From cb4ad63a593557c8d7c4ca2dfeb359a0be4ea082 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 29 Nov 2018 14:41:41 +0100 Subject: [PATCH 1/9] [WIP] thumbnails for segmentation layer --- app/controllers/DataSetController.scala | 4 +- build.sbt | 1 + .../util/image/ImageCreator.scala | 105 ++++++++++-------- 3 files changed, 60 insertions(+), 50 deletions(-) diff --git a/app/controllers/DataSetController.scala b/app/controllers/DataSetController.scala index 68ee33118e3..de2da0d0fa4 100755 --- a/app/controllers/DataSetController.scala +++ b/app/controllers/DataSetController.scala @@ -54,8 +54,8 @@ class DataSetController @Inject()(userService: UserService, val width = Math.clamp(w.getOrElse(DefaultThumbnailWidth), 1, MaxThumbnailHeight) val height = Math.clamp(h.getOrElse(DefaultThumbnailHeight), 1, MaxThumbnailHeight) cache.get[Array[Byte]](s"thumbnail-$organizationName*$dataSetName*$dataLayerName-$width-$height") match { - case Some(a) => - Fox.successful(a) + /*case Some(a) => + Fox.successful(a)*/ case _ => { val defaultCenterOpt = dataSet.defaultConfiguration.flatMap(c => c.configuration.get("position").flatMap(jsValue => JsonHelper.jsResultToOpt(jsValue.validate[Point3D]))) diff --git a/build.sbt b/build.sbt index 8500f0eaa9d..39060cbda29 100644 --- a/build.sbt +++ b/build.sbt @@ -8,6 +8,7 @@ ThisBuild / scapegoatVersion := "1.3.8" ThisBuild / scalacOptions ++= Seq( "-Xmax-classfile-name","100", "-target:jvm-1.8", + "-verbose", "-feature", "-deprecation", "-language:implicitConversions", diff --git a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala index 4ad35cd4bb6..da3d3753b18 100644 --- a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala +++ b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala @@ -16,16 +16,16 @@ case class CombinedImage(pages: List[CombinedPage]) case class CombinedPage(image: BufferedImage, info: List[ImagePartInfo], pageInfo: PageInfo) case class ImageCreatorParameters( - bytesPerElement: Int, - useHalfBytes: Boolean, - slideWidth: Int = 128, - slideHeight: Int = 128, - imagesPerRow: Int = 8, - imagesPerColumn: Int = Int.MaxValue, - imageWidth: Option[Int] = None, - imageHeight: Option[Int] = None, - blackAndWhite: Boolean - ) + bytesPerElement: Int, + useHalfBytes: Boolean, + slideWidth: Int = 128, + slideHeight: Int = 128, + imagesPerRow: Int = 8, + imagesPerColumn: Int = Int.MaxValue, + imageWidth: Option[Int] = None, + imageHeight: Option[Int] = None, + blackAndWhite: Boolean +) object ImageCreator extends LazyLogging { @@ -39,26 +39,28 @@ object ImageCreator extends LazyLogging { def calculateSprites(data: Array[Byte], params: ImageCreatorParameters, targetType: Int): List[BufferedImage] = { val imageData = - if(params.useHalfBytes) { + if (params.useHalfBytes) { val r = new Array[Byte](data.length * 2) - data.zipWithIndex.foreach{ + data.zipWithIndex.foreach { case (b, idx) => - r(2*idx) =(b & 0xF0).toByte - r(2*idx + 1)=(b & 0x0F << 4).toByte + r(2 * idx) = (b & 0xF0).toByte + r(2 * idx + 1) = (b & 0x0F << 4).toByte } r - } else if(params.blackAndWhite) { - data.map(d => if(d != 0x00) 0xFF.toByte else 0x00.toByte) + } else if (params.blackAndWhite) { + data.map(d => if (d != 0x00) 0xFF.toByte else 0x00.toByte) } else data + val slidingSize = params.slideHeight * params.slideWidth * params.bytesPerElement - imageData.sliding(slidingSize, slidingSize).toList.flatMap { - slice => - createBufferedImageFromBytes(slice, targetType, params) + imageData.sliding(slidingSize, slidingSize).toList.flatMap { slice => + createBufferedImageFromBytes(slice, targetType, params) } } - def createSpriteSheet(bufferedImages: List[BufferedImage], params: ImageCreatorParameters, targetType: Int): Option[CombinedImage] = { + def createSpriteSheet(bufferedImages: List[BufferedImage], + params: ImageCreatorParameters, + targetType: Int): Option[CombinedImage] = if (bufferedImages.isEmpty) { logger.warn("No images supplied for sprite sheet generation.") None @@ -67,41 +69,41 @@ object ImageCreator extends LazyLogging { val subpartHeight = params.slideHeight val imagesPerPage = math.min(params.imagesPerColumn.toLong * params.imagesPerRow, Int.MaxValue).toInt - val pages = bufferedImages.sliding(imagesPerPage, imagesPerPage).zipWithIndex.map { - case (pageImages, page) => - val depth = math.ceil(pageImages.size.toFloat / params.imagesPerRow).toInt - val imageWidth = params.imageWidth.getOrElse(subpartWidth * params.imagesPerRow) - val imageHeight = params.imageHeight.getOrElse(subpartHeight * depth) - - val finalImage = new BufferedImage(imageWidth, imageHeight, targetType) - - val info = pageImages.zipWithIndex.map { - case (image, idx) => - assert(image.getWidth() == subpartWidth, "Wrong image size!") - assert(image.getHeight() == subpartHeight, "Wrong image size!") - val w = idx % params.imagesPerRow * params.slideWidth - val h = idx / params.imagesPerRow * params.slideHeight - finalImage.createGraphics().drawImage( - image, w, h, null) - ImagePartInfo(page, w, h, subpartHeight, subpartWidth) - } - CombinedPage(finalImage, info, PageInfo(page, page * imagesPerPage, pageImages.size)) - }.toList + val pages = bufferedImages + .sliding(imagesPerPage, imagesPerPage) + .zipWithIndex + .map { + case (pageImages, page) => + val depth = math.ceil(pageImages.size.toFloat / params.imagesPerRow).toInt + val imageWidth = params.imageWidth.getOrElse(subpartWidth * params.imagesPerRow) + val imageHeight = params.imageHeight.getOrElse(subpartHeight * depth) + + val finalImage = new BufferedImage(imageWidth, imageHeight, targetType) + + val info = pageImages.zipWithIndex.map { + case (image, idx) => + assert(image.getWidth() == subpartWidth, "Wrong image size!") + assert(image.getHeight() == subpartHeight, "Wrong image size!") + val w = idx % params.imagesPerRow * params.slideWidth + val h = idx / params.imagesPerRow * params.slideHeight + finalImage.createGraphics().drawImage(image, w, h, null) + ImagePartInfo(page, w, h, subpartHeight, subpartWidth) + } + CombinedPage(finalImage, info, PageInfo(page, page * imagesPerPage, pageImages.size)) + } + .toList Some(CombinedImage(pages)) } - } - def convertToType(sourceImage: BufferedImage, targetType: Int): BufferedImage = { + def convertToType(sourceImage: BufferedImage, targetType: Int): BufferedImage = sourceImage.getType() match { case e if e == targetType => sourceImage case _ => - val image = new BufferedImage(sourceImage.getWidth(), - sourceImage.getHeight(), targetType) + val image = new BufferedImage(sourceImage.getWidth(), sourceImage.getHeight(), targetType) image.getGraphics().drawImage(sourceImage, 0, 0, null) image } - } def toRGBArray(b: Array[Byte], bytesPerElement: Int) = { val colored = new Array[Int](b.length / bytesPerElement) @@ -129,15 +131,22 @@ object ImageCreator extends LazyLogging { colored } - def createBufferedImageFromBytes(b: Array[Byte], targetType: Int, params: ImageCreatorParameters): Option[BufferedImage] = { + def createBufferedImageFromBytes(b: Array[Byte], + targetType: Int, + params: ImageCreatorParameters): Option[BufferedImage] = try { val bufferedImage = new BufferedImage(params.slideWidth, params.slideHeight, targetType) - bufferedImage.setRGB(0, 0, params.slideWidth, params.slideHeight, toRGBArray(b, params.bytesPerElement), 0, params.slideWidth) + bufferedImage.setRGB(0, + 0, + params.slideWidth, + params.slideHeight, + toRGBArray(b, params.bytesPerElement), + 0, + params.slideWidth) Some(bufferedImage) } catch { case e: IOException => logger.error("IOException while converting byte array to buffered image.", e) None } - } } From 85b9112372ac2500729dcf9a6bdabe97fc3e7573 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 29 Nov 2018 18:07:17 +0100 Subject: [PATCH 2/9] [WIP] add segmentation thumbnail and blend it over normal thumbnail on hover #3489 --- .../javascripts/dashboard/dataset_panel.js | 28 +++++++++++++++- .../model/accessors/dataset_accessor.js | 12 +++++++ app/assets/stylesheets/_dashboard.less | 7 ++++ .../util/image/ImageCreator.scala | 32 ++++++++++++++++++- 4 files changed, 77 insertions(+), 2 deletions(-) diff --git a/app/assets/javascripts/dashboard/dataset_panel.js b/app/assets/javascripts/dashboard/dataset_panel.js index c4da6b65b5e..0d808ddabb1 100644 --- a/app/assets/javascripts/dashboard/dataset_panel.js +++ b/app/assets/javascripts/dashboard/dataset_panel.js @@ -6,7 +6,11 @@ import _ from "lodash"; import type { APIDataset } from "admin/api_flow_types"; import { formatScale } from "libs/format_utils"; -import { getThumbnailURL, hasSegmentation } from "oxalis/model/accessors/dataset_accessor"; +import { + getThumbnailURL, + hasSegmentation, + getSegmentationThumbnailURL, +} from "oxalis/model/accessors/dataset_accessor"; const columnSpan = { xs: 24, sm: 24, md: 24, lg: 12, xl: 12, xxl: 8 }; const thumbnailDimension = 500; @@ -57,10 +61,12 @@ function ThumbnailAndDescription({ thumbnailURL, description, name, + segmentationThumbnailURL, }: { thumbnailURL: string, name: string, description: React.Element<*> | string, + segmentationThumbnailURL: ?string, }) { return ( @@ -74,6 +80,20 @@ function ThumbnailAndDescription({ height: "100%", }} /> + {segmentationThumbnailURL ? ( +
+ ) : null}
@@ -91,6 +111,9 @@ function ThumbnailAndDescriptionFromDataset({ dataset }: { dataset: APIDataset } thumbnailURL={getThumbnailURL(dataset)} name={getDisplayName(dataset)} description={getDescription(dataset)} + segmentationThumbnailURL={ + hasSegmentation(dataset) ? getSegmentationThumbnailURL(dataset) : null + } /> ); } @@ -149,6 +172,9 @@ class DatasetPanel extends React.PureComponent { thumbnailURL={getThumbnailURL(datasets[0])} name={groupName} description={multiDescription} + segmentationThumbnailURL={ + hasSegmentation(datasets[0]) ? getSegmentationThumbnailURL(datasets[0]) : null + } /> ); diff --git a/app/assets/javascripts/oxalis/model/accessors/dataset_accessor.js b/app/assets/javascripts/oxalis/model/accessors/dataset_accessor.js index a8b2a112276..ad667e0b6c3 100644 --- a/app/assets/javascripts/oxalis/model/accessors/dataset_accessor.js +++ b/app/assets/javascripts/oxalis/model/accessors/dataset_accessor.js @@ -183,4 +183,16 @@ export function getThumbnailURL(dataset: APIDataset): string { return ""; } +export function getSegmentationThumbnailURL(dataset: APIDataset): string { + const datasetName = dataset.name; + const organizationName = dataset.owningOrganization; + const segmentationLayer = getSegmentationLayer(dataset); + if (segmentationLayer) { + return `/api/datasets/${organizationName}/${datasetName}/layers/${ + segmentationLayer.name + }/thumbnail`; + } + return ""; +} + export default {}; diff --git a/app/assets/stylesheets/_dashboard.less b/app/assets/stylesheets/_dashboard.less index 5b9064402cc..b84abb04aee 100644 --- a/app/assets/stylesheets/_dashboard.less +++ b/app/assets/stylesheets/_dashboard.less @@ -32,6 +32,13 @@ transition: all 0.3s ease-in-out; } + .dataset-thumbnail-image.segmentation { + opacity: 0; + &:hover { + opacity: 0.2; + } + } + @media @smartphones { height: 55%; width: 100%; diff --git a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala index da3d3753b18..6e82567b150 100644 --- a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala +++ b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala @@ -121,7 +121,8 @@ object ImageCreator extends LazyLogging { case 3 => (0xFF << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) case 4 => - ((b(idx + 3) & 0xFF) << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) + toTestRGB(b(idx)) + //((b(idx + 3) & 0xFF) << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) case _ => throw new Exception("Can't handle " + bytesPerElement + " bytes per element in Image creator.") } @@ -131,6 +132,35 @@ object ImageCreator extends LazyLogging { colored } + def hsvToRgb(hsv: Array[Double]): Int = { + val K = Array(1.0, 2.0 / 3.0, 1.0 / 3.0, 3.0) + val p = Array.ofDim[Double](3) + for (i <- 0 to 2) { + val x = hsv(0) + K(i) + val decimal = x.toInt + val fract = x - decimal + p(i) = Math.abs(fract * 6.0 - K(3)) + } + val returnVal = Array.ofDim[Double](3) + for (i <- 0 to 2) { + val x = K(0) + val cl = com.scalableminds.util.tools.Math.clamp(p(i) - K(0), 0.0, 1.0) + val ret = x * (1 - hsv(1)) + cl * hsv(1) + returnVal(i) = hsv(2) * ret + } + val end = returnVal.map(x => (x * 255).toByte) + (0xFF << 24) | ((end(0) & 0xFF) << 16) | ((end(1) & 0xFF) << 8) | ((end(2) & 0xFF) << 0) + } + + def toTestRGB(b: Byte) = + b match { + case 0 => (0x64 << 24) | (0x64 << 16) | (0x64 << 8) | (0x64 << 0) + case _ => + val golden_ratio = 0.618033988749895 + val value = ((b & 0xFF) * golden_ratio) % 1.0 + hsvToRgb(Array(value, 1.0, 1.0, 1.0)) + } + def createBufferedImageFromBytes(b: Array[Byte], targetType: Int, params: ImageCreatorParameters): Option[BufferedImage] = From fb53d2b0d9a1f1e58624fe33a3950412c4f0afb2 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 6 Dec 2018 10:25:00 +0100 Subject: [PATCH 3/9] update snapshots #3507 --- .../test/enzyme/snapshot.e2e.js.md | 20 +++++++++++------- .../test/enzyme/snapshot.e2e.js.snap | Bin 31393 -> 31512 bytes 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/app/assets/javascripts/test/snapshots/public/test-bundle/test/enzyme/snapshot.e2e.js.md b/app/assets/javascripts/test/snapshots/public/test-bundle/test/enzyme/snapshot.e2e.js.md index 4e715e9ba8b..17ff8030c53 100644 --- a/app/assets/javascripts/test/snapshots/public/test-bundle/test/enzyme/snapshot.e2e.js.md +++ b/app/assets/javascripts/test/snapshots/public/test-bundle/test/enzyme/snapshot.e2e.js.md @@ -121,9 +121,10 @@ Generated by [AVA](https://ava.li).
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zj|f+)p`hBEjx^Mi@nTpZ-ExGo?AxMaBLYx`Wu57%CZdQ1pZq8@LW5RH{1=`Z`bF&A zCC!iMI7spZ&+^mK>yNB=R~ce%9=y9868Un(ES#~f`X97g%}k1A?E0Bv=F{;Hn-;iz>9oW?kHVr2wqI=cmx&te1+I*Ve1sZ4^4J;5T~Caq-c%QJtEpAI9XwHfbN z=7UM~o4!po2G|Edy|S@}PhN0vYx49A(2|XToE)*{0gi@eRHg)5)_@tez`iATh(Wtj*#rY9CVU2r~>0{PM5FwEB*H|G`#uq;$ys zRWId~A$LpUlpo(AfHA#``0`bUtx(3L2C3bD~2EOjNBQ8zrk j6o-7?BMMo7(j(vEg7tD7hE_MGKOllbC>pmcP$2&gxUoGr From 975b28a1c0b216d7a2f9a08b8db42755dc890ac2 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 6 Dec 2018 13:19:47 +0100 Subject: [PATCH 4/9] improve implementation for hsvTorgb #3507 --- .../util/image/ImageCreator.scala | 46 +++++++++---------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala index 6e82567b150..f942cb1ecef 100644 --- a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala +++ b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala @@ -121,8 +121,7 @@ object ImageCreator extends LazyLogging { case 3 => (0xFF << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) case 4 => - toTestRGB(b(idx)) - //((b(idx + 3) & 0xFF) << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) + idToRGB(b(idx)) case _ => throw new Exception("Can't handle " + bytesPerElement + " bytes per element in Image creator.") } @@ -132,34 +131,35 @@ object ImageCreator extends LazyLogging { colored } - def hsvToRgb(hsv: Array[Double]): Int = { - val K = Array(1.0, 2.0 / 3.0, 1.0 / 3.0, 3.0) - val p = Array.ofDim[Double](3) - for (i <- 0 to 2) { - val x = hsv(0) + K(i) - val decimal = x.toInt - val fract = x - decimal - p(i) = Math.abs(fract * 6.0 - K(3)) - } - val returnVal = Array.ofDim[Double](3) - for (i <- 0 to 2) { - val x = K(0) - val cl = com.scalableminds.util.tools.Math.clamp(p(i) - K(0), 0.0, 1.0) - val ret = x * (1 - hsv(1)) + cl * hsv(1) - returnVal(i) = hsv(2) * ret + def idToRGB(b: Byte) = { + def hueToRGB(h: Double): Int = { + + val i: Double = Math.floor(h * 6f) + val f: Double = h * 6f - i + + val (r, g, b) = i % 6 match { + case 0 => (1.0, f, 0.0) + case 1 => (1.0 - f, 1.0, 0.0) + case 2 => (0.0, 1.0, f) + case 3 => (0.0, 1.0 - f, 1.0) + case 4 => (f, 0.0, 1.0) + case 5 => (1.0, 0.0, 1.0 - f) + } + + val rByte = (r * 255).toByte + val gByte = (g * 255).toByte + val bByte = (b * 