From 5c7f92d392f1d832725aaadd6ffee82b494609bb Mon Sep 17 00:00:00 2001
From: Matthew Kelley <matthew.curtis.kelley@gmail.com>
Date: Sat, 7 Mar 2020 12:20:39 -0700
Subject: [PATCH 1/3] Fix DBA to work with Julia 1.x

---
 Project.toml     |  3 ++-
 src/dba.jl       | 16 +++++++++-------
 test/runtests.jl |  8 ++++++++
 3 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/Project.toml b/Project.toml
index 9c4c01e..7a514c6 100644
--- a/Project.toml
+++ b/Project.toml
@@ -4,6 +4,7 @@ uuid = "c3fb160f-4a10-5553-b683-e707b00e83ce"
 [deps]
 BinDeps = "9e28174c-4ba2-5203-b857-d8d62c4213ee"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
@@ -13,4 +14,4 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-julia = "≥ 0.7.0"
\ No newline at end of file
+julia = "≥ 0.7.0"
diff --git a/src/dba.jl b/src/dba.jl
index f748153..8e37066 100644
--- a/src/dba.jl
+++ b/src/dba.jl
@@ -1,3 +1,5 @@
+using LinearAlgebra
+
 """
     DBAResult(cost,converged,iterations,cost_trace)
 
@@ -18,14 +20,14 @@ and the current estimate of the average sequence.
 
 Example usage:
 
-    x = [1,2,2,3,3,4]
-    y = [1,3,4]
-    z = [1,2,2,4]
+    x = Sequence([1., 2., 2., 3., 3., 4.])
+    y = Sequence([1., 3., 4.])
+    z = Sequence([1., 2., 2., 4.])
     avg,result = dba([x,y,z])
 """
 function dba(
         sequences::AbstractVector{T},
-        method::DTWMethod,
+        method::DTWMethod = ClassicDTW(),
         dist::SemiMetric = SqEuclidean();
         init_center::T = rand(sequences),
         iterations::Int = 1000,
@@ -111,13 +113,13 @@ function dba_iteration!(
     total_cost = 0.0
 
     # store stats for barycenter averages
-    scale!(counts,0)
-    scale!(newavg,0)
+    rmul!(counts,0)
+    rmul!(newavg,0)
 
     # main ploop
     for seq in sequences
         # time warp signal versus average
-        # if one of the two is empty, use unconstrained window. If both are nonempty, but not the same lenght, distpath will throw error
+        # if one of the two is empty, use unconstrained window. If both are nonempty, but not the same length, distpath will throw error
         if isempty(i2min) && isempty(i2max)
           cost, i1, i2 = distpath(d, oldavg, seq)
         else
diff --git a/test/runtests.jl b/test/runtests.jl
index ead2b07..b80ede0 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -298,3 +298,11 @@ end
     @test px == qx
     @test py == qy
 end
+
+@testset "DBA" begin
+    x = Sequence([1., 2., 2., 3., 3., 4.])
+    y = Sequence([1., 3., 4.])
+    z = Sequence([1., 2., 2., 4.])
+    avg, _ = dba([x, y, z], init_center=z)
+    @test avg == [1.0, 1.75, 2.75, 4.0]
+end

From 78c36f8f9f04aab45f94edb36a5e5d284bef4d54 Mon Sep 17 00:00:00 2001
From: Matthew Kelley <matthew.curtis.kelley@gmail.com>
Date: Sun, 8 Mar 2020 15:31:00 -0600
Subject: [PATCH 2/3] Update dba to work with multi-dim Sequences

---
 src/dba.jl      |  3 ++-
 src/sequence.jl | 12 ++----------
 2 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/src/dba.jl b/src/dba.jl
index 8e37066..5cc954d 100644
--- a/src/dba.jl
+++ b/src/dba.jl
@@ -46,7 +46,8 @@ function dba(
     dbavg = deepcopy(init_center)
 
     # storage for each iteration
-    newavg = Sequence(zeros(length(dbavg)))
+#     newavg = Sequence(zeros(size(dbavg)))
+    newavg = Sequence(zeros(size(dbavg.val)))
     counts = zeros(Int, length(dbavg))
 
     # variables storing optimization progress
diff --git a/src/sequence.jl b/src/sequence.jl
index 1e95f42..5354b33 100644
--- a/src/sequence.jl
+++ b/src/sequence.jl
@@ -37,14 +37,6 @@ end
     :( x.val[@ntuple($N, (n-> n==$N ? i : Colon()))...] = val )
 end
 
-# convert a sequence back into an array
-# in case sequences have different lenght, throw error
-function seq_to_array(seq::AbstractVector{T}) where T <: Sequence
-  len_seq = length(seq[1])
-  arr = zeros(typeof(seq[1][1]),len_seq,length(seq))
-  for i=1:length(seq)
-    length(seq[i]) != len_seq ? error("Sequences do not have the same length, cannot construct array") : nothing
-    arr[:,i] = seq[i][:]
-  end
-  return arr
+function seq_to_array(seq::Sequence{N}) where N
+    return cat(seq..., dims=N)
 end

From 5b6b67f6936ea2dfbd12c32dc26703909879bff2 Mon Sep 17 00:00:00 2001
From: Matthew Kelley <matthew.curtis.kelley@gmail.com>
Date: Sun, 8 Mar 2020 15:43:40 -0600
Subject: [PATCH 3/3] Remove commented line

---
 src/dba.jl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/dba.jl b/src/dba.jl
index 5cc954d..89cb115 100644
--- a/src/dba.jl
+++ b/src/dba.jl
@@ -46,7 +46,6 @@ function dba(
     dbavg = deepcopy(init_center)
 
     # storage for each iteration
-#     newavg = Sequence(zeros(size(dbavg)))
     newavg = Sequence(zeros(size(dbavg.val)))
     counts = zeros(Int, length(dbavg))