Re: [Pytables-users] Error reading attribute with compound data type

[Anthony S. <sc...@gm...>]

On Wed, Nov 28, 2012 at 1:03 AM, Antonio Valentino <
ant...@ti...> wrote:

> Hi Anthony, hi dashesy,
>
>
> Il giorno 28/nov/2012, alle ore 00:57, Anthony Scopatz <sc...@gm...>
> ha scritto:
>
> > This [1] seems to indicate that this kind of thing should be supported
> via numpy structured arrays.  However, I bet that this data set did not
> start out as a numpy structured array.  This might explain the problem if
> the flavor is wrong.  I would think that a fix should be relatively easy.
> >
> > Be Well
> > Anthony
> >
> > 1.
> http://pytables.github.com/usersguide/libref/declarative_classes.html?highlight=attr#the-attributeset-class
> >
>
> I'm not sure that PyTables is able to handle variable length strings in
> compound data types at the moment.
>

Oops, I didn't notice that...  Antonio is right, the variable length part
of this is probably your issue.


>
> >
> > On Tue, Nov 27, 2012 at 5:17 PM, dashesy <da...@gm...> wrote:
> > I have a file that has attributes with nested compound type, when
> > reading it with PyTables 2.4.0 I get this error:
> >
> > C:\Python27\lib\site-packages\tables\attributeset.py:293:
> > DataTypeWarning: Unsupported type for attribute 'BmiRoot' in node '/'.
> > Offending HDF5 class: 6
> >   value = self._g_getAttr(self._v_node, name)
> > C:\Python27\lib\site-packages\tables\attributeset.py:293:
> > DataTypeWarning: Unsupported type for attribute 'BmiChanExt' in node
> > 'channel00001'. Offending HDF5 class: 6
> >   value = self._g_getAttr(self._v_node, name)
> >
>
> Yes, it is not clear
>
> > Hard to say what exactly happens, just wanted to know if this is not
> > already fixed in newer versions I will be more than happy to work on
> > it, any pointers as to where to look is appreciated.
> >
>
> I don't thing that there are changes that can impact on this issue.
> Anyway you can give a try to the development branch [1]
>
> Any help is very appreciated
>
> [1] https://github.com/PyTables/PyTables
>
>
> > Here is the (partial) dump of the file (for brevity I deleted
> > non-related data parts but can provide the full file if needed):
> >
> > HDF5 "pause5-10-5.ns2.h5" {
> > GROUP "/" {
> >    ATTRIBUTE "BmiRoot" {
> >       DATATYPE  "/BmiRootAttr_t"
> >       DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
> >       DATA {
> >       (0): {
> >             1,
> >             0,
> >             0,
> >             1,
> >             "2008-12-02 22:57:02.251000",
> >             "1 kS/s",
> >             ""
> >          }
> >       }
> >    }
> >    DATATYPE "BmiRootAttr_t" H5T_COMPOUND {
> >       H5T_STD_U32LE "MajorVersion";
> >       H5T_STD_U32LE "MinorVersion";
> >       H5T_STD_U32LE "Flags";
> >       H5T_STD_U32LE "GroupCount";
> >       H5T_STRING {
> >          STRSIZE H5T_VARIABLE;
> >          STRPAD H5T_STR_NULLTERM;
> >          CSET H5T_CSET_ASCII;
> >          CTYPE H5T_C_S1;
> >       } "Date";
> >       H5T_STRING {
> >          STRSIZE H5T_VARIABLE;
> >          STRPAD H5T_STR_NULLTERM;
> >          CSET H5T_CSET_ASCII;
> >          CTYPE H5T_C_S1;
> >       } "Application";
> >       H5T_STRING {
> >          STRSIZE H5T_VARIABLE;
> >          STRPAD H5T_STR_NULLTERM;
> >          CSET H5T_CSET_ASCII;
> >          CTYPE H5T_C_S1;
> >       } "Comment";
> >    }
> >    GROUP "channel" {
