alternaria_viewer.cpp File Reference

View an Alternaria_model in an OpenGL environment. More...

#include <config.h>
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cassert>
#include <iostream>
#include <sstream>
#include <vector>
#include <inttypes.h>
#include <jwsc/math/constants.h>
#include <jwsc/vector/vector.h>
#include <jwsc/vector/vector_math.h>
#include <jwsc/matrix/matrix.h>
#include <jwsc/matrix/matrix_math.h>
#include <jwsc/image/image.h>
#include <jwsc/image/image_io.h>
#include <jwsc/imgblock/imgblock.h>
#include <jwsc/imgblock/imgblock_io.h>
#include <jwsc/imgblock/surface.h>
#include <jwsc++/base/option.h>
#include <jwsc++/base/exception.h>
#include <jwsc++/graphics/camera.h>
#include "imaging_model.h"
#include "psf_model.h"
#include "structure.h"
#include "spore.h"
#include "hypha.h"
#include "alternaria_model.h"

Go to the source code of this file.

Classes
struct	Alternaria_viewer_modes
	Modes the viewer can be in. More...
Defines
#define	REDBLUE   1
#define	REDGREEN   2
#define	REDCYAN   3
#define	BLUERED   4
#define	GREENRED   5
#define	CYANRED   6
#define	VIEW_WIDTH   800
#define	VIEW_HEIGHT   800
#define	APERTURE   60.0f
#define	CLIP_NEAR   10.0f
#define	CLIP_FAR   3000.0f
#define	GLASSES_TYPE   REDCYAN
#define	CAPTURE_FMT   "capture-%04u.tiff"
#define	MODEL_COMPARE_FNAME   0
#define	SURF_COMPARE_FNAME   0
#define	SURF_PATCH_SIZE   2.0
#define	OBJECT_SCALE   1.0
#define	CENTROID_MIN   -5000.0f
#define	CENTROID_MAX   5000.0f
#define	LENGTH_MU   40.0f
#define	LENGTH_SIGMA   4.0f
#define	LENGTH_MIN   1.f
#define	LENGTH_MAX   1000.0f
#define	WIDTH_MU   15.0f
#define	WIDTH_SIGMA   1.0f
#define	WIDTH_MIN   1.0f
#define	WIDTH_MAX   1000.0f
#define	DWIDTH_SIGMA   0.05f
#define	DWIDTH_MIN   -100.0f
#define	DWIDTH_MAX   100.0f
#define	THETA_MU   0
#define	THETA_SIGMA   0.2f
#define	THETA_MIN   0
#define	THETA_MAX   JWSC_PI
#define	PSI_MIN   -JWSC_PI
#define	PSI_MAX   JWSC_PI
#define	OPACITY_MU   0.9f
#define	OPACITY_SIGMA   0.2f
#define	OPACITY_MIN   0.0f
#define	OPACITY_MAX   1.0f
#define	DIST_MU   0.5f
#define	DIST_SIGMA   0.1f
#define	DIST_MIN   0
#define	DIST_MAX   1.0f
Functions
void	init_modes ()
	Initialize the viewer modes.
void	init_camera () throw (Arg_error)
	Initializes the camera to default values.
void	clean_up ()
	Cleans up the program to prepare for exit.
void	reset ()
	Resets the state of the viewer.
void	render_world_axis ()
	Renders the 3D world axis.
void	render_focal_plane ()
	Renders the focal plane.
void	render_model_compare ()
	Renders the Alternaria model to compare with.
void	render_surface_compare ()
	Renders the surface of an Alternaria to compare with.
void	render_scene ()
	Renders the scene into the viewer.
void	display_glut_anaglyph ()
	Display the model as an anaglyph (3D stereo pair).
void	display_glut_regular ()
	Display the model under normal conditions.
void	display_glut ()
	Display callback for the GLUT library.
void	reshape_glut (int w, int h)
	Reshape callback for the GLUT library.
void	keyboard_glut (unsigned char key, int a, int b)
	Keyboard callback for the GLUT library.
void	mouse_glut (int button, int state, int x, int y)
	Mouse callback for the GLUT library.
void	main_menu_glut (int id)
	Main menu callback for the GLUT library.
void	option_menu_glut (int id)
	Option submenu callback for the GLUT library.
void	navigation_menu_glut (int id)
	Keyboard navigation submenu callback for the GLUT library.
void	focal_length_menu_glut (int id)
	Focal length submenu callback for the GLUT library.
void	clipping_menu_glut (int id)
	Clipping plane submenu callback for the GLUT library.
void	init_glut (int argc, char **argv)
