Standalone Viewer Package

MPIViewers/Project.toml

@@ -0,0 +1,64 @@
+name = "MPIViewers"
+uuid = "8bda2715-69d8-46f6-8f4f-eacbc82b6e08"
+authors = ["Tobias Knopp <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+Cairo = "159f3aea-2a34-519c-b102-8c37f9878175"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+Gtk4 = "9db2cae5-386f-4011-9d63-a5602296539b"
+Gtk4Makie = "478199e7-b407-4926-87ea-7196203a28d8"
+Graphics = "a2bd30eb-e257-5431-a919-1863eab51364"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+ImageUtils = "8ad4436d-4835-5a14-8bce-3ae014d2950b"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
+MPIFiles = "371237a9-e6c1-5201-9adb-3d8cfa78fa9f"
+MPIReco = "e4246700-6248-511e-8146-a1d1f47669d2"
+MPISphericalHarmonics = "2527f7a4-0af4-4016-a944-036fbac19de9"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SphericalHarmonicExpansions = "504afa71-bae7-47b4-8ec9-3851161806ac"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
+[compat]
+Cairo = "1.0"
+Colors = "0.12"
+FFTW = "1.3"
+FileIO = "1.6"
+Graphics = "1.1"
+HDF5 = "0.15, 0.16"
+ImageUtils = "0.2"
+Images = "0.23, 0.24, 0.25"
+LoggingExtras = ">= 0.4.2"
+MPIFiles = "0.15, 0.16"
+MPIReco = "0.7"
+MPISphericalHarmonics = "0.0.10"
+Reexport = "1.0"
+CairoMakie = "0.12"
+julia = "1.10"
+Gtk4 = "0.7"
+Gtk4Makie = "0.2, 0.3"
+
+
+[extras]
+HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test", "HTTP"]

MPIViewers/src/3DViewer/3DViewer.jl

@@ -0,0 +1,51 @@
+abstract type Abstract3DViewerMode end
+modeName(m::Abstract3DViewerMode) = string(typeof(m))
+
+#=
+ At the moment it is not possible to update a GtkMakieWidget with new plots.
+ This means we either have to create a new GtkMakieWidget to update the plot
+ or we hook into the observables of the plots.
+
+ The second approach breaks for certain plots, for example for isovolumes (if the isovalue changed).
+=# 
+abstract type Abstract3DViewerModeRedrawType end
+struct ObservableRedraw <: Abstract3DViewerModeRedrawType end
+struct WidgetRedraw <: Abstract3DViewerModeRedrawType end
+redrawType(::Abstract3DViewerMode) = ObservableRedraw()
+
+include("3DViewerWidget.jl")
+include("VolumeMode.jl")
+include("SectionalMode.jl")
+include("IsoSurfaceMode.jl")
+
+function updateData!(m::Abstract3DViewerMode, arr)
+  # NOP
+end
+
+function showData!(gm::Gtk4Makie.GtkGLMakie, mode, data; kwargs...)
+  fig = Figure()
+  lscene = LScene(fig[1,1])
+  res = showData!(WidgetRedraw(), lscene, mode, data; kwargs...)
+  push!(gm, fig)
+  return res
+end
+
+export DataViewer3D, DataViewer3DWidget
+mutable struct DataViewer3D
+  w::Gtk4.GtkWindowLeaf
+  dvw::DataViewer3DWidget
+end
+
+function DataViewer3D(imFG; kwargs...)
+  dv = DataViewer3D(; kwargs...)
+  updateData!(dv.dvw,imFG)
+  return dv
+end
+
+function DataViewer3D(; kwargs...)
+  w = GtkWindow("Data Viewer 3D",800,600)
+  dw = DataViewer3DWidget(; kwargs...)
+  push!(w,dw)
+  show(w)
+  return DataViewer3D(w,dw)
+end

