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
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