Commit 0cb69ff2 authored by Vladimír Ulman's avatar Vladimír Ulman
Browse files

Updated all configs with the [sofa] section (which is used only 

if explicitly enabled during Cmake) and some new items in the
[testing] section (content of the [testing] section is optional).

M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR-correctSize.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-singleCell-correctSize.ini
M    config/config-middleVOI-highSNR.ini
parent d2c780a7

config/config-middleVOI-highSNR.ini

+160 −0
Original line number Diff line number Diff line
@@ -113,6 +113,13 @@ cell nonrigid strong deformation = 0.7 
; short sequences:

cell sparse nonrigid deformations = false



;

; Refer to the [sofa] section for parameters related to performing

; non-rigid deformations with the SOFA framework.

;

; Note that the SOFA option must be also enabled in the CMake.

;



;

; How far a cell can "see" when it is trying to move

; to region with lower density of cells (in microns).
@@ -148,6 +155,138 @@ number of frames per cell cycle = 50 
intensity of nonspecific staining = 2





[sofa]

;

; Note that the SOFA option must be also enabled in the CMake in order

; to make the simulator consider the content of this section.

;



;

; The simulation with the SOFA works in two modes:

; - Export mode:	the simulator starts as usual, creates its internal structures etc.,

; 						but then, instead of actually starting the simulation itself, it

; 						rather exports relevant data for the SOFA including the initial scene*

; 						images, and quits

; - Play mode:		the simulator starts as usual except that some structures/data is

;						not created but rather imported from the SOFA data, the simulation is

;						then started as usual (except for some new SOFA stuff in the atomic

;						functions... ;-)

;

; The play mode is default unless this option equals to 1 (one).

; Set this one to 0 (zero) to work in the play mode.

export mode = 0



; Re-export mode... well, the export mode can be `crippled' if this parameter

; is available (not commented out) and, of course, if the export mode is on.

; That is, the simulator will do export mode but instead of creating every piece

; of the cell right from the scratch, it reads (as if in play mode) the shape of

; cell (cytoplasm), nucleus, and both nucleoli (if enabled in the CMake). The chromatin

; is, however, generated from the scratch and deformation magnitudes as well.

;

; The purpose of this mode is to create and export ``new'' cells without

; the need to re-mesh them in the SOFA. That's why the mask/shape stuff is

; re-read while all the rest is created new.

crippled export mode that plays = 1



;

; For creating new data for a new frame of the simulator, the SOFA usually requires to

; calculate several (however, fixed) internal iterations (which are, however, exported

; as well). This parameter specifies multiplication factor to match simulator frame no.

; with corresponding frame no. of the SOFA. In other words, this parameter minus one tells

; how many internal iterations were used in the SOFA.

frame skip step = 5



;

; Provide template file names used when exporting data to the SOFA:

; Include one '%u' for the cell ID. One can disable certain export

; by disabling/commenting respective parameter.

;

; Note: BP stands for "Boundary Points" -- yes, it has relevance

; to the Cell::BPLists.

;

; Note: "mask voxels" make up an initial cell mask. The file will

; contain the same number of lines as there are voxels in the mask.

;

; The syntax follows that of the standard C library printf() function.

export name nucleus mask img    = ID%02u_init_nucleusMask.mhd

;export name nucleus mask voxels = ID%02u_init_nucleusMask_coordinates.txt

;export name nucleus mask grid   = ID%02u_init_gridPoints.txt

export name nucleus BP          = ID%02u_init_nucleusOuterBoundaryPoints.txt

export name nucleoli1 BP        = ID%02u_init_nucleoli1OuterBoundaryPoints.txt

export name nucleoli2 BP        = ID%02u_init_nucleoli2OuterBoundaryPoints.txt

export name chromatin molecules = ID%02u_init_chromatinPoints.txt

;export name nucleus deform img  = ID%02u_init_nucleusOuterBoundaryPoints_DeformationMagnitudes.ics



;

; Similar stuff but for deformation hints for particular cells.

; Use somewhere first '%u' for the cell ID, later '%lu' for frame

; number.

export name nucleus deformation = ID%.2u_T%03lu_nucleusOuterBoundaryPoints_DeformationMagnitudes.txt



;

; This number minus one gives number of voxels between two

; nearby grid lines.

export mask grid stepping = 7



;

; Provide template file names used when importing data from the SOFA:

; Include first '%u' for the cell ID and second '%lu' for frame number.

