Support more fields, add github conf files

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

@@ -0,0 +1,40 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+    tags: ['*']
+  pull_request:
+  workflow_dispatch:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.10'
+          - 'pre'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -0,0 +1,31 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -1,7 +1,7 @@
 name = "WykoOPDReader"
 uuid = "6da23c8c-444c-4310-aaa6-9150b66cb193"
 authors = ["Jaakko Ruohio <jaakkor2@gmail.com>"]
-version = "0.1.0"
+version = "0.1.1"
 
 [compat]
 julia = "1.10"

src/WykoOPDReader.jl

@@ -1,13 +1,14 @@
 """
     WykoOPDReader
 
-Reader for WYKO data sets (.opd) implemented in Julia.
+Reader for WYKO OPD data sets (.opd) implemented in Julia.
 Exports `readopd`.
 """
 module WykoOPDReader
 
-export readopd
+export readopd, prepplot
 
 include("reader.jl")
+include("util.jl")
 
 end

src/reader.jl

@@ -1,7 +1,7 @@
 """
     readopd(fn)
 
-Read Wyko data set from file `fn`.
+Read Wyko OPD data set from file `fn`.
 
 # Example
 
@@ -10,14 +10,17 @@ using WykoOPDReader
 fn = joinpath(pathof(WykoOPDReader), "..", "..", "test", "demo.opd")
 data = readopd(fn)
 
+# data to plot
+z = data["RAW_DATA"] * (haskey(data, "Wavelength") ? data["Wavelength"]/1000 : 1.0)
+(; x, y, colormap, nan_color) = prepplot(data)
+
 using GLMakie
-colormap = [:NavyBlue, :royalblue3, :LightGreen, :Red]
-nan_color = :black
-autolimitaspect = data["Aspect"]
 fig = Figure()
-ax = Axis(fig[1,1]; autolimitaspect)
-hm = heatmap!(ax, data["RAW_DATA"]; colormap, nan_color)
+ax = Axis(fig[1,1], aspect = DataAspect())
+hm = heatmap!(ax, x, y, z; colormap, nan_color)
+hm.inspector_label = (plot, index, position) -> "\$(x[index[1]]) \$(y[index[2]]) \$(position[3])"
 Colorbar(fig[1,2], hm, width = Relative(1/10))
+DataInspector()
 ```
 """
 function readopd(fn)
@@ -33,22 +36,26 @@ function readopd(fn)
         push!(entries, readentry(io))
     end
     for i = 2:n_entries
-        (; name, type, len) = entries[i]
+        (; name, type, len, dunno) = entries[i]
+#        name == "" || @show name, type, len, dunno, "OPP"
         if name == ""
             continue
         elseif type == 3
             push!(data, name => readimage(io))
         elseif type == 5
             push!(data, name => readstring(io, len))
-        elseif entries[i].type == 6
+        elseif type == 6
             push!(data, name => readint(io, len))
-        elseif entries[i].type == 7
+        elseif type in [7,8] # 7=Float32, 8=Float64
             push!(data, name => readfloat(io, len))
+        elseif type == 15
+            push!(data, name => read15(io, len))
         else
-            @show "This is unknown: ", name, type, len
+            @show "This is unknown: ", name, type, len, dunno
         end
     end
     close(io)
+    data = replaceshortkeys(data)
     return data
 end
 
@@ -76,3 +83,78 @@ end
 readstring(io, n) = rstrip(String(read(io, n)), '\0')
 readfloat(io, n) = reinterpret(n == 4 ? Float32 : Float64, read(io, n))[1]
 readint(io, n) = reinterpret(n == 4 ? Int32 : n == 2 ? Int16 : Int8, read(io, n))[1]
+
+function read15(io, n)
+    readnext(io)
+end
+
+function readnext(io)
+    type = read(io, 1)[1]
+    if type == 1 # bool?
+        reinterpret(Bool, read(io, 1)[1])
+    elseif type == 6
+        reinterpret(Int32, read(io, 4))[1]
+    elseif type == 10
+        reinterpret(Int64, read(io, 8))[1]
+    elseif type == 12
+        reinterpret(Float32, read(io, 4))[1]
+    elseif type == 13
+        reinterpret(Float64, read(io, 8))[1]
+    elseif type == 14
+        len = reinterpret(Int32, read(io, 4))[1]
+        s1 = String(read(io, len))
+        read(io, 1)
+        n = read(io, 1)[1]
+        v1 = read(io, n)
+        s1, v1
+    elseif type == 21 # TimeStamp
+        read(io, 1)
+        reinterpret(Int64, read(io, 8)) # ANSI Date (64-bit value representing the number of 100-nanosecond intervals since January 1, 1601.)
+    elseif type == 66
+        len = reinterpret(Int32, read(io, 4))[1]
+        s1 = String(read(io, len))
+        lenbytes = read(io, 1)[1]
+        len = reinterpret(lenbytes == 1 ? UInt8 : UInt16, read(io, lenbytes))[1]
+        len = reinterpret(Int32, read(io, 4))[1]
+        s2 = String(read(io, len))
+        s1, s2
+    else
+        lenbytes = read(io, 1)[1]
+        len = reinterpret(lenbytes == 1 ? UInt8 : UInt16, read(io, lenbytes))[1]
+        if type == 18
+            String(read(io, len))
+        elseif type == 19
+            v = reinterpret(Float64, read(io, 8))[1]
+            len1 = reinterpret(Int32, read(io, 4))[1]
+            s1 = String(read(io, len1))
+            len2 = reinterpret(Int32, read(io, 4))[1]
+            s2 = String(read(io, len2))
+            sc = reinterpret(Float64, read(io, 8))[1]
+            read(io, len - 8 - 4 - len1 - 4 - len2 - 8) # TODO some bytes unprocessed
+            v, s1, s2, sc
+        elseif type == 125
+            res = Dict{String,Any}()
+            while true
+                len1 = reinterpret(Int32, read(io, 4))[1]
+                if len1 == 0
+                    read(io, 3)
+                    break
+                end
+                s1 = String(read(io, len1))
+                v1 = readnext(io)
+                push!(res, s1 => v1)
+            end
+            res
+        else
+            @show "$type unhandled, please add code"
+            read(io, len)
+        end
+    end
+end
+
+function replaceshortkeys(data)
+    key_short2long = "\xcaxtendedKe\xfds"
+    haskey(data, key_short2long) || return data
+    map = data[key_short2long]
+    Dict((haskey(map, k) ? map[k] : k) => v for (k,v) in data if k != key_short2long)
+end

src/util.jl

@@ -0,0 +1,11 @@
+
+function prepplot(data)
+    k = findfirst(x->isa(x, Matrix), data)
+    x = range(0, stop = size(data[k], 1))
+    y = range(0, stop = size(data[k], 2))
+    x = x * data["Pixel_size"] * 1000 # µm
+    y = y * data["Pixel_size"] * data["Aspect"] * 1000 # µm
+    colormap = [:NavyBlue, :royalblue3, :LightGreen, :Red]
+    nan_color = :black
+    return (; x, y, colormap, nan_color)
+end