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Update for Makie 0.24 #53
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01bfff6
Prune dependencies
mkitti ba17756
Qualify dependencies under ShroffCelegansModels
mkitti 66c7464
Update fix_annotation_ap_axis.jl for Makie 0.24
mkitti 4540214
Fix CI
mkitti 6f525b4
Make cache loading optional
mkitti 10a6cec
Working web apps
mkitti a97973b
Set compat with Dates to 1
mkitti da10d3c
Update web Manifest.toml
mkitti 9ceb850
Use 0.0.0.0 and SHROFF_HOST env var for portability
mkitti 28e4625
Add resave_for_ben.jl
mkitti a81429b
Update loading.jl with config_2026_03_19_v2.json
mkitti 0e6733b
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
mkitti ecee33d
Updates from Windows local dev
mkitti ffe8641
Update Project.toml and Manifest.toml files
mkitti bc7b228
Update scripts
mkitti f9b999d
Add configuration
mkitti cc8e14b
Enable query params in fix_annotation_ap_axis
mkitti e5f8fff
Add linux config v2, conversion script, and update config path
mkitti b623a1a
Add deployment directory copied from shroff-data-for-mark
mkitti d606228
Adapt deployment for repo-based build context
mkitti 2358c8a
Add multithreading to Julia
mkitti 227ec07
Use annotation and timepoint query strings
mkitti 0ddadf9
Identify outlier timepoints via URL
mkitti cddd7a4
Create a base Docker image with just dependencies
mkitti 0a3a6ee
Add initial raw_zscore_analysis function
mkitti 2302198
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
mkitti 5494adb
Update deployment, use base image, annotation changes
mkitti e410a2d
Collect annotation changes path into a single function
mkitti e11b812
Remove redundant AnnotationChanges constructor
mkitti 491450d
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
mkitti f11f263
Add task to download annotation_changes.h5 to a dated file
mkitti 7ca8521
Add win-64 platform
mkitti 292a621
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
mkitti f66092a
Add download_annotation_changes.jl script
mkitti 112d954
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
mkitti d113aad
Use a local dest in download_annotation_changes.jl
mkitti f29d596
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
mkitti be6f87f
Add zscores as a web app
mkitti 037eed2
Set up deployment for zscore-analysis, testing
mkitti 847dfb4
Fix zscore analysis and Win and Linux paths
mkitti 26e987e
Add modified time tracking, add get_avg_models
mkitti a619e1f
Use get_group_annotation_positions_over_time
mkitti 8732792
Add daily mtime tracking for integrated annotations
mkitti fab5730
Mirror modified-times deployment to shroff-data (prod)
mkitti 95566e3
Restore Main-scope names removed by commenting out makie.jl include
mkitti 827d32e
Merge branch 'main' into web_makie_0_24
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| # Config Change Summary | ||
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| ## 2024-09-05 v1 → 2026-03-19 v2 | ||
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| Settings (folderpaths, voxel scale, outlier removal, interpolation, warping, smoothing, mipav_output) are unchanged. | ||
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| ### Removed paths (5) | ||
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| **JCC596_NU** — 3 old paths replaced by re-processed `Untwisting_Redo` equivalents: | ||
| - `JCC596_NU/Untwisting/082619_JCC596_NU/JCC596_NU/Pos3/SPIMB_result/Reg_Sample/Decon_registered` | ||
| - `JCC596_NU/Untwisting/091119_JCC596_NU/JCC596_NU/JCC596_NU/JCC596_NU/Pos2/SPIMB_result/Reg_Sample/Decon_registered` | ||
| - `JCC596_NU/Untwisting/091119_JCC596_NU/JCC596_NU/JCC596_NU/JCC596_NU/Pos3/SPIMB_result/Reg_Sample/Decon_registered` | ||
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| **DCR4221** — UTP 1 dataset dropped; strain now has 4 datasets (UTP 2–5): | ||
| - `Non-model C elegans folders/Untwisting_Paper/DCR4221/063014_lattices_Javier - UTP 1/Decon_reg` | ||
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| **RW10752_NU Pos2** — old path replaced: | ||
| - `RW10752_NU/Untwisting/031219_RW10752_NU/RW10752_NU/RW10752_NU/Pos2/Old/Decon_registered` | ||
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| ### Added paths (13) | ||
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| **JCC596_NU** — 3 replacement paths under `Untwisting_Redo`: | ||