; One can disable certain import by disabling/commenting respective parameter.

;

; The syntax follows that of the standard C library printf() function.

import name nucleus BP          = ../deformationsID01-10/ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

import name nucleoli1 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

import name nucleoli2 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

import name chromatin molecules = ../deformationsID01-10/ID%02u_T%03lu_chromatinPoints.txt



; import name nucleus BP          = ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

; import name nucleoli1 BP        = ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

; import name nucleoli2 BP        = ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

; import name chromatin molecules = ID%02u_T%03lu_gridPoints.txt



;

; In the play mode, one can re-position the cells imported from the SOFA

; to one's own reference positions. To achieve that, a new cell centre

; and/or additional rotation to the current shape may be specified.

; The rotation is understood around the z-axis, i.e., in the xy-plane.

;

; The centre position is given in microns relative to the scene [0,0,0],

; as three (positive) real numbers separated with white space.

; The angle is given, for user convenience, in degrees.

;ID01 initial position = 40.6   43		4.5

;ID01 initial rotation = 45



; clusters

ID01 initial position = 12 12 5.5

ID02 initial position = 19 14.5 5.5

ID02 initial rotation = 45

ID07 initial position = 14 20 5.5



ID04 initial position = 38.5 22 5.5

ID04 initial rotation = -90

ID05 initial position = 40 12 5.5

ID09 initial position = 45 18 5.5



ID03 initial position = 16 42 5.5

ID03 initial rotation = 25

ID08 initial position = 19.5 48 5.5



ID06 initial position = 44 41.5 5.5

ID10 initial position = 47 47.5 5.5



; grid positions

;yy; ID01 initial position = 9 15 5.5

;yy; ID02 initial position = 22.5 15 5.5

;yy; ID03 initial position = 37.5 15 5.5

;yy; ID04 initial position = 51 15 5.5

;yy; ID05 initial position = 9 30 5.5

;yy; ID06 initial position = 22.5 30 5.5

;yy; ID07 initial position = 37.5 30 5.5

;yy; ID08 initial position = 51 30 5.5

;yy; ID09 initial position = 9 45 5.5

;yy; ID10 initial position = 22.5 45 5.5





;

;-------------- characteristics of scheduler -------------------

;
@@ -293,3 +432,24 @@ level = 1 
; Used in both Scheduler constructors. Should be positive natural number.

;cell initial G2 life = 25



;

; If rigid movement of cells is enabled in the CMake, this parameter can

; disable it. It cannot, however, enable it if the rigid movement is disabled

; in the CMake (as the code is simply missing in the simulator binary then).

;

; Presence of the parameter with any value disables the movements,

; and vice versa.

;disable rigid movement = 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



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

; images will not render all chromatin but, instead, only the chromatin

; which is listed in the parameter.

;

; Note that the number of chromatin present in the simulation is defined

; in the [cell] section of this configuration file. So, the numbers listed

; in this parameter should range from 0 up to (the number of chromatin minus 1).

;territories show only these chromatins = 15 30 45

config/config-middleVOI-lowSNR.ini

+160 −0
Original line number Diff line number Diff line
@@ -113,6 +113,13 @@ cell nonrigid strong deformation = 0.7 
; short sequences:

cell sparse nonrigid deformations = false



;

; Refer to the [sofa] section for parameters related to performing

; non-rigid deformations with the SOFA framework.

;

; Note that the SOFA option must be also enabled in the CMake.

;



;

; How far a cell can "see" when it is trying to move

; to region with lower density of cells (in microns).
@@ -148,6 +155,138 @@ number of frames per cell cycle = 50 
intensity of nonspecific staining = 2





[sofa]

;

; Note that the SOFA option must be also enabled in the CMake in order

; to make the simulator consider the content of this section.

;



;

; The simulation with the SOFA works in two modes:

; - Export mode:	the simulator starts as usual, creates its internal structures etc.,

; 						but then, instead of actually starting the simulation itself, it

; 						rather exports relevant data for the SOFA including the initial scene*

; 						images, and quits

; - Play mode:		the simulator starts as usual except that some structures/data is

;						not created but rather imported from the SOFA data, the simulation is

;						then started as usual (except for some new SOFA stuff in the atomic

;						functions... ;-)

;

; The play mode is default unless this option equals to 1 (one).

