Changes between Version 2 and Version 3 of Examples/Brain


Ignore:
Timestamp:
04/11/17 12:01:06 (7 years ago)
Author:
Herwig Zilken
Comment:

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  • Examples/Brain

    v2 v3  
    6868So the grid spacing is 1.0/31076=3.21792e-5 for the Y- and Z-axis. The X-axis is the direction of the slice cutting, therefore it's grid spacing is larger by a factor of 40, resulting in 40*3.21792e-5=1.2872e-3.
    6969
    70 
     70'''Fullsize Version:'''
    7171{{{
    7272#!xml
    … …  
    9595}}}
    9696
    97 To
     97As the dataset is relatively large (200 GB), we decided to generate a second xdmf file which only reads a subsampled version of the data (every 4th pixel in Y- and Z-direction, 12.5 GB). This can be done via the "hyperslab" construct and adds a little bit more complexity to the description. Please note that the grid spacing has to be adapted to the subsampled grid size accordingly.
    9898
     99'''Subsampled Version:'''
     100{{{
     101#!xml
     102<?xml version ="1.0" ?>
     103<!DOCTYPE xdmf SYSTEM "Xdmf.dtd" []>
     104<Xdmf Version="2.0">
     105<Domain>
     106<Grid Name="Brain" GridType="Uniform">
     107<Topology TopologyType="3DCoRectMesh" NumberOfElements="234 7180 7760"/>
     108<Geometry GeometryType="ORIGIN_DXDYDZ">
     109        <DataItem Dimensions="3" NumberType="Float" Precision="4" Format="XML">
     110                 -0.151 -0.4626 -0.5
     111        </DataItem>
     112        <DataItem Dimensions="3" NumberType="Float" Precision="4" Format="XML">
     113                1.28866e-3 1.28866e-4 1.28866e-4
     114        </DataItem>
     115</Geometry>
     116<Attribute Name="PLI" AttributeType="Scalar" Center="Node">
     117    <DataItem ItemType="Hyperslab" Dimensions="234 7180 7760" NumberType="UChar" Precision="1">
     118        <DataItem Dimensions="3 3" Format="XML">
     119           0 0 0
     120           1 4 4
     121           234 7180 7760
     122        </DataItem>
     123        <DataItem Dimensions="234 28721 31076" NumberType="UChar" Precision="1" Format="HDF">
     124                Vervet_Sehrinde.h5:/PLI
     125        </DataItem>
     126   </DataItem>
     127</Attribute>
     128</Grid>
     129</Domain>
     130</Xdmf>
     131
     132}}}
     133
     134== Prototyping the movie
     135Later we will generate the movie by controlling the rendering process in !ParaView via a Python-script (pvpython). Before we can do this, we need to find out good camera positions for camera flights, proper color- and transparency-tables, maybe a volume of interest and so on.
     136
     137To find out the necessary parameters, the data can be loaded with the !ParaView GUI first. There one can interactively adjust camera positions, color tables, .....
     138It is also very helpful to open the Python-Trace window of !ParaView, where most parameter changes made in the GUI are shown as Python commands. Those commands can, with little changes, be used in the final Python script for the movie generation.
     139
     140== Generating the movie with a Python script