1 Introduction
- 1.1 Limitations with Rarr
- 1.2 Example data
2 Quick start guide
3 Additional details
4 Appendix
- Session info

1 Introduction

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It’s design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Zarr is experiencing increasing adoption in a number of scientific fields, where multi-dimensional data are prevalent. In particular as a back-end to the The Open Microscopy Environment’s OME-NGFF format for storing bioimaging data in the cloud.

Rarr is intended to be a simple interface to reading and writing individual Zarr arrays. It is developed in R and C with no reliance on external libraries or APIs for interfacing with the Zarr arrays. Additional compression libraries (e.g. blosc) are bundled with Rarr to provide support for datasets compressed using these tools.

1.1 Limitations with Rarr

If you know about Zarr arrays already, you’ll probably be aware they can be stored in hierarchical groups, where additional meta data can explain the relationship between the arrays. Currently, Rarr is not designed to be aware of these hierarchical Zarr array collections. However, the component arrays can be read individually by providing the path to them directly.

Currently, there are also limitations on the Zarr datatypes that can be accessed using Rarr. For now most numeric types can be read into R, although in some instances e.g. 64-bit integers there is potential for loss of information. Writing is more limited with support only for datatypes that are supported natively in R and only using the column-first representation.

1.2 Example data

The are some example Zarr arrays included with the package. These were created using the Zarr Python implementation and are primarily intended for testing the functionality of Rarr. You can use the code below to list the complete set on your system, however it’s a long list so we don’t show the output here.

list.dirs(
  system.file("extdata", "zarr_examples", package = "Rarr"),
  recursive = TRUE
) |>
  grep(pattern = "zarr$", value = TRUE)

2 Quick start guide

2.1 Installation and setup

If you want to quickly get started reading an existing Zarr array with the package, this section should have the essentials covered. First, we need to install Rarr111 you only need to do the installation step once with the commands below.

## we need BiocManager to perform the installation
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
## install Rarr
BiocManager::install("Rarr")

Once Rarr is installed, we have to load it into our R session:

library(Rarr)

Rarr can be used to read files either on local disk or on remote S3 storage systems. First lets take a look at reading from a local file.

2.2 Reading a from a local Zarr array

To demonstrate reading a local file, we’ll pick the example file containing 32-bit integers arranged in the “column first” ordering.

zarr_example <- system.file(
  "extdata", "zarr_examples", "column-first", "int32.zarr",
  package = "Rarr"
)

2.2.1 Exploring the data

We can get an summary of the array properties, such as its shape and datatype, using the function zarr_overview()222 This is essentially reading and formatting the array metadata that accompanies any Zarr array..

zarr_overview(zarr_example)

## Type: Array
## Path: /tmp/RtmpHaxDDq/Rinst31e1e6703dbd16/Rarr/extdata/zarr_examples/column-first/int32.zarr
## Shape: 30 x 20 x 10
## Chunk Shape: 10 x 10 x 5
## No. of Chunks: 12 (3 x 2 x 2)
## Data Type: int32
## Endianness: little
## Compressor: blosc

You can use this to check that the location is a valid Zarr array, and that the shape and datatype of the array content are what you are expecting. For example, we can see in the output above that the data type (int32) corresponds to what we expect.

2.2.2 Reading the Zarr array

The summary information retrieved above is required, as to read the array with Rarr you need to know the shape and size of the array (unless you want to read the entire array). From the previous output we can see our example array has three dimensions of size 30 x 20 x 10. We can select the subset we want to extract using a list. The list must have the same length as the number of dimensions in our array, with each element of the list corresponding to the indices you want to extract in that dimension.

index <- list(1:4, 1:2, 1)

We then extract the subset using read_zarr_array():

read_zarr_array(zarr_example, index = index)

## , , 1
## 
##      [,1] [,2]
## [1,]    1    2
## [2,]    1    0
## [3,]    1    0
## [4,]    1    0

2.3 Reading from S3 storage

Reading files in S3 storage works in a very similar fashion to local disk. This time the path needs to be a URL to the Zarr array. We can again use zarr_overview() to quickly retrieve the array metadata.

