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

Implmentace photobleachingu a sjednocení funkce GenerateRandomPosition, která byla doposud implementovaná 2x skoro stejně na odlišných místech.

M    src/cell_05_Cytokinesis.cpp
M    src/molecule.h
M    src/cellChr.cpp
M    src/dots.h
M    src/cell.cpp
M    src/cell.h
M    src/cell_07_SPhase.cpp

A    src/tools/getline_profile.cpp - reads out voxel values along specified line
M    CMakeLists.txt				- added getline_profile.cpp

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

to support the 3D-to-2D conversion.

A    src/tools/suggest_planes.cpp		- based on histogram analysis, suggests most occupied planes
													  for every frame of the given sequence
A    src/tools/remove_small_masks.cpp - removes small masks :-)

Added printing of the Copyright and License info:
M    src/tools/apply_mask.cpp
M    src/tools/correct_tracks.cpp
M    src/tools/extract_flow.cpp
M    src/tools/getMax.cpp
M    src/tools/merge_images.cpp	- can now also merge 3 images
M    src/tools/relabel_mask.cpp	- also prints help
M    src/tools/remove_label.cpp	- also now reads ID from command line

M    CMakeLists.txt		- added the new files 

M    src/tools/getrange.cpp - also reports how many unique pixel values are there in the image

Added a new tool that replaces pixel value with some other (used for relabeling of masks):
A    src/tools/relabel_mask.cpp
M    CMakeLists.txt

Updated scripts for cropping:
M    scripts/cropping_and_postprocessing/applymask.txt
M    scripts/cropping_and_postprocessing/resample.txt
M    scripts/cropping_and_postprocessing/postprocessing3D.txt
M    scripts/cropping_and_postprocessing/resample2.txt

This one is not used anymore:
D    scripts/cropping_and_postprocessing/postprocessing2D.txt

Added some helper scripts for cropping of ISOtropic mask and phantom images:
A    scripts/cropping_and_postprocessing
A    scripts/cropping_and_postprocessing/applymask.txt
A    scripts/cropping_and_postprocessing/postprocessing2D.txt
A    scripts/cropping_and_postprocessing/resample.txt
A    scripts/cropping_and_postprocessing/postprocessing3D.txt
A    scripts/cropping_and_postprocessing/resample2.txt
A    scripts/cropping_and_postprocessing/resample3.txt
A    scripts/cropping_and_postprocessing/subsample.txt

Added the GNU license comments at the beginning of each file:
M    src/tools/imagetognuplot.cpp
M    src/tools/imageinfo.cpp
M    src/tools/getslice.cpp
M    src/tools/floattogray16.cpp
M    src/tools/dt.cpp
M    src/tools/rotate90.cpp
M    src/tools/correct_tracks.cpp
M    src/tools/resample.cpp
M    src/tools/readFFvector.cpp
M    src/tools/equalize.cpp
M    src/tools/log.cpp
M    src/tools/gauss.cpp
M    src/tools/getMax.cpp
M    ...

-> gtgen-ng was renamed to mitopacq (spelled as MitoPacq in official documents)
-> tools renamed to scripts, src/tools introduced
-> many tools from the CBIA Optical flow collection of tools was
	adopted in this archive, you'll find them in src/tools as well as
	former src/toolbox/motion etc.

M    Doxyfile					- changed gtgen-ng to mitopacq
M    CMakeLists.txt			- adds the new tools
									- the binary gtgen-ng renamed to mitopacq

M    scripts/finalize.sh	- changed the name of the binary: gtgen-ng -> mitopacq
M    scripts/visualize_scheduling/prepareSchedulingPlot.sh  - ranamed gtgen-ng to mitopacq

M    src/main.cpp				- changed advice at the end: gtgen-ng -> mitopacq
M    src/scheduler.cpp		- changed the name of the lock file: gtgen-ng -> mitopacq

D    tools
D    src/toolbox/tracks
D    src/toolbox/motion
A    src/tools
A    src/tools/imagetognuplot.cpp
A    src/tools/imageinfo.cpp
A    src/tools/getslice.cpp
A    src/tools/floattogray16.cpp
A    src/tools/dt.cpp
A    src/tools/rotate90.cpp
A  + src/tools/correct_tracks.cpp
A    src/tools/resample.cpp
A    src/tools/readFFvector.cpp
A    src/tools/equalize.cpp
A    src/tools/log.cpp
A    src/tools/gauss.cpp
D    scripts/getMax.cpp
A  + src/tools/getMax.cpp
A    src/tools/pointstovtklegacy.cpp
A    src/tools/getrange.cpp
A  + src/tools/remove_label.cpp
A    src/tools/threshold.cpp
A    src/tools/median.cpp
A    src/tools/histogram.cpp
A    src/tools/changeformat.cpp
A    src/tools/imagetovtklegacy.cpp
A  + src/tools/apply_mask.cpp
A  + src/tools/extract_flow.cpp
A    src/tools/setoffset.cpp
A    src/tools/crop.cpp
A    src/tools/historyimage.cpp
A    src/tools/divide.cpp
A    src/tools/compose.cpp
A    src/tools/substract.cpp
A    src/tools/transpose.cpp
A    src/tools/multiply.cpp
A    src/tools/convolution.cpp
A    src/tools/setresolution.cpp
A    src/tools/floattogray8.cpp
A    src/tools/makeaf.cpp
A  + src/tools/merge_images.cpp
A    src/tools/build3D.cpp
A    src/tools/graytogray.cpp
A    src/tools/flip.cpp
A    src/tools/graytofloat.cpp
A  + scripts
D    scripts/batch_cmd.sh

SVN archive svn://sarapis:2201/of/tags/ISBI2013.

