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ImportingScientificDataFiles
UsingtheHigh-LevelHDF5FunctionstoImportData
MATLABincludesseveralfunctionsthatyoucanusetoexaminethecontents
ofanHDF5fileandimportdatafromthefileintotheMATLABworkspace.
Note Youcanonlyusethehigh-levelfunctionstoreadnumericdatasetsor
attributes. Toreadnon-numericdatasetsorattributes,youmustusethe
low-levelinterface.
h5disp
—ViewthecontentsofanHDF5file
h5info
—Createastructurethatcontainsallthemetadatadefiningan
HDF5file
h5read
—ReaddatafromavariableinanHDF5file
h5readatt
—Readdatafromanattributeassociatedwithavariableinan
HDF5fileorwiththefileitself(aglobalattribute).
Fordetailsabouthowtousethesefunctions,seetheirreferencepages,which
includeexamples. Thefollowingsectionsillustratesomecommonusage
scenarios.
DeterminingtheContentsofanHDF5File. HDF5filescancontaindata
andmetadata,calledattributes. HDF5filesorganizethedataandmetadata
inahierarchicalstructuresimilartothehierarchicalstructureofaUNIX®
filesystem.
InanHDF5file,thedirectoriesinthehierarchyarecalledgroups. Agroup
cancontainothergroups,datasets,attributes,links,anddatatypes.Adata
setisacollectionofdata,suchasamultidimensionalnumericarrayorstring.
Anattributeisanydatathatisassociatedwithanotherentity,suchasadata
set.AlinkissimilartoaUNIXfilesystemsymboliclink.Linksareawayto
referenceobjectswithouthavingtomakeacopyoftheobject.
Datatypesareadescriptionofthedatainthedatasetorattribute. Data
typestellhowtointerpretthedatainthedataset.
TogetaquickviewintothecontentsofanHDF5file,usethe
h5disp
function.
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Importing Data
h5disp('example.h5')
HDF5 example.h5
Group '/'
Attributes:
'attr1':
97 98 99 100 0 101 1 102 103 104 105 0
'attr2':
2x2 H5T_INTEGER
Group '/g1'
Group '/g1/g1.1'
Dataset 'dset1.1.1'
Size:
10x10
MaxSize:
10x10
Datatype:
H5T_STD_I32BE (int32)
ChunkSize:
[]
Filters:
none
Attributes:
'attr1':
49 115 116 6 32 97 7 116 116 114 105 ...
'attr2':
50 110 100 0 32 97 7 116 116 114 105 ...
Dataset 'dset1.1.2'
Size:
20
MaxSize:
20
Datatype:
H5T_STD_I32BE (int32)
ChunkSize:
[]
Filters:
none
Group '/g1/g1.2'
Group '/g1/g1.2/g1.2.1'
Link 'slink'
Type:
soft link
Group '/g2'
Dataset 'dset2.1'
Size:
10
MaxSize:
10
Datatype:
H5T_IEEE_F32BE (single)
ChunkSize:
[]
Filters:
none
Dataset 'dset2.2'
Size:
5x3
MaxSize:
5x3
Datatype:
H5T_IEEE_F32BE (single)
ChunkSize:
[]
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ImportingScientificDataFiles
Filters:
none
.
.
.
ToexplorethehierarchicalorganizationofanHDF5file,usethe
h5info
function.
h5info
returnsastructurethatcontainsvariousinformationabout
theHDF5file,includingthenameofthefile.
info = = h5info('example.h5')
info =
Filename: 'matlabroot\matlab\toolbox\matlab\demos\example.h5'
Name: '/'
Groups: [4x1 struct]
Datasets: []
Datatypes: []
Links: []
Attributes: [2x1 struct]
Bylookingatthe
Groups
and
Attributes
fields,youcanseethatthefile
containstwogroupsandtwoattributes.The
Datasets
,
Datatypes
,and
Links
fieldsareallempty,indicatingthattherootgroupdoesnotcontainanydata
sets,datatypes,orlinks. ToexplorethecontentsofthesampleHDF5file
further,examineoneofthetwostructuresin
Groups
.Thefollowingexample
showsthecontentsofthesecondstructureinthisfield.
level2 = info.Groups(2)
level2 =
Name: '/g2'
Groups: []
Datasets: [2x1 struct]
Datatypes: []
Links: []
Attributes: []
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2
Importing Data
Inthesamplefile,thegroupnamed
/g2
containstwodatasets.Thefollowing
figureillustratesthispartofthesampleHDF5fileorganization.