s3_address <- "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr/0"
zarr_overview(s3_address)

## Type: Array
## Path: https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr/0/
## Shape: 50 x 494 x 464
## Chunk Shape: 1 x 494 x 464
## No. of Chunks: 50 (50 x 1 x 1)
## Data Type: float64
## Endianness: little
## Compressor: blosc

The output above indicates that the array is stored in 50 chunks, each containing a slice of the overall data. In the example below we use the index argument to extract the first and tenth slices from the array. Choosing to read only 2 of the 50 slices is much faster than if we opted to download the entire array before accessing the data.

z2 <- read_zarr_array(s3_address, index = list(c(1, 10), NULL, NULL))

We then plot our two slices on top of one another using the image() function.

## plot the first slice in blue
image(log2(z2[1, , ]),
  col = hsv(h = 0.6, v = 1, s = 1, alpha = 0:100 / 100),
  asp = dim(z2)[2] / dim(z2)[3], axes = FALSE
)
## overlay the tenth slice in green
image(log2(z2[2, , ]),
  col = hsv(h = 0.3, v = 1, s = 1, alpha = 0:100 / 100),
  asp = dim(z2)[2] / dim(z2)[3], axes = FALSE, add = TRUE
)

Note: if you receive the error message "Error in stop(aws_error(request$error)) : bad error message" it is likely you have some AWS credentials available in to your R session, which are being inappropriately used to access this public bucket. Please see the section 3.3 for details on how to set credentials for a specific request.

2.4 Writing to a Zarr array

Up until now we’ve only covered reading existing Zarr array into R. However, Rarr can also be used to write R data to disk following the Zarr specification. To explore this, lets create an example array we want to save as a Zarr. In this case it’s going to be a three dimensional array and store the values 1 to 600.

x <- array(1:600, dim = c(10, 10, 6))

path_to_new_zarr <- file.path(tempdir(), "new.zarr")
write_zarr_array(x = x, zarr_array_path = path_to_new_zarr, chunk_dim = c(10, 5, 1))

We can check that the contents of the Zarr array is what we’re expecting. Since the contents of the whole array will be too large to display here, we use the index argument to extract rows 6 to 10, from the 10th column and 1st slice. That should be the values 96, 97, 98, 99, 100, but retaining the 3-dimensional array structure of the original array. The second line below uses identical() to confirm that reading the whole Zarr returns something equivalent to our original input x.

read_zarr_array(zarr_array_path = path_to_new_zarr, index = list(6:10, 10, 1))

## , , 1
## 
##      [,1]
## [1,]   96
## [2,]   97
## [3,]   98
## [4,]   99
## [5,]  100

identical(read_zarr_array(zarr_array_path = path_to_new_zarr), x)

## [1] TRUE

3 Additional details

3.1 Working with Zarr metadata

By default the zarr_overview() function prints a summary of the array to screen, so you can get a quick idea of the array properties. However, there are times when it might be useful to compute on that metadata, in which case printing to screen isn’t very helpful. If his is the case the function also has the argument as_data_frame which toggles whether to print the output to screen, as seen before above, or to return a data.frame containing the array details.

zarr_overview(zarr_example, as_data_frame = TRUE)

##                                                                                     path
## 1 /tmp/RtmpHaxDDq/Rinst31e1e6703dbd16/Rarr/extdata/zarr_examples/column-first/int32.zarr
##   nchunks data_type compressor        dim chunk_dim
## 1      12     int32      blosc 30, 20, 10 10, 10, 5

3.2 Using credentials to access S3 buckets

If you’re accessing data in a private S3 bucket, you can set the environment variables AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY to store your credentials. For example, lets try reading a file in a private S3 bucket:

zarr_overview("https://s3.embl.de/rarr-testing/bzip2.zarr")

## Error: AccessDenied (HTTP 403). Access Denied.

We can see the “Access Denied” message in our output, indicating that we don’t have permission to access this resource as an anonymous user. However, if we use the key pair below, which gives read-only access to the objects in the rarr-testing bucket, we’re now able to interrogate the files with functions in Rarr.

