geozarr_array: GeoZarr Array
In geozarr: GeoZarr Conventions for Geospatial Data in Zarr Stores
geozarr_array R Documentation
GeoZarr Array
Description
This class implements a GeoZarr array. A GeoZarr array is like a
regular Zarr array but it has attributes and/or associated Zarr arrays that
provide a coordinate system for the array.
Super classes
zarr::zarr_object -> zarr::zarr_node -> zarr::zarr_array -> geozarr_array
Active bindings
coordinate_system(read-only) Retrieve the coordinate system of
this array.
Methods
Public methods
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Inherited methods
zarr::zarr_object$print_attributes()zarr::zarr_node$absolute_path()zarr::zarr_node$append_array_attribute()zarr::zarr_node$attribute()zarr::zarr_node$delete_attribute()zarr::zarr_node$relative_path()zarr::zarr_node$save()zarr::zarr_node$set_attribute()zarr::zarr_node$walk_path()zarr::zarr_array$flush()zarr::zarr_array$hierarchy_nodes()zarr::zarr_array$print()zarr::zarr_array$promote()zarr::zarr_array$read()zarr::zarr_array$resize()zarr::zarr_array$write()
geozarr_array$new()
Initialize a new GeoZarr array.
Usage
geozarr_array$new(name, metadata, parent, store, coord_sys)
Arguments
nameThe name of the GeoZarr array.
metadataList with the metadata of the array.
parentThe parent zarr_group instance of this new array, can be
missing or NULL if the Zarr object should have just this array.
storeThe zarr_store instance to persist data in.
coord_sysOptional, an instance of CoordinateSystem providing
the coordinate system of the array. If not provided, the coordinate
system is constructed from the metadata of the array persisted in the
store.
Returns
An instance of geozarr_array.
geozarr_array$post_open()
Perform any processing after the Zarr hierarchy is in place
and out-of-group references can be resolved.
Usage
geozarr_array$post_open()
Returns
Self, invisibly.
geozarr_array$build_coordsys()
Build the coordinate system of the GeoZarr array if it has
not been set yet. This should only be called when the Zarr hierarchy is
in place and out-of-group references can be resolved, particularly for
the cs convention.
Usage
geozarr_array$build_coordsys()
Returns
Self, invisibly.
geozarr_array$subset()
This method extracts a subset of values from the GeoZarr
array, with the range along each axis to extract expressed in
coordinate values of the domain of each axis.
Usage
geozarr_array$subset(
...,
.name = NULL,
.location = NULL,
.rightmost.closed = FALSE
)
Arguments
...One or more arguments of the form axis = range. The "axis"
part should be the name of an axis or its abbreviation X, Y, Z or
T. The "range" part is a vector of values representing coordinates
along the axis where to extract data. Axis abbreviations and names are
case-sensitive and can be specified in any order. If values for the
range per axis fall outside of the extent of the axis, the range is
clipped to the extent of the axis.
.nameThe name of the GeoZarr array to be created. If omitted, an
array will be created at the root of a new in-memory Zarr store.
.locationOptional. If supplied, either an existing zarr_group
in a zarr object, or a character string giving the location on a
local file system where to persist the data. If the argument is a
zarr_group, argument .name must be provided. If the argument gives
the location for a new Zarr store then the location must be writable by
the calling code. As per the Zarr specification, it is recommended to
use a location that ends in ".zarr" when providing a location for a new
store. If argument .name is given then the geozarr_array will be
created in the root of the zarr store with that name. If the .name
argument is not given, a single-array Zarr store will be created. If
the location argument is not given, a zarr object is created in
memory.
.rightmost.closedOptional. Single logical value to indicate if
the upper boundary of range in each axis should be included.
Details
The range of values along each axis to be subset is expressed in
coordinates of the domain of the axis. Any axes for which no selection
is made in the ... argument are extracted in whole. Coordinates can
be specified in a variety of ways that are specific to the nature of
the axis. For numeric axes it should (resolve to) be a vector of real
values from which the range is computed. For time axes a vector of
character timestamps, POSIXct or Date values must be specified. As
with numeric values, only the two extreme values in the vector will be
used. For character axes the order in the axis will be used, with the
first and last value in the supplied range.
