# pliman 3.0.0
## New Functions
* Introduced the `mosaic_*()` family of functions for high-throughput phenotyping, enabling efficient analysis of large-scale image data.
* Added the `shapefile_*()` functions for handling and manipulating shapefiles, providing streamlined spatial data management.

## Minor Improvements
* Fixed a documentation bug related to missing references.
* Additional performance enhancements and minor bug fixes.

# pliman 2.2.0
## New functions
* `mosaic_analyze()` to analyze orthomosaics.

## Minor improvements
* Imports the [poorman](https://github.com/nathaneastwood/poorman) package for data manipulation.
# pliman 2.1.0
## 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 
* Arguments r, g, b, re, and nir now included in `analyze_objects()`, `analyze_objects_shp()`, and `image_view()`, allowing to correctly choose the image band.
* `image_segment_mask()` now has a `col_background` argument.
* Argument `width_at` included in `analyze_objects()`.

# pliman 2.0.1
## 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
## New functions
* `analyze_objects_iter()` to execute an interactive section of `analyze_objects()`.
* `measure_disease_byl()` to measure disease severity '`by` `l`eaf' in an image with several leaves.

* `object_split()` to split multiples objects of an image into a list of images.
* `pca()`, `plot.pca()`, `get_biplot()` as helper functions to perform Principal Component Analysis.
* `rownames_to_column()`, `column_to_rownames()`, `separate_col()`, `round_cols()` as helper functions to manipulate data.

* A set of `poly_*()` function to analyze polygons. All of them are based on a set of coordinate points describing the edge of the object(s). See ?`utils_polygon` for more details.

* `get_wd_here()` and `set_wd_here()` to deal with working directories.

* `apply_fun_to_imgs()` to apply a function (or functions) to a set of images stored in the working directory.

* `make_brush()`, `make_mask()`, and `image_segment_mask()` to create masks and segment images based on such a mask.

* `image_segment_manual()`, `image segment kmeans()`, and `image_segment_mask()` to perform image segmentation in different ways.

* A new family of `efourier_*()` functions to performs Elliptical Fourier Analysis.
   - `efourier()`:	Elliptical Fourier Analysis
   - `efourier_coefs()`:	Get Fourier coefficients
   - `efourier_error()`:	Erros between the original and reconstructed outline
   - `efourier_inv()`:	Inverse Elliptical Fourier Analysis
   - `efourier_norm()`:	Normalized Fourier coefficients
   - `efourier_power()`:	Power in Fourier Analysis
   - `efourier_shape()`:	Draw shapes based on Fourier coefficients
   
* A new family of `landmarks_*()` functions to handle landmarks
   - `landmarks()`: Create image landmarks
   - `landmarks_add()`:	Artificially inflates the number of landmarks
   - `landmarks_angle()`:	Angles between landmarks
   - `landmarks_dist()`:	Distances between landmarks
   - `landmarks_regradi()`:	Pseudolandmarks with equally spaced angles
   
* `object_edge()` to detect edges in images using Sobel-Feldman Operator.

* A new family of `*_shp()` functions to analyze shape files.
   - `image_shp()` to construct a shape file from an image.
   - `object_split_shp()` to splits image objects based on a shapefile.
   - `analyze_objects_shp()` to analyze objects using shapefiles.
   - `measure_disease_shp()` to measure disease using shapefiles.
   
* New `plot_index()` function to plot an image index using raster package, and optionaly using the mapview package to show the image index.

* New `image_view()` function to create an interactive map view of an image. This function allows users to interactively edit and analyze an image using [mapview](https://r-spatial.github.io/mapview/) and [mapedit](https://github.com/r-spatial/mapedit) packages.

* New `image_prepare_mv()` function to prepare an image to be analyzed for `analyze_objects_shp()`. This function aligns and crops the image using either base or mapview visualization.

## 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](https://r-spatial.github.io/mapview/) package is used, allowing the users to draw shapes like points and polygons with [mapedit](https://github.com/r-spatial/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](https://ieeexplore.ieee.org/document/4309314) 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
* `get_measures()` now remove known objects from the results when using the `id` argument.
* The right-hand of argument `measure` in `get_measures()` now accepts a numeric object stored in the global environment.
* `analyze_objects()` now returns the objects `object_index` and `object_rgb` when the argument `pattern` is used. Thanks to [João Paulo Oliveira Ribeiro](https://www.researchgate.net/profile/Joao-Paulo-Ribeiro) for alerting me regarding this issue.
* New argument `reference` in `analyze_objects()` to adjust measures using a reference object in the image.
* Argument `object_index` in `analyze_objects()` now recognizes the names of built-in indexes (see ?`pliman_indexes()`).
* `plot.image_index()` not limits the number of pixels to reduce plotting time.
* `show_image` argument changed with `plot` to standardize the argument across functions.
* `rgb_to_hsb()` optimized using `C++`.
* Change `rows` and `cols` with `nrow` and `ncol`, respectively, in functions `analyze_objects_shp()`, `image_shp()`, `measure_disease_shp()`, and `object_split_shp()`, to standardize the arguments across functions.




# pliman 1.1.0
## 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](https://github.com/nathaneastwood/poorman/blob/master/R/pipe.R) 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](https://pkgdown.r-lib.org/news/index.html#bootstrap-2-0-0) in the package site.


# pliman 1.0.0
## New functions
* `analyze_objects()` is now used as the main function to compute the number and shape of objects.
* `measure_disease()` is now used as the main function to perform phytopatometry studies. The function can compute symptomatic area, as well as the number and shape of lesions.
* `image_segment_iter()` is used to performs iterative image segmentation.
* `conv_hull()`, `poly_area()`, `poly_mass()`, `poly_spline()`, `plot_contour()`, and `plot_ellipse()` as utilities for analyzing polygons.
* `dpi()` to compute the resolution (dots per inch) of an image.
* `tune_tolerance()` for tunning the `tolerance` parameter.

## 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
## 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
* 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.
