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Color TrackScheme Hierarchy according to the time point (Issue 213) #231

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wants to merge 64 commits into from
Closed

Color TrackScheme Hierarchy according to the time point (Issue 213) #231

wants to merge 64 commits into from

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stefanhahmann
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Closes #213

maarzt and others added 18 commits March 21, 2023 13:58
@maarzt
Add new ColorUtils class
2be5a39
@maarzt
Add new method isBeforeTimepoint to interface ModelGraphProperties an…
9ce35a3 
…d according implementations
@maarzt
PaintGraph renderer fade branches, spots and labels according to the …
b469391 
…specified background color
@maarzt
Add new property faded to ScreenEdge and ScreenVertex
ef49f7f
@maarzt
Add timepoint model for fading visualisation of future timepoints
f437c88
@maarzt
Add option fade future timepoints to TrackSchemeStyle
cc75f8c
@maarzt
Refactor some variable names
4615a8b
@maarzt
Improve javadoc for ColorUtils
ecd6897
@stefanhahmann @maarzt
Add isAfterTimepoint methods
084a739
@stefanhahmann @maarzt
Add new class TimepointAndNumberOfSpotsLabel
a3a0e3c 
* Use this class to display and update the current timepoint and the number of spots at that timepoint according to the current timepoint model
@maarzt
TrackSchemePanel: refactoring to reduce code duplication
0852306
@maarzt
LineageTreeLayoutImp: improve code formatting
9744ea1
@maarzt
Refactoring: reuse ColorUtils.mixColors in ColorMap and PaintGraph
7406066 
This reduces code duplication.
@maarzt
LineageTreeLayoutImp: add colorGenerater as constructor parameter
a443062 
This unifies the way how: SelectModel, GraphColorGenerator and TimepointModel,
are initialized and used in the LineageTreeLayout class.
@maarzt
Refactor LineageTreeLayoutImp and LongEdgesLineageTreeLayout
65c1bd1 
Extract method addScreenEdge form cropAndScale. This change reduces code
duplication between the two implementations of cropAndScale.
@stefanhahmann
Fix some javadoc typos
6de9caf
@stefanhahmann
Remove unrequired methods isBeforeTimepoint/isAfterTimepoint
cc56c0f
@stefanhahmann
Add new classes FadedModel, FadedModelAdapter and DefaultFadedModel
d7e3e4d 
* Use these classes to perform fading in TrackSchemeHierachy view
@stefanhahmann stefanhahmann mentioned this pull request Mar 27, 2023
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maarzt
maarzt reviewed Mar 30, 2023
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@maarzt maarzt left a comment

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We are getting closer 👍

src/main/java/org/mastodon/views/trackscheme/LineageTreeLayoutImp.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/views/trackscheme/LineageTreeLayoutImp.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/views/trackscheme/display/PaintGraph.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/views/trackscheme/display/style/TrackSchemeStyle.java Show resolved Hide resolved
src/main/java/org/mastodon/mamut/MamutBranchViewTrackScheme.java Show resolved Hide resolved
src/main/java/org/mastodon/views/trackscheme/display/TrackSchemePanel.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/views/trackscheme/display/TrackSchemePanel.java Show resolved Hide resolved
@stefanhahmann
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The PR somehow introduces a bug when rendering the the TrackScheme Branch. The bug is triggered by resorting the TrackScheme using one of the plugins in mastodon-tomancak. For example "Plugins > Trees Management > Flip Descendants".

GIF 05 05 2023 14-45-05 GIF 05 05 2023 14-45-05

This need to be clarified before merging.

Thanks for pointing this out.

This bug was unfortunately introduced by this commit: 7406066

It should now be resolved by this commit: 37717dc

@tinevez
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tinevez commented May 11, 2023

Ready for review?

@stefanhahmann
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Ready for review?

Yes.
@maarzt reviewed already extensively, but since the changes are massive, a second review would be good.

@tinevez
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tinevez commented May 17, 2023

Sorry I am late on this. Will work on it

@stefanhahmann
Add some more javadoc to scaleAlpha() method to clarify how return va…
91c1ee2 
…lues should be used with java.util.Color objects
@stefanhahmann
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Sorry I am late on this. Will work on it

@tinevez may we kindly remind you on this review? we would love to have this finished/merged.

@tinevez
Add a section label for hierarchy graph in TrackSchem settings editor.
f62cc6a
@tinevez
Center and shrink the timepoint and number of spots panel in the sett…
a074bed 
…ings panel.

Its size was too big to accomodate the default width of TrackScheme
windows. Now we need to center and shrink the other widgets.
@tinevez
Tweak the alignment and size of the settings panel widgets.
cf51d53 
So that
- we have some space to display them all with the default
window width,
- their texts are all aligned vertically on the same baseline,
- the font used is the same everywhere.
@tinevez
Move Mamut specific class to mamut package.
4ed51d6
@tinevez
Fix minor eclipse warnings.
cc18d70
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tinevez commented Jun 29, 2023

I made a PR for your PR with minor changes, mainly sizing the opportunity to fix the look of the settings panel.
Take them if you feel like it.
To me otherwise it is good to be merged to dev.

stefanhahmann and others added 4 commits June 30, 2023 09:40
@stefanhahmann
Merge pull request #17 from mastodon-sc/issue-213-2
9305d9c 
* Adds section label in TrackScheme settings editor
* Changes to the TrackScheme Toolbar UI
@stefanhahmann
Avoid abbreviation of Regen button
b541613 
* Add a tooltip with some explanation of the function of the button
@stefanhahmann
Increase the preferred size of the group locks toggle buttons
3162483 
* On a windows machine the group lock ids (the numbers) where not shown, but "..." instead
* I think only preferred size is need to set the size
@stefanhahmann
Use "timepoint" as label instead of "t"
0deefa7 
* I think it is better to avoid abbreviations in user interfaces. What might be clear to us (t = timepoint) may not be so clear for a newbie user.
@stefanhahmann
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Hi @tinevez,

I merged your PR stefanhahmann#17.

However after merging the toolbar of the trackscheme windows looked like this on my (windows) machine:

grafik

Thus, I increased the size of the Group Locks Panel again: 3162483

Also, I think, it is better to avoid abbreviations in user interfaces. Thus I made these changes:

which make the toolbar of trackscheme window look like this on my windows:

grafik

Hope you agree?

@tinevez
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tinevez commented Jun 30, 2023

Go for it!

@stefanhahmann
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Go for it!

@maarzt may I ask you to merge (I do not have the rights to do so)? If you have questions regarding the remaining conflict, you may contact me.

@tinevez
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tinevez commented Jun 30, 2023

Merged! But I had to do it via a local branch I had rights on.
This PR can be marked as merged and closed.

@stefanhahmann stefanhahmann deleted the issue-213-2 branch September 21, 2023 07:49
@stefanhahmann stefanhahmann mentioned this pull request Jun 25, 2024
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@maarzt maarzt maarzt approved these changes

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3 participants
@stefanhahmann @maarzt @tinevez