#include <GLFW/glfw3.h>
#include <GL/glu.h>
#include "tinyfiledialogs.h"
#include <fstream>
#include <sstream>
#include <iostream>
#include <vector>
#include <cmath>
#include <algorithm>
#include <map>
#include <array>
#include <tuple>

Include dependency graph for swc_viewer.cpp:

Classes
struct	SWCNode
	Structure representing a single node in an SWC neuron morphology. More...

Functions
void	printHelpText ()
	Prints keyboard and mouse controls to the console. More...

std::vector< SWCNode >	loadSWC (const std::string &filename)
	Loads neuron data from an SWC file. More...

void	computeBounds (const std::vector< SWCNode > &nodes, float &minX, float &maxX, float &minY, float &maxY, float &minZ, float &maxZ, float &centerX, float &centerY, float &centerZ, float &radius)

void	openNeuronFile (std::vector< SWCNode > &nodes, float &minX, float &maxX, float &minY, float &maxY, float &minZ, float &maxZ, float &centerX, float &centerY, float &centerZ, float &radius)

void	setColorByType (int type)
	Sets the OpenGL color based on SWC node type. More...

void	drawSimpleSphere (const SWCNode &node, float size=0.5f)

void	drawSimpleLine (const SWCNode &a, const SWCNode &b)
	Draws a simple line between two nodes. More...

void	drawSphere (const SWCNode &node, int slices=6, int stacks=6)
	Draws a sphere with specified geometric detail. More...

void	drawCylinder (const SWCNode &a, const SWCNode &b, int segments=6)
	Draws a cylinder connecting two nodes. More...

void	drawBoundingBox (float minX, float maxX, float minY, float maxY, float minZ, float maxZ)

void	renderSWC (const std::vector< SWCNode > &nodes)
	Renders a complete SWC neuron morphology. More...

void	keyCallback (GLFWwindow *window, int key, int scancode, int action, int mods)
	Handles keyboard input events. More...

void	mouseButtonCallback (GLFWwindow *window, int button, int action, int mods)
	Handles mouse button input events. More...

void	cursorPosCallback (GLFWwindow *window, double xpos, double ypos)
	Handles mouse cursor movement. More...

void	scrollCallback (GLFWwindow *window, double xoffset, double yoffset)
	Handles mouse scroll events. More...

void	setupLighting ()

void	setupCamera (float cx, float cy, float cz, float radius, int width, int height)

int	main (int argc, char **argv)

Variables
int	renderMode = 1
	Current rendering mode (1-5) More...

float	rotateX = 0.0f
	Camera rotation around X and Y axes (in degrees) More...

float	rotateY = 0.0f

float	zoom = 1.0f
	Camera zoom factor (higher values = more zoomed in) More...

float	panX = 0.0f
	Camera pan offset in X and Y directions. More...

float	panY = 0.0f

bool	dragging = false
	Mouse drag state flags. More...

bool	rightDragging = false

double	lastX
	Last recorded mouse cursor position. More...

double	lastY

Function Documentation

◆ computeBounds()

void computeBounds	(	const std::vector< SWCNode > &	nodes,
		float &	minX,
		float &	maxX,
		float &	minY,
		float &	maxY,
		float &	minZ,
		float &	maxZ,
		float &	centerX,
		float &	centerY,
		float &	centerZ,
		float &	radius
	)

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◆ cursorPosCallback()

void cursorPosCallback	(	GLFWwindow *	window,
		double	xpos,
		double	ypos
	)

Handles mouse cursor movement.

Updates camera orientation or position based on mouse movement when:

Left button is held: Rotate view
Right button is held: Pan view
Middle button is held: Zoom view

Parameters

window	The GLFW window that received the event
xpos	The new cursor x-coordinate, relative to the left edge of the content area
ypos	The new cursor y-coordinate, relative to the top edge of the content area

Handles mouse cursor movement.

