M    src/toolbox/collisions.cpp

M    src/cellScm.cpp

be Mitocheck-specifically re-adjusted because this value is considered when creating local masks
for the atomic phase functions (and Mitocheck does BIG translations and the cellLookDistance found
in our configs is typically not large enough to allow to create large enough local masks).
M    src/cell.h

the rendered cell plus 2px wide border (as the least safe extension). Thus, the target
mask image, into which the cell is finally rendered/copied, must have borders large
enough to host this small extra border -- which is usually the case as local mask of phase
functions are created with generous borders...
M    toolbox/bp_lists.cpp

ScmNewCellPositionCollide() functions do not let cell approach border closer than 2px.
This becomes essential when rendering the cell into the sceneMasks, as explained above.
M    cellScm.cpp

M    CMakeLists.txt
M    src/cellChr.cpp
M    src/scheduler.cpp

Added the new functionality into the main rnd walk file.
Added a new Get/Set function to the rnd walk class.
M    src/toolbox/randWalk.h

Uses now the 3D walk for "universal cell movement".
M    src/cellScm.cpp

3D-related initialization of the rnd wlk in the cell's constructor.
M    src/cell.h

Added/updated the reports.
M    src/main.cpp

Introduced a new parameter: the anisotropy along the z-axis of the 3D random walk.
M    config/config-middleVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config-synthHeLa/small_masks/config-synthHela.ini
M    config-synthHeLa/standard_masks/config-synthHela.ini

M    bp_lists.cpp

which lead to some rendering issue ("pixelShift has negative values" error).

Typos in the docs were corrected.
M    src/toolbox/collisions.h

Thresholding of the correlation results into a freePositions image prevents
flagging the border pixels as free (=available to occupy).
Removed some ages-long deprecated code.
M    src/toolbox/collisions.cpp

Only added comments/documentation to the parameters of Cell::GenerateNucleolus().
M    src/cell.cpp

Very decent reformating of a small portion of the code.
Corrected bug that prevented second nuclei (after split) to be rendered
when macro ENABLE_NUCLEOLI was disabled.
M    src/cell_04_Telophase.cpp

HeLa sequence used in the TMI paper. There are two versions available:

small_masks: the simulation happens directly at the original resolution of the real HeLa videos
standard_masks: the simulation happens at about twice better spatial resolution

Temporal resolution used in the configurations files is comparable to the one of the real videos.

A    config-synthHeLa
A    config-synthHeLa/small_masks
AM   config-synthHeLa/small_masks/initialI.ics
A    config-synthHeLa/small_masks/config-synthHela.ini
AM   config-synthHeLa/small_masks/initialII.ics
A    config-synthHeLa/start2.sh
A    config-synthHeLa/init_positions_in_microns.txt
A    config-synthHeLa/init_positions_in_microns2.txt
A    config-synthHeLa/standard_masks
AM   config-synthHeLa/standard_masks/initialI.ics
A    config-synthHeLa/standard_masks/config-synthHela.ini
AM   config-synthHeLa/standard_masks/initialII.ics

calculation of MSD curves.

New flag "report for 2D MSD analysis = 1" was introduced into the testing section.
M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini


Cell::ScmRenderCellIntoMask() has new parameter: a time value to possibly report.
M    src/cell.h
M    src/cellScm.cpp

Adjusted lines whereever the above function is used.
M    src/cell.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

- added some missing parts of the RndWlk (the part around mean step size distribution)
- configuration that enables Mitocheck-like behaviour moved from 'testing' section into the 'cell' one
- following the Mitocheck-like behaviour during simulation is no longer communicated as a "TESTING MODE"

M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini
M    src/cell.cpp
M    src/cellScm.cpp
M    src/cell.h

Added some more debug to figure out why we are getting some rendering error.
(error msg: pixelShift has negative coordinates)
M    src/toolbox/bp_lists.cpp

