Merge pull request #1432 from e-sensing/dev

Pre-release 1.5.4

Author: gilbertocamara

CRAN-SUBMISSION

@@ -1,6 +1,6 @@
 Package: sits
 Type: Package
-Version: 1.5.3-1
+Version: 1.5.4
 Title: Satellite Image Time Series Analysis for Earth Observation Data Cubes
 Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = 'rolfsimoes@gmail.com'),
              person('Gilberto', 'Camara', role = c('aut', 'cre', 'ths'), email = 'gilberto.camara.inpe@gmail.com'),
@@ -65,7 +65,7 @@ Imports:
     tibble (>= 3.3.0),
     tidyr (>= 1.3.0),
     tmap (>= 4.1),
-    torch (>= 0.15.0),
+    torch (>= 0.16.3),
     units,
     utils
 Suggests:
@@ -76,7 +76,6 @@ Suggests:
     covr,
     dendextend,
     dtwclust,
-    DiagrammeR,
     digest,
     e1071,
     exactextractr,
@@ -97,6 +96,7 @@ Suggests:
     RColorBrewer,
     RcppArmadillo (>= 14.0.0),
     scales,
+    snic,
     spdep,
     stars,
     stringr,
@@ -110,7 +110,7 @@ Config/testthat/start-first: cube, raster, regularize, data, ml
 LinkingTo:
     Rcpp,
     RcppArmadillo
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate: 
     'api_accessors.R'
     'api_accuracy.R'

DESCRIPTION

@@ -7,8 +7,10 @@ S3method("sits_bands<-",default)
 S3method("sits_bands<-",raster_cube)
 S3method("sits_bands<-",sits)
 S3method("sits_labels<-",class_cube)
+S3method("sits_labels<-",class_vector_cube)
 S3method("sits_labels<-",default)
 S3method("sits_labels<-",probs_cube)
+S3method("sits_labels<-",probs_vector_cube)
 S3method("sits_labels<-",sits)
 S3method(.accuracy_get_validation,csv)
 S3method(.accuracy_get_validation,data.frame)
@@ -21,6 +23,9 @@ S3method(.check_samples,default)
 S3method(.check_samples,sits)
 S3method(.cube_adjust_crs,default)
 S3method(.cube_adjust_crs,grd_cube)
+S3method(.cube_area_freq,class_cube)
+S3method(.cube_area_freq,class_vector_cube)
+S3method(.cube_area_freq,default)
 S3method(.cube_as_sf,default)
 S3method(.cube_as_sf,raster_cube)
 S3method(.cube_bands,default)
@@ -294,6 +299,7 @@ S3method(.tile_paths,default)
 S3method(.tile_paths,raster_cube)
 S3method(.tile_period,default)
 S3method(.tile_period,raster_cube)
+S3method(.tile_read_block,class_cube)
 S3method(.tile_read_block,default)
 S3method(.tile_read_block,derived_cube)
 S3method(.tile_read_block,eo_cube)
@@ -340,6 +346,7 @@ S3method(plot,sar_cube)
 S3method(plot,sits)
 S3method(plot,sits_accuracy)
 S3method(plot,sits_cluster)
+S3method(plot,sits_model)
 S3method(plot,som_clean_samples)
 S3method(plot,som_evaluate_cluster)
 S3method(plot,som_map)
@@ -390,6 +397,8 @@ S3method(sits_clean,class_cube)
 S3method(sits_clean,default)
 S3method(sits_clean,derived_cube)
 S3method(sits_clean,raster_cube)
+S3method(sits_colors_qgis,class_cube)
+S3method(sits_colors_qgis,class_vector_cube)
 S3method(sits_combine_predictions,average)
 S3method(sits_combine_predictions,default)
 S3method(sits_combine_predictions,uncertainty)
@@ -503,6 +512,9 @@ S3method(summary,variance_cube)
 export("sits_bands<-")
 export("sits_labels<-")
 export(impute_linear)
+export(impute_mean)
+export(impute_mean_window)
+export(impute_median)
 export(sits_accuracy)
 export(sits_accuracy_summary)
 export(sits_add_base_cube)
@@ -575,6 +587,7 @@ export(sits_sgolay)
 export(sits_show_prediction)
 export(sits_slic)
 export(sits_smooth)
+export(sits_snic)
 export(sits_som_clean_samples)
 export(sits_som_evaluate_cluster)
 export(sits_som_map)

