rpipe 0.0.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (104) hide show
  1. data/.document +5 -0
  2. data/.gitignore +23 -0
  3. data/LICENSE +20 -0
  4. data/README +0 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +78 -0
  7. data/VERSION +1 -0
  8. data/bin/create_driver.rb +79 -0
  9. data/bin/rpipe +131 -0
  10. data/bin/swallow_batch_run.rb +21 -0
  11. data/lib/core_additions.rb +5 -0
  12. data/lib/custom_methods/JohnsonMerit220Visit1Preproc.m +26 -0
  13. data/lib/custom_methods/JohnsonMerit220Visit1Preproc.rb +43 -0
  14. data/lib/custom_methods/JohnsonMerit220Visit1Preproc_job.m +80 -0
  15. data/lib/custom_methods/JohnsonMerit220Visit1Stats.m +74 -0
  16. data/lib/custom_methods/JohnsonMerit220Visit1Stats.rb +63 -0
  17. data/lib/custom_methods/JohnsonMerit220Visit1Stats_job.m +63 -0
  18. data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m +26 -0
  19. data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb +41 -0
  20. data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m +69 -0
  21. data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m +76 -0
  22. data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb +67 -0
  23. data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m +59 -0
  24. data/lib/custom_methods/ReconWithHello.rb +7 -0
  25. data/lib/default_logger.rb +13 -0
  26. data/lib/default_methods/default_preproc.rb +76 -0
  27. data/lib/default_methods/default_recon.rb +80 -0
  28. data/lib/default_methods/default_stats.rb +94 -0
  29. data/lib/default_methods/recon/physionoise_helper.rb +69 -0
  30. data/lib/default_methods/recon/raw_sequence.rb +109 -0
  31. data/lib/generators/job_generator.rb +36 -0
  32. data/lib/generators/preproc_job_generator.rb +31 -0
  33. data/lib/generators/recon_job_generator.rb +76 -0
  34. data/lib/generators/stats_job_generator.rb +70 -0
  35. data/lib/generators/workflow_generator.rb +128 -0
  36. data/lib/global_additions.rb +18 -0
  37. data/lib/logfile.rb +310 -0
  38. data/lib/matlab_helpers/CreateFunctionalVolumeStruct.m +6 -0
  39. data/lib/matlab_helpers/import_csv.m +32 -0
  40. data/lib/matlab_helpers/matlab_queue.rb +37 -0
  41. data/lib/matlab_helpers/prepare_onsets_xls.m +30 -0
  42. data/lib/rpipe.rb +254 -0
  43. data/rpipe.gemspec +177 -0
  44. data/spec/generators/preproc_job_generator_spec.rb +27 -0
  45. data/spec/generators/recon_job_generator_spec.rb +33 -0
  46. data/spec/generators/stats_job_generator_spec.rb +50 -0
  47. data/spec/generators/workflow_generator_spec.rb +97 -0
  48. data/spec/helper_spec.rb +40 -0
  49. data/spec/integration/johnson.merit220.visit1_spec.rb +47 -0
  50. data/spec/integration/johnson.tbi.longitudinal.snod_spec.rb +48 -0
  51. data/spec/logfile_spec.rb +96 -0
  52. data/spec/matlab_queue_spec.rb +40 -0
  53. data/spec/merit220_stats_spec.rb +81 -0
  54. data/spec/physio_spec.rb +98 -0
  55. data/test/drivers/merit220_workflow_sample.yml +15 -0
  56. data/test/drivers/mrt00000.yml +65 -0
  57. data/test/drivers/mrt00015.yml +62 -0
  58. data/test/drivers/mrt00015_hello.yml +41 -0
  59. data/test/drivers/mrt00015_withphys.yml +81 -0
  60. data/test/drivers/tbi000.yml +129 -0
  61. data/test/drivers/tbi000_separatevisits.yml +137 -0
  62. data/test/drivers/tmp.yml +58 -0
  63. data/test/fixtures/faces3_recognitionA.mat +0 -0
  64. data/test/fixtures/faces3_recognitionA.txt +86 -0
  65. data/test/fixtures/faces3_recognitionA_equal.csv +25 -0
  66. data/test/fixtures/faces3_recognitionA_unequal.csv +21 -0
  67. data/test/fixtures/faces3_recognitionB_incmisses.txt +86 -0
  68. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt +13360 -0
  69. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt +13360 -0
  70. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt +13360 -0
  71. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt +13360 -0
  72. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt +13360 -0
  73. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt +13360 -0
  74. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt +334 -0
  75. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt +334 -0
  76. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt +334 -0
  77. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt +334 -0
  78. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt +334 -0
  79. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt +334 -0
  80. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt +334 -0
  81. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt +9106 -0
  82. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt +9106 -0
  83. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt +167 -0
  84. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt +167 -0
  85. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt +167 -0
