M    CMakeLists.txt
M    src/cell.cpp
M    src/cell.h
M    src/cellChr.cpp
M    src/cellSOFA.cpp
M    src/cellScm.cpp
M    src/cell_00_Samplephase.cpp
M    src/cell_01_Prophase.cpp
M    src/cell_02_Metaphase.cpp
M    src/cell_03_Anaphase.cpp
M    src/cell_04_Telophase.cpp
M    src/cell_05_Cytokinesis.cpp
M    src/cell_06_G1Phase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_08_G2Phase.cpp
M    src/dots.cpp
M    src/dots.h
M    src/macros.h
M    src/main.cpp
M    src/molecule.cpp
M    src/molecule.h
M    src/scheduler.cpp
M    src/scheduler.h
M    src/settings.h
M    src/toolbox/bp_lists.h
M    src/toolbox/cell_movement.h
M    src/toolbox/collisions.cpp
M    src/toolbox/collisions.h
M    src/toolbox/deformations.cpp
M    src/toolbox/deformations.h
M    src/toolbox/finalpreview.cpp
M    src/toolbox/finalpreview.h
M    src/toolbox/flowfields.h
A    src/toolbox/hungarian/README
M    src/toolbox/importexport.h
M    src/toolbox/perlin.h
M    src/toolbox/rnd_generators.cpp
M    src/toolbox/rnd_generators.h
M    src/toolbox/shape_rendering.cpp
M    src/toolbox/shape_rendering.h
M    src/toolbox/user_abort.cpp
M    src/toolbox/user_abort.h
M    src/types.h

It is intentionally called a displacement, instead of velocity, to stress the fact
that the class does not deal with time variable at all.

Added one more state handling of a real number generator (because of the disp. distro).

Added UseCorrectedUniformDistribution() for the turning angle distribution which
actually creates not uniform distribution, but after drawing random samples from it,
the produced distribution is some-what nearly uniform (quite unlike from the one
produced with UseUniformDistribution()).

Added RandomWalk::ReadyToStartSimulation() indicator for those who are not sure...
M    toolbox/randWalk.h


Adjusted to provide similar trajectory data as the real example.
M    toolbox/walks.cc

Now produces:
+ series of images with trajectories of individual walks
+ single image of labeled trajectories
+ histogram of finishing positions of all trajectories
+ data for the MSD analysis in the same format as is used in the analyzer of real sequences

M    toolbox/walks.cc

M    toolbox/walks.cc

Functions are provided also for standard turning ang. distributions.
Inteface has changed...
M    toolbox/randWalk.h

Sample controlling program.
M    toolbox/walks.cc

A    toolbox/randWalk.h

And a sample program showing how to use it.
A    toolbox/walks.cc

(used to be depending only on time which produces exactly the same sequences
when executed at the very same time, e.g., from a script)

M    rnd_generators.cpp

M    src/toolbox/cell_movement.cpp

Speed-up tuning for MovsMask determination.
M    src/cellScm.cpp

Re-adjusted to meet the real original data again.
M    TMI/config-711extVOI-highSNR.ini

M    src/toolbox/bp_lists.cpp

Some report has decenlty changed.
M    src/cell.cpp

Some more tweaks for the TMI paper.
M    src/cellScm.cpp

M    src/cell_02_Metaphase.cpp

M    src/cell.h
M    src/cellChr.cpp

And made use of them where appropriate...
M    src/cell_00_Samplephase.cpp
M    src/cell_01_Prophase.cpp
M    src/cell_02_Metaphase.cpp
M    src/cell_03_Anaphase.cpp
M    src/cell_04_Telophase.cpp
M    src/cell_05_Cytokinesis.cpp

velocity/movement stuff for the TMI paper.

This was run on eight instances in paralel (givin 40 initial cells).
A    TMI
A    TMI/config-711extVOI-highSNR.ini
AM   TMI/initial_mask_7-11_extended.tif

The restarting of chromatin was disabled by RESTART_PERIOD=1000.
Cell cycle has increased length variability.
M    src/cell.h

Disabled some stats reporting functions.
M    src/cellChr.cpp

Velocity span increased.
M    src/cellScm.cpp

Only 2x noFramesPerCellCycle should be generated.
M    src/main.cpp

Added tweak to avoid having auxiliarly images greater than sceneMasks.
M    src/toolbox/bp_lists.cpp

