Merge pull request #114 from timholy/teh/indices

Support display of non-1 arrays

src/ImageView.jl

@@ -47,7 +47,4 @@ export # types
     toplevel,
     write_to_png
 
-@deprecate view imshow
-@deprecate viewlabeled imshowlabeled
-
 end

src/annotations.jl

@@ -121,7 +121,7 @@ type AnnotationLines{R<:Union{Real, Tuple{Real, Real}}, T}
     coordinate_order::Vector{Int}
 
     function AnnotationLines(lines::T, z, t, linecolor, linewidth, coord_order_str)
-        ord = sortperm(coord_order_str.data)
+        ord = sortperm(Vector{UInt8}(coord_order_str))
         @assert coord_order_str[ord] == "xxyy"
         new(lines, z, t, linecolor, linewidth, ord)
     end
@@ -149,7 +149,7 @@ AnnotationLine(pt1::Tuple{Real,Real}, pt2::Tuple{Real,Real}; args...) =
     AnnotationLine((pt1, pt2); args...)
 
 function AnnotationLine(c1::Real, c2::Real, c3::Real, c4::Real; coord_order="xyxy", args...)
-    ord = sortperm(coord_order.data)
+    ord = sortperm(Vector{UInt8}(coord_order))
     @assert coord_order[ord] == "xxyy"
     (x1,x2,y1,y2) = [c1,c2,c3,c4][ord]
     AnnotationLine((Float64(x1), Float64(y1)),
@@ -171,7 +171,7 @@ end
 
 function AnnotationBox(c1::Real, c2::Real, c3::Real, c4::Real; z = NaN, t = NaN,
                        color=RGB(1,1,1), linewidth=1.0, coord_order="xyxy")
-    ord = sortperm(coord_order.data)
+    ord = sortperm(Vector{UInt8}(coord_order))
     @assert coord_order[ord] == "xxyy"
     (x1, x2, y1, y2) = [c1, c2, c3, c4][ord]
     (x1, x2) = minmax(x1, x2)

src/display.jl

@@ -42,7 +42,7 @@ type ImageCanvas
 
     function ImageCanvas(fmt::Int32, props::Dict)
         ps = get(props, :pixelspacing, nothing)
-        aspect_x_per_y = is(ps, nothing) ? nothing : ps[1]/ps[2]
+        aspect_x_per_y = ps == nothing ? nothing : ps[1]/ps[2]
         if haskey(props, :render!)
             render! = props[:render!]
         else
@@ -76,7 +76,7 @@ parent(imgc::ImageCanvas) = Tk.parent(imgc.c)
 toplevel(imgc::ImageCanvas) = Tk.toplevel(canvas(imgc))
 
 function setbb!(imgc::ImageCanvas, w, h)
-    if !is(imgc.aspect_x_per_y, nothing)
+    if imgc.aspect_x_per_y != nothing
         wc = width(imgc.c)
         hc = height(imgc.c)
         sx = min(wc/w, imgc.aspect_x_per_y*hc/h)
@@ -115,9 +115,11 @@ end
 import Base.getindex
 function getindex(img2::ImageSlice2d, x::Real, y::Real)
     P = img2.imorig
-    indexes = RangeIndex[1:size(P,d) for d = 1:ndims(P)]
-    indexes[img2.xdim] = clamp(convert(Int, x), 1, size(P,img2.xdim))
-    indexes[img2.ydim] = clamp(convert(Int, y), 1, size(P,img2.ydim))
+    indsP = indices(P)
+    indsx, indsy = indsP[img2.xdim], indsP[img2.ydim]
+    indexes = RangeIndex[map(UnitRange, indsP)...]
+    indexes[img2.xdim] = clamp(convert(Int, x), first(indsx), last(indsx))
+    indexes[img2.ydim] = clamp(convert(Int, y), first(indsy), last(indsy))
     if img2.zdim > 0
         indexes[img2.zdim] = img2.zindex
     end
@@ -154,13 +156,14 @@ function ImageSlice2d(img::AbstractArray, props::Dict)
     end
     props[:transpose] = xdim > ydim
     # Start at z=1, t=1
-    pindexes = parentindexes(img)
+    pindexes = map(UnitRange, _parentindexes(img))
     pdims = parentdims(img)
-    indexes = ntuple(i -> (i == zdim || i == tdim) ? 1 : (1:size(img, i)), ndims(img))
+    inds = map(UnitRange, indices(img))
+    indexes = ntuple(i -> (i == zdim || i == tdim) ? 1 : inds[i], ndims(img))
     imslice = Base.view(img, indexes...)
-    bb = BoundingBox(0, size(img, xdim), 0, size(img, ydim))
-    sz = size(imslice)
-    ImageSlice2d(img, imslice, pdims, pindexes, size(imslice), bb, 1, 1, xdim, ydim, zdim, tdim)
+    indsx, indsy = inds[xdim], inds[ydim]
+    bb = BoundingBox(first(indsx)-1, last(indsx), first(indsy)-1, last(indsy))
+    ImageSlice2d(img, imslice, pdims, pindexes, _size(imslice), bb, 1, 1, xdim, ydim, zdim, tdim)
 end
 
