Add option to calculate segment index for an existing volume tracing #7325

MichaelBuessemeyer · 2023-09-07T15:45:59Z

This PR adds a new button to the volume layer menu options that allows the user to calculate the segment index for the volume annotation.

URL of deployed dev instance (used for testing):

https://___.webknossos.xyz

Steps to test:

I recommend testing locally as the backend currently sets hasSegmentIndex to true as default for new annotations.

In file AnnotationService.scala change hasSegmentIndex = Some(fallbackLayer.isEmpty) to hasSegmentIndex = Some(false) (in line 166)
Create a new annotation with a volume annotation without a fallback layer
Use the new option in the dropdown menu of the volume layer and click the "Add segment index to this layer" button.
A modal should open up informing about this feature
Click the "Calculate Segment Index" button
The modal should not close, the backend should do a short calculation and afterwards the whole page should reload.
The option to calculate the segment index should no longer exist in a real world scenario as the index has already be calculated (but might still be possible during testing due to the changes in AnnotationService.scala)

Issues:

fixes #7144

(Please delete unneeded items, merge only when none are left open)

Updated changelog

…-segment-index-button

MichaelBuessemeyer · 2023-09-21T07:36:54Z

frontend/javascripts/oxalis/view/left-border-tabs/modals/downsample_volume_modal.tsx

-      visible
+      open
    >


There was a warning that the property visible will be renamed to open and the renaming would be enforced by the next major version of antd. That's why I already changed this here.

philippotto

Great! I left some feedback :)

philippotto · 2023-09-21T08:20:32Z

frontend/javascripts/admin/admin_rest_api.ts

@@ -1068,6 +1068,15 @@ export async function downsampleSegmentation(
    },
  );
 }
+
+export async function addSegmentIndex(annotationId: string, tracingId: string): Promise<Object> {


can you make Object more precise?

philippotto · 2023-09-21T08:27:51Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

+      return null;
+    }
+    return (
+      <Tooltip title="Add segment index to this layer">


Suggested change

<Tooltip title="Add segment index to this layer">

<Tooltip title="Add segment index to this layer. This enables certain features, such as computing segment statistics. This operation only has to be performed once and is done automatically for new annotations.">

or move it into the modal.

I moved it into the modal 👍

philippotto · 2023-09-21T08:28:51Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

    ];
-    const items = possibleItems.filter((el) => el);
+    const items = possibleItems.filter((el) => el && "label" in el && el.label != null);


is this to satisfy TS? Do you know why it wasn't necessary before?

Yeah, sadly this is necessary to satisfy TS. As I added a label in 624 label: this.getAddSegmentIndexButton(readableName, maybeVolumeTracing) where getAddSegmentIndexButton might return null, there is the option of {label: null, key: string} which wasn't covered by the typing before :/

philippotto · 2023-09-21T08:29:54Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

+  showAddSegmentIndexModal = (volumeTracing: VolumeTracing, layerName: string) => {
+    this.setState({
+      volumeTracingToAddSegmentIndex: volumeTracing,
+      volumeLayerNameToAddSegmentIndex: layerName,


For volume annotations, the layer name is equal to volumeTracing.tracingId afaik. Therefore, you should only need one state variable instead of two.

Afaik the tracingId is the numeric identifier (like 1-23143143-4254534-5) but here I need the readable name given to layer. The readable name is passed to showAddSegmentIndexModal as you can see in line 624.
To make it more explicit that the readable name is used, I renamed the variable layerName in this method to readableName as done in getLayerSettingsHeader

This is an example tracing id I printed to the console: tracingId: "0aa32bb0-d1d6-4e34-b1f9-f88e1053c050

philippotto · 2023-09-21T08:51:20Z

frontend/javascripts/oxalis/view/left-border-tabs/modals/add_segment_index_modal.tsx

+        }}
+      >
+        Note that this action might take a few minutes. Afterwards, the annotation is reloaded.
+        Also, the version history of the volume data will be reset.


this is very important and should be marked in an orange alert box or something similar.

I used an Alert warning text for this 👍
for reference: https://ant.design/components/alert

philippotto · 2023-09-21T08:52:16Z

frontend/javascripts/oxalis/view/left-border-tabs/modals/add_segment_index_modal.tsx

+      open
+    >
+      <p>
+        This will calculate the segment index for the volume annotation layer "{volumeLayerName}".


feel free to add a sentence like "this enables features, such as computing segment statistics."

…-segment-index-button

MichaelBuessemeyer

Thanks for your feedback 👣Philipp. I think I covered everything 👍

MichaelBuessemeyer · 2023-09-28T08:31:04Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

+      return null;
+    }
+    return (
+      <Tooltip title="Add segment index to this layer">


I moved it into the modal 👍

MichaelBuessemeyer · 2023-09-28T08:45:34Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

    ];
-    const items = possibleItems.filter((el) => el);
+    const items = possibleItems.filter((el) => el && "label" in el && el.label != null);


Yeah, sadly this is necessary to satisfy TS. As I added a label in 624 label: this.getAddSegmentIndexButton(readableName, maybeVolumeTracing) where getAddSegmentIndexButton might return null, there is the option of {label: null, key: string} which wasn't covered by the typing before :/

MichaelBuessemeyer · 2023-09-28T08:48:46Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

