Add FSLeyes plugin #182

Stoyan-I-A · 2019-03-10T21:42:42Z

This PR implements the following changes:

Changed numpy and scikit-image versions
Implemented a GUI design for the plugin
Implemented an image loader for the plugin
Implemented buttons on the control panel of the plugin to apply a prediction model
Implemented a button to load existing masks
"Active" images/masks are determined by their visibility status (eye icon on the overlay list)
added the following tools : watershed segmentation, axon auto-fill

Fixes #159, Fixes #162, Fixes #191, Fixes #192, Fixes #193, Fixes #201, Fixes #209

TODO

Write tests for the plugin (and add to Travis) - Will be adressed in Write tests for the FSLeyes plugin #224

How to test / install

The installation procedure can by found here : https://github.com/neuropoly/axondeepseg/blob/FSLeyes_integration/docs/source/documentation.rst

Tools description

Tooltips were added to the GUI. If you hover your cursor over a button on the plugin, a description should popup

- Implemented the GUI design - The user can now select which model to apply by selecting it in the ComboBox

coveralls · 2019-03-10T22:01:33Z

Coverage increased (+0.1%) to 82.812% when pulling 2fe999d on FSLeyes_integration into f216bb8 on master.

ads_plugin.py

It is now possible to save segmentation masks

mathieuboudreau · 2019-03-22T10:56:01Z

@Stoyan-I-A please add a short description in your commit message in addition to noting the Issue #. The reason being that it makes parsing through the commit log a lot easier (i.e. I don't have to click on the issues to know what was meant to be done in a commit).

mathieuboudreau · 2019-03-22T11:39:56Z

I tried loading this plugin, but encountered an error:

System: MacOS 10.14.3

Steps followed:

Created & activated a new conda virtual environment (conda create -n ads_venv python=3.6 & conda activate ads_venv)
Installed ADS inside the venv (pip install -e .)
Installed FSLeyes inside the venv (~~pip install FSLeyes~~ conda install -c conda-forge fsleyes)
Opened FSLeyes from the command line (fsleyes)
Clicked Files --> Load plugin and selected ads_plugin.py

Three more notes:

which fsleyes confirmed that I'm using the fsleyes inside my venv: /Users/mathieuboudreau/anaconda3/envs/ads_venv/bin/fsleyes
fsleyes --version says that I'm using version 0.27.3+build0
I did have an old FSL installation on my system beforehand (and thus FSLeyes)

Any thoughts @Stoyan-I-A ?

- Added the watershed algorithm using a chunk of the code that was used to compute the morphometrics. That should be changed in the future since it is basically copying code that is used elsewhere. - Added the axon filling tool. This tool performs flood-fill at the locations of the centroids of the axon-myelin mask.

The centroids are now calculated with the myelin array rather than the axon array when trying to fill the axons.

Stoyan-I-A · 2019-03-25T22:39:36Z

@mathieuboudreau
I think the error message comes from a package that I was importing. But I am no longer using it, so I'll remove it from the imports.

mathieuboudreau · 2019-03-27T12:56:56Z

Thanks for the clarification @Stoyan-I-A . I can't test it at the moment unfortunately, as I can't even get FSLeyes to open in my venv anymore. Maybe the steps I reported above aren't exactly what I did, because I don't know what else could have changed. I'm getting this now:


(ads_182) mathieuboudreau@brassens:~$ fsleyes 
This program needs access to the screen. Please run with a
Framework build of python, and only when you are logged in
on the main display of your Mac.

I'll let you know once I debug this and I'm able to test your updated setup.

(Edit: woops, sorry about closing for a brief second, it was a misclick.)

mathieuboudreau · 2019-03-27T13:38:12Z

I think installing fsleyes with conda install -c conda-forge fsleyes instead of pip resolved it for me, so I'll change my above steps and test it out again later.

Now, I'm able to open fsleyes within the venv, and install the plugin without the above error occuring.

After that, I was a bit of a loss of where to go to test out your plugin as not instructions appeared, and nothing in the GUI changed. After digging around, I found that there was an option called "ADScontrol" unter Settings --> Ortho View 1, is that what I'm suppose to click?

I did so, and got this error.

Afterwards, nothing else appeared on the GUI, still the basic FSLeyes GUI options.