 parentdims(A::AbstractArray) = [1:ndims(A);]
@@ -179,7 +182,7 @@ function _reslice!(img2::ImageSlice2d)
     if img2.tdim > 0
         newindexes[img2.tdim] = newindexes[img2.tdim][img2.tindex]
     end
-    img2.imslice = Base.view(parent(img2.imorig), newindexes...)
+    img2.imslice = Base.view(_parent(img2.imorig), newindexes...)
     img2
 end
 
@@ -317,7 +320,7 @@ end
 # Display a labeled image: in the status bar that shows information about the pixel under the mouse pointer,
 # display the label value rather than the pixel value.
 function imshowlabeled(img::AbstractArray, label::AbstractArray; proplist...)
-    size(img) == size(label) || throw(DimensionMismatch("size $(size(label)) of label array disagrees with size $(size(img)) of the image"))
+    indices(img) == indices(label) || throw(DimensionMismatch("indices $(indices(label)) of label array disagree with indices $(indices(img)) of the image"))
     if isa(img, ImageMeta) && !isa(label, ImageMeta)
         label = shareproperties(img, label)
     end
@@ -380,7 +383,7 @@ function canvasgrid(ny, nx; w = 800, h = 600, pad=0, name="ImageView")
     grid(frame, 1, 1, sticky="nsew")
     grid_rowconfigure(win, 1, weight=1)
     grid_columnconfigure(win, 1, weight=1)
-    c = Array(Canvas, ny, nx)
+    c = Array{Canvas}(ny, nx)
     for j = 1:nx
         for i = 1:ny
             c1 = Canvas(frame, w/nx, h/ny)
@@ -474,7 +477,7 @@ function redraw(imgc::ImageCanvas)
     hbb = height(bb)
     rectangle(r, bb.xmin, bb.ymin, wbb, hbb)
     # In cases of transparency, paint the background color
-    if imgc.surfaceformat == Cairo.FORMAT_ARGB32 && !is(imgc.background, nothing)
+    if imgc.surfaceformat == Cairo.FORMAT_ARGB32 && imgc.background != nothing
         if isa(imgc.background, CairoPattern)
             set_source(r, imgc.background)
         else
@@ -511,7 +514,7 @@ function resize(imgc::ImageCanvas, img2::ImageSlice2d)
     setbb!(imgc, w, h)
     set_coordinates(imgc, img2.zoombb)
     r = getgc(imgc.c)
-    if !is(imgc.aspect_x_per_y, nothing)
+    if imgc.aspect_x_per_y != nothing
         fill(r, imgc.perimeter)
     end
     redraw(imgc)
@@ -577,8 +580,9 @@ function zoomwheel(imgc::ImageCanvas, img2::ImageSlice2d, delta, x, y)
         xmn, xmx = centeredclip(xu, width(img2)/2, xrange(img2))
         ymn, ymx = centeredclip(yu, height(img2)/2, yrange(img2))
     else
-        xmn, xmx = centeredclip(xu, 2*width(img2), (1,sizex(img2)), xrange(img2))
-        ymn, ymx = centeredclip(yu, 2*height(img2), (1,sizey(img2)), yrange(img2))
+        indsx, indsy = indicesx(img2), indicesy(img2)
+        xmn, xmx = centeredclip(xu, 2*width(img2), (first(indsx),last(indsx)), xrange(img2))
+        ymn, ymx = centeredclip(yu, 2*height(img2), (first(indsy),last(indsy)), yrange(img2))
     end
     zoombb(imgc, img2, BoundingBox(floor(xmn)-1, ceil(xmx), floor(ymn)-1, ceil(ymx)))
 end
@@ -663,10 +667,10 @@ end
 
