[RSDK-1705] add colormap for SLAM UI #2160

JohnN193 · 2023-04-04T18:11:20Z

This PR is updating the SLAM 2D render to apply a greyscale color map to the pointcloud based on the color attribute's probabilities. The code assumes that colors to range from 0 to 100 in the blue/z channel, and sets the colormap accordingly.

Tested with fake slam and a large offline cartographer dataset on mac, and an offline orbslam dataset on a pi using an appimage and local config.

ticket: https://viam.atlassian.net/browse/RSDK-1705

nicksanford · 2023-04-05T17:40:14Z

AppImages ready! http://packages.viam.com/apps/viam-server/viam-server-pr-2160-x86_64.AppImage http://packages.viam.com/apps/viam-server/viam-server-pr-2160-aarch64.AppImage

This is awesome! I didn't know this github workflow existed!!!

nicksanford · 2023-04-05T17:51:51Z

web/frontend/src/components/slam-2d-render.vue

@@ -8,6 +8,36 @@ import { MapControls } from 'three/examples/jsm/controls/OrbitControls';
 import { PCDLoader } from 'three/examples/jsm/loaders/PCDLoader';
 import type { commonApi } from '@viamrobotics/sdk';

+/*
+ * // Leaving additional color map commented for if we want to change to a different scheme.
+ * // const colorMapViridis = [


Mind adding the url that defined this color map?

nicksanford · 2023-04-05T17:51:57Z

web/frontend/src/components/slam-2d-render.vue

+ * // ]
+ */
+
+// this color map is greyscale


Mind adding the url that defined this color map?

nicksanford · 2023-04-05T17:55:38Z

web/frontend/src/components/slam-2d-render.vue

@@ -78,6 +108,21 @@ const disposeScene = () => {
  scene.clear();
 };

+// Find the desired color bucket for a given probability. This assumes the probability will be a value from 0 to 100
+const probToColorMapBucket = (normProb: number, numBuckets: number): number => {


Could you please add unit tests for this function that shows how it behaves with probabilities both within the expected range & outside the expected range and with varied numbers of buckets?

You should be able to follow a similar pattern to what is done here: https://github.com/viamrobotics/rdk/blob/main/web/frontend/tests/unit/Base.spec.ts#L1

I'm happy to pair with you on it.

No current unit testing framework is set up yet for RDK, recommend just moving forward without tests until we complete https://viam.atlassian.net/browse/APP-1600

cool stuff, added a ticket for SLAM to make some tests after that one https://viam.atlassian.net/browse/RSDK-2606

nicksanford · 2023-04-05T17:57:49Z

web/frontend/src/components/slam-2d-render.vue

+ * Map the color of a pixel to a color bucket value.
+ * normProb is the probability value normalized by the size of a byte(255) to be between 0 to 1.
+ */
+const colorBuckets = (normProb: number): THREE.Vector3 => {


Can this also be unit tested?

added a ticket to unit test this https://viam.atlassian.net/browse/RSDK-2606

web/frontend/src/components/slam-2d-render.vue

nicksanford · 2023-04-05T18:04:20Z

web/frontend/src/components/slam-2d-render.vue

+  if (colors instanceof THREE.BufferAttribute || colors instanceof THREE.InterleavedBufferAttribute) {
+    for (let i = 0; i < colors.count; i += 1) {
+      const colorMapPoint = colorBuckets(colors.getZ(i));
+      colors.setXYZ(i, colorMapPoint.x, colorMapPoint.y, colorMapPoint.z);


@micheal-parks Just confirming: Is this the idiomatic way to set the color scheme of points in three.js?

@micheal-parks do you know why three.js uses setXYZ instead of something like setRGB for colors? Is it because the color type is a more generic THREE.BufferAttribute

Exactly, it's because the BufferAttribute class is used for any all sorts of vector data, like colors, vertices, normals ,etc, and the authors haven't added a setRGB alias function

nicksanford · 2023-04-05T18:04:40Z

web/frontend/src/components/slam-2d-render.vue

+  // if the PCD has a color attribute defined, convert those colors using the colorMap
+  if (colors instanceof THREE.BufferAttribute || colors instanceof THREE.InterleavedBufferAttribute) {
+    for (let i = 0; i < colors.count; i += 1) {
+      const colorMapPoint = colorBuckets(colors.getZ(i));


[q] Why do we get the probability number from Z?