NAMESPACE

@@ -1,6 +1,23 @@
 # SITS Release History
 
-# What's new in SITS version 1.5.3
+# What's new in SITS version 1.5
+
+### New features in SITS version 1.5.4
+* Fix bug in `sits_summary()` in obtaining the variance summary with multiple tiles
+* Add new plot type in `sits_accuracy()` function (`"confusion_matrix"`)
+* Add new `type` parameter in `sits_accuracy()` function for selecting plot type
+* Improve `plot.som_evaluate_cluster` function to include a `legend` parameter
+* Add new `sits_snic` segmentation function based on the [snic](https://cran.r-project.org/package=snic) package
+* Add `pkgdown` [documentation website](https://e-sensing.github.io/sits/) for the `sits` package
+* Add new imputation functions: `impute_mean()`, `impute_median()`, and `impute_mean_window()`
+* Improve validation messages in the `sits_accuracy()` function
+* Add `sits_labels<-` support for `probs_vector_cube` and `probs_class_cube`
+* Extend the `sits_colors_qgis()` function to export `sits` color palettes to QGIS for vector cubes
+* Fix area calculations in `sits_summary()`
+* Add `res` parameter to the `sits_mosaic()` function to allow generating mosaics at different resolutions
+
+### Hotfix version 1.5.3-1
+* Replace `arma::is_finite` with `std::isfinite`
 
 ### Hotfix version 1.5.3-1
 * Improve documentation for `sits_labels`
@@ -32,8 +49,7 @@
 * Include label parameter on `sits_select()`
 * General bug fixes
 
-# What's new in SITS version 1.5.2 
-
+### New features in SITS version 1.5.2
 * Include `exclusion_mask` parameter in `sits_classify()` and `sits_smooth()`
 * Support classification data cubes with NA values
 * Support for multiple tiling system in `sits_regularize()`, including MGRS and Brazil Data Cube grids
@@ -51,8 +67,7 @@
 * Support for interactive visualization with SOM samples
 * General bug fixes
 
-# What's new in SITS version 1.5.1
-
+### New features in SITS version 1.5.1
 * Support for ESA World Cover map
 * Support for Digital Earth Australia products
 * Support for Digital Earth Africa geomedian products
@@ -120,7 +135,6 @@
 * Corrected errors in labelling of classified cubes
 * Created a factory of functions for segmentation
 
-
 ### New features in SITS version 1.4.0
 * New function for image segmentation based on `supercells` package
 * New version of `sits_get_data()` to extract average values of time series based on segments
@@ -144,7 +158,7 @@
 * Organize and clean internal APIs 
 * General bug fixes 
 
-# What's new in SITS version 1.2.0
+# What's new in SITS version 1.2
 
 ### Hotfix version 1.2.0-4
 * Fix `.raster_file_blocksize.terra()` bug (issue #918)
@@ -172,7 +186,7 @@
 *  Support for operations on CLOUD band in `sits_apply()`
 *  Bug fixes and internal re-engineering for better code maintenance
 
-# What's new in SITS version 1.1.0
+# What's new in SITS version 1.1
 
 ### Hotfix version 1.1.0-8
 * Fix support to BDC cubes in `sits_regularize()` (issue #848)
@@ -212,14 +226,14 @@
 * Change Microsoft Planetary Computer source name to `"MPC"`
 * Fix several bugs and improve performance
 
-# What's new in SITS version 1.0.0
-* Available on CRAN.
+# What's new in SITS version 1.0
 
 ### New features in SITS version 1.0.0
+* Available on CRAN.
 * Hotfix to improve `sits_whittaker()` function to process cube.
 * Update documentation to match CRAN standards
 
-# What's new in SITS version  0.17.0
+# What's new in SITS version 0.17
 
 ### New features in SITS version 0.17.0
 * Introduced new classifier model `sits_lighttae()`
@@ -245,7 +259,7 @@ confidence
 * Improve several internal functions performances
 * Fix several bugs
 
-# What's new in SITS version 0.16.3
+# What's new in SITS version 0.16
 
 ### New features in SITS version 0.16.3
 * reimplemented all deep learning functions using `torch` package and remove `keras` dependence
@@ -259,16 +273,12 @@ confidence
 * Update `plot()` parameters on raster cubes
 * Support multi-tile for classified cube in `sits_view()`
 
-# What's new in SITS version 0.16.2
-
 ### New features in SITS version 0.16.2
 * Improve `sits_get_data()` to accept tibbles
 * Remove multiples progress bar from `sits_cube()`
 * Improve `sits_regularize()` to process in parallel by tiles, bands, and dates
 * Improve `sits_regularize()` to check malformed files
 
-# What's new in SITS version 0.16.1
-
 ### New features in SITS version 0.16.1
 * Update `AWS_NO_SIGN_REQUEST` environment variable
 * Solved bug in `.gc_get_valid_interval()` function.
@@ -277,8 +287,6 @@ confidence
 * `sits_cube` function for `local cubes` has a new parameter called `multicores`.
 * Print `F1 score` in `sits_kfold_validate` with more than 2 labels.
 