+  showAddSegmentIndexModal = (volumeTracing: VolumeTracing, layerName: string) => {
+    this.setState({
+      volumeTracingToAddSegmentIndex: volumeTracing,
+      volumeLayerNameToAddSegmentIndex: layerName,


Afaik the tracingId is the numeric identifier (like 1-23143143-4254534-5) but here I need the readable name given to layer. The readable name is passed to showAddSegmentIndexModal as you can see in line 624.
To make it more explicit that the readable name is used, I renamed the variable layerName in this method to readableName as done in getLayerSettingsHeader

MichaelBuessemeyer · 2023-09-28T08:54:48Z

frontend/javascripts/oxalis/view/left-border-tabs/modals/add_segment_index_modal.tsx

+        }}
+      >
+        Note that this action might take a few minutes. Afterwards, the annotation is reloaded.
+        Also, the version history of the volume data will be reset.


I used an Alert warning text for this 👍
for reference: https://ant.design/components/alert

MichaelBuessemeyer · 2023-09-28T09:03:50Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

+  showAddSegmentIndexModal = (volumeTracing: VolumeTracing, layerName: string) => {
+    this.setState({
+      volumeTracingToAddSegmentIndex: volumeTracing,
+      volumeLayerNameToAddSegmentIndex: layerName,


This is an example tracing id I printed to the console: tracingId: "0aa32bb0-d1d6-4e34-b1f9-f88e1053c050

hotzenklotz · 2023-10-09T12:48:19Z

frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx

+      <Tooltip title="Add segment index to this layer">
+        <div onClick={() => this.showAddSegmentIndexModal(volumeTracing, readableName)}>
+          <PlusOutlined />
+          Add segment index


No user will know what a "segment index" is. This is a highly technical feature name exposed to the Average Joe.
Perhaps call it "Enable Segment Statistics"?

hotzenklotz · 2023-10-09T12:59:45Z

For the record, I am not a big fan of this feature:

By default, we "downgrade" all existing volume annotations by denying them the super cool new stats. This is a major let down for all existing users.
We expose a highly technical term that most users will not understand.
Even if I find the button, I am very afraid by the "Lose all history" part. Will my annotation be deleted?
Even if I decide to go through with this, I still have to wait for the result. If this is a slow operation, we might as well roll it out automatically over a long period to all existing, old volume annotations.

From my point of view, we should automatically built the index for existing volume annotations to make the segment stats shine. Whether this includes the full version history or not is up for debate.

philippotto · 2023-10-11T14:53:10Z

Ok, then the PR is put on ice for now, right? Also see discussion at https://scm.slack.com/archives/C5AKLAV0B/p1697006098538059.

fm3 · 2023-11-06T08:53:18Z

We decided to add the option for a full migration of all volume annotation layers instead of the button to add the segment index just for a single one. So I’d say this PR is supserseded by #7376

fm3 and others added 6 commits July 17, 2023 11:25

Add route to add segment index to existing volume annotations

2d553b2

add missing messages entry

e1cb8c2

add modal asking for add segment index confirmation

0195ab0

fix linting

efa2752

Merge branch 'master' of github.com:scalableminds/webknossos into add…

f8e418a

…-segment-index-button

Merge branch 'master' of github.com:scalableminds/webknossos into add…

1a066b0

…-segment-index-button

MichaelBuessemeyer self-assigned this Sep 21, 2023

MichaelBuessemeyer added frontend new feature labels Sep 21, 2023

MichaelBuessemeyer commented Sep 21, 2023

View reviewed changes

small fixes & add changelog entry

3ffd4bc

MichaelBuessemeyer requested a review from philippotto September 21, 2023 08:16

MichaelBuessemeyer marked this pull request as ready for review September 21, 2023 08:16

philippotto requested changes Sep 21, 2023

View reviewed changes

MichaelBuessemeyer added 2 commits September 28, 2023 10:28

Merge branch 'master' of github.com:scalableminds/webknossos into add…

444bb97

…-segment-index-button

apply review feedback

82b803f

MichaelBuessemeyer commented Sep 28, 2023

View reviewed changes

MichaelBuessemeyer requested a review from philippotto September 28, 2023 09:17

Merge branch 'master' into add-segment-index-button

7528c95

hotzenklotz reviewed Oct 9, 2023

View reviewed changes

fm3 closed this Nov 6, 2023

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Add option to calculate segment index for an existing volume tracing #7325

Add option to calculate segment index for an existing volume tracing #7325

MichaelBuessemeyer commented Sep 7, 2023 •

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fm3 commented Nov 6, 2023

	<Tooltip title="Add segment index to this layer">
	<Tooltip title="Add segment index to this layer. This enables certain features, such as computing segment statistics. This operation only has to be performed once and is done automatically for new annotations.">

Add option to calculate segment index for an existing volume tracing #7325

Add option to calculate segment index for an existing volume tracing #7325

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MichaelBuessemeyer commented Sep 7, 2023 • edited Loading

URL of deployed dev instance (used for testing):

Steps to test:

Issues:

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hotzenklotz commented Oct 9, 2023

philippotto commented Oct 11, 2023

fm3 commented Nov 6, 2023

MichaelBuessemeyer commented Sep 7, 2023 •

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