netcdf-nmatrix 0.8.0

data/ruby-netcdf.gemspec

@@ -0,0 +1,33 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "netcdf-nmatrix"
+  spec.version       = Ruby::Netcdf::VERSION
+  spec.authors           = ["Takeshi Horinouchi", "Tsuyoshi Koshiro",\
+    "Shigenori Otsuka", "Seiya Nishizawa", "T Sakakima", "Edmund Highcock"]
+  spec.email            = ['edmundhighcock@users.sourceforge.net']
+
+  #if spec.respond_to?(:metadata)
+  #  spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com' to prevent pushes to rubygems.org, or delete to allow pushes to any server."
+  #end
+
+  spec.summary          = %q{Ruby interface to NetCDF which uses NMatrix}
+  spec.description      = %q{A Ruby interface for reading and writing NetCDF files. NetCDF-NMatrix is a rewrite of the previous ruby-netcdf gem which uses NMatrix instead of NArray, and so is compatible with SciRuby.}
+
+  spec.homepage         = 'https://github.com/edmundhighcock/ruby-netcdf'
+  spec.licenses         = ["GFD Dennou Club"]
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.test_files    = spec.files.grep(%r{^(test|demo)/})
+  #spec.bindir        = "exe"
+  #spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.required_ruby_version = Gem::Requirement.new(">= 1.6")
+  spec.add_runtime_dependency(%q<nmatrix>, [">= 0.2"])
+
+  spec.extensions << "extconf.rb"
+end

data/test/aref_aset.rb

@@ -0,0 +1,37 @@
+require 'numru/netcdf'
+include NumRu
+s = 'tmp.nc'
+f = NetCDF.create(s)
+f.redef
+dx = f.def_dim('x',5)
+dy = f.def_dim('y',3)
+v = f.def_var('x','sfloat',[dx])
+v2 = f.def_var('x2',NArray::SFLOAT,[dx])
+vxy = f.def_var('xy','sfloat',[dx,dy])
+f.enddef
+v.put([1,2,3,4,5])
+p 'testing []= ...'
+v[{0..3=>2}]=[100,500]
+v[1]=999
+v[3..4]=[-99,-99]
+v2.put(666)
+v2[0..2]=777
+vxy.put(NArray.sfloat(5,3).indgen!)
+vxy[[2,0],[0,2,1]] = [[1,2],[3,4],[5,6]]
+vxy[1,[2,0,1]] = [10,20,30]
+vxy[[4,3],2] = [100,200]
+
+f.close
+
+f = NetCDF.open(s)
+v = f.var('x')
+p 'testing [] ...'
+p '*0*',v[{0..3=>2}]
+p '*1*',v[1]
+p '*2*',v[3..4],v.rank
+p '*3*',v[[2,0,0]]
+vxy = f.var('xy')
+p '*4*',vxy[[2,0],[0,2,1]]
+p '*5*',vxy[1,[2,0,1]]
+p '*6*',vxy[[4,3],2]
+f.close

data/test/char_var.rb

@@ -0,0 +1,25 @@
+## test of "char" variables
+
+require 'numru/netcdf'
+include NumRu
+s = 'tmp.nc'
+f = NetCDF.create(s)
+d = f.def_dim('x',5)
+v = f.def_var('x','char',[d])
+tv = f.def_var('text','char',[d])
+f.enddef
+v.put( NArray.byte(5).indgen! )
+tv.put( NArray.to_na("hello","byte",5) )
+tv.put( NArray.to_na("LO","byte",2), 'start'=>[3] )
+tv.put( NArray.to_na("H","byte",1), 'index'=>[0] )
+f.close
+
+f = NetCDF.open(s)
+v = f.var('x')
+p v.get
+tv = f.var('text')
+p tv.get
+p tv.get.to_s
+
+
+