  86. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt +167 -0
  87. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt +167 -0
  88. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt +167 -0
  89. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt +167 -0
  90. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt +13360 -0
  91. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt +9106 -0
  92. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt +9106 -0
  93. data/test/fixtures/ruport_summary.yml +123 -0
  94. data/test/fixtures/valid_scans.yaml +35 -0
  95. data/test/helper.rb +10 -0
  96. data/test/test_dynamic_method_inclusion.rb +10 -0
  97. data/test/test_includes.rb +11 -0
  98. data/test/test_integrative_johnson.merit220.visit1.rb +31 -0
  99. data/test/test_preproc.rb +11 -0
  100. data/test/test_recon.rb +11 -0
  101. data/test/test_rpipe.rb +19 -0
  102. data/vendor/output_catcher.rb +93 -0
  103. data/vendor/trollop.rb +781 -0
  104. metadata +260 -0
metadata ADDED
@@ -0,0 +1,260 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: rpipe
3
+ version: !ruby/object:Gem::Version
4
+ hash: 29
5
+ prerelease: false
6
+ segments:
7
+ - 0
8
+ - 0
9
+ - 1
10
+ version: 0.0.1
11
+ platform: ruby
12
+ authors:
13
+ - Kristopher Kosmatka
14
+ - Erik Kastman
15
+ autorequire:
16
+ bindir: bin
17
+ cert_chain: []
18
+
19
+ date: 2010-07-15 00:00:00 -05:00
20
+ default_executable:
21
+ dependencies:
22
+ - !ruby/object:Gem::Dependency
23
+ name: thoughtbot-shoulda
24
+ prerelease: false
25
+ requirement: &id001 !ruby/object:Gem::Requirement
26
+ none: false
27
+ requirements:
28
+ - - ">="
29
+ - !ruby/object:Gem::Version
30
+ hash: 3
31
+ segments:
32
+ - 0
33
+ version: "0"
34
+ type: :development
35
+ version_requirements: *id001
36
+ - !ruby/object:Gem::Dependency
37
+ name: metamri
38
+ prerelease: false
39
+ requirement: &id002 !ruby/object:Gem::Requirement
40
+ none: false
41
+ requirements:
42
+ - - ">="
43
+ - !ruby/object:Gem::Version
44
+ hash: 3
45
+ segments:
46
+ - 0
47
+ version: "0"
48
+ type: :runtime
49
+ version_requirements: *id002
50
+ - !ruby/object:Gem::Dependency
51
+ name: log4r
52
+ prerelease: false
53
+ requirement: &id003 !ruby/object:Gem::Requirement
54
+ none: false
55
+ requirements:
56
+ - - ">="
57
+ - !ruby/object:Gem::Version
58
+ hash: 3
59
+ segments:
60
+ - 0
61
+ version: "0"
62
+ type: :runtime
63
+ version_requirements: *id003
64
+ - !ruby/object:Gem::Dependency
65
+ name: POpen4
66
+ prerelease: false
67
+ requirement: &id004 !ruby/object:Gem::Requirement
68
+ none: false
69
+ requirements:
70
+ - - ">="
71
+ - !ruby/object:Gem::Version
72
+ hash: 3
73
+ segments:
74
+ - 0
75
+ version: "0"
76
+ type: :runtime
77
+ version_requirements: *id004
78
+ - !ruby/object:Gem::Dependency
79
+ name: ruport
80
+ prerelease: false
81
+ requirement: &id005 !ruby/object:Gem::Requirement
82
+ none: false
83
+ requirements:
84
+ - - ">="
85
+ - !ruby/object:Gem::Version
86
+ hash: 3
87
+ segments:
88
+ - 0
89
+ version: "0"
90
+ type: :runtime
91
+ version_requirements: *id005
92
+ description: Neuroimaging preprocessing the Ruby way
93
+ email: kjkosmatka@gmail.com
94
+ executables:
95
+ - rpipe
96
+ - swallow_batch_run.rb
97
+ - create_driver.rb
98
+ extensions: []
99
+
100
+ extra_rdoc_files:
101
+ - LICENSE
102
+ - README
103
+ - README.rdoc
104
+ files:
105
+ - .document
106
+ - .gitignore
107
+ - LICENSE
108
+ - README
109
+ - README.rdoc
110
+ - Rakefile
111
+ - VERSION
112
+ - bin/create_driver.rb
113
+ - bin/rpipe
114
+ - bin/swallow_batch_run.rb
115
+ - lib/core_additions.rb
116
+ - lib/custom_methods/JohnsonMerit220Visit1Preproc.m
117
+ - lib/custom_methods/JohnsonMerit220Visit1Preproc.rb
118
+ - lib/custom_methods/JohnsonMerit220Visit1Preproc_job.m
119
+ - lib/custom_methods/JohnsonMerit220Visit1Stats.m
120
+ - lib/custom_methods/JohnsonMerit220Visit1Stats.rb
121
+ - lib/custom_methods/JohnsonMerit220Visit1Stats_job.m
122
+ - lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m
123
+ - lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb
124
+ - lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m
125
+ - lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m
126
+ - lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb
127
+ - lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m
128
+ - lib/custom_methods/ReconWithHello.rb
129
+ - lib/default_logger.rb
130
+ - lib/default_methods/default_preproc.rb
131
+ - lib/default_methods/default_recon.rb
132
+ - lib/default_methods/default_stats.rb
133
+ - lib/default_methods/recon/physionoise_helper.rb
134
+ - lib/default_methods/recon/raw_sequence.rb
135
+ - lib/generators/job_generator.rb
136
+ - lib/generators/preproc_job_generator.rb
137
+ - lib/generators/recon_job_generator.rb
138
