Convert to Trajectory Object

Description

Converts an object of type 'data.frame' or similar into a 'Trajectory' object. The 'data.frame' should contain columns 'x' and 'y' representing the coordinates.

Usage

as.trajectory(x, delta_time = 1)

Arguments

Value

A 'Trajectory' object containing the coordinates from the 'data.frame'.

Calculate the Centroid of Object

Description

This function calculates the centroid of a set of points contained in an object of class 'trajectory'. The centroid is the average of the coordinates of all the points.

Usage

centroid(obj)

Arguments

Value

A numeric vector containing the coordinates of the centroid of the points stored in 'obj$points'.

Detect Circles in a Maze Image

Description

The function first applies the Canny edge detection algorithm to the input image. It then detects circles corresponding to the board and holes using the detectCircles function. The function filters the detected hole circles based on their distance from the board circle, ensuring they fall within acceptable ranges relative to the specified radii. Finally, it calculates the median radius and angle differences of the remaining circles and constructs a circular representation for the holes based on these parameters.

Usage

detectBarnes(im, boardRadius, holeRadius, sigma = 25, plot = TRUE)

Arguments

Details

Detects circles representing boards and holes in a given image of a maze. It utilizes edge detection to identify potential circle patterns based on specified radius parameters. The function returns the detected circles' coordinates, along with additional information about the board and hole radii.

Value

A list containing:

Examples

path <- system.file('extdata/data.tiff', package='BioTrajectory')
im <- tiff::readTIFF(path)
im <- imager::as.cimg(t(im[,,1]))
Barnes <- detectBarnes(im, boardRadius=207, holeRadius=13, sigma=25)

Calculates distances to a target point

Description

Given a dataset of points, it computes the Euclidean distances from each point to a specified target point. The function also identifies contiguous segments of points that fall within a specified radius around the target.

Usage

distanceToTarget(data, target, targetRadious = 0)

Arguments

Value

A list containing:

Calculates the total distance traveled through a series of points.

Description

Computes the cumulative distance between consecutive points in a given set of coordinates. It sums the Euclidean distances between each pair of adjacent points, providing the total distance traveled along the path defined by the points.

Usage

distanceTraveled(data)

Arguments

Value

A numeric value representing the total distance traveled through the points.

Estimate the Radius of a Circle Fitting Four Points

Description

This function estimates the center and radius of a circle that best fits four points provided by the user. The user interacts with the plot to select four points, and the function optimizes the parameters (center and radius) using a least squares approach.

Usage

getRadius(frame)

Arguments

Details

The function plots the provided 'frame' and then uses the 'locator()' function to allow the user to click on four points. The function then performs optimization using the 'optim()' function to minimize the difference between the selected points and the circle's equation.

The objective function ('ftemp') calculates the sum of squared differences between the points and the expected distance from the circle's center.

Value

A vector of length 3, where: - The first element is the x-coordinate of the circle center (cx). - The second element is the y-coordinate of the circle center (cy). - The third element is the radius of the circle (r).

Examples

if(interactive()){
path <- system.file('extdata/data.tiff', package='BioTrajectory')
im <- tiff::readTIFF(path)
im <- imager::as.cimg(t(im[,,1]))
frame <- plot(im)
circle_params <- getRadius(frame)
print(circle_params)
}

Get Object Trajectory from Image Sequence

Description

This function calculates the trajectory of an object in a sequence of images. It compares each frame to a background image to detect movement. The function identifies the largest object in each frame and calculates its centroid coordinates across the sequence.

Usage

getTrajectory(listImages, Barnes, iBackground, iBegin, iEnd)

Arguments

Details

The function reads the images from 'listImages' and compares each frame to the background image specified by 'iBackground'. Background subtraction is performed using the 'removeBackground()' function, followed by thresholding to identify significant changes between the background and the current frame. The largest connected component in the thresholded image is assumed to be the object of interest, and its centroid is calculated.

