RubyGems - rpipe - Versions diffs - 0.0.1 - Mend

rpipe 0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (104) hide show

data/.document +5 -0
data/.gitignore +23 -0
data/LICENSE +20 -0
data/README +0 -0
data/README.rdoc +33 -0
data/Rakefile +78 -0
data/VERSION +1 -0
data/bin/create_driver.rb +79 -0
data/bin/rpipe +131 -0
data/bin/swallow_batch_run.rb +21 -0
data/lib/core_additions.rb +5 -0
data/lib/custom_methods/JohnsonMerit220Visit1Preproc.m +26 -0
data/lib/custom_methods/JohnsonMerit220Visit1Preproc.rb +43 -0
data/lib/custom_methods/JohnsonMerit220Visit1Preproc_job.m +80 -0
data/lib/custom_methods/JohnsonMerit220Visit1Stats.m +74 -0
data/lib/custom_methods/JohnsonMerit220Visit1Stats.rb +63 -0
data/lib/custom_methods/JohnsonMerit220Visit1Stats_job.m +63 -0
data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m +26 -0
data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb +41 -0
data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m +69 -0
data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m +76 -0
data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb +67 -0
data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m +59 -0
data/lib/custom_methods/ReconWithHello.rb +7 -0
data/lib/default_logger.rb +13 -0
data/lib/default_methods/default_preproc.rb +76 -0
data/lib/default_methods/default_recon.rb +80 -0
data/lib/default_methods/default_stats.rb +94 -0
data/lib/default_methods/recon/physionoise_helper.rb +69 -0
data/lib/default_methods/recon/raw_sequence.rb +109 -0
data/lib/generators/job_generator.rb +36 -0
data/lib/generators/preproc_job_generator.rb +31 -0
data/lib/generators/recon_job_generator.rb +76 -0
data/lib/generators/stats_job_generator.rb +70 -0
data/lib/generators/workflow_generator.rb +128 -0
data/lib/global_additions.rb +18 -0
data/lib/logfile.rb +310 -0
data/lib/matlab_helpers/CreateFunctionalVolumeStruct.m +6 -0
data/lib/matlab_helpers/import_csv.m +32 -0
data/lib/matlab_helpers/matlab_queue.rb +37 -0
data/lib/matlab_helpers/prepare_onsets_xls.m +30 -0
data/lib/rpipe.rb +254 -0
data/rpipe.gemspec +177 -0
data/spec/generators/preproc_job_generator_spec.rb +27 -0
data/spec/generators/recon_job_generator_spec.rb +33 -0
data/spec/generators/stats_job_generator_spec.rb +50 -0
data/spec/generators/workflow_generator_spec.rb +97 -0
data/spec/helper_spec.rb +40 -0
data/spec/integration/johnson.merit220.visit1_spec.rb +47 -0
data/spec/integration/johnson.tbi.longitudinal.snod_spec.rb +48 -0
data/spec/logfile_spec.rb +96 -0
data/spec/matlab_queue_spec.rb +40 -0
data/spec/merit220_stats_spec.rb +81 -0
data/spec/physio_spec.rb +98 -0
data/test/drivers/merit220_workflow_sample.yml +15 -0
data/test/drivers/mrt00000.yml +65 -0
data/test/drivers/mrt00015.yml +62 -0
data/test/drivers/mrt00015_hello.yml +41 -0
data/test/drivers/mrt00015_withphys.yml +81 -0
data/test/drivers/tbi000.yml +129 -0
data/test/drivers/tbi000_separatevisits.yml +137 -0
data/test/drivers/tmp.yml +58 -0
data/test/fixtures/faces3_recognitionA.mat +0 -0
data/test/fixtures/faces3_recognitionA.txt +86 -0
data/test/fixtures/faces3_recognitionA_equal.csv +25 -0
data/test/fixtures/faces3_recognitionA_unequal.csv +21 -0
data/test/fixtures/faces3_recognitionB_incmisses.txt +86 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt +334 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt +9106 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt +9106 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt +167 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt +13360 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt +9106 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt +9106 -0
data/test/fixtures/ruport_summary.yml +123 -0
data/test/fixtures/valid_scans.yaml +35 -0
data/test/helper.rb +10 -0
data/test/test_dynamic_method_inclusion.rb +10 -0
data/test/test_includes.rb +11 -0
data/test/test_integrative_johnson.merit220.visit1.rb +31 -0
data/test/test_preproc.rb +11 -0
data/test/test_recon.rb +11 -0
data/test/test_rpipe.rb +19 -0
data/vendor/output_catcher.rb +93 -0
data/vendor/trollop.rb +781 -0
metadata +260 -0

