Copyright (C) 2013-2016 Centre for Biomedical I... Copyright (C) 2013-2016 Centre for Biomedical Image Analysis (CBIA)
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
main.cpp::main(): starting time: Tue 2017-11-28, 10:03:45
main.cpp::main(): supplied configuration file: config-smallVOI-highSNR.ini
main.cpp::main(): stdlib generator seeded with 1511859825
main.cpp::makeReport():
enabled features: + extended comments (DEBUG) + parallel convolutions + parallel processing of cell phases
+ 3D rigid motion
+ phantoms
+ cell masks
+ TIFF images + ST images at z=60
+ testing mode: watch out for TESTING MODE messages
main.cpp::makeReport():
constants used: cellDiameter=7 um, nucleolusDiameter=1.4 um, coverage=400 %
cellNonRigidDeformation=0.15 um, cellNonRigidStrongDeformation=0.7 um
(mean) noFramesPerCellCycle=50 frames, cellSparseNonRigidDeformations=false
cellMagnitudeOfMovementPerFrame=0.4 um, VarianceOf_cellMagnitudeOfMovementPerFrame=0.3 um
cometCellMagnitudeOfMovementPerFrame=0.5 um, cellLookDistance=0.6 um
cellMovementDirectionality=0.5 um, cellMovement3Danisotropy=0.3 um
main.cpp::makeReport(): Mitocheck HeLa movement is simulated, watch out for MITOCHECK MODE messages.
Some movement constants may be ignored then.
main.cpp::main(): using the pregenerated image initial_mask_after_005.ics
scheduler.cpp::Scheduler(): mask res. minus ini file res.=(-1.14441e-05,-1.14441e-05,-1.14441e-05), L2=3.92902e-10
scheduler.cpp::Scheduler(): mask image is compatible with ini file
scheduler.cpp::Scheduler(): sceneSize = (84.9308,84.9308,11.8854)um, sceneOffset = (0,0,0)um
scheduler.cpp::Scheduler(): sceneRes = (8.07716,8.07716,8.07716)px/um
cell.h::Cell(): cell params loading started
cell.h::Cell(): cell params loaded
rnd_generators.cpp::GetRandomGauss(): randomness started with seed 80817072
cell.h::Cell(): first stronger non-rigid will occur at frame 6
cell.h::Cell(): MITOCHECK MODE: enforcing custom turning angle distribution ala Mitocheck.
randWalk.h::SetZstepLimit(): new Z anisotropy value: 0 [no units]
rnd_generators.cpp::GetRandomUniform(): randomness started with seed 80817072
cell.h::Cell(): MITOCHECK MODE: enforcing mean step size of 1.56085 microns ala Mitocheck.
cell.h::Cell(): MITOCHECK MODE: enforcing new cellLookDistance of size 2.89889 microns due to Mitocheck.
randWalk.h::ResetXYHeading(): new XY heading angle: 0.389556 radians
cell.h::Cell(): new cell created with ID=1 and timePoint=0
cell.h::Cell(): new cell has cycle length 59 frames
scheduler.cpp::Scheduler(): TESTING MODE: fixing initial G2 phase life to 50 frames.
cell.h::SetDelay(): delay: 50
cell.cpp::ReadMaskInG2Phase(): Using mask image ID=1 for this cell with ID=1
bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 162620 points (10298 outer) with centre at (15.5124,20.9451,9.42636)
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=1 into source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=1 with centre at (15.5124,20.9451,9.42636) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(11.7616,17.3328,7.30454) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.42835,7.18074,4.3332) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(95,140,59) pixels
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00317201 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00560099 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.00030601 seconds
cellScm.cpp::ScmRenderCellIntoMask(): 49412 dots were added (ID 1 )
bp_lists.cpp::AllocateAndZeroNewMask(): points span x=12.0092 to 18.9423; y=17.5804 to 24.2659; z=7.55216 to 11.3901
bp_lists.cpp::AllocateAndZeroNewMask(): new image at (10.2759,15.8471,6.68551) of size (10.2759,10.1521,5.57126) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (10.2759,15.8471,6.68551) of size (10.2759,10.1521,5.57126) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(1.48567,1.48567,0.619029) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.42835,7.18074,4.3332) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(12,12,4) pixels
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00351799 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.005303 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000273019 seconds
cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes
cell.cpp::GetCellPolarityAndCentreVector(): axis1: (-0.995932,0.00624961,0.0898907)
cell.cpp::GetCellPolarityAndCentreVector(): axis2: (0.00225511,0.999008,-0.0444692)
cell.cpp::GetCellPolarityAndCentreVector(): axis3: (0.0900794,0.0440856,0.994958)
cell.cpp::GetCellPolarityAndCentreVector(): val1: 8.29274e+06
cell.cpp::GetCellPolarityAndCentreVector(): val2: 7.5124e+06
cell.cpp::GetCellPolarityAndCentreVector(): val3: 2.2231e+06
cell.cpp::GetCellPolarityAndCentreVector(): polarity vector is: (-0.995932,0.00624961,0.0898907)
cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (15.4757,20.9232,9.40924)
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleus mask.
bp_lists.cpp::ResetBoundaryPoints(): source image at (11.7616,17.3328,7.30454) of size (7.55216,7.30454,4.45701) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 139637 points (8843 outer) with centre at (15.5004,20.9548,9.43355)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleus mask created successfully.
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleoli.
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 12996
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (14.3008,20.3673,8.35812)
bp_lists.cpp::ResetBoundaryPoints(): source image at (14.3008,20.3673,8.35812) of size (2.72373,2.72373,2.72373) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 5023 points (337 outer) with centre at (15.7332,21.821,9.79273)
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 7778
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (14.1592,17.8734,8.58792)
bp_lists.cpp::ResetBoundaryPoints(): source image at (14.1592,17.8734,8.58792) of size (3.09515,3.09515,3.09515) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 4639 points (313 outer) with centre at (15.7449,19.4219,10.1436)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleoli generated successfully.
cellChr.cpp::ChrInitialDistribution(): 40657 pixels were found in the mask
cellChr.cpp::ChrInitialDistribution(): going to use 3536 molecules for a chromosome, as 162656 is required total
cell.cpp::GenerateDotDistributionInG2Phase(): Seeds placed for the new chromosomes.
cellChr.cpp::ChrUpdateStats(): operation took 0.035396 seconds, percentil is 0.9
cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1
cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.125746 seconds
cell.cpp::GenerateDotDistributionInG2Phase(): Initial generation of dots and molecules finished.
cell.h::Cell(): cell params loading started
cell.h::Cell(): cell params loaded
cell.h::Cell(): first stronger non-rigid will occur at frame 8
cell.h::Cell(): MITOCHECK MODE: enforcing custom turning angle distribution ala Mitocheck.
randWalk.h::SetZstepLimit(): new Z anisotropy value: 0 [no units]
cell.h::Cell(): MITOCHECK MODE: enforcing mean step size of 1.63578 microns ala Mitocheck.
cell.h::Cell(): MITOCHECK MODE: enforcing new cellLookDistance of size 2.97757 microns due to Mitocheck.
randWalk.h::ResetXYHeading(): new XY heading angle: 3.04377 radians
cell.h::Cell(): new cell created with ID=2 and timePoint=0
cell.h::Cell(): new cell has cycle length 47 frames
scheduler.cpp::Scheduler(): TESTING MODE: fixing initial G2 phase life to 50 frames.
cell.h::SetDelay(): delay: 50
cell.cpp::ReadMaskInG2Phase(): Using mask image ID=2 for this cell with ID=2
bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 206114 points (13028 outer) with centre at (4.2114,12.6927,8.51112)
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=2 into source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=2 with centre at (4.2114,12.6927,8.51112) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(0.742835,8.66641,5.44746) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(6.93313,8.17118,6.3141) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(6,69,44) pixels
bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003933 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00847501 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000309005 seconds
cellScm.cpp::ScmRenderCellIntoMask(): 74945 dots were added (ID 2 )
bp_lists.cpp::AllocateAndZeroNewMask(): points span x=0.990447 to 7.42835; y=8.91402 to 16.59; z=5.69507 to 11.5139
bp_lists.cpp::AllocateAndZeroNewMask(): new image at (-1.23806,7.05693,4.45701) of size (10.7711,11.2663,8.29499) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (-1.23806,7.05693,4.45701) of size (10.7711,11.2663,8.29499) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(1.98089,1.60947,0.990447) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(6.93313,8.17118,6.3141) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(16,12,8) pixels
bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.004186 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00831498 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000378013 seconds
cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes
cell.cpp::GetCellPolarityAndCentreVector(): axis1: (0.446656,0.89442,0.0226188)
cell.cpp::GetCellPolarityAndCentreVector(): axis2: (0.888306,-0.446337,0.108143)
cell.cpp::GetCellPolarityAndCentreVector(): axis3: (-0.106821,0.0282104,0.993878)
cell.cpp::GetCellPolarityAndCentreVector(): val1: 1.51019e+07
cell.cpp::GetCellPolarityAndCentreVector(): val2: 9.01446e+06
cell.cpp::GetCellPolarityAndCentreVector(): val3: 8.11753e+06
cell.cpp::GetCellPolarityAndCentreVector(): polarity vector is: (0.446656,0.89442,0.0226187)
cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (4.08559,12.6282,8.4188)
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleus mask.
bp_lists.cpp::ResetBoundaryPoints(): source image at (0.742835,8.66641,5.44746) of size (7.05693,8.17118,6.4379) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 181701 points (11481 outer) with centre at (4.20299,12.6881,8.51786)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleus mask created successfully.
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleoli.
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 26063
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (3.66744,12.7053,6.39117)
bp_lists.cpp::ResetBoundaryPoints(): source image at (3.66744,12.7053,6.39117) of size (2.72373,2.72373,2.72373) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 4947 points (333 outer) with centre at (5.123,14.1222,7.78538)
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 22855
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (3.89473,10.085,6.37085)
bp_lists.cpp::ResetBoundaryPoints(): source image at (3.89473,10.085,6.37085) of size (2.84753,2.84753,2.84753) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 4811 points (323 outer) with centre at (5.30642,11.5166,7.79557)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleoli generated successfully.
cellChr.cpp::ChrInitialDistribution(): 63951 pixels were found in the mask
cellChr.cpp::ChrInitialDistribution(): going to use 5564 molecules for a chromosome, as 255944 is required total
cell.cpp::GenerateDotDistributionInG2Phase(): Seeds placed for the new chromosomes.
cellChr.cpp::ChrUpdateStats(): operation took 0.056556 seconds, percentil is 0.9
cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2
cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.125643 seconds
cell.cpp::GenerateDotDistributionInG2Phase(): Initial generation of dots and molecules finished.
cell.h::Cell(): cell params loading started
cell.h::Cell(): cell params loaded
cell.h::Cell(): first stronger non-rigid will occur at frame 6
cell.h::Cell(): MITOCHECK MODE: enforcing custom turning angle distribution ala Mitocheck.
randWalk.h::SetZstepLimit(): new Z anisotropy value: 0 [no units]
cell.h::Cell(): MITOCHECK MODE: enforcing mean step size of 1.97383 microns ala Mitocheck.
cell.h::Cell(): MITOCHECK MODE: enforcing new cellLookDistance of size 3.33253 microns due to Mitocheck.
randWalk.h::ResetXYHeading(): new XY heading angle: 4.05445 radians
cell.h::Cell(): new cell created with ID=3 and timePoint=0
cell.h::Cell(): new cell has cycle length 48 frames
scheduler.cpp::Scheduler(): TESTING MODE: fixing initial G2 phase life to 50 frames.
cell.h::SetDelay(): delay: 50
cell.cpp::ReadMaskInG2Phase(): Using mask image ID=3 for this cell with ID=3
bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 227771 points (14387 outer) with centre at (65.6855,78.7756,8.11595)
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=3 into source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=3 with centre at (65.6855,78.7756,8.11595) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(62.0267,75.0263,4.3332) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.30455,7.67596,7.30454) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(500,606,35) pixels
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.004641 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00887901 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000438988 seconds
cellScm.cpp::ScmRenderCellIntoMask(): 89053 dots were added (ID 3 )
bp_lists.cpp::AllocateAndZeroNewMask(): points span x=62.2743 to 69.0836; y=75.2739 to 82.4547; z=4.58082 to 11.3901
bp_lists.cpp::AllocateAndZeroNewMask(): new image at (60.2934,73.4169,3.09515) of size (10.6473,10.7711,9.65685) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (60.2934,73.4169,3.09515) of size (10.6473,10.7711,9.65685) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(1.73328,1.60947,1.23806) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.30455,7.67596,7.30454) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(13,12,10) pixels
bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00424701 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.009047 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000762999 seconds
cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes
cell.cpp::GetCellPolarityAndCentreVector(): axis1: (-0.459513,0.880147,-0.119117)
cell.cpp::GetCellPolarityAndCentreVector(): axis2: (-0.34423,-0.0528533,0.937397)
cell.cpp::GetCellPolarityAndCentreVector(): axis3: (0.818751,0.47175,0.32726)
cell.cpp::GetCellPolarityAndCentreVector(): val1: 1.66659e+07
cell.cpp::GetCellPolarityAndCentreVector(): val2: 1.28382e+07
cell.cpp::GetCellPolarityAndCentreVector(): val3: 1.2104e+07
cell.cpp::GetCellPolarityAndCentreVector(): polarity vector is: (-0.459513,0.880147,-0.119117)
cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (65.6171,78.7405,8.04738)
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleus mask.
bp_lists.cpp::ResetBoundaryPoints(): source image at (62.0267,75.0263,4.3332) of size (7.42835,7.79977,7.42835) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 203775 points (12867 outer) with centre at (65.6878,78.7665,8.12728)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleus mask created successfully.
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleoli.
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 33956
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (64.5241,76.5332,5.09728)
bp_lists.cpp::ResetBoundaryPoints(): source image at (64.5241,76.5332,5.09728) of size (2.84753,2.84753,2.84753) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 5005 points (337 outer) with centre at (65.9906,77.9697,6.56495)
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 28529
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (66.0893,77.8508,6.66249)
bp_lists.cpp::ResetBoundaryPoints(): source image at (66.0893,77.8508,6.66249) of size (2.97134,2.97134,2.97134) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 5400 points (360 outer) with centre at (67.6148,79.3633,8.18358)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleoli generated successfully.
cellChr.cpp::ChrInitialDistribution(): 76950 pixels were found in the mask
cellChr.cpp::ChrInitialDistribution(): going to use 6692 molecules for a chromosome, as 307832 is required total
cell.cpp::GenerateDotDistributionInG2Phase(): Seeds placed for the new chromosomes.
cellChr.cpp::ChrUpdateStats(): operation took 0.069254 seconds, percentil is 0.9
cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3
cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.126568 seconds
cell.cpp::GenerateDotDistributionInG2Phase(): Initial generation of dots and molecules finished.
cell.h::Cell(): cell params loading started
cell.h::Cell(): cell params loaded
cell.h::Cell(): first stronger non-rigid will occur at frame 5
cell.h::Cell(): MITOCHECK MODE: enforcing custom turning angle distribution ala Mitocheck.
randWalk.h::SetZstepLimit(): new Z anisotropy value: 0 [no units]
cell.h::Cell(): MITOCHECK MODE: enforcing mean step size of 1.76402 microns ala Mitocheck.
cell.h::Cell(): MITOCHECK MODE: enforcing new cellLookDistance of size 3.11222 microns due to Mitocheck.
randWalk.h::ResetXYHeading(): new XY heading angle: 5.86584 radians
cell.h::Cell(): new cell created with ID=4 and timePoint=0
cell.h::Cell(): new cell has cycle length 44 frames
scheduler.cpp::Scheduler(): TESTING MODE: fixing initial G2 phase life to 50 frames.
cell.h::SetDelay(): delay: 50
cell.cpp::ReadMaskInG2Phase(): Using mask image ID=4 for this cell with ID=4
bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 194515 points (12301 outer) with centre at (7.10498,39.2767,8.69833)
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=4 into source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=4 with centre at (7.10498,39.2767,8.69833) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(2.47612,36.3989,5.69507) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(9.16163,5.81887,5.94268) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(19,294,46) pixels
bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00359696 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.006194 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000371039 seconds
cellScm.cpp::ScmRenderCellIntoMask(): 67660 dots were added (ID 4 )
bp_lists.cpp::AllocateAndZeroNewMask(): points span x=2.72373 to 11.3901; y=36.6465 to 41.9702; z=5.94268 to 11.3901
bp_lists.cpp::AllocateAndZeroNewMask(): new image at (0.619029,33.5514,4.70462) of size (12.752,11.5139,7.79977) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (0.619029,33.5514,4.70462) of size (12.752,11.5139,7.79977) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(1.85709,2.84753,0.990447) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(9.16163,5.81887,5.94268) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(14,23,8) pixels
bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00366795 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.006504 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000311017 seconds
cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes
cell.cpp::GetCellPolarityAndCentreVector(): axis1: (-0.992967,0.117178,-0.0168827)
cell.cpp::GetCellPolarityAndCentreVector(): axis2: (-0.0477915,-0.266281,0.96271)
cell.cpp::GetCellPolarityAndCentreVector(): axis3: (0.108313,0.956747,0.270008)
cell.cpp::GetCellPolarityAndCentreVector(): val1: 1.69069e+07
cell.cpp::GetCellPolarityAndCentreVector(): val2: 6.38e+06
cell.cpp::GetCellPolarityAndCentreVector(): val3: 6.11529e+06
cell.cpp::GetCellPolarityAndCentreVector(): polarity vector is: (-0.992967,0.117178,-0.0168827)
cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (7.05693,39.2464,8.66641)
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleus mask.
bp_lists.cpp::ResetBoundaryPoints(): source image at (2.47612,36.3989,5.69507) of size (9.16163,5.94268,6.06649) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 171382 points (10834 outer) with centre at (7.10369,39.2685,8.69279)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleus mask created successfully.
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleoli.
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 21994
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (6.59677,36.5578,7.58722)
bp_lists.cpp::ResetBoundaryPoints(): source image at (6.59677,36.5578,7.58722) of size (2.84753,2.84753,2.84753) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 4739 points (317 outer) with centre at (8.018,37.9903,9.05414)
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 22313
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (5.35675,38.4129,5.72817)
bp_lists.cpp::ResetBoundaryPoints(): source image at (5.35675,38.4129,5.72817) of size (3.34276,3.34276,3.34276) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 2480 points (176 outer) with centre at (7.06471,40.1173,7.42698)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleoli generated successfully.
cellChr.cpp::ChrInitialDistribution(): 57510 pixels were found in the mask
cellChr.cpp::ChrInitialDistribution(): going to use 5004 molecules for a chromosome, as 230184 is required total
cell.cpp::GenerateDotDistributionInG2Phase(): Seeds placed for the new chromosomes.
cellChr.cpp::ChrUpdateStats(): operation took 0.055576 seconds, percentil is 0.9
cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4
cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.132891 seconds
cell.cpp::GenerateDotDistributionInG2Phase(): Initial generation of dots and molecules finished.
cell.h::Cell(): cell params loading started
cell.h::Cell(): cell params loaded
cell.h::Cell(): first stronger non-rigid will occur at frame 8
cell.h::Cell(): MITOCHECK MODE: enforcing custom turning angle distribution ala Mitocheck.
randWalk.h::SetZstepLimit(): new Z anisotropy value: 0 [no units]
cell.h::Cell(): MITOCHECK MODE: enforcing mean step size of 2.27762 microns ala Mitocheck.
cell.h::Cell(): MITOCHECK MODE: enforcing new cellLookDistance of size 3.6515 microns due to Mitocheck.
randWalk.h::ResetXYHeading(): new XY heading angle: 4.27761 radians
cell.h::Cell(): new cell created with ID=5 and timePoint=0
cell.h::Cell(): new cell has cycle length 50 frames
scheduler.cpp::Scheduler(): TESTING MODE: fixing initial G2 phase life to 50 frames.
cell.h::SetDelay(): delay: 50
cell.cpp::ReadMaskInG2Phase(): Using mask image ID=5 for this cell with ID=5
bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 194326 points (12292 outer) with centre at (54.287,32.3327,8.54858)
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=5 into source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=5 with centre at (54.287,32.3327,8.54858) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(50.6366,28.7229,5.44746) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.55215,7.05693,6.06649) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(409,232,44) pixels
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003775 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00755399 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000322998 seconds
cellScm.cpp::ScmRenderCellIntoMask(): 67965 dots were added (ID 5 )
bp_lists.cpp::AllocateAndZeroNewMask(): points span x=50.8842 to 57.9411; y=28.9706 to 35.5323; z=5.69507 to 11.2663
bp_lists.cpp::AllocateAndZeroNewMask(): new image at (49.1509,26.9897,4.45701) of size (10.5235,10.3997,7.92357) in microns
bp_lists.cpp::RenderBPListIntoMask(): source image at (49.1509,26.9897,4.45701) of size (10.5235,10.3997,7.92357) in microns
bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(1.48567,1.73328,0.990447) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.55215,7.05693,6.06649) microns (including 2px frame)
bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(12,13,8) pixels
bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00376004 seconds
bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.007559 seconds
bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000321984 seconds
cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes
cell.cpp::GetCellPolarityAndCentreVector(): axis1: (-0.862198,-0.155211,0.482208)
cell.cpp::GetCellPolarityAndCentreVector(): axis2: (-0.219933,0.972203,-0.0803166)
cell.cpp::GetCellPolarityAndCentreVector(): axis3: (0.456338,0.175302,0.872367)
cell.cpp::GetCellPolarityAndCentreVector(): val1: 1.21635e+07
cell.cpp::GetCellPolarityAndCentreVector(): val2: 9.74009e+06
cell.cpp::GetCellPolarityAndCentreVector(): val3: 5.70827e+06
cell.cpp::GetCellPolarityAndCentreVector(): polarity vector is: (-0.862198,-0.155211,0.482208)
cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (54.2269,32.3133,8.5426)
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleus mask.
bp_lists.cpp::ResetBoundaryPoints(): source image at (50.6366,28.7229,5.44746) of size (7.67596,7.18074,6.19029) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 171687 points (10857 outer) with centre at (54.2837,32.3419,8.54549)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleus mask created successfully.
cell.cpp::GenerateDotDistributionInG2Phase(): Generating nucleoli.
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 20961
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (51.7851,31.3571,6.34834)
bp_lists.cpp::ResetBoundaryPoints(): source image at (51.7851,31.3571,6.34834) of size (2.84753,2.84753,2.84753) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 5438 points (362 outer) with centre at (53.2222,32.8082,7.8087)
collisions.cpp::LocateAllFreePositions(): dilation of space image
collisions.cpp::LocateAllFreePositions(): drawing border line
collisions.cpp::LocateAllFreePositions(): performing convolution
collisions.cpp::LocateAllFreePositions(): thresholding convolution result
collisions.cpp::FindPosition(): sum of free positions: 16805
collisions.cpp::FindPosition(): searching finished
cell.cpp::GenerateNucleolus(): attempt number: 1
cell.cpp::GenerateNucleolus(): shift: (52.1819,29.4016,7.85944)
bp_lists.cpp::ResetBoundaryPoints(): source image at (52.1819,29.4016,7.85944) of size (2.84753,2.84753,2.84753) in microns
bp_lists.cpp::ResetBoundaryPoints(): new list contains 5512 points (370 outer) with centre at (53.5893,30.8345,9.2899)
cell.cpp::GenerateDotDistributionInG2Phase(): Nucleoli generated successfully.
cellChr.cpp::ChrInitialDistribution(): 57358 pixels were found in the mask
cellChr.cpp::ChrInitialDistribution(): going to use 4988 molecules for a chromosome, as 229448 is required total
cell.cpp::GenerateDotDistributionInG2Phase(): Seeds placed for the new chromosomes.
cellChr.cpp::ChrUpdateStats(): operation took 0.05022 seconds, percentil is 0.9
cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5
cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.126609 seconds
cell.cpp::GenerateDotDistributionInG2Phase(): Initial generation of dots and molecules finished.
main.cpp::main(): going to work with scene of size (686,686,96) in pixels
scheduler.cpp::PnInitArray(): Starting to load from cache file pnArray.cache
scheduler.cpp::PnInitArray(): Discovered: RealWidth=197, pnSizes[]=198,197,197,18
scheduler.cpp::PnInitArray(): Reading power noise image of size 527 MBytes
scheduler.cpp::PnInitArray(): Finished
scheduler.cpp::PrintPhaseBudgets(): Overview of lengths of cell phases (in number of frames) when mean cell cycle length is 50.
scheduler.cpp::PrintPhaseBudgets(): G1Phase: 3 times 8 frames, 24 frames in total
scheduler.cpp::PrintPhaseBudgets(): SPhase: 2 times 8 frames, 16 frames in total
scheduler.cpp::PrintPhaseBudgets(): G2Phase: 8 frames
scheduler.cpp::PrintPhaseBudgets(): Prophase: 1 frames
scheduler.cpp::PrintPhaseBudgets(): Metaphase: 2 frames
scheduler.cpp::PrintPhaseBudgets(): Anaphase: 1 frames
scheduler.cpp::PrintPhaseBudgets(): Telophase: 1 frames
scheduler.cpp::PrintPhaseBudgets(): Cytokinesis: 1 frames
main.cpp::main(): TESTING MODE: doing just single Run() of length (at least) 1 frames.
scheduler.cpp::Run_st(): Detected available hardware threads: 56
scheduler.cpp::Run_st(): Starting 16 worker threads!

