Integrating code into bestie template #3

Till223 · 2025-02-03T13:12:18Z

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Docs were updated and workflow is passing

renamed heuristic functions

codecov · 2025-02-09T18:05:44Z

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removed plotting inside of the algorithm added plotting in runner.jl using the interim results

…m (RideUnfold, OriginalRide)

ReneSkukies · 2025-02-11T10:55:19Z

Project.toml

 version = "0.1.0"

+[deps]


There are several dependencies here that are unlikely to be part of the package in the end. These are e.g. CairoMakie, UnfoldSim, or Revise.

I understand that these are needed for package development, but ultimately they are too big of a dependence to be included. You could instead have a playground/ dev environment and then "dev UnfoldRIDE" to your local path in that.

Ok, I've switched to using the /test/Project.toml for now, but I'll think about making a dedicated dev environment. It sounds like a good idea.
The main Project.toml should be clean now.

I dont see it yet, forgot to push?

moved non module files to test, mainly runner.jl and runner_matlab_samp.jl

behinger · 2025-02-13T11:39:57Z

Project.toml

 version = "0.1.0"

+[deps]


I dont see it yet, forgot to push?

behinger · 2025-02-13T11:40:18Z

Project.toml

+Distributions = "0.25.117"
+FFTW = "1.8.1"
+Parameters = "0.12.3"
+Peaks = "0.5.3"


Suggested change

Peaks = "0.5.3"

Peaks = "0.5"

don't fix on bugfix versions, but feature / major versions

ReneSkukies

I am not sure if you need to address everything, and some stuff is for later review, but a bit of work still there.

One of the most important things for now are the documentation and the docstrings. This can be a different PR though, and can be done after you finish writing the thesis.

ReneSkukies · 2025-02-11T11:04:48Z

src/ride/ride_structs.jl

+
+abstract type RideModus end
+struct RideOriginal <: RideModus end
+struct RideUnfold <: RideModus end


Suggested change

struct RideUnfold <: RideModus end

struct UnfoldRide <: RideModus end

For consistency, I would probably keep this the same as in Unfold.jl (where the types are names e.g. UnfoldLineraModel)

But then you'd have to rename RideOriginal to OriginalRide as well I guess

renamed them to ModusRide, OriginalRide and UnfoldRide

can I propose AbstractRIDE, UnfoldRIDE and ClassicRIDE / OriginalRIDE?

I agree with Bene, that would make it more clear

Sure, that works. I think I like ClassicRIDE more than OriginalRIDE.

ReneSkukies · 2025-02-11T11:08:45Z

src/ride/ride_unfold_algorithm.jl

+    @debug "Running RIDE algorithm with cfg: $cfg"
+    ## data_preparation
+    data_reshaped = reshape(data, (1, :))
+    evts_s = @subset(evts, :event .== 'S')


This should be more general. You usually can't assume people call their events S or R. Especially given the char type.

It's ok for the initial push though. Can be refactored later

ReneSkukies · 2025-02-11T11:10:13Z

src/ride/ride_unfold_algorithm.jl

@@ -0,0 +1,158 @@
+function ride_algorithm(Modus::Type{RideUnfold}, data, evts, cfg::RideConfig)


It's good practice to directly write some docstrings with the function.

src/ride/ride_unfold_methods.jl

ReneSkukies · 2025-02-17T09:16:52Z

src/ride/ride_original_algorithm.jl

@@ -0,0 +1,232 @@
+function ride_algorithm(Modus::Type{RideOriginal}, data, evts, cfg::RideConfig)


Please provide docstrings with the functions; for exported functions like here use:
https://unfoldtoolbox.github.io/UnfoldSim.jl/previews/PR138/developer_docs/#Docstring-templates

test/test-ride_shared_methods.jl

ReneSkukies · 2025-02-17T11:41:08Z

test/test-ride_shared_methods.jl

Pleas comment on what is happening

test/test-runner.jl

test/Project.toml

…l testing cleaned up Project.toml and test/Project.toml

Co-authored-by: René Skukies <[email protected]>

ReneSkukies

Some more comments and then we can merge ;)
And then tackle documentation 🐙

ReneSkukies · 2025-02-18T10:37:56Z

Project.toml

-Revise = "3.7.2"
-StableRNGs = "1.0.2"
-Statistics = "1.11.1"
+CairoMakie = "0.13"


I don't think you need a compat for CairoMakie if it's not part of you package ;)

ReneSkukies · 2025-02-18T10:42:40Z

src/ride/ride_structs.jl

-abstract type RideModus end
-struct RideOriginal <: RideModus end
-struct RideUnfold <: RideModus end
+abstract type ModusRide end


Suggested change

abstract type ModusRide end

abstract type AbstractRide end

As Bene suggested I would rename this

ReneSkukies · 2025-02-18T10:43:22Z

src/ride/ride_structs.jl

+struct OriginalRide <: ModusRide end
+struct UnfoldRide <: ModusRide end


Suggested change

struct OriginalRide <: ModusRide end

struct UnfoldRide <: ModusRide end

struct OriginalRide <: AbstractRide end

struct UnfoldRide <: AbstractRide end

added function to run the classic version one time for every channel modified the unfold version to be able to work with multiple channels as input

