update for interface change in CoordinateTransformations

REQUIRE

@@ -1,24 +1,24 @@
 julia 0.6
-Images
-Interpolations
-AffineTransforms 0.2.1
-StaticArrays
+Images 0.14.0 0.15.0
+Interpolations 0.7.3 0.7.3+
+AffineTransforms 0.2.3 0.2.3+
+StaticArrays 0.7.2 0.7.2+
 NLsolve
-MathProgBase 0.4
-Ipopt
-IterativeSolvers 0.3
+MathProgBase 0.7.2 0.7.2+
+Ipopt 0.4.0 0.4.0+
+IterativeSolvers 0.6.0 0.6.0+
 CUDArt
-CUFFT
-HDF5
-JLD
-Reexport
+CUFFT 0.0.4 0.0.4+
+HDF5 0.9.3 0.9.3+
+JLD 0.8.3 0.8.3+
+Reexport 0.1.0 0.1.0+
 ForwardDiff 0.2.0
-ProgressMeter
-AxisArrays
-Ratios
-Compat 0.44
-ColorTypes
-OffsetArrays
+ProgressMeter 0.5.6 0.5.6+
+AxisArrays 0.2.1 0.2.1+
+Ratios 0.3.0 0.3.0+
+Compat 1.0.1 1.0.1+
+ColorTypes 0.6.7 0.6.7+
+OffsetArrays 0.6.0 0.6.0+
 Optim
 CoordinateTransformations
-Rotations
+Rotations 0.7.2 0.7.2+

deps/build.jl

@@ -22,6 +22,11 @@ else
     end
 end
 
+if VERSION < v"0.7.0"
+    Pkg.checkout("ImageAxes", "julia0.6")
+    Pkg.pin("ImageAxes")
+end
+
 basedir = splitdir(splitdir(@__FILE__)[1])[1]
 cd(joinpath(basedir, "src")) do
     run(`make`)

src/qd_rigid.jl

@@ -139,7 +139,7 @@ end
 
 ###########  Rigid Transformation (rotation + translation) Search ############
 
-update_SD(SD, tfm::Union{LinearMap, AffineMap}) = update_SD(SD, tfm.m)
+update_SD(SD, tfm::Union{LinearMap, AffineMap}) = update_SD(SD, tfm.linear)
 update_SD(SD, tfm::Transformation) = SD
 update_SD(SD::AbstractArray, m::StaticArray) = update_SD(SD, Array(m))
 update_SD(SD::AbstractArray, m::AbstractArray) = m\SD*m

test/register_affine.jl

@@ -53,7 +53,7 @@ end
 
     tfm, mm = qd_translate(fixed, moving, mxshift; maxevals=1000, thresh=thresh, rtol=0)
 
-    @test sum(abs.(tfm0.v - tfm.v)) < 1e-3
+    @test sum(abs.(tfm0.translation - tfm.translation)) < 1e-3
 
     #3D
     moving = rand(30,30,30)
@@ -67,7 +67,7 @@ end
 
     tfm, mm = qd_translate(fixed, moving, mxshift; maxevals=1000, thresh=thresh, rtol=0)
 
-    @test sum(abs.(tfm0.v - tfm.v)) < 0.1
+    @test sum(abs.(tfm0.translation - tfm.translation)) < 0.1
 
     ######Rotations + Translations
     #2D
@@ -85,7 +85,7 @@ end
 
     tfm, mm = qd_rigid(centered(fixed), moving, mxshift, mxrot, minwidth_rot, SD; thresh=thresh, maxevals=1000, rtol=0, fvalue=1e-8)
 
-    @test sum(abs.(tfm0.m - tfm.m)) < 1e-3
+    @test sum(abs.(tfm0.linear - tfm.linear)) < 1e-3
 
     #3D
     moving = centered(rand(30,30,30))
@@ -102,7 +102,7 @@ end
 
     tfm, mm = qd_rigid(centered(fixed), moving, mxshift, mxrot, minwidth_rot, SD; thresh=thresh, maxevals=1000, rtol=0)
 
-    @test sum(abs.(vcat(tfm0.m[:], tfm0.v) - vcat(RotXYZ(tfm.m)[:], tfm.v))) < 0.1
+    @test sum(abs.(vcat(tfm0.linear[:], tfm0.translation) - vcat(RotXYZ(tfm.linear)[:], tfm.translation))) < 0.1
 
 #NOTE: the 2D test below fails rarely and the 3D test fails often, apparently because full affine is too difficult with these images
     #####General Affine Transformations
@@ -122,7 +122,7 @@ end
 
     tfm, mm = qd_affine(centered(fixed), moving, mxshift, SD; thresh=thresh, maxevals=1500, rtol=0, fvalue=1e-6)
 