data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt ADDED Viewed

@@ -0,0 +1,334 @@
+0.031301
+0.028625
+0.029183
+0.028828
+0.029435
+0.032300
+0.035956
+0.039312
+0.043229
+0.045889
+0.046012
+0.045951
+0.044516
+0.042746
+0.039001
+0.031897
+0.026165
+0.026130
+0.028396
+0.027608
+0.024320
+0.022133
+0.030481
+0.041382
+0.050571
+0.058462
+0.068387
+0.083591
+0.094109
+0.089681
+0.085620
+0.086944
+0.089314
+0.081129
+0.069371
+0.061031
+0.055399
+0.049254
+0.044138
+0.038423
+0.036104
+0.033939
+0.035464
+0.042985
+0.050003
+0.054395
+0.058455
+0.057382
+0.052976
+0.049381
+0.045499
+0.042193
+0.041505
+0.041682
+0.041563
+0.041682
+0.041294
+0.039639
+0.037865
+0.037223
+0.037425
+0.036802
+0.035156
+0.033545
+0.035940
+0.039537
+0.044746
+0.053083
+0.059639
+0.062183
+0.064037
+0.064667
+0.064330
+0.069410
+0.079584
+0.084907
+0.084429
+0.087144
+0.098225
+0.105459
+0.100692
+0.096015
+0.095505
+0.095264
+0.091177
+0.085989
+0.079954
+0.072773
+0.067466
+0.062954
+0.061157
+0.067578
+0.073481
+0.074561
+0.074244
+0.073007
+0.070284
+0.071392
+0.076286
+0.080717
+0.085980
+0.089370
+0.087365
+0.084642
+0.080381
+0.075606
+0.071304
+0.066793
+0.062844
+0.058204
+0.057959
+0.073562
+0.087929
+0.087986
+0.085275
+0.088595
+0.093935
+0.091181
+0.082860
+0.079416
+0.079552
+0.078912
+0.076462
+0.074638
+0.074291
+0.074556
+0.076127
+0.078787
+0.079448
+0.079628
+0.078490
+0.076346
+0.072999
+0.066768
+0.060351
+0.054613
+0.048574
+0.045833
+0.046030
+0.046645
+0.050561
+0.054231
+0.056892
+0.058582
+0.064130
+0.073786
+0.080212
+0.082830
+0.083419
+0.076808
+0.070305
+0.065482
+0.061511
+0.058284
+0.056801
+0.052951
+0.045732
+0.038851
+0.040104
+0.044350
+0.044575
+0.040421
+0.038443
+0.043005
+0.049044
+0.059088
+0.073637
+0.077689
+0.072544
+0.068457
+0.064086
+0.059984
+0.055999
+0.052014
+0.048345
+0.044362
+0.042541
+0.046153
+0.049860
+0.052140
+0.054253
+0.052479
+0.046187
+0.042297
+0.043624
+0.045459
+0.043607
+0.039362
+0.039095
+0.044805
+0.050368
+0.056465
+0.062723
+0.067538
+0.072362
+0.070936
+0.061764
+0.054524
+0.048469
+0.043213
+0.041318
+0.041756
+0.042631
+0.047045
+0.049654
+0.048925
+0.046409
+0.047295
+0.048872
+0.052284
+0.058299
+0.064221
+0.066598
+0.068707
+0.060040
+0.045770
+0.036180
+0.032970
+0.029530
+0.028981
+0.029002
+0.027992
+0.024397
+0.022261
+0.029250
+0.041142
+0.046781
+0.049200
+0.048453
+0.039281
+0.028449
+0.027662
+0.033403
+0.038766
+0.046599
+0.053495
+0.052022
+0.047800
+0.042836
+0.035415
+0.029923
+0.030510
+0.032559
+0.032225
+0.030449
+0.029065
+0.029035
+0.028932
+0.035380
+0.047834
+0.054917
+0.055138
+0.054506
+0.049761
+0.043839
+0.040518
+0.038841
+0.037078
+0.035316
+0.033654
+0.030864
+0.027516
+0.024946
+0.025064
+0.024840
+0.027286
+0.030505
+0.034568
+0.039776
+0.045827
+0.056769
+0.070272
+0.076028
+0.078410
+0.076822
+0.069803
+0.063209
+0.055298
+0.047690
+0.043020
+0.039538
+0.037176
+0.037454
+0.036975
+0.034264
+0.030598
+0.030258
+0.034557
+0.034982
+0.022665
+0.007098
+0.000000
+0.004757
+0.008526
+0.015628
+0.023539
+0.030609
+0.035825
+0.040592
+0.038736
+0.034769
+0.033839
+0.035514
+0.038776
+0.051812
+0.065678
+0.061425
+0.048089
+0.041039
+0.039156
+0.037099
+0.031223
+0.024646
+0.019567
+0.016841
+0.013904
+0.015771
+0.019054
+0.020599
+0.018845
+0.017568
+0.015845
+0.014599
+0.012887
+0.011721
+0.009966
+0.011265
+0.014279
+0.017507
+0.022099
+0.027009
+0.031882
+0.037567
+0.039925