255).toByte + (0xFF << 24) | ((rByte & 0xFF) << 16) | ((gByte & 0xFF) << 8) | ((bByte & 0xFF) << 0) } - val end = returnVal.map(x => (x * 255).toByte) - (0xFF << 24) | ((end(0) & 0xFF) << 16) | ((end(1) & 0xFF) << 8) | ((end(2) & 0xFF) << 0) - } - def toTestRGB(b: Byte) = b match { case 0 => (0x64 << 24) | (0x64 << 16) | (0x64 << 8) | (0x64 << 0) case _ => val golden_ratio = 0.618033988749895 - val value = ((b & 0xFF) * golden_ratio) % 1.0 - hsvToRgb(Array(value, 1.0, 1.0, 1.0)) + val hue = ((b & 0xFF) * golden_ratio) % 1.0 + hueToRGB(hue) } + } def createBufferedImageFromBytes(b: Array[Byte], targetType: Int, From 3578d04d5d2a1a3e720a83f631a2c5163f3b753c Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 6 Dec 2018 13:23:10 +0100 Subject: [PATCH 5/9] remove development changes #3507 --- app/controllers/DataSetController.scala | 4 ++-- build.sbt | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/app/controllers/DataSetController.scala b/app/controllers/DataSetController.scala index de2da0d0fa4..68ee33118e3 100755 --- a/app/controllers/DataSetController.scala +++ b/app/controllers/DataSetController.scala @@ -54,8 +54,8 @@ class DataSetController @Inject()(userService: UserService, val width = Math.clamp(w.getOrElse(DefaultThumbnailWidth), 1, MaxThumbnailHeight) val height = Math.clamp(h.getOrElse(DefaultThumbnailHeight), 1, MaxThumbnailHeight) cache.get[Array[Byte]](s"thumbnail-$organizationName*$dataSetName*$dataLayerName-$width-$height") match { - /*case Some(a) => - Fox.successful(a)*/ + case Some(a) => + Fox.successful(a) case _ => { val defaultCenterOpt = dataSet.defaultConfiguration.flatMap(c => c.configuration.get("position").flatMap(jsValue => JsonHelper.jsResultToOpt(jsValue.validate[Point3D]))) diff --git a/build.sbt b/build.sbt index 39060cbda29..8500f0eaa9d 100644 --- a/build.sbt +++ b/build.sbt @@ -8,7 +8,6 @@ ThisBuild / scapegoatVersion := "1.3.8" ThisBuild / scalacOptions ++= Seq( "-Xmax-classfile-name","100", "-target:jvm-1.8", - "-verbose", "-feature", "-deprecation", "-language:implicitConversions", From eb067a1b70d629a05079b9338eb13bcb4695f3b3 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 6 Dec 2018 13:31:42 +0100 Subject: [PATCH 6/9] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 037ba0f1868..aca616f0f10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md). ### Added - Added the possibility to specify a recommended user configuration in a task type. The recommended configuration will be shown to users when they trace a task with a different task type and the configuration can be accepted or declined. [#3466](https://github.com/scalableminds/webknossos/pull/3466) +- Added a second thumbnail for the datasets which have a segmentation layer and this segmentation thumbnail will be shown on hover over the other thumbnail. [#3507](https://github.com/scalableminds/webknossos/pull/3507) ### Changed From 2e120b30ebf582c8b237419d2f898a08729fb325 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 6 Dec 2018 14:01:45 +0100 Subject: [PATCH 7/9] also make a colorful segmentation thumbnail for 2 byte segmentations #3507 --- .../scala/com/scalableminds/util/image/ImageCreator.scala | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala index f942cb1ecef..42ebacf93d4 100644 --- a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala +++ b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala @@ -116,8 +116,9 @@ object ImageCreator extends LazyLogging { val gray = b(idx) (0xFF << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) case 2 => - val gray = b(idx) - (b(idx + 1) << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) + idToRGB(b(idx)) + //val gray = b(idx) + //(b(idx + 1) << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) case 3 => (0xFF << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) case 4 => From a9fd26573942ea7a0009754b2cb9ba695c04b60a Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 6 Dec 2018 15:16:11 +0100 Subject: [PATCH 8/9] make overlay work at the same time as the zoom effect and support 8 byte segmentations #3507 --- app/assets/stylesheets/_dashboard.less | 22 +++++++++---------- .../util/image/ImageCreator.scala | 4 ++-- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/app/assets/stylesheets/_dashboard.less b/app/assets/stylesheets/_dashboard.less index b84abb04aee..121a0a08fa7 100644 --- a/app/assets/stylesheets/_dashboard.less +++ b/app/assets/stylesheets/_dashboard.less @@ -28,17 +28,6 @@ background-color: #e8e8e8; position: relative; - .dataset-thumbnail-image { - transition: all 0.3s ease-in-out; - } - - .dataset-thumbnail-image.segmentation { - opacity: 0; - &:hover { - opacity: 0.2; - } - } - @media @smartphones { height: 55%; width: 100%; @@ -46,6 +35,17 @@ } } +.dataset-thumbnail-image { + transition: all 0.3s ease-in-out; + &.segmentation { + opacity: 0; + } +} + +.spotlight-item-card:hover .dataset-thumbnail-image.segmentation { + opacity: 0.2; +} + .dataset-description { position: absolute; display: inline-block; diff --git a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala index 42ebacf93d4..1a61ac3e6c8 100644 --- a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala +++ b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala @@ -117,12 +117,12 @@ object ImageCreator extends LazyLogging { (0xFF << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) case 2 => idToRGB(b(idx)) - //val gray = b(idx) - //(b(idx + 1) << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) case 3 => (0xFF << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) case 4 => idToRGB(b(idx)) + case 8 => + idToRGB(b(idx)) case _ => throw new Exception("Can't handle " + bytesPerElement + " bytes per element in Image creator.") } From f9461b213f4e53d559ee186dfbf2127f044d9531 Mon Sep 17 00:00:00 2001 From: Youri K Date: Thu, 20 Dec 2018 11:27:05 +0100 Subject: [PATCH 9/9] check if requested layer is segmentation so only there the data gets interpreted as id #3507 --- .../util/image/ImageCreator.scala | 40 +- .../controllers/BinaryDataController.scala | 505 +++++++++--------- 2 files changed, 288 insertions(+), 257 deletions(-) diff --git a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala index 1a61ac3e6c8..62c94e38ee8 100644 --- a/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala +++ b/util/src/main/scala/com/scalableminds/util/image/ImageCreator.scala @@ -24,7 +24,8 @@ case class ImageCreatorParameters( imagesPerColumn: Int = Int.MaxValue, imageWidth: Option[Int] = None, imageHeight: Option[Int] = None, - blackAndWhite: Boolean + blackAndWhite: Boolean, + isSegmentation: Boolean = false ) object ImageCreator extends LazyLogging { @@ -105,27 +106,30 @@ object ImageCreator extends LazyLogging { image } - def toRGBArray(b: Array[Byte], bytesPerElement: Int) = { + def toRGBArray(b: Array[Byte], bytesPerElement: Int, isSegmentation: Boolean) = { val colored = new Array[Int](b.length / bytesPerElement) var idx = 0 val l = b.length while (idx + bytesPerElement <= l) { colored(idx / bytesPerElement) = { - bytesPerElement match { - case 1 => - val gray = b(idx) - (0xFF << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) - case 2 => - idToRGB(b(idx)) - case 3 => - (0xFF << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) - case 4 => - idToRGB(b(idx)) - case 8 => - idToRGB(b(idx)) - case _ => - throw new Exception("Can't handle " + bytesPerElement + " bytes per element in Image creator.") - } + if (isSegmentation) + idToRGB(b(idx)) + else + bytesPerElement match { + case 1 => + val gray = b(idx) + (0xFF << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) + case 2 => + val gray = b(idx) + (b(idx + 1) << 24) | ((gray & 0xFF) << 16) | ((gray & 0xFF) << 8) | ((gray & 0xFF) << 0) + case 3 => + (0xFF << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) + case 4 => + ((b(idx + 3) & 0xFF) << 24) | ((b(idx) & 0xFF) << 16) | ((b(idx + 1) & 0xFF) << 8) | ((b(idx + 2) & 0xFF) << 0) + case _ => + throw new Exception( + "Can't handle " + bytesPerElement + " bytes per element in Image creator for a color layer.") + } } idx += bytesPerElement } @@ -171,7 +175,7 @@ object ImageCreator extends LazyLogging { 0, params.slideWidth, params.slideHeight, - toRGBArray(b, params.bytesPerElement), + toRGBArray(b, params.bytesPerElement, params.isSegmentation), 0, params.slideWidth) Some(bufferedImage) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/BinaryDataController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/BinaryDataController.scala index ddc879cce0f..547d9854040 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/BinaryDataController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/BinaryDataController.scala @@ -9,8 +9,12 @@ import com.google.inject.Inject import com.scalableminds.util.geometry.Point3D import com.scalableminds.webknossos.datastore.services._ import com.scalableminds.webknossos.datastore.models._ -import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSource, DataSourceId, SegmentationLayer} -import com.scalableminds.webknossos.datastore.models.requests.{DataServiceDataRequest, DataServiceMappingRequest, DataServiceRequestSettings} +import com.scalableminds.webknossos.datastore.models.datasource._ +import com.scalableminds.webknossos.datastore.models.requests.{ + DataServiceDataRequest, + DataServiceMappingRequest, + DataServiceRequestSettings +} import com.scalableminds.webknossos.datastore.models.DataRequestCollection._ import com.scalableminds.webknossos.datastore.models.{DataRequest, ImageThumbnail, WebKnossosDataRequest} import com.scalableminds.util.image.{ImageCreator, ImageCreatorParameters, JPEGWriter} @@ -26,13 +30,11 @@ import play.api.mvc.{PlayBodyParsers, ResponseHeader, Result} import scala.concurrent.{ExecutionContext, Future} class BinaryDataController @Inject()( - dataSourceRepository: DataSourceRepository, - config: DataStoreConfig, - accessTokenService: DataStoreAccessTokenService, - binaryDataServiceHolder: BinaryDataServiceHolder) - (implicit ec: ExecutionContext, - bodyParsers: PlayBodyParsers) - extends Controller { + dataSourceRepository: DataSourceRepository, + config: DataStoreConfig, + accessTokenService: DataStoreAccessTokenService, + binaryDataServiceHolder: BinaryDataServiceHolder)(implicit ec: ExecutionContext, bodyParsers: PlayBodyParsers) + extends Controller { val binaryDataService = binaryDataServiceHolder.binaryDataService @@ -40,279 +42,302 @@ class BinaryDataController @Inject()( * Handles requests for raw binary data via HTTP POST from webKnossos. */ def requestViaWebKnossos( - organizationName: String, - dataSetName: String, - dataLayerName: String - ) = Action.async(validateJson[List[WebKnossosDataRequest]]) { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) - (data, indices) <- requestData(dataSource, dataLayer, request.body) - } yield Ok(data).withHeaders(getMissingBucketsHeaders(indices): _*) - } + organizationName: String, + dataSetName: String, + dataLayerName: String + ) = Action.async(validateJson[List[WebKnossosDataRequest]]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) + (data, indices) <- requestData(dataSource, dataLayer, request.body) + } yield Ok(data).withHeaders(getMissingBucketsHeaders(indices): _*) } + } } - def getMissingBucketsHeaders(indices: List[Int]): Seq[(String, String)] = { - List(("MISSING-BUCKETS" -> formatMissingBucketList(indices)), ("Access-Control-Expose-Headers" -> "MISSING-BUCKETS")) - } + def getMissingBucketsHeaders(indices: List[Int]): Seq[(String, String)] = + List(("MISSING-BUCKETS" -> formatMissingBucketList(indices)), + ("Access-Control-Expose-Headers" -> "MISSING-BUCKETS")) - def formatMissingBucketList(indices: List[Int]): String = { + def formatMissingBucketList(indices: List[Int]): String = "[" + indices.mkString(", ") + "]" - } /** * Handles requests for raw binary data via HTTP GET. */ def requestRawCuboid( - organizationName: String, - dataSetName: String, - dataLayerName: String, - x: Int, - y: Int, - z: Int, - width: Int, - height: Int, - depth: Int, - resolution: Int, - halfByte: Boolean - ) = Action.async { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) - request = DataRequest( - new VoxelPosition(x, y, z, dataLayer.lookUpResolution(resolution)), - width, - height, - depth, - DataServiceRequestSettings(halfByte = halfByte) - ) - (data, indices) <- requestData(dataSource, dataLayer, request) - } yield Ok(data).withHeaders(getMissingBucketsHeaders(indices): _*) - } + organizationName: String, + dataSetName: String, + dataLayerName: String, + x: Int, + y: Int, + z: Int, + width: Int, + height: Int, + depth: Int, + resolution: Int, + halfByte: Boolean + ) = Action.async { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) + request = DataRequest( + new VoxelPosition(x, y, z, dataLayer.lookUpResolution(resolution)), + width, + height, + depth, + DataServiceRequestSettings(halfByte = halfByte) + ) + (data, indices) <- requestData(dataSource, dataLayer, request) + } yield Ok(data).withHeaders(getMissingBucketsHeaders(indices): _*) } + } } /** * Handles requests for raw binary data via HTTP GET for debugging. */ def requestViaAjaxDebug( - organizationName: String, - dataSetName: String, - dataLayerName: String, - cubeSize: Int, - x: Int, - y: Int, - z: Int, - resolution: Int, - halfByte: Boolean - ) = - requestRawCuboid(organizationName, dataSetName, dataLayerName, x, y, z, cubeSize, cubeSize, cubeSize, resolution, halfByte) + organizationName: String, + dataSetName: String, + dataLayerName: String, + cubeSize: Int, + x: Int, + y: Int, + z: Int, + resolution: Int, + halfByte: Boolean + ) = + requestRawCuboid(organizationName, + dataSetName, + dataLayerName, + x, + y, + z, + cubeSize, + cubeSize, + cubeSize, + resolution, + halfByte) /** * Handles a request for raw binary data via a HTTP GET. Used by knossos. */ - def requestViaKnossos( - organizationName: String, - dataSetName: String, - dataLayerName: String, - resolution: Int, - x: Int, y: Int, z: Int, - cubeSize: Int) = Action.async { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) - request = DataRequest( - new VoxelPosition(x * cubeSize * resolution, - y * cubeSize * resolution, - z * cubeSize * resolution, - Point3D(resolution, resolution, resolution)), - cubeSize, - cubeSize, - cubeSize) - (data, indices) <- requestData(dataSource, dataLayer, request) - } yield Ok(data).withHeaders(getMissingBucketsHeaders(indices): _*) - } + def requestViaKnossos(organizationName: String, + dataSetName: String, + dataLayerName: String, + resolution: Int, + x: Int, + y: Int, + z: Int, + cubeSize: Int) = Action.async { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) + request = DataRequest( + new VoxelPosition(x * cubeSize * resolution, + y * cubeSize * resolution, + z * cubeSize * resolution, + Point3D(resolution, resolution, resolution)), + cubeSize, + cubeSize, + cubeSize + ) + (data, indices) <- requestData(dataSource, dataLayer, request) + } yield Ok(data).withHeaders(getMissingBucketsHeaders(indices): _*) } + } } /** * Handles requests for data sprite sheets. */ def requestSpriteSheet( - organizationName: String, - dataSetName: String, - dataLayerName: String, - cubeSize: Int, - imagesPerRow: Int, - x: Int, - y: Int, - z: Int, - resolution: Int, - halfByte: Boolean - ) = Action.async(parse.raw) { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) - dataRequest = DataRequest( - new VoxelPosition(x, y, z, dataLayer.lookUpResolution(resolution)), - cubeSize, - cubeSize, - cubeSize, - DataServiceRequestSettings(halfByte = halfByte)) - imageProvider <- respondWithSpriteSheet(dataSource, dataLayer, dataRequest, imagesPerRow, blackAndWhite = false) - } yield { - Result( - header = ResponseHeader(200), - body = HttpEntity.Streamed(StreamConverters.asOutputStream().mapMaterializedValue { - outputStream => imageProvider(outputStream) - }, None, Some(contentTypeJpeg))) - } + organizationName: