apply PR feedback #3, use newest model with slightly different normal…

…ization, make floodfill_threshold configurable

frontend/javascripts/oxalis/model/sagas/automatic_brush_saga.js

@@ -30,7 +30,6 @@ const outputExtent = 100;
 const inputContextExtent = 20;
 const inputExtent = outputExtent + 2 * inputContextExtent;
 const NUM_PREDICT_SLICES = 3;
-const FLOODFILL_THRESHOLD = 0.7;
 
 // Will remove model validation, NaN checks, and other correctness checks in favor of performance
 if (process.env.NODE_ENV === "production") tf.enableProdMode();
@@ -85,7 +84,10 @@ const getPredictionForTile = async (
   });
 
   const { mean, stdDev } = await meanAndStdDevFromDataset(dataset, colorLayerName);
-  const tensorArray = new Float32Array(new Uint8Array(cuboidData)).map(el => (el - mean) / stdDev);
+  const tensorArray = new Float32Array(new Uint8Array(cuboidData)).map(
+    // This is how the model was trained
+    el => ((el - mean) / stdDev) * (1 / 3) ** 0.5,
+  );
   // 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;
   const { useWebworker, useGPU } = getUseWebworkerAndGPU();
@@ -125,6 +127,8 @@ export default function* inferSegmentInViewport(
   const activeViewport = yield* select(state => state.viewModeData.plane.activeViewport);
   if (activeViewport === "TDView") return;
 
+  const FLOODFILL_THRESHOLD = window.floodfillThreshold || 0.6;
+
   let aborted = false;
   const toastConfig = {
     onClose: () => {

package.json

@@ -161,7 +161,6 @@
     "mini-css-extract-plugin": "^0.4.0",
     "mjs": "^1.0.0",
     "moment": "^2.21.0",
-    "n-dimensional-flood-fill": "^1.0.0",
     "nanoevents": "^1.0.2",
     "pako": "^0.2.8",
     "pretty-bytes": "^5.1.0",

yarn.lock

@@ -7746,11 +7746,6 @@ [email protected]:
   resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-0.0.7.tgz#3075ce93bc21b8fab43e1bc4da7e8115ed1e7bab"
   integrity sha1-MHXOk7whuPq0PhvE2n6BFe0ee6s=
 
-n-dimensional-flood-fill@^1.0.0:
-  version "1.0.0"
-  resolved "https://registry.yarnpkg.com/n-dimensional-flood-fill/-/n-dimensional-flood-fill-1.0.0.tgz#c1b99ed55901f9edcd50e86997ee355109b3601b"
-  integrity sha1-wbme1VkB+e3NUOhpl+41UQmzYBs=
-
 n-gram@^1.0.0:
   version "1.1.0"
   resolved "https://registry.yarnpkg.com/n-gram/-/n-gram-1.1.0.tgz#c07fb7d6d59aa42d10fbf680fc4c46a30766c1ee"