Commit 7597bfcd authored by Vladimír Ulman's avatar Vladimír Ulman Committed by Vladimír Ulman
Browse files

Finalized 'Mitocheck movements': 

- added some missing parts of the RndWlk (the part around mean step size distribution)
- configuration that enables Mitocheck-like behaviour moved from 'testing' section into the 'cell' one
- following the Mitocheck-like behaviour during simulation is no longer communicated as a "TESTING MODE"

M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini
M    src/cell.cpp
M    src/cellScm.cpp
M    src/cell.h

Added some more debug to figure out why we are getting some rendering error.
(error msg: pixelShift has negative coordinates)
M    src/toolbox/bp_lists.cpp
parent bc3e1c0a

config/config-711extVOI-highSNR.ini

+14 −5
Original line number Diff line number Diff line
@@ -91,6 +91,20 @@ variance of the cell magnitude of movement per frame = 0.3 
; random movement (no persistence)

directionality of cell motility = 0.5



;

; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'directionality of cell motility'.

use Mitocheck turning angle distribution = 1

;

; If this parameter is present, the cells displacement size distribution, that

; also influences cell trajectory character, reproduces the one measured from

; a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'cell magnitude of movement per frame'

; and 'variance of the cell magnitude of movement per frame'.

use Mitocheck step size distribution = 1



;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.
@@ -314,11 +328,6 @@ level = 1 
; and vice versa.

;disable rigid movement = 1



; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

use Mitocheck turning angle distribution = 1



; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1

config/config-middleVOI-highSNR.ini

+14 −5
Original line number Diff line number Diff line
@@ -91,6 +91,20 @@ variance of the cell magnitude of movement per frame = 0.3 
; random movement (no persistence)

directionality of cell motility = 0.5



;

; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'directionality of cell motility'.

use Mitocheck turning angle distribution = 1

;

; If this parameter is present, the cells displacement size distribution, that

; also influences cell trajectory character, reproduces the one measured from

; a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'cell magnitude of movement per frame'

; and 'variance of the cell magnitude of movement per frame'.

use Mitocheck step size distribution = 1



;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.
@@ -456,11 +470,6 @@ level = 1 
; and vice versa.

;disable rigid movement = 1



; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

use Mitocheck turning angle distribution = 1



; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1

config/config-middleVOI-lowSNR.ini

+14 −5
Original line number Diff line number Diff line
@@ -91,6 +91,20 @@ variance of the cell magnitude of movement per frame = 0.3 
; random movement (no persistence)

directionality of cell motility = 0.5



;

; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'directionality of cell motility'.

use Mitocheck turning angle distribution = 1

;

; If this parameter is present, the cells displacement size distribution, that

; also influences cell trajectory character, reproduces the one measured from

; a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'cell magnitude of movement per frame'

; and 'variance of the cell magnitude of movement per frame'.

use Mitocheck step size distribution = 1



;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.
@@ -456,11 +470,6 @@ level = 1 
; and vice versa.

;disable rigid movement = 1



; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

use Mitocheck turning angle distribution = 1



; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1

config/config-smallVOI-highSNR.ini

+14 −5
Original line number Diff line number Diff line
@@ -91,6 +91,20 @@ variance of the cell magnitude of movement per frame = 0.3 
; random movement (no persistence)

directionality of cell motility = 0.5



;

; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'directionality of cell motility'.

use Mitocheck turning angle distribution = 1

;

; If this parameter is present, the cells displacement size distribution, that

; also influences cell trajectory character, reproduces the one measured from

; a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'cell magnitude of movement per frame'

; and 'variance of the cell magnitude of movement per frame'.

use Mitocheck step size distribution = 1



;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.
@@ -455,11 +469,6 @@ level = 1 
; and vice versa.

;disable rigid movement = 1



; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

use Mitocheck turning angle distribution = 1



; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1

config/config-smallVOI-lowSNR.ini

+14 −5
Original line number Diff line number Diff line
@@ -91,6 +91,20 @@ variance of the cell magnitude of movement per frame = 0.3 
; random movement (no persistence)

directionality of cell motility = 0.5



;

; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'directionality of cell motility'.

use Mitocheck turning angle distribution = 1

;

; If this parameter is present, the cells displacement size distribution, that

; also influences cell trajectory character, reproduces the one measured from

; a certain dataset from the Mitocheck project.

; This parameters obsoletes the 'cell magnitude of movement per frame'

; and 'variance of the cell magnitude of movement per frame'.

use Mitocheck step size distribution = 1



;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.
@@ -456,11 +470,6 @@ level = 1 
; and vice versa.

;disable rigid movement = 1



; If this parameter is present, the cells turning angle distribution, that

; defines persistency of cell motion as well as it's trajectory character,

; reproduces the one measured from a certain dataset from the Mitocheck project.

use Mitocheck turning angle distribution = 1



; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1