String, + dataSetName: String, + dataLayerName: String, + cubeSize: Int, + imagesPerRow: Int, + x: Int, + y: Int, + z: Int, + resolution: Int, + halfByte: Boolean + ) = Action.async(parse.raw) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) + dataRequest = DataRequest(new VoxelPosition(x, y, z, dataLayer.lookUpResolution(resolution)), + cubeSize, + cubeSize, + cubeSize, + DataServiceRequestSettings(halfByte = halfByte)) + imageProvider <- respondWithSpriteSheet(dataSource, + dataLayer, + dataRequest, + imagesPerRow, + blackAndWhite = false) + } yield { + Result( + header = ResponseHeader(200), + body = HttpEntity.Streamed(StreamConverters.asOutputStream().mapMaterializedValue { outputStream => + imageProvider(outputStream) + }, None, Some(contentTypeJpeg)) + ) } } + } } /** * Handles requests for data images. */ - def requestImage( - organizationName: String, - dataSetName: String, - dataLayerName: String, - width: Int, - height: Int, - x: Int, - y: Int, - z: Int, - resolution: Int, - halfByte: Boolean, - blackAndWhite: Boolean) = Action.async(parse.raw) { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) - dataRequest = DataRequest( - new VoxelPosition(x, y, z, dataLayer.lookUpResolution(resolution)), - width, - height, - 1, - DataServiceRequestSettings(halfByte = halfByte)) - imageProvider <- respondWithSpriteSheet(dataSource, dataLayer, dataRequest, 1, blackAndWhite) - } yield { - Result( - header = ResponseHeader(200), - body = HttpEntity.Streamed(StreamConverters.asOutputStream().mapMaterializedValue { - outputStream => imageProvider(outputStream) - }, None, Some(contentTypeJpeg))) - } + def requestImage(organizationName: String, + dataSetName: String, + dataLayerName: String, + width: Int, + height: Int, + x: Int, + y: Int, + z: Int, + resolution: Int, + halfByte: Boolean, + blackAndWhite: Boolean) = Action.async(parse.raw) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) + dataRequest = DataRequest(new VoxelPosition(x, y, z, dataLayer.lookUpResolution(resolution)), + width, + height, + 1, + DataServiceRequestSettings(halfByte = halfByte)) + imageProvider <- respondWithSpriteSheet(dataSource, dataLayer, dataRequest, 1, blackAndWhite) + } yield { + Result( + header = ResponseHeader(200), + body = HttpEntity.Streamed(StreamConverters.asOutputStream().mapMaterializedValue { outputStream => + imageProvider(outputStream) + }, None, Some(contentTypeJpeg)) + ) } } + } } /** * Handles requests for dataset thumbnail images as JPEG. */ - def requestImageThumbnailJpeg( - organizationName: String, - dataSetName: String, - dataLayerName: String, - width: Int, - height: Int, - centerX: Option[Int], - centerY: Option[Int], - centerZ: Option[Int], - zoom: Option[Double]) = Action.async(parse.raw) { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - thumbnailProvider <- respondWithImageThumbnail(organizationName, dataSetName, dataLayerName, width, height, centerX, centerY, centerZ, zoom) - } yield { - Result( - header = ResponseHeader(200), - body = HttpEntity.Streamed(StreamConverters.asOutputStream().mapMaterializedValue { - outputStream => thumbnailProvider(outputStream) - }, None, Some(contentTypeJpeg))) - } + def requestImageThumbnailJpeg(organizationName: String, + dataSetName: String, + dataLayerName: String, + width: Int, + height: Int, + centerX: Option[Int], + centerY: Option[Int], + centerZ: Option[Int], + zoom: Option[Double]) = Action.async(parse.raw) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + thumbnailProvider <- respondWithImageThumbnail(organizationName, + dataSetName, + dataLayerName, + width, + height, + centerX, + centerY, + centerZ, + zoom) + } yield { + Result( + header = ResponseHeader(200), + body = HttpEntity.Streamed(StreamConverters.asOutputStream().mapMaterializedValue { outputStream => + thumbnailProvider(outputStream) + }, None, Some(contentTypeJpeg)) + ) } } + } } /** * Handles requests for dataset thumbnail images as base64-encoded JSON. */ def requestImageThumbnailJson( - organizationName: String, - dataSetName: String, - dataLayerName: String, - width: Int, - height: Int, - centerX: Option[Int], - centerY: Option[Int], - centerZ: Option[Int], - zoom: Option[Double] - ) = Action.async(parse.raw) { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - thumbnailProvider <- respondWithImageThumbnail(organizationName, dataSetName, dataLayerName, width, height, centerX, centerY, centerZ, zoom) - } yield { - val os = new ByteArrayOutputStream() - thumbnailProvider(Base64.getEncoder.wrap(os)) - Ok(Json.toJson(ImageThumbnail(contentTypeJpeg, os.toString))) - } + organizationName: String, + dataSetName: String, + dataLayerName: String, + width: Int, + height: Int, + centerX: Option[Int], + centerY: Option[Int], + centerZ: Option[Int], + zoom: Option[Double] + ) = Action.async(parse.raw) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + thumbnailProvider <- respondWithImageThumbnail(organizationName, + dataSetName, + dataLayerName, + width, + height, + centerX, + centerY, + centerZ, + zoom) + } yield { + val os = new ByteArrayOutputStream() + thumbnailProvider(Base64.getEncoder.wrap(os)) + Ok(Json.toJson(ImageThumbnail(contentTypeJpeg, os.toString))) } } + } } /** * Handles mapping requests. */ def requestMapping( - organizationName: String, - dataSetName: String, - dataLayerName: String, - mappingName: String - ) = Action.async { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { - AllowRemoteOrigin { - for { - (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) - segmentationLayer <- tryo(dataLayer.asInstanceOf[SegmentationLayer]).toFox ?