Sys.setenv(
  "AWS_ACCESS_KEY_ID" = "V352gmotks4ZyhfU",
  "AWS_SECRET_ACCESS_KEY" = "2jveausI91c8P3c7OCRIOrxdLbp3LNW8"
)
zarr_overview("https://s3.embl.de/rarr-testing/bzip2.zarr")

## Type: Array
## Path: https://s3.embl.de/rarr-testing/bzip2.zarr/
## Shape: 20 x 10
## Chunk Shape: 10 x 10
## No. of Chunks: 2 (2 x 1)
## Data Type: int32
## Endianness: little
## Compressor: bz2

Behind the scenes Rarr makes use of the paws suite of packages (https://paws-r.github.io/) to interact with S3 storage. A comprehensive overview of the multiple ways credentials can be set and used by paws can be found at https://github.com/paws-r/paws/blob/main/docs/credentials.md. If setting environment variables as above doesn’t work or is inappropriate for your use case please refer to that document for other options.

3.3 Creating an S3 client

Although Rarr will try its best to find appropriate credentials and settings to access a bucket, it is not always successful. Once such example is when you have AWS credentials set somewhere and you try to access a public bucket. We can see an example of this below, where we access the same public bucket used in 2.3, but it now fails because we have set the AWS_ACCESS_KEY_ID environment variable in the previous section.

s3_address <- "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr/0"
zarr_overview(s3_address)

## Error:

You might encounter similar problems if you’re trying to access multiple buckets each of which require different credentials. The solution here is to create an “s3_client” using paws.storage::s3(), which contains all the required details for accessing a particular bucket. Doing so will prevent Rarr from trying to determine things on its own, and gives you complete control over the settings used to communicate with the S3 bucket. Here’s an example that will let us access the failing bucket by creating a client with anonymous credentials.

s3_client <- paws.storage::s3(
  config = list(
    credentials = list(anonymous = TRUE), 
    region = "auto",
    endpoint = "https://uk1s3.embassy.ebi.ac.uk")
  )

If you’re accessing a public bucket, the most important step is to provide a credentials list with anonymous = TRUE. Doing so ensures that no attempts to find other credentials are made, and prevents the problems seen above. If you’re using files on Amazon AWS storage you’ll need to set the region to whatever is appropriate for your data e.g. "us-east-2", "eu-west-3", etc. For other S3 providers that don’t have regions use the value "auto" as in the example below. Finally the endpoint argument is the full hostname of the server where your files can be found. For more information on creating an S3 client see the paws.storage documentation.

We can then pass our s3_client to zarr_overview() and it now works successfully.

zarr_overview(s3_address, s3_client = s3_client)

## Type: Array
## Path: https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr/0/
## Shape: 50 x 494 x 464
## Chunk Shape: 1 x 494 x 464
## No. of Chunks: 50 (50 x 1 x 1)
## Data Type: float64
## Endianness: little
## Compressor: blosc

Most functions in Rarr have the s3_client argument and it can be applied in the same way.

3.4 Writing subsets of data

One of the key features of the Zarr specification is that the arrays are chunked, allowing rapid access to the required data without needed to read or write everything else. If you want to modify a subset of a Zarr array, it is very inefficient to write all chunks to disk, which is what write_zarr_array() does. Instead, Rarr provides two functions for reducing the amount of writing required if the circumstances allow: create_empty_zarr_array() and update_zarr_array().

