reduced printout and bugfix with naming viewers

RainerHeintzmann · May 7, 2024 · 96491f3 · 96491f3 · RainerHeintzmann · May 7, 2024
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Showing 5 changed files with 47 additions and 39 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "View5D"
 uuid = "90d841e0-6953-4e90-9f3a-43681da8e949"
 authors = ["rheintzmann <[email protected]>"]
-version = "0.4.5"
+version = "0.5"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
@@ -17,12 +17,12 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 [compat]
 AxisArrays = "0.4.3,0.4.6"
 Colors = "0.12.7, 0.12.8"
-ImageCore = "0.8.21, 0.9"
-JavaCall = "0.7.7, 0.7.8"
+ImageCore = "0.8.21, 0.9, 0.10"
+JavaCall = "0.7.7, 0.7.8, 0.8"
 StaticArrays = "1"
-Unitful = "1.7.0 - 1.12"
-julia = "1, 1.6"
-NDTools = "0.4, 0.5"
+Unitful = "1"
+julia = "1, 1.6, 1.7, 1.8, 1.9, 1.10"
+NDTools = "0.4, 0.5, 0.6"
 
 [extras]
 JavaCall = "494afd89-becb-516b-aafa-70d2670c0337"

diff --git a/src/rois.jl b/src/rois.jl
@@ -57,19 +57,24 @@ The user interaction is saved in a file `coord_filename` and reloaded automatica
 
 #arguments
 + `data` : data to extract the regions of interest from
++ `positions`: if supplied, the positions are used instead of selecting them interactively
++ `viewer`: a pre-existing viewer to use for the user interaction
 + `overwrite`: boolean flag indicating weather a pre-existing file should be loaded or overwritten.
 + `coord_filename`: filname where to save the user-interaction to
 + `roi_size` : size of the region of interest to extract
 + `do_save`:   boolean defining whether to serialize the user interaction to disk
 + `confirm_selected`: if true, a prompt waits for user interaction finished.
++ `verbose`: if true, the number of selected ROIs is printed
 
 #returns
 a tuple of the extracted ROIs and the selected positions
 The latter can be resupplied via the `positions` argument
 """
-function get_rois(data; positions=nothing, viewer=nothing, overwrite=false, confirm_selected=true, do_save=true, coord_filename="selected_coordinates.coords", roi_size=(16,16))
+function get_rois(data; positions=nothing, viewer=nothing, overwrite=false, confirm_selected=true, do_save=true, coord_filename="selected_coordinates.coords", roi_size=(16,16), verbose=false)
     bp = get_positions(data; positions=positions, viewer=viewer, overwrite=overwrite, confirm_selected=confirm_selected, do_save=do_save, coord_filename=coord_filename)
-    println("$(length(bp)) ROIs selected.")
+    if verbose
+        println("$(length(bp)) ROIs selected.")
+    end
     rois = []
     for n in 1:length(bp)
         pos = Tuple(round.(Int,bp[n]))

diff --git a/src/shorthands.jl b/src/shorthands.jl
@@ -114,7 +114,9 @@ created data 3
 function vt(data, viewer=nothing; gamma=nothing, element=0, time=0, show_phase=false, keep_zero=false, name=nothing, title=nothing, times_linked=false)
 viewer = get_viewer(viewer, ignore_nothing=true);
 viewer = vv(data, viewer; gamma=gamma, mode=DisplAddTime, element=element, time=time, show_phase=show_phase, keep_zero=keep_zero, name=name, title=title)
-set_times_linked(times_linked, viewer)
+if !isnothing(viewer)
+    set_times_linked(times_linked, viewer)
+end
 end
 
 """
@@ -170,27 +172,26 @@ alt_name=nothing
 viewer=nothing  # by default the active viewer is used
 value = ""
 for ex in exs
-    varname = sprint(Base.show_unquoted, ex)
+    varname = sprint(Base.show_unquoted, ex);
     if isnothing(alt_name)            
-        name = :(println($(esc(varname))*" = ",
-            begin local value=display_array($(esc(ex)),$(esc(varname)),$(mystarter),$(esc(viewer))) end))
+        name = :(begin local value=display_array($(esc(ex)),$(esc(varname)),$(mystarter),$(esc(viewer))) end)
     else
-        name = :(println($(esc(varname))*" = ",
-            begin local value=display_array($(esc(ex)),$(esc(alt_name)),$(mystarter),$(esc(viewer))) end))
+        name = :(begin local value=display_array($(esc(ex)),$(esc(alt_name)),$(mystarter),$(esc(viewer))) end)
     end
-
     push!(blk.args, name)
+
     if typeof(ex)==String
-        alt_name = ex
+        alt_name = ex  # define this alt_name for the next round. It will generate the expression "alt_name = nothing" which has no effect.
     else 
         alt_name = nothing
+        if typeof(ex) == Symbol # && typeof(eval(ex)) == JavaCall.JavaObject{Symbol("view5d.View5D")}
+            viewer=ex;  # if a viewer is provided as argument, it will be used for display in the next (and future) rounds.
+        end
     end
-    if typeof(ex) == Symbol # && typeof(eval(ex)) == JavaCall.JavaObject{Symbol("view5d.View5D")}
-        viewer=ex
-    end
+
 end
-isempty(exs) || push!(blk.args, :value) # the second part ensures that the result of the display is the viewer
-return blk # blk
+isempty(exs) || push!(blk.args, :value); # the second part ensures that the result of the display is the viewer
+return blk; # blk
 end
 