	Initializes the GLUT to default values.
void	init_gl ()
	Initializes the GL to default values.
void	print_usage (void)
	Prints the usage of the program.
void	process_help_opt (void)
	Processes the 'help' program options.
void	process_version_opt (void)
	Processes the 'version' program options.
void	process_view_size_opt (const char *arg) throw (Arg_error)
	Processes the 'view-size' program options.
void	process_glasses_opt (const char *arg) throw (Arg_error)
	Processes the 'glasses' program options.
void	process_capture_opt (const char *arg) throw (Arg_error)
	Processes the 'capture' program options.
void	process_surf_compare_opt (const char *arg) throw (Arg_error)
	Processes the 'surf-compare' program options.
void	process_surf_scale_opt (const char *arg) throw (Arg_error)
	Processes the 'surf-scale' program options.
void	process_patch_size_opt (const char *arg) throw (Arg_error)
	Processes the 'patch-size' program options.
void	process_model_compare_opt (const char *arg) throw (Arg_error)
	Processes the 'model-compare' program options.
void	init_options ()
	Initialize the options.
void	init_densities ()
	Initializes the density parameters.
void	read_model_compare () throw (Exception)
	Reads the Alternaria model to compare, if there is one.
void	read_surface_compare () throw (Exception)
	Reads the Alternaria surface to compare, if there is one.
int	main (int argc, char **argv)
	Main function for alternaria_viewer.
Variables
Options *	opts = 0
	Program options.
uint32_t	view_width = VIEW_WIDTH
	Width of the viewing window.
uint32_t	view_height = VIEW_HEIGHT
	Height of the viewing window.
float	aperture = APERTURE
	Viewing aperture.
float	clip_near = CLIP_NEAR
	Near clipping plane.
float	clip_far = CLIP_FAR
	Far clipping plane.
int	glasses_type = GLASSES_TYPE
	Anaglyph glasses type.
const char *	capture_fmt = CAPTURE_FMT
	Printf-formatted file to write captured view images to.
const char *	model_compare_fname = MODEL_COMPARE_FNAME
	Name of the model file to compare Alternaria models with.
const char *	surface_compare_fname = SURF_COMPARE_FNAME
	Name of the surface file to compare Alternaria models with.
float	object_scale = OBJECT_SCALE
	Scale of the objects.
Stereo_camera_f *	camera = 0
	3D viewing camera.
GLUquadric *	quad_fill = 0
	Filled quadric.
GLUquadric *	quad_wire = 0
	Wire-frame quadric.
PSF_model *	psf = 0
	PSF_model to test.
Alternaria *	alternaria = 0
	Alternaria to test.
Alternaria *	model_compare = 0
	Alternaria model to compare with.
list< Surface_patch_f * > *	surface_compare = 0
	Alternaria surface to compare with.
Imaging_scale *	surface_scale = 0
	Number of world unit coordinates per image pixel.
float	surface_patch_size = SURF_PATCH_SIZE
	Size of the patch representing each surface point.
Imaging_model_density *	imaging_d = 0
	Imaging_model density.
PSF_model_density *	psf_d = 0
	PSF_model density.
Apical_hypha_density *	apical_hypha_d = 0
	Apical_hypha density.
Lateral_hypha_density *	lateral_hypha_d = 0
	Lateral_hypha density.
Spore_density *	spore_d = 0
	Spore density.
Alternaria_density *	alt_d = 0
	Alternaria density.
Structure *	highlight = 0
	Pointer to the currently selected Structure in alternaria to modify.
struct Alternaria_viewer_modes	modes

---

Detailed Description

View an Alternaria_model in an OpenGL environment.

Author:

Joseph Schlecht

License:

Creative Commons BY-NC-SA 3.0

Definition in file alternaria_viewer.cpp.

---

Define Documentation

#define REDBLUE   1

Definition at line 96 of file alternaria_viewer.cpp.

#define REDGREEN   2

Definition at line 97 of file alternaria_viewer.cpp.

#define REDCYAN   3

Definition at line 98 of file alternaria_viewer.cpp.