scheduler.cpp::Run_st(): All worker threads hav... scheduler.cpp::Run_st(): All worker threads have finished without errors!
scheduler.cpp::ReleaseOldScenes(): scene #7 saved
scheduler.cpp::ReleaseOldScenes(): scene #8 saved
scheduler.cpp::ReleaseOldScenes(): scene #9 saved
scheduler.cpp::~Scheduler(): Destructing scheduler
scheduler.cpp::~Scheduler(): deleting cell with ID = 1
scheduler.cpp::~Scheduler(): deleting cell with ID = 2
scheduler.cpp::~Scheduler(): deleting cell with ID = 3
scheduler.cpp::~Scheduler(): deleting cell with ID = 4
scheduler.cpp::~Scheduler(): deleting cell with ID = 5
scheduler.cpp::~Scheduler(): Saving spatiotemporal mask image
scheduler.cpp::~Scheduler(): Saving spatiotemporal phantom image
main.cpp::main(): Happy end! :-)
main.cpp::main():
main.cpp::main(): Now, inspect the results. If you are happy with them, please run:
main.cpp::main(): $> ./scripts/finalize.sh config-smallVOI-highSNR.ini
main.cpp::main():
main.cpp::main(): stopping time: Tue 2017-11-28, 10:04:28

scheduler.cpp::RunFeeder_st(): Started processi... scheduler.cpp::RunFeeder_st(): Started processing of cell with ID=1 on frame no. 0 at Tue 2017-11-28, 10:04:03, there are 5 cells currently in the system

