[WIP] update transparent plotting demo

[Remi-Gau]

Summary by Sourcery

Updates the transparent plotting demo to use the new BIDS-Model structure and improve the visualisation of results, including ROI contours.

Enhancements:

• Updates the transparent plotting demo to use the new BIDS-Model structure.
• Improves the visualisation of results, including ROI contours.
• Uses the montage settings from the model.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request streamlines the transparent plotting demo by reading the configuration directly from the model, simplifying the layer configuration, and removing redundant steps. This results in a cleaner and more efficient implementation.

Updated class diagram for layers configuration

classDiagram
    class sd_config_layers {
        -layers
        +init(layer_types)
    }

    note for sd_config_layers "The number of layers has been reduced from 4 to 3. The contour layer for the left ROI has been removed."

Loading

File-Level Changes

Change	Details	Files
Streamlined the configuration process for transparent plotting by directly utilizing the information from the model and removing redundant steps.	Removed manual specification of results and directly read them from the model. Removed BIDS layout querying for ROI files. Consolidated ROI contour plotting to use a single mask file. Removed the fourth layer related to ROI contour. Updated opacity range for the dual-coded layer. Set slice display settings based on the model configuration.	demos/MoAE/moae_03_slice_display.m
Updated the layers configuration to use a single contour file.	Replaced the right and left ROI files with a single contour file. Removed the fourth layer related to the left ROI file.	demos/MoAE/moae_03_slice_display.m

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[sourcery-ai]

Hey @Remi-Gau - I've reviewed your changes - here's some feedback:

Overall Comments:

• It might be helpful to include a brief explanation of the purpose of this demo in the description.
• Consider adding comments to explain the purpose of key variables and sections of code to improve readability.

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[codecov]

Codecov Report

Attention: Patch coverage is 69.56522% with 7 lines in your changes missing coverage. Please review.

Project coverage is 53.86%. Comparing base (f53979a) to head (ea2c383).
Report is 161 commits behind head on main.

Files with missing lines	Patch %	Lines
src/stats/results/checkMontage.m	69.56%	7 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (f53979a) and HEAD (ea2c383). Click for more details.

HEAD has 6 uploads less than BASE

Flag	BASE (f53979a)	HEAD (ea2c383)
cli	1	0
ubuntu-latest_matlab-R2023a_fast	1	0
octave	2	1
ubuntu-latest_matlab-R2023a_slow	1	0
macos-latest_matlab-R2023a_fast	1	0
macos-latest_matlab-R2023a_slow	1	0

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #1354       +/-   ##
===========================================
- Coverage   79.57%   53.86%   -25.72%     
===========================================
  Files         285      285               
  Lines        7742     7758       +16     
  Branches       40        0       -40     
===========================================
- Hits         6161     4179     -1982     
- Misses       1565     3579     +2014     
+ Partials       16        0       -16     

Flag	Coverage Δ
cli	?
macos-latest_matlab-R2023a_fast	?
macos-latest_matlab-R2023a_slow	?
octave	53.86% <69.56%> (-21.86%)	⬇️
ubuntu-latest_matlab-R2023a_fast	?
ubuntu-latest_matlab-R2023a_slow	?

Flags with carried forward coverage won't be shown. Click here to find out more.

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