We make the assumption in our current slam implementation that probability will live in the blue channel of the PCD, by setting the color integer to a value from 0 to 100. 100 is less than 255 so only the blue channel needs to be evaluated. The way the color attributes appear to work for three.js is the RGB fields correspond to xyz fields. I did not dive into three.js documentation to see how loader.parse explicitly handles this

I'm a little confused b/c I thought that we put the probability data in the R channel here: https://github.com/viamrobotics/viam-cartographer/pull/25/files#diff-92ff8a5cd3a57430d78c6ba3b61a91d1810399b77613eece3c55841868d2822eR56

@jeremyrhyde @JohnN193 am I missing something?

ah yeah, cairo has probability encoded in the R channel, but after we math out the probability value, pass that char into the integer field of the PCD. the integer field(calling it rgb for simplicity) works as follows

int rgb = 0;
rgb = rgb | (red << 16);
rgb = rgb | (green << 8);
rgb = rgb | (blue << 0);
viam::utils::writeIntToBufferInBytes(pcd_data, RGB);

I am not 100% certain how the pcdloader is handling the 4 byte integer, but experimentally this was found to be the Z channel(for cartographer PCDs the other two channels are 0)

Awesome! Thanks for explaining!!! Would you mind please creating a ticket for the fact that currently the remote-control frontend & any users of slam need to have intimate knowledge of how the specific slam algo implementation encodes probability information the color integer value in the PCD (which currently only works for cartographer) so there is product awareness & we can prioritize when to come back to it to make it more generic / type safe / documented & add a comment at the top of this file with both the assumption this component makes about the PCD color information & a link to the ticket to come back to re assess those assumptions?

ticket: https://viam.atlassian.net/browse/RSDK-2605

Thanks for explaining!

It sounds like since carto_grpc_server is returning a PCD with format "x y z rgb" and putting a probability value 0-100 in the 'rgb' field. Since 0-100 is guaranteed to be less than 255, the probability will end up in the lowest byte, so we're able to pull it out by looking at the 'b' channel.

Agreed this is pretty roundabout. To consider in RSDK-2605: I wonder if we could use a PCD format "x y z intensity" and store the probability in intensity, since it looks like the PCDLoader would be able to pull it out as a single value: https://github.com/mrdoob/three.js/blob/0fbae6f682f6e13dd9eb8acde02e4f50c0b73935/examples/jsm/loaders/PCDLoader.js#L429.

(In that case I think we'd need to use setXYZW below)

nicksanford · 2023-04-05T18:05:36Z

web/frontend/src/components/slam-2d-render.vue

+ */
+const colorBuckets = (normProb: number): THREE.Vector3 => {
+  return colorMapGrey.map(([red, green, blue]) =>
+    new THREE.Vector3(red, green, blue).multiplyScalar(1 / 255))[probToColorMapBucket(normProb, colorMapGrey.length)]!;


What does the .multiplyScalar(1 / 255) do?

this normalizes the pixels of colorMapGrey. So the vector3 will contain values of 0 to 1 instead of 0 to 255, which would match the expected values that colors wants

GPUs usually like data normalized to 0-1 :)

Co-authored-by: nicksanford <nicholascsanford@gmail.com>

jeremyrhyde

LGTM, requesting a re-review since I had some open questions and want to understand them before signing off.

jeremyrhyde · 2023-04-06T16:21:18Z

web/frontend/src/components/slam-2d-render.vue

+ * ticket to add testing: https://viam.atlassian.net/browse/RSDK-2606
+ */
+const probToColorMapBucket = (normProb: number, numBuckets: number): number => {
+  const prob = Math.max(Math.min(100, normProb * 255), 0);


[q] Isn't the normProb an integer between 1-100, why do we need to multiply it by 255? I would expect this to be:

const prob = Math.max(Math.min(100, normProb), 0);

the PCD loader actually sets the values on a scale from 0 to 1, which is why I referred to it as a normalized probability(normProb for short)

Hmm @JohnN193 , for my understanding is it really a scale from 0 to 1, or is it 0 to 100/255?

Also, "normalized" seems to be its own concept in BufferAttribute so it'd be nice to avoid a name could be confused with that... could we simply call it 'probability'?

