rapidtide 2.9.5__py3-none-any.whl → 3.1.3__py3-none-any.whl

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 (405) hide show
  1. cloud/gmscalc-HCPYA +1 -1
  2. cloud/mount-and-run +2 -0
  3. cloud/rapidtide-HCPYA +3 -3
  4. rapidtide/Colortables.py +538 -38
  5. rapidtide/OrthoImageItem.py +1094 -51
  6. rapidtide/RapidtideDataset.py +1709 -114
  7. rapidtide/__init__.py +0 -8
  8. rapidtide/_version.py +4 -4
  9. rapidtide/calccoherence.py +242 -97
  10. rapidtide/calcnullsimfunc.py +240 -140
  11. rapidtide/calcsimfunc.py +314 -129
  12. rapidtide/correlate.py +1211 -389
  13. rapidtide/data/examples/src/testLD +56 -0
  14. rapidtide/data/examples/src/test_findmaxlag.py +2 -2
  15. rapidtide/data/examples/src/test_mlregressallt.py +32 -17
  16. rapidtide/data/examples/src/testalign +1 -1
  17. rapidtide/data/examples/src/testatlasaverage +35 -7
  18. rapidtide/data/examples/src/testboth +21 -0
  19. rapidtide/data/examples/src/testcifti +11 -0
  20. rapidtide/data/examples/src/testdelayvar +13 -0
  21. rapidtide/data/examples/src/testdlfilt +25 -0
  22. rapidtide/data/examples/src/testfft +35 -0
  23. rapidtide/data/examples/src/testfileorfloat +37 -0
  24. rapidtide/data/examples/src/testfmri +94 -27
  25. rapidtide/data/examples/src/testfuncs +3 -3
  26. rapidtide/data/examples/src/testglmfilt +8 -6
  27. rapidtide/data/examples/src/testhappy +84 -51
  28. rapidtide/data/examples/src/testinitdelay +19 -0
  29. rapidtide/data/examples/src/testmodels +33 -0
  30. rapidtide/data/examples/src/testnewrefine +26 -0
  31. rapidtide/data/examples/src/testnoiseamp +21 -0
  32. rapidtide/data/examples/src/testppgproc +17 -0
  33. rapidtide/data/examples/src/testrefineonly +22 -0
  34. rapidtide/data/examples/src/testretro +26 -13
  35. rapidtide/data/examples/src/testretrolagtcs +16 -0
  36. rapidtide/data/examples/src/testrolloff +11 -0
  37. rapidtide/data/examples/src/testsimdata +45 -28
  38. rapidtide/data/models/model_cnn_pytorch/loss.png +0 -0
  39. rapidtide/data/models/model_cnn_pytorch/loss.txt +1 -0
  40. rapidtide/data/models/model_cnn_pytorch/model.pth +0 -0
  41. rapidtide/data/models/model_cnn_pytorch/model_meta.json +68 -0
  42. rapidtide/data/models/model_cnn_pytorch_fulldata/loss.png +0 -0
  43. rapidtide/data/models/model_cnn_pytorch_fulldata/loss.txt +1 -0
  44. rapidtide/data/models/model_cnn_pytorch_fulldata/model.pth +0 -0
  45. rapidtide/data/models/model_cnn_pytorch_fulldata/model_meta.json +80 -0
  46. rapidtide/data/models/model_cnnbp_pytorch_fullldata/loss.png +0 -0
  47. rapidtide/data/models/model_cnnbp_pytorch_fullldata/loss.txt +1 -0
  48. rapidtide/data/models/model_cnnbp_pytorch_fullldata/model.pth +0 -0
  49. rapidtide/data/models/model_cnnbp_pytorch_fullldata/model_meta.json +138 -0
  50. rapidtide/data/models/model_cnnfft_pytorch_fulldata/loss.png +0 -0
  51. rapidtide/data/models/model_cnnfft_pytorch_fulldata/loss.txt +1 -0
  52. rapidtide/data/models/model_cnnfft_pytorch_fulldata/model.pth +0 -0
  53. rapidtide/data/models/model_cnnfft_pytorch_fulldata/model_meta.json +128 -0
  54. rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/loss.png +0 -0
  55. rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/loss.txt +1 -0
  56. rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/model.pth +0 -0
  57. rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/model_meta.json +49 -0
