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made julia 0.4 compatible
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@meggart
meggart committed Apr 2, 2015
1 parent 9014a35 commit 742f13f
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Showing 5 changed files with 71 additions and 72 deletions.
2 changes: 1 addition & 1 deletion REQUIRE
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
julia 0.3-
julia 0.4-
BinDeps
@osx Homebrew
Compat
76 changes: 38 additions & 38 deletions src/NetCDF.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,22 +23,22 @@ type NcDim
ncid::Integer
dimid::Integer
varid::Integer
name::String
name::ASCIIString
dimlen::Integer
vals::AbstractArray
atts::Dict{Any,Any}
atts::Dict
end

NcDim(name::String,dimlength::Integer;values::Union(AbstractArray,Number)=[],atts::Dict{Any,Any}=Dict{Any,Any}())=
NcDim(name::AbstractString,dimlength::Integer;values::Union(AbstractArray,Number)=[],atts::Dict=Dict{Any,Any}())=
begin
(length(values)>0 && length(values)!=dimlength) ? error("Dimension value vector must have the same length as dimlength!") : nothing
NcDim(-1,-1,-1,name,dimlength,values,atts)
NcDim(-1,-1,-1,ascii(name),dimlength,values,atts)
end

NcDim(name::String,values::AbstractArray;atts::Dict{Any,Any}=Dict{Any,Any}())=
NcDim(name,length(values),values=values,atts=atts)
NcDim(name::String,values::AbstractArray,atts::Dict{Any,Any})=
NcDim(name,length(values),values=values,atts=atts)
NcDim(name::AbstractString,values::AbstractArray;atts::Dict=Dict())=
NcDim(ascii(name),length(values),values=values,atts=atts)
NcDim(name::AbstractString,values::AbstractArray,atts::Dict)=
NcDim(ascii(name),length(values),values=values,atts=atts)


type NcVar
Expand All @@ -47,33 +47,33 @@ type NcVar
ndim::Integer
natts::Integer
nctype::Integer
name::String
name::ASCIIString
dimids::Array{}
dim::Array{NcDim}
atts::Dict{Any,Any}
atts::Dict
compress::Integer
end

function NcVar(name::String,dimin::Union(NcDim,Array{NcDim,1});atts::Dict{Any,Any}=Dict{Any,Any}(),t::Union(DataType,Integer)=Float64,compress::Integer=-1)
dim=[dimin]
return NcVar(-1,-1,length(dim),length(atts), typeof(t)==DataType ? jltype2nctype[t] : t,name,Array(Int,length(dim)),dim,atts,compress)
function NcVar(name::AbstractString,dimin::Union(NcDim,Array{NcDim,1});atts::Dict=Dict{Any,Any}(),t::Union(DataType,Integer)=Float64,compress::Integer=-1)
dim=[dimin;]
return NcVar(-1,-1,length(dim),length(atts), typeof(t)==DataType ? jltype2nctype[t] : t,ascii(name),Array(Int,length(dim)),dim,atts,compress)
end
NcVar(name::String,dimin::Union(NcDim,Array{NcDim,1}),atts::Dict{Any,Any},t::Union(DataType,Integer)=Float64)=NcVar(-1,-1,length(dimin),length(atts), typeof(t)==DataType ? jltype2nctype[t] : t,name,Array(Int,length(dimin)),dimin,atts,-1)
NcVar(name::AbstractString,dimin::Union(NcDim,Array{NcDim,1}),atts::Dict,t::Union(DataType,Integer)=Float64)=NcVar(-1,-1,length(dimin),length(atts), typeof(t)==DataType ? jltype2nctype[t] : t,ascii(name),Array(Int,length(dimin)),dimin,atts,-1)

type NcFile
ncid::Integer
nvar::Integer
ndim::Integer
ngatts::Integer
vars::Dict{String,NcVar}
dim::Dict{String,NcDim}
gatts::Dict{Any,Any}
vars::Dict{ASCIIString,NcVar}
dim::Dict{ASCIIString,NcDim}
gatts::Dict
nunlimdimid::Integer
name::String
omode::Uint16
in_def_mode::Bool
end
NcFile(ncid::Integer,nvar::Integer,ndim::Integer,ngatts::Integer,vars::Dict{String,NcVar},dim::Dict{String,NcDim},gatts::Dict{Any,Any},nunlimdimid::Integer,name::String,omode::Uint16)=NcFile(ncid,nvar,ndim,ngatts,vars,dim,gatts,nunlimdimid,name,omode,false)
NcFile(ncid::Integer,nvar::Integer,ndim::Integer,ngatts::Integer,vars::Dict{ASCIIString,NcVar},dim::Dict{ASCIIString,NcDim},gatts::Dict{Any,Any},nunlimdimid::Integer,name::String,omode::Uint16)=NcFile(ncid,nvar,ndim,ngatts,vars,dim,gatts,nunlimdimid,name,omode,false)

include("netcdf_helpers.jl")

