Analyzes objects in an image — analyze

analyze_objects() provides tools for counting and extracting object features (e.g., area, perimeter, radius, pixel intensity) in an image. See more at the Details section.
analyze_objects_iter() provides an iterative section to measure object features using an object with a known area.
plot.anal_obj() produces a histogram for the R, G, and B values when argument object_index is used in the function analyze_objects().

Usage

analyze_objects(
  img,
  foreground = NULL,
  background = NULL,
  pick_palettes = FALSE,
  segment_objects = TRUE,
  viewer = get_pliman_viewer(),
  reference = FALSE,
  reference_area = NULL,
  back_fore_index = "R/(G/B)",
  fore_ref_index = "B-R",
  reference_larger = FALSE,
  reference_smaller = FALSE,
  pattern = NULL,
  parallel = FALSE,
  workers = NULL,
  watershed = TRUE,
  veins = FALSE,
  sigma_veins = 1,
  ab_angles = FALSE,
  ab_angles_percentiles = c(0.25, 0.75),
  width_at = FALSE,
  width_at_percentiles = c(0.05, 0.25, 0.5, 0.75, 0.95),
  haralick = FALSE,
  har_nbins = 32,
  har_scales = 1,
  har_band = 1,
  pcv = FALSE,
  pcv_niter = 100,
  resize = FALSE,
  trim = FALSE,
  fill_hull = FALSE,
  filter = FALSE,
  invert = FALSE,
  object_size = "medium",
  index = "NB",
  r = 1,
  g = 2,
  b = 3,
  re = 4,
  nir = 5,
  object_index = NULL,
  pixel_level_index = FALSE,
  return_mask = FALSE,
  efourier = FALSE,
  nharm = 10,
  threshold = "Otsu",
  k = 0.1,
  windowsize = NULL,
  tolerance = NULL,
  extension = NULL,
  lower_noise = 0.1,
  lower_size = NULL,
  upper_size = NULL,
  topn_lower = NULL,
  topn_upper = NULL,
  lower_eccent = NULL,
  upper_eccent = NULL,
  lower_circ = NULL,
  upper_circ = NULL,
  randomize = TRUE,
  nrows = 1000,
  plot = TRUE,
  show_original = TRUE,
  show_chull = FALSE,
  show_contour = TRUE,
  contour_col = "red",
  contour_size = 1,
  show_lw = FALSE,
  show_background = TRUE,
  show_segmentation = FALSE,
  col_foreground = NULL,
  col_background = NULL,
  marker = FALSE,
  marker_col = NULL,
  marker_size = NULL,
  save_image = FALSE,
  prefix = "proc_",
  dir_original = NULL,
  dir_processed = NULL,
  verbose = TRUE
)

# S3 method for anal_obj
plot(
  x,
  which = "measure",
  measure = "area",
  type = c("density", "histogram"),
  ...
)

analyze_objects_iter(pattern, known_area, verbose = TRUE, ...)

Arguments

img

The image to be analyzed.

foreground, background

A color palette for the foregrond and background, respectively (optional). If a chacarceter is used (eg., foreground = "fore"), the function will search in the current working directory a valid image named "fore".

pick_palettes

Logical argument indicating wheater the user needs to pick up the color palettes for foreground and background for the image. If TRUE pick_palette() will be called internally so that the user can sample color points representing foreground and background.

segment_objects

Segment objects in the image? Defaults to TRUE. In this case, objects are segmented using the index defined in the index argument, and each object is analyzed individually. If segment_objects = FALSE is used, the objects are not segmented and the entire image is analyzed. This is useful, for example, when analyzing an image without background, where an object_index could be computed for the entire image, like the index of a crop canopy.

viewer

The viewer option. This option controls the type of viewer to use for interactive plotting (eg., when pick_palettes = TRUE). If not provided, the value is retrieved using get_pliman_viewer().

reference

Logical to indicate if a reference object is present in the image. This is useful to adjust measures when images are not obtained with standard resolution (e.g., field images). See more in the details section.

reference_area

The known area of the reference objects. The measures of all the objects in the image will be corrected using the same unit of the area informed here.

