Workpackage 4a at IPSL Development of diagnostics and visualization tools Patrick Brockmann Update:  20/10/2004

Definition
IPSL answers to questionnaires
Presentations
Examples of netCDF files at the CF conventions
Survey on the different identified graphic packages
    Ferret
    VCS
    VTK

This workpackage intends to provide a library that can generate output from PRISM models,
to provide a flexible library of tools to facilitate processing and analysis of data in the common PRISM data format,
to promote sharing of data and analysis programmes and
to provide highend and low-end graphical interfaces to display the data.

Considered delivrable D4a5:
Review of existing graphics packages and definition of common requirements for graphics
for ordinary analysis purposes (low-end) and high-quality presentational purposes (highend).

Official PRISM site: http://prism.enes.org

Figure of the Prism components

 

I/O processing library functionalities

 

High-level usability requirements of the Data Analysis & Display System

 

Graphical user interface for PRISM

• KNMI - Utrecht - 26-27 June 2002
  
PDF slides
 
• Met Office - Hadley Center - Bracknell - 21-22 October 2002
  
PDF slides (see also references in VTK paragraph below)


• Paris - IPSL - 3-4 April 2003
  PDF slides
  
  
• KNMI - Utrecht - 11-12 September 2003
  PDF slides
  
  
• DKRZ - Hamburg - 24-25 February 2004
  PDF slides


• KNMI - Utrecht - 7-8 October 2004
  PDF slides

• You will find there (http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/prism/gridsCF/) some grids taken from the
  
Ocean Carbon-Cycle Model Intercomparison Project (OCMIP) which were originallly written
following the GDT convention. CF convention was not existing at that time.
They have been converted to the CF convention and can be a good start to evaluate the
different graphic packages identified in PRISM WP4a.
Those metafiles contain metadata which should be located in each model ouput file.
Here, we do not respect the idea of a self described file with all information needed to make
processing and visualization. But this solution was choosen to avoid redundancy and save
some extra place. Anyway this aspect will be handled by XML description (as proposed
in CDML - see CDAT) of netcdf files which propose a description on how a dataset is
partionned into files or/and where to find metadata.
• Notes: The "cgi-bin/nph-dods" URL part must be remove to make the dowload possible.
In brief, when you browse an URL with a cgi-bin/nph-dods, you access to the file through
a cgi-bin program which allow you to get the "DODS Dataset Access Form".
If you what to download a file, just remove this cgi-bin/nph-dods part.
 
• You can find output of a simulation of the IPSL coupled models from http://dods.ipsl.jussieu.fr/fast/atlas/2L27_SE_2030_2039_output

You will find atmospheric model output (files with _histmnth.nc extension)
and ocean model output (files with grid_T.nc extension).

Ferret

VCS

VTK

With a special focus on

• Handling of CF conventions
• Isocontours
• Data structure proposed by software to handle irregular grids
• Section (cut plane, from profiles)
• Overlays
• Probe (synchronous probe over multiple windows, variables)
• Interaction with Python scripting language
• Interaction with the Python processing module CDMS - Climate Data Management System
• Remote access with OPeNDAP/DODS
  

• Informations: Ferret

• Example:
  
Here is a typical script to plot irregular grids as polygon maps (no isocontours).



yes? set window 1
yes? def sym DB=http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/prism
yes? use "http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/ocmip/phase2/MPIM/CFC/MPIM_SurfTS_1940.nc"
yes? go CF_map_cylin.jnl MPIM 0 SST[l=1] 10 /lev=25
yes? go land
yes? message
yes? let var_masked=if mask[k=1,d=MPIM_gridCF.nc] eq 1 then SSS
yes? go CF_map_cylin.jnl MPIM 0 var_masked[l=1] 10 /lev=25
yes? go land
yes? message
yes? go CF_map_cylin.jnl MPIM 0 var_masked[l=1] 10 /lev=25/line

Note that both model output and the CF grid file are get from the DODS server at IPSL.
You can try this example without any other installation except Ferret (Release > 5.70) and
having downloaded example scripts.

This functionnality has been used to design a simple diagnostic tool
to check correctness of coupled models output here at IPSL.
See http://dods.ipsl.jussieu.fr/fast/ to get a better idea.
 

• Informations: CDAT and VCS - Visualization Control System
  
 
• Example:
  
The script vcs_demo.py  covers a prototype of application using CDMS to read the grid file and the var file,
combining the masks using fonctions from cdms.MV and using the new meshfill method (on developpement)
from VCS to plot the variable as a polygons plot.

You can get MPIM_gridCF.nc, IPSL.ORCA4_gridCF.nc and CPL84_1m_0204_0204_grid_T.nc files from
the DODS IPSL server (see previous paragraph "Examples of netCDF files at the CF conventions").
Type vcs_demo.py -h to get usage.
Note that you can also use it with cdml files (xml built with cdscan from CDMS package which allow you
to aggregate files from time or level dimensions).
Some calls and plots produced with it:


> python -i vcs_demo.py -m -p linear MPIM_gridCF.nc MPIM_gridCF.nc bathy

> python -i vcs_demo.py -m -p linear IPSL.ORCA4_gridCF.nc CPL84_1m_0204_0204_grid_T.nc sosstsst

• Informations: VTK
  
The Visualization ToolKit (VTK) is an open source, freely available software
 system for 3D computer graphics, image processing, and visualization.
VTK has been implemented on nearly every Unix-based platform and PC's (Windows NT and Windows95).
VTK applications can be written directly in C++, Tcl, Java, or Python.

• A prototype of application developped during PRISM project
  
• http://dods.ipsl.jussieu.fr/vtk/VTK_Mapper/VTK_Mapper.pdf