#define BLUERED   4

Definition at line 99 of file alternaria_viewer.cpp.

#define GREENRED   5

Definition at line 100 of file alternaria_viewer.cpp.

#define CYANRED   6

Definition at line 101 of file alternaria_viewer.cpp.

#define VIEW_WIDTH   800

Definition at line 104 of file alternaria_viewer.cpp.

#define VIEW_HEIGHT   800

Definition at line 105 of file alternaria_viewer.cpp.

#define APERTURE   60.0f

Definition at line 106 of file alternaria_viewer.cpp.

#define CLIP_NEAR   10.0f

Definition at line 107 of file alternaria_viewer.cpp.

#define CLIP_FAR   3000.0f

Definition at line 108 of file alternaria_viewer.cpp.

#define GLASSES_TYPE   REDCYAN

Definition at line 109 of file alternaria_viewer.cpp.

#define CAPTURE_FMT   "capture-%04u.tiff"

Definition at line 110 of file alternaria_viewer.cpp.

#define MODEL_COMPARE_FNAME   0

Definition at line 111 of file alternaria_viewer.cpp.

#define SURF_COMPARE_FNAME   0

Definition at line 112 of file alternaria_viewer.cpp.

#define SURF_PATCH_SIZE   2.0

Definition at line 113 of file alternaria_viewer.cpp.

#define OBJECT_SCALE   1.0

Definition at line 114 of file alternaria_viewer.cpp.

#define CENTROID_MIN   -5000.0f

Definition at line 116 of file alternaria_viewer.cpp.

#define CENTROID_MAX   5000.0f

Definition at line 117 of file alternaria_viewer.cpp.

#define LENGTH_MU   40.0f

Definition at line 118 of file alternaria_viewer.cpp.

#define LENGTH_SIGMA   4.0f

Definition at line 119 of file alternaria_viewer.cpp.

#define LENGTH_MIN   1.f

Definition at line 120 of file alternaria_viewer.cpp.

#define LENGTH_MAX   1000.0f

Definition at line 121 of file alternaria_viewer.cpp.

#define WIDTH_MU   15.0f

Definition at line 122 of file alternaria_viewer.cpp.

#define WIDTH_SIGMA   1.0f

Definition at line 123 of file alternaria_viewer.cpp.

#define WIDTH_MIN   1.0f

Definition at line 124 of file alternaria_viewer.cpp.

#define WIDTH_MAX   1000.0f

Definition at line 125 of file alternaria_viewer.cpp.

#define DWIDTH_SIGMA   0.05f

Definition at line 126 of file alternaria_viewer.cpp.

#define DWIDTH_MIN   -100.0f

Definition at line 127 of file alternaria_viewer.cpp.

#define DWIDTH_MAX   100.0f

Definition at line 128 of file alternaria_viewer.cpp.

#define THETA_MU   0

Definition at line 129 of file alternaria_viewer.cpp.

#define THETA_SIGMA   0.2f

Definition at line 130 of file alternaria_viewer.cpp.

#define THETA_MIN   0

Definition at line 131 of file alternaria_viewer.cpp.

#define THETA_MAX   JWSC_PI

Definition at line 132 of file alternaria_viewer.cpp.

#define PSI_MIN   -JWSC_PI

Definition at line 133 of file alternaria_viewer.cpp.

#define PSI_MAX   JWSC_PI

Definition at line 134 of file alternaria_viewer.cpp.

#define OPACITY_MU   0.9f

Definition at line 135 of file alternaria_viewer.cpp.

#define OPACITY_SIGMA   0.2f

Definition at line 136 of file alternaria_viewer.cpp.

#define OPACITY_MIN   0.0f

Definition at line 137 of file alternaria_viewer.cpp.

#define OPACITY_MAX   1.0f

Definition at line 138 of file alternaria_viewer.cpp.

#define DIST_MU   0.5f

Definition at line 139 of file alternaria_viewer.cpp.

#define DIST_SIGMA   0.1f

Definition at line 140 of file alternaria_viewer.cpp.

#define DIST_MIN   0

Definition at line 141 of file alternaria_viewer.cpp.

#define DIST_MAX   1.0f

Definition at line 142 of file alternaria_viewer.cpp.

---

Function Documentation

void init_modes

(

)

Initialize the viewer modes.

