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Single section vasculature fails to load due to empty connectivity #173

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eleftherioszisis opened this issue Mar 11, 2020 · 0 comments
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@eleftherioszisis
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eleftherioszisis commented Mar 11, 2020

I tried to load an one section vasculature dataset, but MorphIO doesn't load it due to the empty connectivity dataset.
test_single_section_sg.zip

from morphio.vasculature import Vasculature

v = Vasculature('test_single_section.h5')

Traceback:

---------------------------------------------------------------------------
RawDataError                              Traceback (most recent call last)
<ipython-input-3-43b259418727> in <module>
----> 1 m = morphio.vasculature.Vasculature('test_single_section_sg.h5')

RawDataError: Opening vasculature file 'test_single_section_sg.h5': bad number of dimensions in connectivity dataspace

h5dump:

HDF5 "test_single_section_sg.h5" {
GROUP "/" {
   DATASET "connectivity" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( 0 ) / ( 0 ) }
      DATA {
      }
   }
   DATASET "points" {
      DATATYPE  H5T_IEEE_F32LE
      DATASPACE  SIMPLE { ( 3, 4 ) / ( 3, 4 ) }
      DATA {
      (0,0): 0.685519, 0.68087, 0.39709, 1,
      (1,0): 0.512065, 0.125548, 0.0812268, 1,
      (2,0): 0.832563, 0.221666, 0.261854, 1
      }
   }
   DATASET "structure" {
      DATATYPE  H5T_STD_U64LE
      DATASPACE  SIMPLE { ( 1, 2 ) / ( 1, 2 ) }
      DATA {
      (0,0): 0, 0
      }
   }
}
}

@eleftherioszisis eleftherioszisis changed the title Single section vasculature fails to load due to emtpy connectivity Single section vasculature fails to load due to empty connectivity Mar 11, 2020
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