Computing mismatch with OffsetArrays

[Cody-G]

Continued from #81 (comment)

It seems that we're not handling OffsetArrays correctly. The full stacktrace I get when changing that particular line is:

QuadDIRECT tests with random images: Error During Test
  Got an exception of type ErrorException outside of a @test
  size not supported for arrays with axes (0:51, 0:51); see http://docs.julialang.org/en/latest/devdocs/offset-arrays/
  Stacktrace:
   [1] errmsg(::OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}}) at /home/cody/.julia/v0.6/OffsetArrays/src/OffsetArrays.jl:91
   [2] safe_get!(::Array{Float64,2}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::Tuple{UnitRange{Int64},UnitRange{Int64}}, ::Float64) at /home/cody/.julia/v0.6/BlockRegistration/src/RegisterMismatchCommon.jl:406
   [3] #mismatch!#46(::Symbol, ::Function, ::CenterIndexedArrays.CenterIndexedArray{RegisterCore.NumDenom{Float64},2,Array{RegisterCore.NumDenom{Float64},2}}, ::RegisterMismatch.CMStorage{Float64,2}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}) at /home/cody/.julia/v0.6/BlockRegistration/src/RegisterMismatch.jl:136
   [4] (::RegisterMismatch.#kw##mismatch!)(::Array{Any,1}, ::RegisterMismatch.#mismatch!, ::CenterIndexedArrays.CenterIndexedArray{RegisterCore.NumDenom{Float64},2,Array{RegisterCore.NumDenom{Float64},2}}, ::RegisterMismatch.CMStorage{Float64,2}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}) at ./<missing>:0
   [5] #mismatch#43(::Symbol, ::Function, ::Type{Float64}, ::SubArray{Float64,2,Array{Float64,2},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::Array{Int64,1}) at /home/cody/.julia/v0.6/BlockRegistration/src/RegisterMismatch.jl:121
   [6] (::RegisterMismatch.#kw##mismatch)(::Array{Any,1}, ::RegisterMismatch.#mismatch, ::Type{Float64}, ::SubArray{Float64,2,Array{Float64,2},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::Array{Int64,1}) at ./<missing>:0 (repeats 2 times)
   [7] #best_shift#1(::Symbol, ::CoordinateTransformations.IdentityTransformation, ::Function, ::SubArray{Float64,2,Array{Float64,2},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::Array{Int64,1}, ::Float64) at /home/cody/.julia/v0.6/BlockRegistration/src/qd_rigid.jl:19
   [8] (::RegisterOptimize.#kw##best_shift)(::Array{Any,1}, ::RegisterOptimize.#best_shift, ::SubArray{Float64,2,Array{Float64,2},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::SubArray{Float64,2,OffsetArrays.OffsetArray{Float64,2,Array{Float64,2}},Tuple{UnitRange{Int64},UnitRange{Int64}},false}, ::Array{Int64,1}, ::Float64) at ./<missing>:0
   [9] #rigid_mm_fast#23(::CoordinateTransformations.IdentityTransformation, ::Function, ::Array{Float64,1}, ::Array{Int64,1}, ::Array{Float64,2}, ::Array{Float64,2}, ::Float64, ::Array{Float64,2}) at /home/cody/.julia/v0.6/BlockRegistration/src/qd_rigid.jl:157
   [10] (::RegisterOptimize.#kw##rigid_mm_fast)(::Array{Any,1}, ::RegisterOptimize.#rigid_mm_fast, ::Array{Float64,1}, ::Array{Int64,1}, ::Array{Float64,2}, ::Array{Float64,2}, ::Float64, ::Array{Float64,2}) at ./<missing>:0
   [11] split!(::QuadDIRECT.Box{Float64,1}, ::RegisterOptimize.#f#29{CoordinateTransformations.IdentityTransformation,Float64,Array{Float64,2},Array{Float64,2},Array{Int64,1},Array{Float64,2}}, ::Array{Float64,1}, ::Int64, ::Array{Float64,1}, ::Float64, ::Float64, ::Float64, ::Float64) at /home/cody/.julia/v0.6/QuadDIRECT.jl/src/algorithm.jl:48
   [12] _init(::Function, ::Array{Float64,1}, ::Tuple{Array{Float64,1}}, ::Array{Float64,1}, ::Array{Float64,1}) at /home/cody/.julia/v0.6/QuadDIRECT.jl/src/algorithm.jl:31
   [13] init(::Function, ::Tuple{Array{Float64,1}}, ::Array{Float64,1}, ::Array{Float64,1}) at /home/cody/.julia/v0.6/QuadDIRECT.jl/src/algorithm.jl:20
   [14] #analyze#45(::Array{Any,1}, ::Function, ::Function, ::Tuple{Array{Float64,1}}, ::Array{Float64,1}, ::Array{Float64,1}) at /home/cody/.julia/v0.6/QuadDIRECT.jl/src/algorithm.jl:515
   [15] (::QuadDIRECT.#kw##analyze)(::Array{Any,1}, ::QuadDIRECT.#analyze, ::Function, ::Tuple{Array{Float64,1}}, ::Array{Float64,1}, ::Array{Float64,1}) at ./<missing>:0
   [16] #_analyze#8(::Array{Any,1}, ::Function, ::Function, ::Array{Float64,1}, ::Array{Float64,1}) at /home/cody/.julia/v0.6/BlockRegistration/src/qd_rigid.jl:72
   [17] (::RegisterOptimize.#kw##_analyze)(::Array{Any,1}, ::RegisterOptimize.#_analyze, ::Function, ::Array{Float64,1}, ::Array{Float64,1}) at ./<missing>:0
   [18] #qd_rigid_coarse#25(::CoordinateTransformations.IdentityTransformation, ::Float64, ::Array{Any,1}, ::Function, ::Array{Float64,2}, ::Array{Float64,2}, ::Array{Int64,1}, ::Array{Float64,1}, ::Array{Float64,1}, ::Array{Float64,2}) at /home/cody/.julia/v0.6/BlockRegistration/src/qd_rigid.jl:190
   [19] (::RegisterOptimize.#kw##qd_rigid_coarse)(::Array{Any,1}, ::RegisterOptimize.#qd_rigid_coarse, ::Array{Float64,2}, ::Array{Float64,2}, ::Array{Int64,1}, ::Array{Float64,1}, ::Array{Float64,1}, ::Array{Float64,2}) at ./<missing>:0
   [20] #qd_rigid#37(::Float64, ::CoordinateTransformations.IdentityTransformation, ::Array{Any,1}, ::Function, ::Array{Float64,2}, ::Array{Float64,2}, ::Array{Int64,1}, ::Float64, ::Array{Float64,1}, ::Array{Float64,2}) at /home/cody/.julia/v0.6/BlockRegistration/src/qd_rigid.jl:240
   [21] (::RegisterOptimize.#kw##qd_rigid)(::Array{Any,1}, ::RegisterOptimize.#qd_rigid, ::Array{Float64,2}, ::Array{Float64,2}, ::Array{Int64,1}, ::Float64, ::Array{Float64,1}, ::Array{Float64,2}) at ./<missing>:0
   [22] macro expansion at /home/cody/.julia/v0.6/BlockRegistration/test/register_affine.jl:88 [inlined]
   [23] macro expansion at ./test.jl:860 [inlined]
   [24] anonymous at ./<missing>:?
   [25] include_from_node1(::String) at ./loading.jl:576
   [26] include(::String) at ./sysimg.jl:14
   [27] eval(::Module, ::Any) at ./boot.jl:235
   [28] eval_user_input(::Any, ::Base.REPL.REPLBackend) at ./REPL.jl:66
   [29] macro expansion at ./REPL.jl:97 [inlined]
   [30] (::Base.REPL.##1#2{Base.REPL.REPLBackend})() at ./event.jl:73