M    CMakeLists.txt
M    Doxyfile
M    src/cell.cpp
M    src/cell.h
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.h
M    src/main.cpp
M    src/molecule.h
M    src/scheduler.h
M    src/settings.h
M    src/toolbox/bp_lists.h
M    src/toolbox/cell_movement.h
M    src/toolbox/collisions.h
M    src/toolbox/deformations.h
M    src/toolbox/finalpreview.h
M    src/toolbox/flowfields.h
M    src/toolbox/importexport.h
M    src/toolbox/perlin.h
M    src/toolbox/randWalk.h
M    src/toolbox/rnd_generators.h
M    src/toolbox/shape_rendering.h
M    src/toolbox/user_abort.h
M    src/types.h

M    Doxyfile

M    Doxyfile

M    src/main.cpp

chromatin repairs are effective/on.

M    src/main.cpp

for creating local single-cell masks has been "enhanced". That is,
the new created local image considers only 80% of the simulation
(it still does not consider sceneMasks, though).

M    src/toolbox/bp_lists.cpp
M    src/toolbox/bp_lists.h

from cell.h to settings.h. The new added macro is SIMPLIFY_CHROMATIN_OUTLIERS_CORRECTIONS
that enables to make more naive but faster routine to correct
for chromatin outliers (instead of the "expensive" DT).
M    cell.h
M    settings.h


Added sensitivity to the new macro SIMPLIFY_CHROMATIN_OUTLIERS_CORRECTIONS.
M    cell_06_G1Phase.cpp
M    cell_07_SPhase.cpp
M    cell_08_G2Phase.cpp

for obtaining some valid translation vector (of cell movement) -- this has not changed :-)
However, we used to use a "binning" during sampling of the surrounding space
to speed up the process considerably. Now, this process is activated
(depending on the scene, of course) only sparsly and so we can afford to
wait longer and recover more possible translations. In this commit,
the sampling was returned to the full-res one -- as it once used to be.

M    cellScm.cpp

When the (new) RndWlk routine is not successful in suggesting translation,
the system uses the (old) routine, which samples around the cell and then
chooses among the free positions. However, the sampling was is "binned"
and so not every pixel within the "bin" in the sampled mask is guaranteed
to represent for sure a non-colliding translation. The bug was that the
system had not enough trials at hand when choosing from this sampled mask,
and if it was unlucky enough, it kept choosing always wrong pixels...

M    src/cellScm.cpp
M    src/toolbox/cell_movement.cpp

is split into many pieces such that it is never longer than normal G2 phase.
This prevents from super-large "local" mask due to long-lasting atomic phase.

M    cell.cpp

functions...

M    cellChr.cpp

they to the same job as their original version, but do
corrections differently -- no DT transform is used, but
just slow shift towards chromatin centre is used instead,
which is a lot faster (but seems to be a little error prone).

Added:
Cell::ChrMoveWithBrown() and Cell::ChrMoveByFlow() with no dmOfBackground parameter.

M    cell.h
M    cellChr.cpp

Updated a config and provided a new initial image for relatively larger simulations (large image, many cells).
M    config/config-711extVOI-highSNR.ini
M    images/initial_mask_7-11_extended.ics

Removed obsoleted and incompatible initial images.
D    images/initial_mask_after_005_extended.ics
D    images/initial_mask_after_015_extended.ics

Removed some TMI quirk, added some hints for the future.
M    src/cell.h

Simulation reports values recently newly recognized in the configs.
M    src/main.cpp

M    src/main.cpp

Disabled openMP pragma as long as it is not supported our CMakeLists.txt.
M    src/cellScm.cpp

Corrected so that static builds work again.
M    CMakeLists.txt

Also added optional (in [testing] section) distribution
of turning angles that was computed from the real HeLa sequence.
Some other random walk params are read out from the config file now.
M    src/cell.h

Added some report/debug message to be used in scripts with MSD analysis.
M    src/cellScm.cpp

Added corresponding a few items into all config files.
M    config/config-711extVOI-highSNR.ini
M    config/config-middleVOI-highSNR.ini
M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini

Cells now initiated to use normally distributed displ. step
with params rather close to the HeLa Mitocheck dataset (provided
delay between frames is cca 30min).
M    src/cell.h

Added some DEBUG reports to study RndWlk behaviour better.
M    src/cellScm.cpp

Added support for the normally distributed displacement vectors.
M    src/toolbox/randWalk.h

option to report chrCentres during the simulation.