data/test/clone.rb

@@ -0,0 +1,54 @@
+require 'numru/netcdf'
+include NumRu
+s = 'tmp.nc'
+#f = NetCDF.new(s,'rw')
+f = NetCDF.create(s)
+f.redef
+d = f.def_dim('x',3)
+v = f.def_var('x','sfloat',[d])
+a = f.put_att('long_name','xx')
+f.enddef
+v.put([1,2,3])
+f.taint
+f.freeze
+f2 = f.clone
+p 'netcdf  clone'
+p f.path, f2.path   
+p f.tainted?, f2.tainted?, f.frozen?, f2.frozen?  
+
+p 'netcdf  dup'
+f3 = f.dup
+p f.tainted?, f3.tainted?, f.frozen?, f3.frozen?  
+
+p 'netcdfdim'
+d.taint
+d2 = d.clone
+d3 = d.dup
+p d.tainted?, d2.tainted?, d3.tainted?
+
+p 'netcdfvar'
+v.taint
+v2 = v.clone
+v3 = v.dup
+p v.tainted?, v2.tainted?, v3.tainted?
+
+p 'netcdfatt'
+a.taint
+a2 = a.clone
+a3 = a.dup
+p a.tainted?, a2.tainted?, a3.tainted?
+
+f.close
+
+p 'narray (for reference)'
+a = NArray.float(3)
+a.taint
+b = a.clone
+p a.tainted?, b.tainted?  
+b = a.dup
+p a.tainted?, b.tainted?  
+
+
+
+
+

data/test/create_tmp.rb

@@ -0,0 +1,15 @@
+require 'numru/netcdf'
+
+$DEBUG = true
+include NumRu
+file = NetCDF.create_tmp
+file.def_dim('x',5)
+file.put_att("history", __FILE__ )
+p file.path
+p file.att("history").get
+print "environment variable TEMP ="+(ENV['TEMP'] || '')+"\n"
+file2=file
+print "000\n"
+file.close
+GC.start
+print "aaa\n"

data/test/def_var_with_dim.rb

@@ -0,0 +1,14 @@
+require 'numru/netcdf'
+include NumRu
+file = NetCDF.create("tmp.nc")
+var1 = file.def_var_with_dim("var1","sfloat",[6],["x"])
+var2 = file.def_var_with_dim("var2","sfloat",[6,3],["x","y"])
+var3 = file.def_var_with_dim("var3","sfloat",[3],["y"])
+var3 = file.def_var_with_dim("var4","sfloat",[0],["t"])
+att = var1.put_att("long_name","test")
+file.close
+
+p var1 == nil
+p file == nil
+p att == nil
+p att == att, var1 ==var1, file == file

data/test/factor_offset.rb

@@ -0,0 +1,53 @@
+require 'numru/netcdf'
+include NumRu
+
+s = 'tmp.nc'
+f = NetCDF.create(s)
+
+nx = 10
+d = f.def_dim('x',nx)
+v1 = f.def_var('v1','sint',[d])
+v2 = f.def_var('v2','sint',[d])
+v3 = f.def_var('v3','int',[d])
+v1.put_att('scale_factor',0.1,'sfloat')
+v1.put_att('add_offset',100.0,'sfloat')
+v2.put_att('scale_factor',0.1,'sfloat')
+v2.put_att('add_offset',100.0,'sfloat')
+v3.put_att('scale_factor',0.1,'sfloat')
+v3.put_att('add_offset',100.0,'sfloat')
+f.enddef
+v1.put( NArray.sint(nx).indgen!+100 )
+v2.scaled_put( NArray.float(nx).indgen!+100 )
+v3.scaled_put( NArray.float(nx).indgen!+100 )
+f.close
+
+
+print "** originally unscaled\n"
+f = NetCDF.open(s)
+v1 = f.var('v1')
+v11 = v1.get
+v12 = v1.scaled_get
+p v11
+p v12
+
+print "** originally scaled\n"
+v2 = f.var('v2')
+v21 = v2.get
+v22 = v2.scaled_get
+p v21
+p v22
+
+print "** originally sclaed (int --> double)\n"
+v3 = f.var('v3')
+v31 = v3.get
+v32 = v3.scaled_get
+p v31
+p v32
+
+print "** unpack type fixed to sfloat\n"
+NetCDFVar.unpack_type = NArray::SFLOAT
+v33 = v3.scaled_get
+p v33
+NetCDFVar.unpack_type = NArray::INT
+v33 = v3.scaled_get
+p v33

data/test/putatt.cdl

@@ -0,0 +1,23 @@
+netcdf tmp {
+dimensions:
+	x = 5 ;
+variables:
+	float x(x) ;
+		x:long_name = "test variable" ;
+		x:int_att = 123s ;
+		x:float_att = 0.333333333333333 ;
+		x:float_array = 0.1, 0.2, 30. ;
+		x:sfloat_narray = 0.f, 0.3333333f, 0.6666667f ;
+		x:float_narray = 0., 1., 2. ;
+		x:sint_narray = 0s, 1s, 2s ;
+		x:int2float = 10. ;
+		x:changed = "changed to text" ;
+
+// global attributes:
+		:history = "2001-12-23" ;
+		:int_att = 123s ;
+		:sfloat_att = 0.3333333f ;
+data:
+
+ x = _, _, _, _, _ ;
+}

