The HDF5 installation provides several useful tools for inspecting HDF5 files.
lstagner@computer:~/TEST$ h5ls test_geometry.h5 nbi Group npa Group spec Group lstagner@computer:~/TEST$ h5ls test_geometry.h5/nbi adist Dataset {1} aoffy Dataset {1} aoffz Dataset {1} ashape Dataset {1} awidy Dataset {1} awidz Dataset {1} axis Dataset {3} data_source Dataset {SCALAR} divy Dataset {3} divz Dataset {3} focy Dataset {SCALAR} focz Dataset {SCALAR} name Dataset {SCALAR} naperture Dataset {SCALAR} shape Dataset {SCALAR} src Dataset {3} widy Dataset {SCALAR} widz Dataset {SCALAR} lstagner@computer:~/TEST$ h5ls -v test_geometry.h5/nbi/src Opened "test_geometry.h5" with sec2 driver. src Dataset {3/3} Attribute: description scalar Type: 47-byte null-terminated ASCII string Data: "Position of the center of the beam source grid" Attribute: units scalar Type: 3-byte null-terminated ASCII string Data: "cm" Location: 1:5024 Links: 1 Chunks: {3} 24 bytes Storage: 24 logical bytes, 20 allocated bytes, 120.00% utilization Filter-0: shuffle-2 OPT {8} Filter-1: deflate-1 OPT {9} Type: native double lstagner@computer:~/TEST$ h5ls -d test_geometry.h5/nbi/src src Dataset {3} Data: (0) 0, -532, 0
The IDL routine read_hdf5.pro is provided to read any HDF5 file.
IDL> f = read_hdf5("./test_geometry.h5") IDL> help,f ** Structure <284b698>, 4 tags, length=2224, data length=2194, refs=1: NBI STRUCT -> <Anonymous> Array[1] NPA STRUCT -> <Anonymous> Array[1] SPEC STRUCT -> <Anonymous> Array[1] DESCRIPTION STRING 'Geometric quantities for FIDASIM' IDL> help,f.nbi ** Structure <27fb4d8>, 20 tags, length=752, data length=734, refs=2: ADIST STRUCT -> <Anonymous> Array[1] AOFFY STRUCT -> <Anonymous> Array[1] AOFFZ STRUCT -> <Anonymous> Array[1] ASHAPE STRUCT -> <Anonymous> Array[1] AWIDY STRUCT -> <Anonymous> Array[1] AWIDZ STRUCT -> <Anonymous> Array[1] AXIS STRUCT -> <Anonymous> Array[1] DATA_SOURCE STRUCT -> <Anonymous> Array[1] DIVY STRUCT -> <Anonymous> Array[1] DIVZ STRUCT -> <Anonymous> Array[1] FOCY STRUCT -> <Anonymous> Array[1] FOCZ STRUCT -> <Anonymous> Array[1] NAME STRUCT -> <Anonymous> Array[1] NAPERTURE STRUCT -> <Anonymous> Array[1] SHAPE STRUCT -> <Anonymous> Array[1] SRC STRUCT -> <Anonymous> Array[1] WIDY STRUCT -> <Anonymous> Array[1] WIDZ STRUCT -> <Anonymous> Array[1] DESCRIPTION STRING 'Neutral Beam Geometry' COORDINATE_SYSTEM STRING 'Right-handed cartesian' IDL> help,f.nbi.src ** Structure <27f5908>, 3 tags, length=56, data length=56, refs=2: DESCRIPTION STRING 'Position of the center of the beam source grid' UNITS STRING 'cm' DATA DOUBLE Array[3]
The h5py library can be used to read and write HDF5 files.
>>> import h5py as h5 >>> f = h5.File("./test_geometry.h5") >>> [k for k in f.keys()] ['nbi', 'npa', 'spec'] >>> [k for k in f['nbi'].keys()] ['adist', 'aoffy', 'aoffz', 'ashape', 'awidy', 'awidz', 'axis', 'data_source', 'divy', 'divz', 'focy', 'focz', 'name', 'naperture', 'shape', 'src', 'widy', 'widz'] >>> f["/nbi/src"].value array([ 0., -532., 0.])
The HDF5.jl library can be used to read and write HDF5 files.
julia> using HDF5 julia> f = h5open("test_geometry.h5") HDF5 data file: test_geometry.h5 julia> names(f) 3-element Array{ByteString,1}: "nbi" "npa" "spec" julia> names(f["/nbi"]) 11-element Array{ByteString,1}: "adist" "aoffy" "aoffz" "ashape" "awidy" "awidz" "axis" "data_source" "divy" "divz" "focy" "focz" "name" "naperture" "shape" "src" "widy" "widz" julia> read(f["/nbi/src"]) 3-element Array{Float64,1}: 0.0 -532.0 0.0 julia> h5read("test_geometry.h5","/nbi/src") 3-element Array{Float64,1}: 0.0 -532.0 0.0