  58. rapidtide/data/models/model_revised_tf2/model.keras +0 -0
  59. rapidtide/data/models/{model_serdar → model_revised_tf2}/model_meta.json +1 -1
  60. rapidtide/data/models/model_serdar2_tf2/model.keras +0 -0
  61. rapidtide/data/models/{model_serdar2 → model_serdar2_tf2}/model_meta.json +1 -1
  62. rapidtide/data/models/model_serdar_tf2/model.keras +0 -0
  63. rapidtide/data/models/{model_revised → model_serdar_tf2}/model_meta.json +1 -1
  64. rapidtide/data/reference/HCP1200v2_MTT_2mm.nii.gz +0 -0
  65. rapidtide/data/reference/HCP1200v2_binmask_2mm.nii.gz +0 -0
  66. rapidtide/data/reference/HCP1200v2_csf_2mm.nii.gz +0 -0
  67. rapidtide/data/reference/HCP1200v2_gray_2mm.nii.gz +0 -0
  68. rapidtide/data/reference/HCP1200v2_graylaghist.json +7 -0
  69. rapidtide/data/reference/HCP1200v2_graylaghist.tsv.gz +0 -0
  70. rapidtide/data/reference/HCP1200v2_laghist.json +7 -0
  71. rapidtide/data/reference/HCP1200v2_laghist.tsv.gz +0 -0
  72. rapidtide/data/reference/HCP1200v2_mask_2mm.nii.gz +0 -0
  73. rapidtide/data/reference/HCP1200v2_maxcorr_2mm.nii.gz +0 -0
  74. rapidtide/data/reference/HCP1200v2_maxtime_2mm.nii.gz +0 -0
  75. rapidtide/data/reference/HCP1200v2_maxwidth_2mm.nii.gz +0 -0
  76. rapidtide/data/reference/HCP1200v2_negmask_2mm.nii.gz +0 -0
  77. rapidtide/data/reference/HCP1200v2_timepercentile_2mm.nii.gz +0 -0
  78. rapidtide/data/reference/HCP1200v2_white_2mm.nii.gz +0 -0
  79. rapidtide/data/reference/HCP1200v2_whitelaghist.json +7 -0
  80. rapidtide/data/reference/HCP1200v2_whitelaghist.tsv.gz +0 -0
  81. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2.xml +131 -0
  82. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2_regions.txt +60 -0
  83. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2_space-MNI152NLin6Asym_2mm.nii.gz +0 -0
  84. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm.nii.gz +0 -0
  85. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm_mask.nii.gz +0 -0
  86. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin6Asym_2mm_mask.nii.gz +0 -0
  87. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL2_space-MNI152NLin6Asym_2mm_mask.nii.gz +0 -0
  88. rapidtide/data/reference/MNI152_T1_1mm_Brain_FAST_seg.nii.gz +0 -0
  89. rapidtide/data/reference/MNI152_T1_1mm_Brain_Mask.nii.gz +0 -0
  90. rapidtide/data/reference/MNI152_T1_2mm_Brain_FAST_seg.nii.gz +0 -0
  91. rapidtide/data/reference/MNI152_T1_2mm_Brain_Mask.nii.gz +0 -0
  92. rapidtide/decorators.py +91 -0
  93. rapidtide/dlfilter.py +2553 -414
  94. rapidtide/dlfiltertorch.py +5201 -0
  95. rapidtide/externaltools.py +328 -13
  96. rapidtide/fMRIData_class.py +178 -0
  97. rapidtide/ffttools.py +168 -0
  98. rapidtide/filter.py +2704 -1462
  99. rapidtide/fit.py +2361 -579
  100. rapidtide/genericmultiproc.py +197 -0
  101. rapidtide/happy_supportfuncs.py +3255 -548
  102. rapidtide/helper_classes.py +590 -1181
  103. rapidtide/io.py +2569 -468
  104. rapidtide/linfitfiltpass.py +784 -0
  105. rapidtide/makelaggedtcs.py +267 -97
  106. rapidtide/maskutil.py +555 -25
  107. rapidtide/miscmath.py +867 -137
  108. rapidtide/multiproc.py +217 -44
  109. rapidtide/patchmatch.py +752 -0
  110. rapidtide/peakeval.py +32 -32
  111. rapidtide/ppgproc.py +2205 -0
  112. rapidtide/qualitycheck.py +353 -40
  113. rapidtide/refinedelay.py +854 -0
  114. rapidtide/refineregressor.py +939 -0
