WIP: Fix precomputed reading

scalableminds · Jan 19, 2023 · 2b80411 · 2b80411
1 parent 4f48a8b
commit 2b80411
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Showing 4 changed files with 9 additions and 8 deletions.
diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/Compressor.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/Compressor.scala
@@ -9,7 +9,7 @@ import org.apache.commons.compress.compressors.gzip.{
 import org.blosc.{BufferSizes, IBloscDll, JBlosc}
 import play.api.libs.json.{Format, JsResult, JsValue, Json}
 
-import java.awt.image.BufferedImage
+import java.awt.image.{BufferedImage, DataBufferByte}
 import java.io._
 import java.nio.ByteBuffer
 import java.util
@@ -274,8 +274,11 @@ class JpegCompressor() extends Compressor {
   @throws[IOException]
   override def uncompress(is: InputStream, os: OutputStream): Unit = {
     val iis: ImageInputStream = createImageInputStream(is)
-    val ios = createImageOutputStream(os)
     val bi: BufferedImage = ImageIO.read(iis: ImageInputStream)
-    ImageIO.write(bi, "bmp", ios)
+    val raster = bi.getRaster
+    val dbb: DataBufferByte = raster.getDataBuffer.asInstanceOf[DataBufferByte]
+    val width = raster.getWidth
+    val data = dbb.getData.grouped(width).toList.transpose
+    os.write(data.flatten.toArray)
   }
 }
diff --git a/...os-datastore/app/com/scalableminds/webknossos/datastore/datareaders/FileSystemStore.scala b/...os-datastore/app/com/scalableminds/webknossos/datastore/datareaders/FileSystemStore.scala
@@ -1,10 +1,8 @@
 package com.scalableminds.webknossos.datastore.datareaders
 
-import com.scalableminds.webknossos.datastore.storage.httpsfilesystem.HttpsPath
 import net.liftweb.util.Helpers.tryo
 
-import java.net.URI
-import java.nio.file.{FileSystem, Files, Path, Paths}
+import java.nio.file.{FileSystem, Files, Path}
 
 class FileSystemStore(val internalRoot: Path) {
   def readBytes(key: String): Option[Array[Byte]] = {

diff --git a/...os-datastore/app/com/scalableminds/webknossos/datastore/datareaders/MultiArrayUtils.scala b/...os-datastore/app/com/scalableminds/webknossos/datastore/datareaders/MultiArrayUtils.scala
@@ -130,7 +130,8 @@ object MultiArrayUtils {
      */
     val permutation = axisOrder.permutation(source.getRank)
     val flippedIfNeeded = if (flip) permutation.reverse else permutation
-    source.permute(flippedIfNeeded)
+    val permutationHack = Array(0, 2, 1)
+    source.permute(permutationHack)
   }
 
 }
diff --git a/...app/com/scalableminds/webknossos/datastore/datareaders/precomputed/PrecomputedArray.scala b/...app/com/scalableminds/webknossos/datastore/datareaders/precomputed/PrecomputedArray.scala
@@ -82,7 +82,6 @@ class PrecomputedArray(relativePath: DatasetPath,
         .min(header.precomputedScale.size(i))
       s"$beginOffset-$endOffset"
     })
-    //logger.info(s"${header.precomputedScale.key}: Getting chunk ${chunkIndex(0)},${chunkIndex(1)},${chunkIndex(2)}, resulting in ${coordinates.mkString(header.dimension_separator.toString)}")
     coordinates.mkString(header.dimension_separator.toString)
   }