 ### Utilities ###
 function allocate_surface!(imgc::ImageCanvas, w, h)
-    buf = Array(UInt32, w, h)
+    buf = Array{UInt32}(w, h)
     imgc.surface = CairoImageSurface(buf, imgc.surfaceformat, flipxy = false)
     if imgc.transpose
-        imgc.renderbuf = Array(UInt32, h, w)
+        imgc.renderbuf = Array{UInt32}(h, w)
     end
 end
 
@@ -698,7 +702,7 @@ end
 
 # Create a checkerboard pattern (for use with transparency)
 function checker(checkersize::Int; light = 0xffb0b0b0, dark = 0xff404040)
-    buf = Array(UInt32, 2checkersize, 2checkersize)
+    buf = Array{UInt32}(2checkersize, 2checkersize)
     fill!(buf, light)
     buf[1:checkersize,checkersize+1:2checkersize] = dark
     buf[checkersize+1:2checkersize,1:checkersize] = dark
@@ -713,7 +717,7 @@ end
 function rendersize(w::Integer, h::Integer, r)
     ww = w
     wh = h
-    if !is(r, nothing)
+    if r != nothing
         if r > 1
             ww = round(Integer, w*r)
         else
@@ -744,7 +748,7 @@ function resetfirst!(s::SubArray)
     pstride = 1
     for j = 1:length(s.indexes)
         newfirst += (first(s.indexes[j])-1)*pstride
-        pstride *= size(s.parent, j)
+        pstride *= length(indices(s.parent, j))
     end
     s.first_index = newfirst
     s
@@ -772,3 +776,12 @@ function write_to_png(imgc::ImageCanvas, filename)
     ctx = copy(imgc.c.backcc, imgc.canvasbb)
     Cairo.write_to_png(ctx.surface, filename)
 end
+
+# Non-1 index utilities
+_parentindexes(V::SubArray) = V.indexes
+_parentindexes(a::AbstractArray) = indices(a)
+_size(a::AbstractArray) = map(length, indices(a))
+indicesx(img2::ImageSlice2d) = img2.indexes[img2.xdim]
+indicesy(img2::ImageSlice2d) = img2.indexes[img2.ydim]
+_parent(a::AbstractArray) = parent(a)
+_parent(a::AxisArray) = a

src/navigation.jl

@@ -169,7 +169,7 @@ end
 # callback is an array of 5 entries, the 5th being the edit box
 function addbuttons(f, sz, bkg, pad, index, orientation, callback, rng)
     rotflag = orientation == "z"
-    ctrl = Array(Any, 7)
+    ctrl = Array{Any}(7)
     ctrl[1], ctrl[2], ctrl[3], ctrl[4] = arrowheads(sz, rotflag)
     mask = trues(sz)
     const color = ("black", "green", "green", "black")

test/REQUIRE

@@ -1,2 +1,3 @@
 TestImages
 ImageMagick
+OffsetArrays

test/simple.jl

@@ -1,5 +1,5 @@
 import ImageView
-using Images
+using Images, OffsetArrays
 
 # Grayscale
 ImageView.imshow(rand(Gray{N0f8}, 10, 10))
@@ -21,3 +21,7 @@ A[1,2,2] = NaN
 A[1,3,3] = -Inf
 A[1,4,4] = Inf
 ImageView.imshow(colorview(RGB, A))
+
+# Non-1 indices
+A = OffsetArray(rand(11, 10), -5:5, 0:9)
+ret = ImageView.imshow(A)

test/test4d.jl

@@ -6,11 +6,11 @@ sz = [201, 301, 31]
 center = [(s+1)>>1 for s in sz]  # ceil(Int, sz/2)
 C3 = Bool[(i-center[1])^2+(j-center[2])^2 <= k^2 for i = 1:sz[1], j = 1:sz[2], k = sz[3]:-1:1]
 cmap1 = round(UInt32, linspace(0,255,60))
-cmap = Array(UInt32, length(cmap1))
+cmap = Array{UInt32}(length(cmap1))
 for i = 1:length(cmap)
     cmap[i] = cmap1[i]<<16 + cmap1[end-i+1]<<8 + cmap1[i]
 end
-C4 = Array(UInt32, sz..., length(cmap))
+C4 = Array{UInt32}(sz..., length(cmap))
 for i = 1:length(cmap)
     C4[:,:,:,i] = C3*cmap[i]
 end