  115. rapidtide/resample.py +725 -204
  116. rapidtide/scripts/__init__.py +1 -0
  117. rapidtide/scripts/{adjustoffset → adjustoffset.py} +7 -2
  118. rapidtide/scripts/{aligntcs → aligntcs.py} +7 -2
  119. rapidtide/scripts/{applydlfilter → applydlfilter.py} +7 -2
  120. rapidtide/scripts/applyppgproc.py +28 -0
  121. rapidtide/scripts/{atlasaverage → atlasaverage.py} +7 -2
  122. rapidtide/scripts/{atlastool → atlastool.py} +7 -2
  123. rapidtide/scripts/{calcicc → calcicc.py} +7 -2
  124. rapidtide/scripts/{calctexticc → calctexticc.py} +7 -2
  125. rapidtide/scripts/{calcttest → calcttest.py} +7 -2
  126. rapidtide/scripts/{ccorrica → ccorrica.py} +7 -2
  127. rapidtide/scripts/delayvar.py +28 -0
  128. rapidtide/scripts/{diffrois → diffrois.py} +7 -2
  129. rapidtide/scripts/{endtidalproc → endtidalproc.py} +7 -2
  130. rapidtide/scripts/{fdica → fdica.py} +7 -2
  131. rapidtide/scripts/{filtnifti → filtnifti.py} +7 -2
  132. rapidtide/scripts/{filttc → filttc.py} +7 -2
  133. rapidtide/scripts/{fingerprint → fingerprint.py} +20 -16
  134. rapidtide/scripts/{fixtr → fixtr.py} +7 -2
  135. rapidtide/scripts/{gmscalc → gmscalc.py} +7 -2
  136. rapidtide/scripts/{happy → happy.py} +7 -2
  137. rapidtide/scripts/{happy2std → happy2std.py} +7 -2
  138. rapidtide/scripts/{happywarp → happywarp.py} +8 -4
  139. rapidtide/scripts/{histnifti → histnifti.py} +7 -2
  140. rapidtide/scripts/{histtc → histtc.py} +7 -2
  141. rapidtide/scripts/{glmfilt → linfitfilt.py} +7 -4
  142. rapidtide/scripts/{localflow → localflow.py} +7 -2
  143. rapidtide/scripts/{mergequality → mergequality.py} +7 -2
  144. rapidtide/scripts/{pairproc → pairproc.py} +7 -2
  145. rapidtide/scripts/{pairwisemergenifti → pairwisemergenifti.py} +7 -2
  146. rapidtide/scripts/{physiofreq → physiofreq.py} +7 -2
  147. rapidtide/scripts/{pixelcomp → pixelcomp.py} +7 -2
  148. rapidtide/scripts/{plethquality → plethquality.py} +7 -2
  149. rapidtide/scripts/{polyfitim → polyfitim.py} +7 -2
  150. rapidtide/scripts/{proj2flow → proj2flow.py} +7 -2
  151. rapidtide/scripts/{rankimage → rankimage.py} +7 -2
  152. rapidtide/scripts/{rapidtide → rapidtide.py} +7 -2
  153. rapidtide/scripts/{rapidtide2std → rapidtide2std.py} +7 -2
  154. rapidtide/scripts/{resamplenifti → resamplenifti.py} +7 -2
  155. rapidtide/scripts/{resampletc → resampletc.py} +7 -2
  156. rapidtide/scripts/retrolagtcs.py +28 -0
  157. rapidtide/scripts/retroregress.py +28 -0
  158. rapidtide/scripts/{roisummarize → roisummarize.py} +7 -2
  159. rapidtide/scripts/{runqualitycheck → runqualitycheck.py} +7 -2
  160. rapidtide/scripts/{showarbcorr → showarbcorr.py} +7 -2
  161. rapidtide/scripts/{showhist → showhist.py} +7 -2
  162. rapidtide/scripts/{showstxcorr → showstxcorr.py} +7 -2
  163. rapidtide/scripts/{showtc → showtc.py} +7 -2
  164. rapidtide/scripts/{showxcorr_legacy → showxcorr_legacy.py} +8 -8
  165. rapidtide/scripts/{showxcorrx → showxcorrx.py} +7 -2
  166. rapidtide/scripts/{showxy → showxy.py} +7 -2
  167. rapidtide/scripts/{simdata → simdata.py} +7 -2
  168. rapidtide/scripts/{spatialdecomp → spatialdecomp.py} +7 -2
  169. rapidtide/scripts/{spatialfit → spatialfit.py} +7 -2
  170. rapidtide/scripts/{spatialmi → spatialmi.py} +7 -2
  171. rapidtide/scripts/{spectrogram → spectrogram.py} +7 -2
  172. rapidtide/scripts/stupidramtricks.py +238 -0
