Read med file exported from Gmsh

Now the package can also read med files exported from Gmsh. There is
some small differences how element sets are internally written to .h5
file and also looks that node / element id numbers are not explicitly
defined by Gmesh. Closes issue #16.

src/read_aster_mesh.jl

@@ -98,9 +98,19 @@ function get_element_sets(med::MEDFile, mesh_name::String)::Dict{Int64, Vector{S
     if !haskey(mesh, "ELEME")
         return element_sets
     end
-    for (k, v) in mesh["ELEME"]
-        elset_id = parse(Int, split(k, '_')[2])
-        element_sets[elset_id] = collect(to_ascii(d) for d in v["GRO"]["NOM"])
+    elset_keys = sort(collect(keys(mesh["ELEME"])))
+    for (i, k) in enumerate(elset_keys)
+        v = mesh["ELEME"][k]
+        if startswith(k, "FAM") # exported from Salome
+            elset_id = parse(Int, split(k, '_')[2])
+        else # exported from Gmsh
+            elset_id = -i
+        end
+        if !isempty(v)
+            element_sets[elset_id] = map(strip, collect(to_ascii(d) for d in v["GRO"]["NOM"]))
+        else
+            element_sets[elset_id] = [""]
+        end
     end
     return element_sets
 end
@@ -110,9 +120,9 @@ function get_nodes(med::MEDFile, nsets::Dict{Int, Vector{String}}, mesh_name::St
     @assert length(increments) == 1
     increment = first(increments)
     nodes = med.data["ENS_MAA"][mesh_name][increment]["NOE"]
-    node_ids = nodes["NUM"]
     nset_ids = nodes["FAM"]
-    nnodes = length(node_ids)
+    nnodes = length(nset_ids)
+    node_ids = get(nodes, "NUM", collect(1:nnodes))
     node_coords = nodes["COO"]
     dim = round(Int, length(node_coords)/nnodes)
     node_coords = reshape(node_coords, nnodes, dim)'
@@ -136,8 +146,8 @@ function get_connectivity(med::MEDFile, elsets::Dict{Int64, Vector{String}}, mes
     for eltype in keys(all_elements)
         elements = all_elements[eltype]
         elset_ids = elements["FAM"]
-        element_ids = elements["NUM"]
-        nelements = length(element_ids)
+        nelements = length(elset_ids)
+        element_ids = get(elements, "NUM", collect(1:nelements))
         element_connectivity = elements["NOD"]
         element_dim = round(Int, length(element_connectivity)/nelements)
         element_connectivity = reshape(element_connectivity, nelements, element_dim)'

test/runtests.jl

@@ -8,6 +8,7 @@ include(joinpath("..", "docs", "make.jl"))
 @testset "AsterReader.jl" begin
     include("test_read_aster_mesh.jl")
     include("test_read_aster_results.jl")
+    include("test_read_gmsh_med.jl")
 end
 
 include(joinpath("..", "docs", "deploy.jl"))

test/test_read_gmsh_med.jl

@@ -0,0 +1,12 @@
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/AsterReader.jl/blob/master/LICENSE
+
+using FEMBase, Test, AsterReader
+using AsterReader: aster_parse_nodes, aster_read_mesh, MEDFile, get_element_sets
+
+datadir = first(splitext(basename(@__FILE__)))
+
+@testset "test med file exported from gmsh, issue #16" begin
+    mesh_file = joinpath(datadir, "t1.med")
+    mesh = aster_read_mesh(mesh_file)
+end