Update Manifest.toml and refactor scalebar functionality in MakieRecipes.jl

- Downgraded Julia version from 1.11.3 to 1.11.1.
- Updated ElectroPhysiology dependency version from 0.5.40 to 0.5.45 and adjusted git-tree-sha1.
- Refactored scalebar functionality to improve parameter handling and documentation, enhancing usability in plot visualizations.
- Revised test script to reflect changes in scale bar parameters and data loading for improved clarity in experimental analysis.

Author: mattar13

Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.3"
+julia_version = "1.11.1"
 manifest_format = "2.0"
 project_hash = "264a14f240d43fd1743b9a93abff69dec12397af"
 
@@ -299,9 +299,9 @@ version = "1.6.0"
 
 [[deps.ElectroPhysiology]]
 deps = ["CurveFit", "DSP", "Dates", "FileIO", "ImageMagick", "Images", "OffsetArrays", "Polynomials", "ProgressMeter", "Requires", "SparseArrays", "Statistics", "TimeZones"]
-git-tree-sha1 = "dfb4f67fbb08b55046a29b780c045d78c0d42c7a"
+git-tree-sha1 = "d6410f4992c0de040aaac703b254787ebb7734c9"
 uuid = "da7a9670-f599-43ac-b818-143f8bf87d45"
-version = "0.5.40"
+version = "0.5.45"
 
 [[deps.ExprTools]]
 git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec"

src/PhysMakie/MakieRecipes.jl

@@ -294,24 +294,27 @@ end
 export stimulustiming!
 
 """
-    @recipe(ScaleBar)
+    scalebar!(ax; origin=(0.0, 0.0), length_x=nothing, length_y=nothing,
+             color=:black, linewidth=2.0, text_color=:black, fontsize=12,
+             x_label=nothing, y_label=nothing, offset_x_ratio=0.02, offset_y_ratio=0.02)
 
-A recipe for adding scale bars to plots. This recipe adds:
+Add scale bars to a plot. This function adds:
 1. An optional x-scale bar (horizontal)
 2. An optional y-scale bar (vertical)
 
-# Attributes
-- `start_x`: Starting x-position for the x-scale bar (default: nothing, meaning no x-scale bar)
-- `length_x`: Length of the x-scale bar in data units (default: 1.0)
-- `start_y`: Starting y-position for the y-scale bar (default: nothing, meaning no y-scale bar)
-- `length_y`: Length of the y-scale bar in data units (default: 1.0)
+# Arguments
+- `ax`: The axis to add scale bars to
+- `origin`: (x,y) position where the scale bars will start (default: (0.0, 0.0))
+- `length_x`: Length of the x-scale bar in data units (default: nothing, meaning no x-scale bar)
+- `length_y`: Length of the y-scale bar in data units (default: nothing, meaning no y-scale bar)
 - `color`: Color of the scale bars (default: :black)
 - `linewidth`: Width of the scale bars (default: 2.0)
 - `text_color`: Color of the scale bar labels (default: :black)
 - `fontsize`: Size of the scale bar labels (default: 12)
 - `x_label`: Label for the x-scale bar (default: nothing, will use length_x value)
 - `y_label`: Label for the y-scale bar (default: nothing, will use length_y value)
-- `offset_ratio`: Ratio of axis range to use for text offset (default: 0.02)
+- `offset_x_ratio`: Ratio of x-axis range to use for text offset (default: 0.02)
+- `offset_y_ratio`: Ratio of y-axis range to use for text offset (default: 0.02)
 