Expand Down Expand Up @@ -179,27 +179,27 @@ function putvar{T<:Integer}(nc::NcFile,varname::String,vals::Array;start::Array{
haskey(nc.vars,varname) ? nothing : error("No variable $varname in file $nc.name")
nc.vars[varname].ndim==length(start) ? nothing : error("Length of start vector does not equal number of NetCDF variable dimensions")
nc.vars[varname].ndim==length(count) ? nothing : error("Length of count vector does not equal number of NetCDF variable dimensions")
start=int(start).-1
start=map(Int,start).-1
for i=1:length(start)
count[i] = count[i] < 0 ? nc.vars[varname].dim[i].dimlen - start[i] : count[i]
start[i]+count[i] > nc.vars[varname].dim[i].dimlen ? error("In dimension $(nc.vars[varname].dim[i].name) start+count exceeds dimension bounds: $(start[i])+$(count[i]) > $(nc.vars[varname].dim[i].dimlen)") : nothing
end
count=uint(count[length(count):-1:1])
start=uint(start[length(start):-1:1])
count=map(UInt,count[length(count):-1:1])
start=map(UInt,start[length(start):-1:1])
x=vals
varid=nc.vars[varname].varid
if nc.vars[varname].nctype==NC_DOUBLE
_nc_put_vara_double_c(ncid,varid,start,count,float64(x))
_nc_put_vara_double_c(ncid,varid,start,count,map(Float64,x))
elseif nc.vars[varname].nctype==NC_FLOAT
_nc_put_vara_float_c(ncid,varid,start,count,float32(x))
_nc_put_vara_float_c(ncid,varid,start,count,map(Float32,x))
elseif nc.vars[varname].nctype==NC_INT
_nc_put_vara_int_c(ncid,varid,start,count,int32(x))
_nc_put_vara_int_c(ncid,varid,start,count,map(Int32,x))
elseif nc.vars[varname].nctype==NC_SHORT
_nc_put_vara_short_c(ncid,varid,start,count,int16(x))
_nc_put_vara_short_c(ncid,varid,start,count,map(Int16,x))
elseif nc.vars[varname].nctype==NC_CHAR
_nc_put_vara_text_c(ncid,varid,start,count,ascii(x))
elseif nc.vars[varname].nctype==NC_BYTE
_nc_put_vara_schar_c(ncid,varid,start,count,int8(x))
_nc_put_vara_schar_c(ncid,varid,start,count,map(Int8,x))
end
NC_VERBOSE ? println("Successfully wrote to file ",ncid) : nothing
end
Expand Down Expand Up @@ -232,9 +232,9 @@ function ncclose()
end
end