; Set this one to 0 (zero) to work in the play mode.

export mode = 0



; Re-export mode... well, the export mode can be `crippled' if this parameter

; is available (not commented out) and, of course, if the export mode is on.

; That is, the simulator will do export mode but instead of creating every piece

; of the cell right from the scratch, it reads (as if in play mode) the shape of

; cell (cytoplasm), nucleus, and both nucleoli (if enabled in the CMake). The chromatin

; is, however, generated from the scratch and deformation magnitudes as well.

;

; The purpose of this mode is to create and export ``new'' cells without

; the need to re-mesh them in the SOFA. That's why the mask/shape stuff is

; re-read while all the rest is created new.

crippled export mode that plays = 1



;

; For creating new data for a new frame of the simulator, the SOFA usually requires to

; calculate several (however, fixed) internal iterations (which are, however, exported

; as well). This parameter specifies multiplication factor to match simulator frame no.

; with corresponding frame no. of the SOFA. In other words, this parameter minus one tells

; how many internal iterations were used in the SOFA.

frame skip step = 5



;

; Provide template file names used when exporting data to the SOFA:

; Include one '%u' for the cell ID. One can disable certain export

; by disabling/commenting respective parameter.

;

; Note: BP stands for "Boundary Points" -- yes, it has relevance

; to the Cell::BPLists.

;

; Note: "mask voxels" make up an initial cell mask. The file will

; contain the same number of lines as there are voxels in the mask.

;

; The syntax follows that of the standard C library printf() function.

export name nucleus mask img    = ID%02u_init_nucleusMask.mhd

;export name nucleus mask voxels = ID%02u_init_nucleusMask_coordinates.txt

;export name nucleus mask grid   = ID%02u_init_gridPoints.txt

export name nucleus BP          = ID%02u_init_nucleusOuterBoundaryPoints.txt

export name nucleoli1 BP        = ID%02u_init_nucleoli1OuterBoundaryPoints.txt

export name nucleoli2 BP        = ID%02u_init_nucleoli2OuterBoundaryPoints.txt

export name chromatin molecules = ID%02u_init_chromatinPoints.txt

;export name nucleus deform img  = ID%02u_init_nucleusOuterBoundaryPoints_DeformationMagnitudes.ics



;

; Similar stuff but for deformation hints for particular cells.

; Use somewhere first '%u' for the cell ID, later '%lu' for frame

; number.

export name nucleus deformation = ID%.2u_T%03lu_nucleusOuterBoundaryPoints_DeformationMagnitudes.txt



;

; This number minus one gives number of voxels between two

; nearby grid lines.

export mask grid stepping = 7



;

; Provide template file names used when importing data from the SOFA:

; Include first '%u' for the cell ID and second '%lu' for frame number.

; One can disable certain import by disabling/commenting respective parameter.

;

; The syntax follows that of the standard C library printf() function.

import name nucleus BP          = ../deformationsID01-10/ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

import name nucleoli1 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

import name nucleoli2 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

import name chromatin molecules = ../deformationsID01-10/ID%02u_T%03lu_chromatinPoints.txt



; import name nucleus BP          = ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

; import name nucleoli1 BP        = ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

; import name nucleoli2 BP        = ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

; import name chromatin molecules = ID%02u_T%03lu_gridPoints.txt



;

; In the play mode, one can re-position the cells imported from the SOFA

; to one's own reference positions. To achieve that, a new cell centre

; and/or additional rotation to the current shape may be specified.

; The rotation is understood around the z-axis, i.e., in the xy-plane.

;

; The centre position is given in microns relative to the scene [0,0,0],

; as three (positive) real numbers separated with white space.

; The angle is given, for user convenience, in degrees.

;ID01 initial position = 40.6   43		4.5

;ID01 initial rotation = 45



; clusters

ID01 initial position = 12 12 5.5

ID02 initial position = 19 14.5 5.5

ID02 initial rotation = 45

ID07 initial position = 14 20 5.5



ID04 initial position = 38.5 22 5.5

ID04 initial rotation = -90

ID05 initial position = 40 12 5.5

ID09 initial position = 45 18 5.5



ID03 initial position = 16 42 5.5

ID03 initial rotation = 25

ID08 initial position = 19.5 48 5.5



ID06 initial position = 44 41.5 5.5

ID10 initial position = 47 47.5 5.5



; grid positions

;yy; ID01 initial position = 9 15 5.5

;yy; ID02 initial position = 22.5 15 5.5

;yy; ID03 initial position = 37.5 15 5.5

;yy; ID04 initial position = 51 15 5.5

;yy; ID05 initial position = 9 30 5.5

;yy; ID06 initial position = 22.5 30 5.5

;yy; ID07 initial position = 37.5 30 5.5

;yy; ID08 initial position = 51 30 5.5

;yy; ID09 initial position = 9 45 5.5

;yy; ID10 initial position = 22.5 45 5.5





;

;-------------- characteristics of scheduler -------------------

;
@@ -293,3 +432,24 @@ level = 1 
; Used in both Scheduler constructors. Should be positive natural number.