MPIViewers/src/3DViewer/3DViewerWidget.jl

@@ -0,0 +1,202 @@
+mutable struct DataViewer3DWidget{A, C} <: Gtk4.GtkGrid
+  handle::Ptr{Gtk4.GObject}
+  lscene::LScene
+  scene::Scene
+  axis::A
+  cam::C
+  gm::Gtk4Makie.GtkGLMakie
+  # Controls
+  controlGrid::GtkGrid
+  modeCb::GtkComboBoxText
+  modeOpt::GtkMenuButton
+  frameAdj::GtkAdjustment
+  channelAdj::GtkAdjustment
+  cmapCb::GtkComboBoxText
+  cmin::GtkScaleButton
+  cmax::GtkScaleButton
+  # Data
+  data::AbstractArray
+  # Mode
+  modes::Vector{<:Abstract3DViewerMode}
+end
+
+function DataViewer3DWidget(; modes = [VolumeMode, SectionalMode, IsoSurfaceMode])
+  grid = GtkGrid()
+  handle = grid.handle
+
+  # Setup the controls
+  controls = GtkGrid()
+  controls.column_spacing = 5
+  controls.row_spacing = 5
+
+  # Mode selection
+  # We have to initialize the modeBox and the options later
+  # Once the viewer exits we can initialize the modes with the viewer as parent
+  # And then fill out our options
+  modeBox = GtkComboBoxText()
+  controls[1, 1] = GtkLabel("Mode")
+  controls[1, 2] = modeBox
+  modeOptions = GtkMenuButton()
+  controls[2, 1] = GtkLabel("Options")
+  controls[2, 2] = modeOptions
+  controls[3, 1:2] = GtkSeparator(:v)
+
+  # Frame/Time Selection
+  frameAdj = GtkAdjustment(1, 1, 1, 1, 1, 1)
+  frameSlider = GtkSpinButton(frameAdj, 1, 0)
+  controls[4, 1] = GtkLabel("Frames")
+  controls[4, 2] = frameSlider
+  channelAdj = GtkAdjustment(1, 1, 1, 1, 1, 1)
+  channelSlider = GtkSpinButton(channelAdj, 1, 0)
+  controls[5, 1] = GtkLabel("Channels")
+  controls[5, 2] = channelSlider
+  controls[6, 1:2] = GtkSeparator(:v)
+
+  # Colormap Selection
+  colormapBox = GtkComboBoxText()
+  cmaps =  important_cmaps()
+  foreach(cm -> push!(colormapBox, cm), cmaps)
+  controls[7, 1] = GtkLabel("Colormap")
+  controls[7, 2] = colormapBox
+  colormapBox.active = 5 # viridis
+  cmin = GtkScaleButton(0, 99, 1, ["audio-volume-low"])
+  cmax = GtkScaleButton(1, 100, 1, ["audio-volume-high"])
+  cmin.value = 0
+  cmax.value = 100
+  controls[8, 1] = GtkLabel("Min")
+  controls[8, 2] = cmin
+  controls[9, 1] = GtkLabel("Max")
+  controls[9, 2] = cmax
+
+  grid[1, 1] = controls
+
+  # Setup the 3D viewing widget
+  fig = Figure()
+  lscene = LScene(fig[1,1])
+  scene = lscene.scene
+  cam = scene.camera_controls
+  axis = first(scene.plots) # Initial plot is an axis for LScene
+  gm = GtkMakieWidget()
+  push!(gm, fig)
+
+  grid[1, 2] = gm
+
+  viewer = DataViewer3DWidget(handle, lscene, scene, axis, cam, gm, controls, modeBox, modeOptions, frameAdj, channelAdj, colormapBox, cmin, cmax, [], Abstract3DViewerMode[])
+
+  # Initialize the modes
+  modes = map(mode -> mode(viewer), modes)
+  for mode in modes
+    push!(modeBox, modeName(mode))
+  end
+  modeBox.active = 0
+  modeOptions.popover = popover(first(modes))
+  viewer.modes = modes
+
+  initCallbacks(viewer)
+
+  return viewer
+end
+
+function initCallbacks(m::DataViewer3DWidget)
+  signal_connect(m.modeCb, "changed") do widget
+    foreach(mode -> mode.active = false, m.modes)
+    mode = m.modes[m.modeCb.active + 1]
+    mode.active = true
+    m.modeOpt.popover = popover(mode)
+    showData!(WidgetRedraw(), m)
+  end
+
+  signal_connect(m.frameAdj, "value_changed") do widget
+    showData!(m)
+  end
+  signal_connect(m.channelAdj, "value_changed") do widget
+    showData!(m)
+  end
+
+  signal_connect(m.cmapCb, "changed") do widget
+    showData!(m)
+  end
+
+  signal_connect(m.cmin, "value_changed") do widget, val
+    showData!(m)
+  end
+  signal_connect(m.cmax, "value_changed") do widget, val
+    showData!(m)
+  end
+end
+
+
+function updateData!(m::DataViewer3DWidget, file::Union{MDFFile, String})
+  imMeta = loadRecoData(file)
+  updateData!(m, imMeta)
+end
+
+# TODO handle 3 and 4 dim ImageMeta
+function updateData!(m::DataViewer3DWidget, imMeta::ImageMeta{T, 5}) where T
+  m.data = imMeta
+  m.frameAdj.upper = size(m.data, 5)
+  m.channelAdj.upper = size(m.data, 1)
+  map(mode -> updateData!(mode, m.data), m.modes)
+  showData!(WidgetRedraw(), m)
+end
+
+function updateData!(m::DataViewer3DWidget, array::AbstractArray{T, 5}) where T
+  m.data = array
+  m.frameAdj.upper = size(m.data, 5)
+  m.channelAdj.upper = size(m.data, 1)
+  m.cmin = 0
+  m.cmax = 100
+  map(mode -> updateData!(mode, m.data), m.modes)
+  showData!(WidgetRedraw(), m)
+end
+
+function prepareData(m::DataViewer3DWidget)
+  frame = round(Int64, m.frameAdj.value)
+  channel = round(Int64, m.channelAdj.value)
+  data = ustrip.(m.data[channel, :, :, :, frame])
+  return data
+end
+
+function prepareDrawKwargs(m::DataViewer3DWidget)
+  dict = Dict{Symbol, Any}()
+  max = maximum(m.data)
+  cmin = (m.cmin.value/100) * max
+  cmax = (m.cmax.value/100) * max
+  dict[:cparams] = ColoringParams(cmin, cmax, Gtk4.active_text(m.cmapCb))
+  return dict
+end
+
+showData!(m::DataViewer3DWidget) = showData!(redrawType(m.modes[m.modeCb.active + 1]), m)
+
+function showData!(::WidgetRedraw, m::DataViewer3DWidget)
+  # Prepare new GtkMakieWidget
+  delete!(m, m[1, 2])
+  m.gm = GtkMakieWidget()
+  m[1, 2] = m.gm
+
+  mode = m.modes[m.modeCb.active + 1]
+  data = prepareData(m)  
+  kwargs = prepareDrawKwargs(m)
+  lscene = showData!(m.gm, mode, data; kwargs...)
+
+  m.lscene = lscene
+  m.scene = lscene.scene
+  m.axis = first(m.scene.plots)
+
+  # Set the camera to the old position
+  eyeposition = m.cam.eyeposition[]
+  upvector = m.cam.upvector[]
+  lookat = m.cam.lookat[]
+  m.cam = m.scene.camera_controls
+  update_cam!(m.scene, eyeposition, lookat, upvector)
+  return nothing
+end
+
+function showData!(re::ObservableRedraw, m::DataViewer3DWidget)
+  # TODO move these into a function
+  mode = m.modes[m.modeCb.active + 1]
+  data = prepareData(m)
+  kwargs = prepareDrawKwargs(m)
+  showData!(re, m.lscene, mode, data; kwargs...)
+  return nothing
+end