data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt ADDED Viewed

@@ -0,0 +1,334 @@
+0.387541
+0.466773
+0.448018
+0.418485
+0.348200
+0.296984
+0.231474
+0.177464
+0.114078
+0.057627
+0.005374
+0.018398
+0.030155
+0.048732
+0.059982
+0.078719
+0.081711
+0.086532
+0.084784
+0.090925
+0.087036
+0.117259
+0.171491
+0.231840
+0.259638
+0.226066
+0.192077
+0.158779
+0.122637
+0.100049
+0.122900
+0.152512
+0.177192
+0.223394
+0.304282
+0.379087
+0.354388
+0.289266
+0.235631
+0.172958
+0.132019
+0.115558
+0.099384
+0.082963
+0.066734
+0.050616
+0.033966
+0.042859
+0.072381
+0.095677
+0.125026
+0.138318
+0.123797
+0.107664
+0.092384
+0.076195
+0.060872
+0.045790
+0.040485
+0.035308
+0.031210
+0.025880
+0.021805
+0.016536
+0.012682
+0.029786
+0.063432
+0.090257
+0.124330
+0.138982
+0.129634
+0.117206
+0.108882
+0.093504
+0.105120
+0.264201
+0.447930
+0.430818
+0.344071
+0.271313
+0.190110
+0.124145
+0.133063
+0.157832
+0.180472
+0.193217
+0.170691
+0.149656
+0.126243
+0.104978
+0.081776
+0.069668
+0.063316
+0.056123
+0.049470
+0.042313
+0.035651
+0.029227
+0.031853
+0.035184
+0.039459
+0.042355
+0.046979
+0.049876
+0.062251
+0.073518
+0.088789
+0.097339
+0.127598
+0.242189
+0.380397
+0.391503
+0.316196
+0.258693
+0.188302
+0.139104
+0.131758
+0.132302
+0.128799
+0.128923
+0.121024
+0.109645
+0.097188
+0.085888
+0.073504
+0.062038
+0.051979
+0.045148
+0.036992
+0.029916
+0.021948
+0.014680
+0.006922
+0.000000
+0.016314
+0.046114
+0.071494
+0.100997
+0.120741
+0.112228
+0.099243
+0.088031
+0.075339
+0.063965
+0.052447
+0.050512
+0.047561
+0.046863
+0.043295
+0.043460
+0.038888
+0.078978
+0.143354
+0.208034
+0.244443
+0.221101
+0.204383
+0.181122
+0.167863
+0.164243
+0.164262
+0.161373
+0.160673
+0.152988
+0.147668
+0.139446
+0.134261
+0.125796
+0.120455
+0.111619
+0.106626
+0.097120
+0.096837
+0.104191
+0.115259
+0.122322
+0.133579
+0.125047
+0.114578
+0.099584
+0.091194
+0.072941
+0.081899
+0.192170
+0.339028
+0.373346
+0.307443
+0.251432
+0.193158
+0.128703
+0.123870
+0.311296
+0.460354
+0.413580
+0.330368
+0.257791
+0.177266
+0.111056
+0.108772
+0.124857
+0.134119
+0.148663
+0.142347
+0.128203
+0.113605
+0.100148
+0.085145
+0.073828
+0.071936
+0.071771
+0.070844
+0.070481
+0.069743
+0.068068
+0.064226
+0.060952
+0.057274
+0.053855
+0.050344
+0.046276
+0.040856
+0.035418
+0.030103
+0.024530
+0.019377
+0.013519
+0.010176
+0.029142
+0.057015
+0.080981
+0.109348
+0.125047
+0.121321
+0.114942
+0.111967
+0.102999
+0.118122
+0.180695
+0.249158
+0.288482
+0.253052
+0.218923
+0.181922
+0.147726
+0.139065
+0.147169
+0.149358
+0.156593
+0.148336
+0.130169
+0.112183
+0.094319
+0.076493
+0.057942
+0.047247
+0.052315
+0.055461
+0.060321
+0.063744
+0.068420
+0.075373
+0.085759
+0.094557
+0.104429
+0.116572
+0.174087
+0.246578
+0.304068
+0.276145
+0.230970
+0.189609
+0.145715
+0.108017
+0.108886
+0.119184
+0.126949
+0.136384
+0.142131
+0.145018
+0.149689
+0.148360
+0.207788
+0.447206
+0.547408
+0.438627
+0.345469
+0.237059
+0.179579
+0.162774
+0.142560
+0.124467
+0.103896
+0.095235
+0.110025
+0.123040
+0.138060
+0.150234
+0.156605
+0.160230
+0.165613
+0.169452
+0.177439
+0.183653
+0.192861
+0.193968
+0.179387
+0.160601
+0.146472
+0.124483
+0.142538
+0.212150
+0.282583
+0.301483
+0.253199
+0.219265
+0.173994
+0.138819
+0.093852
+0.059193
+0.012173
+0.000357
+0.026773
+0.057192
+0.082337
+0.114205
+0.112928
+0.099683
+0.082857
+0.072123
+0.053306
+0.044549
+0.027362
+0.118562
+0.220960