regionlock.cpp::checkAndLock(): Total time spen... regionlock.cpp::checkAndLock(): Total time spent waiting (all threads): 0m 0s

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, STARTING G2-phase at timePoint=0

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=12.0092 to 18.9423; y=17.5804 to 24.2659; z=7.55216 to 11.3901

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(181,183,22) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.006552 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00625901 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000231996 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.20103e-05 seconds

rnd_generators.cpp::GetRandomGauss(): randomnes... rnd_generators.cpp::GetRandomGauss(): randomness started with seed 117284384

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 40685 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

rnd_generators.cpp::GetRandomUniform(): randomn... rnd_generators.cpp::GetRandomUniform(): randomness started with seed 117284384

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.89855,-0.0742222,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 9.74327deg clockwise around (15.5124,20.9451,9.42636) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 463... bp_lists.cpp::MoveBPListAndCentre(): moving 4639 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(78,138,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00325698 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000262022 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 49729 dot... cellScm.cpp::ScmRenderCellIntoMask(): 49729 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(165,181,22) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00285602 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(188,209,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.00136e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 40902 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=1 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-0.692059,0.575373,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 10.392deg clockwise around (13.6127,20.8712,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 502... bp_lists.cpp::MoveBPListAndCentre(): moving 5023 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(72,143,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00393301 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000310004 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 49968 dot... cellScm.cpp::ScmRenderCellIntoMask(): 49968 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(159,185,22) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00352502 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000171006 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.69873e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41065 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=2 with sync

cellScm.cpp::ScmUniversalMovement(): MITOCHECK ... cellScm.cpp::ScmUniversalMovement(): MITOCHECK MODE: trying 3x longer step ala Mitocheck.

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-4.67993,3.75476,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 5.00174deg clockwise around (12.9206,21.4465,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): new object... bp_lists.cpp::MoveBPListAndCentre(): new object mask centre is (8.22549,25.2052,9.43379)

bp_lists.cpp::MoveBPListAndCentre(): moving 463... bp_lists.cpp::MoveBPListAndCentre(): moving 4639 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(34,173,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00326398 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.006574 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.00029102 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 50002 dot... cellScm.cpp::ScmRenderCellIntoMask(): 50002 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00282699 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000119984 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09673e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41176 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrUpdateStats(): operation took 0... cellChr.cpp::ChrUpdateStats(): operation took 0.039882 seconds, percentil is 0.9

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=3 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (2.25986,1.06912,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -7.54688deg clockwise around (8.24068,25.2013,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 502... bp_lists.cpp::MoveBPListAndCentre(): moving 5023 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00403601 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.00030902 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 49870 dot... cellScm.cpp::ScmRenderCellIntoMask(): 49870 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(139,225,22) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00343302 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000156999 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.29938e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41019 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.123117 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=4 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.54957,-1.69965,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -2.96197deg clockwise around (10.5005,26.2704,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 502... bp_lists.cpp::MoveBPListAndCentre(): moving 5023 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 463... bp_lists.cpp::MoveBPListAndCentre(): moving 4639 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(65,168,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00391099 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000322998 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 49828 dot... cellScm.cpp::ScmRenderCellIntoMask(): 49828 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(152,211,22) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003335 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(180,221,36) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.40071e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41000 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.116027 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=5 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0.139328,1.39305,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -0.047114deg clockwise around (12.0501,24.5707,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 463... bp_lists.cpp::MoveBPListAndCentre(): moving 4639 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003973 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000328995 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 49865 dot... cellScm.cpp::ScmRenderCellIntoMask(): 49865 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00336599 seconds

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000144005 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 2.2009e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 40997 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.124646 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=6 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.51694,1.72884,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 8.14554deg clockwise around (12.1894,25.9638,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 463... bp_lists.cpp::MoveBPListAndCentre(): moving 4639 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(53,193,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00355697 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000256002 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 49969 dot... cellScm.cpp::ScmRenderCellIntoMask(): 49969 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(141,236,22) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00308597 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(163,264,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09673e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41091 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=7 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.79791,0.086633,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 8.38968deg clockwise around (10.6725,27.6926,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 463... bp_lists.cpp::MoveBPListAndCentre(): moving 4639 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(39,194,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00323999 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000259042 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 50085 dot... cellScm.cpp::ScmRenderCellIntoMask(): 50085 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00279099 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000124991 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 2.10404e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41142 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.118664 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=1, doing G2-phase at timePoint=8 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (2.00992,-0.608469,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -8.48561deg clockwise around (8.87459,27.7793,9.42653) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 162... bp_lists.cpp::MoveBPListAndCentre(): moving 162620 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 139... bp_lists.cpp::MoveBPListAndCentre(): moving 139637 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 502... bp_lists.cpp::MoveBPListAndCentre(): moving 5023 dots with flow field at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:61--189, y:105--233, z:12--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(55,189,59) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00322601 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.006946 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000256002 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 50055 dot... cellScm.cpp::ScmRenderCellIntoMask(): 50055 dots were added (ID 1 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.002776 seconds

