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Fix deprecation warnings

Browse Source 
* Add docstrings
* Refactor code
* Module level docstring giving an example
This commit is contained in:
Jukka Aho
2018-09-06 12:02:56 +03:00
parent 1357e7e46d
commit ca911e5e87
15 changed files with 539 additions and 432 deletions
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src/io.jl
+45 -44
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@@ -36,7 +36,7 @@ function Xdmf(name::String; version="3.0", overwrite=false)
if isfile(h5file)
if overwrite
info("Result file $h5file exists, removing old file.")
@debug("Result file $h5file exists, removing old file.")
rm(h5file)
else
error("Result file $h5file exists, use Xdmf($name; overwrite=true) to rewrite results")
@@ -45,7 +45,7 @@ function Xdmf(name::String; version="3.0", overwrite=false)
if isfile(xmlfile)
if overwrite
info("Result file $xmlfile exists, removing old file.")
@debug("Result file $xmlfile exists, removing old file.")
rm(xmlfile)
else
error("Result file $xmlfile exists, use Xdmf($name; overwrite=true) to rewrite results")
@@ -209,9 +209,9 @@ function traverse(xdmf::Xdmf, x::XMLElement, attr_name::String)
items = split(attr_name, '/')
new_item = xdmf_filter(childs, first(items))
if new_item == nothing
info("traverse: childs:")
@debug("traverse: childs:")
for child in childs
info(LightXML.name(child))
@debug(LightXML.name(child))
end
error("traverse: failed, items = $items, xdmf_filter not find child")
end
@@ -261,9 +261,13 @@ function save!(xdmf::Xdmf)
save_file(doc, xmffile(xdmf))
end
function Base.close(xdmf::Xdmf)
close(xdmf.hdf)
end
function new_dataitem(xdmf::Xdmf, path::String, data::Array{T,N}) where {T,N}
dataitem = new_element("DataItem")
datatype = replace("$T", "64", "")
datatype = replace("$T", "64" => "")
dimensions = join(reverse(size(data)), " ")
set_attribute(dataitem, "DataType", datatype)
set_attribute(dataitem, "Dimensions", dimensions)
@@ -271,7 +275,7 @@ function new_dataitem(xdmf::Xdmf, path::String, data::Array{T,N}) where {T,N}
if xdmf.format == "HDF"
hdf = basename(h5file(xdmf))
if exists(xdmf.hdf, path)
info("Xdmf: $path already existing in h5 file, not overwriting.")
@debug("Xdmf: $path already existing in h5 file, not overwriting.")
else
write(xdmf.hdf, path, data)
end
@@ -324,6 +328,28 @@ global const xdmf_element_mapping = Dict(
"Wedge15" => "Wedge_15",
"Hex20" => "Hex_20")
"""
get_spatial_collection()
Return a SpatialCollection at given time either by creating new one or returning
existing one.
"""
function get_spatial_collection(temporal_collection, time)
for spatial_collection in get_elements_by_tagname(temporal_collection, "Grid")
time_element = find_element(spatial_collection, "Time")
time_value = Meta.parse(attribute(time_element, "Value"; required=true))
isapprox(time_value, time) && return spatial_collection
end
# did not find, create new one
spatial_collection = new_child(temporal_collection, "Grid")
set_attribute(spatial_collection, "GridType", "Collection")
set_attribute(spatial_collection, "Name", "Problems")
set_attribute(spatial_collection, "CollectionType", "Spatial")
time_element = new_child(spatial_collection, "Time")
set_attribute(time_element, "Value", time)
return spatial_collection
end
"""
update_xdmf!(xdmf, problem, time, fields)
@@ -337,20 +363,20 @@ julia> update_xdmf!(p1, 0.0, ["displacement", "temperature"])
"""
function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vector)
info("Xdmf: storing fields $fields of problem $(problem.name) at time $time")
@debug("Xdmf: storing fields $fields of problem $(problem.name) at time $time")
# 1. find domain
xml = xdmf.xml
domain = find_element(xml, "Domain")
if domain == nothing
info("Xdmf: Domain not found, creating.")
@debug("Xdmf: Domain not found, creating.")
domain = new_child(xml, "Domain")
end
# 2. find for TemporalCollection
temporal_collection = find_element(domain, "Grid")
if temporal_collection == nothing
info("Xdmf: Temporal collection not found, creating.")
