Class: CodeRunner::Trinity::NetcdfSmartReader

Inherits:
Object
  • Object
show all
Defined in:
lib/trinitycrmod/read_netcdf.rb

Instance Method Summary collapse

Constructor Details

#initialize(file) ⇒ NetcdfSmartReader

Returns a new instance of NetcdfSmartReader.



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# File 'lib/trinitycrmod/read_netcdf.rb', line 40

def initialize(file)
  @file = file
end

Instance Method Details

#axiskit(variable, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 102

def axiskit(variable, options)
  case variable
  when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval'
    return GraphKit::AxisKit.autocreate(data: GSL::Vector.linspace(1, sz=@file.dim(variable).length, sz), title: variable)
  end
  GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, ''))
end

#check_no_r(non_flat_dims) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 117

def check_no_r(non_flat_dims)
  raise "Please specify the r index for real or imaginary" if non_flat_dims.include? @file.dim('r')
end

#dim_end(name, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 89

def dim_end(name, options)
  sym = name.to_sym
  if i=options[sym + :_index]
    return i-1
  elsif i=options[sym + :_element]
    return i
  elsif i=options[sym + :max]
    return i
  else
    return -1
  end
end

#dim_start(name, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 74

def dim_start(name, options)
  sym = name.to_sym
  if i=options[sym + :_index]
    return i-1
  elsif i=options[sym + :_element]
    return i
  elsif i=options[sym + :min]
    return i
  else
    return 0
  end
end

#dimension_variable_name(n) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 109

def dimension_variable_name(n)
  case n
  when 't','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval'
    n
  else
    raise "Unknown dimension #{n}"
  end
end

#dimensions(varname) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 43

def dimensions(varname)
  #p 'varname', varname
  raise "Unknown variable #{varname}" unless @file.var(varname)
  @file.var(varname).dims
end

#ends(dims, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 86

def ends(dims, options)
  dims.map{|d| dim_end(d.name, options)}
end

#graphkit(variable, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 120

def graphkit(variable, options)
  non_flat_dims=dimensions(variable).find_all{|dim| dim_start(dim.name, options) != dim_end(dim.name, options) and dim.length != 1}
  check_no_r(non_flat_dims)
  axiskits = non_flat_dims.map{|dim| dimvar = dimension_variable_name(dim.name); axiskit(dimvar, options)} + [axiskit(variable, options)]
  hash = {}
  axes = [:x, :y, :z, :f]
  axiskits.each_with_index{|ax, i| hash[axes[i]] = ax}
  kit = GraphKit.autocreate(hash)
  opts = options.dup
  opts.delete(:modify_variable)
  opts.delete(:graphkit_name)
  #kit.data[0].title += " with options: " + opts.to_s
  kit.data[0].title += " " + opts.to_s.gsub(/_(index|element)/, '')
  if kit.zlabel
    kit.zlabel = "'#{kit.zlabel}' rotate by 90"
    #kit.zlabel = nil
  end
  kit
end

#read_variable(varname, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 48

def read_variable(varname, options)
  #start = get_start(dims, options)
  dims = dimensions(varname)
  narray = @file.var(varname).get('start'=>starts(dims, options), 'end'=>ends(dims, options))
  if options[:modify_variable]
    myhsh = dims.inject({}){|hsh, dim|
      opts = options.dup
      opts[:modify_variable] = nil
      dimval = read_variable(dimension_variable_name(dim.name), opts)
      hsh[dim.name] = dimval
      hsh
    }
    narray = options[:modify_variable].call(varname, narray, myhsh)
  elsif options[:invert_matrix]
    narray = GSL::Linalg::LU.invert(narray.to_gm_view).to_na_ref
  end
  shape = narray.shape
  shape.delete_if{|i| i==1}
  #p 'shape', shape; STDIN.gets
  narray.reshape!(*shape)
  narray

end

#starts(dims, options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 71

def starts(dims, options)
  dims.map{|d| dim_start(d.name, options)}
end