back_fore_index

A character value to indicate the index to segment the foreground (objects and reference) from the background. Defaults to "R/(G/B)". This index is optimized to segment white backgrounds from green leaves and a blue reference object.

fore_ref_index

A character value to indicate the index to segment objects and the reference object. It can be either an available index in pliman (see pliman_indexes() or an own index computed with the R, G, and B bands. Defaults to "B-R". This index is optimized to segment green leaves from a blue reference object after a white background has been removed.

reference_larger, reference_smaller

Logical argument indicating when the larger/smaller object in the image must be used as the reference object. This only is valid when reference is set to TRUE and reference_area indicates the area of the reference object. IMPORTANT. When reference_smaller is used, objects with an area smaller than 1% of the mean of all the objects are ignored. This is used to remove possible noise in the image such as dust. So, be sure the reference object has an area that will be not removed by that cutpoint.

pattern

A pattern of file name used to identify images to be imported. For example, if pattern = "im" all images in the current working directory that the name matches the pattern (e.g., img1.-, image1.-, im2.-) will be imported as a list. Providing any number as pattern (e.g., pattern = "1") will select images that are named as 1.-, 2.-, and so on. An error will be returned if the pattern matches any file that is not supported (e.g., img1.pdf).

parallel

If TRUE 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, especially when pattern is used is informed. When object_index is informed, multiple sections will be used to extract the RGB values for each object in the image. This may significantly speed up processing time when an image has lots of objects (say >1000).

workers

A positive numeric scalar or a function specifying the number of parallel processes that can be active at the same time. By default, the number of sections is set up to 30% of available cores.

watershed

If TRUE (default) performs watershed-based object detection. This will detect objects even when they are touching one other. If FALSE, all pixels for each connected set of foreground pixels are set to a unique object. This is faster but is not able to segment touching objects.

veins

Logical argument indicating whether vein features are computed. This will call object_edge() and applies the Sobel-Feldman Operator to detect edges. The result is the proportion of edges in relation to the entire area of the object(s) in the image. Note that THIS WILL BE AN OPERATION ON AN IMAGE LEVEL, NOT OBJECT!.

sigma_veins

Gaussian kernel standard deviation used in the gaussian blur in the edge detection algorithm

ab_angles

Logical argument indicating whether apex and base angles should be computed. Defaults to FALSE. If TRUE, poly_apex_base_angle() are called and the base and apex angles are computed considering the 25th and 75th percentiles of the object height. These percentiles can be changed with the argument ab_angles_percentiles.

ab_angles_percentiles

The percentiles indicating the heights of the object for which the angle should be computed (from the apex and the bottom). Defaults to c(0.25, 0.75), which means considering the 25th and 75th percentiles of the object height.

width_at

Logical. If TRUE, the widths of the object at a given set of quantiles of the height are computed.

width_at_percentiles

A vector of heights along the vertical axis of the object at which the width will be computed. The default value is c(0.05, 0.25, 0.5, 0.75, 0.95), which means the function will return the width at the 5th, 25th, 50th, 75th, and 95th percentiles of the object's height.

haralick

Logical value indicating whether Haralick features are computed. Defaults to FALSE.

har_nbins

An integer indicating the number of bins using to compute the Haralick matrix. Defaults to 32. See Details

har_scales

A integer vector indicating the number of scales to use to compute the Haralick features. See Details.

har_band

The band to compute the Haralick features (1 = R, 2 = G, 3 = B). Defaults to 1.

pcv

Computes the Perimeter Complexity Value? Defaults to FALSE.

pcv_niter

An integer specifying the number of smoothing iterations for computing the Perimeter Complexity Value. Defaults to 100.

resize

Resize the image before processing? Defaults to FALSE. Use a numeric value of range 0-100 (proportion of the size of the original image).

trim

Number of pixels removed from edges in the analysis. The edges of images are often shaded, which can affect image analysis. The edges of images can be removed by specifying the number of pixels. Defaults to FALSE (no trimmed edges).

