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Fix the no soma h5 morphologies#288

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tomdele merged 6 commits intocleanup_morphologyHDF5from
fix_no_soma
Apr 23, 2021
Merged

Fix the no soma h5 morphologies#288
tomdele merged 6 commits intocleanup_morphologyHDF5from
fix_no_soma

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@tomdele tomdele commented Apr 16, 2021

Fix the no soma morphologies. The single-neurite.h5 is :

HDF5 "single-neurite.h5" {
GROUP "/" {
   DATASET "points" {
      DATATYPE  H5T_IEEE_F32LE
      DATASPACE  SIMPLE { ( 3, 4 ) / ( 3, 4 ) }
      DATA {
      (0,0): 4, 0, 0, 2,
      (1,0): 5, 0, 0, 2,
      (2,0): 6, 0, 0, 2
      }
   }
   DATASET "structure" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SIMPLE { ( 1, 3 ) / ( 1, 3 ) }
      DATA {
      (0,0): 0, 2, 0
      }
   }
}
}

@tomdele tomdele marked this pull request as ready for review April 16, 2021 14:37
@tomdele tomdele requested a review from mgeplf April 16, 2021 14:37
@tomdele tomdele linked an issue Apr 16, 2021 that may be closed by this pull request
@tomdele tomdele mentioned this pull request Apr 20, 2021
@tomdele tomdele requested a review from asanin-epfl April 22, 2021 16:57
@tomdele tomdele merged commit 2a888cf into cleanup_morphologyHDF5 Apr 23, 2021
@tomdele tomdele deleted the fix_no_soma branch April 23, 2021 09:15
@asanin-epfl
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Could be useful to check for soma types in the new added tests, but it's up to you

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tomdele commented Apr 23, 2021

Good idea. I will do it. I need to rebase on your test PR anyway.

tomdele added a commit that referenced this pull request Apr 23, 2021
* Fix the no soma h5 morphologies
* wrong type for the structure
* fix data again
* Remove the size necessarily equal to zero.
* remove cassert
* Multiple sections soma
@asanin-epfl
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What test PR? Do I have one?

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tomdele commented Apr 23, 2021

I meant your pytest PR

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tomdele commented Apr 23, 2021

Rah not PR (we merged it already) commit.

mgeplf added a commit that referenced this pull request May 5, 2021
* make which datasets belong to which versions more clear
* don't use try/catch to detect if datasets exist
* try and clarify where member variables are read & saved
* removed member variables _points, _pointsDims, _sections, since their locality can be kept local
* fix version numbering in tests/data/h5/v1/endoplasmic-reticulum.h5 / mitochondria.h5
* Fix the no soma h5 morphologies (#288)
* Add tests for somatypes
* test for extra somas/out of order during traversal of sections
* 100 % coverage for src/readers/morphologyHDF5.cpp
* added explicit glia tests
* variable rename, use static_cast

Co-authored-by: tomdele <thomas.delemontex@epfl.ch>
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MorphIO H5 reader always interprets first section as soma

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