Here, one should find the version that's been used
for generating of the official training data for
the Cell tracking challenge at ISBI2014.

A    tools
A    tools/visualize_scheduling
A    tools/visualize_scheduling/reformatSchedulingPlot.cpp
AM   tools/visualize_scheduling/prepareSchedulingPlot.sh
A    tools/visualize_cell_volumes
A    tools/visualize_cell_volumes/volume.gp
A    tools/3D_to_2D.sh
A    tools/getMax.cpp
A    tools/aura.fi.muni.cz
AM   tools/finalize.sh
AM   tools/serialCrop.sh
A    tools/batch_cmd.sh
AM   tools/serialCompose.sh
A    Doxyfile
A    config
A    config/config-middleVOI-lowSNR.ini
A    config/config-smallVOI-highSNR-correctSize.ini
A    config/config-singleCell.ini
A    config/config-smallVOI-highSNR.ini
A    config/config-smallVOI-lowSNR.ini
A    config/config-middleVOI-highSNR.ini
A    doc
AM   doc/ukoly_ISBI2014.jpg
AM   doc/ISBI2013_ChallegeDatasets_configuration.jpg
AM   doc/cbia_logo.png
A    doc/paralel_execution.txt
AM   doc/ISBI2013_TrainingDatasets_configuration.jpg
AM   doc/ISBI2014_New_Train_and_ChallDatasets_configuration.jpg
AM   doc/internals-scheme.pdf
AM   doc/casovani_bunky.jpg
AM   doc/ISBI2014_Old_Train_and_ChallDatasets_configuration.jpg
A    images
AM   images/initial_mask_after_005.ics
AM   images/initial_single_cell.ics
A    images/initial
AM   images/initial/ID6_C10_SceneSizeB_ready.ics
AM   images/initial/ID1_C15_SceneSizeS_ready.ics
AM   images/initial/ID5_C4_SceneSizeS_ready.ics
AM   images/initial/ID4_C33_SceneSizeB_ready.ics
AM   images/initial/ID5_C5_SceneSizeS_ready.ics
AM   images/initial/ID2_C8_SceneSizeS_ready.ics
AM   images/initial/initial_mask_after_005_extended.ics
AM   images/initial/initial_mask_after_015_extended.ics
AM   images/initial/ID6_C9_SceneSizeB_ready.ics
AM   images/initial/ID3_C10_SceneSizeS_ready.ics
A    TODO
A    src
A    src/cell_08_G2Phase.cpp
A    src/cell_00_Samplephase.cpp
A    src/molecule.cpp
A    src/settings.h
A    src/toolbox
A    src/toolbox/flowfields.cpp
A    src/toolbox/perlin.h
A    src/toolbox/cell_movement.h
A    src/toolbox/deformations.h
A    src/toolbox/finalpreview.h
A    src/toolbox/shape_rendering.h
A    src/toolbox/flowfields.h
A    src/toolbox/user_abort.cpp
A    src/toolbox/tracks
A    src/toolbox/tracks/apply_mask.cpp
A    src/toolbox/tracks/merge_images.cpp
A    src/toolbox/tracks/correct_tracks.cpp
A    src/toolbox/tracks/remove_label.cpp
A    src/toolbox/user_abort.h
A    src/toolbox/rnd_generators.cpp
A    src/toolbox/collisions.cpp
A    src/toolbox/bp_lists.cpp
A    src/toolbox/rnd_generators.h
A    src/toolbox/collisions.h
A    src/toolbox/bp_lists.h
A    src/toolbox/motion
A    src/toolbox/motion/extract_flow.cpp
A    src/toolbox/cell_movement.cpp
A    src/toolbox/perlin.cpp
A    src/toolbox/deformations.cpp
A    src/toolbox/hungarian
A    src/toolbox/hungarian/Hungarian.h
A    src/toolbox/hungarian/BipartiteGraph.cpp
A    src/toolbox/hungarian/Assignment.cpp
A    src/toolbox/hungarian/Matrix.h
A    src/toolbox/hungarian/BipartiteGraph.h
A    src/toolbox/hungarian/Hungarian.cpp
A    src/toolbox/hungarian/Assignment.h
A    src/toolbox/finalpreview.cpp
A    src/toolbox/shape_rendering.cpp
A    src/cell_05_Cytokinesis.cpp
A    src/cell_02_Metaphase.cpp
A    src/types.h
A    src/dots.cpp
A    src/molecule.h
A    src/cellChr.cpp
A    src/scheduler.cpp
A    src/dots.h
A    src/cell.cpp
A    src/cell_01_Prophase.cpp
A    src/cell_03_Anaphase.cpp
A    src/cellScm.cpp
A    src/scheduler.h
A    src/cell.h
A    src/main.cpp
A    src/cell_04_Telophase.cpp
A    src/cell_07_SPhase.cpp
A    src/macros.h
A    src/cell_06_G1Phase.cpp
A    readme.txt
A    CMakeLists.txt