tokfile 0.0.3 → 0.0.4

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Files changed (5) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/lib/tokfile/ogyropsi.rb +165 -160
  4. data/tokfile.gemspec +4 -4
  5. metadata +3 -3
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data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.0.3
1
+ 0.0.4
data/lib/tokfile/ogyropsi.rb CHANGED
@@ -2,61 +2,65 @@
2
2
  # A class for interacting with files of format ogyropsi,
3
3
  # an input format for GENE and GYRO that is output by CHEASE
4
4
  #
5
- class TokFile::Ogyropsi
6
- # Create the object. Read data from filename if it exists.
7
- # Otherwise do nothing.
8
- def initialize(filename)
9
- @filename = filename
10
- return unless FileTest.exist? @filename
11
- @lines = File.read(filename).split("\n")
12
- #for i in 1...@lines.size
13
- vb2 = TokFile.verbosity > 1
14
- if vb2
15
- eputs
16
- eputs "Reading data from ogyropsi filename #{filename}."
17
- eputs
18
- end
19
- i = 0
20
- sz = @lines.size
21
- total_size = 0
22
- while i < sz
23
-
24
- var = @lines[i].gsub(/\s/, '').downcase.to_sym
25
- var = :pr if var == :p
26
- j=i+1
27
- j+=1 while j < sz and not @lines[j] =~ /^\s*[A-Za-z]/
28
- val = @lines.slice(i+1...j).join(' ').sub(/\A\s+/, '').sub(/\s+\Z/, '').split(/\s+/).map{|s| eval(s)}
29
- vsz = val.size
30
- total_size += vsz
31
- if vb2
32
- Terminal.erewind(1)
33
- eputs "#{var}(#{vsz})#{Terminal::CLEAR_LINE}" if vb2
34
- end
35
- self.class.attr_accessor var
36
- case val.size
37
- when 1
38
- set(var, val[0])
39
- when @npsi, @nchi
40
- set(var, val.to_gslv)
41
- when @npsi*@nchi
42
- set(var, GSL::Matrix.alloc(*val.pieces(@nchi)))
43
- else
44
- raise "Unknown size for #{var}"
45
- end
46
- i=j
47
- end
48
-
49
- if vb2
50
- Terminal.erewind(1)
51
- eputs "Read total data size of #{total_size.to_f * 8.0/1.0e6} MB"
52
- end
53
- if TokFile.verbosity > 0
54
- eputs <<EOF
5
+ class TokFile
6
+ def self.verbosity
7
+ 0
8
+ end
9
+ class Ogyropsi
10
+ # Create the object. Read data from filename if it exists.
11
+ # Otherwise do nothing.
12
+ def initialize(filename)
13
+ @filename = filename
14
+ return unless FileTest.exist? @filename
15
+ @lines = File.read(filename).split("\n")
16
+ #for i in 1...@lines.size
17
+ vb2 = TokFile.verbosity > 1
18
+ if vb2
19
+ eputs
20
+ eputs "Reading data from ogyropsi filename #{filename}."
21
+ eputs
22
+ end
23
+ i = 0
24
+ sz = @lines.size
25
+ total_size = 0
26
+ while i < sz
27
+
28
+ var = @lines[i].gsub(/\s/, '').downcase.to_sym
29
+ var = :pr if var == :p
30
+ j=i+1
31
+ j+=1 while j < sz and not @lines[j] =~ /^\s*[A-Za-z]/
32
+ val = @lines.slice(i+1...j).join(' ').sub(/\A\s+/, '').sub(/\s+\Z/, '').split(/\s+/).map{|s| eval(s)}
33
+ vsz = val.size
34
+ total_size += vsz
35
+ if vb2
36
+ Terminal.erewind(1)
37
+ eputs "#{var}(#{vsz})#{Terminal::CLEAR_LINE}" if vb2
38
+ end
39
+ self.class.attr_accessor var
40
+ case val.size
41
+ when 1
42
+ set(var, val[0])
43
+ when @npsi, @nchi
44
+ set(var, val.to_gslv)
45
+ when @npsi*@nchi
46
+ set(var, GSL::Matrix.alloc(*val.pieces(@nchi)))
47
+ else
48
+ raise "Unknown size for #{var}"
49
+ end
50
+ i=j
51
+ end
52
+
53
+ if vb2
54
+ Terminal.erewind(1)
55
+ eputs "Read total data size of #{total_size.to_f * 8.0/1.0e6} MB"
56
+ end
57
+ if TokFile.verbosity > 0
58
+ eputs <<EOF
55
59
  -----------------------------------------
56
60
  Tokfile
57
61
  -----------------------------------------
58
62
  Successfully read an ogyropsi file called
59
- #{filename}
63
+ #{filename}
60
64
  with the following parameters:
61
65
 
62
66
  npsi = #@npsi
@@ -64,114 +68,114 @@ nchi = #@nchi
64
68
  -----------------------------------------
65
69
  EOF
66
70
 