function create(name::String,varlist::Union(Array{NcVar},NcVar);gatts::Dict{Any,Any}=Dict{Any,Any}(),mode::Uint16=NC_NETCDF4)
function create(name::String,varlist::Union(Array{NcVar},NcVar);gatts::Dict=Dict{Any,Any}(),mode::Uint16=NC_NETCDF4)
ida=Array(Int32,1)
vars=Dict{String,NcVar}();
vars=Dict{ASCIIString,NcVar}();
#Create the file
_nc_create_c(name,mode,ida);
id=ida[1];
Expand All @@ -250,9 +250,9 @@ function create(name::String,varlist::Union(Array{NcVar},NcVar);gatts::Dict{Any,
end
end
nunlim=0;
ndim=int32(length(dims));
ndim=Int32(length(dims));
#Create Dimensions in the file
dim=Dict{String,NcDim}();
dim=Dict{ASCIIString,NcDim}();
for d in dims
dima=Array(Int32,1);
NC_VERBOSE? println("Dimension length ", d.dimlen) : nothing
Expand All @@ -279,9 +279,9 @@ function create(name::String,varlist::Union(Array{NcVar},NcVar);gatts::Dict{Any,
i=i+1
end
vara=Array(Int32,1);
dumids=int32(v.dimids)
dumids=map(Int32,v.dimids)
NC_VERBOSE ? println(dumids) : nothing
_nc_def_var_c(id,v.name,int32(v.nctype),v.ndim,int32(dumids[v.ndim:-1:1]),vara);
_nc_def_var_c(id,v.name,Int32(v.nctype),v.ndim,map(Int32,dumids[v.ndim:-1:1]),vara);
v.varid=vara[1];
vars[v.name]=v;
if v.compress > -1
Expand All @@ -290,7 +290,7 @@ function create(name::String,varlist::Union(Array{NcVar},NcVar);gatts::Dict{Any,
v.compress=-1
else
v.compress=max(v.compress,9)
_nc_def_var_deflate_c(int32(id),int32(v.varid),int32(1),int32(1),int32(v.compress));
_nc_def_var_deflate_c(Int32(id),Int32(v.varid),Int32(1),Int32(1),Int32(v.compress));
end
end
putatt(id,v.varid,v.atts)
Expand Down Expand Up @@ -345,13 +345,13 @@ function open(fil::String; mode::Integer=NC_NOWRITE, readdimvar::Bool=false)
(ndim,nvar,ngatt,nunlimdimid)=_ncf_inq(ncid)
NC_VERBOSE ? println(ndim,nvar,ngatt,nunlimdimid) : nothing
#Create ncdf object
ncf=NcFile(ncid,nvar-ndim,ndim,ngatt,Dict{String,NcVar}(),Dict{String,NcDim}(),Dict{Any,Any}(),nunlimdimid,abspath(fil),mode)
ncf=NcFile(ncid,nvar-ndim,ndim,ngatt,Dict{ASCIIString,NcVar}(),Dict{ASCIIString,NcDim}(),Dict{Any,Any}(),nunlimdimid,abspath(fil),mode)
#Read global attributes
ncf.gatts=_nc_getatts_all(ncid,NC_GLOBAL,ngatt)
#Read dimensions
for dimid = 0:ndim-1
(name,dimlen)=_nc_inq_dim(ncid,dimid)
ncf.dim[name]=NcDim(ncid,dimid,-1,name,dimlen,[1:dimlen],Dict{Any,Any}())
ncf.dim[name]=NcDim(ncid,dimid,-1,name,dimlen,[1:dimlen;],Dict{Any,Any}())
end
#Read variable information
for varid = 0:nvar-1
Expand All @@ -366,7 +366,7 @@ function open(fil::String; mode::Integer=NC_NOWRITE, readdimvar::Bool=false)
vdim[i]=ncf.dim[getdimnamebyid(ncf,did)]
i=i+1
end
ncf.vars[name]=NcVar(ncid,varid,vndim,natts,nctype,name,int(dimids[vndim:-1:1]),vdim[vndim:-1:1],atts,0)
ncf.vars[name]=NcVar(ncid,varid,vndim,natts,nctype,name,map(Int,dimids[vndim:-1:1]),vdim[vndim:-1:1],atts,0)
end
readdimvar==true ? _readdimvars(ncf) : nothing
currentNcFiles[abspath(ncf.name)]=ncf
Expand Down Expand Up @@ -455,12 +455,12 @@ function nccreate(fil::String,varname::String,dims...;atts::Dict=Dict{Any,Any}()
end
# Create variable
vara=Array(Int32,1);
dumids=int32(v.dimids)
dumids=map(Int32,v.dimids)
if (!nc.in_def_mode)
_nc_redef_c(nc.ncid)
nc.in_def_mode=true
end
_nc_def_var_c(nc.ncid,v.name,v.nctype,v.ndim,int32(dumids[v.ndim:-1:1]),vara);
_nc_def_var_c(nc.ncid,v.name,v.nctype,v.ndim,map(Int32,dumids[v.ndim:-1:1]),vara);
v.varid=vara[1];
nc.vars[v.name]=v;
putatt(nc.ncid,v.varid,atts)
Expand Down
2 changes: 1 addition & 1 deletion src/netcdf_c_wrappers.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ const NC_NETCDF4 =0x1000 # Use netCDF-4/HDF5 format. Mode flag for nc_creat
@osx_only begin
# Add Homebrew/lib to the DL_LOAD_PATH
const brew_prefix = Pkg.dir("Homebrew", "deps", "usr")
push!(DL_LOAD_PATH, joinpath(brew_prefix, "lib"))
push!(Libdl.DL_LOAD_PATH, joinpath(brew_prefix, "lib"))
end
ncname= @windows ? "netcdf" : "libnetcdf"