Definition at line 284 of file alternaria_viewer.cpp.

void init_camera

(

)

throw (Arg_error)

Initializes the camera to default values.

Definition at line 298 of file alternaria_viewer.cpp.

void clean_up

(

)

Cleans up the program to prepare for exit.

Used to check for memory leaks.

Definition at line 319 of file alternaria_viewer.cpp.

void reset

(

)

Resets the state of the viewer.

Definition at line 348 of file alternaria_viewer.cpp.

void render_world_axis

(

)

Renders the 3D world axis.

Definition at line 358 of file alternaria_viewer.cpp.

void render_focal_plane

(

)

Renders the focal plane.

Definition at line 409 of file alternaria_viewer.cpp.

void render_model_compare

(

)

Renders the Alternaria model to compare with.

Definition at line 459 of file alternaria_viewer.cpp.

void render_surface_compare

(

)

Renders the surface of an Alternaria to compare with.

Definition at line 471 of file alternaria_viewer.cpp.

void render_scene

(

)

Renders the scene into the viewer.

Definition at line 518 of file alternaria_viewer.cpp.

void display_glut_anaglyph

(

)

Display the model as an anaglyph (3D stereo pair).

Reset the color mask.

Definition at line 548 of file alternaria_viewer.cpp.

void display_glut_regular

(

)

Display the model under normal conditions.

Definition at line 653 of file alternaria_viewer.cpp.

void display_glut

(

)

Display callback for the GLUT library.

Definition at line 686 of file alternaria_viewer.cpp.

void reshape_glut	(	int	w,
		int	h
	)

Reshape callback for the GLUT library.

Definition at line 709 of file alternaria_viewer.cpp.

void keyboard_glut	(	unsigned char	key,
		int	a,
		int	b
	)

Keyboard callback for the GLUT library.

Definition at line 718 of file alternaria_viewer.cpp.

void mouse_glut	(	int	button,
		int	state,
		int	x,
		int	y
	)

Mouse callback for the GLUT library.

Definition at line 995 of file alternaria_viewer.cpp.

void main_menu_glut

(

int

id

)

Main menu callback for the GLUT library.

Definition at line 1050 of file alternaria_viewer.cpp.

void option_menu_glut

(

int

id

)

Option submenu callback for the GLUT library.

Definition at line 1068 of file alternaria_viewer.cpp.

void navigation_menu_glut

(

int

id

)

Keyboard navigation submenu callback for the GLUT library.

Definition at line 1088 of file alternaria_viewer.cpp.

void focal_length_menu_glut

(

int

id

)

Focal length submenu callback for the GLUT library.

Definition at line 1108 of file alternaria_viewer.cpp.

void clipping_menu_glut

(

int

id

)

Clipping plane submenu callback for the GLUT library.

Definition at line 1124 of file alternaria_viewer.cpp.

void init_glut	(	int	argc,
		char **	argv
	)

Initializes the GLUT to default values.

Definition at line 1138 of file alternaria_viewer.cpp.

void init_gl

(

)

Initializes the GL to default values.

Definition at line 1181 of file alternaria_viewer.cpp.

void print_usage

(

void

)

Prints the usage of the program.

Definition at line 1245 of file alternaria_viewer.cpp.

void process_help_opt

(

void

)

Processes the 'help' program options.

Definition at line 1253 of file alternaria_viewer.cpp.

void process_version_opt

(

void

)

Processes the 'version' program options.

Definition at line 1260 of file alternaria_viewer.cpp.

void process_view_size_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'view-size' program options.

Definition at line 1267 of file alternaria_viewer.cpp.

void process_glasses_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'glasses' program options.

Definition at line 1288 of file alternaria_viewer.cpp.

void process_capture_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'capture' program options.

Definition at line 1313 of file alternaria_viewer.cpp.

void process_surf_compare_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'surf-compare' program options.

Definition at line 1323 of file alternaria_viewer.cpp.

void process_surf_scale_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'surf-scale' program options.

Definition at line 1333 of file alternaria_viewer.cpp.

void process_patch_size_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'patch-size' program options.

Definition at line 1358 of file alternaria_viewer.cpp.

void process_model_compare_opt

(

const char *

arg

)

throw (Arg_error)

Processes the 'model-compare' program options.

Definition at line 1371 of file alternaria_viewer.cpp.

void init_options

(

)

Initialize the options.

