- Jul 10, 2015
-
-
Vladimír Ulman authored
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
-
- Jul 03, 2015
-
-
Vladimír Ulman authored
M src/cell_02_Metaphase.cpp
-
Vladimír Ulman authored
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
-
- Jul 02, 2015
-
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
- May 10, 2015
-
-
Vladimír Ulman authored
-
- May 06, 2015
-
-
Vladimír Ulman authored
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
-
- May 05, 2015
-
-
Vladimír Ulman authored
M src/scheduler.cpp
-
- Jan 28, 2015
-
-
Vladimír Ulman authored
A src/tools/calc2DFFfromChrPointsXZ.cpp M CMakeLists.txt
-
- Jan 27, 2015
-
-
Vladimír Ulman authored
(besides the already created image with average vector counts). M src/tools/calc2DFFfromChrPoints.cpp
-
Vladimír Ulman authored
M src/tools/getline_profile.cpp
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
- Nov 29, 2014
-
-
Vladimír Ulman authored
- 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
-
- Nov 28, 2014
-
-
Vladimír Ulman authored
M src/cell_08_G2Phase.cpp
-
Vladimír Ulman authored
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
-
- Nov 27, 2014
-
-
Vladimír Ulman authored
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()
-
- Nov 26, 2014
-
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
(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
-
- Nov 21, 2014
-
-
Vladimír Ulman authored
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"
-
- Nov 20, 2014
-
-
Vladimír Ulman authored
position in the very first frame as well
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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...
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
- Nov 19, 2014
-
-
Vladimír Ulman authored
" 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
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
- Nov 18, 2014
-
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
- Nov 10, 2014
-
-
Vladimír Ulman authored
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
-
- Nov 06, 2014
-
-
Vladimír Ulman authored
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
-
Vladimír Ulman authored
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
-
- Nov 05, 2014
-
-
David Svoboda authored
- 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
-
- Jun 27, 2014
-
-
David Svoboda authored
* 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
-