Followups for OME-TIFF export

CHANGELOG.unreleased.md

@@ -16,7 +16,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - If an annotation that others are allowed to edit is opened, it will now be automatically locked. This prevents conflicts when multiple users try to edit it at the same time. [#6819](https://github.com/scalableminds/webknossos/pull/6819)
 - Added new mesh-related menu items to the context menu when a mesh is hovered in the 3d viewport. [#](https://github.com/scalableminds/webknossos/pull/6813)
 - Highlight 'organization owner' in Admin>User page. [#6832](https://github.com/scalableminds/webknossos/pull/6832
-- Added OME-TIFF export for bounding boxes. [#6838](https://github.com/scalableminds/webknossos/pull/6838)
+- Added OME-TIFF export for bounding boxes. [#6838](https://github.com/scalableminds/webknossos/pull/6838) [#6874](https://github.com/scalableminds/webknossos/pull/6874)
 - Added functions to get and set segment colors to the frontend API (`api.data.{getSegmentColor,setSegmentColor}`). [#6853](https://github.com/scalableminds/webknossos/pull/6853)
 
 ### Changed

app/controllers/JobsController.scala

@@ -235,7 +235,7 @@ class JobsController @Inject()(jobDAO: JobDAO,
           dataSet <- dataSetDAO.findOneByNameAndOrganizationName(dataSetName, organizationName) ?~> Messages(
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND
-          _ <- jobService.assertTiffExportBoundingBoxLimits(bbox)
+          _ <- jobService.assertTiffExportBoundingBoxLimits(bbox, mag)
           userAuthToken <- wkSilhouetteEnvironment.combinedAuthenticatorService.findOrCreateToken(
             request.identity.loginInfo)
           command = "export_tiff"

app/models/job/Job.scala

@@ -1,7 +1,7 @@
 package models.job
 
 import com.scalableminds.util.accesscontext.{DBAccessContext, GlobalAccessContext}
-import com.scalableminds.util.geometry.BoundingBox
+import com.scalableminds.util.geometry.{BoundingBox, Vec3Int}
 import com.scalableminds.util.mvc.Formatter
 import com.scalableminds.util.time.Instant
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
@@ -365,11 +365,13 @@ class JobService @Inject()(wkConf: WkConf,
       _ <- workerDAO.findOneByDataStore(dataStoreName)
     } yield ()
 
-  def assertTiffExportBoundingBoxLimits(bbox: String): Fox[Unit] =
+  def assertTiffExportBoundingBoxLimits(boundingBox: String, mag: Option[String]): Fox[Unit] =
     for {
-      boundingBox <- BoundingBox.fromLiteral(bbox).toFox ?~> "job.export.tiff.invalidBoundingBox"
-      _ <- bool2Fox(boundingBox.volume <= wkConf.Features.exportTiffMaxVolumeMVx * 1024 * 1024) ?~> "job.export.tiff.volumeExceeded"
-      _ <- bool2Fox(boundingBox.dimensions.maxDim <= wkConf.Features.exportTiffMaxEdgeLengthVx) ?~> "job.export.tiff.edgeLengthExceeded"
+      parsedBoundingBox <- BoundingBox.fromLiteral(boundingBox).toFox ?~> "job.export.tiff.invalidBoundingBox"
+      parsedMag <- Vec3Int.fromMagLiteral(mag.getOrElse("1-1-1"), true) ?~> "job.export.tiff.invalidMag"
+      boundingBoxInMag = parsedBoundingBox / parsedMag
+      _ <- bool2Fox(boundingBoxInMag.volume <= wkConf.Features.exportTiffMaxVolumeMVx * 1024 * 1024) ?~> "job.export.tiff.volumeExceeded"
+      _ <- bool2Fox(boundingBoxInMag.dimensions.maxDim <= wkConf.Features.exportTiffMaxEdgeLengthVx) ?~> "job.export.tiff.edgeLengthExceeded"
     } yield ()
 
 }

conf/messages

@@ -285,6 +285,7 @@ job.disabled = Long-running jobs are not enabled for this WEBKNOSSOS instance.
 job.worker.notFound = Could not find this worker in the database.
 job.export.fileNotFound = Exported file not found. The link may be expired.
 job.export.tiff.invalidBoundingBox = The selected bounding box could not be parsed, must be x,y,z,width,height,depth
+job.export.tiff.invalidMag = The selected mag could not be parsed, must be x-y-z
 job.export.tiff.volumeExceeded = The volume of the selected bounding box is too large.
 job.export.tiff.edgeLengthExceeded = An edge length of the selected bounding box is too large.
 job.inferNuclei.notAllowed.organization = Currently nuclei inferral is only allowed for datasets of your own organization.

frontend/javascripts/admin/admin_rest_api.ts

@@ -1,4 +1,3 @@
-import { saveAs } from "file-saver";
 import ResumableJS from "resumablejs";
 import _ from "lodash";
 import dayjs from "dayjs";
@@ -985,6 +984,15 @@ export function convertToHybridTracing(
   });
 }
 