-# What's new in SITS version 0.16.0
-
 ### New features in SITS version 0.16.0-1
 * hotfix `sits_cube()` function to tolerate malformed paths from STAC service;
 
@@ -290,8 +298,7 @@ confidence
 * Improve `sits_regularize()` by taking least cloud cover by default method to compose images
 * Bug fixes;
 
-
-# What's new in SITS version 0.15.1
+# What's new in SITS version 0.15
 
 ### New features in SITS version 0.15.1-1
 * Fix bug in `sits_regularize` that generated images with artifacts
@@ -319,8 +326,6 @@ confidence
 * `sits_regularize()` is producing *Float64* images as output
 * Full support for Microsoft Planetary Computing
 
-# What's new in SITS version 0.15.0 
-
 ### New features in SITS version 0.15.0-4
 * Change `gdalcubes_chunk_size` in "config.yml" to improve `sits_regularize()`.
 
@@ -365,7 +370,7 @@ confidence
 * Remove `S2_10-1` BDC collection from config
 * Other bug fixes
 
-# What's new in SITS version 0.14.1
+# What's new in SITS version 0.14
 
 ### New features in SITS version 0.14.1-1
 
@@ -387,9 +392,6 @@ confidence
 * Fix partial merge configuration file
 * Change bbox to roi in sits
 
-
-# What's new in SITS version 0.14.0
-
 ### New features in SITS version 0.14.0-2
 
 * fix `sits_bbox()` function 
@@ -411,7 +413,7 @@ confidence
 * Add parameters `origin` and `collection` to `sits_cube.local_cube()` function
 * Fix LOCAL source examples and tests
 
-# What's new in SITS version 0.13.1
+# What's new in SITS version 0.13
 
 ### New features in SITS version 0.13.1
 
@@ -421,28 +423,20 @@ confidence
 * fix deprecated warnings in keras package 
 * bug fixes 
 
-# What's new in SITS version 0.13.0-3
-
 ### New features in SITS version 0.13.0-3
 
 * Update documentation in Machine Learning methods
 * Hotfix bug in neuron labelling
 
-# What's new in SITS version 0.13.0-2
-
 ### New features in SITS version 0.13.0-2
 
 * Bug fixes in BDC MODIS cube
 
-# What's new in SITS version 0.13.0-1
-
 ### New features in SITS version 0.13.0-1
 
 * Bug fixes in check STAC bands
 * Change Landsat-8 (LC8_30-1) product metadata for BDC source
 
-# What's new in SITS version 0.13
-
 ### New features in SITS version 0.13.0
 
 * Create API for source cube

NEWS.md

@@ -65,6 +65,46 @@ C_glcm_correlation <- function(x, angles, nrows, ncols, n_grey, window_size) {
     .Call(`_sits_C_glcm_correlation`, x, angles, nrows, ncols, n_grey, window_size)
 }
 
+C_interp_mean_window_vec <- function(data, k, weighting) {
+    .Call(`_sits_C_interp_mean_window_vec`, data, k, weighting)
+}
+
+C_interp_mean_window_mat <- function(data, k, weighting) {
+    .Call(`_sits_C_interp_mean_window_mat`, data, k, weighting)
+}
+
+linear_interp <- function(mtx) {
+    .Call(`_sits_linear_interp`, mtx)
+}
+
+linear_interp_vec <- function(vec) {
+    .Call(`_sits_linear_interp_vec`, vec)
+}
+
+C_mask_na <- function(x) {
+    .Call(`_sits_C_mask_na`, x)
+}
+
+C_fill_na <- function(x, fill) {
+    .Call(`_sits_C_fill_na`, x, fill)
+}
+
+C_interp_mean_vec <- function(data) {
+    .Call(`_sits_C_interp_mean_vec`, data)
+}
+
+C_interp_mean_mat <- function(data) {
+    .Call(`_sits_C_interp_mean_mat`, data)
+}
+
+C_interp_median_vec <- function(data) {
+    .Call(`_sits_C_interp_median_vec`, data)
+}
+
+C_interp_median_mat <- function(data) {
+    .Call(`_sits_C_interp_median_mat`, data)
+}
+
 C_kernel_median <- function(x, ncols, nrows, band, window_size) {
     .Call(`_sits_C_kernel_median`, x, ncols, nrows, band, window_size)
 }
@@ -125,22 +165,6 @@ C_label_max_prob <- function(x) {
     .Call(`_sits_C_label_max_prob`, x)
 }
 
-linear_interp <- function(mtx) {
-    .Call(`_sits_linear_interp`, mtx)
-}
-
-linear_interp_vec <- function(vec) {
-    .Call(`_sits_linear_interp_vec`, vec)
-}
-
-C_mask_na <- function(x) {
-    .Call(`_sits_C_mask_na`, x)
-}
-
-C_fill_na <- function(x, fill) {
-    .Call(`_sits_C_fill_na`, x, fill)
-}
-
 batch_calc <- function(n_pixels, max_lines_per_batch) {
     .Call(`_sits_batch_calc`, n_pixels, max_lines_per_batch)
 }