I'm on a MacOS 10.14.3, in the git branch FSLeyes_integration, and at the git commit 85692ca4dd1.

mathieuboudreau · 2019-03-27T13:44:30Z

Scratch that last point, I had an older version of the plugin in the plugin folder for some reason. The current one has the directory changes you made recently. Now I get this error:

I opened fsleyes from my axondeepseg/ folder on the commandline, so it appears the path handling still needs some tweaking.

mathieuboudreau · 2019-03-27T14:08:59Z

I resolved the bug in commit fd63f2f (wrong filename, only printing the module path instead of concatenating it) and made the code a bit more robust for OS-independence. Now the plugin loads for me 🎉!

jcohenadad · 2019-03-27T14:18:21Z

Awesome!! Thank you @mathieuboudreau and @Stoyan-I-A for your contribution

jcohenadad · 2019-03-27T15:58:03Z

It would be nice to reorganize plugin window like that:

jcohenadad · 2019-09-03T16:00:17Z

@Stoyan-I-A I did a git pull, then (after activating the environment):

conda uninstall fsleyes
yes | conda install -c conda-forge fsleyes>=0.30.1
fsleyes &

When loading the plugin, a window pops up with the following error message: Error installing plugin file, Details: no module named: 'wx.lib.agw.hyperlink'

And the terminal output says:

Failed to load plugin file /Users/julien/.fsleyes/plugins/ads_plugin.py: cannot import name 'ImageOps'
objc[12735]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff9e4be3d8) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x12f69ef50). One of the two will be used. Which one is undefined.
   ERROR           status.pyc  164: reportIfError   - Error installing plugin file: An error occurred installing the plugin file.

UPDATE: 2019-09-03 12:02:54:

After uninstall/reinstall again:

conda uninstall fsleyes
yes | conda install -c conda-forge fsleyes>=0.30.1

Opening FSLeyes, no need to relead the plugin (still there), and it works fine (i can open the plugin and it works).

Additional, info about PIL (maybe overwritten by fsleyes install):

>>> import PIL
>>> PIL.__version__
'6.1.0'

mathieuboudreau · 2019-09-06T13:03:03Z

@Stoyan-I-A I tried to follow the steps for debugging the GUI in the wiki (https://github.com/neuropoly/axondeepseg/wiki/How-to-test-the-plugin-script-in-debug-mode), however the instructions weren't clear/detailed enough for me to be able to do so on my computer.

Could you possibly take a video screen capture of you following the steps required to do so as an example, and I'll try to follow that along, and I'll fill in the missing information that I thought I would have needed in the wiki? One large issue I think may be that your steps may not be identical for all IDEs (I use Visual Studio Code).

Stoyan-I-A · 2019-09-06T21:50:51Z

@mathieuboudreau I'll see what I can do. Do you think it would help if I added pictures?

mathieuboudreau · 2019-09-06T22:19:13Z

We'll see after I see the video, it depznds on how exact some instructuions might need to be.

- The plugin now checks suffixes instead of the entire name - The fill option now creates a new corrected axon overlay - The plugin now verifies if another version is present in the ADS directory

Stoyan-I-A · 2019-09-08T02:31:23Z

@mathieuboudreau I added the video to AxonDeepSeg's google drive.
https://drive.google.com/open?id=1O5TFJZT2dD6XiUQxeJvI1lpEclS1CLB7

Stoyan-I-A · 2019-09-08T02:39:44Z

why duplicating the hard-coded version information? (see Line 2)

I found it easier to check the version this way. But I should change this.

jcohenadad · 2019-09-08T19:23:32Z

why duplicating the hard-coded version information? (see Line 2)

I found it easier to check the version this way. But I should change this.

sorry i missed that on line 2, the version is a comment (part of the header). I would definitely remove this from the header (if we change the version in the future, we need to update both the code and the header, which is prone to errors).

moreover, instead of having the version lost in the code, i would create a global variable and put it at the top of the file, so it is visible by anyone reading your code. Something like:

VERSION = '2.0.1'

that you can put right after all the imports.

mathieuboudreau · 2019-09-10T16:24:19Z

ads_plugin.py

@@ -36,6 +34,8 @@

 from AxonDeepSeg.morphometrics.compute_morphometrics import *

+VERSION = "0.2.2"


I would specify in the name that it's the plugin version, to avoid confusion with the ADS version. so maybe rename it to PLUGIN_VERSION

mathieuboudreau · 2019-09-13T17:16:17Z

@Stoyan-I-A I updated instructions for debugging with a bit more details, it works for me now! https://github.com/neuropoly/axondeepseg/wiki/fsleyes-plugin

mathieuboudreau · 2019-09-18T12:36:22Z

Do we know if this plugin/fsleyes will/should work on Windows OS?

Stoyan-I-A · 2019-09-18T20:18:08Z

Do we know if this plugin/fsleyes will/should work on Windows OS?