If the range of coordinate values for an axis in argument ... extends
the valid range of the axis, the extracted data will start at the
beginning for smaller values and extend to the end for larger values.
If the values envelope the valid range the entire axis will be
extracted in the result. If the range of coordinate values for any axis
are all either smaller or larger than the valid range of the axis then
nothing is extracted and NULL is returned.
The extracted data has the same dimensional structure as the data in
the array, with degenerate dimensions preserved. The order of the axes
in argument ... does not reorder the axes in the result.
Arguments following ... must be explicitly named, like
.rightmost.closed = TRUE, to avoid the argument being treated as an
axis name.
As an example, to extract values of a variable for Australia for the
year 2020, where the first axis in GeoZarr array x is the longitude,
the second axis is the latitude, both in degrees, and the third (and
final) axis is time, the values are extracted by x$subset(X = c(112, 154), Y = c(-9, -44), T = c("2020-01-01", "2021-01-01")). Note that
this works equally well for projected coordinate reference systems -
the key is that the specification in argument ... uses the same
domain of values as the respective axes in x use.
Returns
If the .location argument is a zarr_group, the new Zarr
geozarr_array is returned, with a subset of data from this GeoZarr
array, having the axes and attributes of this GeoZarr array. Otherwise,
the zarr object that is newly created and which contains the
geozarr_array instance, or an error if the zarr object could not be
created. If one or more of the selectors in the ... argument fall
entirely outside of the range of the axis NULL is returned.
geozarr_array$write_external_coordinates()
Write any external coordinates of this array to the
underlying Zarr store. The metadata of this array is scanned for ref
objects in the cs convention attributes. The values of the external
coordinates are taken from the CoordinateSystem instance of this
array.
Usage
geozarr_array$write_external_coordinates()
Returns
Self, invisibly.
geozarr documentation built on Sept. 16, 2026, 1:07 a.m.
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| geozarr_array | R Documentation |
GeoZarr Array
Description
This class implements a GeoZarr array. A GeoZarr array is like a regular Zarr array but it has attributes and/or associated Zarr arrays that provide a coordinate system for the array.
Super classes
zarr::zarr_object -> zarr::zarr_node -> zarr::zarr_array -> geozarr_array
Active bindings
coordinate_system(read-only) Retrieve the coordinate system of this array.
Methods
Public methods
Inherited methods
zarr::zarr_object$print_attributes()zarr::zarr_node$absolute_path()zarr::zarr_node$append_array_attribute()zarr::zarr_node$attribute()zarr::zarr_node$delete_attribute()zarr::zarr_node$relative_path()zarr::zarr_node$save()zarr::zarr_node$set_attribute()zarr::zarr_node$walk_path()zarr::zarr_array$flush()zarr::zarr_array$hierarchy_nodes()zarr::zarr_array$print()zarr::zarr_array$promote()zarr::zarr_array$read()zarr::zarr_array$resize()zarr::zarr_array$write()
geozarr_array$new()
Initialize a new GeoZarr array.
Usage
geozarr_array$new(name, metadata, parent, store, coord_sys)
Arguments
nameThe name of the GeoZarr array.
metadataList with the metadata of the array.
parentThe parent
zarr_groupinstance of this new array, can be missing orNULLif the Zarr object should have just this array.storeThe zarr_store instance to persist data in.
coord_sysOptional, an instance of CoordinateSystem providing the coordinate system of the array. If not provided, the coordinate system is constructed from the metadata of the array persisted in the store.
Returns
An instance of geozarr_array.
geozarr_array$post_open()
Perform any processing after the Zarr hierarchy is in place and out-of-group references can be resolved.