fill_hull

Fill holes in the binary image? Defaults to FALSE. This is useful to fill holes in objects that have portions with a color similar to the background. IMPORTANT: Objects touching each other can be combined into one single object, which may underestimate the number of objects in an image.

filter

Performs median filtering in the binary image? See more at image_filter(). Defaults to FALSE. Use a positive integer to define the size of the median filtering. Larger values are effective at removing noise, but adversely affect edges.

invert

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).

object_size

The size of the object. Used to automatically set up tolerance and extension parameters. One of the following. "small" (e.g, wheat grains), "medium" (e.g, soybean grains), "large"(e.g, peanut grains), and "elarge" (e.g, soybean pods)`.

index

A character value specifying the target mode for conversion to binary image when foreground and background are not declared. Defaults to "NB" (normalized blue). See image_index() for more details. User can also calculate your own index using the bands names, e.g. index = "R+B/G"

r, g, b, re, nir

The red, green, blue, red-edge, and near-infrared bands of the image, respectively. Defaults to 1, 2, 3, 4, and 5, respectively. If a multispectral image is provided (5 bands), check the order of bands, which are frequently presented in the 'BGR' format.

object_index

Defaults to FALSE. If an index is informed, the average value for each object is returned. It can be the R, G, and B values or any operation involving them, e.g., object_index = "R/B". In this case, it will return for each object in the image, the average value of the R/B ratio. Use pliman_indexes_eq() to see the equations of available indexes.

pixel_level_index

Return the indexes computed in object_index in the pixel level? Defaults to FALSE to avoid returning large data.frames.

return_mask

Returns the mask for the analyzed image? Defaults to FALSE.

efourier

Logical argument indicating if Elliptical Fourier should be computed for each object. This will call efourier() internally. It efourier = TRUE is used, both standard and normalized Fourier coefficients are returned.

nharm

An integer indicating the number of harmonics to use. Defaults to 10. For more details see efourier().

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.

k

a numeric in the range 0-1. when k is high, local threshold values tend to be lower. when k is low, local threshold value tend to be higher.

windowsize

windowsize controls the number of local neighborhood in adaptive thresholding. By default it is set to 1/3 * minxy, where minxy is the minimum dimension of the image (in pixels).

tolerance

The minimum height of the object in the units of image intensity between its highest point (seed) and the point where it contacts another object (checked for every contact pixel). If the height is smaller than the tolerance, the object will be combined with one of its neighbors, which is the highest.

extension

Radius of the neighborhood in pixels for the detection of neighboring objects. Higher value smooths out small objects.

lower_noise

To prevent noise from affecting the image analysis, objects with lesser than 10% of the mean area of all objects are removed (lower_noise = 0.1). Increasing this value will remove larger noises (such as dust points), but can remove desired objects too. To define an explicit lower or upper size, use the lower_size and upper_size arguments.

lower_size, upper_size

Lower and upper limits for size for the image analysis. Plant images often contain dirt and dust. Upper limit is set to NULL, i.e., no upper limit used. One can set a known area or use lower_limit = 0 to select all objects (not advised). Objects that matches the size of a given range of sizes can be selected by setting up the two arguments. For example, if lower_size = 120 and upper_size = 140, objects with size greater than or equal 120 and less than or equal 140 will be considered.

topn_lower, topn_upper

Select the top n objects based on its area. topn_lower selects the n elements with the smallest area whereas topn_upper selects the n objects with the largest area.

lower_eccent, upper_eccent, lower_circ, upper_circ

Lower and upper limit for object eccentricity/circularity for the image analysis. Users may use these arguments to remove objects such as square papers for scale (low eccentricity) or cut petioles (high eccentricity) from the images. Defaults to NULL (i.e., no lower and upper limits).

randomize

Randomize the lines before training the model?

nrows

The number of lines to be used in training step. Defaults to 2000.

plot

Show image after processing?

show_original

Show the count objects in the original image?

show_chull

Show the convex hull around the objects? Defaults to FALSE.

show_contour

Show a contour line around the objects? Defaults to TRUE.

contour_col, contour_size

The color and size for the contour line around objects. Defaults to contour_col = "red" and contour_size = 1.