| - `JCC596_NU/Untwisting_Redo/082619_Pos3` | ||
| - `JCC596_NU/Untwisting_Redo/091119_Pos2` | ||
| - `JCC596_NU/Untwisting_Redo/091119_Pos3` | ||
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| **RW10752_NU Pos2** — replacement path: | ||
| - `RW10752_NU/Untwisting/031219_RW10752_NU/RW10752_NU/RW10752_NU/Pos2/SPIMB/For_Tracking/For_Tracking` | ||
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| **RW10131_retracked** — new strain, 3 positions (2024 SLS268 imaging): | ||
| - `RW10131/Data/2024_SLS268/20240401/RW10131_SLS6_New/Pos4/SPIMB/Reg_Sample/For_Tracking` | ||
| - `RW10131/Data/2024_SLS268/20240429/SLS268_RW10131_SLS6/Pos1/SPIMB/Reg_Sample/For_Tracking` | ||
| - `RW10131/Data/2024_SLS268/20240507/Pos1/SPIMA/Reg_Sample/For_Tracking` | ||
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| **RW10598_retracked** — new strain, 3 positions (2023 re-tracking): | ||
| - `RW10598/2023_Data/Tracking/20230718/RW10598_NU/Pos1/SPIMB/Reg_Sample/For_Tracking` | ||
| - `RW10598/2023_Data/Tracking/20230718/RW10598_NU/Pos2/SPIMB/Reg_Sample/For_Tracking` | ||
| - `RW10598/2023_Data/Tracking/20230719/RW10598_NU/Pos4/SPIMB/Reg_Sample/For_Tracking` | ||
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| **RW10896_retracked** — new strain, 3 positions (2023 imaging): | ||
| - `RW10896/Postwitching/2023_imaging/20231129/RW10896_NU/Pos1/SPIMB/Registered_Volumes/For_Tracking` | ||
| - `RW10896/Postwitching/2023_imaging/20231129/RW10896_NU/Pos2/SPIMB/Registered_Volumes/For_Tracking` | ||
| - `RW10896/Postwitching/2023_imaging/20231129/RW10896_NU/Pos3/SPIMB/Registered_Volumes/For_Tracking` |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| #!/usr/bin/env julia | ||
| # Converts Windows-style paths in a config JSON to Unix-style paths. | ||
| # Usage: julia convert_windows_paths.jl [input.json [output.json]] | ||
| # | ||
| # Default input: config/windows/config_2026_03_19_v2.json | ||
| # Default output: config/linux/config_2026_03_19_v2.json | ||
| # | ||
| # Path mapping applied: | ||
| # X:\shrofflab\ → /nearline/shroff/shrofflab/ | ||
| # remaining backslashes → forward slashes | ||
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| using JSON3 | ||
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| const WINDOWS_PREFIX = Regex("^[A-Za-z]:\\\\shrofflab\\\\", "i") | ||
| const UNIX_PREFIX = "/nearline/shroff/shrofflab/" | ||
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| function convert_path(s::AbstractString) | ||
| s = replace(s, WINDOWS_PREFIX => UNIX_PREFIX) | ||
| replace(s, '\\' => '/') | ||
| end | ||
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| function convert_value(v) | ||
| if v isa AbstractString | ||
| return convert_path(v) | ||
| elseif v isa AbstractDict | ||
| return Dict(k => convert_value(val) for (k, val) in v) | ||
| elseif v isa AbstractArray | ||
| return [convert_value(el) for el in v] | ||
| else | ||
| return v | ||
| end | ||
| end | ||
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| function main() | ||
| script_dir = dirname(abspath(@__FILE__)) | ||
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| input_path = length(ARGS) >= 1 ? ARGS[1] : | ||
| joinpath(script_dir, "windows", "config_2026_03_19_v2.json") | ||
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| default_output_dir = joinpath(script_dir, "linux") | ||
| output_path = length(ARGS) >= 2 ? ARGS[2] : | ||
| joinpath(default_output_dir, basename(input_path)) | ||
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| isfile(input_path) || error("Input file not found: $input_path") | ||
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| config = open(input_path) do io | ||
| JSON3.read(io, Dict{String,Any}) | ||
| end | ||
| converted = convert_value(config) | ||
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| mkpath(dirname(output_path)) | ||
| open(output_path, "w") do io | ||
| JSON3.write(io, converted) | ||
| println(io) # trailing newline | ||
| end | ||
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| println("Wrote converted config to: $output_path") | ||
| end | ||
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| main() |
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i usually just test on 1 and 1.10