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fix documentation of zarr-array
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@dblodgett-usgs
dblodgett-usgs committed Jul 1, 2024
1 parent 1cde108 commit 00d1382
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Showing 2 changed files with 53 additions and 118 deletions.
60 changes: 30 additions & 30 deletions R/zarr-array.R
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
#' oindex TODO
#' @keywords internal
oindex = NULL,
#' @description
#' method_description
#' (Re)load metadata from store without synchronization (file locking).
load_metadata_nosync = function() {

Expand Down Expand Up @@ -135,27 +135,27 @@ ZarrArray <- R6::R6Class("ZarrArray",
}
private$dtype <- normalize_dtype(meta$dtype, object_codec = object_codec)
},
#' @description
#' method_description
#' Load or reload metadata from store.
load_metadata = function() {
private$load_metadata_nosync()
# TODO: support for synchronization
},
#' @description
#' method_description
#' Referesh metadata if not cached without synchronization (file locking).
refresh_metadata_nosync = function() {
if(!private$cache_metadata && !private$is_view) {
private$load_metadata_nosync()
}
},
#' @description
#' method_description
#' Refresh metadata from store if not cached.
refresh_metadata = function() {
if(!private$cache_metadata) {
private$load_metadata()
}
},
#' @description
#' method_description
#' Write metadata to store without synchronization (file locking).
flush_metadata_nosync = function() {
if(private$is_view) {
Expand Down Expand Up @@ -188,13 +188,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
encoded_meta <- private$store$metadata_class$encode_array_metadata(zarray_meta)
private$store$set_item(mkey, encoded_meta)
},
#' @description
#' method_description
#' TODO
chunk_key = function(chunk_coords) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L2063
return(paste0(private$key_prefix, do.call(paste, c(as.list(chunk_coords), sep = private$dimension_separator))))
},
#' @description
#' method_description
#' TODO
compute_cdata_shape = function() {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L428
Expand All @@ -212,7 +212,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
cdata_shape <- as.numeric(cdata_shape)
return(cdata_shape)
},
#' @description
#' method_description
#' Resize an array without synchronization (file locking)
resize_nosync = function(...) {
# Note: When resizing an array, the data are not rearranged in any way.
Expand Down Expand Up @@ -252,7 +252,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
}
}
},
#' @description
#' method_description
#' TODO
get_basic_selection_zd = function(selection = NA, out = NA, fields = NA) {
# Special case basic selection for zero-dimensional array
Expand Down Expand Up @@ -296,13 +296,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
}
return(out)
},
#' @description
#' method_description
#' TODO
get_basic_selection_nd = function(selection = NA, out = NA, fields = NA) {
indexer <- BasicIndexer$new(selection, self)
return(private$get_selection(indexer, out = out, fields = fields))
},
#' @description
#' method_description
#' TODO
get_selection = function(indexer, out = NA, fields = NA) {
# Reference: https://github.com/gzuidhof/zarr.js/blob/292804/src/core/index.ts#L304
Expand Down Expand Up @@ -359,7 +359,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
return(out)

},
#' @description
#' method_description
#' TODO
set_basic_selection_zd = function(selection, value, fields = NA) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/core.py#L1625
Expand Down Expand Up @@ -422,13 +422,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
c_data <- private$encode_chunk(chunk_raw)
self$get_chunk_store()$set_item(c_key, c_data)
},
#' @description
#' method_description
#' TODO
set_basic_selection_nd = function(selection, value, fields = NA) {
indexer <- BasicIndexer$new(selection, self)
return(private$set_selection(indexer, value = value, fields = fields))
},
#' @description
#' method_description
#' TODO
set_selection = function(indexer, value, fields = NA) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L1682
Expand Down Expand Up @@ -491,13 +491,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
return()
}
},
#' @description
#' method_description
#' TODO
process_chunk = function(out, cdata, chunk_selection, drop_axes, out_is_ndarray, fields, out_selection, partial_read_decode = FALSE) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L1755
# TODO
},
#' @description
#' method_description
#' TODO
get_chunk_value = function(proj, indexer, value, selection_shape) {
# Reference: https://github.com/gzuidhof/zarr.js/blob/15e3a3f00eb19f0133018fb65f002311ea53bb7c/src/core/index.ts#L550
Expand All @@ -517,12 +517,12 @@ ZarrArray <- R6::R6Class("ZarrArray",
}
return(chunk_value)
},
#' @description
#' method_description
#' TODO
chunk_buffer_to_raw_array = function(decoded_chunk) {
# TODO
},
#' @description
#' method_description
#' For parallel usage
chunk_getitem_part1 = function(chunk_coords, chunk_selection, out, out_selection, drop_axes = NA, fields = NA) {
if(length(chunk_coords) != length(private$chunks)) {
Expand All @@ -543,7 +543,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
})
return(result)
},
#' @description
#' method_description
#' For parallel usage
chunk_getitem_part2 = function(part1_result, chunk_coords, chunk_selection, out, out_selection, drop_axes = NA, fields = NA) {
c_key <- private$chunk_key(chunk_coords)
Expand Down Expand Up @@ -586,7 +586,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
}
}
},
#' @description
#' method_description
#' For non-parallel usage
chunk_getitem = function(chunk_coords, chunk_selection, out, out_selection, drop_axes = NA, fields = NA) {
# TODO
Expand Down Expand Up @@ -634,12 +634,12 @@ ZarrArray <- R6::R6Class("ZarrArray",
}
})
},
#' @description
#' method_description
#' TODO
chunk_getitems = function(lchunk_coords, lchunk_selection, out, lout_selection, drop_axes = NA, fields = NA) {
# TODO
},
#' @description
#' method_description
#' TODO
chunk_setitem = function(chunk_coords, chunk_selection, value, fields = NA) {
# Reference: https://github.com/gzuidhof/zarr.js/blob/15e3a3f00eb19f0133018fb65f002311ea53bb7c/src/core/index.ts#L625
Expand Down Expand Up @@ -717,30 +717,30 @@ ZarrArray <- R6::R6Class("ZarrArray",
chunk_data <- private$encode_chunk(chunk_raw)
self$get_chunk_store()$set_item(chunk_key, chunk_data)
},
#' @description
#' method_description
#' TODO
chunk_setitem_nosync = function(chunk_coords, chunk_selection, value, fields = NA) {
# TODO
},
#' @description
#' method_description
#' TODO
chunk_setitems = function(lchunk_coords, lchunk_selection, values, fields = NA) {
# TODO
},
#' @description
#' method_description
#' TODO
process_for_setitem = function(ckey, chunk_selection, value, fields = NA) {
# TODO
},
chunk_delitem = function(ckey) {
# TODO
},
#' @description
#' method_description
#' TODO
chunk_delitems = function(ckeys) {
# TODO
},
#' @description
#' method_description
#' TODO
decode_chunk = function(cdata, start = NA, nitems = NA, expected_shape = NA) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/core.py#L2066
Expand Down Expand Up @@ -782,7 +782,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
# ensure correct chunk shape
return(chunk)
},
#' @description
#' method_description
#' TODO
encode_chunk = function(chunk_as_raw) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/core.py#L2105
Expand Down Expand Up @@ -813,7 +813,7 @@ ZarrArray <- R6::R6Class("ZarrArray",

return(cdata)
},
#' @description
#' method_description
#' TODO
append_nosync = function(data, axis = 0) {
# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L2141
Expand All @@ -822,7 +822,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
),
public = list(
#' @description
#' Create a new Array instance.
#' Create a new ZarrArray instance.
#' @param store Array store already initialized.
#' @param path character path
#' @param read_only logical read only?
Expand Down
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