show_lw

If TRUE, plots the length and width lines on each object calling plot_lw().

show_background

Show the background? Defaults to TRUE. A white background is shown by default when show_original = FALSE.

show_segmentation

Shows the object segmentation colored with random permutations. Defaults to FALSE.

col_foreground, col_background

Foreground and background color after image processing. Defaults to NULL, in which "black", and "white" are used, respectively.

marker, marker_col, marker_size

The type, color and size of the object marker. Defaults to NULL, which plots the object id. Use marker = "point" to show a point in each object or marker = FALSE to omit object marker.

save_image

Save the image after processing? The image is saved in the current working directory named as proc_* where * is the image name given in img.

prefix

The prefix to be included in the processed images. Defaults to "proc_".

dir_original, dir_processed

The directory containing the original and processed images. Defaults to NULL. In this case, the function will search for the image img in the current working directory. After processing, when save_image = TRUE, the processed image will be also saved in such a directory. It can be either a full path, e.g., "C:/Desktop/imgs", or a subfolder within the current working directory, e.g., "/imgs".

verbose

If TRUE (default) a summary is shown in the console.

x

An object of class anal_obj.

which

Which to plot. Either 'measure' (object measures) or 'index' (object index). Defaults to "measure".

measure

The measure to plot. Defaults to "area".

type

The type of plot. Either "hist" or "density". Partial matches are recognized.

...

Depends on the function:

For analyze_objects_iter(), further arguments passed on to analyze_objects().

known_area

The known area of the template object.

Value

analyze_objects() returns a list with the following objects:

results A data frame with the following variables for each object in the image:
- id: object identification.
- x,y: x and y coordinates for the center of mass of the object.
- area: area of the object (in pixels).
- area_ch: the area of the convex hull around object (in pixels).
- perimeter: perimeter (in pixels).
- radius_min, radius_mean, and radius_max: The minimum, mean, and maximum radius (in pixels), respectively.
- radius_sd: standard deviation of the mean radius (in pixels).
- diam_min, diam_mean, and diam_max: The minimum, mean, and maximum diameter (in pixels), respectively.
- major_axis, minor_axis: elliptical fit for major and minor axes (in pixels).
- caliper: The longest distance between any two points on the margin of the object. See poly_caliper() for more details
- length, width The length and width of objects (in pixels). These measures are obtained as the range of x and y coordinates after aligning each object with poly_align().
- radius_ratio: radius ratio given by radius_max / radius_min.
- theta: object angle (in radians).
- eccentricity: elliptical eccentricity computed using the ratio of the eigen values (inertia axes of coordinates).
- form_factor (Wu et al., 2007): the difference between a leaf and a circle. It is defined as 4*pi*A/P, where A is the area and P is the perimeter of the object.
- narrow_factor (Wu et al., 2007): Narrow factor (caliper / length).
- asp_ratio (Wu et al., 2007): Aspect ratio (length / width).
- rectangularity (Wu et al., 2007): The similarity between a leaf and a rectangle (length * width/ area).
- pd_ratio (Wu et al., 2007): Ratio of perimeter to diameter (perimeter / caliper)
- plw_ratio (Wu et al., 2007): Perimeter ratio of length and width (perimeter / (length + width))
- solidity: object solidity given by area / area_ch.
- convexity: The convexity of the object computed using the ratio between the perimeter of the convex hull and the perimeter of the polygon.
- elongation: The elongation of the object computed as 1 - width / length.
- circularity: The object circularity given by perimeter ^ 2 / area.
- circularity_haralick: The Haralick's circularity (CH), computed as CH = m/sd, where m and sd are the mean and standard deviations from each pixels of the perimeter to the centroid of the object.
- circularity_norm: The normalized circularity (Cn), to be unity for a circle. This measure is computed as Cn = perimeter ^ 2 / 4*pi*area and is invariant under translation, rotation, scaling transformations, and dimensionless.
- asm: The angular second-moment feature.
- con: The contrast feature
- cor: Correlation measures the linear dependency of gray levels of neighboring pixels.
- var: The variance of gray levels pixels.
- idm: The Inverse Difference Moment (IDM), i.e., the local homogeneity.
- sav: The Sum Average.
- sva: The Sum Variance.
- sen: Sum Entropy.
- dva: Difference Variance.
- den: Difference Entropy
- f12: Difference Variance.
- f13: The angular second-moment feature.
statistics: A data frame with the summary statistics for the area of the objects.
count: If pattern is used, shows the number of objects in each image.
obj_rgb: If object_index is used, returns the R, G, and B values for each pixel of each object.
object_index: If object_index is used, returns the index computed for each object.
Elliptical Fourier Analysis: If efourier = TRUE is used, the following objects are returned.
- efourier: The Fourier coefficients. For more details see efourier().
- efourier_norm: The normalized Fourier coefficients. For more details see efourier_norm().
- efourier_error: The error between original data and reconstructed outline. For more details see efourier_error().
- efourier_power: The spectrum of harmonic Fourier power. For more details see efourier_power().
veins: If veins = TRUE is used, returns, for each image, the proportion of veins (in fact the object edges) related to the total object(s)' area.
analyze_objects_iter() returns a data.frame containing the features described in the results object of analyze_objects().
plot.anal_obj() returns a trellis object containing the distribution of the pixels, optionally for each object when facet = TRUE is used.

