added support for colormaps. Bugsfix with @ve

Project.toml

@@ -16,13 +16,13 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 AxisArrays = "0.4.3,0.4.6"
-Colors = "0.12.7, 0.12.8"
+Colors = "0.12.7, 0.12.8, 0.13"
 ImageCore = "0.8.21, 0.9, 0.10"
 JavaCall = "0.7.7, 0.7.8, 0.8"
+NDTools = "0.4, 0.5, 0.6, 0.7"
 StaticArrays = "1"
 Unitful = "1"
 julia = "1, 1.6, 1.7, 1.8, 1.9, 1.10"
-NDTools = "0.4, 0.5, 0.6, 0.7"
 
 [extras]
 JavaCall = "494afd89-becb-516b-aafa-70d2670c0337"

src/shorthands.jl

@@ -13,16 +13,16 @@ This is just a shorthand for the function `view5d`. See `view5d` for arguments d
 See documentation of `view5d` for explanation of the parameters.
 """
 function vv(data, viewer=nothing; gamma=nothing, mode::DisplayMode =DisplNew, element=0, time=0, show_phase=false, keep_zero=false, name=nothing, title=nothing)
-view5d(data, viewer; gamma=gamma, mode=mode, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
+    view5d(data, viewer; gamma=gamma, mode=mode, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
 end
 
 function display_array(arr, name, disp=vv, viewer=nothing) # AbstractArray{N,T} where {N,T}
-v=disp(arr,viewer; name=name)
-if isnothing(v)
-    v= nothing # repr(begin local value = arr end) # returns a representation (a String)
-end
-return v
-# return "in_view5d"
+    v=disp(arr,viewer; name=name)
+    if isnothing(v)
+        v= nothing # repr(begin local value = arr end) # returns a representation (a String)
+    end
+    return v
+    # return "in_view5d"
 end
 
 # function display_array(ex, name, disp=vv, viewer=nothing)
@@ -60,13 +60,13 @@ See documentation of `view5d` for explanation of the parameters.
 `elements_linked`: determines wether all elements are linked together (no indidual scaling and same color)
 """
 function ve(data, viewer=nothing; gamma=nothing, element=0, time=0, show_phase=false, keep_zero=false, name=nothing, title=nothing, elements_linked=false)
-viewer = get_viewer(viewer, ignore_nothing=true)
-if isnothing(viewer)
-    vv(data, viewer; gamma=gamma, mode=DisplAddElement, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
-else
-    set_elements_linked(elements_linked, viewer)
-    vv(data, viewer; gamma=gamma, mode=DisplAddElement, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
-end
+    viewer = get_viewer(viewer, ignore_nothing=true)
+    if isnothing(viewer)
+        vv(data, viewer; gamma=gamma, mode=DisplAddElement, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
+    else
+        set_elements_linked(elements_linked, viewer)
+        vv(data, viewer; gamma=gamma, mode=DisplAddElement, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
+    end
 end
 
 """
@@ -166,7 +166,7 @@ end
 
 
 ## just a non-exported helper function to be used in the various macros below
-function do_start(exs;mystarter=vv)
+function do_start(exs; mystarter=vv)
 blk = Expr(:block)
 alt_name=nothing
 viewer=nothing  # by default the active viewer is used

src/viewer_core.jl

@@ -10,7 +10,8 @@ export set_display_size, set_active_viewer, set_properties, clear_active
 export get_viewer_history, close_all, hide_all, to_front_all
 export export_marker_lists, import_marker_lists, delete_all_marker_lists, export_markers_string, empty_marker_list
 export DisplayMode, DisplAddElement, DisplAddTime, DisplNew, DisplReplace
-export set_view5d_default_size
+export set_view5d_default_size, add_colormap
+export get_active_element, get_active_time, set_position, set_colormap_no
 # export list_methods, java_memory
 # export init_layout, invalidate 
 
@@ -170,6 +171,73 @@ function set_gamma(gamma=1.0, myviewer=nothing; element=0)
     update_panels(myviewer)
 end
 
