  find_library(LIB_PTHREAD pthread)

		  set(LIBS ${LIBS} ${LIB_GSL} ${LIB_GOMP} ${LIB_PTHREAD})

		  set_target_properties(mitogen PROPERTIES LINK_SEARCH_START_STATIC ON)

		  set_target_properties(getMax PROPERTIES LINK_SEARCH_START_STATIC ON)

else (BUILD_STATIC)

		  find_library(LIB_FFTW_SINGLE_THREADS fftw3f_threads)

		  find_library(LIB_FFTW_SINGLE fftw3f)

		  set(LIBS ${LIBS} ${LIB_FFTW_SINGLE_THREADS} ${LIB_FFTW_SINGLE})

endif (BUILD_STATIC)

# link the targets with the required libraries

target_link_libraries(mitogen	${LIBS})

target_link_libraries(getMax	${LIBS})

;

;--------------- characteristics of one 'universal' cell ----------------

;

[cell]

; Should be 46 for humans.

chromosome count = 46

; Lengths of phases of cell cycle

; (in percents)

;

; Well, they sum up to only 95% (not 100%) and that is because

; there is Cell::SetDelay() executed after cytokinesis, which

; delays, that is, lengthen/enlarges, the budget of the G1 phase

; by 0% to 10%  (with mean of 5%) of the cell cycle length.

; So the \e durationOfG1Phase ranges, in fact, from 45% to 55%

; yielding new total of 95% to 105% (with mean at 100%).

;

; times correspond to literature

duration of G1 phase = 45.0

duration of S phase = 30.0

duration of G2 phase = 15.0

duration of prophase = 1.25

duration of metaphase = 2.85

duration of anaphase = 0.25

duration of telophase = 0.325

duration of cytokinesis = 0.325

;

;testing:

;durationOfG1Phase = 1.0

;durationOfSPhase = 1.0

;durationOfG2Phase = 1.0

;durationOfProphase = 1.0

;durationOfMetaphase = 1.0

;durationOfAnaphase = 1.0

;durationOfTelophase = 20.0

;durationOfCytokinesis = 1.0

;

;

; amount of fluorophore molecules filling the nucleus interior

; (in percents)

;

coverage = 300.0

;

; The average diameter of standard cell (in microns)

;

cell diameter = 7.0

;

; A diameter of nucleolus (in microns)

;

nucleolus diameter = 1.4

;

; How far a cell can normally move between frames (in microns)

;

; When setting this value, take into account how many

; frames are used to sample cell cycle, which correlates

; with time delay between acquisition of frames in real

; situation

;

; Default value is based on our observation that a cell

; moves 1.5-2.0um/frame if time-sampling is 9.5min/frame,

; and about 1um/frame if time-sampling is 5min/frame. Thus,

; both cases yield "average" velocities of 0.184um/min and 0.2um/min.

; We use 0.19um/min and 23.75hrs/cycle.

;

; This value must not be greater than cellLookDistance.

;

; Erik data:

; cellMagnitudeOfMovementPerFrame = 0.6 

;

; short sequences

cell magnitude of movement per frame = 0.85

;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.

;

comet cell magnitude of movement per frame = 0.5

;

; maximum magnitude of vectors used for usual and occuring-most-of-the-time

; non-rigid deformation of cells (in microns)

;

; short sequence:

cell nonrigid deformation = 0.15

;

; maximum magnitude of vectors used for "strong" non-rigid

; deformation of cells (in microns); this deformation typically

; happens just occasionally and, unlike the deformations driven

; with the cellNonRigidDeformation constant, one usually notices it;

; if set to zero, the "strong" deformation is disabled

;

; observed from Erik's data:

; cellNonRigidStrongDeformation = 1.0

;

; short sequence:

cell nonrigid strong deformation = 0.7

;

; Should or shouldn't non-rigid deformations (if available) be done

; in every frame. It is good to disable them when noFramesPerCellCycle

; is more than 60.

;

; Erik's data:

; const bool cellSparseNonRigidDeformations=true;

;

; short sequences:

cell sparse nonrigid deformations = false

;

; How far a cell can "see" when it is trying to move

; to region with lower density of cells (in microns).

;

; The higher the value is, the greater outlook a cell has

; and the higher chance it flows into less dense region (

; and the higher time demand for the simulation :-).

;

; This value must not be less than cellMagnitudeOfMovementPerFrame.

