Cannot read HDF5 data


#1

I can see the file structure OK in HDFview 3/.1 but when I try to look at the data I get the following message:

An error occurred while loading data for the table:

Failed to read scalar dataset:Can’t open directory or file.

The data is Chunked in quite large sizes 8192 X 1 or 4096 X 1.

Regards,

Rob


#2

Rob, can you send us the output of h5dump -pBH <your file>? What’s your OS? Maybe there’s a dangling reference via an external link. G.


#3

Hi Gerd,

Thank you for your reply. I am using windows 10. I cannot look at any data no matter how small the sample I would like to see is.

Here is the dump. I have put 1/2 in as the file became too large and will send the rest in another email just in case you need it.

regards,

Rob

HDF5 “D1_31012017.h5” {

SUPER_BLOCK {

SUPERBLOCK_VERSION 0

FREELIST_VERSION 0

SYMBOLTABLE_VERSION 0

OBJECTHEADER_VERSION 0

OFFSET_SIZE 8

LENGTH_SIZE 8

BTREE_RANK 16

BTREE_LEAF 4

ISTORE_K 32

FILE_SPACE_STRATEGY H5F_FSPACE_STRATEGY_FSM_AGGR

FREE_SPACE_PERSIST FALSE

FREE_SPACE_SECTION_THRESHOLD 1

FILE_SPACE_PAGE_SIZE 4096

USER_BLOCK {

  USERBLOCK_SIZE 0

}

}

GROUP “/” {

ATTRIBUTE “CLASS” {

  DATATYPE  H5T_STRING {

     STRSIZE 5;

     STRPAD H5T_STR_NULLTERM;

     CSET H5T_CSET_UTF8;

     CTYPE H5T_C_S1;

  }

  DATASPACE  SCALAR

}

ATTRIBUTE “PYTABLES_FORMAT_VERSION” {

  DATATYPE  H5T_STRING {

     STRSIZE 3;

     STRPAD H5T_STR_NULLTERM;

     CSET H5T_CSET_UTF8;

     CTYPE H5T_C_S1;

  }

  DATASPACE  SCALAR

}

ATTRIBUTE “TITLE” {

  DATATYPE  H5T_STRING {

     STRSIZE 1;

     STRPAD H5T_STR_NULLTERM;

     CSET H5T_CSET_UTF8;

     CTYPE H5T_C_S1;

  }

  DATASPACE  NULL

}

ATTRIBUTE “VERSION” {

  DATATYPE  H5T_STRING {

     STRSIZE 3;

     STRPAD H5T_STR_NULLTERM;

     CSET H5T_CSET_UTF8;

     CTYPE H5T_C_S1;

  }

  DATASPACE  SCALAR

}

GROUP “S1” {

  ATTRIBUTE "CLASS" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "TITLE" {

     DATATYPE  H5T_STRING {

        STRSIZE 1;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  NULL

  }

  ATTRIBUTE "VERSION" {

     DATATYPE  H5T_STRING {

        STRSIZE 3;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "axis0_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "axis1_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "block0_items_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "block1_items_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "encoding" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "nblocks" {

     DATATYPE  H5T_STD_I32LE

     DATASPACE  SCALAR

  }

  ATTRIBUTE "ndim" {

     DATATYPE  H5T_STD_I32LE

     DATASPACE  SCALAR

  }

  ATTRIBUTE "pandas_type" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "pandas_version" {

     DATATYPE  H5T_STRING {

        STRSIZE 6;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  DATASET "axis0" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_ASCII;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SIMPLE { ( 5 ) / ( 13107 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 13107 )

        SIZE 326 (0.077:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 5 65535 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "axis1" {

     DATATYPE  H5T_STD_I64LE

     DATASPACE  SIMPLE { ( 324000 ) / ( 324000 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 8192 )

        SIZE 237813 (10.899:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 8 65536 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "freq" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "index_class" {

        DATATYPE  H5T_STRING {

           STRSIZE 8;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 10;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 9;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "block0_items" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_ASCII;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SIMPLE { ( 1 ) / ( 13107 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 13107 )

        SIZE 312 (0.016:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 5 65535 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "block0_values" {

     DATATYPE  H5T_STD_I64LE

     DATASPACE  SIMPLE { ( 324000, 1 ) / ( 324000, 1 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 8192, 1 )

        SIZE 11640 (222.680:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 8 65536 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "block1_items" {

     DATATYPE  H5T_STRING {

        STRSIZE 3;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_ASCII;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SIMPLE { ( 4 ) / ( 21845 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 21845 )

        SIZE 314 (0.038:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 3 65535 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "block1_values" {

     DATATYPE  H5T_IEEE_F64LE

     DATASPACE  SIMPLE { ( 324000, 4 ) / ( 324000, 4 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 2048, 4 )

        SIZE 9362132 (1.107:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 8 65536 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

}

GROUP “S2” {

  ATTRIBUTE "CLASS" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "TITLE" {

     DATATYPE  H5T_STRING {

        STRSIZE 1;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  NULL

  }

  ATTRIBUTE "VERSION" {

     DATATYPE  H5T_STRING {

        STRSIZE 3;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "axis0_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "axis1_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "block0_items_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "block1_items_variety" {