Definition at line 1381 of file alternaria_viewer.cpp.

void init_densities

(

)

Initializes the density parameters.

Definition at line 1430 of file alternaria_viewer.cpp.

void read_model_compare

(

)

throw (Exception)

Reads the Alternaria model to compare, if there is one.

Definition at line 1464 of file alternaria_viewer.cpp.

void read_surface_compare

(

)

throw (Exception)

Reads the Alternaria surface to compare, if there is one.

Definition at line 1479 of file alternaria_viewer.cpp.

int main	(	int	argc,
		char **	argv
	)

Main function for alternaria_viewer.

Definition at line 1526 of file alternaria_viewer.cpp.

---

Variable Documentation

Options* opts = 0

Program options.

Definition at line 161 of file alternaria_viewer.cpp.

uint32_t view_width = VIEW_WIDTH

Width of the viewing window.

Definition at line 164 of file alternaria_viewer.cpp.

uint32_t view_height = VIEW_HEIGHT

Height of the viewing window.

Definition at line 167 of file alternaria_viewer.cpp.

float aperture = APERTURE

Viewing aperture.

Definition at line 170 of file alternaria_viewer.cpp.

float clip_near = CLIP_NEAR

Near clipping plane.

Definition at line 173 of file alternaria_viewer.cpp.

float clip_far = CLIP_FAR

Far clipping plane.

Definition at line 176 of file alternaria_viewer.cpp.

int glasses_type = GLASSES_TYPE

Anaglyph glasses type.

Definition at line 179 of file alternaria_viewer.cpp.

const char* capture_fmt = CAPTURE_FMT

Printf-formatted file to write captured view images to.

Definition at line 182 of file alternaria_viewer.cpp.

const char* model_compare_fname = MODEL_COMPARE_FNAME

Name of the model file to compare Alternaria models with.

Definition at line 185 of file alternaria_viewer.cpp.

const char* surface_compare_fname = SURF_COMPARE_FNAME

Name of the surface file to compare Alternaria models with.

Definition at line 188 of file alternaria_viewer.cpp.

float object_scale = OBJECT_SCALE

Scale of the objects.

Definition at line 191 of file alternaria_viewer.cpp.

Stereo_camera_f* camera = 0

3D viewing camera.

Definition at line 194 of file alternaria_viewer.cpp.

GLUquadric* quad_fill = 0

Filled quadric.

Definition at line 197 of file alternaria_viewer.cpp.

GLUquadric* quad_wire = 0

Wire-frame quadric.

Definition at line 200 of file alternaria_viewer.cpp.

PSF_model* psf = 0

PSF_model to test.

Definition at line 203 of file alternaria_viewer.cpp.

Alternaria* alternaria = 0

Alternaria to test.

Definition at line 206 of file alternaria_viewer.cpp.

Alternaria* model_compare = 0

Alternaria model to compare with.

Definition at line 209 of file alternaria_viewer.cpp.

list<Surface_patch_f*>* surface_compare = 0

Alternaria surface to compare with.

Definition at line 212 of file alternaria_viewer.cpp.

Imaging_scale* surface_scale = 0

Number of world unit coordinates per image pixel.

Definition at line 215 of file alternaria_viewer.cpp.

float surface_patch_size = SURF_PATCH_SIZE

Size of the patch representing each surface point.

Definition at line 218 of file alternaria_viewer.cpp.

Imaging_model_density* imaging_d = 0

Imaging_model density.

Definition at line 221 of file alternaria_viewer.cpp.

PSF_model_density* psf_d = 0

PSF_model density.

Definition at line 224 of file alternaria_viewer.cpp.

Apical_hypha_density* apical_hypha_d = 0

Apical_hypha density.

Definition at line 227 of file alternaria_viewer.cpp.

Lateral_hypha_density* lateral_hypha_d = 0

Lateral_hypha density.

Definition at line 230 of file alternaria_viewer.cpp.

Spore_density* spore_d = 0

Spore density.

Definition at line 233 of file alternaria_viewer.cpp.

Alternaria_density* alt_d = 0

Alternaria density.

Definition at line 236 of file alternaria_viewer.cpp.

Structure* highlight = 0

Pointer to the currently selected Structure in alternaria to modify.

Definition at line 242 of file alternaria_viewer.cpp.

struct Alternaria_viewer_modes modes