+ - lib/generators/stats_job_generator.rb
139
+ - lib/generators/workflow_generator.rb
140
+ - lib/global_additions.rb
141
+ - lib/logfile.rb
142
+ - lib/matlab_helpers/CreateFunctionalVolumeStruct.m
143
+ - lib/matlab_helpers/import_csv.m
144
+ - lib/matlab_helpers/matlab_queue.rb
145
+ - lib/matlab_helpers/prepare_onsets_xls.m
146
+ - lib/rpipe.rb
147
+ - rpipe.gemspec
148
+ - spec/generators/preproc_job_generator_spec.rb
149
+ - spec/generators/recon_job_generator_spec.rb
150
+ - spec/generators/stats_job_generator_spec.rb
151
+ - spec/generators/workflow_generator_spec.rb
152
+ - spec/helper_spec.rb
153
+ - spec/integration/johnson.merit220.visit1_spec.rb
154
+ - spec/integration/johnson.tbi.longitudinal.snod_spec.rb
155
+ - spec/logfile_spec.rb
156
+ - spec/matlab_queue_spec.rb
157
+ - spec/merit220_stats_spec.rb
158
+ - spec/physio_spec.rb
159
+ - test/drivers/merit220_workflow_sample.yml
160
+ - test/drivers/mrt00000.yml
161
+ - test/drivers/mrt00015.yml
162
+ - test/drivers/mrt00015_hello.yml
163
+ - test/drivers/mrt00015_withphys.yml
164
+ - test/drivers/tbi000.yml
165
+ - test/drivers/tbi000_separatevisits.yml
166
+ - test/drivers/tmp.yml
167
+ - test/fixtures/faces3_recognitionA.mat
168
+ - test/fixtures/faces3_recognitionA.txt
169
+ - test/fixtures/faces3_recognitionA_equal.csv
170
+ - test/fixtures/faces3_recognitionA_unequal.csv
171
+ - test/fixtures/faces3_recognitionB_incmisses.txt
172
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt
173
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt
174
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt
175
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt
176
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt
177
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt
178
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt
179
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt
180
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt
181
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt
182
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt
183
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt
184
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt
185
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt
186
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt
187
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt
188
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt
189
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt
190
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt
191
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt
192
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt
193
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt
194
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt
195
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt
196
+ - test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt
197
+ - test/fixtures/ruport_summary.yml
198
+ - test/fixtures/valid_scans.yaml
199
+ - test/helper.rb
200
+ - test/test_dynamic_method_inclusion.rb
201
+ - test/test_includes.rb
202
+ - test/test_integrative_johnson.merit220.visit1.rb
203
+ - test/test_preproc.rb
204
+ - test/test_recon.rb
205
+ - test/test_rpipe.rb
206
+ - vendor/output_catcher.rb
207
+ - vendor/trollop.rb
208
+ has_rdoc: true
209
+ homepage: http://github.com/brainmap/rpipe
210
+ licenses: []
211
+
212
+ post_install_message:
213
+ rdoc_options:
214
+ - --charset=UTF-8
215
+ require_paths:
216
+ - lib
217
+ required_ruby_version: !ruby/object:Gem::Requirement
218
+ none: false
219
+ requirements:
220
+ - - ">="
221
+ - !ruby/object:Gem::Version
222
+ hash: 3
223
+ segments:
224
+ - 0
225
+ version: "0"
226
+ required_rubygems_version: !ruby/object:Gem::Requirement
227
+ none: false
228
+ requirements:
229
+ - - ">="
230
+ - !ruby/object:Gem::Version
231
+ hash: 3
232
+ segments:
233
+ - 0
234
+ version: "0"
235
+ requirements: []
236
+
237
+ rubyforge_project:
238
+ rubygems_version: 1.3.7
239
+ signing_key:
240
+ specification_version: 3
241
+ summary: Neuroimaging preprocessing the Ruby way
242
+ test_files:
243
+ - spec/generators/preproc_job_generator_spec.rb
244
+ - spec/generators/stats_job_generator_spec.rb
245
+ - spec/generators/recon_job_generator_spec.rb
246
+ - spec/generators/workflow_generator_spec.rb
247
+ - spec/matlab_queue_spec.rb
248
+ - spec/logfile_spec.rb
249
+ - spec/physio_spec.rb
250
+ - spec/integration/johnson.merit220.visit1_spec.rb
251
+ - spec/integration/johnson.tbi.longitudinal.snod_spec.rb
252
+ - spec/merit220_stats_spec.rb
253
+ - spec/helper_spec.rb
254
+ - test/helper.rb
255
+ - test/test_dynamic_method_inclusion.rb
256
+ - test/test_includes.rb
257
+ - test/test_integrative_johnson.merit220.visit1.rb
258
+ - test/test_preproc.rb
259
+ - test/test_recon.rb
260
+ - test/test_rpipe.rb