67
- end
68
-
69
- # A GraphKit::MultiKit containing summary information about the
70
- # contents of the file.
71
- def summary_graphkit
72
- multkit = GraphKit::MultiKit.new([:pr, :dpdpsi, :f, :fdfdpsi, :q, :shear, :ti, :te].map{|name|
73
- kit = GraphKit.quick_create([@psi, send(name)])
74
- kit.title = name.to_s
75
- kit.ylabel = nil
76
- kit.xlabel = 'psi'
77
- kit
78
- })
79
- multkit.gp.multiplot = "layout 3,3"
80
- kit = @npsi.times.map{|i| GraphKit.quick_create([@r.col(i), @z.col(i)])}.sum
81
- kit.data.each{|dk| dk.gp.with = 'l'}
82
- multkit.push kit
83
- multkit
84
- end
85
-
86
- # Read selected data from the given file object,
87
- # overwriting current values where present.
88
- def read_data(file_object, data_group, time)
89
- # Convert to an object of class Tokfile::Ogyropsi if necessary
90
- file_object = file_object.internal_representation(time).to_ogyropsi unless file_object.kind_of? TokFile::Ogyropsi
91
- VARIABLES.each do |var|
92
- next unless in_data_group(data_group, var)
93
- varname = instance_varname(var)
94
- if data_group=="all"
95
- set(varname, file_object.send(varname)) if file_object.send(varname)
96
- else
97
- if file_object.send(varname)
98
- input = file_object.send(varname)
99
- case input
100
- when Integer, Float
101
- set(varname, input)
102
- when GSL::Vector
103
- case input.size
104
- when file_object.npsi
105
- #interp = GSL::Interp.alloc('cspline', file_object.npsi)
106
- #ep [file_object.psi.max, file_object.psi.min, @psi.max, @psi.min, 'end']
107
- #ep input
108
- #set(varname, interp.eval(file_object.psi, input, @psi))
109
- interp = GSL::ScatterInterp.alloc(:linear, [file_object.psi, input], false)
110
- set(varname, @psi.collect{|ps| interp.eval(ps)})
111
- end
112
- end
113
- end
114
- end
115
-
116
- end
117
-
118
- end
119
-
120
- def instance_varname(var)
121
- varname = var.downcase.to_sym
122
- varname = :pr if varname == :p
123
- varname
124
- end
125
-
126
- def in_data_group(data_group, var)
127
- return true if data_group == "all"
128
- case var
129
- when /D?[NT][IE](DPSI)?/i, /ZEFF/i, /^p$|dpdpsi/i
130
- data_group == 'profiles'
131
- else
132
- data_group == 'geometry'
133
- end
134
- end
135
-
136
- # Write contents to @filename
137
- def write
138
- File.open(@filename, 'w') do |file|
139
- VARIABLES.each do |var|
140
- varname = instance_varname(var)
141
- file.puts var
142
- val = send(varname)
143
- case val
144
- when Integer, Float
145
- file.puts " #{val}"
146
- when GSL::Vector
147
- for i in 0...val.size
148
- file.print(sprintf(" %16.9E", val[i]))
149
- file.print("\n") if (i+1)%5 == 0
150
- end
151
- file.print("\n") unless val.size%5==0
152
- when GSL::Matrix
153
- # Note that fortran and hence this file is column major
154
- k = 0
155
- for i in 0...val.shape[0]
156
- for j in 0...val.shape[1]
157
- file.print(sprintf(" %16.9E", val[i,j]))
158
- file.print("\n") if (k+=1)%5 == 0
159
- end
160
- end
161
- file.print("\n") unless k%5==0
162
- end
163
- end
164
- end
165
- end
166
-
167
-
168
-
169
-
170
-
171
-
172
- end
173
-
174
- VARIABLES = %w{
71
+ end
72
+ end
73
+
74
+ # A GraphKit::MultiKit containing summary information about the
75
+ # contents of the file.
76
+ def summary_graphkit
77
+ multkit = GraphKit::MultiKit.new([:pr, :dpdpsi, :f, :fdfdpsi, :q, :shear, :ti, :te].map{|name|
78
+ kit = GraphKit.quick_create([@psi, send(name)])
79
+ kit.title = name.to_s
80
+ kit.ylabel = nil
81
+ kit.xlabel = 'psi'
82
+ kit
83
+ })
84
+ multkit.gp.multiplot = "layout 3,3"
85
+ kit = @npsi.times.map{|i| GraphKit.quick_create([@r.col(i), @z.col(i)])}.sum
86
+ kit.data.each{|dk| dk.gp.with = 'l'}
87
+ multkit.push kit
88
+ multkit
89
+ end
90
+
91
+ # Read selected data from the given file object,
92
+ # overwriting current values where present.
93
+ def read_data(file_object, data_group, time)
94
+ # Convert to an object of class Tokfile::Ogyropsi if necessary
95
+ file_object = file_object.internal_representation(time).to_ogyropsi unless file_object.kind_of? TokFile::Ogyropsi
96
+ VARIABLES.each do |var|
97
+ next unless in_data_group(data_group, var)
98
+ varname = instance_varname(var)
99
+ if data_group=="all"
100
+ set(varname, file_object.send(varname)) if file_object.send(varname)
101
+ else
102
+ if file_object.send(varname)
103
+ input = file_object.send(varname)
104
+ case input
105
+ when Integer, Float
106
+ set(varname, input)
107
+ when GSL::Vector
108
+ case input.size
109
+ when file_object.npsi
110
+ #interp = GSL::Interp.alloc('cspline', file_object.npsi)
111
+ #ep [file_object.psi.max, file_object.psi.min, @psi.max, @psi.min, 'end']
112
+ #ep input
113
+ #set(varname, interp.eval(file_object.psi, input, @psi))
114
+ interp = GSL::ScatterInterp.alloc(:linear, [file_object.psi, input], false)
115
+ set(varname, @psi.collect{|ps| interp.eval(ps)})
116
+ end
117
+ end
118
+ end
119
+ end
120
+
121
+ end
122
+
123
+ end
124
+
125
+ def instance_varname(var)
126
+ varname = var.downcase.to_sym
127
+ varname = :pr if varname == :p
128
+ varname
129
+ end
130
+
131
+ def in_data_group(data_group, var)
132
+ return true if data_group == "all"
133
+ case var
134
+ when /D?[NT][IE](DPSI)?/i, /ZEFF/i, /^p$|dpdpsi/i
135
+ data_group == 'profiles'
136
+ else
137
+ data_group == 'geometry'
138
+ end
139
+ end
140
+
141
+ # Write contents to @filename
142
+ def write
143
+ File.open(@filename, 'w') do |file|
144
+ VARIABLES.each do |var|
145
+ varname = instance_varname(var)
146
+ file.puts var
147
+ val = send(varname)
148
+ case val
149
+ when Integer, Float
150
+ file.puts " #{val}"
151
+ when GSL::Vector
152
+ for i in 0...val.size
153
+ file.print(sprintf(" %16.9E", val[i]))
154
+ file.print("\n") if (i+1)%5 == 0
155
+ end
156
+ file.print("\n") unless val.size%5==0
157
+ when GSL::Matrix
158
+ # Note that fortran and hence this file is column major
159
+ k = 0
160
+ for i in 0...val.shape[0]
161
+ for j in 0...val.shape[1]
162
+ file.print(sprintf(" %16.9E", val[i,j]))
163
+ file.print("\n") if (k+=1)%5 == 0
164
+ end
165
+ end
166
+ file.print("\n") unless k%5==0
167
+ end
168
+ end
169
+ end
170
+ end
171
+
172
+
173
+
174
+
175
+
176
+
177
+
178
+ VARIABLES = %w{
175
179
 
