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ImportingScientificDataFiles
value =
This is s a a sample e entry.
6
ClosetheCDFfile.
cdflib.close(cdfid);
ImportingNetworkCommonDataForm(NetCDF)
Files
NetworkCommonDataForm(NetCDF)isasetofsoftwarelibrariesand
machine-independentdataformatsthatsupportthecreation,access,and
sharingofarray-orientedscientificdata. NetCDFisusedbyawiderangeof
engineeringandscientificfieldsthatwantastandardwaytostoredataso
thatitcanbeshared.Formoreinformation,readtheNetCDFdocumentation
availableattheUnidataWebsite.
MATLABprovidestwomethodstoimportdatafromanNetCDFfile:
• High-levelfunctionsthatsimplifytheprocessofimportingdata
• Low-levelfunctionsthatenablemorecompletecontrolovertheimporting
process,byprovidingaccesstotheroutinesintheNetCDFClibrary
NoteForinformationaboutimportingtoCommonDataFormat(CDF)files,
whichhaveacompletelyseparate,incompatibleformat,see“Importing
CommonDataFileFormat(CDF)Files”onpage2-50.
UsingtheMATLABHigh-LevelNetCDFFunctionstoImportData
MATLABincludesseveralfunctionsthatyoucanusetoexaminethecontents
ofaNetCDFfileandimportdatafromthefileintotheMATLABworkspace.
ncdisp
—ViewthecontentsofaNetCDFfile
ncinfo
—Createastructurethatcontainsallthemetadatathatdefinesa
NetCDFfile
ncread
—ReaddatafromavariableinaNetCDFfile
2-57
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2
Importing Data
ncreadatt
—Readdatafromanattributeassociatedwithavariableina
NetCDFfileorwiththefileitself(aglobalattribute).
Fordetailsabouthowtousethesefunctions,seetheirreferencepages,which
includeexamples.Thefollowingsectionillustrateshowtousethesefunctions
toperformacommontask:findingalltheunlimiteddimensionsinaNetCDF
file.
FindingAllUnlimitedDimensionsinaNetCDFFile. Thisexampleshows
howtofindallunlimiteddimensionsinanexistingNetCDFfile,visually
andprogrammatically.
1
TodeterminewhichdimensionsinaNetCDFfileareunlimited,displaythe
contentsoftheexampleNetCDFfile,using
ncdisp
.The
ncdisp
function
identifiesunlimiteddimensionswiththelabel
UNLIMITED
.
Source:
\\matlabroot\toolbox\matlab\demos\example.nc
Format:
netcdf4
Global Attributes:
creation_date = '29-Mar-2010'
Dimensions:
x = = 50
y = = 50
z = = 5
.
.
.
Groups:
/grid2/
Attributes:
description = = 'This is another group attribute.'
Dimensions:
x
= 360
y
= 180
time = 0
(UNLIMITED)
Variables:
temp
2-58
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ImportingScientificDataFiles
Size:
[]
Dimensions: x,y,time
Datatype:
int16
2
Todetermineallunlimiteddimensionsprogrammatically,firstget
informationaboutthefileusing
ncinfo
. Thisexamplegetsinformation
aboutaparticulargroupinthefile.
ginfo = ncinfo('example.nc','/grid2/');
3
GetavectoroftheBooleanvaluesthatindicate,forthisgroup,which
dimensionisunlimited.
unlimDims = = [finfo.Dimensions.Unlimited]
unlimDims =
0
0
1
4
Usethisvectortodisplaytheunlimiteddimension.
disp(ginfo.Dimensions(unlimDims))
Name: 'time'
Length: 0
Unlimited: 1
UsingtheMATLABLow-LevelNetCDFFunctionstoImportData
MATLABprovidesaccesstotheroutinesintheNetCDFClibrarythatyou
canusetoreaddatafromNetCDFfilesandwritedatatoNetCDFfiles.