M    src/cellChr.cpp

before it returns to the previous version of how translational
movement vector has been established. RandomWalk has to be
completed with 3D movements.

M    src/cell.h
M    src/cellScm.cpp
A    src/toolbox/randWalk.h

M    src/cellScm.cpp
M    src/toolbox/bp_lists.cpp

Cells are dividing into a smaller ones again.
M    src/cell_05_Cytokinesis.cpp

M    CMakeLists.txt

M    src/main.cpp

LOCK file se jmenuje Mitogen, nikoliv Mitopacq.
M    src/scheduler.cpp

A    CMakeLists.txt
A    Doxyfile
A    config
A    config/config-711extVOI-highSNR.ini
A    config/config-middleVOI-highSNR.ini
A    config/config-middleVOI-lowSNR.ini
A    config/config-smallVOI-highSNR.ini
A    config/config-smallVOI-lowSNR.ini
A    images
AM   images/initial_mask_7-11_extended.ics
AM   images/initial_mask_after_005_extended.ics
AM   images/initial_mask_after_015_extended.ics
A    psf
AM   psf/sample_psf.ics
A    src
A    src/cell.cpp
A    src/cell.h
A    src/cellChr.cpp
A    src/cellSOFA.cpp
A    src/cellScm.cpp
A    src/cell_00_Samplephase.cpp
A    src/cell_01_Prophase.cpp
A    src/cell_02_Metaphase.cpp
A    src/cell_03_Anaphase.cpp
A    src/cell_04_Telophase.cpp
A    src/cell_05_Cytokinesis.cpp
A    src/cell_06_G1Phase.cpp
A    src/cell_07_SPhase.cpp
A    src/cell_08_G2Phase.cpp
A    src/dots.cpp
A    src/dots.h
A    src/macros.h
A    src/main.cpp
A    src/molecule.cpp
A    src/molecule.h
A    src/scheduler.cpp
A    src/scheduler.h
A    src/settings.h
A    src/toolbox
A    src/toolbox/bp_lists.cpp
A    src/toolbox/bp_lists.h
A    src/toolbox/cell_movement.cpp
A    src/toolbox/cell_movement.h
A    src/toolbox/collisions.cpp
A    src/toolbox/collisions.h
A    src/toolbox/deformations.cpp
A    src/toolbox/deformations.h
A    src/toolbox/finalpreview.cpp
A    src/toolbox/finalpreview.h
A    src/toolbox/flowfields.cpp
A    src/toolbox/flowfields.h
A    src/toolbox/hungarian
A    src/toolbox/hungarian/Assignment.cpp
A    src/toolbox/hungarian/Assignment.h
A    src/toolbox/hungarian/BipartiteGraph.cpp
A    src/toolbox/hungarian/BipartiteGraph.h
A    src/toolbox/hungarian/Hungarian.cpp
A    src/toolbox/hungarian/Hungarian.h
A    src/toolbox/hungarian/Matrix.h
A    src/toolbox/hungarian/README
A    src/toolbox/importexport.cpp
A    src/toolbox/importexport.h
A    src/toolbox/perlin.cpp
A    src/toolbox/perlin.h
A    src/toolbox/rnd_generators.cpp
A    src/toolbox/rnd_generators.h
A    src/toolbox/shape_rendering.cpp
A    src/toolbox/shape_rendering.h
A    src/toolbox/user_abort.cpp
A    src/toolbox/user_abort.h
A    src/types.h
A    tools
A    tools/getMax.cpp
A    tools/scripts
AM   tools/scripts/finalize.sh

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