CMAKE options:
BUILD_STATIC                     OFF                                                                                         
CMAKE_INSTALL_PREFIX             /usr/local                                                                                  
DEBUG_VERSION                    ON                                                                                          
DOCUMENTATION                    OFF                                                                                         
DO_EVENTS_SYNCHRONIZED           OFF                                                                                         
DO_FLAT_2DMOTION                 ON                                                                                          
DO_MULTITHREADING                ON                                                                                          
DO_NONRIGID_MOTION               OFF                                                                                         
DO_PHOTOBLEACHING                OFF                                                                                         
DO_RIGID_MOTION                  ON                                                                                          
ENABLE_NUCLEOLI                  OFF                                                                                         
HIGH_SNR                         ON                                                                                          
INC_CYTOPACQ                     /usr/local/include                                                                          
INC_GSL                          /usr/include                                                                                
INC_I3D                          /usr/local/include                                                                          
INC_INIPARSER                    /usr/local/include                                                                          
LIB_ACQUIGEN                     /usr/local/lib/libacquigen.so                                                               
LIB_CYTOGEN                      /usr/local/lib/libcytogen.so                                                                
LIB_DL                           /usr/lib/x86_64-linux-gnu/libdl.so                                                          
LIB_FFTW_SINGLE                  /usr/lib/x86_64-linux-gnu/libfftw3f.so                                                      
LIB_FFTW_SINGLE_THREADS          /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so                                              
LIB_GSL                          /usr/lib/libgsl.so                                                                          
LIB_I3DALGO                      /usr/local/lib/libi3dalgo.so                                                                
LIB_I3DCORE                      /usr/local/lib/libi3dcore.so                                                                
LIB_INIPARSER                    /usr/local/lib/libiniparser.so                                                              
LIB_OPTIGEN                      /usr/local/lib/liboptigen.so                                                                
SAVE_ANISOTROPIC_GT              OFF                                                                                         
SAVE_FINAL                       OFF                                                                                         
SAVE_FLOWFIELDS                  OFF                                                                                         
SAVE_NUCLEI                      OFF                                                                                         
SAVE_TIFFS                       OFF                                                                                         
SHOW_CENTRES                     OFF                                                                                         
SHOW_TERRITORIES                 OFF                                                                                         
SOFA_CONNECTOR                   OFF                                                                                         
USE_REAL_PSF                     OFF                                                                                         

Reports how long cell cycle a new cell has chosen.
M    cell.h

Couldn't compile when ENABLE_NUCLEOLI was off.
M    cellSOFA.cpp

Added parellel search for MovsMasks values
(when seeking possible translations in ScmUniversalMovement()).
M    cellScm.cpp

Corrected an error when using AllocateAndZeroNewMask()
M    cell_06_G1Phase.cpp

Render...() and SoftRender...() now do FloodFill in a tight-copy
of the cell (used to do along a copy of the input image), which
results in a lot faster overall rendering.
M    toolbox/bp_lists.cpp

M    src/tools/imageinfo.cpp

Has one new parameter that drives whether the output image should be saved as binary.
M    src/tools/threshold.cpp

if explicitly enabled during Cmake) and some new items in the
[testing] section (content of the [testing] section is optional).

M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR-correctSize.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-singleCell-correctSize.ini
M    config/config-middleVOI-highSNR.ini

M    src/scheduler.cpp

A    src/tools/calc2DFFfromChrPointsXZ.cpp
M    CMakeLists.txt

(besides the already created image with average vector counts).

M    src/tools/calc2DFFfromChrPoints.cpp

M    src/tools/getline_profile.cpp

M    CMakeLists.txt
A    src/tools/calc2DFFfromChrPoints.cpp

Added units to the displayed information.
M    src/tools/imageinfo.cpp

New param in the crop whether to zero offset of the output image or not.
M    src/tools/crop.cpp

A bug in printing out the line profile was corrected.
M    src/tools/getline_profile.cpp

the Mitopacq starts to produce also ID%02u_T%03lu_chromatinPoints.txt
files with positions of the chromatin molecules.
By tracking these, one can establish a GT flow field of the phantom
texture changes (- a subject of a tool coming in the next commit).

M    src/cell.cpp
M    src/cell_08_G2Phase.cpp

- cells can enter G2 phase atomic function again and again
  now even when SOFA is enabled in the CMake
  (so simulation can "interleave the cells", unlike "one does all after another")

- cell movement routine can now rescue cells when in collision

M    src/cell.cpp					- Cell::DoNextPhase keeps cell running in G2
M    src/cell.h					- when SOFA: added slsRotation and slsTranslation
										  (which used to be local in the G2)
M    src/cell_08_G2Phase.cpp	- added code looking for smallest translation when cell
										  has 'mustMove' true

M    src/cell_08_G2Phase.cpp

polarity (movement goes in this direction) and velocity of movement
(ability to rotate increases with velocity).

M    src/cell_08_G2Phase.cpp	- new movement code
										- corrected bug when cell is forced to stay
										  on the current position

M    src/cell.h			- typo in docs
M    src/cellSOFA.cpp	- debug report change, word 'doing' is reserved for 'greping' logs

M    src/cell.cpp		- Both initial cell mask creating functions (called from
							  the Scheduler's constructors) now also init the polarity vector
							- added implementation of GetCellPolarityAndCentreVector(),
							  which is basically a SVD calculation over given mask image
							- GenerateCentrosomes() now makes use of the above function

M    src/cell.h		- add the Cell::scmCellPolarityVector and Cell::ScmResetCellPolarityVector()
							  that updates it
							- added declaration for the GetCellPolarityAndCentreVector()

M    src/cellScm.cpp	- implementation of Cell::ScmResetCellPolarityVector() that
							  also uses GetCellPolarityAndCentreVector()

a mode, in which T000 shape files (cell, nucl* masks) are read
but (only) chromatin and deformation magnitures are generated new.

