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Include field data (such as time information) in parallel VTK files (#…
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…140)

* Write field data to PVTK files as well

Field data such as the current time are now also written to PVTK files,
in addition to the VTK files associated to each "process". This seems to
be needed for ParaView to have access to the field data.

* Update tests

* Add notes to docs on including time information

* Try to fix tests on Julia 1.6
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@jipolanco
jipolanco committed Apr 4, 2024
1 parent 8813546 commit 7eb6761
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Showing 6 changed files with 121 additions and 47 deletions.
19 changes: 15 additions & 4 deletions docs/src/grids/datasets.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ vtk_grid("fields", x, y, z) do vtk
vtk["Pressure"] = rand(Nx - 1, Ny - 1, Nz - 1) # scalar field attached to cells
vtk["Velocity"] = rand(3, Nx, Ny, Nz) # vector field attached to points
vtk["VelocityGradients"] = rand(3, 3, Nx, Ny, Nz) # 3×3 tensor field attached to points
vtk["date"] = "31/10/2021" # metadata ("field data" in VTK)
vtk["time"] = 0.42 # metadata ("field data" in VTK)
vtk["Date"] = "31/10/2021" # metadata ("field data" in VTK)
vtk["TimeValue"] = 0.42 # metadata ("field data" in VTK)
end
```

Expand All @@ -25,6 +25,17 @@ input.
In particular, note that the `Pressure` field is attached to cells instead of points, since it has dimensions ``(N_x - 1) × (N_y - 1) × (N_z - 1)``, which is the number of cells in structured files (see [Cells in structured formats](@ref)).
For more control, see [Dataset types](@ref) below.

!!! note "Time values"

As a sidenote, the `TimeValue` field used above [is special](https://docs.vtk.org/en/latest/design_documents/IOXMLTimeInFieldData.html#field-data-as-time-meta-data-in-vtk-xml-file-formats),
as it is interpreted by VTK and ParaView as the time associated to the dataset.
This can be convenient when writing time series data (for example, results from a simulation at different timesteps).

Other alternatives for including time information are to use [ParaView collections](@ref) (`.pvd` format), or to generate
[JSON `.series` files](https://gitlab.kitware.com/paraview/paraview/-/blob/v5.5.0/Documentation/release/ParaView-5.5.0.md#json-based-new-meta-file-format-for-series-added)
(the latter can't be currently done by WriteVTK, but the format is very simple).


## Passing tuples of arrays

Note that, in the example above, the `Velocity` vector field is passed as a single ``3 × N_x × N_y × N_z`` array, which is the layout ultimately used in VTK formats.
Expand Down Expand Up @@ -124,8 +135,8 @@ vtk_grid("fields_explicit", x, y, z) do vtk
vtk["Pressure", VTKCellData()] = rand(Nx - 1, Ny - 1, Nz - 1)
vtk["Velocity", VTKPointData()] = rand(3, Nx, Ny, Nz)
vtk["VelocityGradients", VTKPointData()] = rand(3, 3, Nx, Ny, Nz)
vtk["date", VTKFieldData()] = "31/10/2021"
vtk["time", VTKFieldData()] = 0.42
vtk["Date", VTKFieldData()] = "31/10/2021"
vtk["TimeValue", VTKFieldData()] = 0.42
end
```

Expand Down
10 changes: 10 additions & 0 deletions src/WriteVTK.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,16 @@ end
DatasetFile(dtype, xdoc::XMLDocument, fname::AbstractString, args...; kwargs...) =
DatasetFile(xdoc, add_extension(fname, dtype), xml_name(dtype), args...; kwargs...)

function data_format(vtk::DatasetFile)
if vtk.appended
:appended
elseif vtk.ascii
:ascii
else
:inline
end
end

function show(io::IO, vtk::DatasetFile)
open_str = isopen(vtk) ? "open" : "closed"
print(io, "VTK file '$(vtk.path)' ($(vtk.grid_type) file, $open_str)")
Expand Down
42 changes: 40 additions & 2 deletions src/gridtypes/pvtk_grid.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,11 @@ struct PVTKFile <: VTKFile
path::String
end

# This is just to make a PVTKFile work like a DatasetFile.
# Only used when writing VTKFieldData to a PVTK file.
# Note that data is always written as text (ASCII).
data_format(::PVTKFile) = :ascii

# Returns true if the arguments do *not* contain any cell vectors.
_pvtk_is_structured(x::AbstractVector{<:AbstractMeshCell}, args...) = Val(false)
_pvtk_is_structured(x, args...) = _pvtk_is_structured(args...)
Expand Down Expand Up @@ -130,11 +135,44 @@ end