ClassicRIDE just runs multiple times, once for each channel, then outputs a Vector of RideResults UnfoldRIDE adapted to handle multiple channels throughout the algorithm

wrote tutorial code for data simulation

…the size of one epoch changed output C_latencies to present latencies from stimulus onset instead of latencies from epoch onset adjusted plotting to work with new outputs

changed UnfoldModeRIDE and ClassicRIDE parameters to UnfoldMode and ClassicMode and AbstractMode

fixed a bug in heuristic2

…de_classic_algorithm.jl and ride/ride_classic_methods.jl

deleted unused code

updated index.md

Multi channel processing + Various changes

Till223 added 2 commits February 3, 2025 14:11

integrating code into bestie template

73057e5

implemented dspfilter()

d7ae8e9

renamed heuristic functions

Till223 added 7 commits February 10, 2025 13:38

added interim result saving

dea3662

removed plotting inside of the algorithm added plotting in runner.jl using the interim results

added integration test test-runner.jl

599ecbb

replaced CairoMakie in tests with UnicodePlots

38408d2

formatting

033e871

adjusted test to not give 30000 results

5ce51d7

removed trailing whitespaces

249ad0d

added separate integration testsets for both versions of the algorith…

e1a96cd

…m (RideUnfold, OriginalRide)

ReneSkukies reviewed Feb 11, 2025

View reviewed changes

Till223 added 3 commits February 11, 2025 12:28

cleaned up Project.toml

4674028

moved non module files to test, mainly runner.jl and runner_matlab_samp.jl

Merge remote-tracking branch 'remotes/origin/main' into initial_commit

fa442dc

added missing manual test files

35aea38

behinger reviewed Feb 13, 2025

View reviewed changes

ReneSkukies reviewed Feb 17, 2025

View reviewed changes

Till223 and others added 3 commits February 17, 2025 15:29

added dev/ folder to hold files only related to development and manua…

4a83fce

…l testing cleaned up Project.toml and test/Project.toml

renamed ModusRide, OriginalRide, UnfoldRide

20e692c

added TODO suggestion

eaf1f2b

Co-authored-by: René Skukies <[email protected]>

ReneSkukies reviewed Feb 18, 2025

View reviewed changes

Till223 added 10 commits February 27, 2025 09:53

WIP multi channel support

60fa7ee

added function to run the classic version one time for every channel modified the unfold version to be able to work with multiple channels as input

minor changes

230c5ed

Merge branch 'initial_commit' into multi_channel

eded07f

wip minor changes

3aa596a

working implementation of multi channel processing.

776bf97

ClassicRIDE just runs multiple times, once for each channel, then outputs a Vector of RideResults UnfoldRIDE adapted to handle multiple channels throughout the algorithm

minor changes

48c31ca

simplified data simulation code

3ed823a

wrote tutorial code for data simulation

changed algorithm output to contain S,C,R with zero padding to match …

155eb97

…the size of one epoch changed output C_latencies to present latencies from stimulus onset instead of latencies from epoch onset adjusted plotting to work with new outputs

changed results to contain the raw_erp, mainly to make plotting easier

68eb4e9

changed UnfoldModeRIDE and ClassicRIDE parameters to UnfoldMode and ClassicMode and AbstractMode

updated git.ignore

148ce76

Till223 and others added 20 commits March 24, 2025 23:16

moved matlab data to /dev/data

5af1327

changed simulated_data path to dev/data/

34c1342

added matlab_RIDE with scripts used during UnfoldRIDE development

5e6a9c7

forgot to save these

6fa9e0a

script to create a sysimage

c0b1eaa

fixed tests

8d4f136

fixed a bug in heuristic2

renamed ride_original_algorithm.jl and ride_original_methods.jl to ri…

9332d6e

…de_classic_algorithm.jl and ride/ride_classic_methods.jl

added comments for ride_shared_methods.jl

ad5e060

moved matlab_RIDE to other repository

b7169d3

fixed a bug in ride_unfold_algorithm.jl

07f665b

added wiki pages and code

2478234

fixed an issue with the plotting

7ba61cf

deleted unused code

added landing page index.md

1e0573f

updated README.md

ac757b2

fixed tests

bfccd78

updated index.md

formatting

40491ab

removed template remnant

fde6665

added docstrings for ride_structs.jl

5f309b4

Update make.jl to deploy predocs

96b92d6

Merge pull request #5 from unfoldtoolbox/multi_channel

2946816

Multi channel processing + Various changes

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Integrating code into bestie template #3

Integrating code into bestie template #3

Till223 commented Feb 3, 2025

codecov bot commented Feb 9, 2025

ReneSkukies Feb 11, 2025

Till223 Feb 11, 2025

behinger Feb 13, 2025

behinger Feb 13, 2025

behinger Feb 13, 2025

ReneSkukies left a comment

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Till223 Feb 17, 2025

behinger Feb 17, 2025

ReneSkukies Feb 17, 2025

Till223 Feb 17, 2025

ReneSkukies Feb 11, 2025

ReneSkukies Feb 17, 2025

ReneSkukies Feb 11, 2025

ReneSkukies Feb 17, 2025

ReneSkukies Feb 17, 2025

ReneSkukies left a comment

ReneSkukies Feb 18, 2025

ReneSkukies Feb 18, 2025

ReneSkukies Feb 18, 2025

	struct RideUnfold <: RideModus end
	struct UnfoldRide <: RideModus end

		@@ -0,0 +1,158 @@
		function ride_algorithm(Modus::Type{RideUnfold}, data, evts, cfg::RideConfig)

		@@ -0,0 +1,232 @@
		function ride_algorithm(Modus::Type{RideOriginal}, data, evts, cfg::RideConfig)

		struct OriginalRide <: ModusRide end
		struct UnfoldRide <: ModusRide end

Integrating code into bestie template #3

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Till223 commented Feb 3, 2025

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codecov bot commented Feb 9, 2025

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