~> Messages("dataLayer.notFound") - mappingRequest = DataServiceMappingRequest(dataSource, segmentationLayer, mappingName) - result <- binaryDataService.handleMappingRequest(mappingRequest) - } yield { - Ok(result) - } + organizationName: String, + dataSetName: String, + dataLayerName: String, + mappingName: String + ) = Action.async { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName))) { + AllowRemoteOrigin { + for { + (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) + segmentationLayer <- tryo(dataLayer.asInstanceOf[SegmentationLayer]).toFox ?~> Messages("dataLayer.notFound") + mappingRequest = DataServiceMappingRequest(dataSource, segmentationLayer, mappingName) + result <- binaryDataService.handleMappingRequest(mappingRequest) + } yield { + Ok(result) } } + } } - private def getDataSourceAndDataLayer(organizationName: String, dataSetName: String, dataLayerName: String)(implicit m: MessagesProvider): Fox[(DataSource, DataLayer)] = { + private def getDataSourceAndDataLayer(organizationName: String, dataSetName: String, dataLayerName: String)( + implicit m: MessagesProvider): Fox[(DataSource, DataLayer)] = for { - dataSource <- dataSourceRepository.findUsable(DataSourceId(dataSetName, organizationName)).toFox ?~> Messages("dataSource.notFound") ~> 404 + dataSource <- dataSourceRepository.findUsable(DataSourceId(dataSetName, organizationName)).toFox ?~> Messages( + "dataSource.notFound") ~> 404 dataLayer <- dataSource.getDataLayer(dataLayerName) ?~> Messages("dataLayer.notFound", dataLayerName) ~> 404 } yield { (dataSource, dataLayer) } - } private def requestData( - dataSource: DataSource, - dataLayer: DataLayer, - dataRequests: DataRequestCollection - ): Fox[(Array[Byte], List[Int])] = { + dataSource: DataSource, + dataLayer: DataLayer, + dataRequests: DataRequestCollection + ): Fox[(Array[Byte], List[Int])] = { val requests = dataRequests.map(r => DataServiceDataRequest(dataSource, dataLayer, r.cuboid(dataLayer), r.settings)) binaryDataService.handleDataRequests(requests) } @@ -320,22 +345,26 @@ class BinaryDataController @Inject()( private def contentTypeJpeg = "image/jpeg" private def respondWithSpriteSheet( - dataSource: DataSource, - dataLayer: DataLayer, - request: DataRequest, - imagesPerRow: Int, - blackAndWhite: Boolean - )(implicit m: MessagesProvider): Fox[(OutputStream) => Unit] = { + dataSource: DataSource, + dataLayer: DataLayer, + request: DataRequest, + imagesPerRow: Int, + blackAndWhite: Boolean + )(implicit m: MessagesProvider): Fox[(OutputStream) => Unit] = { val params = ImageCreatorParameters( dataLayer.bytesPerElement, request.settings.halfByte, request.cuboid(dataLayer).width, request.cuboid(dataLayer).height, imagesPerRow, - blackAndWhite = blackAndWhite) + blackAndWhite = blackAndWhite, + isSegmentation = dataLayer.category == Category.segmentation + ) for { (data, indices) <- requestData(dataSource, dataLayer, request) - dataWithFallback = if (data.length == 0) new Array[Byte](params.slideHeight * params.slideWidth * params.bytesPerElement) else data + dataWithFallback = if (data.length == 0) + new Array[Byte](params.slideHeight * params.slideWidth * params.bytesPerElement) + else data spriteSheet <- ImageCreator.spriteSheetFor(dataWithFallback, params) ?~> Messages("image.create.failed") firstSheet <- spriteSheet.pages.headOption ?~> Messages("image.page.failed") } yield { @@ -344,16 +373,16 @@ class BinaryDataController @Inject()( } private def respondWithImageThumbnail( - organizationName: String, - dataSetName: String, - dataLayerName: String, - width: Int, - height: Int, - centerX: Option[Int], - centerY: Option[Int], - centerZ: Option[Int], - zoom: Option[Double] - )(implicit m: MessagesProvider): Fox[(OutputStream) => Unit] = { + organizationName: String, + dataSetName: String, + dataLayerName: String, + width: Int, + height: Int, + centerX: Option[Int], + centerY: Option[Int], + centerZ: Option[Int], + zoom: Option[Double] + )(implicit m: MessagesProvider): Fox[(OutputStream) => Unit] = for { (dataSource, dataLayer) <- getDataSourceAndDataLayer(organizationName, dataSetName, dataLayerName) position = ImageThumbnail.goodThumbnailParameters(dataLayer, width, height, centerX, centerY, centerZ, zoom) @@ -362,16 +391,14 @@ class BinaryDataController @Inject()( } yield { image } - } - def clearCache(organizationName: String, dataSetName: String) = Action.async { - implicit request => - accessTokenService.validateAccess(UserAccessRequest.administrateDataSources) { - AllowRemoteOrigin { - val count = binaryDataService.clearCache(organizationName, dataSetName) - Future.successful(Ok("Closed " + count + " file handles")) - } + def clearCache(organizationName: String, dataSetName: String) = Action.async { implicit request => + accessTokenService.validateAccess(UserAccessRequest.administrateDataSources) { + AllowRemoteOrigin { + val count = binaryDataService.clearCache(organizationName, dataSetName) + Future.successful(Ok("Closed " + count + " file handles")) } + } } }