;cell initial G2 life = 25



;

; If rigid movement of cells is enabled in the CMake, this parameter can

; disable it. It cannot, however, enable it if the rigid movement is disabled

; in the CMake (as the code is simply missing in the simulator binary then).

;

; Presence of the parameter with any value disables the movements,

; and vice versa.

;disable rigid movement = 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



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

; images will not render all chromatin but, instead, only the chromatin

; which is listed in the parameter.

;

; Note that the number of chromatin present in the simulation is defined

; in the [cell] section of this configuration file. So, the numbers listed

; in this parameter should range from 0 up to (the number of chromatin minus 1).

;territories show only these chromatins = 15 30 45

config/config-singleCell-correctSize.ini

+160 −0
Original line number Diff line number Diff line
@@ -113,6 +113,13 @@ cell nonrigid strong deformation = 1.4 
; short sequences:

cell sparse nonrigid deformations = false



;

; Refer to the [sofa] section for parameters related to performing

; non-rigid deformations with the SOFA framework.

;

; Note that the SOFA option must be also enabled in the CMake.

;



;

; How far a cell can "see" when it is trying to move

; to region with lower density of cells (in microns).
@@ -148,6 +155,138 @@ number of frames per cell cycle = 50 
intensity of nonspecific staining = 2





[sofa]

;

; Note that the SOFA option must be also enabled in the CMake in order

; to make the simulator consider the content of this section.

;



;

; The simulation with the SOFA works in two modes:

; - Export mode:	the simulator starts as usual, creates its internal structures etc.,

; 						but then, instead of actually starting the simulation itself, it

; 						rather exports relevant data for the SOFA including the initial scene*

; 						images, and quits

; - Play mode:		the simulator starts as usual except that some structures/data is

;						not created but rather imported from the SOFA data, the simulation is

;						then started as usual (except for some new SOFA stuff in the atomic

;						functions... ;-)

;

; The play mode is default unless this option equals to 1 (one).

; Set this one to 0 (zero) to work in the play mode.

export mode = 0



; Re-export mode... well, the export mode can be `crippled' if this parameter

; is available (not commented out) and, of course, if the export mode is on.

; That is, the simulator will do export mode but instead of creating every piece

; of the cell right from the scratch, it reads (as if in play mode) the shape of

; cell (cytoplasm), nucleus, and both nucleoli (if enabled in the CMake). The chromatin

; is, however, generated from the scratch and deformation magnitudes as well.

;

; The purpose of this mode is to create and export ``new'' cells without

; the need to re-mesh them in the SOFA. That's why the mask/shape stuff is

; re-read while all the rest is created new.

crippled export mode that plays = 1



;

; For creating new data for a new frame of the simulator, the SOFA usually requires to

; calculate several (however, fixed) internal iterations (which are, however, exported

; as well). This parameter specifies multiplication factor to match simulator frame no.

; with corresponding frame no. of the SOFA. In other words, this parameter minus one tells

; how many internal iterations were used in the SOFA.

frame skip step = 5



;

; Provide template file names used when exporting data to the SOFA:

; Include one '%u' for the cell ID. One can disable certain export

; by disabling/commenting respective parameter.

;

; Note: BP stands for "Boundary Points" -- yes, it has relevance

; to the Cell::BPLists.

;

; Note: "mask voxels" make up an initial cell mask. The file will

; contain the same number of lines as there are voxels in the mask.