data/test/putatt.rb

@@ -0,0 +1,56 @@
+require 'numru/netcdf'
+include NumRu
+s = 'tmp.nc'
+f = NetCDF.create(s)
+d = f.def_dim('x',5)
+v = f.def_var('x','sfloat',[d])
+
+require 'date'
+att = f.put_att("history", Date.today.to_s )
+p att.get, f.att("history").get
+att = f.put_att("int_att",123)
+att = f.put_att("sfloat_att",1.0/3.0,'sfloat')
+att = f.put_att("sfloat_att2",2.0/3.0,NArray::SFLOAT)
+att = v.put_att("long_name",'test variable')
+att = v.put_att("int_att",123)
+p att.get, v.att("int_att").get
+att = v.put_att("float_att",1.0/3.0)
+att = v.put_att("float_array",[0.1, 0.2, 30])
+att = v.put_att("sfloat_narray",NArray.sfloat(3).indgen!/3)
+att = v.put_att("float_narray",NArray.float(3).indgen!)
+att = v.put_att("sint_narray",NArray.sint(3).indgen!)
+att = v.put_att("int2float",10,'float')
+att = att = v.put_att("dummy",10,'float')
+att.put('changed to text')
+att.name = 'changed'
+begin
+   v.put_att("destined_to_fail",9.8,'complex')
+rescue
+   print "*1* exception raised as expected -- (",
+         __FILE__,":",__LINE__,") ", $!,"\n"
+end
+begin
+   v.put_att("destined_to_fail",9.8,'string')
+rescue
+   print "*2* exception raised as expected -- (",
+         __FILE__,":",__LINE__,") ", $!,"\n"
+end
+
+begin
+   v.put_att("destined_to_fail",'hello','int')
+rescue
+   print "*3* exception raised as expected -- (",
+         __FILE__,":",__LINE__,") ", $!,"\n"
+end
+
+begin
+   v.put_att("destined_to_fail",[10,30,'sss'])
+rescue
+   print "*4* exception raised as expected -- (",
+         __FILE__,":",__LINE__,") ", $!,"\n"
+end
+
+
+f.close
+
+print `ncdump tmp.nc`

data/test/test.cdl

@@ -0,0 +1,31 @@
+netcdf test {
+dimensions:
+	x = 15 ;
+	y = 10 ;
+	z = 10 ;
+variables:
+	short test_sint(x) ;
+	byte test_byte(y) ;
+	byte test_byte2(z, y) ;
+	int test_int(y) ;
+	float test_sfloat(z) ;
+	double test_float(y) ;
+	byte test_byte_vara(z, y) ;
+		test_byte_vara:min to max of byte_vara = 0b, 20b ;
+	short test_sint_vara(z, y) ;
+		test_sint_vara:string = "%%%%%" ;
+	int test_int_vara(z, y) ;
+		test_int_vara:min to max of int_vara = 0, 60 ;
+	float test_sfloat_vara(z, y) ;
+		test_sfloat_vara:min to max of float_vara = 0.01f, 5.5f ;
+	double test_float_vara(z, y) ;
+		test_float_vara:min_to max of double_vara = 0.0001, 5.5555 ;
+
+// global attributes:
+		:type_byte = 6b ;
+		:type_short = 222s, 333s, 444s ;
+		:type_int = 2222s, 3333s, 4444s ;
+		:type_float = 2.22f, 3.33f, 4.44f ;
+		:type_double = 2.222, 3.333, 4.444 ;
+		:string = "netCDF for Ruby" ;
+}