[note to self] carto_grpc_server sends back a value from 0-100, then PCDLoader divides by 255. We multiply by 255 here to bring it back to 0-100.

Yeah for our implementation of a PCD from cartographer, normProb goes from 0-100/255. Because that isn’t a range I can guarantee for all slam algos I added the max/min bounds.

Fine with calling it probability. I picked the name just because I saw it was normalized but I don’t feel strongly about it

Cool, calling it probability sounds good to me. Free tor resolve from my side.

jeremyrhyde · 2023-04-06T16:23:14Z

web/frontend/src/components/slam-2d-render.vue

@@ -8,6 +8,42 @@ import { MapControls } from 'three/examples/jsm/controls/OrbitControls';
 import { PCDLoader } from 'three/examples/jsm/loaders/PCDLoader';
 import type { commonApi } from '@viamrobotics/sdk';

+/*
+ * // Leaving additional color map commented for if we want to change to a different scheme.


[minor] expand on this comment to state that this schema is used to map probability values (probability value ranges?) to colors specified by the schema

tweaked the comment to try being more reflective of what the usage is

jeremyrhyde · 2023-04-06T16:26:34Z

web/frontend/src/components/slam-2d-render.vue

+  if (colors instanceof THREE.BufferAttribute || colors instanceof THREE.InterleavedBufferAttribute) {
+    for (let i = 0; i < colors.count; i += 1) {
+      const colorMapPoint = colorBuckets(colors.getZ(i));
+      colors.setXYZ(i, colorMapPoint.x, colorMapPoint.y, colorMapPoint.z);


@micheal-parks do you know why three.js uses setXYZ instead of something like setRGB for colors? Is it because the color type is a more generic THREE.BufferAttribute

jeremyrhyde · 2023-04-06T16:27:14Z

web/frontend/src/components/slam-2d-render.vue

+ * // Leaving additional color map commented for if we want to change to a different scheme.
+ * generated with: https://waldyrious.net/viridis-palette-generator/
+ * more info: https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html
+ * // const colorMapViridis = [


[q] Why are we storing the colorMapViridis here if we are using the grayscale one?

I left the viridis colormap commented out so we could easily swap to it if after testing we found the greyscale color map did not perform the way we wanted

Gotcha so the colorMapViridis is given to that grayscaler to produce our grayscale map?

the viridis color map is a separate mapping from the greyscale color map

@EshaMaharishi just confirming we are alright having this alternative color schema as a comment in this file

Generally I think it's better to remove unused code than leave it commented out, but I don't feel very strongly in this case if we think it's useful to have it available

On second thought, I think we should remove it. It's not great to accumulate commented out code in a codebase. It'll always be in the git history if we need it.

jeremyrhyde

LGTM, just pinged @EshaMaharishi regarding the color schema comment but I am fine with whichever outcome we decide on

jeremyrhyde · 2023-04-06T21:58:58Z

web/frontend/src/components/slam-2d-render.vue

@@ -8,6 +8,44 @@ import { MapControls } from 'three/examples/jsm/controls/OrbitControls';
 import { PCDLoader } from 'three/examples/jsm/loaders/PCDLoader';
 import type { commonApi } from '@viamrobotics/sdk';

+/*
+ * this color map is greyscale. The color map is being used map probability values of a PCD


thanks for the comment update!

EshaMaharishi

LGTM mod comment about the name 'normProb'

web/frontend/src/components/slam-2d-render.vue

EshaMaharishi · 2023-04-07T01:13:19Z

web/frontend/src/components/slam-2d-render.vue

+  // if the PCD has a color attribute defined, convert those colors using the colorMap
+  if (colors instanceof THREE.BufferAttribute || colors instanceof THREE.InterleavedBufferAttribute) {
+    for (let i = 0; i < colors.count; i += 1) {
+      const colorMapPoint = colorBuckets(colors.getZ(i));


Thanks for explaining!

It sounds like since carto_grpc_server is returning a PCD with format "x y z rgb" and putting a probability value 0-100 in the 'rgb' field. Since 0-100 is guaranteed to be less than 255, the probability will end up in the lowest byte, so we're able to pull it out by looking at the 'b' channel.

Agreed this is pretty roundabout. To consider in RSDK-2605: I wonder if we could use a PCD format "x y z intensity" and store the probability in intensity, since it looks like the PCDLoader would be able to pull it out as a single value: https://github.com/mrdoob/three.js/blob/0fbae6f682f6e13dd9eb8acde02e4f50c0b73935/examples/jsm/loaders/PCDLoader.js#L429.

