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

default settings of the simulator without having the need to adjust
the source code and to recompile it afterwards.

As a result: New section '[testing]' has been introduced into config files.
This section is mandatory but may be empty. Unlike the other sections, whose
content is fixed and must be strictly present, the content of this one is first
checked for presence and secondly, if found, certain action is taken (usually
overriding of default behaviour in the simulator).

Added sample full-featured configuration for the testing mode.
M    ISBI2015/config-smallVOI-lowSNR.ini

These files were modified to become sensitive to the testing mode configuration options.
M    src/main.cpp
M    src/cell.cpp
M    src/cell.h
M    src/cellScm.cpp
M    src/scheduler.cpp

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.

And corrected the importexport.cpp to compile...

AM   ISBI2015/isbi2015-cisteExport5.tar
M    src/toolbox/importexport.cpp

files. Basically, they only import/export point coordinates to/from
given text files now.

M    CMakeLists.txt
A    src/toolbox/importexport.cpp
A    src/toolbox/importexport.h

M    src/cell.h         - some typos in the docs corrected
                        - added declaration of ScmXYTranslationalMovement()
M    src/cellScm.cpp    - added implementation of ScmXYTranslationalMovement()
M    src/cellChr.cpp    - removed debug report related to the RandomWalk initialization of chromatin

M    src/cell_06_G1Phase.cpp		- correction to avoid "reconstruction" of chromatin in the very first frame
M    src/cell_07_SPhase.cpp		- ditto
M    src/cell_08_G2Phase.cpp		- ditto
											- a bug in the initialization before use of the GenerateCentrosomes() function
M    src/cell_00_Samplephase.cpp	- the same correction related to the previous bug

M    src/toolbox/bp_lists.cpp		- some pointers in the Rendering...() functions were made const
M    src/toolbox/bp_lists.h		- litte polishing of the docs

M    src/cell.cpp						- slightly "improved" :-) error report in the GenerateCentrosomes() function

The modified config file along with two sample initial masks.
Masks should not change as Igor has already created meshes for
some cells from the masks. Also the modified source codes are
added.

A    ISBI2015/config-smallVOI-lowSNR.ini
AM   ISBI2015/initial_mask_after_005-1stSet-David.ics
AM   ISBI2015/initial_mask_after_005-2ndSet-Vlado.ics
AM   ISBI2015/isbi2015-cisteExport3.tar

M    src/cell.cpp		- just added a comment to test something some day later
M    src/cell.h		- just added one comment regarding strong non-rigid deformation into the constructor
M    src/cell_04_Telophase.cpp	 - typo corrected

- random walk
- potlačený Brown
- úpravy parametrů ve finalpreview

M    src/cell.cpp
M    src/cell.h
M    src/cellChr.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/main.cpp
M    src/scheduler.cpp
M    src/toolbox/finalpreview.cpp
M    src/toolbox/flowfields.cpp
M    src/toolbox/rnd_generators.cpp
M    src/toolbox/rnd_generators.h
M    src/toolbox/shape_rendering.h

* A new function "ChrRepairDistrWieghted" for an improvement of dot distribution.

* A bug in photobleaching, that caused blinking of images, repaired. Previously, 
the conversion float->unsigned was performed by truncating the float value. Now, the 
conversion is called after 'roundf' function.

M    TODO
M    src/cell.cpp
M    src/cell.h
M    src/cellChr.cpp
M    src/cell_06_G1Phase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_08_G2Phase.cpp

				- corrected example of gnuplot commands

M    src/cell.cpp	- ChrRepairDistribution() and ChrRepairDistrLocally() were moved cellChr.cpp
M    src/cellChr.cpp	- included the two functions
			- cosmetic reorganization of functions to form semantically coherent groups

M    cell.h		- added two new functions: Cell::ChrGetCentreOfMass() and Cell::ChrGetCentreOfLowDensity()
M    cellChr.cpp	- ... and their implementation

M    cellScm.cpp	- added commented-out sample of how to use them

M    CMakeLists.txt

			  the method Cell::ChrUpdateStats() -- since Cell::ChrReportStats
			  reports all together, there was no reason to keep the updating
			  functions parted
M    cellChr.cpp	- the asimilation here...

M    cell_06_G1Phase.cpp - removed now unneccessary calls to ChrUpdateDensities()
M    cell_07_SPhase.cpp  - ditto
M    cell_08_G2Phase.cpp - ditto

				- do dilation around overcrowded points correctly
				- do it within the limits of the maskNucleus
				- than erode by 1px to get further from the maskNucleus boundaries
				- insert not-overcrowded points as additional constraints to
				  account for when choosing new distribution for the overcrowded points

M    cell.h		- ChrUpdateStats() now takes a new parameter: the percentil,
			  which is used when computing Cell::chrSpreads
M    cellChr.cpp	- implements the changes in the ChrUpdateStats()
			- added a new macro REPORT_CHRDOT_DISTRIBUTIONS_IN_ChrUpdateStats
			  that can report chromosome territory distributions for gnuplot
			  (the macro is not controlled from the Cmake, at least not yet...)