data/test/test.rb

@@ -0,0 +1,195 @@
+##require 'numru/netcdf' 
+## // to test before make install -->
+require 'nmatrix'
+require '../netcdfraw'  
+require '../lib/netcdf'
+## <-- to test before make install //
+
+include NumRu
+
+filename = "test.nc"
+print "creating ",filename,"...\n"
+file=NetCDF.create(filename,false,false)
+
+dimx=file.def_dim("x",15)
+dimy=file.def_dim("y",10)
+dimz=file.def_dim("z",10)
+
+batt = file.put_att("type_byte",5,"byte")
+file.put_att("type_short",[222,333,444],"int16")
+file.put_att("type_int",[2222,3333,4444])
+file.put_att("type_float",[2.22,3.33,4.44],"float32")
+file.put_att("type_double",[2.222,3.333,4.444])
+string = file.put_attraw("string","netCDF for Ruby","string")
+batt.put(6,"byte")
+
+int16_var=file.def_var("test_int16","int16",["x"])
+byte_var=file.def_var("test_byte","byte",["y"])
+byte_var2=file.def_var("test_byte2","byte",[dimy,dimz])
+int_var=file.def_var("test_int","int32",["y"])
+sfloat_var=file.def_var("test_sfloat","float32",["z"])
+float_var=file.def_var("test_float","float64",["y"])
+
+a=NMatrix.seq([10], dtype: :int16)
+b=NMatrix.ones([10], dtype: :int16) * 7.0
+c=NMatrix.bindgen([10])
+d=NMatrix.seq([10], dtype: :int32)
+e=NMatrix.ones([10], dtype: :float32) * 1.111
+f=NMatrix.ones([10], dtype: :float64) * 5.5555555
+file.enddef
+file2 = file
+(file2 == file)
+
+
+byte_var.put_var_byte(c)
+int_var.put_var_int(d)
+sfloat_var.put_var_sfloat(e)
+float_var.put_var_float(f)
+
+file.redef
+byte_vara=file.def_var("test_byte_vara","byte",[dimy,dimz]);
+int16_vara=file.def_var("test_int16_vara","int16",["y","z"]);
+int_vara=file.def_var("test_int_vara","int32",["y","z"]);
+sfloat_vara=file.def_var("test_sfloat_vara","float32",["y","z"]);
+float_vara=file.def_var("test_float_vara","float64",["y","z"]);
+file.enddef
+
+byte_vara2 = byte_vara
+(byte_vara2 == byte_vara)
+
+g=NMatrix.bindgen([10,10])
+h=NMatrix.bindgen([2,3])
+gh=NMatrix.ones([1,1], dtype: :byte) * 33
+k=NMatrix.seq([10,10], dtype: :int16)
+l=NMatrix.seq([2,3], dtype: :int16)
+kl=NMatrix.ones([1,1], dtype: :int16) * 44
+m=NMatrix.seq([10,10], dtype: :int32)
+n=NMatrix.seq([2,3], dtype: :int32)
+mn=NMatrix.ones([1,1], dtype: :int32) * 55
+o=NMatrix.ones([10,10], dtype: :float32) * 1.234567
+p=NMatrix.ones([2,3], dtype: :float32) * 2.345678
+op=NMatrix.ones([1,1], dtype: :float32) * 3.4
+q=NMatrix.ones([10,10], dtype: :float64) * 1.234
+r=NMatrix.ones([2,3], dtype: :float64) * 2.345
+qr=NMatrix.ones([1,1], dtype: :float64) * 4.5
+s=NMatrix.ones([2,2], dtype: :float64) * 10.0
+
+
+
+byte_vara.put(g)
+byte_vara.put(h,{"start"=>[3,5]})
+byte_vara.put(g,{"start"=>[0,0],"end"=>[9,9]})
+byte_vara.put(h,{"start"=>[-8,2]})
+byte_vara.put(h,{"start"=>[0,0],"stride"=>[2,3]})
+byte_vara.put(h,{'start'=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+byte_vara.put(gh,{"index"=>[4,7]})
+
+int16_vara.put(k)
+int16_vara.put(l,{"start"=>[3,5]})
+int16_vara.put(k,{"start"=>[0,0],"end"=>[9,9]})
+int16_vara.put(l,{"start"=>[-8,2]})
+int16_vara.put(l,{"start"=>[0,0],"stride"=>[2,3]})
+int16_vara.put(l,{"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+int16_vara.put(kl,{"index"=>[4,7]})
+
+int_vara.put(m)
+int_vara.put(n,{"start"=>[3,5]})
+int_vara.put(m,{"start"=>[0,0],"end"=>[9,9]})
