tokfile 0.0.3 → 0.0.4
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/tokfile/ogyropsi.rb +165 -160
- data/tokfile.gemspec +4 -4
- metadata +3 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 062d056c77137d0588181f62d8d782a0e919703e
|
4
|
+
data.tar.gz: 0669f4b12c8d7413854240f290d481a319b7670b
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 40f5a4581ae863de2363f102b23abf4eda8810e31e8039fb6137ffd47256cfa10bdccca9a8c3867d0cbb41b81f307de842d017e948a49534c91a966e922a45b1
|
7
|
+
data.tar.gz: f33976293ca398d92e7c6bc86ebc0efe3d8f6bda2b2c1e6252e3867c297749cc17d5681f8d38168710e28c26d08602bdeed3fc16d2192f2e65261e0073426502
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.0.
|
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
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
14
|
-
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
-
|
25
|
-
|
26
|
-
|
27
|
-
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
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
|
-
|
68
|
-
|
69
|
-
|
70
|
-
|
71
|
-
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
|
76
|
-
|
77
|
-
|
78
|
-
|
79
|
-
|
80
|
-
|
81
|
-
|
82
|
-
|
83
|
-
|
84
|
-
|
85
|
-
|
86
|
-
|
87
|
-
|
88
|
-
|
89
|
-
|
90
|
-
|
91
|
-
|
92
|
-
|
93
|
-
|
94
|
-
|
95
|
-
|
96
|
-
|
97
|
-
|
98
|
-
|
99
|
-
|
100
|
-
|
101
|
-
|
102
|
-
|
103
|
-
|
104
|
-
|
105
|
-
|
106
|
-
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
|
112
|
-
|
113
|
-
|
114
|
-
|
115
|
-
|
116
|
-
|
117
|
-
|
118
|
-
|
119
|
-
|
120
|
-
|
121
|
-
|
122
|
-
|
123
|
-
|
124
|
-
|
125
|
-
|
126
|
-
|
127
|
-
|
128
|
-
|
129
|
-
|
130
|
-
|
131
|
-
|
132
|
-
|
133
|
-
|
134
|
-
|
135
|
-
|
136
|
-
|
137
|
-
|
138
|
-
|
139
|
-
|
140
|
-
|
141
|
-
|
142
|
-
|
143
|
-
|
144
|
-
|
145
|
-
|
146
|
-
|
147
|
-
|
148
|
-
|
149
|
-
|
150
|
-
|
151
|
-
|
152
|
-
|
153
|
-
|
154
|
-
|
155
|
-
|
156
|
-
|
157
|
-
|
158
|
-
|
159
|
-
|
160
|
-
|
161
|
-
|
162
|
-
|
163
|
-
|
164
|
-
|
165
|
-
|
166
|
-
|
167
|
-
|
168
|
-
|
169
|
-
|
170
|
-
|
171
|
-
|
172
|
-
|
173
|
-
|
174
|
-
|
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.
|
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.
|
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-
|
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.
|
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.
|
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-
|
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.
|
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
|