  173. rapidtide/scripts/{synthASL → synthASL.py} +7 -2
  174. rapidtide/scripts/{tcfrom2col → tcfrom2col.py} +7 -2
  175. rapidtide/scripts/{tcfrom3col → tcfrom3col.py} +7 -2
  176. rapidtide/scripts/{temporaldecomp → temporaldecomp.py} +7 -2
  177. rapidtide/scripts/{testhrv → testhrv.py} +1 -1
  178. rapidtide/scripts/{threeD → threeD.py} +7 -2
  179. rapidtide/scripts/{tidepool → tidepool.py} +7 -2
  180. rapidtide/scripts/{variabilityizer → variabilityizer.py} +7 -2
  181. rapidtide/simFuncClasses.py +2113 -0
  182. rapidtide/simfuncfit.py +312 -108
  183. rapidtide/stats.py +579 -247
  184. rapidtide/tests/.coveragerc +27 -6
  185. rapidtide-2.9.5.data/scripts/fdica → rapidtide/tests/cleanposttest +4 -6
  186. rapidtide/tests/happycomp +9 -0
  187. rapidtide/tests/resethappytargets +1 -1
  188. rapidtide/tests/resetrapidtidetargets +1 -1
  189. rapidtide/tests/resettargets +1 -1
  190. rapidtide/tests/runlocaltest +3 -3
  191. rapidtide/tests/showkernels +1 -1
  192. rapidtide/tests/test_aliasedcorrelate.py +4 -4
  193. rapidtide/tests/test_aligntcs.py +1 -1
  194. rapidtide/tests/test_calcicc.py +1 -1
  195. rapidtide/tests/test_cleanregressor.py +184 -0
  196. rapidtide/tests/test_congrid.py +70 -81
  197. rapidtide/tests/test_correlate.py +1 -1
  198. rapidtide/tests/test_corrpass.py +4 -4
  199. rapidtide/tests/test_delayestimation.py +54 -59
  200. rapidtide/tests/test_dlfiltertorch.py +437 -0
  201. rapidtide/tests/test_doresample.py +2 -2
  202. rapidtide/tests/test_externaltools.py +69 -0
  203. rapidtide/tests/test_fastresampler.py +9 -5
  204. rapidtide/tests/test_filter.py +96 -57
  205. rapidtide/tests/test_findmaxlag.py +50 -19
  206. rapidtide/tests/test_fullrunhappy_v1.py +15 -10
  207. rapidtide/tests/test_fullrunhappy_v2.py +19 -13
  208. rapidtide/tests/test_fullrunhappy_v3.py +28 -13
  209. rapidtide/tests/test_fullrunhappy_v4.py +30 -11
  210. rapidtide/tests/test_fullrunhappy_v5.py +62 -0
  211. rapidtide/tests/test_fullrunrapidtide_v1.py +61 -7
  212. rapidtide/tests/test_fullrunrapidtide_v2.py +27 -15
  213. rapidtide/tests/test_fullrunrapidtide_v3.py +28 -8
  214. rapidtide/tests/test_fullrunrapidtide_v4.py +16 -8
  215. rapidtide/tests/test_fullrunrapidtide_v5.py +15 -6
  216. rapidtide/tests/test_fullrunrapidtide_v6.py +142 -0
  217. rapidtide/tests/test_fullrunrapidtide_v7.py +114 -0
  218. rapidtide/tests/test_fullrunrapidtide_v8.py +66 -0
  219. rapidtide/tests/test_getparsers.py +158 -0
  220. rapidtide/tests/test_io.py +59 -18
  221. rapidtide/tests/{test_glmpass.py → test_linfitfiltpass.py} +10 -10
  222. rapidtide/tests/test_mi.py +1 -1
  223. rapidtide/tests/test_miscmath.py +1 -1
  224. rapidtide/tests/test_motionregress.py +5 -5
  225. rapidtide/tests/test_nullcorr.py +6 -9
  226. rapidtide/tests/test_padvec.py +216 -0
  227. rapidtide/tests/test_parserfuncs.py +101 -0
  228. rapidtide/tests/test_phaseanalysis.py +1 -1
  229. rapidtide/tests/test_rapidtideparser.py +59 -53
  230. rapidtide/tests/test_refinedelay.py +296 -0
  231. rapidtide/tests/test_runmisc.py +5 -5
  232. rapidtide/tests/test_sharedmem.py +60 -0
  233. rapidtide/tests/test_simroundtrip.py +132 -0
  234. rapidtide/tests/test_simulate.py +1 -1
  235. rapidtide/tests/test_stcorrelate.py +4 -2
  236. rapidtide/tests/test_timeshift.py +2 -2
  237. rapidtide/tests/test_valtoindex.py +1 -1