...but a minimal case to trigger the error is:

using BlockRegistration, RegisterMismatch, OffsetArrays
a = OffsetArray(ones(10,10), (-1:8, -1:8))
b = copy(a)
mismatch(a,b,(2,2))

The issue comes from calling size on an OffsetArray here, and I think we'll also need a new fillfixed! method because it relies on size as well: https://github.com/HolyLab/BlockRegistration/blob/master/src/RegisterMismatch.jl#L259-L271

[timholy]

The right way to fix this is to redesign how we handle indices in RegisterMismatch & RegisterMismatchCuda. Consequently this may take a while so in the meantime keep working around this.

[timholy]

Wow, there is so much old code here. I am going to run FemtoCleaner locally to update a bunch of stuff. Should we get #81 in before I do that? Anyone else have anything brewing? @ChantalJuntao? I don't want to make your life difficult in terms of merging.

[Cody-G]

#81 is almost ready, but when I added tests with anisotropic sampling I discovered more bugs...working on those now. But I'm guessing it won't be too bad to rebase that on whatever you do, because I think all of the old code you are talking about is outside of the QuadDIRECT-based methods? So unless the interface changes a ton I don't think it will be an issue for me.

[timholy]

OK, I may go ahead then, at least locally. Since the whole QuadDIRECT section is newer it was written using more modern syntax. So hopefully it won't be a bad merge.

[Cody-G]

Fixed by HolyLab/RegisterMismatch.jl#6

[timholy]

Sweet. It's always a good sign when fixing one bug fixes others---a clear indication that we're adopting the right abstractions.