NEWS.md

In rcaiman: CAnopy IMage ANalysis

rcaiman 1.2.0

Breaking changes

• ootb_mblt() was updated and results from this version will be different to those from previous version.

New features

• New calc_co() provides canopy openness calculation for hemispherical images.
• New correct_vignetting() to correct the vignetting effect and doing so standardize radiometry.
• New crop_caim() allows cropping after reading, complementing read_caim().
• New crosscalibrate_lens() allows geometrical cross-calibration.
• New extract_radiometry() helps to built a function to correct the vignetting effect with correct_vignetting().
• New extract_sky_points_simple() to obtain sky points without the need of a working binarized image.
• fisheye_to_equidistant() is now able to interpolate. It gains the m argument.

Minor improvements and fixes

• calc_zenith_colrow() is former calc_zenith_raster_coord().
• calibrate_lens gains a more extensive output.
• extract_rl() default values were changed.
• Fix extrac_sky_points(). Now, dist_to_plan works as intended.
• find_sky_pixels_nonnull() gains intercept and w.
• fit_cie_sky_model() output was simplified, it does not return a raster anymore. It has to be calculated from the model with cie_sky_model_raster().
• interpolate_sky_points() changes g for r. This acknowledge a change made in the code but not reflected in the arguments or documentation. The change was to approximate the function as much as possible to the Lang et al. (2010) method in which this function was based.
• Fix an issue in extract_sky_points() due to a change on the behavior of large data.frame naming.
• ootb_obia() gains w_red.
• ootb_sky_reconstruction() was updated.
• row_col_from_zenith_azimuth() and zenith_azimuth_from_row_col() now uses different arguments because they were reprogrammed to overcome limitations in azimuth angle computations and unintentional side effects.
• thr_mblt() is former thr_image().

rcaiman 1.1.1

New features

• ootb_obia() gains gamma

Minor improvements and fixes

• ootb_mblt() now can detect when find_sky_pixels() fails to deliver a good mask, and switch to find a mask by applying a global threshold calculated with IsoData.This last method will works well since the failure of find_sky_pixels() is associated with extremely open forest, in which circumstances it will not produce comission errors.

rcaiman 1.0.7

Breaking changes

• Now rcaiman depends on terra package instead of raster since key dependencies of the latter package are on the course of losing maintenance by 2023 (https://r-spatial.org/book/sp-raster.html). This implied changes in the whole code. Although maximum efforts were made to maintain the behavior of functions, it may happen that scripts running well with version 0.1.1 fails with this new version.
• A major bug on local_fuzzy_thresholding() was fixed. This affected the main function enhance_caim() since it internally uses local_fuzzy_thresholding(). If possible, results from scripts using local_fuzzy_thresholding() or enhace_caim() should be recalculated with this new version.

New features

• New HSP functions family enables a dynamic workflow between R and the HSP software package ().
• azimuth_image() gains rotation, which allows processing images with the top oriented to any known azimuth angle. Previously, by default it assumed that the top was oriented to the north.
• New chessboard() provides chessboard segmentation.
• New cie_sky_model_raster() produces CIE sky images of any resolution from custom parameterized CIE sky models. The CIE sky model implementation is based on Pascal code by Mait Lang.
• New colorfulness() provides a method to quantify image colorfulness.
• New deffuzify() is an alternative to apply_thr() for turning fuzzy classification into Boolean.
• New extract_dn() facilitates the extraction of digital numbers from canopy photographs. The extraction is based on raster coordinates obtained automatically with extract_sky_points() or manually with third-party software.
• New extract_rl() facilitates the extraction of relative luminance from hemispherical photographs. This function uses objects from extract_sky_points() and returns objects essential to fit_cie_sky_model().
• New extract_sky_points() to automatically extract sky points from canopy photographs.
• New extract_sun_coord() to automatically extract sun coordinates from canopy photographs. Objects returned by this function are essential to fit_cie_sky_model().
• New find_sky_pixels_nonnull_criteria() offers a method for fine-tuning working binarized images, which are the input of many functions, such as extract_sky_points() and extract_sun_coord(). The method is based on the assumption that the threshold can be tuned as long as no new cells with zero gaps are obtained (the so-called null cells).
• New fisheye_to_pano() provides a method to reproject from hemispherical to cylindrical.
• New fit_cie_sky_model() uses maximum likelihood to estimate the coefficients of the CIE sky model that best fit to data sampled from a canopy photograph. Then, those coefficients can be used to produce and image with cie_sky_model_raster().
• fit_coneshaped_model() now works with the point-like data objects returned by extract_rl() and returns a function that can easily produce a raster when SpatRaster objects are provided as arguments. As a result, the function is faster and more versatile.

R r <- read_caim() z <- zenith_image(ncol(r), lens("Nikon_FCE9")) a <- azimuth_image(z) g <- sky_grid_segmentation(z, a, 10) bin <- find_sky_pixels(r, z, a) sky_points <- extract_sky_points(r, bin, g) sky_points <- extract_rl(r, z, a, sky_points, NULL) model <- fit_coneshaped_model(sky_points$sky_points) model$fun(60, 10) model$fun(z, a) New interpolate_sky_points() provides a method to produce raster images from point-like data, such as the objects returned by extract_dn() or extract_rl(). New Mask_sunlit_canopy() is a wrapper function around membership_to_color() that facilitates masking sunlit canopy. New obia() is a revised version of the object-based image analysis presented in . New ootb_obia() is a revised version of the full workflow presented in , which includes enhance_caim() and obia(). New ootb_sky_reconstruction() provides an easy to use function that will build an above canopy image from a single below canopy image, by means of fit_cie_sky_model() and interpolate_sky_points(). New polar_qtree() provides quad-tree segmentation in the polar space. New qtree() provides classical quad-tree segmentation New thr_isodata() is an alternative implementation of the IsoData method from the autothresholdr package.

Minor improvements and fixes

• Examples of restricted view photography were added, broadening the scope of the package since most new users search for code templates on the examples in order to get started.
• Now apply_thr() turns NA values from r to 0. This allows to quickly produce binarized images without NA values.
• calc_zenith_raster_coord() is former calc_zenith_raster_coordinates().
• enhance_caim() gains thr and fuzziness, and default values for all arguments except caim. This makes the functions easier for new users and more flexible for advanced users.
• expand_noncircular() now produces the expected output when zenith_colrow is far from the image center, not only when it is close to it.
• extract_feature() gains ignore_label_0 since it cannot handle NA values as expected after changing dependency from raster to terra.
• find_sky_pixels() now uses sample size percentage.
• fisheye_to_equidistant() is former reproject_to_equidistant(). Now the resolution of the output is 1, and the extension is derived from radius. Previously, and incorrectly, the resolution was different from 1 since while the dimension was computed from radius, as it should, the extension was taken from z.
• fix_reconstructed_sky() is former fix_predicted_sky().
• normalize() gains force_range and defaults values for mn and mx.
• ootb_mblt() now uses find_sky_pixels_nonnull_criteria() and gains two arguments, bin and fix_sky_cs, which allows quick customization.
• read_caim() now is allowed to read any raster image that terra::raster() can read. Of course, the georeferencing is turned off by assigning a local projection and manipulating extension and resolution, as usual.

R f <- system.file("ex/elev.tif", package="terra") read_caim(f) terra::rast(f) In regional_thresholding(), method gains the thr_isodata method. As a consequence of changing dependency from raster to terra, rings_segmentation(), sectors_segmentation(), and sky_grid_segmentation() return 0 outside the circular image instead of NA.

rcaiman documentation built on Nov. 15, 2023, 1:08 a.m.