> >       DATATYPE "BmiChanAttr_t" H5T_COMPOUND {
> >          H5T_STD_U16LE "ID";
> >          H5T_IEEE_F32LE "Clock";
> >          H5T_IEEE_F32LE "SampleRate";
> >          H5T_STD_U8LE "SampleBits";
> >       }
> >       DATATYPE "BmiChanExt2Attr_t" H5T_COMPOUND {
> >          H5T_STD_I32LE "DigitalMin";
> >          H5T_STD_I32LE "DigitalMax";
> >          H5T_STD_I32LE "AnalogMin";
> >          H5T_STD_I32LE "AnalogMax";
> >          H5T_STRING {
> >             STRSIZE 16;
> >             STRPAD H5T_STR_NULLTERM;
> >             CSET H5T_CSET_ASCII;
> >             CTYPE H5T_C_S1;
> >          } "AnalogUnit";
> >       }
> >       DATATYPE "BmiChanExtAttr_t" H5T_COMPOUND {
> >          H5T_IEEE_F64LE "NanoVoltsPerLSB";
> >          H5T_COMPOUND {
> >             H5T_STD_U32LE "HighPassFreq";
> >             H5T_STD_U32LE "HighPassOrder";
> >             H5T_STD_U16LE "HighPassType";
> >             H5T_STD_U32LE "LowPassFreq";
> >             H5T_STD_U32LE "LowPassOrder";
> >             H5T_STD_U16LE "LowPassType";
> >          } "Filter";
> >          H5T_STD_U8LE "PhysicalConnector";
> >          H5T_STD_U8LE "ConnectorPin";
> >          H5T_STRING {
> >             STRSIZE H5T_VARIABLE;
> >             STRPAD H5T_STR_NULLTERM;
> >             CSET H5T_CSET_ASCII;
> >             CTYPE H5T_C_S1;
> >          } "Label";
> >       }
> >       DATATYPE "BmiChanFiltAttr_t" H5T_COMPOUND {
> >          H5T_STD_U32LE "HighPassFreq";
> >          H5T_STD_U32LE "HighPassOrder";
> >          H5T_STD_U16LE "HighPassType";
> >          H5T_STD_U32LE "LowPassFreq";
> >          H5T_STD_U32LE "LowPassOrder";
> >          H5T_STD_U16LE "LowPassType";
> >       }
> >       GROUP "channel00001" {
> >          ATTRIBUTE "BmiChan" {
> >             DATATYPE  "/channel/BmiChanAttr_t"
> >             DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
> >             DATA {
> >             (0): {
> >                   1,
> >                   30000,
> >                   1000,
> >                   16
> >                }
> >             }
> >          }
> >          ATTRIBUTE "BmiChanExt" {
> >             DATATYPE  "/channel/BmiChanExtAttr_t"
> >             DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
> >             DATA {
> >             (0): {
> >                   1000,
> >                   {
> >                      750000,
> >                      4,
> >                      1,
> >                      7500,
> >                      3,
> >                      1
> >                   },
> >                   1,
> >                   1,
> >                   "elec1"
> >                }
> >             }
> >          }
> >          ATTRIBUTE "BmiChanExt2" {
> >             DATATYPE  "/channel/BmiChanExt2Attr_t"
> >             DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
> >             DATA {
> >             (0): {
> >                   -8191,
> >                   8191,
> >                   -8191,
> >                   8191,
> >                   "uV"
> >                }
> >             }
> >          }
> >          DATASET "continuous_set" {
> >             DATATYPE  H5T_STD_I16LE
> >             DATASPACE  SIMPLE { ( 631 ) / ( H5S_UNLIMITED ) }
> >             DATA {...
> >             }
> >          }
> >       }
> >    }
> > }
> > }
>
>
> --
> Antonio Valentino
>
>
>
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