Parameters

[in]	window	The GLFW window that received the event
[in]	xpos	The new x-coordinate of the cursor, in screen coordinates
[in]	ypos	The new y-coordinate of the cursor, in screen coordinates

This callback function processes mouse movement to implement interactive 3D view manipulation. It provides the following functionality:

Left-drag: Rotates the view around the X and Y axes
Right-drag: Pans the view in the X and Y directions

The function uses the difference between the current and last cursor positions to calculate the amount of rotation or panning to apply. The actual view transformation is applied in the main rendering loop using the global state variables modified by this function.

Note: The function updates the lastX and lastY variables to track cursor movement between frames; Rotation and panning speeds are scaled by constant factors (0.3f and 1.5f)

See also: mouseButtonCallback() for enabling/disabling rotation and panning; GLFW cursor position documentation: https://www.glfw.org/docs/latest/input_guide.html#cursor_pos

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◆ drawBoundingBox()

void drawBoundingBox	(	float	minX,
		float	maxX,
		float	minY,
		float	maxY,
		float	minZ,
		float	maxZ
	)

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◆ drawCylinder()

void drawCylinder	(	const SWCNode &	a,
		const SWCNode &	b,
		int	segments = `6`
	)

Draws a cylinder connecting two nodes.

Parameters

a	First node (start of cylinder)
b	Second node (end of cylinder)
segments	Number of radial segments for the cylinder [default: 6]

Renders a tapered cylinder that connects two nodes, with the radius at each end determined by the nodes' radii. The cylinder is colored according to the first node's type.

Draws a cylinder connecting two nodes.

Parameters

[in]	a	The starting node of the cylinder
[in]	b	The ending node of the cylinder
[in]	segments	The number of sides around the cylinder

This function draws a tapered cylinder connecting two nodes in 3D space. The cylinder's radius at each end is determined by the radius property of the corresponding node, allowing for smooth tapering of neurites.

The function handles the necessary coordinate system transformations to orient the cylinder correctly between the two points in 3D space. It uses OpenGL's matrix stack to ensure the transformations don't affect subsequent rendering operations.

Note: The cylinder is drawn with smooth normals for proper lighting; If the nodes are coincident (distance = 0), the function returns early; The 57.2957795f constant converts radians to degrees (180/π); Uses legacy OpenGL immediate mode rendering

See also: gluCylinder() for details on the underlying GLU primitive

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◆ drawSimpleLine()

void drawSimpleLine	(	const SWCNode &	a,
		const SWCNode &	b
	)

Draws a simple line between two nodes.

Parameters

a	First node (start point)
b	Second node (end point)

Renders a line in 3D space between two nodes using immediate mode OpenGL. The line width is determined by the nodes' radii.

Draws a simple line between two nodes.

Parameters

[in]	a	The starting node of the line
[in]	b	The ending node of the line

This function renders a simple line segment between two nodes in 3D space using OpenGL's immediate mode line rendering. The line is drawn with the current OpenGL color and line width settings.

The function is typically used for wireframe representations of neuron morphologies or for debug visualization.

Note: The line is drawn with the current OpenGL color; Uses legacy OpenGL immediate mode rendering (glBegin/glEnd); For more complex line rendering (e.g., with thickness), consider using geometry shaders or other modern OpenGL techniques

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◆ drawSimpleSphere()

void drawSimpleSphere	(	const SWCNode &	node,
		float	size = `0.5f`
	)

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◆ drawSphere()

void drawSphere	(	const SWCNode &	node,
		int	slices = `6`,
		int	stacks = `6`
	)

Draws a sphere with specified geometric detail.

Parameters

node	The SWC node to draw
slices	Number of subdivisions around the z-axis (longitude) [default: 6]
stacks	Number of subdivisions along the z-axis (latitude) [default: 6]

Uses GLU quadric objects to render a sphere with the specified level of detail. The sphere is colored according to the node's type.

Draws a sphere with specified geometric detail.

Parameters

[in]	node	The SWCNode containing the position and radius for the sphere
[in]	slices	The number of subdivisions around the Z axis (longitude)
[in]	stacks	The number of subdivisions along the Z axis (latitude)

This function draws a sphere using OpenGL's GLU quadric primitives with smooth normal vectors for proper lighting calculations. The sphere's radius is taken from the node's radius property, and its position is set to the node's coordinates.