Instead of directly returning the centroid coordinates, the function now creates an object of class 'trayectoria' to store the calculated centroids. The coordinates of the object in each frame are added to the 'trayectoria' object. If no object is detected in a frame, the corresponding coordinates are set to 'NA'. The resulting 'trayectoria' object is returned, which allows users to further manipulate and analyze the trajectory of the object across frames.

The returned 'trayectoria' object contains methods for extracting and analyzing the coordinates, making it easier to track the object over time.

Value

An object of class 'trayectoria' containing the points (coordinates) of the object in each frame. The 'trayectoria' object will include the 'x' and 'y' coordinates. If no object is detected in a frame, the corresponding coordinates will be set to 'NA' in the 'trayectoria' object.

Examples

# Not run:
path <- system.file('extdata/frames', package='BioTrajectory')
images <- list.files(path, full.names = TRUE)
B  <- list(c1 = structure(list(x = 342L, y = 263L), row.names = 1L, class = "data.frame"),
    boardRadius = 207, c2 = structure(list(x = c(157L, 172L, 202L, 245L,
    297L, 352L, 408L, 455L, 494L, 517L, 522L, 507L, 476L, 430L,
    375L, 318L, 262L, 215L, 180L, 160L), y = c(242L, 188L, 141L,
    105L, 85L, 80L, 93L, 124L, 166L, 219L, 277L, 334L, 383L,
    420L, 440L, 442L, 426L, 394L, 350L, 298L), class = "data.frame")), holeRadius = 13)

trajectory <- getTrajectory(images, B, 1, 1, 2)
print(trajectory) 

Creates a heatmap from a trajectory.

Description

Generates a heatmap based on the density of points in a trajectory. It utilizes kernel density estimation to visualize the concentration of points, allowing for adjustments in color palette and plotting limits.

Usage

heatmapFromTrajectory(data, plim = NULL, plot.pal = TRUE, ...)

Arguments

Value

A matrix of density values corresponding to the heatmap.

Interpolates a trajectory

Description

Given a dataset of points, it interpolates to generate intermediate points between them.

Usage

interpolateTrajectory(data, n = 4)

Arguments

Value

An object of class 'trayectoria', which contains the 'x' and 'y' coordinates, including both the original points and any interpolated points. The 'trayectoria' object allows users to store, manipulate, and analyze the coordinates of the object across frames. If no object is detected in a frame, the corresponding coordinates will be set to 'NA'.

Check if Object is a Trajectory

Description

Checks if an object is of class 'Trajectory'.

Usage

is.trajectory(x)

Arguments

Value

A logical value ('TRUE' or 'FALSE') indicating whether the object is of class 'Trajectory'.

Check if the first and last points of a "trajectory" object are within a given tolerance

Description

This function checks if the distance between the first and last points in an object of class 'trajectory' is smaller than a specified tolerance 'tol'. The distance is calculated using the Euclidean distance between the two points.

Usage

isClosed(obj, tol = 1e-06)

Arguments

Value

A logical value ('TRUE' or 'FALSE'), indicating whether the distance between the first and last points is smaller than 'tol'.

Length of the Trajectory

Description

Calculates the total length of the trajectory, which is the sum of the distances between consecutive points in the 'Trajectory' object.

Usage

## S3 method for class 'trajectory'
length(x)

Arguments

Value

A numeric value representing the total length of the trajectory.

Finds the nearest targets to a set of points within a specified radius.

Description

Calculates the distances between a set of points and target locations. It identifies the nearest target for each point and checks if the distance is within a specified radius. If a target is found within the radius, its index and distance are returned; otherwise, -1 is returned for both.

Usage

nearestTarget(data, targets, r)

Arguments

Value

A data frame with two columns:

Calculate the normals from tangents of a trajectory object

Description

This function computes the normal vectors at each point of an object of class 'trajectory' by rotating the tangent vectors 90 degrees.

Usage

normalVectors(obj)

Arguments

Value

A matrix of the same dimensions as 'obj$points' with the normal vectors. Each row represents a normal vector at a given point, which is obtained by rotating the corresponding tangent vector by 90 degrees.

