Hi Anthony, hi dashesy,
Il giorno 28/nov/2012, alle ore 00:57, Anthony Scopatz <scop...@gmail.com> 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. > > On Tue, Nov 27, 2012 at 5:17 PM, dashesy <dash...@gmail.com> 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 ------------------------------------------------------------------------------ Keep yourself connected to Go Parallel: INSIGHTS What's next for parallel hardware, programming and related areas? Interviews and blogs by thought leaders keep you ahead of the curve. http://goparallel.sourceforge.net _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
