Performs image rotation and reflection
image autocrop() Crops automatically an image to the area of objects.
image_crop() Crops an image to the desired area.
image_trim() Remove pixels from the edges of an image (20 by default).
image_dimension() Gives the dimension (width and height) of an image.
image_rotate() Rotates the image clockwise by the given angle.
image_horizontal() Converts (if needed) an image to a horizontal image.
image_vertical() Converts (if needed) an image to a vertical image.
image_hreflect() Performs horizontal reflection of the image.
image_vreflect() Performs vertical reflection of the image.
image_resize() Resize the image. See more at EBImage::resize().
image_contrast() Improve contrast locally by performing adaptive
histogram equalization. See more at EBImage::clahe().
image_dilate() Performs image dilatation. See more at EBImage::dilate().
image_erode() Performs image erosion. See more at EBImage::erode().
image_opening() Performs an erosion followed by a dilation. See more at
EBImage::opening().
image_closing() Performs a dilation followed by an erosion. See more at
EBImage::closing().
image_filter() Performs median filtering in constant time. See more at
EBImage::medianFilter().
image_blur() Performs blurring filter of images. See more at
EBImage::gblur().
image_skeleton() Performs image skeletonization.
image_autocrop(
img,
index = "NB",
edge = 5,
opening = 5,
closing = FALSE,
filter = FALSE,
invert = FALSE,
threshold = "Otsu",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)image_crop(
img,
width = NULL,
height = NULL,
viewer = get_pliman_viewer(),
downsample = NULL,
max_pixels = 1e+06,
show = "rgb",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_dimension(img, parallel = FALSE, workers = NULL, verbose = TRUE)
image_rotate(
img,
angle,
bg_col = "white",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = TRUE
)
image_horizontal(
img,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_vertical(
img,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_hreflect(
img,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_vreflect(
img,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_resize(
img,
rel_size = 100,
width,
height,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_trim(
img,
edge = NULL,
top = NULL,
bottom = NULL,
left = NULL,
right = NULL,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_dilate(
img,
kern = NULL,
size = NULL,
shape = "disc",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_erode(
img,
kern = NULL,
size = NULL,
shape = "disc",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_opening(
img,
kern = NULL,
size = NULL,
shape = "disc",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_closing(
img,
kern = NULL,
size = NULL,
shape = "disc",
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_skeleton(
img,
kern = NULL,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE,
...
)
image_thinning(
img,
niter = 3,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE,
...
)
image_filter(
img,
size = 2,
cache = 512,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_blur(
img,
sigma = 3,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_contrast(
img,
parallel = FALSE,
workers = NULL,
verbose = TRUE,
plot = FALSE
)
image_skeleton() returns a binary Image object.
All other functions returns a modified version of image depending on the
image_*() function used.
If image is a list, a list of the same length will be returned.
An image or a list of images of class Image.
The index to segment the image. See image_index() for more
details. Defaults to "NB" (normalized blue).
for image_autocrop() the number of pixels in the edge of the cropped
image. If edge = 0 the image will be cropped to create a bounding rectangle
(x and y coordinates) around the image objects.
for image_trim(), the number of pixels removed from the edges. By
default, 20 pixels are removed from all the edges.
Morphological operations (brush size)
opening performs an erosion followed by a dilation. This helps to
remove small objects while preserving the shape and size of larger objects.
closing performs a dilatation followed by an erosion. This helps to
fill small holes while preserving the shape and size of larger objects.
filter performs median filtering in the binary image. Provide a positive
integer > 1 to indicate the size of the median filtering. Higher values are
more efficient to remove noise in the background but can dramatically impact
the perimeter of objects, mainly for irregular perimeters such as leaves
with serrated edges.
Hierarchically, the operations are performed as opening > closing > filter. The value declared in each argument will define the brush size.
Inverts the binary image if desired. This is useful to process
images with a black background. Defaults to FALSE. If reference = TRUE
is use, invert can be declared as a logical vector of length 2 (eg.,
invert = c(FALSE, TRUE). In this case, the segmentation of objects and
reference from the foreground using back_fore_index is performed using the
default (not inverted), and the segmentation of objects from the reference
is performed by inverting the selection (selecting pixels higher than the
threshold).
The theshold method to be used.
By default (threshold = "Otsu"), a threshold value based
on Otsu's method is used to reduce the grayscale image to a binary image. If
a numeric value is informed, this value will be used as a threshold.
If threshold = "adaptive", adaptive thresholding (Shafait et al. 2008)
is used, and will depend on the k and windowsize arguments.
If any non-numeric value different than "Otsu" and "adaptive" is used,
an iterative section will allow you to choose the threshold based on a
raster plot showing pixel intensity of the index.
Processes the images asynchronously (in parallel) in separate
R sessions running in the background on the same machine. It may speed up
the processing time when image is a list. The number of sections is set
up to 70% of available cores.
A positive numeric scalar or a function specifying the maximum number of parallel processes that can be active at the same time.
If TRUE (default) a summary is shown in the console.
If TRUE plots the modified image. Defaults to FALSE.
For image_resize() the Width and height of the resized image. These arguments
can be missing. In this case, the image is resized according to the
relative size informed in rel_size.
For image_crop() a numeric vector indicating the pixel range (x and y,
respectively) that will be maintained in the cropped image, e.g., width =
100:200
The viewer option. If not provided, the value is retrieved
using get_pliman_viewer(). This option controls the type of viewer to use
for interactive plotting. The available options are "base" and "mapview".
If set to "base", the base R graphics system is used for interactive
plotting. If set to "mapview", the mapview package is used. To set this
argument globally for all functions in the package, you can use the
set_pliman_viewer() function. For example, you can run
set_pliman_viewer("mapview") to set the viewer option to "mapview" for
all functions.
integer; for each dimension the number of
pixels/lines/bands etc that will be skipped; Defaults to NULL, which will
find the best downsampling factor to approximate the max_pixels value.
integer > 0. Maximum number of cells to use for the plot.
If max_pixels < npixels(img), regular sampling is used before plotting.
How to plot in mapview viewer, either "rgb" or "index".
The rotation angle in degrees.
Color used to fill the background pixels, defaults to "white".
The relative size of the resized image. Defaults to 100. For
example, setting rel_size = 50 to an image of width 1280 x 720, the new
image will have a size of 640 x 360.
The number of pixels removed from top,
bottom, left, and right when using image_trim().
An Image object or an array, containing the structuring
element. Defaults to a brushe generated with EBImage::makeBrush().
For image_filter() is the median filter radius (integer). Defaults to 3.
For image_dilate() and image_erode() is an odd number containing the
size of the brush in pixels. Even numbers are rounded to the next odd one.
The default depends on the image resolution and is computed as the image
resolution (megapixels) times 20.
A character vector indicating the shape of the brush. Can be
box, disc, diamond, Gaussian or line. Default is disc.
Additional arguments passed on to image_binary().
The number of iterations to perform in the thinning procedure.
Defaults to 3. Set to NULL to iterate until the binary image is no longer
changing.
The the L2 cache size of the system CPU in kB (integer).
Defaults to 512.
A numeric denoting the standard deviation of the Gaussian filter
used for blurring. Defaults to 3.
Tiago Olivoto tiagoolivoto@gmail.com
if (interactive() && requireNamespace("EBImage")) {
library(pliman)
img <- image_pliman("sev_leaf.jpg")
plot(img)
img <- image_resize(img, 50)
img1 <- image_rotate(img, 45)
img2 <- image_hreflect(img)
img3 <- image_vreflect(img)
img4 <- image_vertical(img)
image_combine(img1, img2, img3, img4)
}
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