class CodeRunner::Trinity::NetcdfSmartReader
Public Class Methods
dimensions()
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# File lib/trinitycrmod/read_netcdf.rb, line 103 def self.dimensions ['t','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval', 'cegrid', 'job', 'conv'] end
new(file)
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# File lib/trinitycrmod/read_netcdf.rb, line 40 def initialize(file) @file = file end
Public Instance Methods
axiskit(variable, options)
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# File lib/trinitycrmod/read_netcdf.rb, line 107 def axiskit(variable, options) case variable when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval', 'job', 'conv' return GraphKit::AxisKit.autocreate( data: GSL::Vector.linspace(1, sz= (de=dim_end(variable,options); de<0 ? de+@file.dim(variable).length : de) - (ds=dim_start(variable,options); ds<0 ? ds+@file.dim(variable).length : ds) + 1, 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/, '').sub(/.*rho.*The definition.*/, 'rho')) end
check_no_r(non_flat_dims)
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# File lib/trinitycrmod/read_netcdf.rb, line 127 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)
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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] or i=options[sym] return i-1 elsif i=options[sym + :_element] return i elsif i=options[sym + :max] #if sym == :conv #return [i, @file.var('conv_final') return i else return -1 end end
dim_start(name, options)
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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] or i = options[sym] 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)
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# File lib/trinitycrmod/read_netcdf.rb, line 119 def dimension_variable_name(n) case n when *self.class.dimensions n else raise "Unknown dimension #{n}" end end
dimensions(varname)
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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)
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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)
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# File lib/trinitycrmod/read_netcdf.rb, line 130 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)/, '') kit.data[0].gp.with = "lp" if kit.zlabel kit.zlabel = "'#{kit.zlabel}' rotate by 90" #kit.zlabel = nil end kit end
read_variable(varname, options)
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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)
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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