Merge pull request #1132 from M3nin0/hotfix/args-merge

hotfix: fix sits_regularize and sits_merge

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sits
 Type: Package
-Version: 1.5.1
+Version: 1.5.0-1
 Title: Satellite Image Time Series Analysis for Earth Observation Data Cubes
 Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = '[email protected]'),
  person('Gilberto', 'Camara', role = c('aut', 'cre'), email = '[email protected]'),
@@ -17,7 +17,7 @@ Description: An end-to-end toolkit for land use and land cover classification
  applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>.
  Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, 
  Brazil Data Cube, and Digital Earth Africa using the Spatio-temporal Asset Catalog (STAC) 
- protocol (<https://stacspec.org/> and the 'gdalcubes' R package 
+ protocol (<https://stacspec.org/>) and the 'gdalcubes' R package 
  developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>.
  Supports visualization methods for images and time series and 
  smoothing filters for dealing with noisy time series.

NAMESPACE

@@ -337,9 +337,6 @@ S3method(sits_cube,default)
 S3method(sits_cube,local_cube)
 S3method(sits_cube,sar_cube)
 S3method(sits_cube,stac_cube)
-S3method(sits_detect_change,default)
-S3method(sits_detect_change,raster_cube)
-S3method(sits_detect_change,sits)
 S3method(sits_get_data,csv)
 S3method(sits_get_data,data.frame)
 S3method(sits_get_data,default)
@@ -443,9 +440,6 @@ export(sits_config)
 export(sits_config_show)
 export(sits_cube)
 export(sits_cube_copy)
-export(sits_detect_change)
-export(sits_detect_change_method)
-export(sits_dtw)
 export(sits_factory_function)
 export(sits_filter)
 export(sits_formula_linear)

NEWS.md

@@ -1,6 +1,16 @@
 # SITS Release History
 
 # What's new in SITS version 1.5
+
+### Hotfix version 1.5.0-1
+* Remove tapply from `.reg_cube_split_assets()` for R 4.X compatibility
+* Fix `sits_merge()` function that was not merging `SAR` and `OPTICAL` cubes
+* Rename n_input_pixels back to input_pixels for compatibility with models trained in old versions of the package
+* Fix torch usage in Apple M3 by turning off MPS technology
+* Fix date parameter usage in `sits_view()`
+* Improve `plot()` performance using raster overviews
+* Include support for PLANET Mosaic product
+
 ### New features in SITS version 1.5.0
 * Support for SENTINEL-1-RTC and SENTINEL-2-L2A in CDSE
 * Include support for DEA products SENTINEL-1-RTC, LS5-SR, LS7-SR, LS9-SR, ALOS-PALSAR-MOSAIC, NDVI ANOMALY, DAILY CHIRPS, MONTHLY CHIRPS and DEM-30

R/api_detect_changes.R

@@ -143,7 +143,7 @@
  # Fill with zeros remaining NA pixels
  values <- C_fill_na(values, 0)
  # Used to check values (below)
- n_input_pixels <- nrow(values)
+ input_pixels <- nrow(values)
  # Include names in cube predictors
  colnames(values) <- .pred_features_name(
  .ml_bands(cd_method), tile_timeline
@@ -163,7 +163,7 @@
  # Are the results consistent with the data input?
  .check_processed_values(
  values = values,
- n_input_pixels = n_input_pixels
+ input_pixels = input_pixels
  )
  # Log here
  .debug_log(

R/api_regularize.R

@@ -42,7 +42,7 @@
  breaks = timeline,
  labels = FALSE
  )
- fi_groups <- unname(tapply(fi, groups, list))
+ fi_groups <- unname(split(fi, groups))
  assets <- .common_size(
  .discard(tile, "file_info"),
  feature = timeline[unique(groups)],

R/sits_detect_change.R

@@ -38,7 +38,6 @@
 #' each point (tibble of class "sits")
 #' or a data cube indicating detections in each pixel
 #' (tibble of class "detections_cube").
-#' @export
 sits_detect_change <- function(data,
  cd_method,
  ...,
@@ -49,7 +48,6 @@ sits_detect_change <- function(data,
 }
 
 #' @rdname sits_detect_change
-#' @export
 sits_detect_change.sits <- function(data,
  cd_method,
  ...,
@@ -74,7 +72,6 @@ sits_detect_change.sits <- function(data,
 }
 
 #' @rdname sits_detect_change
-#' @export
 sits_detect_change.raster_cube <- function(data,
  cd_method, ...,
  roi = NULL,
@@ -180,7 +177,6 @@ sits_detect_change.raster_cube <- function(data,
 }
 
 #' @rdname sits_detect_change
-#' @export
 sits_detect_change.default <- function(data, cd_method, ...) {
  stop("Input should be a sits tibble or a data cube")
 }

R/sits_detect_change_method.R

@@ -12,8 +12,6 @@
 #' @return Change detection method prepared
 #' to be passed to
 #' \code{\link[sits]{sits_detect_change}}
-#' @export
-#'
 sits_detect_change_method <- function(samples, cd_method = sits_dtw()) {
  # set caller to show in errors
  .check_set_caller("sits_detect_change_method")

R/sits_dtw.R

@@ -19,8 +19,6 @@
 #' used in operations with data cubes.
 #' @return Change detection method prepared to be passed to
 #' \code{\link[sits]{sits_detect_change_method}}
-#' @export
-#'
 sits_dtw <-
  function(samples = NULL,
  ...,

R/sits_merge.R

@@ -132,10 +132,10 @@ sits_merge.raster_cube <- function(data1, data2, ...) {
  .data[["tile"]]
  )
 
- if (inherits(data2, "raster_cube")) {
- return(.merge_equal_cube(data1, data2))
- } else {
+ if (inherits(data2, "sar_cube")) {
  return(.merge_distinct_cube(data1, data2))
+ } else {
+ return(.merge_equal_cube(data1, data2))
  }
 }
 
@@ -152,8 +152,8 @@ sits_merge.raster_cube <- function(data1, data2, ...) {
 
 .merge_distinct_cube <- function(data1, data2) {
  # Get cubes timeline
- d1_tl <- unique(as.Date(unlist(.cube_timeline(data1))))
- d2_tl <- unique(as.Date(unlist(.cube_timeline(data2))))
+ d1_tl <- unique(as.Date(.cube_timeline(data1)[[1]]))
+ d2_tl <- unique(as.Date(.cube_timeline(data2)[[1]]))
 
  # get intervals
  d1_period <- as.numeric(

inst/extdata/sources/config_source_planet.yaml

@@ -0,0 +1,30 @@
+sources:
+ PLANET :
+ s3_class : ["planet_cube", "stac_cube", "eo_cube",
+ "raster_cube"]
+ collections :
+ MOSAIC :
+ bands :
+ B01 : &planet_mosaic_4m
+ missing_value : 0
+ minimum_value : 1
+ maximum_value : 65534
+ scale_factor : 0.01
+ offset_value : 0
+ resolution : 4.77
+ band_name : "blue"
+ data_type : "INT2U"
+ B02 : 
+ <<: *planet_mosaic_4m
+ band_name : "green"
+ B03 :
+ <<: *planet_mosaic_4m
+ band_name : "red"
+ B04 :
+ <<: *planet_mosaic_4m
+ band_name : "nir"
+ satellite : "PLANETSCOPE"
+ sensor : "MOSAIC"
+ collection_name: "planet-mosaic"
+ ext_tolerance: 0
+ grid_system : ""