-    @test sum(abs.(vcat(tfm0.m[:], tfm0.v) - vcat(tfm.m[:], tfm.v))) < 0.1
+    @test sum(abs.(vcat(tfm0.linear[:], tfm0.translation) - vcat(tfm.linear[:], tfm.translation))) < 0.1
 
     #The tests below fail.  Probably two factors contributing to failure:
     # 1) Full affine 3D is a lot of parameters so it's just difficuilt (12 parameters)
@@ -146,7 +146,7 @@ end
     #tfm, mm = qd_affine(centered(fixed), centered(moving), mxshift, SD; thresh=thresh, rtol=0, fvalue=1e-4);
 
     #@test mm <= 1e-4
-    #@test sum(abs.(vcat(tfm0.m[:], tfm0.v) - vcat(tfm.m[:], tfm.v))) < 0.1
+    #@test sum(abs.(vcat(tfm0.linear[:], tfm0.translation) - vcat(tfm.linear[:], tfm.translation))) < 0.1
 
     #not random
     #moving = zeros(10,10,10);
@@ -165,12 +165,12 @@ end
     #thresh = 0.5 * sum(abs2.(fixed[.!(isnan.(fixed))]));
     #mxshift = [5;5;5];
     #SD = eye(ndims(fixed));
-    #@test RegisterOptimize.aff(vcat(tfm00.v[:], tfm00.m[:]), fixed, SD) == tfm0
+    #@test RegisterOptimize.aff(vcat(tfm00.translation[:], tfm00.linear[:]), fixed, SD) == tfm0
 
     #tfm, mm = qd_affine(centered(fixed), centered(moving), mxshift, SD; thresh=thresh, rtol=0, fvalue=1e-4);
 
     #@test mm <= 1e-4
-    #@test sum(abs.(vcat(tfm0.m[:], tfm0.v) - vcat(tfm.m[:], tfm.v))) < 0.1
+    #@test sum(abs.(vcat(tfm0.linear[:], tfm0.translation) - vcat(tfm.linear[:], tfm.translation))) < 0.1
 
 end #tests with random images
 
@@ -185,8 +185,8 @@ function fixedmov(img, tfm)
 end
 
 #helpers to convert Transformations to AffineMaps
-to_affine(tfm::Translation) = AffineMap(eye(length(tfm.v)), tfm.v)
-to_affine(tfm::LinearMap) = AffineMap(eye(length(tfm.v)), tfm.v)
+to_affine(tfm::Translation) = AffineMap(eye(length(tfm.translation)), tfm.translation)
+to_affine(tfm::LinearMap) = AffineMap(eye(length(tfm.translation)), tfm.translation)
 to_affine(tfm::AffineMap) = tfm
 
 #Helper to test that a found transform is (roughly) the inverse of the original transform
@@ -195,9 +195,9 @@ function tfmtest(tfm, tfminv)
     diagtol = 0.005
     offdiagtol = 0.005
     vtol = 0.1
-    @test all(x->(1-diagtol < x < 1+diagtol), diag(comp.m))
-    @test all(x->(-offdiagtol < x < offdiagtol), comp.m.-diagm(diag(comp.m)))
-    @test all(abs.(comp.v) .< vtol)
+    @test all(x->(1-diagtol < x < 1+diagtol), diag(comp.linear))
+    @test all(x->(-offdiagtol < x < offdiagtol), comp.linear.-diagm(diag(comp.linear)))
+    @test all(abs.(comp.translation) .< vtol)
 end
 
 # tests with standard images
@@ -235,7 +235,7 @@ end
     #make it harder with nonuniform scaling
     scale = @SMatrix [1.005 0; 0 0.995]
     SD = eye(2)
-    tfm = AffineMap(tfm.m*scale, tfm.v)
+    tfm = AffineMap(tfm.linear*scale, tfm.translation)
     mxshift = (100,100) #make sure this isn't too small
     fixed, moving = fixedmov(centered(img), tfm)
     tform, mm = qd_affine(centered(fixed), centered(moving), mxshift, SD; maxevals=1000, rtol=0, fvalue=0.0002)
@@ -245,7 +245,7 @@ end
     SD = diagm([0.5; 1.0])
     tfm = Translation(@SVector([14.3, 17.8]))∘LinearMap(SD\RotMatrix(0.01)*SD)
     scale = @SMatrix [1.005 0; 0 0.995]
-    tfm = AffineMap(tfm.m*scale, tfm.v)
+    tfm = AffineMap(tfm.linear*scale, tfm.translation)
     fixed, moving = fixedmov(centered(img), tfm)
     tform, mm = qd_affine(centered(fixed), centered(moving), mxshift, SD; maxevals=1000, rtol=0, fvalue=0.0002)
     tfmtest(tfm, tform)