# Add point and cell data as usual
function Base.setindex!(
pvtk::PVTKFile, data, name::AbstractString, args...,
pvtk::PVTKFile, data, name::AbstractString, loc::AbstractFieldData,
)
pvtk.vtk[name, loc] = data
end

# In the case of field data, also add it to the pvtk file.
# Otherwise field data (typically the time / "TimeValue") is not seen by ParaView.
function Base.setindex!(
pvtk::PVTKFile, data, name::AbstractString, loc::VTKFieldData,
)
pvtk.vtk[name, loc] = data
if pvtk.pvtkargs.ismain
add_field_data(pvtk, data, name, loc)
end
data
end

# Used in add_field_data.
# We need to find the PUnstructuredGrid / PStructuredGrid / ... node.
function find_base_xml_node_to_add_field(pvtk::PVTKFile, loc)
xroot = root(pvtk.xdoc)
pgrid_type = "P" * pvtk.vtk.grid_type
find_element(xroot, pgrid_type)
end

# If `loc` was not passed, try to guess which kind of data was passed.
function Base.setindex!(
pvtk::PVTKFile, data, name::AbstractString,
)
pvtk.vtk[name, args...] = data
loc = guess_data_location(data, pvtk.vtk) :: AbstractFieldData
pvtk[name, loc] = data
end

# Write XML attribute.
# Example:
#
# pvtk[VTKCellData()] = Dict("HigherOrderDegrees" => "HigherOrderDegreesDataset")
#
function Base.setindex!(
pvtk::PVTKFile, attributes, loc::AbstractFieldData,
)
Expand Down
47 changes: 29 additions & 18 deletions src/write_data.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -110,17 +110,23 @@ function write_array(io, data::Tuple)
n
end

function add_data_ascii(xml, x::Union{Number,String})
function add_data_ascii(xml, x::Union{Number,AbstractString})
add_text(xml, " ")
add_text(xml, string(x))
end

add_data_ascii(xml, x::AbstractArray) = map(v -> add_data_ascii(xml, v), x)
function add_data_ascii(xml, x::AbstractArray)
for v ∈ x
add_data_ascii(xml, v)
end
nothing
end

function add_data_ascii(xml, data::Tuple)
for i in eachindex(data...), x in data
add_data_ascii(xml, x[i])
end
nothing
end

function set_num_components(xDA, vtk, data, loc)
Expand Down Expand Up @@ -173,9 +179,10 @@ function data_to_xml(vtk, xParent, data, name,
set_attribute(xDA, "ComponentName$(i - 1)", n) # 0-based
end
end
if vtk.appended
fmt = data_format(vtk)
if fmt === :appended
data_to_xml_appended(vtk, xDA, data)
elseif vtk.ascii
elseif fmt === :ascii
data_to_xml_ascii(vtk, xDA, data)
else
data_to_xml_inline(vtk, xDA, data)
Expand Down Expand Up @@ -209,7 +216,7 @@ containing the size of the data array in bytes.
"""
function data_to_xml_appended(vtk::DatasetFile, xDA::XMLElement, data)
@assert vtk.appended
@assert data_format(vtk) === :appended

buf = vtk.buf # append buffer
compress = vtk.compression_level > 0
Expand Down Expand Up @@ -258,7 +265,7 @@ end
Add inline, base64-encoded data to VTK XML file.
"""
function data_to_xml_inline(vtk::DatasetFile, xDA::XMLElement, data)
@assert !vtk.appended && !vtk.ascii
@assert data_format(vtk) === :inline
compress = vtk.compression_level > 0

# DataArray node
Expand Down Expand Up @@ -305,8 +312,8 @@ end
Add inline data to VTK XML file in ASCII format.
"""
function data_to_xml_ascii(vtk::DatasetFile, xDA::XMLElement, data)
@assert !vtk.appended && vtk.ascii
function data_to_xml_ascii(vtk::VTKFile, xDA::XMLElement, data)
@assert data_format(vtk) === :ascii
set_attribute(xDA, "format", "ascii")
add_text(xDA, "\n")
add_data_ascii(xDA, data)
Expand All @@ -320,18 +327,10 @@ end
Add either point or cell data to VTK file.
"""
function add_field_data(vtk::DatasetFile, data, name::AbstractString,
function add_field_data(vtk::VTKFile, data, name::AbstractString,
loc::AbstractFieldData;
component_names::Union{AbstractVector, Nothing}=nothing)
# Find Piece node.
xroot = root(vtk.xdoc)
xGrid = find_element(xroot, vtk.grid_type)

xbase = if loc === VTKFieldData()
xGrid
else
find_element(xGrid, "Piece")
end
xbase = find_base_xml_node_to_add_field(vtk, loc)