@debug("Xdmf: Temporal collection not found, creating.")
temporal_collection = new_child(domain, "Grid")
set_attribute(temporal_collection, "GridType", "Collection")
set_attribute(temporal_collection, "Name", "Time")
@@ -361,43 +387,18 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
collection_type = attribute(temporal_collection, "CollectionType"; required=true)
@assert collection_type == "Temporal"
# 3. find for SpatialCollection at given time
spatial_collection = nothing
spatial_collection_exists = false
for spatial_collection in get_elements_by_tagname(temporal_collection, "Grid")
time_element = find_element(spatial_collection, "Time")
time_value = parse(attribute(time_element, "Value"; required=true))
if isapprox(time_value, time)
info("Xdmf: SpatialCollection for time $time already exists.")
spatial_collection_exists = true
break
end
end
if !spatial_collection_exists
info("Xdmf: SpatialCollection for time $time not found, creating.")
spatial_collection = new_child(temporal_collection, "Grid")
set_attribute(spatial_collection, "GridType", "Collection")
set_attribute(spatial_collection, "Name", "Problems")
set_attribute(spatial_collection, "CollectionType", "Spatial")
time_element = new_child(spatial_collection, "Time")
set_attribute(time_element, "Value", time)
end
# 3.1 make sure that Grid element we found really is SpatialCollection
collection_type = attribute(spatial_collection, "CollectionType"; required=true)
@assert collection_type == "Spatial"
spatial_collection = get_spatial_collection(temporal_collection, time)
for frame in get_elements_by_tagname(spatial_collection, "Grid")
frame_name = attribute(frame, "Name")
if frame_name == problem.name
warn("Xdmf: Already found Grid with name $frame_name for time $time, skipping.")
@warn("Xdmf: Already found Grid with name $frame_name for time $time, skipping.")
return
end
end
frame_name = problem.name
info("Xdmf: Creating Grid for problem $frame_name")
@debug("Xdmf: Creating Grid for problem $frame_name")
frame = new_child(spatial_collection, "Grid")
set_attribute(frame, "Name", frame_name)
@@ -408,7 +409,7 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
X_array = hcat([X_dict[nid] for nid in node_ids]...)
ndim, nnodes = size(X_array)
geom_type = (ndim == 2 ? "XY" : "XYZ")
info("Xdmf: Creating geometry, type = $geom_type, number of nodes = $nnodes")
@debug("Xdmf: Creating geometry, type = $geom_type, number of nodes = $nnodes")
X_dataitem = new_dataitem(xdmf, X_array)
geometry = new_child(frame, "Geometry")
set_attribute(geometry, "Type", geom_type)
@@ -419,12 +420,12 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
nelements = length(all_elements)
element_types = unique(map(get_element_type, all_elements))
nelement_types = length(element_types)
info("Xdmf: Saving topology of $nelements elements total, $nelement_types different element types.")
@debug("Xdmf: Saving topology of $nelements elements total, $nelement_types different element types.")
for element_type in element_types
elements = collect(filter_by_element_type(element_type, all_elements))
nelements = length(elements)
info("Xdmf: $nelements elements of type $element_type")
@debug("Xdmf: $nelements elements of type $element_type")
sort!(elements, by=get_element_id)
element_ids = map(get_element_id, elements)
element_conn = map(element -> [node_mapping[j]-1 for j in get_connectivity(element)], elements)
@@ -446,24 +447,24 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
@assert node_ids == field_node_ids
field_dim = length(field_dict[first(field_node_ids)])
if field_dim == 2
info("Xdmf: Field dimension = 2, extending to 3")
@debug("Xdmf: Field dimension = 2, extending to 3")
for nid in field_node_ids
field_dict[nid] = [field_dict[nid]; 0.0]
end
field_dim = 3
end
field_type = Dict(1 => "Scalar", 3 => "Vector", 6 => "Tensor6")[field_dim]
info("Xdmf: Saving field $field_name, type = $field_type, dimension = $field_dim, center = $field_center")
@debug("Xdmf: Saving field $field_name, type = $field_type, dimension = $field_dim, center = $field_center")
field_array = hcat([field_dict[nid] for nid in field_node_ids]...)
field_dataitem = new_dataitem(xdmf, field_array)
attribute = new_child(frame, "Attribute")
set_attribute(attribute, "Name", ucfirst(field_name))
set_attribute(attribute, "Name", uppercasefirst(field_name))
set_attribute(attribute, "Center", field_center)
set_attribute(attribute, "AttributeType", field_type)
add_child(attribute, field_dataitem)
end
save!(xdmf)
info("Xdmf: all done.")
@debug("Xdmf: all done.")
end