MPIViewers/src/3DViewer/IsoSurfaceMode.jl

@@ -0,0 +1,77 @@
+export IsoSurfaceMode
+
+
+mutable struct IsoSurfaceMode{P} <: Abstract3DViewerMode
+  pop::GtkPopover
+  parent::P
+  active::Bool
+  isoAdj::GtkAdjustment
+  isoMin::GtkLabel
+  isoMax::GtkLabel
+  isorange::GtkEntry
+end
+function IsoSurfaceMode(parent::P) where P  
+  pop = GtkPopover()
+  grid = GtkGrid()
+  grid[1, 1] = GtkLabel("Iso Value:")
+  minLabel = GtkLabel("0.0")
+  maxLabel = GtkLabel("1.0")
+  adj = GtkAdjustment(0.5, 0.0, 1.0, 0.05, 0.05, 0.05)
+  scale = GtkScale(:h, adj)
+  scale.hexpand = true
+  grid[2, 1] = minLabel
+  grid[3, 1] = scale
+  grid[4, 1] = maxLabel
+
+  grid[1, 2] = GtkLabel("Iso Range:")
+  range = GtkEntry()
+  range.text = "0.05"
+  grid[2:4, 2] = range
+
+
+  pop.child = grid
+
+  mode = IsoSurfaceMode(pop, parent, false, adj, minLabel, maxLabel, range)
+
+  initCallbacks!(mode)
+
+  return mode
+end
+
+function initCallbacks!(mode::IsoSurfaceMode)
+  signal_connect(mode.isoAdj, "value_changed") do widget
+    if mode.active
+      showData!(WidgetRedraw(), mode.parent)
+    end
+  end
+  signal_connect(mode.isorange, "changed") do widget
+    if mode.active
+      showData!(WidgetRedraw(), mode.parent)
+    end
+  end
+end
+
+modeName(m::IsoSurfaceMode) = "Iso Surface"
+popover(m::IsoSurfaceMode) = m.pop
+redrawType(::IsoSurfaceMode) = WidgetRedraw()
+
+
+function updateData!(m::IsoSurfaceMode, data)
+  min, max = extrema(data)
+  m.isoAdj.upper = max
+  m.isoAdj.lower = min
+  m.isoAdj.step_increment = (max - min) / 100
+  m.isoMin.label = string(min)
+  m.isoMax.label = string(max)
+end
+
+function showData!(re, scene::LScene, mode::IsoSurfaceMode, data; kwargs...)
+  showData!(re, scene.scene, mode, data; kwargs...)
+  return scene
+end
+function showData!(::WidgetRedraw, scene::Scene, mode::IsoSurfaceMode, data; kwargs...)
+  isovalue = mode.isoAdj.value
+  isoRange = parse(Float64, mode.isorange.text)
+  volume!(scene, data; algorithm=:iso, isovalue=isovalue, isorange=isoRange)
+  return scene
+end