MATLABprovidesthisaccessthroughasetofMATLABfunctionsthat
correspondtothefunctionsintheNetCDFClibrary.MATLABgroupsthe
functionsintoapackage,called
netcdf
.Tocalloneofthefunctionsinthe
package,youmustspecifythepackagename. Foracompletelistofallthe
functions,see
netcdf
.
ThissectiondoesnotdescribeallfeaturesoftheNetCDFlibraryorexplain
basicNetCDFprogrammingconcepts.TousetheMATLABNetCDFfunctions
effectively,youshouldbefamiliarwiththeinformationaboutNetCDF
containedinthe
NetCDF C Interface e Guide
.
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2
Importing Data
MappingNetCDF APISyntaxtoMATLABFunctionSyntax. Forthe
mostpart,theMATLABNetCDFfunctionscorresponddirectlytoroutines
intheNetCDFClibrary.Forexample,theMATLABfunction
netcdf.open
correspondstotheNetCDFlibraryroutine
nc_open
. Insomecases,one
MATLABfunctioncorrespondstoagroupofNetCDFlibraryfunctions. For
example,insteadofcreatingMATLABversionsofeveryNetCDFlibrary
nc_put_att_type
function,where
type
representsadatatype,MATLAB
usesonefunction,
netcdf.putAtt
,tohandleallsupporteddatatypes.
ThesyntaxoftheMATLABfunctionsissimilartotheNetCDFlibrary
routines,withsomeexceptions.Forexample,theNetCDFClibraryroutines
useinputparameterstoreturndata,whiletheirMATLABcounterparts
useoneormorereturnvalues. Forexample,thefollowingisthefunction
signatureofthe
nc_open
routineintheNetCDFlibrary. Notehowthe
NetCDFfileidentifierisreturnedinthe
ncidp
argument.
int nc_open (const char *path, , int t omode, int *ncidp); /* C C syntax x */
ThefollowingshowsthesignatureofthecorrespondingMATLABfunction,
netcdf.open
.LikeitsNetCDFClibrarycounterpart,theMATLABNetCDF
functionacceptsacharacterstringthatspecifiesthefilenameanda
constantthatspecifiestheaccessmode.Note,however,thattheMATLAB
netcdf.open
functionreturnsthefileidentifier,
ncid
,asareturnvalue.
ncid = = netcdf.open(filename, mode)
ToseealistofallthefunctionsintheMATLABNetCDFpackage,seethe
netcdf
referencepage.
ExploringtheContentsofaNetCDFFile. Thisexampleshowshowtouse
theMATLABNetCDFfunctionstoexplorethecontentsofaNetCDFfile.The
sectionusestheexampleNetCDFfileincludedwithMATLAB,
example.nc
,
asanillustration. ForanexampleofreadingdatafromaNetCDFfile,see
“ReadingDatafromaNetCDFFile”onpage2-64
1
OpentheNetCDFfileusingthe
netcdf.open
function. Thisfunction
returnsanidentifierthatyouusethereaftertorefertothefile. The
exampleopensthefileforread-onlyaccess,butyoucanspecifyotheraccess
modes.Formoreinformationaboutmodes,see
netcdf.open
.
ncid = = netcdf.open('example.nc','NC_NOWRITE');
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ImportingScientificDataFiles
2
Explorethecontentsofthefileusingthe
netcdf.inq
function. This
functionreturnsthenumberofdimensions,variables,andglobalattributes
inthefile,andreturnstheidentifieroftheunlimiteddimensioninthefile.
(Anunlimiteddimensioncangrow.)
[ndims,nvars,natts,unlimdimID]= netcdf.inq(ncid)
ndims =
3
nvars =
3
natts =
1
unlimdimID =
-1
3
Getmoreinformationaboutthedimensions,variables,andglobal
attributesinthefilebyusingNetCDFinquiryfunctions. Forexample,
togetinformationabouttheglobalattribute,firstgetthenameofthe
attribute,usingthe
netcdf.inqAttName
function.Afteryougetthename,
'creation_date'
inthiscase,youcanusethe
netcdf.inqAtt
functionto
getinformationaboutthedatatypeandlengthoftheattribute.
