create visualization graph #1011

YukaUU · 2024-07-16T09:50:35Z

Add visualization panel to viewer page.

Summary

Click the icon to the left of the toolbar's tutorial to open the side menu on the right side.
Then, you can see a graph visualizing the annotation information
It shows the relationship between human:annotation vs zooming.

Motivation

To visualize pathologist annotation information

Testing

The graph and the results with collection:Mark.
Annotation:0

Annotation:1

Annotation:9

…ukaUU_anotaiton_log_uI

ただし、ID指定

birm

Can we call this new field something a little more reasable, like viewerState?

Maybe you want to save it somewhere inside, so that each drawn object has its own x,y,zoom, even if they're grouped together? I noted some issues when testing this in #1013

YukaUU · 2024-07-18T10:10:07Z

Can we call this new field something a little more reasable, like viewerState?

OK!
I change new field name.

Maybe you want to save it somewhere inside, so that each drawn object has its own x,y,zoom, even if they're grouped together? I noted some issues when testing this in #1013

That's right.
I will fix it.

YukaUU · 2024-07-18T11:05:50Z

I changed new field name from states to viewerStates.29e4a08

Test

Show x, y and zooming in pop panel

2.log (send data to DB)

3.log:DB collection:Mark

YukaUU · 2024-07-18T15:31:11Z

Maybe you want to save it somewhere inside, so that each drawn object has its own x,y,zoom, even if they're grouped together? I noted some issues when testing this in #1013

Not all annotations saved have (accurate) info saved #1013 #1013 (comment)

I fixed it!

Test

Annotation: Multi mode

log (send data to DB)

3.log:DB collection:Mark

Check pop up panel

…tion

YukaUU · 2024-07-18T16:23:52Z

Delete viewerStates
Past PR did not support Multi Mode.　#966
I fixed it #1011 (comment)
This commit was also deleted.#1011 (comment)

Test

Annotation: Single mode

log:DB collection:Mark

2.Annotation: Multi mode

log:DB collection:Mark

birm

Very close; just one hopefully quick thing I noticed!

birm · 2024-07-19T14:49:36Z

core/extension/openseadragon-canvas-draw-overlay.js

+          viewerStates: {
+            x: StatesHelper.getCurrentStates(true).x,
+            y: StatesHelper.getCurrentStates(true).y,
+            z: StatesHelper.getCurrentStates(true).y


Suggested change

z: StatesHelper.getCurrentStates(true).y

z: StatesHelper.getCurrentStates(true).z

I'm pretty sure this is why this is happening:

I also noticed a mistake in my local and was fixing the same point.
Thank you!!

YukaUU · 2024-07-20T08:47:44Z

@birm
Refactored to remove unnecessary code, etc
I resolved all comments and issue.
（#1011 (review) , #1013)
Please check it

Test

Visualization Graph

log (send data to DB)

log:DB collection:Mark

Pop up panel

Other(It is not related to this PR.)
All fixes in this PR are done, but I found a bug in the Pop Panel display, added to the issue
When two or more annotations overlap, only one of them is displayed when trying to display the PoP Panel. #1014

birm

Great work, and good fixes!

YukaUU added 30 commits June 10, 2024 22:26

add a blank

164d7f9

Merge branch 'yukaUU_GSoC_db_Mark_add_centerPosition_and_Zoom' into y…

fe4eee4

…ukaUU_anotaiton_log_uI

Add log at Toolbar and logAnnotation callback

a2d41a9

add log side menu

fc7ba17

Added opening/closing of side menu/ header

91c0996

add log annotation icon

c2e0231

draft pull request

d9b78d5

add sideMenu on right

a1f8279

add collapsiblelist in Log Panel

08ed4f3

add collapsible list on right side menu

a154cbb

add collapsiblelist in Log Panel

50f70a0

add layers on log panel using $UI.layers,$UI.layers.list

78026e7

add original component

71c3d13

logの情報を取り出す

0fd78db

ただし、ID指定

change function fetchMark : logAnnotaiton

144f139

add loadingLog function

20038b6

add visualizationLayerItems in dataloader

4013f34

create graph in log panel

3d8ef72

add data calculate

7ff366e

create graph

c05437c

fix from log to visualization in subtool

431550c

fix id: 'visualization_panel'

3b0f51b

fix:visualizationSideMenu

1d78faa

fix id and $UI.visualizationList (CollapsibleList )

15e43e1

fix visualizationlist

7ef73f6

fix side menu size

84650dc

fix titleVisualization

bc73fef

fix createVisualizationViewer

3c71ed3

fix VisualizationViewer (is logsViewer instance)

d919cb8

fix $UI.visualizatiomViewer

ffd169a

birm self-requested a review July 17, 2024 17:08

birm mentioned this pull request Jul 17, 2024

Not all annotations saved have (accurate) info saved #1013

Closed

birm requested changes Jul 17, 2024

View reviewed changes

change name from states to viewerStates

10a8801

YukaUU added 6 commits July 18, 2024 21:41

fix

29e4a08

add zooming in each annotation at Multi mode

67c0196

ad zoom data each annotation

467755e

add viewerStates in each annotation at multi mode

7204c13

add viewerStates in each annotation at multi mode

277397e

fix Multi mode on the pencil tool seems to save all annotations

17e6f80

YukaUU added 2 commits July 19, 2024 00:35

fix error This line has a length of 148. Maximum allowed is 125

037c693

delete viewerStates ( previuos commit :added viewerStates each annota…

27c7fd3

…tion

YukaUU added 3 commits July 19, 2024 02:19

fix visualization panel using $D.visualizations.geometries.features

e748f61

fix small bug

a093930

remove viewerStates:image

4e6f480

birm requested changes Jul 19, 2024

View reviewed changes

YukaUU added 4 commits July 19, 2024 23:56

fix point viewerStates

0076c4d

fix small bug

591a265

Remove unused code from viewer.html

eb64052

delete unused code

179d08a

fix comment in visualizationviewer

01ffbd9

birm self-requested a review July 22, 2024 21:58

birm approved these changes Jul 23, 2024

View reviewed changes

birm merged commit 87e0cbd into camicroscope:develop Jul 23, 2024
1 of 2 checks passed

YukaUU mentioned this pull request Jul 25, 2024

all annotations saved have (accurate) info saved #1013 #1015

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create visualization graph #1011

create visualization graph #1011

YukaUU commented Jul 16, 2024 •

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	z: StatesHelper.getCurrentStates(true).y
	z: StatesHelper.getCurrentStates(true).z

create visualization graph #1011

create visualization graph #1011

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YukaUU commented Jul 16, 2024 • edited Loading

Summary

Motivation

Testing

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