 """
@@ -212,7 +213,7 @@ julia> using Unitful, AxisArrays; @vv AxisArray(rand(10,11,12,3,4),(:x,:y,:z,:li
 ```
 """
 macro vv(exs...)
-do_start(exs; mystarter=vv)
+    do_start(exs; mystarter=vv);
 end
 
 """
@@ -235,15 +236,15 @@ rand(5, 4, 7, 1, 2) = in_view5d
 ```
 """
 macro ve(exs...)
-do_start(exs; mystarter=ve)
+    do_start(exs; mystarter=ve)
 end
 
 """
 @vp expressions
 a conveniance macro in its usage similar to `@show`, displaying also phase information using view5d. See `@vv` and `vp` for details. 
 """
 macro vp(exs...)
-do_start(exs; mystarter=vp)
+    do_start(exs; mystarter=vp)
 end
 
 """
@@ -255,7 +256,7 @@ Note that variables of String type or expressions in strings do currently not wo
 ```
 """
 macro vt(exs...)
-do_start(exs; mystarter=vt)
+    do_start(exs; mystarter=vt)
 end
 
 """
@@ -267,19 +268,19 @@ Note that variables of String type or expressions in strings do currently not wo
 ```
 """
 macro vr(exs...)
-do_start(exs; mystarter=vr)
+    do_start(exs; mystarter=vr)
 end
 
 macro vep(exs...)
-do_start(exs; mystarter=vep)
+    do_start(exs; mystarter=vep)
 end
 
 macro vtp(exs...)
-do_start(exs; mystarter=vtp)
+    do_start(exs; mystarter=vtp)
 end
 
 macro vrp(exs...)
-do_start(exs; mystarter=vrp)
+    do_start(exs; mystarter=vrp)
 end
 
 #=  Missing implementations from Java:

diff --git a/src/viewer_core.jl b/src/viewer_core.jl
@@ -930,12 +930,12 @@ function check_alive(viewer)
             if num_elem >= 0
                 return viewer
             else
-                @warn "View5D: viewer not existing."
+                # @warn "View5D: viewer not existing."
                 remove_viewer(viewer)
                 return nothing
             end
         catch
-            @warn "View5D: viewer not existing."
+            # @warn "View5D: viewer not existing."
             remove_viewer(viewer)
             return nothing
         end
@@ -1113,8 +1113,9 @@ Arguments:
 + viewer: viewer to apply normalization to
 + element: element to apply it to
 + min_ratio: the minimum contrast ratio (towards zero) to require to do apply min-max rather that zero to max display normalization
++ verbose: if true, the normalization range is printed to the console
 """
-function optional_normalize_display(data, viewer=nothing; element=0, min_ratio=1e6)
+function optional_normalize_display(data, viewer=nothing; element=0, min_ratio=1e6, verbose=false)
     if !(eltype(data) <: Real)
         data = abs.(data);
     end
@@ -1123,7 +1124,9 @@ function optional_normalize_display(data, viewer=nothing; element=0, min_ratio=1
     if ((mymax - mymin)*min_ratio < mymax)
         mymin = 0;
     end
-    println("display normalized to $(mymin) to $(mymax).")
+    if verbose
+        println("display normalized to $(mymin) to $(mymax).")
+    end
     set_min_max_thresh(mymin, mymax, viewer; element=element)
     update_panels(viewer)
 end

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -9,17 +9,16 @@ data3 = rand(5,5,3,4,2); # more elements
 @testset "start viewers" begin
     v = @vv data1; # start the viewer
     @ve data2; # append along element
-    @vt data3; # append along time
-    @vt data3; # append along time
+    @vt "Hi there" data3 "ignor this" data3; # append along time
     @vr data3; # replace first
     w = @vv data2;
-    @vr v data3; # replace first
+    @vr "Hello" v data3; # replace first
     @test 6 == get_num_times();
     @test 4 == get_num_elements();
     sleep(0.1); hide_viewer() ;
 end
 
-@testset "interaction with markers and roi extraction" begin
+@testset "markers, rois" begin
     v = @vv data1; # start the viewer
     markers = empty_marker_list(2,2)
     markers[1][3]=1.0 
@@ -50,15 +49,15 @@ data1 = rand(5,5,3,1,1) .+ 1im.*rand(5,5,3,1,1);
 data2 = rand(5,5,3,1,1) .+ 1im.*rand(5,5,3,1,1);
 data3 = rand(5,5,3,2,1) .+ 1im.*rand(5,5,3,2,1); # more elements
 
-@testset "complex-valued display" begin
+@testset "complex-vals" begin
     @test nothing != @vp data1; # start a new viewer in phase mode
     @test nothing == set_gamma(1.0);
     @test nothing != @vep data2; # start a new viewer in phase mode
     @vp data3; # new phase viewer
     @vrp data3; # replace phase data
 end
 
-@testset "view5d datatypes" begin
+@testset "datatypes" begin
     @test nothing != view5d(rand(Float32,2,2,2,2,2)) # -> float
     @test nothing != view5d(rand(Float64,2,2,2,2,2)) # -> double
     @test nothing != view5d(rand(ComplexF32,2,2,2,2,2)) # > Complex