Merge pull request #272 from JuliaRobotics/twig/biadjacency

Interface tests pass except for a few compares and renamed to BiadjacencyMatrix

Author: GearsAD

src/BigData/BigData.jl

@@ -10,7 +10,7 @@ include("services/FileDataStore.jl")
 
 export AbstractDataStore
 
-export GeneralBigDataEntry, MongodbBigDataEntry, FileBigDataEntry
+export AbstractBigDataEntry, GeneralBigDataEntry, MongodbBigDataEntry, FileBigDataEntry
 export InMemoryDataStore, FileDataStore
 
 export getBigData, addBigData!, updateBigData!, deleteBigData!, listStoreEntries

src/CloudGraphsDFG/services/CloudGraphsDFG.jl

@@ -36,10 +36,10 @@ end
 # Accessors
 getLabelDict(dfg::CloudGraphsDFG) = dfg.labelDict
 getDescription(dfg::CloudGraphsDFG) = dfg.description
-setDescription(dfg::CloudGraphsDFG, description::String) = dfg.description = description
+setDescription!(dfg::CloudGraphsDFG, description::String) = dfg.description = description
 getAddHistory(dfg::CloudGraphsDFG) = dfg.addHistory
 getSolverParams(dfg::CloudGraphsDFG) = dfg.solverParams
-function setSolverParams(dfg::CloudGraphsDFG, solverParams::T)::T where T <: AbstractParams
+function setSolverParams!(dfg::CloudGraphsDFG, solverParams::T)::T where T <: AbstractParams
     return dfg.solverParams = solverParams
 end
 
@@ -163,7 +163,7 @@ function getFactor(dfg::CloudGraphsDFG, factorId::Int64)::DFGFactor
     factor = dfg.rebuildFactorMetadata!(dfg, factor)
     # GUARANTEED never to bite us in the future...
     # ... TODO: refactor if changed: https://github.com/JuliaRobotics/IncrementalInference.jl/issues/350
-    solverData(factor).fncargvID = factor._variableOrderSymbols
+    getSolverData(factor).fncargvID = factor._variableOrderSymbols
 
     # Add to cache
     push!(dfg.factorCache, factor.label=>factor)

src/Common.jl

@@ -114,7 +114,6 @@ Related
 ls, lsf
 """
 sortDFG(vars::Vector{Symbol})::Vector{Symbol} = sortVarNested(vars)
-
 """
     $SIGNATURES
 
@@ -137,7 +136,7 @@ function getfnctype(data::GenericFunctionNodeData)
   return data.fnc.usrfnc!
 end
 function getfnctype(fact::DFGFactor; solveKey::Symbol=:default)
-  data = solverData(fact) # TODO , solveKey=solveKey)
+  data = getSolverData(fact) # TODO , solveKey=solveKey)
   return getfnctype(data)
 end
 function getfnctype(dfg::T, lbl::Symbol; solveKey::Symbol=:default) where T <: AbstractDFG
@@ -153,7 +152,7 @@ Notes
 - Replaces older `getfnctype`.
 """
 getFactorType(data::GenericFunctionNodeData) = data.fnc.usrfnc!
-getFactorType(fct::DFGFactor) = getFactorType(solverData(fct))
+getFactorType(fct::DFGFactor) = getFactorType(getSolverData(fct))
 function getFactorType(dfg::G, lbl::Symbol) where G <: AbstractDFG
   getFactorType(getFactor(dfg, lbl))
 end
@@ -464,3 +463,29 @@ function hasTagsNeighbors(dfg::InMemoryDFGTypes,
   alltags = union( (ls(dfg, sym) .|> x->getTags(getNeiFnc(dfg,x)))... )
   length(filter(x->x in alltags, tags)) >= (matchAll ? length(tags) : 1)
 end
+
+
+
+#Natural Sorting
+# Adapted from https://rosettacode.org/wiki/Natural_sorting
+# split at digit to not digit change
+splitbynum(x::AbstractString) = split(x, r"(?<=\D)(?=\d)|(?<=\d)(?=\D)")
+#parse to Int
+numstringtonum(arr::Vector{<:AbstractString}) = [(n = tryparse(Int, e)) != nothing ? n : e for e in arr]
+#natural less than
+function natural_lt(x::T, y::T) where T <: AbstractString
+    xarr = numstringtonum(splitbynum(x))
+    yarr = numstringtonum(splitbynum(y))
+    for i in 1:min(length(xarr), length(yarr))
+        if typeof(xarr[i]) != typeof(yarr[i])
+            return isa(xarr[i], Int)
+        elseif xarr[i] == yarr[i]
+            continue
+        else
+            return xarr[i] < yarr[i]
+        end
+    end
+    return length(xarr) < length(yarr)
+end
+
+natural_lt(x::Symbol, y::Symbol) = natural_lt(string(x),string(y))