Combine Two Trajectories

Description

Combines two 'Trajectory' objects by concatenating their points. The result is a new trajectory that contains the coordinates of both input trajectories.

Usage

## S3 method for class 'trajectory'
tr1 | tr2

Arguments

Value

A new 'Trajectory' object containing the concatenated points of the two input trajectories.

Plot the Trajectory

Description

Plots the trajectory by displaying the 'x' and 'y' coordinates as points on a 2D plot. Optionally, you can add a line connecting the points.

Usage

## S3 method for class 'trajectory'
plot(x, ..., stepSize = 0)

Arguments

Value

A plot displaying the trajectory.

Print Summary of the Trajectory

Description

Prints a detailed summary of the trajectory, including statistics for both the 'x' and 'y' coordinates and the total number of frames.

Usage

## S3 method for class 'summary.trajectory'
print(x, ...)

Arguments

Value

Prints the summary directly.

Read and Resize an Image

Description

This function reads an image from a file path and resizes it to a specified number of rows. It supports several image formats, including JPG, JPEG, PNG, TIFF, and TIF. The function also converts the image into a suitable format for further processing.

Usage

readImage(path, resizeRows)

Arguments

Details

The function detects the image format based on the file extension. It currently supports the following formats: JPG, JPEG, PNG, TIFF, and TIF. If the image has more than 3 dimensions (such as an RGBA image with an alpha channel), the alpha channel is discarded. The image is resized only if its height exceeds the specified 'resizeRows'.

Value

A cimg object containing the resized image.

Examples

# Example usage
img_path <- system.file('extdata/data.tiff', package='BioTrajectory')
img <- readImage(img_path, resizeRows = 500)
plot(img)  # Visualizes the resized image

Reads tracking data from a specified file.

Description

Reads a text file containing tracking data, where each line represents coordinates. If a line contains "null", it adds NA values for that entry. Optionally, it can remove rows with NA values.

Usage

readtrackData(file, na.rm = FALSE)

Arguments

Value

An object of class 'trayectoria' containing the points (coordinates) of the object in each frame. The 'trayectoria' object will include the 'x' and 'y' coordinates. If no object is detected in a frame, the corresponding coordinates will be set to 'NA' in the 'trayectoria' object.

Examples

# Read tracking data from a file
path <- system.file('extdata/track.txt', package='BioTrajectory')
tracking_data <- readtrackData(path, na.rm = TRUE)
# Print the resulting data frame
print(tracking_data)

Reverse the points of a trajectory object and create a new trajectory

Description

This function reverses the order of the points in an object of class 'trajectory' and then constructs a new trajectory using the reversed points. The function assumes the existence of a 'trajectory' function that creates a trajectory from the given x and y coordinates, as well as a time step 'delta_time'.

Usage

reverseTrajectory(obj)

Arguments

Value

A new trajectory object created using the reversed points and the original 'delta_time' from 'obj'.

Image Frame Selector and Viewer

Description

This function provides an interactive image frame viewer where the user can navigate through a sequence of images and select a specific one. The viewer uses buttons for navigation (previous and next) and an option to select an image. The function uses the 'rp.control' to create a window for the interface, and 'grid' for displaying images.

Usage

selFrame(image_files)

Arguments

Details

The function displays a sequence of images from the provided file paths, allowing the user to navigate between them using "Previous" and "Next" buttons. The images are displayed using 'grid.raster' from the 'grid' package. A "Select" button allows the user to select the current image, and the function returns the index of the selected image.

Value

The index of the selected image.

Examples

# Not run:
path <- system.file('extdata/frames/', package='BioTrajectory')
image_files <- list.files(path, pattern = "\\.png$", full.names = TRUE)
selFrame(image_files)

Visualizes the distance to the target in a plot.

Description

This function generates a plot of the distance to a target over time or some other associated parameter in the object. It also draws a horizontal line to indicate the target radius and a red segment that shows the start and length of a parameter associated with the 'obj'.