M    cellScm.cpp	- added macro-guards to get rid of a compiler warning
M    scheduler.cpp	- corrected English in some debug messages

responsible for regeneration of distribution of highly concentrated
chromocenters.

M    src/cell.cpp
M    src/cell.h
M    src/cell_06_G1Phase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_08_G2Phase.cpp
M    src/main.cpp
M    src/scheduler.cpp

A    scripts/visualize_chromocentresVariously
A    scripts/visualize_chromocentresVariously/ruzice_fromInitial.bc
A    scripts/visualize_chromocentresVariously/ruzice_pipeline
A    scripts/visualize_chromocentresVariously/ruzice_fromZero.bc
AM   scripts/visualize_chromocentresVariously/ruzice.sh

a some more statistics reporting functions.

M    cell.h						- added Cell::chrDensities,
									- added functions ChrUpdateDensities(), ChrUpdateStats(), ChrReportClosests()
M    cellChr.cpp				- added implementations of the three functions
									- little change in the reports of the ChrRenderIntoPhantoms()

M    cell_06_G1Phase.cpp	- added some debug reports related to the chromosome organization
M    cell_07_SPhase.cpp
M    cell_08_G2Phase.cpp

directly from I3DLIB. Unfortunately, new compilers and more restrictive and do not support 
this type of "transitivity".

M    CMakeLists.txt

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

Implicit option is "ON".


M    src/cell_08_G2Phase.cpp
M    src/cell_05_Cytokinesis.cpp
M    src/cell.cpp
M    src/cell_01_Prophase.cpp
M    src/cell.h
M    src/cell_04_Telophase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_06_G1Phase.cpp
M    CMakeLists.txt

M    src/cellChr.cpp	- added report about positions of chrCentres also into
							  the Cell::ChrRenderIntoPhantoms() with flow fields

Added ';' after all lines with REPORT and DEBUG_REPORT so that code
now looks nicer :-)

M    src/cell_08_G2Phase.cpp
M    src/cell_00_Samplephase.cpp
M    src/toolbox/flowfields.cpp
M    src/toolbox/rnd_generators.cpp
M    src/toolbox/bp_lists.cpp
M    src/toolbox/cell_movement.cpp
M    src/cell_02_Metaphase.cpp
M    src/cell_05_Cytokinesis.cpp
M    src/types.h
M    src/cellChr.cpp
M    src/scheduler.cpp
M    src/cell.cpp
M    src/cell_03_Anaphase.cpp
M    src/cellScm.cpp
M    src/cell.h
M    src/cell_04_Telophase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_06_G1Phase.cpp

by setting the corresponding parameter to zero in the config file.

This info has been added all config files.

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/cellScm.cpp				- little clean-up in the code related to the "stronger"
M    src/cell.h					- in the constructor, added detection for disabling of the "stronger"

M    src/cell_06_G1Phase.cpp	- corrected typo in a comment

M    src/cellChr.cpp				- added debug print of chromocenter coordinates

cell distribution to adjust the cell spread to one's need.

AM   moveCellMasks.zip

and unified output files: sceneMasks* and scenePhantoms* are always
produced and are always isotropic. If requested with the macro,
the *nonISO (typically anisotropic) versions of the above files are
produced as well.

M    CMakeLists.txt		- renamed the macro, revised the other macros and their order
M    src/main.cpp			- corrected reprint of the simulator setting (due to the new name of the macro)
M    src/scheduler.cpp	- exports masks and phantoms isotropic and optionally their anisotropic versions
M    src/settings.h		- revised documentation of the new macro

M    src/toolbox/finalpreview.cpp	- corrected for the new macro
M    src/toolbox/finalpreview.h		- corrected the docs of the PrepareFinalImage() and PrepareFinalPreviewImage()

AM   scripts/extractCellDebugLog.sh		- added new script to extract log lines regarded only to the given cell ID

M    CMakeLists.txt							- (hopefully) clarified the comment for the ISOTROPIC_GROUND_TRUTH option

M    src/cellChr.cpp							- in photobleaching, it now reports "total cell intensity" and "mean dot
													  intensity" in the ChrRenderIntoPhantoms() functions
M    src/main.cpp								- removed the ISBI Challenges settings, currently the generations
													  are simulated without any comets

and coverage is now 400% (owing to the added effect of photobleaching).
Also the paragraph about noFramesPerCellCycle was only cosmetically updated.
Added the intensity of nonspecific staining to all config files as well.

Unified that lowSNR means dynamic range usage to 40%, high means 85%.
Updated everywhere the commentary regarding the 'slice of interest'.


M    config/config-middleVOI-lowSNR.ini		- removed unused option 'comet cell count'
M    config/config-middleVOI-highSNR.ini

M    config/config-smallVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini

M    config/config-smallVOI-highSNR-correctSize.ini
D    config/config-singleCell.ini
A  + config/config-singleCell-correctSize.ini