The function handles the OpenGL matrix stack appropriately and uses the current OpenGL color for rendering. The resolution of the sphere can be controlled through the slices and stacks parameters.

Note: The sphere is drawn with smooth shading (GLU_SMOOTH); Uses legacy OpenGL immediate mode rendering; For high-quality rendering, use at least 16 slices and stacks

See also: drawSimpleSphere() for a faster, lower-quality alternative; gluQuadricNormals() for details on normal generation

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◆ keyCallback()

void keyCallback	(	GLFWwindow *	window,
		int	key,
		int	scancode,
		int	action,
		int	mods
	)

Handles keyboard input events.

Processes key presses and releases to control the visualization:

WASD: Move camera left/right/forward/backward
QE: Move camera up/down
Arrow keys: Rotate view
R: Reset view
Space: Toggle auto-rotation
1-5: Switch between rendering modes
+/-: Adjust rendering parameters
ESC: Close window
H: Toggle help text

Parameters

window	The GLFW window that received the event
key	The keyboard key that was pressed or released
scancode	The system-specific scancode of the key
action	GLFW_PRESS, GLFW_RELEASE or GLFW_REPEAT
mods	Bit field describing which modifier keys were held down

Handles keyboard input events.

Parameters

[in]	window	The GLFW window that received the event
[in]	key	The keyboard key that was pressed or released
[in]	scancode	The system-specific scancode of the key
[in]	action	The key action (GLFW_PRESS, GLFW_RELEASE, or GLFW_REPEAT)
[in]	mods	Bit field describing which modifier keys were held down

This callback function processes keyboard input for controlling the neuron viewer. It implements the following keyboard shortcuts:

F: Refine neuron geometry (halve delta)
Ctrl+F: Coarsen neuron geometry (double delta)
1-6: Switch between different render modes
O: Open a neuron file dialog
R: Reset camera view
H: Show/hide help window
S: Save the current neuron data to file

The function modifies global state for view parameters and triggers updates to the neuron visualization when geometry is refined or coarsened.

Note: The function only processes key press events (GLFW_PRESS); Modifier keys (Ctrl, Shift, Alt) are checked using the mods parameter

See also: GLFW key documentation: https://www.glfw.org/docs/latest/input_guide.html#input_key

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◆ loadSWC()

std::vector<SWCNode> loadSWC ( const std::string & filename )

Loads neuron data from an SWC file.

Parses an SWC (Standardized Waveform Container) file containing neuron morphology data and returns a vector of SWCNode objects.

Parameters

filename Path to the SWC file to load

Returns: std::vector<SWCNode> Vector of nodes representing the neuron morphology

Exceptions

std::runtime_error If the file cannot be opened or is malformed

Note: The SWC format is a standard format for representing neuron morphologies. Each line in the file represents a point in the neuron structure.

See also: http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html

Loads neuron data from an SWC file.

Parameters

[in] filename Path to the SWC or UGX file to load

Returns: std::vector<SWCNode> Vector of SWC nodes representing the neuron

This function loads a neuron morphology from the specified file and returns its nodes as a vector of SWCNode objects. It supports both SWC and UGX file formats and performs preprocessing on the loaded data.

The function:

Reads the neuron data using NeuronGraph's readFromFileUGXorSWC()
Applies preprocessing to the loaded nodes
Converts the node map to a vector for rendering

Note: The function modifies the global graph object; Preprocessing includes validation and cleanup of the neuron structure

Exceptions

std::runtime_error if the file cannot be read or parsed

See also: NeuronGraph::readFromFileUGXorSWC(); NeuronGraph::preprocess()

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◆ main()

int main	(	int	argc,
		char **	argv
	)

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◆ mouseButtonCallback()

void mouseButtonCallback	(	GLFWwindow *	window,
		int	button,
		int	action,
		int	mods
	)

Handles mouse button input events.