+int_vara.put(n,{"start"=>[-8,2]})
+int_vara.put(n,{"start"=>[0,0],"stride"=>[2,3]})
+int_vara.put(n,{"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+int_vara.put(mn,{"index"=>[4,7]})
+
+sfloat_vara.put(o)
+sfloat_vara.put(p,{"start"=>[3,5]})
+sfloat_vara.put(o,{"start"=>[0,0],"end"=>[9,9]})
+sfloat_vara.put(p,{"start"=>[-8,2]})
+sfloat_vara.put(p,{"start"=>[0,0],"stride"=>[2,3]})
+sfloat_vara.put(p,{"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+sfloat_vara.put(op,{"index"=>[4,7]})
+
+float_vara.put(q)
+float_vara.put(r,{"start"=>[3,5]})
+float_vara.put(q,{"start"=>[0,0],"end"=>[9,9]})
+float_vara.put(r,{"start"=>[-8,2]})
+float_vara.put(r,{"start"=>[0,0],"stride"=>[2,3]})
+float_vara.put(r,{"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+float_vara.put(qr,{"index"=>[4,7]})
+
+float_vara.dim_names
+
+
+na_aaa=byte_vara.get({"start"=>[3,5]})
+na_aab=byte_vara.get({"start"=>[0,0],"end"=>[9,9]})
+na_aac=byte_vara.get({"start"=>[-8,2]})
+na_aad=byte_vara.get({"start"=>[0,0],"stride"=>[2,3]})
+na_aae=byte_vara.get({'start'=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+na_aaf=byte_vara.get({"index"=>[4,7]})
+na_aag=byte_vara.get
+
+na_bba=int16_vara.get({"start"=>[3,5]})
+na_bbb=int16_vara.get({"start"=>[0,0],"end"=>[9,9]})
+na_bbc=int16_vara.get({"start"=>[-8,2]})
+na_bbd=int16_vara.get({"start"=>[0,0],"stride"=>[2,3]})
+na_bbf=int16_vara.get({"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+na_bbg=int16_vara.get({"index"=>[4,7]})
+na_bbh=int16_vara.get
+
+na_cca=int_vara.get({"start"=>[3,5]})
+na_ccb=int_vara.get({"start"=>[0,0],"end"=>[9,9]})
+na_ccc=int_vara.get({"start"=>[-8,2]})
+na_ccd=int_vara.get({"start"=>[0,0],"stride"=>[2,3]})
+na_cce=int_vara.get({"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+na_ccf=int_vara.get({"index"=>[4,7]})
+na_ccg=int_vara.get
+
+na_dda=sfloat_vara.get({"start"=>[3,5]})
+na_ddb=sfloat_vara.get({"start"=>[0,0],"end"=>[9,9]})
+na_ddc=sfloat_vara.get({"start"=>[-8,2]})
+na_ddd=sfloat_vara.get({"start"=>[0,0],"stride"=>[2,3]})
+na_dde=sfloat_vara.get({"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+na_ddf=sfloat_vara.get({"index"=>[4,7]})
+na_ddg=sfloat_vara.get
+
+na_eea=float_vara.get({"start"=>[3,5]})
+na_eeb=float_vara.get({"start"=>[0,0],"end"=>[9,9]})
+na_eec=float_vara.get({"start"=>[-8,2]})
+na_eed=float_vara.get({"start"=>[0,0],"stride"=>[2,3]})
+na_eee=float_vara.get({"start"=>[1,1],"end"=>[3,7],"stride"=>[2,3]})
+na_eef=float_vara.get({"index"=>[4,7]})
+na_eeg=float_vara.get
+
+file.redef
+
+copy_byte = string.copy(byte_vara) 
+copy_byte.put([0,20],"byte") 
+copy_byte.name="new_name"
+
+copy_byte2 = copy_byte
+(copy_byte2 == copy_byte)
+
+copy_int16 = string.copy(int16_vara)
+copy_int16.put("%%%%%")
+copy_int = string.copy(int_vara)
+copy_int.put([0,60],"int32")
+copy_sfloat = string.copy(sfloat_vara)
+copy_sfloat.put([0.01,5.5],"float32")
+copy_float = string.copy(float_vara)
+copy_float.put([0.0001,5.5555],"float64")
+file.enddef
+nm = copy_byte.name
+att0 = string.get
+att1 = copy_byte.get
+att2 = copy_int16.get
+att3 = copy_int.get
+att4 = copy_sfloat.get
+att5 = copy_float.get
+file.fill(true)
+file.fill(false)
+
+float_vara.dim_names
+float_vara.att_names
+
+file.close
+exit(0)
+