Usage

showDistanceToTarget(obj, ...)

Arguments

Details

This function generates a line plot of the distance to a target (stored in 'obj$distance'). It also draws a red horizontal line at the value of 'obj$targetRadious' to indicate the target's radius. Additionally, a red vertical segment is drawn to show the start of the range defined by 'obj$r$start' and the length defined by 'obj$r$length'.

Value

A plot showing the relationship between the object's position and the target's position.

Examples

# Create a fictional object with example data
obj <- list(
  distance = rep(c(5, 10, 15, 20, 15, 10, 5),5),
  targetRadious = 12,
  r = list(start = 2, length = 10)
)
# Visualize the distance to the target using the function
showDistanceToTarget(obj)

Apply a moving average filter to the trajectory and create a smoothed trajectory

Description

This function applies a moving average filter to the 'x' and/or 'y' coordinates of a "trajectory" object. The filter is applied using a window of a specified size. The function then creates a new trajectory object using the smoothed coordinates. The filter is applied symmetrically around each point.

Usage

smoothTrajectory(obj, method = c("x", "y", "both"), window = 3)

Arguments

Value

A new trajectory object created using the smoothed 'x' and 'y' coordinates.

Subsample the points of a trajectory object and create a new trajectory

Description

This function subsamples the points of a 'trajectory' object by selecting every 'step'-th point. It then creates a new trajectory using the selected points, adjusting the 'delta_time' accordingly.

Usage

subsampleTrajectory(obj, step = 2)

Arguments

Value

A new trajectory object created using the subsampled points and the adjusted 'delta_time'.

Summary of the Trajectory

Description

Generates a summary of the trajectory, including the minimum, maximum, and mean of the 'x' and 'y' coordinates, as well as the total number of frames.

Usage

## S3 method for class 'trajectory'
summary(object, ...)

Arguments

Value

A summary object containing statistics for both the 'x' and 'y' coordinates of the trajectory.

Calculate the tangent cectors of a trajectory object

Description

This function calculates the unit tangent vectors at each point of the trajectory represented by a 'trajectory' object. The tangent vectors are computed by taking the difference between consecutive points and normalizing them to have unit length.

Usage

tangentVectors(obj)

Arguments

Value

A matrix where each row is a unit tangent vector corresponding to each pair of consecutive points in 'obj$points'.

Trajectory Class

Description

A class representing a trajectory of an object over time, including the 'x' and 'y' coordinates of the object's centroids across frames. It provides methods to manipulate and analyze the trajectory, such as calculating the length, summarizing the trajectory, printing the summary, and plotting the trajectory.

Usage

trajectory(x, y, delta_time = 1)

Arguments

Details

The 'Trajectory' class stores the coordinates of an object across multiple frames. The class provides methods to compute various aspects of the trajectory, such as its length and summary statistics, as well as visualizations. It can also be used to manipulate the trajectory, such as combining it with another trajectory using the '|' operator.

Trim a trajectory object to a subset of points

Description

This function trims the points of a 'trajectory' object by selecting a subset of the points from the specified 'from' to 'to' indices. It then creates a new trajectory using the selected points.

Usage

trimTrajectory(obj, from = 1, to = nrow(obj$points))

Arguments

Value

A new trajectory object created using the subset of points from the 'from' to 'to' indices.

Extract Frames from a Video and Save as Images

Description

This function is a wrapper that simplifies extracting frames from a video. It processes the video file and saves the frames as PNG images in the specified directory. By default, it extracts 15 frames per second.

Usage

videoToFrames(videoPath, outputDir, fps = 15)

Arguments

Value

A list of file paths to the generated images.

Examples

# Not run:
videoPath <- system.file('extdata/video.mp4', package='BioTrajectory')
outputDir <- system.file('extdata/frames/', package='BioTrajectory')
images <- videoToFrames(videoPath, outputDir, fps=15)
print(images)  # Displays the paths to the generated images