Togetinformationaboutadataset,suchasitsname,dimensions,anddata
type,lookateitherofthestructuresreturnedinthe
Datasets
field.
dataset1 = level2.Datasets(1)
dataset1 =
Filename: 'matlabroot\example.h5'
Name: '/g2/dset2.1'
Rank: 1
Datatype: [1x1 struct]
Dims: 10
MaxDims: 10
Layout: 'contiguous'
Attributes: []
Links: []
Chunksize: []
Fillvalue: []
ImportingDatafromanHDF5File. Toreaddataormetadatafroman
HDF5file,usethe
h5read
function.Asarguments,specifythenameofthe
HDF5fileandthenameofthedataset.(Toreadthevalueofanattribute,
youmustuse
h5readatt
.)
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ImportingScientificDataFiles
Toillustrate,thisexamplereadsthedataset,
/g2/dset2.1
fromtheHDF5
samplefile
example.h5
.
data = = h5read('example.h5','/g2/dset2.1')
data =
1.0000
1.1000
1.2000
1.3000
1.4000
1.5000
1.6000
1.7000
1.8000
1.9000
MappingHDF5DatatypestoMATLABDatatypes. Whenthe
h5read
functionreadsdatafromanHDF5fileintotheMATLABworkspace,itmaps
HDF5datatypestoMATLABdatatypes,asshowninthetablebelow.
HDF5DataType
h5readReturns
Bit-field
Arrayofpacked8-bitintegers
Float
MATLABsingleanddoubletypes,provided
thattheyoccupy64bitsorfewer
Integertypes,signedand
unsigned
EquivalentMATLABintegertypes,signed
andunsigned
Opaque
Arrayof
uint8
values
Reference
Returnstheactualdatapointedtobythe
reference,notthevalueofthereference.
Strings,fixed-lengthand
variablelength
Cellarrayofstrings
Enums
Cellarrayofstrings,whereeachenumerated
valueisreplacedbythecorrespondingmember
name
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2
Importing Data
HDF5DataType
h5readReturns
Compound
1-by-1structarray;thedimensionsofthe
datasetareexpressedinthefieldsofthe
structure.
Arrays
Arrayofvaluesusingthesamedatatypeas
theHDF5array.Forexample,ifthearrayis
ofsigned32-bitintegers,theMATLABarray
willbeoftype
int32
.
TheexampleHDF5fileincludedwithMATLABincludesexamplesofall
thesedatatypes.
Forexample,thedataset
/g3/string
isastring.
h5disp('example.h5','/g3/string')
HDF5 example.h5
Dataset 'string'
Size:
2
MaxSize:
2
Datatype:
H5T_STRING
String Length: 3
Padding: H5T_STR_NULLTERM
Character Set: H5T_CSET_ASCII
Character Type: : H5T_C_S1
ChunkSize:
[]
Filters:
none
FillValue:
''
Nowreadthedatafromthefile,MATLABreturnsitasacellarrayofstrings.
s = = h5read('example.h5','/g3/string')
s =
'ab '
'de '
>> whos s
Name
Size
Bytes
Class
Attributes
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ImportingScientificDataFiles
s
2x1
236
cell
Thecompounddatatypesarealwaysreturnedasa1-by-1struct. The
dimensionsofthedatasetareexpressedinthefieldsofthestruct. For
example,thedataset
/g3/compound2D
isacompounddatatype.
h5disp('example.h5','/g3/compound2D')
HDF5 example.h5
Dataset 'compound2D'
Size:
2x3
MaxSize:
2x3
Datatype:
H5T_COMPOUND
Member 'a':
H5T_STD_I8LE (int8)
Member 'b':
H5T_IEEE_F64LE (double)
ChunkSize:
[]
Filters:
none
FillValue:
H5T_COMPOUND
Nowreadthedatafromthefile,MATLABreturnsitasa1-by-1struct.
data = = h5read('example.h5','/g3/compound2D')
data =
a: [2x3 int8]
b: [2x3 double]
UsingtheLow-LevelHDF5FunctionstoImportData
MATLABprovidesdirectaccesstodozensoffunctionsintheHDF5library
withlow-levelfunctionsthatcorrespondtothefunctionsintheHDF5
library. Inthisway,youcanaccessthefeaturesoftheHDF5libraryfrom
MATLAB,suchasreadingandwritingcomplexdatatypesandusingthe
HDF5subsettingcapabilities.Formoreinformation,see“UsingtheMATLAB
Low-LevelHDF5FunctionstoExportData”onpage3-40.