     DATATYPE  H5T_STRING {

        STRSIZE 7;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "encoding" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "nblocks" {

     DATATYPE  H5T_STD_I32LE

     DATASPACE  SCALAR

  }

  ATTRIBUTE "ndim" {

     DATATYPE  H5T_STD_I32LE

     DATASPACE  SCALAR

  }

  ATTRIBUTE "pandas_type" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  ATTRIBUTE "pandas_version" {

     DATATYPE  H5T_STRING {

        STRSIZE 6;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_UTF8;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SCALAR

  }

  DATASET "axis0" {

     DATATYPE  H5T_STRING {

        STRSIZE 5;

        STRPAD H5T_STR_NULLTERM;

        CSET H5T_CSET_ASCII;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SIMPLE { ( 5 ) / ( 13107 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 13107 )

        SIZE 326 (0.077:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 5 65535 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "axis1" {

     DATATYPE  H5T_STD_I64LE

     DATASPACE  SIMPLE { ( 324000 ) / ( 324000 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 8192 )

        SIZE 237813 (10.899:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 8 65536 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

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           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

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        DATASPACE  SCALAR

     }

     ATTRIBUTE "freq" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

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           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "index_class" {

        DATATYPE  H5T_STRING {

           STRSIZE 8;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 10;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 9;

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           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

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     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

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  }

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     DATATYPE  H5T_STRING {

        STRSIZE 5;

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        CSET H5T_CSET_ASCII;

        CTYPE H5T_C_S1;

     }

     DATASPACE  SIMPLE { ( 1 ) / ( 13107 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 13107 )

        SIZE 312 (0.016:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 5 65535 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

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     ATTRIBUTE "kind" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

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           CSET H5T_CSET_UTF8;

           CTYPE H5T_C_S1;

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        DATASPACE  SCALAR

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     ATTRIBUTE "name" {

        DATATYPE  H5T_STRING {

           STRSIZE 2;

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           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

  DATASET "block0_values" {

     DATATYPE  H5T_STD_I64LE

     DATASPACE  SIMPLE { ( 324000, 1 ) / ( 324000, 1 ) }

     STORAGE_LAYOUT {

        CHUNKED ( 8192, 1 )

        SIZE 11640 (222.680:1 COMPRESSION)

     }

     FILTERS {

        USER_DEFINED_FILTER {

           FILTER_ID 32001

           COMMENT blosc

           PARAMS { 2 2 8 65536 9 1 1 }

        }

     }

     FILLVALUE {

        FILL_TIME H5D_FILL_TIME_ALLOC

        VALUE  H5D_FILL_VALUE_DEFAULT

     }

     ALLOCATION_TIME {

        H5D_ALLOC_TIME_INCR

     }

     ATTRIBUTE "CLASS" {

        DATATYPE  H5T_STRING {

           STRSIZE 6;

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           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

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        DATASPACE  SCALAR

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     ATTRIBUTE "TITLE" {

        DATATYPE  H5T_STRING {

           STRSIZE 1;

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           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  NULL

     }

     ATTRIBUTE "VERSION" {

        DATATYPE  H5T_STRING {

           STRSIZE 3;

           STRPAD H5T_STR_NULLTERM;

           CSET H5T_CSET_ASCII;

           CTYPE H5T_C_S1;

        }

        DATASPACE  SCALAR

     }

     ATTRIBUTE "transposed" {

        DATATYPE  H5T_STD_B8LE

        DATASPACE  SCALAR

     }

  }

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#4

The file appears to be a PyTables file, created by pandas. (?) Did you create the file locally, or did you get it from someone else? The datasets appear to be (chunked and) compressed with BLOSC. If HDFView can’t access the BLOSC filter, you’d see an error message like the one you are seeing. The HDF5 library (included in HDFView) will be looking for it in default places, but you can help by setting the HDF5_PLUGIN_PATH variable to the directory where you keep a copy of the BLOSC DLL. You can get the plugins from https://www.hdfgroup.org/downloads/hdf5/ (see under “Filter Plugins (Encode and Decode)”). See also https://www.hdfgroup.org/2018/06/hdf5-or-how-i-learned-to-love-data-compression-and-partial-i-o/ for some related material.


#5

HI Gerd,

Thank you for your reply. I did not make the data set which I think is why I cannot read it.

I do not think I had the the BLOSC filter as I did not have the plugins loaded and I have now done this and I can see the BLOSC files now in “C:\Program Files\HDF_Group\HDF5\1.10.6\lib\plugin” and “C:\Program Files\HDF_Group\HDF5\1.10.6\HDFPLExamples\example\testfiles”.

However HDF5 still produces the same error.

I do not know how to use the “set the HDF5_PLUGIN_PATH variable” command as HDFview may still not know where the BLOSC DLL is.

Regards,

Rob


#6

How about https://www.computerhope.com/issues/ch000549.htm ?
Just create a user variable HDF5_PLUGIN_PATH and set the value to C:\Program Files\HDF_Group\HDF5\1.10.6\lib\plugin?

If you are familiar w/ Python/pandas you should be able to access the data w/o HDFView.

G.


#7

Hi Gerd,

Thank you very much.

he new path in environment variables worked so HDFviewer worked and I can export the files to read in Octave (at present as I maybe able to use Matlab too). .

Regards,

Rob