 # Example
 ```julia
@@ -320,84 +323,63 @@ ax = Axis(fig[1,1])
 # First plot your data
 lines!(ax, x, y)
 # Then add scale bars
-scale_bar!(ax, start_x=0.1, length_x=10.0, start_y=0.1, length_y=5.0)
+scalebar!(ax, origin=(0.1, 0.1), length_x=10.0, length_y=5.0)
 ```
 """
-@recipe(ScaleBar) do scene
-    Attributes(
-        start_x = nothing,
-        length_x = 1.0,
-        start_y = nothing,
-        length_y = 1.0,
-        color = :black,
-        linewidth = 2.0,
-        text_color = :black,
-        fontsize = 12,
-        x_label = nothing,
-        y_label = nothing,
-        offset_ratio = 0.02
-    )
-end
-
-"""
-    Makie.plot!(sb::ScaleBar)
-
-Internal plotting function for ScaleBar recipe. Adds scale bars to the current plot
-based on the specified positions and lengths.
-"""
-function Makie.plot!(sb::ScaleBar)
-    # Get the parent axis
-    ax = sb.parent
-    
-    # Get current axis limits
-    xlims = ax.finallimits[].origin[1], ax.finallimits[].origin[1] + ax.finallimits[].widths[1]
-    ylims = ax.finallimits[].origin[2], ax.finallimits[].origin[2] + ax.finallimits[].widths[2]
-    
-    # Calculate offsets based on axis ranges
-    x_range = xlims[2] - xlims[1]
-    y_range = ylims[2] - ylims[1]
-    offset = sb.offset_ratio[] * min(x_range, y_range)
+function scalebar!(ax;         
+    origin = (0.0, 0.0),
+    length_x = nothing,
+    length_y = nothing,
+    color = :black,
+    linewidth = 2.0,
+    text_color = :black,
+    fontsize = 12,
+    x_label = nothing,
+    y_label = nothing,
+    offset_x_ratio = 10.0,
+    offset_y_ratio = 0.2
+)
+    x_start, y_start = origin
 
-    # Plot x-scale bar if start_x is specified
-    if !isnothing(sb.start_x[])
-        x_start = sb.start_x[]
-        x_end = x_start + sb.length_x[]
-        y_pos = sb.start_y[] === nothing ? ylims[1] + offset : sb.start_y[]
+    # Plot x-scale bar if length_x is specified
+    if !isnothing(length_x)
+        x_end = x_start + length_x
 
-        lines!(sb, [x_start, x_end], [y_pos, y_pos],
-            color = sb.color[],
-            linewidth = sb.linewidth[]
+        lines!(ax, [x_start, x_end], [y_start, y_start],
+            color = color,
+            linewidth = linewidth
         )
 
-        x_label_text = isnothing(sb.x_label[]) ? "$(sb.length_x[])" : sb.x_label[]
-        text!(sb, x_label_text,
-            position = (x_start + sb.length_x[]/2, y_pos - offset),
-            align = (:center, :top),
-            color = sb.text_color[],
-            fontsize = sb.fontsize[]
+        x_label_text = isnothing(x_label) ? "$(length_x)" : x_label
+        text!(ax, x_label_text,
+            position = (x_start + length_x/2, y_start - y_start/offset_x_ratio),
+            align = (:center, :center),
+            color = text_color,
+            fontsize = fontsize
         )
     end
 
-    # Plot y-scale bar if start_y is specified
-    if !isnothing(sb.start_y[])
-        y_start = sb.start_y[]
-        y_end = y_start + sb.length_y[]
-        x_pos = sb.start_x[] === nothing ? xlims[1] + offset : sb.start_x[]
+    # Plot y-scale bar if length_y is specified
+    if !isnothing(length_y)
+        y_end = y_start + length_y
 
-        lines!(sb, [x_pos, x_pos], [y_start, y_end],
-            color = sb.color[],
-            linewidth = sb.linewidth[]
+        lines!(ax, [x_start, x_start], [y_start, y_end],
+            color = color,
+            linewidth = linewidth
         )
 