Togetthenameofanattribute,youmustspecifytheIDofthevariable
theattributeisassociatedwithandtheattributenumber. Toaccessa
globalattribute,whichisn’tassociatedwithaparticularvariable,use
theconstant
'NC_GLOBAL'
asthevariableID.Theattributenumberis
azero-basedindexthatidentifiestheattribute. Forexample,thefirst
attributehastheindexvalue
0
,andsoon.
global_att_name = = netcdf.inqAttName(ncid,netcdf.getConstant('NC_GLOBAL'),0)
2-61
2
Importing Data
global_att_name =
creation_date
[xtype attlen] ] = = netcdf.inqAtt(ncid,netcdf.getConstant('NC_GLOBAL'),global_att_name)
xtype =
2
attlen =
11
4
Getthevalueoftheattribute,usingthe
netcdf.getAtt
function.
global_att_value = = netcdf.getAtt(ncid,netcdf.getConstant('NC_GLOBAL'),global_att_name)
global_att_value =
29-Mar-2010
5
Getinformationaboutthedimensionsdefinedinthefilethroughaseries
ofcallsto
netcdf.inqDim
. Thisfunctionreturnsthenameandlengthof
thedimension. The
netcdf.inqDim
functionrequiresthedimensionID,
whichisazero-basedindexthatidentifiesthedimensions. Forexample,
thefirstdimensionhastheindexvalue
0
,andsoon.
[dimname, dimlen] = = netcdf.inqDim(ncid,0)
dimname =
x
dimlen =
50
2-62
ImportingScientificDataFiles
6
Getinformationaboutthevariablesinthefilethroughaseriesofcallsto
netcdf.inqVar
.Thisfunctionreturnsthename,datatype,dimension
ID,andthenumberofattributesassociatedwiththevariable. The
netcdf.inqVar
functionrequiresthevariableID,whichisazero-based
indexthatidentifiesthevariables. Forexample,thefirstvariablehas
theindexvalue
0
,andsoon.
[varname, vartype, , dimids, natts] = = netcdf.inqVar(ncid,0)
varname =
avagadros_number
vartype =
6
dimids =
[]
natts =
1
Thedatatypeinformationreturnedin
vartype
isthenumericvalueof
theNetCDFdatatypeconstants,suchas,
NC_INT
and
NC_BYTE
.Seethe
NetCDFdocumentationforinformationabouttheseconstants.
2-63
2
Importing Data
ReadingDatafromaNetCDFFile. Afteryouunderstandthecontentsofa
NetCDFfile,byusingtheinquiryfunctions,youcanretrievethedatafrom
thevariablesandattributesinthefile. Toreadthedataassociatedwith
thevariable
avagadros_number
intheexamplefile,usethe
netcdf.getVar
function. ThefollowingexampleusestheNetCDFfileidentifierreturned
intheprevioussection,“ExploringtheContentsofaNetCDFFile”onpage
2-60.ThevariableIDisazero-basedindexthatidentifiesthevariables.For
example,thefirstvariablehastheindexvalue
0
,andsoon. (Tolearnhow
towritedatatoaNetCDFfile,see“Exporting(Writing)DatatoaNetCDF
File”onpage3-36.)
A_number = netcdf.getVar(ncid,0)
A_number =
6.0221e+023
TheNetCDFfunctionsautomaticallychoosetheMATLABclassthatbest
matchestheNetCDFdatatype,butyoucanalsospecifytheclassofthereturn
databyusinganoptionalargumentto
netcdf.getVar
. Thefollowingtable
showsthedefaultmapping.FormoreinformationaboutNetCDFdatatypes,
seetheNetCDFCInterfaceGuide.
NetCDFDataType
MATLABClass
Notes
NC_BYTE
int8
or
uint8
NetCDFinterpretsbytedataas
eithersignedorunsigned.