+export async function downloadWithFilename(downloadUrl: string) {
+  const link = document.createElement("a");
+  link.href = downloadUrl;
+  link.rel = "noopener";
+  document.body.appendChild(link);
+  link.click();
+  document.body.removeChild(link);
+}
+
 export async function downloadAnnotation(
   annotationId: string,
   annotationType: APIAnnotationType,
@@ -1005,24 +1013,7 @@ export async function downloadAnnotation(
   const maybeAmpersand = possibleVersionString === "" && !includeVolumeData ? "" : "&";
 
   const downloadUrl = `/api/annotations/${annotationType}/${annotationId}/download?${possibleVersionString}${maybeAmpersand}${skipVolumeDataString}`;
-  const { buffer, headers } = await Request.receiveArraybuffer(downloadUrl, {
-    extractHeaders: true,
-  });
-
-  // Using headers to determine the name and type of the file.
-  const contentDispositionHeader = headers["content-disposition"];
-  const filenameStartingPart = 'filename="';
-  const filenameStartingPosition =
-    contentDispositionHeader.indexOf(filenameStartingPart) + filenameStartingPart.length;
-  const filenameEndPosition = contentDispositionHeader.indexOf('"', filenameStartingPosition + 1);
-  const filename = contentDispositionHeader.substring(
-    filenameStartingPosition,
-    filenameEndPosition,
-  );
-  const blob = new Blob([buffer], {
-    type: headers["content-type"],
-  });
-  saveAs(blob, filename);
+  await downloadWithFilename(downloadUrl);
 }
 
 // When the annotation is open, please use the corresponding method

frontend/javascripts/oxalis/view/action-bar/download_modal_view.tsx

@@ -10,6 +10,7 @@ import features from "features";
 import {
   doWithToken,
   downloadAnnotation,
+  downloadWithFilename,
   getAuthToken,
   startExportTiffJob,
 } from "admin/admin_rest_api";
@@ -41,7 +42,6 @@ import {
 import { formatBytes, formatScale } from "libs/format_utils";
 import { BoundingBoxType, Vector3 } from "oxalis/constants";
 import { useStartAndPollJob } from "admin/job/job_hooks";
-import { saveAs } from "file-saver";
 const CheckboxGroup = Checkbox.Group;
 const { TabPane } = Tabs;
 const { Paragraph, Text } = Typography;
@@ -290,7 +290,7 @@ function _DownloadModalView({
     async onSuccess(job) {
       if (job.resultLink != null) {
         const token = await doWithToken(async (t) => t);
-        saveAs(`${job.resultLink}?token=${token}`);
+        downloadWithFilename(`${job.resultLink}?token=${token}`);
       }
     },
     onFailure() {

test/backend/MathTestSuite.scala

@@ -0,0 +1,19 @@
+package backend
+
+import com.scalableminds.util.tools.Math.ceilDiv
+import org.scalatestplus.play.PlaySpec
+
+class MathTestSuite extends PlaySpec {
+  "Math" should {
+    "ceilDiv correctly" in {
+      assert(ceilDiv(5, 2) == 3)
+      assert(ceilDiv(-5, 2) == -3)
+      assert(ceilDiv(5, -2) == -3)
+      assert(ceilDiv(-5, -2) == 3)
+      assert(ceilDiv(4, 2) == 2)
+
+      assert(ceilDiv(5L, 2L) == 3L)
+      assert(ceilDiv(4L, 2L) == 2L)
+    }
+  }
+}

util/src/main/scala/com/scalableminds/util/geometry/BoundingBox.scala

@@ -1,5 +1,6 @@
 package com.scalableminds.util.geometry
 
+import com.scalableminds.util.tools.Math.ceilDiv
 import net.liftweb.common.Full
 
 case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
@@ -55,6 +56,10 @@ case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
   def *(that: Vec3Int): BoundingBox =
     BoundingBox(topLeft * that, width * that.x, height * that.y, depth * that.z)
 
+  def /(that: Vec3Int): BoundingBox =
+    // Since floorDiv is used for topLeft, ceilDiv is used for the size to avoid voxels being lost at the border
+    BoundingBox(topLeft / that, ceilDiv(width, that.x), ceilDiv(height, that.y), ceilDiv(depth, that.z))
+
   def toSql: List[Int] =
     List(topLeft.x, topLeft.y, topLeft.z, width, height, depth)
 

util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala

@@ -14,6 +14,9 @@ case class Vec3Int(x: Int, y: Int, z: Int) {
   def *(that: Int): Vec3Int =
     Vec3Int(x * that, y * that, z * that)
 
+  def /(that: Vec3Int): Vec3Int =
+    Vec3Int(x / that.x, y / that.y, z / that.z)
+
   def scale(s: Float): Vec3Int =
     Vec3Int((x * s).toInt, (y * s).toInt, (z * s).toInt)
 

util/src/main/scala/com/scalableminds/util/tools/Math.scala

@@ -30,4 +30,14 @@ object Math {
 
   def stdDev[T: Numeric](xs: Iterable[T]): Double = math.sqrt(variance(xs))
 
+  def ceilDiv(num: Long, divisor: Long): Long = {
+    val sign = num.signum * divisor.signum
+    sign * (num.abs + divisor.abs - 1) / divisor.abs
+  }
+
+  def ceilDiv(num: Int, divisor: Int): Int = {
+    val sign = num.signum * divisor.signum
+    sign * (num.abs + divisor.abs - 1) / divisor.abs
+  }
+
 }