src/CommonAccessors.jl

@@ -58,4 +58,6 @@ $SIGNATURES
 
 Return the internal ID for a variable.
 """
-getInternalId(v::DataLevel1) = v._dfgNodeParams._internalId
+getInternalId(v::DataLevel2) = v._dfgNodeParams._internalId
+
+getInternalId(v::Union{DFGVariableSummary, DFGFactorSummary}) = v._internalId

src/Deprecated.jl

@@ -131,7 +131,7 @@ end
 Retrieve data structure stored in a variable.
 """
 function getData(v::DFGVariable; solveKey::Symbol=:default)::VariableNodeData
-  @warn "getData is deprecated, please use solverData()"
+  @warn "getData is deprecated, please use getSolverData()"
   return v.solverDataDict[solveKey]
 end
 
@@ -153,6 +153,12 @@ end
 Retrieve solver data structure stored in a factor.
 """
 function data(f::DFGFactor)::GenericFunctionNodeData
-  @warn "data() is deprecated, please use solverData()"
+  @warn "data() is deprecated, please use getSolverData()"
   return f.data
 end
+
+
+getLabelDict(dfg::AbstractDFG) = error("getLabelDict is deprecated, consider using listing functions")
+
+setSolverParams(args...) = error("setSolverParams is deprecated, use setSolverParams!")
+setDescription(args...) = error("setSolverParams is deprecated, use setDescription!")

src/DistributedFactorGraphs.jl

@@ -91,7 +91,7 @@ export MeanMaxPPE
 # AbstractDFG Interface
 #--------
 export setSerializationModule!, getSerializationModule
-export getLabelDict, getDescription, setDescription, getAddHistory, getSolverParams, setSolverParams
+export getDescription, setDescription!, getAddHistory, getSolverParams, setSolverParams!
 export getUserData, setUserData!, getRobotData, setRobotData!, getSessionData, setSessionData!
 
 # Not sure these are going to work everywhere, TODO implement in cloud?
@@ -103,10 +103,12 @@ export exists, addVariable!, addFactor!, getVariable, getFactor, updateVariable!
 export getVariables, getVariableIds, getFactors, getFactorIds, ls, lsf
 export isFullyConnected, hasOrphans
 export getNeighbors, _getDuplicatedEmptyDFG, getSubgraphAroundNode, getSubgraph
-export getIncidenceMatrix, getIncidenceMatrixSparse
+export getBiadjacencyMatrix
+
 export toDot, toDotFile
 # Deprecated
 export getAdjacencyMatrix, getAdjacencyMatrixSparse
+export getLabelDict, setSolverParams, setDescription
 #--------
 