(In that case I think we'd need to use setXYZW below)

EshaMaharishi · 2023-04-07T01:44:52Z

web/frontend/src/components/slam-2d-render.vue

+ * ticket to add testing: https://viam.atlassian.net/browse/RSDK-2606
+ */
+const probToColorMapBucket = (normProb: number, numBuckets: number): number => {
+  const prob = Math.max(Math.min(100, normProb * 255), 0);


Hmm @JohnN193 , for my understanding is it really a scale from 0 to 1, or is it 0 to 100/255?

Also, "normalized" seems to be its own concept in BufferAttribute so it'd be nice to avoid a name could be confused with that... could we simply call it 'probability'?

[note to self] carto_grpc_server sends back a value from 0-100, then PCDLoader divides by 255. We multiply by 255 here to bring it back to 0-100.

EshaMaharishi · 2023-04-07T01:57:22Z

web/frontend/src/components/slam-2d-render.vue

+ * // Leaving additional color map commented for if we want to change to a different scheme.
+ * generated with: https://waldyrious.net/viridis-palette-generator/
+ * more info: https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html
+ * // const colorMapViridis = [


Generally I think it's better to remove unused code than leave it commented out, but I don't feel very strongly in this case if we think it's useful to have it available

github-actions · 2023-04-10T20:53:50Z

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github-actions · 2023-04-10T20:53:52Z

AppImages ready!
http://packages.viam.com/apps/viam-server/viam-server-pr-2160-x86_64.AppImage
http://packages.viam.com/apps/viam-server/viam-server-pr-2160-aarch64.AppImage

JohnN193 added 2 commits April 4, 2023 13:42

add color map for slam frontend

0ef1f8c

small tweaks

d8ca9e3

viambot added the safe to test This pull request is marked safe to test from a trusted zone label Apr 4, 2023

linting

066a615

viambot added safe to test This pull request is marked safe to test from a trusted zone and removed safe to test This pull request is marked safe to test from a trusted zone labels Apr 4, 2023

JohnN193 added the appimage Build AppImage of PR label Apr 5, 2023

JohnN193 requested review from EshaMaharishi, nicksanford, jeremyrhyde and micheal-parks April 5, 2023 15:51

JohnN193 marked this pull request as ready for review April 5, 2023 15:51

nicksanford reviewed Apr 5, 2023

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add links to color maps

328a6da

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Apply suggestions from code review

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Co-authored-by: nicksanford <nicholascsanford@gmail.com>

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make lint

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micheal-parks approved these changes Apr 6, 2023

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add comments for tickets

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JohnN193 added 2 commits April 6, 2023 12:15

Merge branch 'main' of github.com:JohnN193/rdk into RSDK-1705-colormap

4d621a8

bump rc version

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JohnN193 requested a review from nicksanford April 6, 2023 16:25

jeremyrhyde suggested changes Apr 6, 2023

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more comments

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JohnN193 requested a review from jeremyrhyde April 6, 2023 21:33

jeremyrhyde approved these changes Apr 6, 2023

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EshaMaharishi approved these changes Apr 7, 2023

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JohnN193 added 2 commits April 10, 2023 16:23

Merge branch 'main' of github.com:JohnN193/rdk into RSDK-1705-colormap

bcefc48

address comments

a6d7e6f

viambot added safe to test This pull request is marked safe to test from a trusted zone and removed safe to test This pull request is marked safe to test from a trusted zone labels Apr 10, 2023

bump RC

daa884a

viambot added safe to test This pull request is marked safe to test from a trusted zone and removed safe to test This pull request is marked safe to test from a trusted zone labels Apr 10, 2023

make lint

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viambot added safe to test This pull request is marked safe to test from a trusted zone and removed safe to test This pull request is marked safe to test from a trusted zone labels Apr 10, 2023

JohnN193 merged commit 97370ce into viamrobotics:main Apr 10, 2023

JohnN193 deleted the RSDK-1705-colormap branch March 22, 2024 17:28

[RSDK-1705] add colormap for SLAM UI #2160

[RSDK-1705] add colormap for SLAM UI #2160

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github-actions bot commented Apr 10, 2023

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