Commit bafde34d authored by David Svoboda's avatar David Svoboda
Browse files

Added parameters for variability of cell body texture. 

Affected files:
- TriangleMesh.*
- overExpressing.cfg
- phosphoDefective.cfg
parent 4f1a9a52

config/overExpressing.cfg

+9 −3
Original line number Original line Diff line number Diff line
@@ -9,9 +9,9 @@ texture_res_z 1 




; Border width is given as percentage of the minimal (axes-aligned) bounding box of the cell.

; Border width is given as percentage of the minimal (axes-aligned) bounding box of the cell.

; NB: The texture image is then given as (1 + 2*percentage/100)*box_size.

; NB: The texture image is then given as (1 + 2*percentage/100)*box_size.

border_width_x  5

border_width_x  75

border_width_y  5

border_width_y  75

border_width_z  5

border_width_z  75





; Parameters related to phantom rendering:

; Parameters related to phantom rendering:

; NB: One can influence the rendered cell type (e.g., overexpressing, phosphodefective) in this section.

; NB: One can influence the rendered cell type (e.g., overexpressing, phosphodefective) in this section.
@@ -34,3 +34,9 @@ filoAxisOrientedDensity 10 
; neighbouring pixel in the direction from filo axis to the envelope

; neighbouring pixel in the direction from filo axis to the envelope

; (surface). This direction is orthogonal to filo axis.

; (surface). This direction is orthogonal to filo axis.

filoContourOrientedDensity	12

filoContourOrientedDensity	12

		

; coarseness of initial Perlin noise in cell body (lower limit)

coarsenessLower 1.0



; coarseness of initial Perlin noise in cell body (upper limit)

coarsenessUpper 2.0

config/phosphoDefective.cfg

+8 −2
Original line number Original line Diff line number Diff line
@@ -26,11 +26,17 @@ PSF ../psf/2013-07-25_1_1_9_0_2_0_0_1_0_0_0_0_9_12.ics 
; multiplicity of how many dots should be pressed between two

; multiplicity of how many dots should be pressed between two

; pixel positions. The neighbouring pixels are understood as

; pixel positions. The neighbouring pixels are understood as

; neighbouring pixel along the direction of filopodium axis

; neighbouring pixel along the direction of filopodium axis

filoAxisOrientedDensity 7	

filoAxisOrientedDensity 5	





; Filopodium parameter:

; Filopodium parameter:

; multiplicity of how many dots should be pressed between two

; multiplicity of how many dots should be pressed between two

; pixel positions. The neighbouring pixels are understood as

; pixel positions. The neighbouring pixels are understood as

; neighbouring pixel in the direction from filo axis to the envelope

; neighbouring pixel in the direction from filo axis to the envelope

; (surface). This direction is orthogonal to filo axis.

; (surface). This direction is orthogonal to filo axis.

filoContourOrientedDensity	9
 
filoContourOrientedDensity	4



; coarseness of initial Perlin noise in cell body (lower limit)

coarsenessLower 1.0



; coarseness of initial Perlin noise in cell body (upper limit)

coarsenessUpper 1.0

src/TriangleMesh.cpp

+7 −2
Original line number Original line Diff line number Diff line
@@ -1428,7 +1428,9 @@ void ActiveMesh::InitDots_body(const i3d::Image3d<i3d::GRAY16>& mask) 




	i3d::Image3d<float> perlinInner,perlinOutside;

	i3d::Image3d<float> perlinInner,perlinOutside;

	perlinInner.CopyMetaData(mask);

	perlinInner.CopyMetaData(mask);

	DoPerlin3D(perlinInner,1.0,0.3,1.0,6);

	float coarseness = GetRandomUniform(this->configFile.coarsenessLower, 

													this->configFile.coarsenessUpper);

	DoPerlin3D(perlinInner,coarseness,0.3,1.0,6);

	Stretch(perlinInner, 0.0f, 1.0f, 4.0f);

	Stretch(perlinInner, 0.0f, 1.0f, 4.0f);

#ifdef SAVE_INTERMEDIATE_IMAGES

#ifdef SAVE_INTERMEDIATE_IMAGES

	perlinInner.SaveImage("2_PerlinAlone_Inner.ics");

	perlinInner.SaveImage("2_PerlinAlone_Inner.ics");
@@ -2395,6 +2397,9 @@ int ActiveMesh::configDataSubClass::ParseConfigFile(const char* fileName) 
	getValueOrDefault("filoAxisOrientedDensity", 10, filoAxisOrientedDensity);

	getValueOrDefault("filoAxisOrientedDensity", 10, filoAxisOrientedDensity);

	getValueOrDefault("filoContourOrientedDensity", 15, filoContourOrientedDensity);

	getValueOrDefault("filoContourOrientedDensity", 15, filoContourOrientedDensity);





	getValueOrDefault("coarsenessLower", 1.0, coarsenessLower);

	getValueOrDefault("coarsenessUpper", 2.0, coarsenessUpper);



	//clear to save some memory

	//clear to save some memory

	keyVal_map.clear();

	keyVal_map.clear();

	return (0);

	return (0);

src/TriangleMesh.h

+5 −0
Original line number Original line Diff line number Diff line
@@ -206,6 +206,11 @@ class ActiveMesh 
		// (surface). This direction is orthogonal to filo axis.

		// (surface). This direction is orthogonal to filo axis.

		int filoContourOrientedDensity;

		int filoContourOrientedDensity;





		// coarseness of initial Perlin noise in cell body (lower limit)

		float coarsenessLower;



		// coarseness of initial Perlin noise in cell body (upper limit)

		float coarsenessUpper;





	 private:

	 private:

		void getValueOrDefault(const char* key,const std::string& defValue, std::string& var);

		void getValueOrDefault(const char* key,const std::string& defValue, std::string& var);