NEWS
spatialdataR 0.99.41
- fix vignette to call 'spatialdataR::transform()' explicitly
- address R CMD check warnings re: undocumented arguments, undefined functions
spatialdataR 0.99.40
- validty & setters now assure that each layer is a completely named list
- 'SpatialDataImage/Label()' now accept single array (previously required list)
- simplified various code bits (e.g., using 'lengths()', 'seq_along()', etc.)
spatialdataR 0.99.39
- class revision: SpatialData slots were base::list, now prototyped
S4Vectors::SimpleList with layer-specific properties & validation
- added 'path()' to retrieve on-disk paths of spatial data elements
spatialdataR 0.99.38
- make use of new BiocGenerics:
data,rotate,scale,sequence,table,transform
spatialdataR 0.99.37
- fix note regarding internal '.mask' generic
- fix conclits with 'base::labels' and 'S4Vectors::transform'
- in mask(), return 'j' instances that mapped to each 'i'
spatialdataR 0.99.36
- fix conflicts with 'base::table' and 'utils::data'
spatialdataR 0.99.35
- bug fix: 'centroids,shape' was previously
returning vertex coordinates for polygons
- class renaming:
sdArray/Frame > SpatialDataArray/Frame,
Image/LabelArray > SpatialDataImage/Label,
Shape/PointFrame > SpatialDataShape/Point
spatialdataR 0.99.34
- omit SpatialData.data everywhere
- improved Point/ShapeFrame constructor
- consolidated sdFrame code, docs, methods
spatialdataR 0.99.33
- added validity checks and tests for Zattrs
- improved handling of 'spatialdata_attrs'
- synchronize tables when subsetting/renaming
- more memory efficient mask(), keeping
an observation of unmapped instances
- revised package 'Description:' field
to align with current capabilities
spatialdataR 0.99.32
- added unit tests for query()
- improved 'table' element validation
- split centroids/extent() code & docs
- revised 'coordTrans' show method of Zattrs
(refactored code, fixed 'sequence' display)
- implemented internal data/meta() get & set
to avoid @-accessiong throughout code base
spatialdataR 0.99.31
- refactored point/shape transformations
- rebrand spatial queries as crop();
keeping table queries as query()
- added object-wide spatial crop()
- added .zattrs contructor
- revised vignette
spatialdataR 0.99.30
- query() by table method draft
- added xNames<-() methods (x = image, label, ...)
- added combine() to make one SpatialData object from two
- 'duckspatial' for handling of points and shapes
- add ShapeFrame construction from matrix & 'sf'
- bug fix in coord trans. graph representation
for when element and space names collide
spatialdataR 0.99.29
- revision of Zarr version-specific .zattrs handling
- added Zarr v3 example dataset 'inst/extdata/blobs_v3'
- reorganization of unit tests to facilitate v3-specific testing
spatialdataR 0.99.28
- validity checks for 'table' elements
- fixed and reenable broken/skipped tests
- spatialdata_attrs utilities (instance_key(), region_key(), region())
spatialdataR 0.99.27
- spatial queries (aka subsetting) by bounding box
(all element types) or polygons (points and shapes),
including unit tests, documentation, visual examples
- masking draft to aggregate information across layers
(image by label, point by shape, shape by shape;
the latter aggregates values in an associated table)
spatialdataR 0.99.26
- added unit tests for existing transformations
- implemented minimal layer-wise validity checks
(Image/LabelArray and Shape/PointFrame elements)
spatialdataR 0.99.25
- improved Zattrs show method (cf., PR #117)
- replace jsonlite::fromJSON() with Rarr::read_zarr_attributes()
for reading .zattrs & rewrite code-/test-base accordingly
spatialdataR 0.99.24
- ZarrArray imported by Bioconductor/ZarrArray
- Rarr replaces pizzarr for importing tables via anndataR
- anndataR replaces zellkonverter
- update basilisk env to spatialdata==0.7.0
- replace spatialdata.read with anndata.read_zarr to read tables
spatialdataR 0.99.22
- split off 'SpatialData.data'
spatialdataR 0.99.21
- use Python's 'spatialdata::read_zarr' for reading tables
spatialdataR 0.99.20
- 'ImageArray' subsetting with multiscales support
- for 'tables', moved 'instance/region_key' to 'int_colData'
spatialdataR 0.99.19
- adding code to improve visualization of transformation network (PR #98)
spatialdataR 0.99.18
- split off 'SpatialData.plot'
spatialdataR 0.99.17
- rewrite of points and labels plotting, including
documented examples and support for tables
- setup 'basilisk' environment to use 'pip'
for 'spatialdata' and 'spatialdata-io'
spatialdataR 0.99.16
- added draft for transformations (tbc)
- added methods for table handling following draft from PR #74
- 'get/setTable' for adding/getting tables
- 'valTable' to retrieve data from an existing table
spatialdataR 0.99.15
- added methods for coordinate transormation handling, namely:
'rmvCT()' for removal and 'addCT()' for adding/appending
- major rewrite of 'ImageArray' plotting & bounding box 'query'
- added vignettes demos of bounding box queries & multiscale plotting
spatialdataR 0.99.14
- added unit tests for image plotting, element & object handling
- element-wise and object-wide subsetting à la '['
- fixed multiscales plotting
spatialdataR 0.99.13
- added 'do_tx_to_ext()' to align spatial elements within Py
- fixed problem with 'basilisk' environment
- added more validity checks
spatialdataR 0.99.12
- complete authors list in DESCRIPTION and vignette
- include more information on elements in show method
- basic vignette sections on data representation, handling etc.
- added 'ggforce' dependency for visualizing circular shapes
spatialdataR 0.99.11
- in 'readSpatialData()', provide option to specify
TRUE/FALSE/index/character to control reading
spatialdataR 0.99.10
- add support for multiscales in 'ImageArray's
including show method to display available scales
spatialdataR 0.99.9
- add 'basilisk'-based interface to Python's 'spatialdata-io'
to support readers across platforms & writing to .zarr
spatialdataR 0.99.8
- updated show method to include information on coordinate systems
spatialdataR 0.99.7
- added utility '.coord2graph()' in coord.R to represent
element-coordinate system relationships as graph
spatialdataR 0.99.6
- option to read 'table' using 'anndataR' instead
of 'anndata+zellkonverter' through 'basilisk'