Read Xdmf: Difference between revisions

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(→‎Reading XDMF Data: Placed code in source tags so it get syntax highlighting. Cleaned up indentation of the code.)
 
Line 7: Line 7:
all stored directly in the XML file.
all stored directly in the XML file.


<?xml version="1.0" ?>
<source lang="xml" line="1">
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf>
<Xdmf>
     <Domain>
     <Domain>
         <Grid Name="TestGrid">
         <Grid Name="TestGrid">
             <Topology Type="Hexahedron" NumberOfElements="2" >
             <Topology Type="Hexahedron" NumberOfElements="2" >
                 <DataItem Format="XML" DataType="Float"
                 <DataItem Format="XML" DataType="Float"
                    Dimensions="2 8">
                          Dimensions="2 8">
                     0 1 7 6  3 4 10 9
                     0 1 7 6  3 4 10 9
                     1 2 8 7  4 5 11 10
                     1 2 8 7  4 5 11 10
Line 22: Line 21:
             </Topology>
             </Topology>
             <Geometry Type="XYZ">
             <Geometry Type="XYZ">
                    <DataItem Format="XML" DataType="Float" Precision="8"
                <DataItem Format="XML" DataType="Float" Precision="8"
                            Dimensions="4 3 3">
                          Dimensions="4 3 3">
                      0.0  0.0  1.0
                    0.0  0.0  1.0
                      1.0  0.0  1.0
                    1.0  0.0  1.0
                      3.0  0.0  2.0
                    3.0  0.0  2.0
                   
                      0.0  1.0  1.0
                    0.0  1.0  1.0
                      1.0  1.0  1.0
                    1.0  1.0  1.0
                      3.0  2.0  2.0
                    3.0  2.0  2.0
                   
                      0.0  0.0  -1.0
                    0.0  0.0  -1.0
                      1.0  0.0  -1.0
                    1.0  0.0  -1.0
                      3.0  0.0  -2.0
                    3.0  0.0  -2.0
                   
                      0.0  1.0  -1.0
                    0.0  1.0  -1.0
                      1.0  1.0  -1.0
                    1.0  1.0  -1.0
                      3.0  2.0  -2.0
                    3.0  2.0  -2.0
                    </DataItem>
                </DataItem>
             </Geometry>
             </Geometry>
             <Attribute Name="NodeValues" Center="Node">
             <Attribute Name="NodeValues" Center="Node">
                 <DataItem Format="XML" DataType="Float" Precision="8"
                 <DataItem Format="XML" DataType="Float" Precision="8"
                        Dimensions="4 3" >
                          Dimensions="4 3" >
                        100 200 300
                    100 200 300
                        300 400 500
                    300 400 500
                        300 400 500
                    300 400 500
                        500 600 700
                    500 600 700
                 </DataItem>
                 </DataItem>
             </Attribute>
             </Attribute>
             <Attribute Name="CellValues" Center="Cell">
             <Attribute Name="CellValues" Center="Cell">
                 <DataItem Format="XML" DataType="Float" Precision="8"
                 <DataItem Format="XML" DataType="Float" Precision="8"
                        Dimensions="2" >
                          Dimensions="2" >
                        100 200
                    100 200
                 </DataItem>
                 </DataItem>
             </Attribute>
             </Attribute>
         </Grid>
         </Grid>
     </Domain>
     </Domain>
</Xdmf>
</Xdmf>
</source>


The XML is stored in the file "MyGrid.xmf". The following Python program demonstrated parsing the XML and
The XML is stored in the file "MyGrid.xmf". The following Python program demonstrated parsing the XML and
retrieving the data values.
retrieving the data values.


from Xdmf import *
<source lang="python" line="1">
reader = XdmfReader.New()
#! /usr/bin/env python
dom = XdmfReader.read('MyGrid.xmf')
from Xdmf import *
# We now have a tree. Find the one and only Grid element
reader = XdmfReader.New()
grid = dom.getUnstruturedGrid(0)
dom = XdmfReader.read('MyGrid.xmf')
# We now have a tree. Find the one and only Grid element
top = grid.GetTopology()
grid = dom.getUnstruturedGrid(0)
print 'Values = ', top.getValuesString()
 