# Find or create "nodetype" (PointData, CellData or FieldData) node.
nodetype = node_type(loc)
Expand All @@ -344,6 +343,18 @@ function add_field_data(vtk::DatasetFile, data, name::AbstractString,
xDA
end

function find_base_xml_node_to_add_field(vtk::DatasetFile, loc)
# Find Piece node.
xroot = root(vtk.xdoc)
xGrid = find_element(xroot, vtk.grid_type)
xbase = if loc === VTKFieldData()
xGrid
else
find_element(xGrid, "Piece")
end
xbase
end

vtk_point_data(args...; kwargs...) = add_field_data(args..., VTKPointData(); kwargs...)
vtk_cell_data(args...; kwargs...) = add_field_data(args..., VTKCellData(); kwargs...)
vtk_field_data(args...; kwargs...) = add_field_data(args..., VTKFieldData(); kwargs...)
Expand Down
46 changes: 23 additions & 23 deletions test/checksums.sha1
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Original file line number Diff line number Diff line change
Expand Up @@ -55,28 +55,28 @@ b20bf14b2531aaf323b891e090d0615d0e943ef6 collection_03.vtr
8005b27b071ed50765d0d859a9e4e84a52c3963c arraydata_2D.vti
d5215c84b3c1630bedd98994963560ff14200dc5 arraydata_3D.vti
aa49366e66d8930fa639a8361d153a95baca361e arrays.vti
2626bef24152fcfe28c810ca68adf473c8fad90c simulation.pvtu
4a0be2eaf5c7ffdb60970f0396a11ef2ab3affca simulation/simulation_1.vtu
3edeb95b6d2f955c8ee5539cb0a64be1f53f0bf1 simulation.pvtu
1348c734f1b79881f6b74461aaee059fa2f01c09 simulation/simulation_1.vtu
ee3ea76e543c6e3a9c1c28d80596b68c5b22d7ac higherorderdegrees.pvtu
9a524fb558d6e8e2a42c6bf704da88c2a835b296 higherorderdegrees/higherorderdegrees_1.vtu
e23c8f0db331e1db635aa5d98b9f1375132e7ffd pimage.pvti
e581d4824d67655584f573743f42788fb26e162c pimage/pimage_1.vti
150ce17cb8ddbb974344954a3193a3373ee1c3fc pimage/pimage_2.vti
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21dd9d15e51720f9d5822bf663c718974094d779 pimage/pimage_6.vti
d35ceff83c6c43b43eefe07007cbba8752cead15 prectilinear.pvtr
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d26dd7cf0570b1fbad8714e16e784f09bb6affed prectilinear/prectilinear_2.vtr
e36a533248051994e7da804bff1b168d2d866bba prectilinear/prectilinear_3.vtr
4b73039f56d1a92fe958a98c86dde64b3fb86b63 prectilinear/prectilinear_4.vtr
87a07f8911949b002501da5bdd5daf497a65d09a prectilinear/prectilinear_5.vtr
4fd1d4de3867230a0636bef0260417ed17b7c17f prectilinear/prectilinear_6.vtr
fc3a26b061585c093520bbb720714d180ca22335 pstructured.pvts
584520780f94c58a9919cb216d116733f8466e0f pstructured/pstructured_1.vts
0ff33138288a96f8f6f4377f2e061748aa702d97 pstructured/pstructured_2.vts
e365dc765a17a288640e04f726cf8a7421559f39 pstructured/pstructured_3.vts
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ad4b841fdf277c6138bbd763f4db2a359c46e400 pstructured/pstructured_3.vts
651905ba5698b503f58d40fc1051267fefa4b49e pstructured/pstructured_4.vts
bba1504744a03b3f9594fcfe63435b7311e030fe pstructured/pstructured_5.vts
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4 changes: 4 additions & 0 deletions test/pvtk_grid.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ function pvtk_unstructured()
pvtk["Processor"] = [1,2]
pvtk["Temperature", VTKPointData()] = y
pvtk["Id", VTKCellData()] = [2, 1]
pvtk["TimeValue"] = 4.2
end
@test isfile(vtufile)
@test vtufile ∈ outfiles
Expand Down Expand Up @@ -73,6 +74,7 @@ function pvtk_imagedata()
) do vtk
vtk["point_data"] = point_data
vtk["process_id"] = processid
vtk["TimeValue"] = 1.2
end
end
end
Expand All @@ -95,6 +97,7 @@ function pvtk_rectilinear()
) do vtk
vtk["point_data"] = point_data
vtk["process_id"] = processid
vtk["TimeValue"] = 3.4
end
end
end
Expand Down Expand Up @@ -124,6 +127,7 @@ function pvtk_structured()
) do vtk
vtk["point_data"] = point_data
vtk["process_id"] = processid
vtk["TimeValue"] = 3.5
end
end
end
Expand Down

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