;

; The syntax follows that of the standard C library printf() function.

export name nucleus mask img    = ID%02u_init_nucleusMask.mhd

;export name nucleus mask voxels = ID%02u_init_nucleusMask_coordinates.txt

;export name nucleus mask grid   = ID%02u_init_gridPoints.txt

export name nucleus BP          = ID%02u_init_nucleusOuterBoundaryPoints.txt

export name nucleoli1 BP        = ID%02u_init_nucleoli1OuterBoundaryPoints.txt

export name nucleoli2 BP        = ID%02u_init_nucleoli2OuterBoundaryPoints.txt

export name chromatin molecules = ID%02u_init_chromatinPoints.txt

;export name nucleus deform img  = ID%02u_init_nucleusOuterBoundaryPoints_DeformationMagnitudes.ics



;

; Similar stuff but for deformation hints for particular cells.

; Use somewhere first '%u' for the cell ID, later '%lu' for frame

; number.

export name nucleus deformation = ID%.2u_T%03lu_nucleusOuterBoundaryPoints_DeformationMagnitudes.txt



;

; This number minus one gives number of voxels between two

; nearby grid lines.

export mask grid stepping = 7



;

; Provide template file names used when importing data from the SOFA:

; Include first '%u' for the cell ID and second '%lu' for frame number.

; One can disable certain import by disabling/commenting respective parameter.

;

; The syntax follows that of the standard C library printf() function.

import name nucleus BP          = ../deformationsID01-10/ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

import name nucleoli1 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

import name nucleoli2 BP        = ../deformationsID01-10/ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

import name chromatin molecules = ../deformationsID01-10/ID%02u_T%03lu_chromatinPoints.txt



; import name nucleus BP          = ID%02u_T%03lu_nucleusOuterBoundaryPoints.txt

; import name nucleoli1 BP        = ID%02u_T%03lu_nucleoli1OuterBoundaryPoints.txt

; import name nucleoli2 BP        = ID%02u_T%03lu_nucleoli2OuterBoundaryPoints.txt

; import name chromatin molecules = ID%02u_T%03lu_gridPoints.txt



;

; In the play mode, one can re-position the cells imported from the SOFA

; to one's own reference positions. To achieve that, a new cell centre

; and/or additional rotation to the current shape may be specified.

; The rotation is understood around the z-axis, i.e., in the xy-plane.

;

; The centre position is given in microns relative to the scene [0,0,0],

; as three (positive) real numbers separated with white space.

; The angle is given, for user convenience, in degrees.

;ID01 initial position = 40.6   43		4.5

;ID01 initial rotation = 45



; clusters

ID01 initial position = 12 12 5.5

ID02 initial position = 19 14.5 5.5

ID02 initial rotation = 45

ID07 initial position = 14 20 5.5



ID04 initial position = 38.5 22 5.5

ID04 initial rotation = -90

ID05 initial position = 40 12 5.5

ID09 initial position = 45 18 5.5



ID03 initial position = 16 42 5.5

ID03 initial rotation = 25

ID08 initial position = 19.5 48 5.5



ID06 initial position = 44 41.5 5.5

ID10 initial position = 47 47.5 5.5



; grid positions

;yy; ID01 initial position = 9 15 5.5

;yy; ID02 initial position = 22.5 15 5.5

;yy; ID03 initial position = 37.5 15 5.5

;yy; ID04 initial position = 51 15 5.5

;yy; ID05 initial position = 9 30 5.5

;yy; ID06 initial position = 22.5 30 5.5

;yy; ID07 initial position = 37.5 30 5.5

;yy; ID08 initial position = 51 30 5.5

;yy; ID09 initial position = 9 45 5.5

;yy; ID10 initial position = 22.5 45 5.5





;

;-------------- characteristics of scheduler -------------------

;
@@ -293,3 +432,24 @@ level = 1 
; Used in both Scheduler constructors. Should be positive natural number.

;cell initial G2 life = 25



;

; If rigid movement of cells is enabled in the CMake, this parameter can

; disable it. It cannot, however, enable it if the rigid movement is disabled

; in the CMake (as the code is simply missing in the simulator binary then).

;

; Presence of the parameter with any value disables the movements,

; and vice versa.

;disable rigid movement = 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



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

; images will not render all chromatin but, instead, only the chromatin

; which is listed in the parameter.

;

; Note that the number of chromatin present in the simulation is defined

; in the [cell] section of this configuration file. So, the numbers listed

; in this parameter should range from 0 up to (the number of chromatin minus 1).

;territories show only these chromatins = 15 30 45

config/config-smallVOI-highSNR-correctSize.ini

+160 −0

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config/config-smallVOI-highSNR.ini

+160 −0

File changed.

Preview size limit exceeded, changes collapsed.