Details

A binary image is first generated to segment the foreground and background. The argument index is useful to choose a proper index to segment the image (see image_binary() for more details). It is also possible to provide color palettes for background and foreground (arguments background and foreground, respectively). When this is used, a general linear model (binomial family) fitted to the RGB values to segment fore- and background.

Then, the number of objects in the foreground is counted. By setting up arguments such as lower_size and upper_size, it is possible to set a threshold for lower and upper sizes of the objects, respectively. The argument object_size can be used to set up pre-defined values of tolerance and extension depending on the image resolution. This will influence the watershed-based object segmentation. Users can also tune up tolerance and extension explicitly for a better precision of watershed segmentation.

If watershed = FALSE is used, all pixels for each connected set of foreground pixels in img are set to a unique object. This is faster, especially for a large number of objects, but it is not able to segment touching objects.

There are some ways to correct the measures based on a reference object. If a reference object with a known area (reference_area) is used in the image and reference = TRUE is used, the measures of the objects will be corrected, considering the unit of measure informed in reference_area. There are two main ways to work with reference objects.

The first, is to provide a reference object that has a contrasting color with both the background and object of interest. In this case, the arguments back_fore_index and fore_ref_index can be used to define an index to first segment the reference object and objects to be measured from the background, then the reference object from objects to be measured.
The second one is to use a reference object that has a similar color to the objects to be measured, but has a contrasting size. For example, if we are counting small brown grains, we can use a brown reference template that has an area larger (says 3 times the area of the grains) and then uses reference_larger = TRUE. With this, the larger object in the image will be used as the reference object. This is particularly useful when images are captured with background light, such as the example 2. Some types: (i) It is suggested that the reference object is not too much larger than the objects of interest (mainly when the watershed = TRUE). In some cases, the reference object can be broken into several pieces due to the watershed algorithm. (ii) Since the reference object will increase the mean area of the object, the argument lower_noise can be increased. By default (lower_noise = 0.1) objects with lesser than 10% of the mean area of all objects are removed. Since the mean area will be increased, increasing lower_noise will remove dust and noises more reliably. The argument reference_smaller can be used in the same way

By using pattern, it is possible to process several images with common pattern names that are stored in the current working directory or in the subdirectory informed in dir_original. To speed up the computation time, one can set parallel = TRUE.

analyze_objects_iter() can be used to process several images using an object with a known area as a template. In this case, all the images in the current working directory that match the pattern will be processed. For each image, the function will compute the features for the objects and show the identification (id) of each object. The user only needs to inform which is the id of the known object. Then, given the known_area, all the measures will be adjusted. In the end, a data.frame with the adjusted measures will be returned. This is useful when the images are taken at different heights. In such cases, the image resolution cannot be conserved. Consequently, the measures cannot be adjusted using the argument dpi from get_measures(), since each image will have a different resolution. NOTE: This will only work in an interactive section.

