Skeletonization (#128)

* method for converting and reverting RPs

* first rudimentary and slow implementation of `skeletonize`

* function barriers and single arrays instead of matrix storing the lines

* debugged single array solution

* debug package compilation

* compute only triangles

* more tests; debugged code w.r.t. main diagonal

* horizontal-histo based on _linehistograms (is slower in fact)

* debugged line counting based on _linehistograms

* final implementation

* fixed tests for ubuntu

* again, try to fix the tests

* can not find the mistake..

* still not...

* make tests work!

* Removed unnecessary deps

* requested changes

* version increase and changelog

* clean `scan_lines!`

* simplify conversion btw standard RP and CRM

* comment horizontalhisto2 back

* fix `revert_close_return_map`

* `create_close_returns_map` without full matrix

* linehistograms based on vertical lines

* simplify verticalhisto

* optimization of verticalhisto

* optimization of "second version" of verticalhisto

* verticalhisto-method replaced and little polishing

* point to the right Data-Repo

* fix tests

* Apply suggestions from code review

Co-authored-by: Helios De Rosario <helios.derosario@gmail.com>
Co-authored-by: George Datseris <datseris.george@gmail.com>

Author: 3 people

.gitignore

@@ -3,3 +3,19 @@
 *.jl.*.cov
 *.jl.mem
 Manifest.toml
+
+RP_gross.csv
+
+RP_klein.csv
+
+test/timeseries/1.csv
+
+test/timeseries/2.csv
+
+test/timeseries/3.csv
+
+test/timeseries/test_time_series_lorenz_standard_N_10000_multivariate.csv
+
+test/timeseries/test_time_series_roessler_N_10000_multivariate.csv
+
+test/timeseries/4.csv

NEWS.md

@@ -1,5 +1,8 @@
 # RecurrenceAnalysis.jl News
 
+## v1.7.0
+- New method of skeletonizing a Recurrence Matrix `skeletonize`, in order to eliminate tangential motion.
+
 ## v1.5.2
 - New, faster formula for `rna[:averagepath]` allowing disconnected graphs.
 

Project.toml

@@ -1,7 +1,7 @@
 name = "RecurrenceAnalysis"
 uuid = "639c3291-70d9-5ea2-8c5b-839eba1ee399"
 repo = "https://github.com/JuliaDynamics/RecurrenceAnalysis.jl.git"
-version = "1.6.4"
+version = "1.7.0"
 
 [deps]
 DelayEmbeddings = "5732040d-69e3-5649-938a-b6b4f237613f"
@@ -25,6 +25,7 @@ julia = "1.5"
 
 [extras]
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -33,4 +34,4 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Statistics", "Test", "SparseArrays", "Random", "DynamicalSystemsBase", "LightGraphs","DataStructures"]
+test = ["Statistics", "Test", "SparseArrays", "Random", "DynamicalSystemsBase", "LightGraphs", "DataStructures", "Downloads"]

src/RecurrenceAnalysis.jl

@@ -45,14 +45,16 @@ export embed,
        nmprt,
        rqa,
        sorteddistances,
+       skeletonize,
        @windowed,
        rna,
        # deprecated:
-       transitivity  
+       transitivity
 
 include("matrices/distance_matrix.jl")
 include("matrices/matrices.jl")
 include("matrices/plot.jl")
+include("matrices/skeletonization.jl")
 include("rqa/histograms.jl")
 include("rqa/rqa.jl")
 include("rqa/radius.jl")

src/matrices/matrices.jl

@@ -218,7 +218,7 @@ JointRecurrenceMatrix(args...; kwargs...) = JointRecurrenceMatrix{WithinRange}(a
 
 """
     JointRecurrenceMatrix(R1, R2; kwargs...)
-    
+
 Create a joint recurrence matrix from given recurrence matrices `R1, R2`.
 """
 function JointRecurrenceMatrix(
@@ -336,7 +336,7 @@ Note that `parallel` may be either `Val(true)` or `Val(false)`.
 """
 function recurrence_matrix(xx::AbstractDataset, yy::AbstractDataset, metric::Metric, ε, ::Val{false})
     x = xx.data
-    y = yy.data    
+    y = yy.data
     @assert ε isa Real || length(ε) == length(y)
     rowvals = Vector{Int}()
     colvals = Vector{Int}()