-        y_label_text = isnothing(sb.y_label[]) ? "$(sb.length_y[])" : sb.y_label[]
-        text!(sb, y_label_text,
-            position = (x_pos - offset, y_start + sb.length_y[]/2),
-            align = (:right, :center),
-            color = sb.text_color[],
-            fontsize = sb.fontsize[],
-            rotation = -pi/2 # Makie uses radians for rotation
+        y_label_text = isnothing(y_label) ? "$(length_y)" : y_label
+        text!(ax, y_label_text,
+            position = (x_start - x_start/offset_y_ratio, y_start + length_y/2),
+            align = (:center, :center),
+            color = text_color,
+            fontsize = fontsize,
+            rotation = pi/2  # Makie uses radians for rotation
         )
     end
 
-    return sb
-end
+    return ax
+end
+
+# Export the function
+export scalebar!

test/Manifest.toml

@@ -1509,11 +1509,11 @@ version = "0.5.3"
 
 [[deps.PhysiologyAnalysis]]
 deps = ["CSV", "Colors", "DataFrames", "Dates", "ElectroPhysiology", "FileIO", "GLMakie", "HypothesisTests", "ImageFiltering", "ImageMagick", "Images", "Interpolations", "LinearAlgebra", "LsqFit", "OffsetArrays", "Peaks", "Polynomials", "ProgressMeter", "Requires", "SparseArrays", "Statistics", "StatsBase"]
-git-tree-sha1 = "f933db47eabc577f1620757a79cc39e6986a6863"
+git-tree-sha1 = "ed78c25f59a444d783271c7b7ba648e5d9408647"
 repo-rev = "main"
 repo-url = "https://github.com/mattar13/PhysiologyAnalysis.jl.git"
 uuid = "69cbc4a0-077e-48a7-9b45-fa8b7014b5ca"
-version = "0.6.42"
+version = "0.6.44"
 
 [[deps.Pixman_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"]

test/revision.jl

@@ -6,33 +6,33 @@ using Pkg; Pkg.activate("test")
 using GLMakie
 using PhysiologyAnalysis
 #using Pkg; Pkg.activate("test")
- 
+
 #Loading data for 10mM Dopamine 
 img_da_10mM_fn = raw"F:\Data\Two Photon\2025-05-19-nirCAT-STR-DPUFF\nirCAT_s2_10mM_mq010.tif"
 stim_da_10mM_fn = raw"F:\Data\Patching\2025-05-19-nirCAT-str\25519016.abf"
-da_10mM_data = load_puffing_data(img_da_10mM_fn, stim_da_10mM_fn, split_channel = false, main_channel = :red)
+da_10mM_data = load_puffing_data(img_da_10mM_fn, stim_da_10mM_fn, split_channel = true, main_channel = :red)
 
+#%%
+PhysiologyPlotting.__init__()
 fig_roi = plot_roi_analysis(da_10mM_data["experiment"], stim_idx = 2)
 
 experiment = da_10mM_data["experiment"]
 getStimulusProtocol(experiment)
 fig, ax = twophotonprojection(experiment, dims = (1, 2))
 stimulustiming!(ax, experiment)
 
-
 scalebar!(ax, 
-    start_x = 40.0,  # Start at 40 seconds
+    origin = (0.5, 0.01),  # Start at 40 seconds
     length_x = 25.0, # 25 second scale bar
-    start_y = 0.005, # Start at 0.005 intensity
-    length_y = 0.1,  # 0.1 intensity scale bar
+    length_y = 0.001,  # 0.1 intensity scale bar
     x_label = "25 s",
-    y_label = "0.1"
+    y_label = "1% df/f"
 )
 fig
 
 #%%
-fig = plot_roi_analysis(data2P, stim_idx = 2)
-display(fig)
-save(raw"H:\Data\Analysis\fig_roi_analysis_striatum_elec.png", fig)
+# fig = plot_roi_analysis(data2P, stim_idx = 2)
+# display(fig)
+# save(raw"H:\Data\Analysis\fig_roi_analysis_striatum_elec.png", fig)
 
 # Save the ROI analysis figure