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[netCDF #NRW-974703]: invalid HDF5 variable size prevents reading range in Java

Hi Garret,

[Oops, that went out before I was done. Here's the complete version ...]

John Caron wrote:
> final Variable variable = 
> file.findVariable("/Chromosomes/Summary.StartIndex");
> 
> indicates a member variable "StartIndex" of the structure "Summary"
> 
> Garret Wilson wrote:
> > I'm not sure I'm following you. Are you saying that the Variable I am
> > reading is a member of a Structure? (yes/no)

Yes.

Opening your dataset in the netCDF-Java ToolsUI [1] "NcDump" tab, I get the 
following

netcdf 
20130212_CN021_P3_222k_B02_WD7195FBPAT10231Nat_Nat_Std_CHTNWD_OP3_14.mip222k.oschp
{
  ...
  group: Chromosomes {
    variables:

     Structure {
       byte Chromosome;
           :_Unsigned = "true";
       int Display_&size;
       char Display(4);
       int StartIndex;
           :_Unsigned = "true";
       int MarkerCount;
           :_Unsigned = "true";
       float MinSignal;
       float MaxSignal;
       float MedianCnState;
       float HomFrequency;
       float HetFrequency;
       float Mosaicism;
       float LOH;
       float MedianSignal;
     } Summary(24);
  }
  ...
}

> > Are you saying that the API documentation "...this returns only the
> > variable's data in the first Structure, so that the Array shape is the
> > same as the Variable" applies to the Variable I am trying to read? (yes/no)

Yes.

Here's a snippet from the netCDF enhanced data model (aka Common Data
Model) about Structures that I think is relevant:

  "A Structure is a type of Variable that contains other Variables,
  analogous to a struct in C, or a row in a relational database. In
  general, the data in a Structure are physically stored close
  together on disk, so that it is efficient to retrieve all of the
  data in a Structure at the same time. A Variable contained in a
  Structure is a member Variable, and can only be read in the
  context of its containing Structure.
  - http://www.unidata.ucar.edu/software/netcdf-java/CDM/

netCDF has two data models:

1) The netCDF-3 data model ("classic") is made up of files,
   dimensions, attributes, and variables where the variables were
   simple multi-dimensional arrays.

2) The netCDF-4 data model ("enhanced") extends the classic model with
   groups, user defined types including structures, and a few other
   things.

Hope that helps explain how Structures fit into the data model
netCDF-Java is working from and how that might affects the API.

Ethan

[1] netCDF-Java ToolsUI
WebStart link:
http://www.unidata.ucar.edu/software/netcdf-java/v4.3/webstart/netCDFtools.jnlp
More info on netCDF-Java page:
http://www.unidata.ucar.edu/software/netcdf-java/documentation.htm


Ticket Details
===================
Ticket ID: NRW-974703
Department: Support netCDF Java
Priority: High
Status: Closed