Processes mouse button presses and releases for:

Left button: Start/end rotation
Right button: Start/end panning
Middle button: Start/end zooming

Parameters

window	The GLFW window that received the event
button	The mouse button that was pressed or released
action	GLFW_PRESS or GLFW_RELEASE
mods	Bit field describing which modifier keys were held down

Handles mouse button input events.

Parameters

[in]	window	The GLFW window that received the event
[in]	button	The mouse button that was pressed or released
[in]	action	The button action (GLFW_PRESS or GLFW_RELEASE)
[in]	mods	Bit field describing which modifier keys were held down

This callback function processes mouse button events to enable interactive 3D view manipulation. It tracks the following interactions:

Left mouse button: Enables view rotation when dragged
Right mouse button: Enables view panning when dragged

The function updates global state variables (dragging, rightDragging) that are used by cursorPosCallback to implement the actual view transformations.

Note: The function tracks both press and release events for smooth interaction; The cursor position is captured on button press for relative movement

See also: cursorPosCallback() for the implementation of the actual view transformations; GLFW mouse button documentation: https://www.glfw.org/docs/latest/input_guide.html#input_mouse_button

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◆ openNeuronFile()

void openNeuronFile	(	std::vector< SWCNode > &	nodes,
		float &	minX,
		float &	maxX,
		float &	minY,
		float &	maxY,
		float &	minZ,
		float &	maxZ,
		float &	centerX,
		float &	centerY,
		float &	centerZ,
		float &	radius
	)

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◆ printHelpText()

void printHelpText ( )

Prints keyboard and mouse controls to the console.

Displays a help message listing all available keyboard shortcuts and mouse controls for the neuron viewer application.

Note: This function is typically called when the application starts or when the user presses the 'H' key.

Prints keyboard and mouse controls to the console.

Displays the application's keyboard and mouse controls to the console. The help text is defined as a global string constant in globals.h.

Note: The help text includes controls for view manipulation, file operations, and rendering modes.

See also: globals.h for the help text definition

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◆ renderSWC()

void renderSWC ( const std::vector< SWCNode > & nodes )

Renders a complete SWC neuron morphology.

Parameters

nodes Vector of SWC nodes to render

This is the main rendering function that draws an entire neuron morphology. It handles the display of all nodes and connections between them, with appropriate coloring based on node types. The function respects the current rendering mode and visualization settings from globals.h.

Renders a complete SWC neuron morphology.

Parameters

[in] nodes A vector of SWCNode objects representing the neuron morphology

This function renders a complete neuron morphology from SWC node data using different rendering modes controlled by the global renderMode variable. The function handles both the rendering of nodes (soma, branch points, etc.) and the connections between them (dendrites, axons).

Supported render modes:

Mode 1: White wireframe lines between nodes
Mode 2: Colored spheres at nodes with white wireframe connections
Mode 3: Yellow simple spheres at node positions
Mode 4: Purple detailed spheres at node positions
Mode 5: Colored tapered cylinders between nodes (no spheres)
Mode 6: Colored detailed spheres with colored tapered cylinders

The function first renders all nodes according to the current render mode, then renders the connections between nodes. Node colors are determined by their SWC type using the setColorByType() function.

Note: The function uses the global renderMode variable to determine rendering style; Parent-child relationships are determined by the node.pid field; The function skips rendering of invalid parent references (pid = -1)

See also: setColorByType() for information about color mapping; drawSphere(), drawCylinder() for the actual rendering primitives

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◆ scrollCallback()

void scrollCallback	(	GLFWwindow *	window,
		double	xoffset,
		double	yoffset
	)

Handles mouse scroll events.

Zooms the view in/out based on vertical scroll input.

Parameters

window	The GLFW window that received the event
xoffset	The scroll offset along the x-axis (unused)
yoffset	The scroll offset along the y-axis (positive = scroll up, negative = scroll down)

Handles mouse scroll events.

Parameters

[in]	window	The GLFW window that received the event
[in]	xoffset	The scroll offset along the x-axis (unused in this implementation)
[in]	yoffset	The scroll offset along the y-axis (positive for scroll up, negative for scroll down)

This callback function processes mouse scroll wheel input to implement smooth zooming of the 3D view. It modifies the global zoom factor based on the vertical scroll amount.