3.4.1 Creating an “empty” array

Despite the name, you can actually think of create_empty_zarr_array() as creating an array where all the values are the same. The Zarr specification allows for “uninitialized” chunks, which are not actually present on disk. In this case, any reading application assumes the entirety of the chunk is filled with a single value, which is found in the array metadata. This allows for very efficient creation of the new array, since only a small metadata file is actually written. However it is necessary to provide some additional details, such as the shape of the array, since there’s no R array to infer these from. Let’s look at an example:

path <- tempfile()
create_empty_zarr_array(
  zarr_array_path = path,
  dim = c(50, 20),
  chunk_dim = c(5, 10),
  data_type = "integer",
  fill_value = 7L
)

First we have to provide a location for the array to be created using the zarr_array_path argument. Then we provide the dimensions of the new array, and the shape of the chunks it should be split into. These two arguments must be compatible with one another i.e. have the same number of dimensions and no value in chunk_dim should exceed the corresponding value in dim. The data_type argument defines what type of values will be stored in the array. This is currently limited to: "integer", "double", and "string"333 Rarr is currently limited to writing Zarr arrays using data types native to R, rather than the full range provided by other implementations.. Finally we use the fill_value argument to provide our default value for the uninitialized chunks. The next few lines check what’s actually been created on our file system. First, we use list.files() to confirm that that only file that’s been created is the .zarray metadata; there are no chunk files. Then we use table() to check the contents of the array, and confirm that when it’s read the resulting array in R is full of 7s, our fill value.

list.files(path, all.files = TRUE, no.. = TRUE)

## [1] ".zarray"

table(read_zarr_array(path))

## 
##    7 
## 1000

3.4.2 Updating a subset of an existing array

Lets assume we want to update the first row of our array to contain the sequence of integers from 1 to 20. In the code below we create an example vector containing the new data. We then use update_zarr_array(), passing the location of the Zarr and the new values to be inserted. Finally, we provide the index argument which defines which elements in the Zarr array should be updated. It’s important that the shape and number of values in x corresponds to the total count of points in the Zarr array we want to update e.g. in this case we’re updating a single row of 20 values.

x <- 1:20
update_zarr_array(
  zarr_array_path = path,
  x = x,
  index = list(1, 1:20)
)

As before, we can take a look at what’s happened on disk and confirm the values are present in the array if we read it into R.

list.files(path, all.files = TRUE, no.. = TRUE)

## [1] ".zarray" "0.0"     "0.1"

read_zarr_array(path, index = list(1:2, 1:5))

##      [,1] [,2] [,3] [,4] [,5]
## [1,]    1    2    3    4    5
## [2,]    7    7    7    7    7

table(read_zarr_array(path))

## 
##   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20 
##   1   1   1   1   1   1 981   1   1   1   1   1   1   1   1   1   1   1   1   1

Here list.files() confirms that there’s now two chunk files that have been created. When we first created the Zarr we specified that the chunks should be 10 columns wide, so by modifying 20 columns we’d expect at least two chunks to be realized on disk. We use read_zarr_array() to confirm visually that the first row contains our sequence of values, whilst the second row is still all 7. We use table() to confirm that the total contents is as expected.

4 Appendix

Session info

## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Rarr_1.2.0       BiocStyle_2.30.0
## 
## loaded via a namespace (and not attached):
##  [1] crayon_1.5.2        httr_1.4.7          cli_3.6.1          
##  [4] knitr_1.44          magick_2.8.1        rlang_1.1.1        
##  [7] xfun_0.40           stringi_1.7.12      jsonlite_1.8.7     
## [10] glue_1.6.2          htmltools_0.5.6.1   sass_0.4.7         
## [13] rmarkdown_2.25      evaluate_0.22       jquerylib_0.1.4    
## [16] fastmap_1.1.1       lifecycle_1.0.3     yaml_2.3.7         
## [19] bookdown_0.36       stringr_1.5.0       BiocManager_1.30.22
## [22] compiler_4.3.1      codetools_0.2-19    Rcpp_1.0.11        
## [25] R.oo_1.25.0         R.utils_2.12.2      digest_0.6.33      
## [28] R6_2.5.1            curl_5.1.0          paws.common_0.6.2  
## [31] paws.storage_0.4.0  magrittr_2.0.3      bslib_0.5.1        
## [34] R.methodsS3_1.8.2   tools_4.3.1         mime_0.12          
## [37] xml2_1.3.5          cachem_1.0.8

Reading Zarr arrays with Rarr

24 October 2023

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