Expand Down
14 changes: 7 additions & 7 deletions src/netcdf_helpers.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ end
function _nc_inq_dim(id::Integer,idim::Integer)
namea=Array(Uint8,NC_MAX_NAME+1);lengtha=Array(Int32,1)
NetCDF._nc_inq_dim_c(id,idim,namea,lengtha)
name=bytestring(convert(Ptr{Uint8}, namea))
name=bytestring(pointer(namea))
dimlen=lengtha[1]
NC_VERBOSE ? println("Successfully read from file") : nothing
NC_VERBOSE ? println("name=",name," dimlen=",dimlen) : nothing
Expand Down Expand Up @@ -54,7 +54,7 @@ function _nc_inq_attname(ncid::Integer,varid::Integer,attnum::Integer)
# Get attribute name from attribute number
namea=Array(Uint8,NC_MAX_NAME+1)
_nc_inq_attname_c(ncid,varid,attnum,namea)
name=bytestring(convert(Ptr{Uint8}, namea))
name=bytestring(pointer(namea))
NC_VERBOSE ? println("Successfully read attribute name") : nothing
NC_VERBOSE ? println("name=",name) : nothing
return name
Expand Down Expand Up @@ -101,11 +101,11 @@ function _nc_put_att(ncid::Integer,varid::Integer,name,val)
elseif (attype==NC_SHORT)
_nc_put_att_short_c(ncid,varid,name,attype,attlen,val)
elseif (attype==NC_INT)
_nc_put_att_int_c(ncid,varid,name,attype,attlen,int32(val))
_nc_put_att_int_c(ncid,varid,name,attype,attlen,map(Int32,val))
elseif (attype==NC_FLOAT)
_nc_put_att_float_c(ncid,varid,name,attype,attlen,val)
elseif (attype==NC_DOUBLE)
_nc_put_att_float_c(ncid,varid,name,NC_FLOAT,attlen,float32(val))
_nc_put_att_float_c(ncid,varid,name,NC_FLOAT,attlen,map(Float32,val))
elseif (attype==NC_BYTE)
_nc_put_att_byte_c(ncid,varid,name,attype,attlen,val)
else
Expand Down Expand Up @@ -154,7 +154,7 @@ function _ncv_inq(nc::NcFile,varid::Integer)
dimids=vndim>0 ? dimida[1:vndim] : []
natts=natta[1]
NC_VERBOSE ? println("Successfully read from file") : nothing
name=bytestring(convert(Ptr{Uint8}, namea))
name=bytestring(pointer(namea))
isdimvar=false
for n in nc.dim
if (n[2].name==name)
Expand Down Expand Up @@ -270,7 +270,7 @@ function parsedimargs(dim)
elseif (typeof(a)<:AbstractArray)
#Assume dimension values are given
if dimvals==nothing
dimvals=float64(a)
dimvals=map(Float64,a)
dimlen=length(dimvals)
else
error ("Dimension values of $name defined more than once")
Expand All @@ -289,7 +289,7 @@ function finalizedim(dimlen,dimvals,dimatts,name)
dimlen=1
end
if ((dimlen!=nothing) & (dimvals==nothing))
dimvals=float64([1:dimlen])
dimvals=map(Float64,[1:dimlen;])
end
if (dimatts==nothing)
dimatts=@Compat.AnyDict("missval"=>-9999)
Expand Down
49 changes: 24 additions & 25 deletions test/runtests.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ end
# Test Medium level Interface
# Test Dimension Creation
d1 = NcDim("Dim1",2;values=[5.0,10.0],atts=@Compat.AnyDict("units"=>"deg C"));
d2 = NcDim("Dim2",[1:10]);
d2 = NcDim("Dim2",[1:10;]);
d3 = NcDim("Dim3",20;atts=@Compat.AnyDict("max"=>10));