The zoom factor is adjusted using an exponential scale (1.1^yoffset) to provide natural-feeling zoom behavior. The zoom level is clamped between 0.05 and 10.0 to prevent extreme zoom levels that might cause rendering issues or numerical instability.

Note: The xoffset parameter is currently unused but included for future compatibility; Zooming is centered on the current view (no focal point adjustment); The 1.1 base value provides a good balance between precision and responsiveness

See also: GLFW scroll documentation: https://www.glfw.org/docs/latest/input_guide.html#scrolling

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◆ setColorByType()

void setColorByType ( int type )

Sets the OpenGL color based on SWC node type.

Parameters

type	SWC node type identifier (1-7)

Maps standard SWC node types to distinct colors for visualization. The color mapping follows the standard SWC color scheme:

1 (Soma): Red
2 (Axon): Blue
3 (Dendrite): Yellow
4 (Apical dendrite): Purple
5-7: Other standard SWC types

Parameters

[in] type The SWC node type identifier

This function maps standard SWC node types to specific colors for visualization. The color mapping is as follows:

Type 1: Red (soma)
Type 2: Green (axon)
Type 3: Blue (basal dendrite)
Type 4: Yellow (apical dendrite)
Type 5: Magenta
Type 6: Cyan
Type 7: Orange
Default: White (for any other type)

The function uses a static map for efficient type-to-color lookup and modifies the current OpenGL color state.

Note: The function modifies the OpenGL current color state; The color map is static and shared across all instances; For custom color schemes, modify the colorMap variable

See also: http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html for SWC format specification

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◆ setupCamera()

void setupCamera	(	float	cx,
		float	cy,
		float	cz,
		float	radius,
		int	width,
		int	height
	)

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◆ setupLighting()

void setupLighting ( )

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Variable Documentation

◆ dragging

bool dragging = false

Mouse drag state flags.

These track the current drag operation:

dragging: True during left-button rotation
rightDragging: True during right-button panning

Mouse drag state flags.

◆ lastX

double lastX

Last recorded mouse cursor position.

Used to calculate mouse movement deltas for smooth camera control.

Last recorded mouse cursor position.

◆ lastY

double lastY

◆ panX

float panX = 0.0f

Camera pan offset in X and Y directions.

These values control the 2D panning of the view:

panX: Horizontal pan (positive = right)
panY: Vertical pan (positive = up)

Camera pan offset in X and Y directions.

◆ panY

float panY = 0.0f

◆ renderMode

int renderMode = 1

Current rendering mode (1-5)

Controls how the neuron is rendered:

1: Basic line rendering
2: Cylinder rendering
3: Spheres at nodes
4: Full 3D rendering
5: Debug rendering mode

Current rendering mode (1-5)

◆ rightDragging

bool rightDragging = false

◆ rotateX

float rotateX = 0.0f

Camera rotation around X and Y axes (in degrees)

These angles control the 3D view orientation:

rotateX: Rotation around the X-axis (vertical rotation)
rotateY: Rotation around the Y-axis (horizontal rotation)

Camera rotation around X and Y axes (in degrees)

◆ rotateY

float rotateY = 0.0f

◆ zoom

float zoom = 1.0f

Camera zoom factor (higher values = more zoomed in)

Classes

Functions

Variables

Function Documentation

◆ computeBounds()

◆ cursorPosCallback()

◆ drawBoundingBox()

◆ drawCylinder()

◆ drawSimpleLine()

◆ drawSimpleSphere()

◆ drawSphere()

◆ keyCallback()

◆ loadSWC()

◆ main()

◆ mouseButtonCallback()

◆ openNeuronFile()

◆ printHelpText()

◆ renderSWC()

◆ scrollCallback()

◆ setColorByType()

◆ setupCamera()

◆ setupLighting()

Variable Documentation

◆ dragging

◆ lastX

◆ lastY

◆ panX

◆ panY

◆ renderMode

◆ rightDragging

◆ rotateX

◆ rotateY

◆ zoom