- Dec 28, 2019
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Vladimir Ulman authored
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Vladimir Ulman authored
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- Mar 15, 2019
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Vladimir Ulman authored
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Vladimír Ulman authored
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- Mar 29, 2017
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Vladimír Ulman authored
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- Feb 23, 2017
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Vladimír Ulman authored
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Vladimír Ulman authored
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- Dec 20, 2016
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Vladimír Ulman authored
M src/tools/imageinfo.cpp
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- Nov 03, 2016
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Vladimír Ulman authored
M CMakeLists.txt - searches now also for Apple's .dylibs M src/cellChr.cpp - on Apple: #include<values.h> -> #include<float.h> M src/scheduler.cpp - ditto
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- Apr 22, 2016
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Vladimír Ulman authored
(note: sh shell cannot handle variable substrings, unlike bash!) M scripts/finalize.sh
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Vladimír Ulman authored
Get max, krome GPL licence, vypisuje radek s "identifikatorem" MAXX M src/tools/getMax.cpp Skript preskakuje lic. texty a hleda radek s MAXX, aby ziskal co potrebuje vedet pro svou praci; A taky vola mitogen namisto mitopacqu... M scripts/finalize.sh LOCK file se jmenuje Mitogen (bylo Mitopacq) M src/scheduler.cpp
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Vladimír Ulman authored
M src/main.cpp
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- Apr 01, 2016
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David Svoboda authored
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
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- Nov 18, 2015
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Vladimír Ulman authored
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
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- Nov 13, 2015
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Vladimír Ulman authored
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
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Vladimír Ulman authored
M toolbox/walks.cc
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Vladimír Ulman authored
Functions are provided also for standard turning ang. distributions. Inteface has changed... M toolbox/randWalk.h Sample controlling program. M toolbox/walks.cc
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- Nov 09, 2015
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Vladimír Ulman authored
A toolbox/randWalk.h And a sample program showing how to use it. A toolbox/walks.cc
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- Jul 29, 2015
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Vladimír Ulman authored
(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
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- Jul 11, 2015
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Vladimír Ulman authored
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
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- Jul 10, 2015
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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
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- Jul 03, 2015
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Vladimír Ulman authored
M src/cell_02_Metaphase.cpp
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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
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- Jul 02, 2015
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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
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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
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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
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- May 10, 2015
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Vladimír Ulman authored
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- May 06, 2015
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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
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- May 05, 2015
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Vladimír Ulman authored
M src/scheduler.cpp
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- Jan 28, 2015
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Vladimír Ulman authored
A src/tools/calc2DFFfromChrPointsXZ.cpp M CMakeLists.txt
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- Jan 27, 2015
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Vladimír Ulman authored
(besides the already created image with average vector counts). M src/tools/calc2DFFfromChrPoints.cpp
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Vladimír Ulman authored
M src/tools/getline_profile.cpp
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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
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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
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- Nov 29, 2014
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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
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- Nov 28, 2014
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Vladimír Ulman authored
M src/cell_08_G2Phase.cpp
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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
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- Nov 27, 2014
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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()
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- Nov 26, 2014
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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
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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
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