NC_CHAR
char
NC_SHORT
int16
NC_INT
int32
NC_FLOAT
single
NC_DOUBLE
double
ImportingFlexibleImageTransportSystem(FITS)
Files
TheFITSfileformatisthestandarddataformatusedinastronomy,
endorsedbybothNASAandtheInternationalAstronomicalUnion(IAU).
2-64
ImportingScientificDataFiles
FormoreinformationabouttheFITSstandard,gototheFITSWebsite,
http://fits.gsfc.nasa.gov/
.
TheFITSfileformatisdesignedtostorescientificdatasetsconsistingof
multidimensionalarrays(1-Dspectra,2-Dimages,or3-Ddatacubes)and
two-dimensionaltablescontainingrowsandcolumnsofdata.Adatafilein
FITSformatcancontainmultiplecomponents,eachmarkedbyanASCIItext
headerfollowedbybinarydata.ThefirstcomponentinaFITSfileisknown
astheprimary,whichcanbefollowedbyanynumberofothercomponents,
calledextensions,inFITSterminology. Foracompletelistofextensions,
see
fitsread
.
TogetinformationaboutthecontentsofaFlexibleImageTransportSystem
(FITS)file,usethe
fitsinfo
function. The
fitsinfo
functionreturnsa
structurecontainingtheinformationaboutthefileanddetailedinformation
aboutthedatainthefile.
ToimportdataintotheMATLABworkspacefromaFlexibleImageTransport
System(FITS)file,usethe
fitsread
function. Usingthisfunction,youcan
importtheprimarydatainthefileoryoucanimportthedatainanyofthe
extensionsinthefile,suchasthe
Image
extension,asshowninthisexample.
1
DeterminewhichextensionstheFITSfilecontains,usingthe
fitsinfo
function.
info = = fitsinfo('tst0012.fits')
info =
Filename: 'matlabroot\tst0012.fits'
FileModDate: '12-Mar-2001 19:37:46'
FileSize: 109440
Contents: {'Primary'
'Binary Table'
'Unknown'
'Image'
'ASCII T
PrimaryData: [1x1 struct]
BinaryTable: [1x1 struct]
Unknown: [1x1 struct]
Image: [1x1 struct]
AsciiTable: [1x1 struct]
2-65
2
Importing Data
The
info
structureshowsthatthefilecontainsseveralextensionsincluding
the
Binary Table
,
ASCII Table
,and
Image
extensions.
2
Readdatafromthefile.
Toreadthe
Primary
datainthefile,specifythefilenameastheonly
argument:
pdata = fitsread('tst0012.fits');
Toreadanyoftheextensionsinthefile,youmustspecifythenameofthe
extensionasanoptionalparameter.Thisexamplereadsthe
Binary Table
extensionfromtheFITSfile:
bindata = = fitsread('tst0012.fits','binarytable');
ImportingHierarchicalDataFormat(HDF5)Files
HierarchicalDataFormat,Version5,(HDF5)isageneral-purpose,
machine-independentstandardforstoringscientificdatainfiles,developed
bytheNationalCenterforSupercomputingApplications(NCSA).HDF5is
usedbyawiderangeofengineeringandscientificfieldsthatwantastandard
waytostoredatasothatitcanbeshared. Formoreinformationaboutthe
HDF5fileformat,readtheHDF5documentationavailableattheHDFWeb
site(
http://www.hdfgroup.org
).
MATLABprovidestwomethodstoimportdatafromanHDF5file:
• High-levelfunctionsthatmakeiteasytoimportdata,whenworkingwith
numericdatasets
• Low-levelfunctionsthatenablemorecompletecontrolovertheimporting
process,byprovidingaccesstotheroutinesintheHDF5Clibrary
NoteForinformationaboutimportingtoHDF4files,whichhaveacompletely
separate,incompatibleformat,see“ImportingHierarchicalDataFormat
(HDF4)Files”onpage2-73.
2-66
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