Support globs and multiple sheets

Author: timholy

Project.toml

@@ -5,6 +5,7 @@ version = "1.0.0"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
 ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
@@ -20,6 +21,7 @@ CounterMarkingImageViewExt = "ImageView"
 
 [compat]
 FileIO = "1"
+Glob = "1"
 ImageCore = "0.10"
 ImageIO = "0.6"
 ImageMorphology = "0.4"

docs/src/index.md

@@ -162,7 +162,7 @@ julia> writexlsx(raw"C:\Users\me\somefolder\mydata.xlsx", seg)
 If you have many images in one folder, you can process them all using a single command:
 
 ```
-julia> process_images("2025-03-15/*.png")
+julia> process_images("2025-03-15/results.xlsx", "2025-03-15/*.png")
 ```
 
 ### Step 8: create a "density map" of marks across multiple images

src/CounterMarking.jl

@@ -5,9 +5,10 @@ using ImageSegmentation
 using ImageMorphology: label_components
 using FileIO
 using XLSX
+using Glob
 
 export segment_image, stimulus_index, spots, Spot, upperleft
-export writexlsx
+export writexlsx, process_images
 export randshow, meanshow
 
 include("segment.jl")

src/xlxs.jl

@@ -36,3 +36,39 @@ function writexlsx(filename::AbstractString, seg::SegmentedImage)
     spotdict, stimulus = spots(seg)
     writexlsx(filename, spotdict, stimulus, imgsize)
 end
+
+"""
+    process_images(outfile::AbstractString, glob::GlobMatch; dirname=pwd())
+    process_images(outfile::AbstractString, glob::AbstractString; dirname=pwd())
+
+Process all images with filenames matching `glob` and save the results to `outfile`.
+Each image will be a separate sheet in the Excel file.
+
+Optionally specify the `dirname` containing the images.
+
+# Examples
+
+To process a collection of images in a different directory, and save the results to
+that same directory:
+
+```julia
+julia> process_images("2025-03-15/results.xlsx", glob"*.png"; dirname="2025-03-15")
+```
+"""
+function process_images(outfile::AbstractString, glob::Glob.GlobMatch; dirname=pwd())
+    i = 0
+    XLSX.openxlsx(outfile; mode="w") do xf
+        for filename in readdir(glob, dirname)
+            img = load(filename)
+            seg = segment_image(img)
+            imgsize = size(labels_map(seg))
+            spotdict, stimulus = spots(seg)
+            sheetname = splitext(basename(filename))[1]
+            sheet = xf[i+=1]
+            XLSX.rename!(sheet, sheetname)
+            makesheet!(sheet, spotdict, stimulus, imgsize)
+        end
+    end
+end
+process_images(outfile::AbstractString, glob::AbstractString; kwargs...) =
+    process_images(outfile, Glob.GlobMatch(glob); kwargs...)

test/runtests.jl

@@ -1,5 +1,6 @@
 using CounterMarking
 using FileIO
+using XLSX
 using Test
 
 @testset "CounterMarking.jl" begin
@@ -38,4 +39,9 @@ using Test
     tmpfile = tempname() * ".xlsx"
     writexlsx(tmpfile, seg)
     @test isfile(tmpfile)
+
+    # Test multi-file writing
+    process_images(tmpfile, glob"*.png"; dirname=testdir)
+    data = XLSX.readtable(tmpfile, "Picture")
+    @test isa(data, XLSX.DataTable)
 end