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Read object features table #84

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Read object features table #84

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emilmelnikov
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@emilmelnikov emilmelnikov commented May 12, 2021 •
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Add the ability to read an object features table from object classification workflow.

Also, refactor and simplify all workflows and associated demos.

Closes #56.

@emilmelnikov
Add base workflow command class
6ffdc8b
@emilmelnikov
Add all existing ilastik workflow commands
0711014
@emilmelnikov
Add an option to create a feature table
3beb25d
@emilmelnikov
Remove old ImageJ commands and executors
fe15eda
@emilmelnikov
Refactor ilastik options
b2e4a53 
* Use special "MESSAGE" visibility for providing path examples

* Remove value auto-loading from persistent storage because
  it interferes with programmatic options usage

* Simplify field labels wording

* Change class name to be more consistent with built-in ImageJ plugins
@emilmelnikov
Update workflow demos
fc4eb68 
* Use new workflow classes

* Describe the demos in a base class comment

* Remove tracking demo because example files are missing from resources
@emilmelnikov emilmelnikov requested a review from wolny May 20, 2021 02:50
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wolny approved these changes May 23, 2021
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This is very nicely done, great job @emilmelnikov! The code is much cleaner than what it was before and I'm glad that the workflows can finally be implemented using the @Plugin annotations, instead of the oldschool GenericCommand (?).
👍 :shipit:

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k-dominik commented May 27, 2021 •
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Are these changes backwards compatible (e.g. will old macros still run)? I've tried some of my old ones, but so far without success.

for Pixel Classification it seems that parameters have been renamed:

  • projectfilename -> project
  • inputimage -> rawdata

I know this sucks, I like the more expressive parameter names, too, but we can't break old macros because of an internal refactor

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Are these changes backwards compatible (e.g. will old macros still run)? I've tried some of my old ones, but so far without success.

for Pixel Classification it seems that parameters have been renamed:

  • projectfilename -> project
  • inputimage -> rawdata

I know this sucks, I like the more expressive parameter names, too, but we can't break old macros because of an internal refactor

Good call, I forgot about macros.

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Just to add now that I looked at the code it is really nice to see reduced amount of duplication and boilerplate for the workflows! I tested generating the tables and this works nicely as well. We'll have to add documentation for this though, as one has to configure the csv export in ilastik first - otherwise it won't work. The real power of the table can be unleashed once we allow for exporting the Object Identities. That way (I think) one could use feature table as colormaps (somehow) :D. We should maybe ask @tischi how to best do it and provide an example.

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emilmelnikov commented May 31, 2021 •
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We'll have to add documentation for this though, as one has to configure the csv export in ilastik first - otherwise it won't work.

Would this work?

image

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emilmelnikov commented May 31, 2021 •
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The real power of the table can be unleashed once we allow for exporting the Object Identities.

I presume we need to change table export in ilastik for this?

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The real power of the table can be unleashed once we allow for exporting the Object Identities.

I presume we need to change table export in ilastik for this?

no, we'd need to allow exporting a different source via --export_source=Object Identities" command line argument.

We'll have to add documentation for this though, as one has to configure the csv export in ilastik first - otherwise it won't work.

Would this work?

image

that's perfect :) users don't even need to look into some docs.

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we'd need to allow exporting a different source via --export_source=Object Identities" command line argument.

Should we address this in a separate PR?

@k-dominik k-dominik mentioned this pull request Jul 19, 2022
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@emilmelnikov emilmelnikov mentioned this pull request Jul 3, 2023
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Superseded by #106.

Object features table could be addressed in a separate PR.

@emilmelnikov emilmelnikov deleted the add-tables branch September 22, 2023 12:31
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@wolny wolny wolny approved these changes

@k-dominik k-dominik Awaiting requested review from k-dominik

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Better output for object classification
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@emilmelnikov @k-dominik @wolny