Definition of the IO interface + HDF5/CGNS implementation

Project.toml

@@ -1,7 +1,7 @@
 name = "Bcube"
 uuid = "cf06320b-b7f3-4748-8003-81a6b6979792"
 authors = ["Ghislain Blanchard, Lokman Bennani and Maxime Bouyges"]
-version = "0.1.11"
+version = "0.1.12"
 
 [deps]
 FEMQuad = "be8e8821-3f6f-54c2-987c-d2773c3a52cb"
@@ -25,9 +25,19 @@ StaticArrays = "1.2"
 Symbolics = "5"
 WriteVTK = "1.12"
 julia = "1.6"
+JLD2 = "0.4.47"
+HDF5 = "0.17"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["Test"]
+
+[weakdeps]
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+
+[extensions]
+JLD2Ext = "JLD2"
+HDF5Ext = "HDF5"

ext/HDF5Ext/HDF5Ext.jl

@@ -0,0 +1,8 @@
+module HDF5Ext
+using Bcube
+using HDF5
+
+include("./common.jl")
+include("./read.jl")
+include("./write.jl")
+end

ext/HDF5Ext/common.jl

@@ -0,0 +1,84 @@
+const BCUBE_ENTITY_TO_CGNS_ENTITY = Dict(
+    Bcube.Node_t => 2,
+    Bcube.Bar2_t => 3,
+    Bcube.Bar3_t => 4,
+    Bcube.Tri3_t => 5,
+    Bcube.Tri6_t => 6,
+    Bcube.Tri9_t => 25,
+    Bcube.Tri10_t => 26,
+    Bcube.Quad4_t => 7,
+    Bcube.Quad8_t => 8,
+    Bcube.Quad9_t => 9,
+    Bcube.Quad16_t => 27,
+    Bcube.Tetra4_t => 10,
+    Bcube.Tetra10_t => 11,
+    Bcube.Pyra5_t => 12,
+    Bcube.Penta6_t => 14,
+    Bcube.Hexa8_t => 17,
+    Bcube.Hexa27_t => 27,
+)
+const CGNS_ENTITY_TO_BCUBE_ENTITY = Dict(v => k for (k, v) in BCUBE_ENTITY_TO_CGNS_ENTITY)
+
+function bcube_entity_to_cgns_entity(::T) where {T <: Bcube.AbstractEntityType}
+    BCUBE_ENTITY_TO_CGNS_ENTITY[T]
+end
+
+cgns_entity_to_bcube_entity(code::Integer) = CGNS_ENTITY_TO_BCUBE_ENTITY[code]()
+
+function get_child(parent; name = "", type = "")
+    child_name = findfirst(child -> child_match(child, name, type), parent)
+    return isnothing(child_name) ? nothing : parent[child_name]
+end
+
+function get_children(parent; name = "", type = "")
+    child_names = findall(child -> child_match(child, name, type), parent)
+    return map(child_name -> parent[child_name], child_names)
+end
+
+function child_match(child, name, type)
+    if get_name(child) == name
+        if length(name) > 0 && length(type) > 0
+            (get_cgns_type(child) == type) && (return true)
+        elseif length(name) > 0
+            return true
+        end
+    end
+
+    if get_cgns_type(child) == type
+        if length(name) > 0 && length(type) > 0
+            (get_name(child) == name) && (return true)
+        elseif length(type) > 0
+            return true
+        end
+    end
+
+    return false
+end
+
+get_name(obj) = String(last(split(HDF5.name(obj), '/')))
+
+get_data_type(obj) = attributes(obj)["type"][]
+
+get_cgns_type(obj) = haskey(attributes(obj), "label") ? attributes(obj)["label"][] : nothing
+
+function get_value(obj)
+    data_type = get_data_type(obj)
+    data = read(obj[" data"])
+    if data_type == "C1"
+        return String(UInt8.(data))
+    elseif data_type in ("I4", "I8", "R4", "R8")
+        return data
+    else
+        error("Datatype '$(data_type)' not handled")
+    end
+end
+
+function get_cgns_base(obj)
+    cgnsBases = get_children(obj; type = "CGNSBase_t")
+    if length(cgnsBases) == 0
+        error("Could not find any CGNSBase_t node in the file")
+    elseif length(cgnsBases) > 1
+        error("The file contains several CGNSBase_t nodes, only one base is supported")
+    end
+    return first(cgnsBases)
+end