Usage
geozarr_array$post_open()
Returns
Self, invisibly.
geozarr_array$build_coordsys()
Build the coordinate system of the GeoZarr array if it has
not been set yet. This should only be called when the Zarr hierarchy is
in place and out-of-group references can be resolved, particularly for
the cs convention.
Usage
geozarr_array$build_coordsys()
Returns
Self, invisibly.
geozarr_array$subset()
This method extracts a subset of values from the GeoZarr array, with the range along each axis to extract expressed in coordinate values of the domain of each axis.
Usage
geozarr_array$subset( ..., .name = NULL, .location = NULL, .rightmost.closed = FALSE )
Arguments
...One or more arguments of the form
axis = range. The "axis" part should be the name of an axis or its abbreviationX,Y,ZorT. The "range" part is a vector of values representing coordinates along the axis where to extract data. Axis abbreviations and names are case-sensitive and can be specified in any order. If values for the range per axis fall outside of the extent of the axis, the range is clipped to the extent of the axis..nameThe name of the GeoZarr array to be created. If omitted, an array will be created at the root of a new in-memory Zarr store.
.locationOptional. If supplied, either an existing zarr_group in a zarr object, or a character string giving the location on a local file system where to persist the data. If the argument is a
zarr_group, argument.namemust be provided. If the argument gives the location for a new Zarr store then the location must be writable by the calling code. As per the Zarr specification, it is recommended to use a location that ends in ".zarr" when providing a location for a new store. If argument.nameis given then thegeozarr_arraywill be created in the root of thezarrstore with that name. If the.nameargument is not given, a single-array Zarr store will be created. If thelocationargument is not given, azarrobject is created in memory..rightmost.closedOptional. Single logical value to indicate if the upper boundary of range in each axis should be included.
Details
The range of values along each axis to be subset is expressed in
coordinates of the domain of the axis. Any axes for which no selection
is made in the ... argument are extracted in whole. Coordinates can
be specified in a variety of ways that are specific to the nature of
the axis. For numeric axes it should (resolve to) be a vector of real
values from which the range is computed. For time axes a vector of
character timestamps, POSIXct or Date values must be specified. As
with numeric values, only the two extreme values in the vector will be
used. For character axes the order in the axis will be used, with the
first and last value in the supplied range.
If the range of coordinate values for an axis in argument ... extends
the valid range of the axis, the extracted data will start at the
beginning for smaller values and extend to the end for larger values.
If the values envelope the valid range the entire axis will be
extracted in the result. If the range of coordinate values for any axis
are all either smaller or larger than the valid range of the axis then
nothing is extracted and NULL is returned.
The extracted data has the same dimensional structure as the data in
the array, with degenerate dimensions preserved. The order of the axes
in argument ... does not reorder the axes in the result.
Arguments following ... must be explicitly named, like
.rightmost.closed = TRUE, to avoid the argument being treated as an
axis name.
As an example, to extract values of a variable for Australia for the
year 2020, where the first axis in GeoZarr array x is the longitude,
the second axis is the latitude, both in degrees, and the third (and
final) axis is time, the values are extracted by x$subset(X = c(112, 154), Y = c(-9, -44), T = c("2020-01-01", "2021-01-01")). Note that
this works equally well for projected coordinate reference systems -
the key is that the specification in argument ... uses the same
domain of values as the respective axes in x use.
Returns
If the .location argument is a zarr_group, the new Zarr
geozarr_array is returned, with a subset of data from this GeoZarr
array, having the axes and attributes of this GeoZarr array. Otherwise,
the zarr object that is newly created and which contains the
geozarr_array instance, or an error if the zarr object could not be
created. If one or more of the selectors in the ... argument fall
entirely outside of the range of the axis NULL is returned.
geozarr_array$write_external_coordinates()
Write any external coordinates of this array to the
underlying Zarr store. The metadata of this array is scanned for ref
objects in the cs convention attributes. The values of the external
coordinates are taken from the CoordinateSystem instance of this
array.
Usage
geozarr_array$write_external_coordinates()
Returns
Self, invisibly.
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