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keller-mark / pizzarr

Slice into Zarr arrays in R 🍕
https://keller-mark.github.io/pizzarr/
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hidivelab zarr

readme

pizzarr pizzarr website

A Zarr implementation for R.

Installation

Installation requires R 4.0.0 or greater.

install.packages("devtools")
devtools::install_github("keller-mark/pizzarr")

Usage

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="<f4", fill_value=NA)

z$set_item("...", a)

selection <- z$get_item(list(slice(1, 2), slice(1, 5)))

print(selection$data)
#      [,1] [,2] [,3] [,4] [,5]
# [1,]    1    3    5    7    9
# [2,]    2    4    6    8   10

Current status

(This section has been adapted from the Rarr project README).

Stores

Store Status
(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 ✔ / ✔ 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

setwd("path/to/pizzarr")
install.packages("devtools")
devtools::install()
devtools::load_all()

Testing

Set TESTTHAT_CPUS=# in .Renviron to run tests in parallel

devtools::check()
devtools::test()

Documentation

install.packages("devtools")
install.packages("pkgdown")
devtools::document()
pkgdown::build_site()

Resources