;

; Erik data:

; cellLookDistance = 1.1f*cellMagnitudeOfMovementPerFrame; 

;

; short sequences:

cell look distance = 6.0

; two presets available: "Erik data" vs. "short sequences"

;

; Default (average) number of frames per cell cycle

;

; Observation: 

; 150 frames/cycle gives 9.5min/frame provided cycle lasts 23.75 hours.

; 285 frames/cycle gives 5min/frame provided cycle lasts 23.75 hours.

;

; Erik data:

; noFramesPerCellCycle = 150

; short sequences:

number of frames per cell cycle = 50

; Eva data:

; noFramesPerCellCycle = 280; 

;

;-------------- characteristics of scheduler -------------------

;

[scheduler]

;

; Number of initial cells put into the process

;

number of initial cells = 10

;

; A constant that defines which slice from fully _ISOtropic_ 3D image

; should be used for spatiotemporal image. The spatiotemporal images

; are created from the ISOtropic images before these are anisotropically

; resampled.

;

slice of interest = 60

;

;---------------- optical system --------------------------------------

;

;

[objective]

name = Zeiss 63x/1.40 Oil DIC (new)

magnification = 63

[microscope]

name = Zeiss S100

magnification = 0.859

[microscope adapter]

magnification = 1

[confocal unit]

name = Atto CARV

magnification = 1

[confocal unit adapter]

magnification = 1

[psf]

;experimentaly measured point spread function

;corresponding to the selected components

;location = /mnt/gryf/COMMON/DATA/PSF/2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

location = 2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

;location = /home/xulman/gryfCOMMON/DATA/PSF/2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

[light source]

;experimentaly measured quadratic surface of uneven illumination

;corresponding to the selected components

b1 = 0.8507717563

b2 = 0.0003232258

b3 = 0.0002796816

b4 = -0.0000000193

b5 = -0.0000003282

b6 = -0.0000002623

[fluorophore]

photobleaching rate = 0.003

[camera]

name = Micromax 1300-YHS

pixel size = 6.7

dynamic range = 12

grid = (1300,1030)

baseline = 550

ADC gain = 6

ADC offset = 0

read out noise = 25

dark current = 0.1

full well depth = 18000

[acquisition]

time = 5000

dynamic range usage = 85

[table]

z step = 0.2

[voi]

; size and shift in microns

size = (86.7,86.7,9.3)

shift = (0,0)

[subpixel precision]

level = 1

;

;--------------- testing mode options ----------------

;

[testing]

;

; When starting the simulation with the '-g' parameter (use given initial

; masks image/file), the following two integer parameters override the span

; of IDs which the simulator searches for. Note that the created cells will

; receive their own IDs, independently of the mask image.

;

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

init mask min label = 7

init mask max label = 11

;

; For non-rigid deformations, the simulator uses a coherent deformation pool

; saved as the Scheduler::pnArray. At the start up, if this data is not found

; in a cache file pnArray.cache on harddisk, a new one is automatically

; created. When creating the new one, its 3D+t size is typically derived from

; the cell diameter (times a factor of 3.5x times scene resolution) and from

; the Scheduler::GetInterphaseBudget(). With this option, one can override

; the default. Typically we want to make it a lot tighter...

;

; Used in the main() function. The factor is a positive real number,

; the length is positive natural one.

;pnArray xyz factor = 2.0

;pnArray z length = 52

;

; The simulator is capable of performing 'strong non-rigid deformations'

; occasionally. The average number of frames between two consecutive

; 'strong deformations' is normally inferred the duration of the G2 cell

; cycle phase. This parameter may override this average delay [in frames].

;

; Used in the Cell constructor and Cell::ScmSuggestNonrigidDeformation().

; Should be positive natural number.

;strong deformation delay = 10

;

; This option overrides the simulation scenario (whatever is currently used,

; e.g., interviewing Scheduler::Run(...) with creation of comets) by calling

; a single Run(X) with X read from this parameter.

;

; Used in the main() function. Should be positive natural number.

;single run length = 1

;

; When starting the simulation, every cell starts initially in the G2 cell

; cycle phase and stays there for some random time. This parameter overrides

; this random time and, actually, fixes it for all cells to the same specified

; value.

;

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

cell initial G2 life = 5

;

; 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

; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1

; If this parameter is present, the routine for rendering territories into

; images will not render all chromatin but, instead, only the chromatin

; which is listed in the parameter.

;

; Note that the number of chromatin present in the simulation is defined

; in the [cell] section of this configuration file. So, the numbers listed

; in this parameter should range from 0 up to (the number of chromatin minus 1).

;territories show only these chromatins = 15 30 45