176
180
  NPSI
177
181
  NCHI
@@ -226,5 +230,6 @@ Jacobian
226
230
  R
227
231
  Z
228
232
 
229
- }
233
+ }
234
+ end
230
235
  end
data/tokfile.gemspec CHANGED
@@ -2,16 +2,16 @@
2
2
  # DO NOT EDIT THIS FILE DIRECTLY
3
3
  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
4
4
  # -*- encoding: utf-8 -*-
5
- # stub: tokfile 0.0.3 ruby lib
5
+ # stub: tokfile 0.0.4 ruby lib
6
6
 
7
7
  Gem::Specification.new do |s|
8
8
  s.name = "tokfile"
9
- s.version = "0.0.3"
9
+ s.version = "0.0.4"
10
10
 
11
11
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
12
12
  s.require_paths = ["lib"]
13
13
  s.authors = ["Edmund Highcock"]
14
- s.date = "2015-04-16"
14
+ s.date = "2015-08-09"
15
15
  s.description = "A tool for working with common tokamak file formats from tools like EFIT, CHEASE, TRANSP, CRONOS etc. Contains commands for plotting a summary of content, manipulating the data within them and most importantly, converting one format to another."
16
16
  s.email = "edmundhighcock@users.sourceforge.net"
17
17
  s.executables = ["tokfile"]
@@ -43,7 +43,7 @@ Gem::Specification.new do |s|
43
43
  ]
44
44
  s.homepage = "http://github.com/edmundhighcock/tokfile"
45
45
  s.licenses = ["GPLv3"]
46
- s.rubygems_version = "2.2.2"
46
+ s.rubygems_version = "2.4.8"
47
47
  s.summary = "A set of tools for testing and manipulating and converting files associated with tokamaks."
48
48
 
49
49
  if s.respond_to? :specification_version then
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: tokfile
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.3
4
+ version: 0.0.4
5
5
  platform: ruby
6
6
  authors:
7
7
  - Edmund Highcock
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2015-04-16 00:00:00.000000000 Z
11
+ date: 2015-08-09 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: coderunner
@@ -174,7 +174,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
174
174
  version: '0'
175
175
  requirements: []
176
176
  rubyforge_project:
177
- rubygems_version: 2.2.2
177
+ rubygems_version: 2.4.8
178
178
  signing_key:
179
179
  specification_version: 4
180
180
  summary: A set of tools for testing and manipulating and converting files associated