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.20103e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 41141 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 162656 'chr' points, ID=1

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.122132 seconds

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (5.32365,21.666,6.68551) of size (11.0187,10.8949,5.57126) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(12,14,4) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00337505 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00876796 seconds

cell.cpp::GetCellPolarityAndCentreVector(): Com... cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes

cell.cpp::GetCellPolarityAndCentreVector(): cen... cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (10.7711,27.1135,9.40924)

cell.cpp::GenerateCentrosomes(): Doing distance... cell.cpp::GenerateCentrosomes(): Doing distance transform

cell.cpp::GenerateCentrosomes(): max dist: 3.51... cell.cpp::GenerateCentrosomes(): max dist: 3.51008

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 166275 points (10539 outer) with centre at (10.8823,27.1675,9.42712)

scheduler.cpp::PnGetMeNonrigidHints(): since pn... scheduler.cpp::PnGetMeNonrigidHints(): since pnArray has size 197,197,197, will use offset 103,43,0

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 143835 points (9123 outer) with centre at (10.8667,27.1691,9.43303)

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 5211 points (351 outer) with centre at (10.7577,28.0595,9.85438)

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-10.5235,-5.07604,4.70462) of size (51.9984,51.8746,9.40924) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 4910 points (332 outer) with centre at (11.6818,25.8523,10.0973)

scheduler.cpp::GetCellCometsLeavingFactor(): th... scheduler.cpp::GetCellCometsLeavingFactor(): there are 5 'living' and 0 'cut away' cells, ratio=inf

regionlock.cpp::checkAndLock(): Total time spen... regionlock.cpp::checkAndLock(): Total time spent waiting (all threads): 0m 0s

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, STARTING G2-phase at timePoint=0

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=2.72373 to 11.3901; y=36.6465 to 41.9702; z=5.94268 to 11.3901

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.004677 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00943804 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.00136e-05 seconds

rnd_generators.cpp::GetRandomGauss(): randomnes... rnd_generators.cpp::GetRandomGauss(): randomness started with seed 18446744072939310688

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57434 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

rnd_generators.cpp::GetRandomUniform(): randomn... rnd_generators.cpp::GetRandomUniform(): randomness started with seed 18446744072939310688

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.79891,1.08347,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 2.09147deg clockwise around (7.10498,39.2767,8.69833) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 473... bp_lists.cpp::MoveBPListAndCentre(): moving 4739 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00467104 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000391006 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 67770 dot... cellScm.cpp::ScmRenderCellIntoMask(): 67770 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00409502 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 7.80225e-05 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.10269e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57581 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.127671 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, doing G2-phase at timePoint=1 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.13417,0.391993,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -22.8992deg clockwise around (8.90473,40.3604,8.69831) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 248... bp_lists.cpp::MoveBPListAndCentre(): moving 2480 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(46,301,46) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00392604 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00904197 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000337005 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68495 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68495 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00342697 seconds

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.00136e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58186 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.117651 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, doing G2-phase at timePoint=2 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0.663099,1.56534,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -4.58201deg clockwise around (10.0389,40.7524,8.69831) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 473... bp_lists.cpp::MoveBPListAndCentre(): moving 4739 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(52,313,46) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00396702 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000367999 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68606 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68606 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00350899 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000128001 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 9.0003e-06 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58341 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.125842 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, doing G2-phase at timePoint=3 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-0.618056,0.328643,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -5.66537deg clockwise around (10.702,42.3177,8.69831) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 473... bp_lists.cpp::MoveBPListAndCentre(): moving 4739 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

cellScm.cpp::ScmRemoveCellFromMask(): 67660 dot... cellScm.cpp::ScmRemoveCellFromMask(): 67660 dots were removed (ID 4)

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00388001 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000376999 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68596 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68596 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003545 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 6.40005e-05 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09971e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58322 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.117182 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, doing G2-phase at timePoint=4 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.40949,0.513159,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -5.36934deg clockwise around (10.0839,42.6464,8.69831) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 248... bp_lists.cpp::MoveBPListAndCentre(): moving 2480 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(38,317,46) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00382698 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000371993 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68647 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68647 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00334102 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 6.2e-05 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09999e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58369 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, doing G2-phase at timePoint=5 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0.64858,1.78587,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -12.2171deg clockwise around (8.67445,43.1595,8.69831) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 473... bp_lists.cpp::MoveBPListAndCentre(): moving 4739 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(46,329,46) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00381601 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.00037396 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68636 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68636 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(182,201,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00365001 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(200,212,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.00136e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58343 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=4, doing G2-phase at timePoint=6 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-0.824814,2.03953,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 23.1934deg clockwise around (9.32303,44.9454,8.69831) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194515 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171382 dots with flow field at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::MoveBPListAndCentre(): new object... bp_lists.cpp::MoveBPListAndCentre(): new object mask centre is (8.49362,46.978,8.69302)

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00403196 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000365973 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68641 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68641 dots were added (ID 4 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003425 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00797296 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 9.95398e-06 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58183 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 230184 'chr' points, ID=4

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.129867 seconds

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003842 seconds

cell.cpp::GetCellPolarityAndCentreVector(): Com... cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes

cell.cpp::GetCellPolarityAndCentreVector(): cen... cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (8.4188,46.9224,8.66641)

cell.cpp::GenerateCentrosomes(): Doing distance... cell.cpp::GenerateCentrosomes(): Doing distance transform

cell.cpp::GenerateCentrosomes(): max dist: 6.14... cell.cpp::GenerateCentrosomes(): max dist: 6.14648

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

scheduler.cpp::PnGetMeNonrigidHints(): since pn... scheduler.cpp::PnGetMeNonrigidHints(): since pnArray has size 197,197,197, will use offset 117,59,14

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-16.7138,16.0948,3.21895) of size (47.5414,46.3034,10.7711) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 2601 points (183 outer) with centre at (8.82133,47.7437,7.39385)

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::SoftRenderBPListIntoMask(): pixel... bp_lists.cpp::SoftRenderBPListIntoMask(): pixelShift=(28,344,39)

bp_lists.cpp::SoftRenderBPListIntoMask(): rende... bp_lists.cpp::SoftRenderBPListIntoMask(): rendering (dilated) object took 0.00425202 seconds

bp_lists.cpp::SoftRenderBPListIntoMask(): flood... bp_lists.cpp::SoftRenderBPListIntoMask(): flooding outside of (dilated) object took 0.017399 seconds

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--121, y:253--381, z:6--95

bp_lists.cpp::SoftRenderBPListIntoMask(): sourc... bp_lists.cpp::SoftRenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::SoftRenderBPListIntoMask(): pixel... bp_lists.cpp::SoftRenderBPListIntoMask(): pixelShift=(28,344,39)

bp_lists.cpp::SoftRenderBPListIntoMask(): rende... bp_lists.cpp::SoftRenderBPListIntoMask(): rendering (dilated) object took 0.004031 seconds

bp_lists.cpp::SoftRenderBPListIntoMask(): flood... bp_lists.cpp::SoftRenderBPListIntoMask(): flooding outside of (dilated) object took 0.017858 seconds

scheduler.cpp::GetCellCometsLeavingFactor(): th... scheduler.cpp::GetCellCometsLeavingFactor(): there are 5 'living' and 0 'cut away' cells, ratio=inf

scheduler.cpp::ReleaseOldScenes(): scene #1 saved scheduler.cpp::ReleaseOldScenes(): scene #1 saved

scheduler.cpp::ReleaseOldScenes(): scene #2 saved scheduler.cpp::ReleaseOldScenes(): scene #2 saved

scheduler.cpp::RunFeeder_st(): Started processi... scheduler.cpp::RunFeeder_st(): Started processing of cell with ID=2 on frame no. 0 at Tue 2017-11-28, 10:04:03, there are 5 cells currently in the system

regionlock.cpp::checkAndLock(): Total time spen... regionlock.cpp::checkAndLock(): Total time spent waiting (all threads): 0m 0s

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, STARTING G2-phase at timePoint=0