The purpose of this mode is to create and export ``new'' cells without
the need to re-mesh them in the SOFA. That's why the mask/shape stuff
is re-read while all the rest is created new.

M    ISBI2015/config-smallVOI-lowSNR.ini
M    src/cell.cpp

and to finalPreview images (only in HIGH_SNR mode)
because of the ISBI2015 paper.

This is the revision at which the data for the paper were prepared.

M    src/cell.cpp
M    src/toolbox/finalpreview.cpp

(and sample lines for them in the config file):

- cell boundary may be drawed before territories themselves
- only listed chromatin molecules can be drawed

M    ISBI2015/config-smallVOI-lowSNR.ini
M    src/cellChr.cpp

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"

								position in the very first frame as well

and, of course, means to push cells to keep to their reference
positions. User may specify her desired reference position with
the config file. If none is specified, the position as it is
imported from the SOFA is used.


M    src/cell.h	- added support for the reference positions
M    src/cellSOFA.cpp - added implementation of the support

M    src/cell.cpp	- both initial cell mask obtaining functions reposition the cell

M    ISBI2015/config-smallVOI-lowSNR.ini
						- added sample specification of the reference position
						- some docs corrected (hopefully improved ;-)

M    src/scheduler.cpp  - patched error that forced scheduler to treat boundary
                          in the user supplied initial mask image as a cell

												  a "SOFA path way" in which 26-neig. dilation is used
												  in order to sustain nice masks (the original pathway
												  broke some masks after non-rigid SOFA deformations)

M    src/toolbox/finalpreview.cpp	- added some tuning for the ISBI2015 paper

the CMake. This is realised in the Cell::GenerateDotDistributionInG2Phase(),
Cell::ReadMaskInG2Phase() and Cell::GenerateMaskInG2Phase(), which are
functions called from the both Scheduler constructors. So, the Scheduler
had not to be modified at all in order for the simulator to be able
to do the import.

M    cell.cpp					- changes in the three functions due to the import


The simulator is now capable of simulating non-moving cells in the G2 with
the SOFA framework doing the non-rigid deformations.

M    cell_08_G2Phase.cpp	- added some SOFA related branch-code ;-)


Now, the simulator is functionally the same as the snapshot pulled in r36:
"the first successfully working single-cell testing implementation of MitoPacq+SOFA."

In fact, it handles now more than just one cell...

calls the same named function from Cell for all cells.

M    scheduler.cpp	- added SOFA_InitialExport()
M    scheduler.h

M    main.cpp			- reports some params from the config [sofa] section in the MakeReport()
							- added code that fires up export of simulator data when
							  SOFA interconnections is enabled and in the export mode

allows it pre-reserve the list (std::vector) to some (over)estimated
length.

This function and the ImportPointList() can now issue a simple warning
to inform user that something may go wrong.

M    importexport.cpp
M    importexport.h

which are implemented in the new file src/cellSOFA.cpp. This is related to
the SOFA framework interconnection.

The functions provide easy way to export various data from the simulator
and to import subset of the data back to the simulator. Most of it is
controlled via the configuration file into which a new section "[sofa]"
has been introduced. This section is only mandatory iff SOFA feature is
turned on in the CMake.

M    CMakeLists.txt		- acknowledges the new cellSOFA.cpp file
A    src/cellSOFA.cpp	- SOFA export and import functions
M    src/cell.h			- added their declarations (with poor doc for now)
								- initialization of Cell::chrCentres is now in
								  the cell's constructor
M    src/cellChr.cpp		- the init of chrCentres has been removed from
								  the Cell::ChrInitialDistribution()

M    ISBI2015/config-smallVOI-lowSNR.ini	- a sample of the [sofa] section

and uses it for the old two: Scheduler::GetInterphaseBudget() and Scheduler::PrintPhaseBudgets().
The latter two functions used to rely on Cell::GetPhaseFrameBudget() in order to
do their job. This had two drawbacks: There had to be at least one cell in the scheduler,
and the reports of the two functions were biased by the used cell's randomized cell cycle length.

M    src/cell.h		- just added a comment in the Cell::GetPhaseFrameBudget()
M    src/scheduler.h		- clarifications in the docs of the budget functions
M    src/scheduler.cpp	- the two old budget functions now rely on the new one
								- added the new one: Scheduler::GetPhaseFrameBudget()
M    src/main.cpp		- decent clean up in the simulation branch of the code

"
Added a snapshot of changes for the first successfully working single-cell
testing implementation of MitoPacq+SOFA.

In the comming revisions, we should arrive to an official MitoPacq+SOFA version
in the main SVN trunk that shall produce the same results as the snapshot above.
"

The simulator is starting to be slightly sensitive to the GTGEN_WITH_SOFA directives.

M    scheduler.cpp			- creates a little less changing pnArray with SOFA
M    toolbox/bp_lists.cpp	- renders only up to scm*OuterBPNumber points

config files. The files were not modified otherwise.
The added section is, however, empty (all is commented out).

M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR-correctSize.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-singleCell-correctSize.ini
M    config/config-middleVOI-highSNR.ini