+"""
+    add_colormap(mymap::Vector{RGB{T}}, myviewer=get_viewer()) where {T}
+adds a colormap to the viewer.
+
+# Arguments:
+* mymap: a colormap as a Vector of RGBs. See https://juliagraphics.github.io/Colors.jl/stable/colormapsandcolorscales/
+* myviewer: the viewer to apply this to. By default the active viewer is used.
+* N: the number of colors in the colormap. Default is 255.
+
+For unclear reasons the use-defined colormaps do not show up in the menu, but are accessible via "c".
+# Example:
+```jldoctest
+julia> v = @vv 2 .*(rand(10,10,10).-0.5)
+julia> add_colormap(diverging_palette(0, 200, 32))
+julia> set_min_max_thresh(-1.0, 1.0, v)
+```
+
+"""
+function add_colormap(mymap::Vector{RGB{T}}, myviewer=get_viewer()) where {T}
+    sz = length(mymap);
+    red = zeros(UInt8, sz)
+    green = zeros(UInt8, sz)
+    blue = zeros(UInt8, sz)
+    red .= (round(UInt8, mymap[p].r*255) for p in 1:sz)
+    green .= (round(UInt8, mymap[p].g*255) for p in 1:sz)
+    blue .= (round(UInt8, mymap[p].b*255) for p in 1:sz)
+    rb = reinterpret(Int8, red)
+    gb = reinterpret(Int8, green)
+    bb = reinterpret(Int8, blue)
+
+    jbyteArr = Vector{jbyte}
+    jcall(myviewer, "add_colormap", Nothing, (jint, jbyteArr, jbyteArr, jbyteArr), sz, rb, gb, bb);
+    update_panels(myviewer)
+end
+
+function set_colormap_no(no, elem= nothing, myviewer=get_viewer())
+    if isnothing(elem)
+        elem=get_active_element(myviewer)
+    end
+    jcall(myviewer, "set_colormap_no", Nothing, (jint, jint), no, elem);
+end
+
+"""
+    add_colormap(cmap_name="RdBu", myviewer=get_viewer(); N=255)
+adds a colormap ny name to the viewer.
+
+# Arguments:
+* cmap_name: a name that the function colormaps in the Colors package accepts. See https://juliagraphics.github.io/Colors.jl/stable/colormapsandcolorscales/ for possible names.
+* myviewer: the viewer to apply this to. By default the active viewer is used.
+* N: the number of colors in the colormap. Default is 255.
+
+For unclear reasons the use-defined colormaps do not show up in the menu, but are accessible via "c".
+# Example:
+```jldoctest
+julia> v = @vv 2 .*(rand(10,10,10).-0.5)
+julia> add_colormap("RdBu")
+```
+"""
+function add_colormap(cmap_name="RdBu", myviewer=get_viewer(); N=255)
+    mymap = colormap(cmap_name, N);
+    add_colormap(mymap, myviewer)
+    if cmap_name == "RdBu"
+        set_min_max_thresh(-1.0, 1.0, myviewer)
+        update_panels(myviewer)
+    end
+end
+
 """
     set_time(mytime=-1, myviewer=nothing)
 
@@ -325,6 +393,28 @@ function get_num_elements(myviewer=nothing)
     num_elem=jcall(myviewer, "getNumElements", jint, ());
 end
 
+"""
+    get_active_element(myviewer=get_viewer(myviewer))
+gets the currently active element number in the viewer
+
+# Arguments
+* `myviewer`: the viewer to apply this to. By default the active viewer is used.
+"""
+function get_active_element(myviewer=get_viewer(myviewer))
+    return jcall(myviewer, "get_active_element", jint, ());
+end
+
+"""
+    get_active_time(myviewer=get_viewer(myviewer))
+gets the currently active time number in the viewer
+
+# Arguments
+* `myviewer`: the viewer to apply this to. By default the active viewer is used.
+"""
+function get_active_time(myviewer=get_viewer(myviewer))
+    return jcall(myviewer, "get_active_time", jint, ());
+end
+
 """
     set_axis_scales_and_units(pixelsize=(1.0,1.0,1.0,1.0,1.0),
         value_name = "intensity",value_unit = "a.u.",
@@ -1069,6 +1159,7 @@ function start_viewer(viewer, myJArr, jtype="jfloat", mode::DisplayMode = DisplN
             throw(ArgumentError("Added elements, the number of times $nt in the viewer need to correspond to the time dimension of this data $sizeT."))
         end
         size3d = sizeX*sizeY*sizeZ
+        e_offset = get_num_elements(viewer)
         for e in 0:sizeE-1
             dummy=jcall(viewer, command, V, (jArr, jint, jint, jint, jint, jint),
                             myJArr[e*size3d+1:end],sizeX, sizeY, sizeZ, sizeE, sizeT); 
@@ -1079,7 +1170,7 @@ function start_viewer(viewer, myJArr, jtype="jfloat", mode::DisplayMode = DisplN
             process_keys("t",viewer)   
             if !isnothing(name)
                 # E = get_num_elements()-1
-                set_element_name(e, name, viewer)
+                set_element_name(e+e_offset, name, viewer)
             end
             myviewer = viewer
             if !isnothing(properties)

test/runtests.jl

@@ -89,3 +89,15 @@ end
     @test nothing == update_panels()
     @test nothing == close_all()
 end
+
+@testset "get functions" begin
+    v = view5d(rand(Float32,2,2,2,2,3))
+    @test 3 == get_num_times(v)
+    @test 2 == get_num_elements(v)
+
+end
+
+@testset "set functions" begin
+    v = view5d(rand(Float32,2,2,2,2,3))
+    set_colormap_no(13, v)
+end