# Release values from data when done
top = grid.GetTopology()
top.release()
print 'Values = ', top.getValuesString()
# Release values from data when done
geo = grid.GetGeometry()
top.release()
print 'Geo Type = ', geo.getType().getName(), ' # Points = ', geo.getNumberPoints()
 
print 'Points = ', geo.getValuesString()
geo = grid.GetGeometry()
geo.release()
print 'Geo Type = ', geo.getType().getName(), ' # Points = ', geo.getNumberPoints()
# for each Attribute, print Light Data and Values
print 'Points = ', geo.getValuesString()
for i in range(grid.getNumberAttributes()) :
geo.release()
# for each Attribute, print Light Data and Values
for i in range(grid.getNumberAttributes()):
     attr = grid.getAttribute(i)
     attr = grid.getAttribute(i)
     print 'Attribute ', i, ' Name = ', attr.getName()
     print 'Attribute ', i, ' Name = ', attr.getName()
Line 87: Line 89:
     print 'Values ', attr.getValuesString()
     print 'Values ', attr.getValuesString()
     attr.release()
     attr.release()
</source>

Latest revision as of 13:59, 20 May 2016

Reading XDMF Data

TwoHex.jpg

The following Xdmf XML file is a simple example of a Uniform Grid that contains two Hexahedron that share a face. There are values centered at the nodes and at the cell centers. The values for geometry, connectivity, and scalars are all stored directly in the XML file.

<source lang="xml" line="1"> <?xml version="1.0" ?> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []> <Xdmf>

   <Domain>
       <Grid Name="TestGrid">
           <Topology Type="Hexahedron" NumberOfElements="2" >
               <DataItem Format="XML" DataType="Float"
                         Dimensions="2 8">
                   0 1 7 6   3 4 10 9
                   1 2 8 7   4 5 11 10
               </DataItem>
           </Topology>
           <Geometry Type="XYZ">
               <DataItem Format="XML" DataType="Float" Precision="8"
                         Dimensions="4 3 3">
                   0.0   0.0   1.0
                   1.0   0.0   1.0
                   3.0   0.0   2.0
                   
                   0.0   1.0   1.0
                   1.0   1.0   1.0
                   3.0   2.0   2.0
                   
                   0.0   0.0   -1.0
                   1.0   0.0   -1.0
                   3.0   0.0   -2.0
                   
                   0.0   1.0   -1.0
                   1.0   1.0   -1.0
                   3.0   2.0   -2.0
               </DataItem>
           </Geometry>
           <Attribute Name="NodeValues" Center="Node">
               <DataItem Format="XML" DataType="Float" Precision="8"
                         Dimensions="4 3" >
                   100 200 300
                   300 400 500
                   300 400 500
                   500 600 700
               </DataItem>
           </Attribute>
           <Attribute Name="CellValues" Center="Cell">
               <DataItem Format="XML" DataType="Float" Precision="8"
                         Dimensions="2" >
                   100 200
               </DataItem>
           </Attribute>
       </Grid>
   </Domain>

</Xdmf> </source>

The XML is stored in the file "MyGrid.xmf". The following Python program demonstrated parsing the XML and retrieving the data values.

<source lang="python" line="1">

  1. ! /usr/bin/env python

from Xdmf import * reader = XdmfReader.New() dom = XdmfReader.read('MyGrid.xmf')

  1. We now have a tree. Find the one and only Grid element

grid = dom.getUnstruturedGrid(0)

top = grid.GetTopology() print 'Values = ', top.getValuesString()

  1. Release values from data when done

top.release()

geo = grid.GetGeometry() print 'Geo Type = ', geo.getType().getName(), ' # Points = ', geo.getNumberPoints() print 'Points = ', geo.getValuesString() geo.release()

  1. for each Attribute, print Light Data and Values

for i in range(grid.getNumberAttributes()):

   attr = grid.getAttribute(i)
   print 'Attribute ', i, ' Name = ', attr.getName()
   # Attribute HeavyData is not Updated by default
   # there could potentially be many causing huge IO
   attr.read()
   print 'Values ', attr.getValuesString()
   attr.release()

</source>