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=0.990447 to 7.42835; y=8.91402 to 16.59; z=5.69507 to 11.5139

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(171,169,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00791 seconds

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000238001 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.8999e-05 seconds

rnd_generators.cpp::GetRandomGauss(): randomnes... rnd_generators.cpp::GetRandomGauss(): randomness started with seed 443762656

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64014 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

regionlock.h::printLockInfo(): SPHERE lock, wai... regionlock.h::printLockInfo(): SPHERE lock, waiting time: 0ms, timePoint: 1-1, sceneType: masks, centre: [4.2114, 12.6927, 8.51112], radius: 8.75

rnd_generators.cpp::GetRandomUniform(): randomn... rnd_generators.cpp::GetRandomUniform(): randomness started with seed 443762656

cellScm.cpp::ScmSuggestTranslationsTowardsEmpty... cellScm.cpp::ScmSuggestTranslationsTowardsEmpty_SS(): MovsMask will have size (49,49,5)

cellScm.cpp::ScmSuggestTranslationsTowardsEmpty... cellScm.cpp::ScmSuggestTranslationsTowardsEmpty_SS(): trouble ahead: colliding even for no movement

cellScm.cpp::ScmSuggestTranslationsTowardsEmpty... cellScm.cpp::ScmSuggestTranslationsTowardsEmpty_SS(): Collision detections took 6.73576 seconds

cellScm.cpp::ScmSuggestTranslationVector(): Got... cellScm.cpp::ScmSuggestTranslationVector(): Got to follow MovsMask, its initial sum is 110.405

cell_movement.cpp::ReadVectorFromPreferenceMap(... cell_movement.cpp::ReadVectorFromPreferenceMap(): returning with vector (0,-0.495223,-0.247612)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0,-0.495223,-0.247612) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -17.5187deg clockwise around (4.2114,12.6927,8.51112) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 494... bp_lists.cpp::MoveBPListAndCentre(): moving 4947 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(2,68,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00409603 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000387967 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75778 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75778 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(168,166,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00375098 seconds

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09673e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64643 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.115713 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=1 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0.571629,-0.182321,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -17.7685deg clockwise around (4.2104,12.1974,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 494... bp_lists.cpp::MoveBPListAndCentre(): moving 4947 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(5,68,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00506103 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.011082 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000446022 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75979 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75979 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(171,166,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00450903 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00954896 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(197,173,33) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.19805e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64875 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=2 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.18861,1.4823,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -0.0902022deg clockwise around (4.78203,12.0151,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 494... bp_lists.cpp::MoveBPListAndCentre(): moving 4947 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(15,80,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00416297 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000382006 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75972 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75972 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(181,178,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00361705 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000113964 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.20401e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64800 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=3 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.50071,0.554853,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -9.19658deg clockwise around (5.97064,13.4974,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 481... bp_lists.cpp::MoveBPListAndCentre(): moving 4811 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(26,85,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00399697 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000365973 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75991 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75991 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): AABB offs... bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(23.808,22.7859,2.59992) microns (including 2px frame)

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(192,184,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00359696 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00771105 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.10269e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64822 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.125238 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=4 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-0.741786,-1.30375,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 15.9436deg clockwise around (7.47135,14.0523,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 481... bp_lists.cpp::MoveBPListAndCentre(): moving 4811 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(22,73,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00393701 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000406027 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75924 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75924 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(187,172,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00352204 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000123978 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.19805e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64794 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=5 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-0.345881,1.25314,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -2.37344deg clockwise around (6.72956,12.7485,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 481... bp_lists.cpp::MoveBPListAndCentre(): moving 4811 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(19,83,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00396299 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000396997 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75976 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75976 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(184,182,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00367701 seconds

bp_lists.cpp::RenderBPListIntoMask(): AABB offs... bp_lists.cpp::RenderBPListIntoMask(): AABB offset =(27.2982,25.8826,4.16267) microns (including 2px frame)

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.20103e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64773 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.131585 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=6 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.45589,-0.663611,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -4.85037deg clockwise around (6.38368,14.0017,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 494... bp_lists.cpp::MoveBPListAndCentre(): moving 4947 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00400302 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00862598 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000376016 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75965 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75965 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(196,177,21) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003546 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.007774 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09971e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64800 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=2, doing G2-phase at timePoint=7 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0.791573,-1.03122,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 24.9706deg clockwise around (7.83957,13.338,8.26368) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 206... bp_lists.cpp::MoveBPListAndCentre(): moving 206114 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 181... bp_lists.cpp::MoveBPListAndCentre(): moving 181701 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::MoveBPListAndCentre(): new object... bp_lists.cpp::MoveBPListAndCentre(): new object mask centre is (8.62243,12.304,8.27027)

bp_lists.cpp::MoveBPListAndCentre(): moving 481... bp_lists.cpp::MoveBPListAndCentre(): moving 4811 dots with flow field at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(39,68,42) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00499201 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.011773 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000437975 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 75525 dot... cellScm.cpp::ScmRenderCellIntoMask(): 75525 dots were added (ID 2 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00451303 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00991398 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000153005 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.19805e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 64432 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 255944 'chr' points, ID=2

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.142627 seconds

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=5.10629 to 12.0829; y=8.69016 to 16.1112; z=5.44746 to 11.2663

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (3.09515,6.93313,4.2094) of size (10.7711,10.8949,8.29499) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(14,12,8) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00839099 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.015705 seconds

cell.cpp::GetCellPolarityAndCentreVector(): Com... cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes

cell.cpp::GetCellPolarityAndCentreVector(): cen... cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (8.5426,12.2568,8.17118)

cell.cpp::GenerateCentrosomes(): Doing distance... cell.cpp::GenerateCentrosomes(): Doing distance transform

cell.cpp::GenerateCentrosomes(): max dist: 7.00... cell.cpp::GenerateCentrosomes(): max dist: 7.00484

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 211671 points (13395 outer) with centre at (8.62866,12.3041,8.26826)

scheduler.cpp::PnGetMeNonrigidHints(): since pn... scheduler.cpp::PnGetMeNonrigidHints(): since pnArray has size 197,197,197, will use offset 27,25,72

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (-20.3042,-12.0092,2.72373) of size (48.9033,49.3985,11.7616) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 4869 points (327 outer) with centre at (9.48837,10.9449,7.49044)

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:0--98, y:38--166, z:4--95

bp_lists.cpp::SoftRenderBPListIntoMask(): sourc... bp_lists.cpp::SoftRenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::SoftRenderBPListIntoMask(): pixel... bp_lists.cpp::SoftRenderBPListIntoMask(): pixelShift=(32,61,35)

bp_lists.cpp::SoftRenderBPListIntoMask(): rende... bp_lists.cpp::SoftRenderBPListIntoMask(): rendering (dilated) object took 0.00463104 seconds

bp_lists.cpp::SoftRenderBPListIntoMask(): flood... bp_lists.cpp::SoftRenderBPListIntoMask(): flooding outside of (dilated) object took 0.016939 seconds

scheduler.cpp::GetCellCometsLeavingFactor(): th... scheduler.cpp::GetCellCometsLeavingFactor(): there are 5 'living' and 0 'cut away' cells, ratio=inf

scheduler.cpp::RunFeeder_st(): Started processi... scheduler.cpp::RunFeeder_st(): Started processing of cell with ID=3 on frame no. 0 at Tue 2017-11-28, 10:04:03, there are 5 cells currently in the system

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, STARTING G2-phase at timePoint=0

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=62.2743 to 69.0836; y=75.2739 to 82.4547; z=4.58082 to 11.3901

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(188,185,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.013622 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.020017 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000317 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.39996e-05 seconds

rnd_generators.cpp::GetRandomGauss(): randomnes... rnd_generators.cpp::GetRandomGauss(): randomness started with seed 18446744071842591488

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 76977 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

rnd_generators.cpp::GetRandomUniform(): randomn... rnd_generators.cpp::GetRandomUniform(): randomness started with seed 18446744071842591488

