apply PR feedback #2

scalableminds · Apr 9, 2019 · 9589321 · 9589321
1 parent 7dcae93
commit 9589321
Show file tree

Hide file tree

Showing 4 changed files with 18 additions and 13 deletions.
diff --git a/frontend/javascripts/libs/floodfill.js b/frontend/javascripts/libs/floodfill.js
@@ -25,12 +25,10 @@ export default function(options: FloodfillOptions) {
   let flooded = [];
   const visits = {};
 
-  // $FlowFixMe Flow doesn't allow to use an array as the key
-  const visited = key => visits[key] === true;
+  const visited = key => visits[key.toString()] === true;
 
   const markAsVisited = key => {
-    // $FlowFixMe Flow doesn't allow to use an array as the key
-    visits[key] = true;
+    visits[key.toString()] = true;
   };
 
   const member = getArgs => getter(getArgs[0], getArgs[1], getArgs[2]);

diff --git a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.js b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.js
@@ -45,6 +45,7 @@ import {
   type Vector3,
   type ContourMode,
   ContourModeEnum,
+  OrthoViews,
   type OrthoView,
   type VolumeTool,
   VolumeToolEnum,
@@ -348,10 +349,12 @@ function* inferSegmentInViewport(action: InferSegmentationInViewportAction): Sag
     const tensorArray = new Float32Array(new Uint8Array(cuboidData)).map(
       el => (el - mean) / stdDev,
     );
+    // When interpreting the 3d data slice as a 2d slice, the x and y axis are flipped only on the YZ plane
+    const isXYflipped = activeViewport === OrthoViews.PLANE_YZ;
 
     return useWebworker
-      ? workerPredict(useGPU, tensorArray.buffer, inputExtent)
-      : mainThreadPredict(useGPU, tf, tensorArray.buffer, inputExtent);
+      ? workerPredict(useGPU, tensorArray.buffer, inputExtent, isXYflipped)
+      : mainThreadPredict(useGPU, tf, tensorArray.buffer, inputExtent, isXYflipped);
   };
 
   function* currentPositionUpdater(): Saga<void> {
@@ -414,11 +417,11 @@ function* inferSegmentInViewport(action: InferSegmentationInViewportAction): Sag
   const seed = clickPosition;
   const seedPrediction = yield* call(getter, ...seed);
   if (seedPrediction) {
-    // The floodfill will run until aborted
-    floodfill({ getter, seed, onFlood });
-
     // Keep updating the current position
-    yield* call(currentPositionUpdater);
+    yield* fork(currentPositionUpdater);
+
+    // The floodfill will run until aborted or exhausted
+    yield* call(floodfill, { getter, seed, onFlood });
   } else {
     Toast.warning("Click position is classified as border, please click inside a segment instead.");
   }

diff --git a/frontend/javascripts/oxalis/workers/tensorflow.impl.js b/frontend/javascripts/oxalis/workers/tensorflow.impl.js
@@ -6,6 +6,7 @@ export default async function predict(
   tf: Object,
   buffer: ArrayBuffer,
   inputExtent: number,
+  isXYflipped: boolean,
 ) {
   if (useGPU) {
     tf.setBackend("webgl");
@@ -21,7 +22,10 @@ export default async function predict(
   }
 
   let tensor = tf.tensor4d(tensorArray, [1, inputExtent, inputExtent, 1]);
-  tensor = tf.transpose(tensor, [0, 2, 1, 3]);
+  // The tensorflow model expects a flipped x/y-axis
+  if (!isXYflipped) {
+    tensor = tf.transpose(tensor, [0, 2, 1, 3]);
+  }
 
   const model = segmentationModel;
   const inferredTensor = model.predict(tensor);

diff --git a/frontend/javascripts/oxalis/workers/tensorflow.worker.js b/frontend/javascripts/oxalis/workers/tensorflow.worker.js
@@ -20,8 +20,8 @@ if (typeof OffscreenCanvas !== "undefined") {
 
 const tf = require("@tensorflow/tfjs");
 
-function predictWrapper(useGPU, buffer: ArrayBuffer, inputExtent: number) {
-  return predict(useGPU, tf, buffer, inputExtent);
+function predictWrapper(useGPU, buffer: ArrayBuffer, inputExtent: number, isXYflipped: boolean) {
+  return predict(useGPU, tf, buffer, inputExtent, isXYflipped);
 }
 
 export default expose<typeof predictWrapper>(predictWrapper);