# Test Variable creation
Expand All @@ -31,16 +31,16 @@ nc3 = NetCDF.create("nc3.nc",vt,mode=NC_CLASSIC_MODEL);
#Test Adding attributes
NetCDF.putatt(nc1,"v1",@Compat.Dict("Additional String attribute"=>"att"))
NetCDF.putatt(nc1,"global",@Compat.Dict("Additional global attribute"=>"gatt"))
NetCDF.putatt(nc1,"global",@Compat.Dict("Additional Int8 attribute"=>int8(20),
"Additional Int16 attribute"=>int16(20),
"Additional Int32 attribute"=>int32(20),
"Additional Float32 attribute"=>float32(20),
"Additional Float64 attribute"=>float64(20)))
NetCDF.putatt(nc1,"v1", @Compat.Dict("Additional Int8 array attribute"=>int8([1:20]),
"Additional Int16 array attribute"=>int16([1:20]),
"Additional Int32 array attribute"=>int32([1:20]),
"Additional Float32 array attribute"=>float32([1:20]),
"Additional Float64 array attribute"=>float64([1:20])))
NetCDF.putatt(nc1,"global",@Compat.Dict("Additional Int8 attribute"=>Int8(20),
"Additional Int16 attribute"=>Int16(20),
"Additional Int32 attribute"=>Int32(20),
"Additional Float32 attribute"=>Float32(20),
"Additional Float64 attribute"=>Float64(20)))
NetCDF.putatt(nc1,"v1", @Compat.Dict("Additional Int8 array attribute"=>map(Int8,[1:20;]),
"Additional Int16 array attribute"=>map(Int16,[1:20;]),
"Additional Int32 array attribute"=>map(Int32,[1:20;]),
"Additional Float32 array attribute"=>map(Float32,[1:20;]),
"Additional Float64 array attribute"=>map(Float64,[1:20;])))


#Test writing data
Expand Down Expand Up @@ -90,28 +90,28 @@ for fn in ("nc1.nc","nc2.nc","nc3.nc")
end
end

nccreate("nc1.nc","v1","Dim1",[1,2,3],@Compat.AnyDict("units"=>"deg C"),"Dim2",[1:10],"Dim3",20,@Compat.AnyDict("max"=>10),
nccreate("nc1.nc","v1","Dim1",[1,2,3],@Compat.AnyDict("units"=>"deg C"),"Dim2",[1:10;],"Dim3",20,@Compat.AnyDict("max"=>10),
mode=NC_NETCDF4)
nccreate("nc2.nc","v2","Dim1",[1,2,3],@Compat.AnyDict("units"=>"deg C"),"Dim2",[1:10],"Dim3",20,@Compat.AnyDict("max"=>10),
nccreate("nc2.nc","v2","Dim1",[1,2,3],@Compat.AnyDict("units"=>"deg C"),"Dim2",[1:10;],"Dim3",20,@Compat.AnyDict("max"=>10),
atts=@Compat.AnyDict("a1"=>"varatts"),gatts=@Compat.AnyDict("Some global attributes"=>2010),mode=NC_64BIT_OFFSET)
nccreate("nc2.nc","v3","Dim1",mode=NC_CLASSIC_MODEL)
tlist = [Float64, Float32, Int32, Int16, Int8]
for i = 1:length(tlist)
nccreate("nc3.nc","vt$i","Dim2",[1:10],t=tlist[i])
nccreate("nc3.nc","vt$i","Dim2",[1:10;],t=tlist[i])
end

ncputatt("nc1.nc","v1",@Compat.Dict("Additional String attribute"=>"att"))
ncputatt("nc1.nc","global",@Compat.Dict("Additional global attribute"=>"gatt"))
ncputatt("nc1.nc","global",@Compat.Dict("Additional Int8 attribute"=>int8(20),
"Additional Int16 attribute"=>int16(20),
"Additional Int32 attribute"=>int32(20),
"Additional Float32 attribute"=>float32(20),
"Additional Float64 attribute"=>float64(20)))
ncputatt("nc1.nc","v1", @Compat.Dict("Additional Int8 array attribute"=>int8([1:20]),
"Additional Int16 array attribute"=>int16([1:20]),
"Additional Int32 array attribute"=>int32([1:20]),
"Additional Float32 array attribute"=>float32([1:20]),
"Additional Float64 array attribute"=>float64([1:20])))
ncputatt("nc1.nc","global",@Compat.Dict("Additional Int8 attribute"=>Int8(20),
"Additional Int16 attribute"=>Int16(20),
"Additional Int32 attribute"=>Int32(20),
"Additional Float32 attribute"=>Float32(20),
"Additional Float64 attribute"=>Float64(20)))
ncputatt("nc1.nc","v1", @Compat.Dict("Additional Int8 array attribute"=>map(Int8,[1:20;]),
"Additional Int16 array attribute"=>map(Int16,[1:20;]),
"Additional Int32 array attribute"=>map(Int32,[1:20;]),
"Additional Float32 array attribute"=>map(Float32,[1:20;]),
"Additional Float64 array attribute"=>map(Float64,[1:20;])))

#First generate the data
x1 = rand(2,10,20)
Expand All @@ -137,5 +137,4 @@ for i=1:length(tlist)
end


ncclose()

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