Additional measures: By default, some measures are not computed, mainly due to computational efficiency when the user only needs simple measures such as area, length, and width.
- If haralick = TRUE, The function computes 13 Haralick texture features for each object based on a gray-level co-occurrence matrix (Haralick et al. 1979). Haralick features depend on the configuration of the parameters har_nbins and har_scales. har_nbins controls the number of bins used to compute the Haralick matrix. A smaller har_nbins can give more accurate estimates of the correlation because the number of events per bin is higher. While a higher value will give more sensitivity. har_scales controls the number of scales used to compute the Haralick features. Since Haralick features compute the correlation of intensities of neighboring pixels it is possible to identify textures with different scales, e.g., a texture that is repeated every two pixels or 10 pixels. By default, the Haralick features are computed with the R band. To chance this default, use the argument har_band. For example, har_band = 2 will compute the features with the green band.
- If efourier = TRUE is used, an Elliptical Fourier Analysis (Kuhl and Giardina, 1982) is computed for each object contour using efourier().
- If veins = TRUE (experimental), vein features are computed. This will call object_edge() and applies the Sobel-Feldman Operator to detect edges. The result is the proportion of edges in relation to the entire area of the object(s) in the image. Note that THIS WILL BE AN OPERATION ON AN IMAGE LEVEL, NOT an OBJECT LEVEL! So, If vein features need to be computed for leaves, it is strongly suggested to use one leaf per image.
- If ab_angles = TRUE the apex and base angles of each object are computed with poly_apex_base_angle(). By default, the function computes the angle from the first pixel of the apex of the object to the two pixels that slice the object at the 25th percentile of the object height (apex angle). The base angle is computed in the same way but from the first base pixel.
- If width_at = TRUE, the width at the 5th, 25th, 50th, 75th, and 95th percentiles of the object height are computed by default. These quantiles can be adjusted with the width_at_percentiles argument.

References

Claude, J. (2008) Morphometrics with R, Use R! series, Springer 316 pp.

Gupta, S., Rosenthal, D. M., Stinchcombe, J. R., & Baucom, R. S. (2020). The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E. New Phytologist, 225(5), 2183–2195. doi:10.1111/NPH.16286

Haralick, R.M., K. Shanmugam, and I. Dinstein. 1973. Textural Features for Image Classification. IEEE Transactions on Systems, Man, and Cybernetics SMC-3(6): 610–621. doi:10.1109/TSMC.1973.4309314

Kuhl, F. P., and Giardina, C. R. (1982). Elliptic Fourier features of a closed contour. Computer Graphics and Image Processing 18, 236–258. doi: doi:10.1016/0146-664X(82)90034-X

Lee, Y., & Lim, W. (2017). Shoelace Formula: Connecting the Area of a Polygon and the Vector Cross Product. The Mathematics Teacher, 110(8), 631–636. doi:10.5951/mathteacher.110.8.0631

Montero, R. S., Bribiesca, E., Santiago, R., & Bribiesca, E. (2009). State of the Art of Compactness and Circularity Measures. International Mathematical Forum, 4(27), 1305–1335.

Chen, C.H., and P.S.P. Wang. 2005. Handbook of Pattern Recognition and Computer Vision. 3rd ed. World Scientific.

Wu, S. G., Bao, F. S., Xu, E. Y., Wang, Y.-X., Chang, Y.-F., and Xiang, Q.-L. (2007). A Leaf Recognition Algorithm for Plant Classification Using Probabilistic Neural Network. in 2007 IEEE International Symposium on Signal Processing and Information Technology, 11–16. doi:10.1109/ISSPIT.2007.4458016

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
library(pliman)
img <- image_pliman("soybean_touch.jpg")
obj <- analyze_objects(img)

obj$statistics
#>        stat        value
#> 1         n 3.000000e+01
#> 2  min_area 1.366000e+03
#> 3 mean_area 2.051300e+03
#> 4  max_area 2.436000e+03
#> 5   sd_area 2.300703e+02
#> 6  sum_area 6.153900e+04
#> 7  coverage 1.151122e-01

