add a few helpers related to pulling data from ZARR

Author: vreuter

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+
+### Added
+* Introduced more basic helper functions for reading from ZARR
+
 ## [v0.5.0] - 2025-06-17
 
 ### Added

build.sbt

@@ -189,7 +189,7 @@ lazy val compileSettings = Def.settings(
   Test / console / scalacOptions := (Compile / console / scalacOptions).value,
 )
 
-lazy val versionNumber = "0.5.0"
+lazy val versionNumber = "0.6.0-SNAPSHOT"
 
 lazy val metadataSettings = Def.settings(
   name := projectName,

modules/zarr/src/main/scala/ZarrArrayExtras.scala

@@ -10,6 +10,21 @@ import at.ac.oeaw.imba.gerlich.gerlib.zarr.OmeZarrIndex.OmeZarrStandardCoordinat
 
 /** Helpers for working with [[com.bc.zarr.ZarrArray]] */
 object ZarrArrayExtras:
+  
+  // TODO: guard against atypical dimension order.
+  private def getXY(za: ZarrArray): Either[String, Dimensions2D] = 
+    za.getShape.toList match {
+      case _ :: _ :: _ :: y :: x :: Nil => new Dimensions2D(x = x, y = y).asRight
+      case dims => s"${dims.length}-D array, not 5-D".asLeft
+    }
+
+  def readFirstFullSize2DFrom5D(za: ZarrArray): Either[String, DataRead2D] = for
+    dims <- getXY(za)
+    data <- Try{ 
+      JzarrTools.readFrom(za, Array(1, 1, 1, dims.y, dims.x), Array(0, 0, 0, 0, 0)) 
+    }.toEither.leftMap(_.getMessage)
+  yield DataRead2D(data, dims)
+
   extension (za: ZarrArray)
     def read(indexMapping: IndexMapping)(
         origin: OmeZarrStandardCoordinate,
@@ -23,4 +38,14 @@ object ZarrArrayExtras:
         .leftMap(e =>
           s"For index mapping $indexMapping and starting from $origin, failed to read block of size $size: ${e.getMessage}"
         )
+  
+  final class Dimensions2D(val x: Int, val y: Int):
+    require(x >= 0, s"x dimension must be nonnegative, not $x")
+    require(y >= 0, s"y dimension must be nonnegative, not $y")
+
+  final class DataRead2D(values: Array[Int], dimensions: Dimensions2D):
+    require(
+      values.length === dimensions.x * dimensions.y, 
+      s"${dimensions.x} * ${dimensions.y} = ${dimensions.x * dimensions.y}, not ${values.length}"
+    )
 end ZarrArrayExtras