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.33184,0.886676,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 12.7049deg clockwise around (65.6855,78.7756,8.11595) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 500... bp_lists.cpp::MoveBPListAndCentre(): moving 5005 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

regionlock.cpp::checkAndLock(): Total time spen... regionlock.cpp::checkAndLock(): Total time spent waiting (all threads): 0m 0s

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(489,613,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.004283 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000434011 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 89605 dot... cellScm.cpp::ScmRenderCellIntoMask(): 89605 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(175,193,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003861 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000117004 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.1012e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77404 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.116893 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=1 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.26454,0.301575,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -11.5871deg clockwise around (64.3537,79.662,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 540... bp_lists.cpp::MoveBPListAndCentre(): moving 5400 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00454099 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000421003 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 89115 dot... cellScm.cpp::ScmRenderCellIntoMask(): 89115 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(187,195,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00395298 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(210,211,36) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.5974e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77008 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.116281 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=2 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.66106,0.693451,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 3.96182deg clockwise around (65.6182,79.9636,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 500... bp_lists.cpp::MoveBPListAndCentre(): moving 5005 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 540... bp_lists.cpp::MoveBPListAndCentre(): moving 5400 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(486,621,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00447997 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000425011 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 89346 dot... cellScm.cpp::ScmRenderCellIntoMask(): 89346 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(173,201,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00398999 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00896999 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.19805e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77184 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=3 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-2.09646,-0.121892,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 14.0769deg clockwise around (63.9572,80.6571,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 540... bp_lists.cpp::MoveBPListAndCentre(): moving 5400 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(469,620,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00454101 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000416011 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 89997 dot... cellScm.cpp::ScmRenderCellIntoMask(): 89997 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(155,200,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00401902 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(190,231,49) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09971e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77725 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.120447 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=4 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-3.19736,-0.129987,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -8.28104deg clockwise around (61.8607,80.5352,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 500... bp_lists.cpp::MoveBPListAndCentre(): moving 5005 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

regionlock.h::printLockInfo(): SPHERE lock, wai... regionlock.h::printLockInfo(): SPHERE lock, waiting time: 0ms, timePoint: 5-5, sceneType: masks, centre: [65.6855, 78.7756, 8.11595], radius: 8.75

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(443,619,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00454098 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00986403 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000431955 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 89658 dot... cellScm.cpp::ScmRenderCellIntoMask(): 89658 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): AABB diag... bp_lists.cpp::RenderBPListIntoMask(): AABB diagonal=(7.06967,7.20562,6.93313) microns (including 2px frame)

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(130,199,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00403303 seconds

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.10269e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77431 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.141767 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=5 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.46544,-0.320133,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 9.90113deg clockwise around (58.6634,80.4052,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 500... bp_lists.cpp::MoveBPListAndCentre(): moving 5005 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 540... bp_lists.cpp::MoveBPListAndCentre(): moving 5400 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(431,616,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00833702 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.017419 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000657022 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 89987 dot... cellScm.cpp::ScmRenderCellIntoMask(): 89987 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(117,196,26) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00561702 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(143,213,36) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.39475e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77713 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.127584 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=6 with sync

regionlock.h::printLockInfo(): SPHERE lock, wai... regionlock.h::printLockInfo(): SPHERE lock, waiting time: 647ms, timePoint: 7-7, sceneType: masks, centre: [57.1979, 80.085, 8.11624], radius: 8.75

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-2.34444,-0.868113,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 5.47241deg clockwise around (57.1979,80.085,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 540... bp_lists.cpp::MoveBPListAndCentre(): moving 5400 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(412,610,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00447899 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000429988 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 90119 dot... cellScm.cpp::ScmRenderCellIntoMask(): 90119 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00391996 seconds

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.29938e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77847 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.117542 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=3, doing G2-phase at timePoint=7 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (0.404024,-1.85655,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 3.94475deg clockwise around (54.8535,79.2169,8.11624) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 227... bp_lists.cpp::MoveBPListAndCentre(): moving 227771 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 203... bp_lists.cpp::MoveBPListAndCentre(): moving 203775 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 540... bp_lists.cpp::MoveBPListAndCentre(): moving 5400 dots with flow field at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00455397 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000434995 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 90118 dot... cellScm.cpp::ScmRenderCellIntoMask(): 90118 dots were added (ID 3 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00396001 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000124991 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.10269e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 77908 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 307832 'chr' points, ID=3

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.129072 seconds

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=51.5814 to 59.0022; y=73.9182 to 80.7358; z=4.58082 to 11.3901

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(12,15,10) pixels

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00555396 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.015908 seconds

cell.cpp::GetCellPolarityAndCentreVector(): Com... cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes

cell.cpp::GetCellPolarityAndCentreVector(): cen... cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (55.2174,77.2548,8.04738)

cell.cpp::GenerateCentrosomes(): Doing distance... cell.cpp::GenerateCentrosomes(): Doing distance transform

cell.cpp::GenerateCentrosomes(): max dist: 9.27... cell.cpp::GenerateCentrosomes(): max dist: 9.27337

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 230376 points (14598 outer) with centre at (55.2656,77.3489,8.11729)

scheduler.cpp::PnGetMeNonrigidHints(): since pn... scheduler.cpp::PnGetMeNonrigidHints(): since pnArray has size 197,197,197, will use offset 93,23,66

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (38.9988,52.1222,1.36186) of size (53.2365,53.3603,13.1234) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 5684 points (380 outer) with centre at (56.6252,78.8363,8.20214)

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:466--594, y:572--685, z:1--95

bp_lists.cpp::SoftRenderBPListIntoMask(): sourc... bp_lists.cpp::SoftRenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::SoftRenderBPListIntoMask(): pixel... bp_lists.cpp::SoftRenderBPListIntoMask(): pixelShift=(408,588,28)

bp_lists.cpp::SoftRenderBPListIntoMask(): rende... bp_lists.cpp::SoftRenderBPListIntoMask(): rendering (dilated) object took 0.00589199 seconds

bp_lists.cpp::SoftRenderBPListIntoMask(): flood... bp_lists.cpp::SoftRenderBPListIntoMask(): flooding outside of (dilated) object took 0.02193 seconds

scheduler.cpp::GetCellCometsLeavingFactor(): th... scheduler.cpp::GetCellCometsLeavingFactor(): there are 5 'living' and 0 'cut away' cells, ratio=inf

scheduler.cpp::ReleaseOldScenes(): scene #3 saved scheduler.cpp::ReleaseOldScenes(): scene #3 saved

scheduler.cpp::ReleaseOldScenes(): scene #4 saved scheduler.cpp::ReleaseOldScenes(): scene #4 saved

scheduler.cpp::ReleaseOldScenes(): scene #5 saved scheduler.cpp::ReleaseOldScenes(): scene #5 saved

scheduler.cpp::ReleaseOldScenes(): scene #6 saved scheduler.cpp::ReleaseOldScenes(): scene #6 saved

scheduler.cpp::RunFeeder_st(): Started processi... scheduler.cpp::RunFeeder_st(): Started processing of cell with ID=5 on frame no. 0 at Tue 2017-11-28, 10:04:03, there are 5 cells currently in the system

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, STARTING G2-phase at timePoint=0

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=50.8842 to 57.9411; y=28.9706 to 35.5323; z=5.69507 to 11.2663

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(203,205,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.0078 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(215,229,35) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000226997 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 2.10032e-05 seconds

rnd_generators.cpp::GetRandomGauss(): randomnes... rnd_generators.cpp::GetRandomGauss(): randomness started with seed 887525312

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57360 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

rnd_generators.cpp::GetRandomUniform(): randomn... rnd_generators.cpp::GetRandomUniform(): randomness started with seed 887525312

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-0.999883,0.0153189,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 1.1575deg clockwise around (54.287,32.3327,8.54858) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 543... bp_lists.cpp::MoveBPListAndCentre(): moving 5438 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(400,231,44) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00470001 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000400007 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68002 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68002 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(194,204,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00447401 seconds

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.5974e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57362 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.117073 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=1 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.92054,0.558146,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 15.4242deg clockwise around (53.2865,32.3486,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 551... bp_lists.cpp::MoveBPListAndCentre(): moving 5512 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(415,235,44) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00395 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000346005 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68607 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68607 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(209,208,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.003425 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000131994 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.29938e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57853 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.117025 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=2 with sync

cellScm.cpp::ScmUniversalMovement(): MITOCHECK ... cellScm.cpp::ScmUniversalMovement(): MITOCHECK MODE: trying 3x longer step ala Mitocheck.