########################### Example 1 #########################
# Enumerate the objects in the original image
# Return the top-5 grains with the largest area
top <-
 analyze_objects(img,
                 marker = "id",
                 topn_upper = 5)

top$results
#>   id        x         y area area_ch perimeter radius_mean radius_min
#> 4  4 344.3132 104.74372 2436  2408.0  185.6102    27.45204   24.31796
#> 9  9 468.0383  55.44180 2311  2278.0  181.0244    26.77622   23.16169
#> 3  3 236.6572 338.80546 2310  2288.5  181.0244    26.69273   23.99117
#> 6  6 405.9755  76.41826 2297  2264.5  178.7817    26.58139   24.07681
#> 2  2 537.0532 400.81350 2289  2261.5  178.1960    26.55606   24.84882
#>   radius_max radius_sd diam_mean diam_min diam_max major_axis minor_axis
#> 4   30.53131 1.7403323  54.90407 48.63592 61.06262   20.76326   18.04194
#> 9   31.04441 2.3392198  53.55243 46.32339 62.08881   20.69928   17.14476
#> 3   29.44025 1.2381808  53.38545 47.98234 58.88049   19.82571   17.91553
#> 6   30.02968 1.6596304  53.16279 48.15362 60.05937   19.82630   17.78272
#> 2   28.70321 0.9660995  53.11211 49.69764 57.40641   19.53438   18.01553
#>    caliper   length    width radius_ratio      theta eccentricity form_factor
#> 4 61.03278 61.02182 51.02160     1.255504 -0.9790241    0.4949248   0.8885535
#> 9 61.18823 61.07428 48.72944     1.340334  1.2628961    0.5603174   0.8862079
#> 3 57.69749 57.20139 51.99249     1.227128 -0.6370637    0.4282680   0.8858245
#> 6 59.48109 59.42578 50.82265     1.247245  1.1427598    0.4421814   0.9030764
#> 2 56.85948 56.53366 52.36854     1.155113 -0.8035065    0.3866007   0.9058576
#>   narrow_factor asp_ratio rectangularity pd_ratio plw_ratio solidity convexity
#> 4      1.000180  1.196000       1.278091 3.041156  1.656592 1.011628 0.9187379
#> 9      1.001866  1.253334       1.287804 2.958484  1.648618 1.014486 0.8658923
#> 3      1.008673  1.100186       1.287464 3.137474  1.657825 1.009395 0.9111738
#> 6      1.000931  1.169277       1.314835 3.005691  1.621626 1.014352 0.8761289
#> 2      1.005763  1.079535       1.293397 3.133971  1.636293 1.012160 0.8794599
#>   elongation circularity circularity_haralick circularity_norm    coverage
#> 4 0.16387934    14.14250             15.77402        0.8584609 0.004556678
#> 9 0.20212827    14.17993             11.44664        0.8555300 0.004322858
#> 3 0.09106255    14.18607             21.55802        0.8551466 0.004320988
#> 6 0.14477098    13.91507             16.01645        0.8718206 0.004296670
#> 2 0.07367508    13.87235             27.48791        0.8745939 0.004281706


#' ########################### Example 1 #########################
# Correct the measures based on the area of the largest object
# note that since the reference object

img <- image_pliman("flax_grains.jpg")
res <-
  analyze_objects(img,
                  index = "GRAY",
                  marker = "point",
                  show_contour = FALSE,
                  reference = TRUE,
                  reference_area = 6,
                  reference_larger = TRUE,
                  lower_noise = 0.3)

# }

# \donttest{
library(pliman)

img <- image_pliman("soy_green.jpg")
# Segment the foreground (grains) using the normalized blue index (NB, default)
# Shows the average value of the blue index in each object

rgb <-
   analyze_objects(img,
                   marker = "id",
                   object_index = "B",
                   pixel_level_index = TRUE)

# density of area
plot(rgb)


# histogram of perimeter
plot(rgb, measure = "perimeter", type = "histogram") # or 'hist'


# density of the blue (B) index
plot(rgb, which = "index")

# }