FSLeyes isn't supported on Windows. I tried to install it with the PyPi package and it wasn't working correctly.

That being said, I did find some instructions to run FSLeyes on Windows with a Linux Subsystem
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows

…w also load jpg/jpeg images

jcohenadad · 2019-10-01T16:14:23Z

When trying to re-install the plugin, an error pops up on FSLeyes:

UPDATE 2019-10-01 12:16:05: Doing a pip install -e . solved it (requirements changed recently)

…mask

mathieuboudreau

Per Julien's recommendation on Slack, and since we've likely reviewed this branch/feature more-or-less 10 times & users are already beginning to use it, I'm going to approve this PR and merge so that I can record a tutorial video for it. Any remaining fixes/changes should now be done by opening small (i.e. single-issue or single-feature) pull requests, and not in another big one like this.

Great job @Stoyan-I-A ! This feature is going to be incredibly useful!

Stoyan-I-A added 4 commits March 4, 2019 18:53

Add files via upload

ec16825

Added a button to run a prediction model on the loaded PNG image

f00c11f

Changed reqs to be compatible with FSLeyes

ee0c338

Issues #162 and #173

37582f4

- Implemented the GUI design - The user can now select which model to apply by selecting it in the ComboBox

jcohenadad reviewed Mar 11, 2019

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jcohenadad reviewed Mar 11, 2019

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jcohenadad and others added 3 commits March 13, 2019 12:58

Merge branch 'master' into FSLeyes_integration

e21c209

Merge branch 'master' into FSLeyes_integration

6070ef7

Issue #191

e716bb1

It is now possible to save segmentation masks

Stoyan-I-A added 2 commits March 24, 2019 21:00

#193 - Changed the method to find the centroids

20e1176

The centroids are now calculated with the myelin array rather than the axon array when trying to fill the axons.

Stoyan-I-A added 2 commits March 25, 2019 18:43

#182 - removed unused package

d7bf190

#182 - changed the logo location

85692ca

mathieuboudreau closed this Mar 27, 2019

mathieuboudreau reopened this Mar 27, 2019

[BUG] Fix logo path & make os-independent

fd63f2f

Antoine Moevus and others added 2 commits April 2, 2019 10:08

Merge branch 'master' into FSLeyes_integration

2e1668f

[FSLeyes integration] - updated the documentation for installing FSLeyes

f49c9ec

[GUI] Add buton to compute and save morphometrics (#256)

30d8b36

Stoyan-I-A added 2 commits September 7, 2019 18:57

#254 #253 #182 - see description

01e8309

- The plugin now checks suffixes instead of the entire name - The fill option now creates a new corrected axon overlay - The plugin now verifies if another version is present in the ADS directory

#182 - removed unnecessary axon_mask check

fabe4c0

#182 - modified how the version is checked

a5552eb

mathieuboudreau reviewed Sep 10, 2019

View reviewed changes

mathieuboudreau added 3 commits September 16, 2019 14:54

Merge branch 'master' into FSLeyes_integration

d0192f8

Result test fail due to upgrade in package

3ff1e65

Update imread to use imageio config param names

e018786

jcohenadad mentioned this pull request Sep 17, 2019

Use adsutils for i/o in ADS plugin #257

Closed

Stoyan-I-A added 3 commits September 23, 2019 17:09

#259 - changed the way the image format is checked. The plugin can no…

9a6f98e

…w also load jpg/jpeg images

#259 - forgot to change plugin version

126d24e

#263 Flipping images when they are loaded into FSLeyes

63be0f4

#182 - the fill_axon tool now uses the centroids found with the axon …

2fe999d

…mask

mathieuboudreau approved these changes Oct 14, 2019

View reviewed changes

mathieuboudreau merged commit 1eb6309 into master Oct 14, 2019

Stoyan-I-A mentioned this pull request Mar 3, 2020

[FSLeyes_integration] Modify the image loading process to make use of the new 2D support #229

Closed

This was referenced May 14, 2020

Verify version of ads_plugin under fsleyes config folder #253

Closed

Identify axon/myelin files based on the suffix #254

Closed

jcohenadad mentioned this pull request Sep 8, 2020

Failing to load ads_plugin: No module named wx.lib.agw.hyperlink #348

Closed

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Add FSLeyes plugin #182

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		@@ -36,6 +34,8 @@

		from AxonDeepSeg.morphometrics.compute_morphometrics import *

		VERSION = "0.2.2"

Add FSLeyes plugin #182

Add FSLeyes plugin #182

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TODO

How to test / install

Tools description

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