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-7.8788,-8.23921,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -5.34483deg clockwise around (55.207,32.9067,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 543... bp_lists.cpp::MoveBPListAndCentre(): moving 5438 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00392601 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.008753 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000323981 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68514 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68514 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00346202 seconds

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(164,150,46) pixels

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.50204e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57727 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=3 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.38711,-2.19908,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 4.70391deg clockwise around (47.3282,24.6675,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 551... bp_lists.cpp::MoveBPListAndCentre(): moving 5512 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(362,151,44) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00400299 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00878301 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000339001 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68621 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68621 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00346801 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000128984 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.09971e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57919 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.120474 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=4 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-2.04068,-1.44416,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 8.47253deg clockwise around (48.7153,22.4684,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 543... bp_lists.cpp::MoveBPListAndCentre(): moving 5438 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 551... bp_lists.cpp::MoveBPListAndCentre(): moving 5512 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

cellScm.cpp::ScmRenderCellIntoMask(): inserting... cellScm.cpp::ScmRenderCellIntoMask(): inserting ID=5 into source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(346,139,44) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00364599 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00929698 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000469029 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68863 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68863 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(140,112,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00410002 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000149965 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000159979 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.99676e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 57976 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.140795 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=5 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.96573,0.987886,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 18.2999deg clockwise around (46.6746,21.0243,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 543... bp_lists.cpp::MoveBPListAndCentre(): moving 5438 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 551... bp_lists.cpp::MoveBPListAndCentre(): moving 5512 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00397199 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00823301 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000348032 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68975 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68975 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(125,121,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00355399 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000144005 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.90139e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58155 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.127034 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=6 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (1.69188,-0.165934,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by 9.56874deg clockwise around (44.7089,22.0122,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 551... bp_lists.cpp::MoveBPListAndCentre(): moving 5512 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00473601 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000395 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68949 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68949 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::RenderBPListIntoMask(): Warning: ... bp_lists.cpp::RenderBPListIntoMask(): Warning: Asked to render outside or at the boundary of the mask image.

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00410599 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000160992 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.40071e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58126 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.116881 seconds

cell_08_G2Phase.cpp::DoG2Phase(): ***** ****... cell_08_G2Phase.cpp::DoG2Phase(): ***** ***** cell ID=5, doing G2-phase at timePoint=7 with sync

cellScm.cpp::ScmUniversalMovement(): Comet vect... cellScm.cpp::ScmUniversalMovement(): Comet vector is (0,0,0), state is 0 (nHTF)

flowfields.cpp::DescribeTranslation(): adding v... flowfields.cpp::DescribeTranslation(): adding vector (-1.42093,0.480575,0) to the flow field

flowfields.cpp::DescribeRotation(): adding rota... flowfields.cpp::DescribeRotation(): adding rotation by -2.55217deg clockwise around (46.4008,21.8462,8.5487) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 194... bp_lists.cpp::MoveBPListAndCentre(): moving 194326 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 171... bp_lists.cpp::MoveBPListAndCentre(): moving 171687 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 543... bp_lists.cpp::MoveBPListAndCentre(): moving 5438 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::MoveBPListAndCentre(): moving 551... bp_lists.cpp::MoveBPListAndCentre(): moving 5512 dots with flow field at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(334,150,44) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00407195 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00820202 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 0.000348032 seconds

cellScm.cpp::ScmRenderCellIntoMask(): 68934 dot... cellScm.cpp::ScmRenderCellIntoMask(): 68934 dots were added (ID 5 )

bp_lists.cpp::RenderBPListIntoMask(): source im... bp_lists.cpp::RenderBPListIntoMask(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(127,123,23) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.00334799 seconds

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.000132978 seconds

bp_lists.cpp::RenderBPListIntoMask(): finishing... bp_lists.cpp::RenderBPListIntoMask(): finishing (eroding) object took 1.20401e-05 seconds

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regenerating distance map, it contains 58113 pixels

cellChr.cpp::FindNearestMaskVoxel(): Regenerati... cellChr.cpp::FindNearestMaskVoxel(): Regeneration finished.

cellChr.cpp::ChrRenderIntoPhantoms(): going to ... cellChr.cpp::ChrRenderIntoPhantoms(): going to render 229448 'chr' points, ID=5

cellChr.cpp::ChrRenderIntoPhantoms(): direct re... cellChr.cpp::ChrRenderIntoPhantoms(): direct rendering chr points took 0.136153 seconds

bp_lists.cpp::AllocateAndZeroNewMask(): points ... bp_lists.cpp::AllocateAndZeroNewMask(): points span x=41.6636 to 48.3153; y=18.9178 to 25.765; z=5.69507 to 11.2663

bp_lists.cpp::RenderBPListIntoMask(): pixelShif... bp_lists.cpp::RenderBPListIntoMask(): pixelShift=(13,12,8) pixels

bp_lists.cpp::RenderBPListIntoMask(): rendering... bp_lists.cpp::RenderBPListIntoMask(): rendering (dilated) object took 0.004659 seconds

bp_lists.cpp::RenderBPListIntoMask(): flooding ... bp_lists.cpp::RenderBPListIntoMask(): flooding outside of (dilated) object took 0.00985801 seconds

cell.cpp::GetCellPolarityAndCentreVector(): Com... cell.cpp::GetCellPolarityAndCentreVector(): Computing principal axes

cell.cpp::GetCellPolarityAndCentreVector(): cen... cell.cpp::GetCellPolarityAndCentreVector(): centroid (in microns): (44.9415,22.285,8.5426)

cell.cpp::GenerateCentrosomes(): Doing distance... cell.cpp::GenerateCentrosomes(): Doing distance transform

cell.cpp::GenerateCentrosomes(): max dist: 6.16... cell.cpp::GenerateCentrosomes(): max dist: 6.16181

cell.cpp::GenerateCentrosomes(): centrosomes ge... cell.cpp::GenerateCentrosomes(): centrosomes generated.

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (0,0,0) of size (84.9308,84.9308,11.8854) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 196603 points (12457 outer) with centre at (44.9849,22.3343,8.54906)

scheduler.cpp::PnGetMeNonrigidHints(): since pn... scheduler.cpp::PnGetMeNonrigidHints(): since pnArray has size 197,197,197, will use offset 93,80,6

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::ResetBoundaryPoints(): source ima... bp_lists.cpp::ResetBoundaryPoints(): source image at (25.7516,3.59037,2.72373) of size (57.3221,57.1983,11.3901) in microns

bp_lists.cpp::ResetBoundaryPoints(): new list c... bp_lists.cpp::ResetBoundaryPoints(): new list contains 5623 points (379 outer) with centre at (45.6824,20.8298,9.23611)

cellScm.cpp::ScmRemoveCellFromMask(): sweeping ... cellScm.cpp::ScmRemoveCellFromMask(): sweeping ranges, x:374--502, y:197--325, z:5--95

bp_lists.cpp::SoftRenderBPListIntoMask(): pixel... bp_lists.cpp::SoftRenderBPListIntoMask(): pixelShift=(328,144,37)

bp_lists.cpp::SoftRenderBPListIntoMask(): rende... bp_lists.cpp::SoftRenderBPListIntoMask(): rendering (dilated) object took 0.00499499 seconds

bp_lists.cpp::SoftRenderBPListIntoMask(): flood... bp_lists.cpp::SoftRenderBPListIntoMask(): flooding outside of (dilated) object took 0.019308 seconds

scheduler.cpp::GetCellCometsLeavingFactor(): th... scheduler.cpp::GetCellCometsLeavingFactor(): there are 5 'living' and 0 'cut away' cells, ratio=inf

scheduler.cpp::ReleaseOldScenes(): scene #0 saved scheduler.cpp::ReleaseOldScenes(): scene #0 saved