# How to push! new row to array in hdf5 file?

**URL:** <https://discourse.julialang.org/t/how-to-push-new-row-to-array-in-hdf5-file/2608>\
**Category:** General Usage\
**Tags:** hdf5\
**Created:** [March 11, 2017, 5:37pm UTC](https://discourse.julialang.org/t/how-to-push-new-row-to-array-in-hdf5-file/2608 "2017-03-11T17:37:44Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![programista](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/programista/32/5372_2.png) [@programista](https://discourse.julialang.org/u/programista)\
**Post date:** [March 11, 2017, 5:37pm UTC](https://discourse.julialang.org/t/how-to-push-new-row-to-array-in-hdf5-file/2608/1 "2017-03-11T17:37:44Z")

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How to push! new row to array in hdf5 file without read and write the array?

```julia
  | | |_| | | | (_| | | Version 0.5.0 (2016-09-19 18:14 UTC)
 _/ |\ __'_|_|_|\__'_| | Official http://julialang.org/ release
|__/ | x86_64-w64-mingw32

julia> using HDF5

julia> hfi=h5open("my_file.h5","w")
HDF5 data file: my_file.h5

julia> close(hfi)

julia> fid = h5open("my_file.h5","r+")
HDF5 data file: my_file.h5

julia> write(fid,"A",rand(5,5))

Is somthing l;ike push! ? :

julia> push!(fid,"A",rand(5)) 
ERROR: MethodError: no method matching push!(::HDF5.HDF5File, ::String)
Closest candidates are:
  push!(::Any, ::Any, ::Any) at abstractarray.jl:1715
  push!(::Any, ::Any, ::Any, ::Any...) at abstractarray.jl:1716
  push!(::Array{Any,1}, ::ANY) at array.jl:486
  ...
 in push!(::HDF5.HDF5File, ::String, ::Array{Float64,1}) at .\abstractarray.jl:1715

```

Paul

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**Author:** ![slowbrain](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/slowbrain/32/2224_2.png) [@slowbrain](https://discourse.julialang.org/u/slowbrain)\
**Post date:** [March 12, 2017, 2:02am UTC](https://discourse.julialang.org/t/how-to-push-new-row-to-array-in-hdf5-file/2608/2 "2017-03-12T02:02:01Z")

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There is `set_dims!` function to achieve what you need.  
However you need to “preallocate” dataset’s dimensions to be able to change them later:

```julia
fid = h5open("my_file.h5","w")
A = d_create(fid, "A", Float64, ((5,5),(-1,-1)), "chunk", (5,5))
A[:,:] = randn(5,5)
close(fid)

fid = h5open("my_file.h5","r+")
A = d_open(fid, "A")
set_dims!(A, (6,5)) # add new row
A[6,:] = -1.
close(fid)

```

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**Author:** ![programista](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/programista/32/5372_2.png) [@programista](https://discourse.julialang.org/u/programista)\
**Post date:** [March 13, 2017, 8:46am UTC](https://discourse.julialang.org/t/how-to-push-new-row-to-array-in-hdf5-file/2608/3 "2017-03-13T08:46:22Z")

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Thanks, is nice working.  
What do this line : ?

|A = d\_create(fid, “A”, Float64, ((5,5),(-1,-1)), “chunk”, (5,5))|

Why my code dosent works ?  
My code  
julia\> using HDF5

julia\> fid=h5open(“file.h5”,“w”)  
HDF5 data file: file.h5

julia\> close(fid)

julia\> fid = h5open(“file.h5”,“r+”)  
HDF5 data file: file.h5

julia\> write(fid,“A”,rand(5,5))

julia\> close(fid)

julia\> fid = h5open(“file.h5”,“r+”)  
HDF5 data file: file.h5

julia\> A = d\_open(fid, “A”)  
HDF5 dataset: /A (file: file.h5)

julia\> size(A)  
(5,5)

julia\> set\_dims!(A, (6,5)) # add new row  
HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:  
#000: /home/abuild/rpmbuild/BUILD/hdf5-1.8.13/src/H5D.c line 1167 in  
H5Dset\_extent(): unable to set extend dataset  
major: Dataset  
minor: Unable to initialize object  
#001: /home/abuild/rpmbuild/BUILD/hdf5-1.8.13/src/H5Dint.c line 2169  
in H5D\_\_set\_extent(): dataset has contiguous stor  
age  
major: Invalid arguments to routine  
minor: Out of range  
ERROR: Error extending dataset dimensions  
in h5d\_set\_extent(::HDF5.HDF5Dataset, ::Array{UInt64,1}) at  
C:\Users\PC.julia\v0.5\HDF5\src\plain.jl:2007  
in set\_dims!(::HDF5.HDF5Dataset, ::Tuple{Int64,Int64}) at  
C:\Users\PC.julia\v0.5\HDF5\src\plain.jl:1178

Paul

W dniu 2017-03-12 o 03:05, Tomas Mikoviny pisze:

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**Author:** ![slowbrain](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/slowbrain/32/2224_2.png) [@slowbrain](https://discourse.julialang.org/u/slowbrain)\
**Post date:** [March 13, 2017, 8:17pm UTC](https://discourse.julialang.org/t/how-to-push-new-row-to-array-in-hdf5-file/2608/4 "2017-03-13T20:17:27Z")

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Everything should make sense once you look at [HDF5 User’s Guide](https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/HDF5_Users_Guide/Datasets/HDF5_Datasets.htm?rhtocid=5.2.0_5#TOC_5_4_5_Storage_Strategiesbc-13) (5.4.5. Storage Strategies).  
Contiguous datasets created with `write` or `d_create` without specifying chunked storage are of fixed size =\> one cannot resize them.  
To define chunks and therefore resizable datasets one needs to follow this scheme:  
(as in [HDF5.jl Mid-level routines](https://github.com/JuliaIO/HDF5.jl/blob/master/doc/hdf5.md#mid-level-routines))

```julia
d = d_create(parent, name, dtype, (dims, max_dims), "chunk", (chunk_dims))
set_dims!(d, new_dims)

```

Please note `max_dims` parameter that defines the limits of dimensions of particular dataset. I had called it “preallocation” in earlier post. If one uses `max_dims` to be `(-1,-1)`, as in example above, you can change any dimension of the dataset freely, as long as it is less then `typemax(Uint)`.