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https://github.com/keller-mark/pizzarr
Slice into Zarr arrays in R 🍕
https://github.com/keller-mark/pizzarr
hidivelab zarr
Last synced: 2 months ago
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Slice into Zarr arrays in R 🍕
- Host: GitHub
- URL: https://github.com/keller-mark/pizzarr
- Owner: keller-mark
- License: mit
- Created: 2021-03-01T17:16:48.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-10-24T21:11:08.000Z (3 months ago)
- Last Synced: 2024-10-26T08:44:36.670Z (2 months ago)
- Topics: hidivelab, zarr
- Language: R
- Homepage: https://keller-mark.github.io/pizzarr/
- Size: 8.3 MB
- Stars: 28
- Watchers: 5
- Forks: 3
- Open Issues: 35
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# pizzarr 
A Zarr implementation for R.
## Installation
Installation requires R 4.0.0 or greater.
```r
install.packages("devtools")
devtools::install_github("keller-mark/pizzarr")
```
## Usage
```r
library(pizzarr)
a <- array(data=1:20, dim=c(2, 10))
# [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
# [1,] 1 3 5 7 9 11 13 15 17 19
# [2,] 2 4 6 8 10 12 14 16 18 20
z <- zarr_create(shape=dim(a), dtype="(reading / writing) |
|-------------------|:------------------------------:|
| `MemoryStore` | ✔ / ✔ |
| `DirectoryStore` | ✔ / ✔ |
| `HttpStore` | ✔ / ❌ |
### Data types
| Zarr Data Type | Status
(reading / writing) | Notes |
|-----------------------|:------------------------------:|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `b1` / `boolean` | ✔ / ✔ | Converted to `logical` in R. |
| `i1` / `int8` | ✔ / ✔ | Converted to `integer` in R. |
| `u1` / `uint8` | ✔ / ✔ | Converted to `integer` in R. |
| `i2` / `int16` | ✔ / ✔ | Converted to `integer` in R. |
| `u2` / `uint16` | ✔ / ✔ | Converted to `integer` in R. |
| `i4` / `int32` | ✔ / ✔ | Converted to `integer` in R. |
| `u4` / `uint32` | ✔ / ✔ | Converted to `integer` in R. |
| `i8` / `int64` | ✔ / ✔ | Converted to `integer` in R. |
| `u8` / `uint64` | ✔ / ✔ | Converted to `integer` in R. |
| `f2` / `float16` | ✔ / ✔ | Converted to `double` in R. |
| `f4` / `float32` | ✔ / ✔ | Converted to `double` in R. |
| `f8` / `float64` | ✔ / ✔ | Converted to `double` in R. |
| `complex` | ❌ / ❌ | |
| `timedelta` | ❌ / ❌ | |
| `datetime` | ❌ / ❌ | |
| `string` | ✔ / ✔ | Converted to `character` in R. |
| `Unicode` | ✔ / ✔ | Converted to `character` in R. |
| `void *` | ❌ / ❌ | |
| Structured data types | ❌ / ❌ | |
| Object data type - [VLenUTF8](https://numcodecs.readthedocs.io/en/stable/vlen.html#vlenutf8) | ✔ / ✔ | Converted to `character` in R. |
Note: no effort is made to assess loss of precision due to conversion.
### Compression tools
| Data Type | Status
(reading / writing) | Notes |
|---------------|:------------------------------:|-----------------------------------------------------------------------------------------------------|
| `zlib / gzip` | ✔ / ✔ | Only system default compression level 6 is enabled for writing. |
| `bzip2` | ✔ / ✔ | Only system default compression level 6 is enabled for writing. |
| `blosc` | ✔ / ✔ | Only system default compression level 5 is enabled for writing. |
| `LZMA` | ✔ / ✔ | Only system default compression level 9 is enabled for writing. |
| `LZ4` | ✔ / ✔ | |
| `Zstd` | ✔ / ✔ | |
## Development
```r
setwd("path/to/pizzarr")
install.packages("devtools")
devtools::install()
devtools::load_all()
```
## Testing
```r
devtools::check()
devtools::test()
```
## Documentation
```r
install.packages("devtools")
install.packages("pkgdown")
devtools::document()
pkgdown::build_site()
```
## Resources
- [Discussion of Zarr in R](https://github.com/zarr-developers/community/issues/18)
- [Rarr](https://github.com/grimbough/Rarr)
- Note: `pizzarr` has an optional dependency on Rarr for Blosc (de)compression.
- R package development
- [R packages](https://r-pkgs.org/)
- [roxygen2 syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html)
- [R6](https://r6.r-lib.org/index.html)
- [R6 roxygen2 syntax](https://www.tidyverse.org/blog/2019/11/roxygen2-7-0-0/#r6-documentation)
- [pkgdown](https://pkgdown.r-lib.org/)
- Zarr implementation
- [zarr_implementations](https://github.com/zarr-developers/zarr_implementations)
- [zarr-python](https://github.com/zarr-developers/zarr-python)
- [LZ4 and ZSTD compression in R](https://github.com/traversc/qs)
- [zarr.js](https://github.com/gzuidhof/zarr.js)
- [zarrita.js](https://github.com/manzt/zarrita.js)
- [v2 spec](https://zarr.readthedocs.io/en/stable/spec/v2.html)