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pliman 2.1.0

CRAN release: 2023-10-14

New functions

  • A new mosaic_*() family of functions to handle orthomosaics from RGB and multispectral images.

  • object_export() and object_export_shp() to export objects from single images to multiple images.

  • image_augment() to augment an image by rotating it multiple times.

Bug fixes

  • Setting save_image = TRUE in measure_disease_byl() now exports the processed images to a local directory, allowing the use of sad() call to the created object.

Minor improvements

pliman 2.0.1

CRAN release: 2023-09-11

New functions

  • object_export_shp() and object_export() to export objects from an image to multiple images in the current working directory.
  • plot_index_shp() to plot rectangles on top of an RGB image, where each rectangle is colored based on a quantitative variable.

Bug fixes

  • Fix bug in poly_center() by calling the column position instead column name (X1)

pliman 2.0.0

CRAN release: 2023-07-15

New functions

New features

  • New viewer option added. Now, iterative functions such as pick_palette() and measure_disease_iter() have an argument viewer. 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, allowing the users to draw shapes like points and polygons with mapedit package. 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.

  • Haralick’s features that quantify pixel texture for image objects were included.

  • Several measures were added in analyze_objects(). The function now wraps some poly_*() functions to compute shape measures such as width, length, elongation, circularity. Haralick’s features are now computed by default. . This improvement was at cost of a slight increase in computation time.

  • analyze_objects(), measure_disease(), and measure_disease_byl() have now a filter argument that applies a median filtering in the binary mask. This is useful to reduce the noise in the segmentation of objects.

  • Arguments reference_larger and reference_smaller were included in analyze_objects() indicating when the larger/smaller object in the image must be used as the reference object.

  • Arguments efourier and nharm included in analyze_objects(). If efourier = TRUE, Elliptical Fourier analysis is computed for each object depending on the number of harmonics (nharm).

  • Logical arguments reference_larger and reference_smaller included in analyze_objects(). Those indicates when the larger/smaller object in the image must be used as the reference object. This only is valid when reference = 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.

  • Rcpp and RcppArmadillo dependencies were included, allowing the implementation of C++ code. This will dramatically reduce the time computing of some functions/procesures. As an example, we wave.

    • Reduction in time processing from more than 5 minutes to less than 1 second using the new object_rgb() function to extract the RGB values from an image (1445 x 1084) with ~1400 objects.
    • Reduction in time processing of the set of *_poly() functions.

Minor changes

pliman 1.1.0

CRAN release: 2021-12-10

New functions

  • measure_disease_iter() to measure disease in an interactive section.
  • pick_count() to count objects in an image manually.
  • pick_palette() to create an image palette by picking up color point(s) from the image
  • pick_rgb() to pick up the RGB values from selected point(s) in the image.
  • summary_index() to summary the index either between and within objects.
  • pliman now exports the foward-pipe operator %>%. Code from poorman package.

Minor changes

  • Deprecated functions in the last version (count_objects(), image_show(), leaf_area(), objects_rgb(), prop_segmented(), and symptomatic_area()) were removed.
  • Use Bootstrap 5 from pkgdown 2.0.0 in the package site.

pliman 1.0.0

CRAN release: 2021-11-09

New functions

Deprecated functions.

  • objects_rgb() will be depracated in the future. Now, to compute an index for each object use the object_index argument in analyze_objects(), for example, analyze_objects(object_index = "B").
  • leaf_area() will be depracated in the future. Now, combine analyze_objects() with get_measures() to obtain the area and shape of objects (leaves).
  • prop_segmented() is now deprecated in favour of image_segment_iter().
  • count_lesions() is now deprecated. Now, to compute the number and shape of lesions, use the argument show_features = TRUE in measure_disease().
  • image_show() is now deprecated in favour of plot().

Minor improvements

  • Include fill_hull argument in symptomatic_area() and count_lesions()
  • Improve image_contrast() function to avoid error regarding image resolution.
  • New argument subfolder in image_export() to export an image to a subfolder.
  • Now EBImage installation is checked when pliman is installed.
  • image_pliman() now returns the image object instead of the path to the image. So, it is not necessarily to call it within image_import().

pliman 0.3.0

CRAN release: 2021-06-10

New functions

  • image_autocrop() for automatic image cropping.
  • image_filter() to perform median-based filtering.
  • image_contrast() to improve contrast by performing adaptive histogram equalization
  • object_coord() to get the object coordinates and (optionally) draw a bounding rectangle around multiple objects in an image.
  • object_id() to get the object identification in an image.
  • object_isolate() to isolate an object from an image.
  • prop_segmented() to perform (iterative) image segmentation with pixels proportion.

Minor improvements

  • New argument filter in count_objects() and prop_segmented().

pliman 0.2.0

CRAN release: 2021-05-15

  • Includes the suggestions given by the CRAN team in the first submission

pliman 0.1.0

  • The first version of pliman package submitted to CRAN.