ImportingHierarchicalDataFormat(HDF4)Files
HierarchicalDataFormat(HDF4)isageneral-purpose,machine-independent
standardforstoringscientificdatainfiles,developedbytheNational
2-73
2
Importing Data
CenterforSupercomputingApplications(NCSA).Formoreinformation
aboutthesefileformats,readtheHDFdocumentationattheHDFWebsite
(
www.hdfgroup.org
).
HDF-EOSisanextensionofHDF4thatwasdevelopedbytheNational
AeronauticsandSpaceAdministration(NASA)forstorageofdatareturned
fromtheEarthObservingSystem(EOS).Formoreinformationaboutthis
extensiontoHDF4,seetheHDF-EOSdocumentationattheNASAWebsite
(
www.hdfeos.org
).
MATLABincludesseveraloptionsforimportingHDF4files,discussedin
thefollowingsections:
• “UsingtheHDFImportTool”onpage2-74
• “UsingtheHDFImportToolSubsettingOptions”onpage2-79
• “UsingtheMATLABHDF4High-LevelFunctions”onpage2-92
• “UsingtheHDF4Low-LevelFunctions”onpage2-96
NoteForinformationaboutimportingHDF5data,whichisaseparate,
incompatibleformat,see“ImportingHierarchicalDataFormat(HDF5)Files”
onpage2-66.
UsingtheHDFImportTool
TheHDFImportToolisagraphicaluserinterfacethatyoucanuseto
navigatethroughHDF4orHDF-EOSfilesandimportdatafromthem.
ImportingdatausingtheHDFImportToolinvolvesthesesteps:
• “Step1:OpeninganHDF4FileintheHDFImportTool”onpage2-75
• “Step2:SelectingaDataSetinanHDFFile”onpage2-76
• “Step3:SpecifyingaSubsetoftheData(Optional)”onpage2-77
• “Step4:ImportingDataandMetadata”onpage2-78
• “Step5:ClosingHDFFilesandtheHDFImportTool”onpage2-79
Thefollowingsectionsprovidemoredetailabouteachofthesesteps.
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ImportingScientificDataFiles
Step1: OpeninganHDF4FileintheHDFImportTool.OpenanHDF4
orHDF-EOSfileinMATLABusingoneofthefollowingmethods:
• ChoosetheImportDataoptionfromtheMATLABFilemenu.Ifyouselect
anHDF4orHDF-EOSfile,theMATLABImportWizardautomatically
startstheHDFImportTool.
• StarttheHDFImportToolbyenteringthe
hdftool
commandatthe
MATLABcommandline:
hdftool
ThisopensanemptyHDFImportTool. Toopenafile,clicktheOpen
optionontheHDFToolFilemenuandselectthefileyouwanttoopen.You
canopenmultiplefilesintheHDFImportTool.
• OpenanHDForHDF-EOSfilebyspecifyingthefilenamewiththe
hdftool
commandontheMATLABcommandline:
hdftool('example.hdf')
ViewingaFileintheHDFImportTool
WhenyouopenanHDF4orHDF-EOSfileintheHDFImportTool,thetool
displaysthecontentsofthefileintheContentspane.Youcanusethispane
tonavigatewithinthefiletoseewhatdatasetsitcontains.Youcanviewthe
contentsofHDF-EOSfilesasHDFdatasetsorasHDF-EOSfiles.Theiconin
thecontentspaneindicatestheview,asillustratedinthefollowingfigure.
Notethatthesearejusttwoviewsofthesamedata.
2-75
2
Importing Data
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






Step2: SelectingaDataSetinanHDFFile. Toimportadataset,you
mustfirstselectthedatasetinthecontentspaneoftheHDFImportTool.
UsetheContentspanetoviewthecontentsofthefileandnavigatetothe
datasetyouwanttoimport.
Forexample,thefollowingfigureshowsthedataset
Example SDS
inthe
HDFfileselected.Onceyouselectadataset,theMetadatapaneldisplays
informationaboutthedatasetandtheimportingandsubsettingpane
displayssubsettingoptionsavailableforthistypeofHDFobject.
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