 # File import and export

src/FileDFG/services/FileDFG.jl

@@ -138,7 +138,7 @@ function loadDFG(dst::String, iifModule, dfgLoadInto::G; loaddir=joinpath("/","t
     # PATCH - To update the fncargvID for factors, it's being cleared somewhere in rebuildFactorMetadata.
     # TEMPORARY
     # TODO: Remove in future
-    map(f->solverData(f).fncargvID = f._variableOrderSymbols, getFactors(dfgLoadInto))
+    map(f->getSolverData(f).fncargvID = f._variableOrderSymbols, getFactors(dfgLoadInto))
 
     return dfgLoadInto
 end

src/GraphsDFG/services/GraphsDFG.jl

@@ -16,14 +16,14 @@ end
 vertex_index(v::GraphsNode) = v.index
 
 # Accessors
-getLabelDict(dfg::GraphsDFG) = dfg.labelDict
-getDescription(dfg::GraphsDFG) = dfg.description
-setDescription(dfg::GraphsDFG, description::String) = dfg.description = description
-getAddHistory(dfg::GraphsDFG) = dfg.addHistory
-getSolverParams(dfg::GraphsDFG) = dfg.solverParams
-function setSolverParams(dfg::GraphsDFG, solverParams::T) where T <: AbstractParams
-    dfg.solverParams = solverParams
-end
+# getLabelDict(dfg::GraphsDFG) = dfg.labelDict
+# getDescription(dfg::GraphsDFG) = dfg.description
+# setDescription(dfg::GraphsDFG, description::String) = dfg.description = description
+# getAddHistory(dfg::GraphsDFG) = dfg.addHistory
+# getSolverParams(dfg::GraphsDFG) = dfg.solverParams
+# function setSolverParams(dfg::GraphsDFG, solverParams::T) where T <: AbstractParams
+#     dfg.solverParams = solverParams
+# end
 
 """
     $(SIGNATURES)

src/LightDFG/LightDFG.jl

@@ -6,10 +6,10 @@ using DocStringExtensions
 import ...DistributedFactorGraphs: AbstractDFG, DFGNode, AbstractDFGVariable, AbstractDFGFactor, AbstractDFGSummary, AbstractParams, NoSolverParams, DFGVariable, DFGFactor
 
 # import DFG functions to extend
-import ...DistributedFactorGraphs:  setSolverParams,
+import ...DistributedFactorGraphs:  setSolverParams!,
                                     getFactor,
-                                    setDescription,
-                                    getLabelDict,
+                                    setDescription!,
+                                    # getLabelDict,
                                     getUserData,
                                     setUserData!,
                                     getRobotData,
@@ -40,8 +40,7 @@ import ...DistributedFactorGraphs:  setSolverParams,
                                     getNeighbors,
                                     getSubgraphAroundNode,
                                     getSubgraph,
-                                    getIncidenceMatrix,
-                                    getIncidenceMatrixSparse,
+                                    getBiadjacencyMatrix,
                                     _getDuplicatedEmptyDFG,
                                     toDot,
                                     toDotFile

src/LightDFG/entities/LightDFG.jl

@@ -56,6 +56,18 @@ LightDFG{T}(g::FactorGraph{Int,DFGVariable,DFGFactor}=FactorGraph{Int,DFGVariabl
 LightDFG(g::FactorGraph{Int,DFGVariable,DFGFactor}=FactorGraph{Int,DFGVariable,DFGFactor}(); params::T=NoSolverParams(), kwargs...)  where T =
         LightDFG{T,DFGVariable,DFGFactor}(g; params=params, kwargs...)
 
+
+LigthDFG(description::String,
+         userId::String,
+         robotId::String,
+         sessionId::String,
+         userData::Dict{Symbol, String},
+         robotData::Dict{Symbol, String},
+         sessionData::Dict{Symbol, String},
+         solverParams::AbstractParams) =
+         LigthDFG(FactorGraph{Int,DFGVariable,DFGFactor}(), description, userId, robotId, sessionId, userData, robotData, sessionData, Symbol[], solverParams)
+
+
 # Fully depcrecate nodeCounter and labelDict
 # Base.propertynames(x::LightDFG, private::Bool=false) =
 #     (:g, :description, :userId, :robotId, :sessionId, :nodeCounter, :labelDict, :addHistory, :solverParams)