  238. rapidtide/tests/test_zRapidtideDataset.py +5 -3
  239. rapidtide/tests/utils.py +10 -9
  240. rapidtide/tidepoolTemplate.py +88 -70
  241. rapidtide/tidepoolTemplate.ui +60 -46
  242. rapidtide/tidepoolTemplate_alt.py +88 -53
  243. rapidtide/tidepoolTemplate_alt.ui +62 -52
  244. rapidtide/tidepoolTemplate_alt_qt6.py +921 -0
  245. rapidtide/tidepoolTemplate_big.py +1125 -0
  246. rapidtide/tidepoolTemplate_big.ui +2386 -0
  247. rapidtide/tidepoolTemplate_big_qt6.py +1129 -0
  248. rapidtide/tidepoolTemplate_qt6.py +793 -0
  249. rapidtide/util.py +1389 -148
  250. rapidtide/voxelData.py +1048 -0
  251. rapidtide/wiener.py +138 -25
  252. rapidtide/wiener2.py +114 -8
  253. rapidtide/workflows/adjustoffset.py +107 -5
  254. rapidtide/workflows/aligntcs.py +86 -3
  255. rapidtide/workflows/applydlfilter.py +231 -89
  256. rapidtide/workflows/applyppgproc.py +540 -0
  257. rapidtide/workflows/atlasaverage.py +309 -48
  258. rapidtide/workflows/atlastool.py +130 -9
  259. rapidtide/workflows/calcSimFuncMap.py +490 -0
  260. rapidtide/workflows/calctexticc.py +202 -10
  261. rapidtide/workflows/ccorrica.py +123 -15
  262. rapidtide/workflows/cleanregressor.py +415 -0
  263. rapidtide/workflows/delayvar.py +1268 -0
  264. rapidtide/workflows/diffrois.py +84 -6
  265. rapidtide/workflows/endtidalproc.py +149 -9
  266. rapidtide/workflows/fdica.py +197 -17
  267. rapidtide/workflows/filtnifti.py +71 -4
  268. rapidtide/workflows/filttc.py +76 -5
  269. rapidtide/workflows/fitSimFuncMap.py +578 -0
  270. rapidtide/workflows/fixtr.py +74 -4
  271. rapidtide/workflows/gmscalc.py +116 -6
  272. rapidtide/workflows/happy.py +1242 -480
  273. rapidtide/workflows/happy2std.py +145 -13
  274. rapidtide/workflows/happy_parser.py +277 -59
  275. rapidtide/workflows/histnifti.py +120 -4
  276. rapidtide/workflows/histtc.py +85 -4
  277. rapidtide/workflows/{glmfilt.py → linfitfilt.py} +128 -14
  278. rapidtide/workflows/localflow.py +329 -29
  279. rapidtide/workflows/mergequality.py +80 -4
  280. rapidtide/workflows/niftidecomp.py +323 -19
  281. rapidtide/workflows/niftistats.py +178 -8
  282. rapidtide/workflows/pairproc.py +99 -5
  283. rapidtide/workflows/pairwisemergenifti.py +86 -3
  284. rapidtide/workflows/parser_funcs.py +1488 -56
  285. rapidtide/workflows/physiofreq.py +139 -12
  286. rapidtide/workflows/pixelcomp.py +211 -9
  287. rapidtide/workflows/plethquality.py +105 -23
  288. rapidtide/workflows/polyfitim.py +159 -19
  289. rapidtide/workflows/proj2flow.py +76 -3
  290. rapidtide/workflows/rankimage.py +115 -8
  291. rapidtide/workflows/rapidtide.py +1833 -1919
  292. rapidtide/workflows/rapidtide2std.py +101 -3
  293. rapidtide/workflows/rapidtide_parser.py +607 -372
  294. rapidtide/workflows/refineDelayMap.py +249 -0
  295. rapidtide/workflows/refineRegressor.py +1215 -0
  296. rapidtide/workflows/regressfrommaps.py +308 -0
  297. rapidtide/workflows/resamplenifti.py +86 -4
  298. rapidtide/workflows/resampletc.py +92 -4
  299. rapidtide/workflows/retrolagtcs.py +442 -0
  300. rapidtide/workflows/retroregress.py +1501 -0
  301. rapidtide/workflows/roisummarize.py +176 -7
  302. rapidtide/workflows/runqualitycheck.py +72 -7
  303. rapidtide/workflows/showarbcorr.py +172 -16
  304. rapidtide/workflows/showhist.py +87 -3
  305. rapidtide/workflows/showstxcorr.py +161 -4
  306. rapidtide/workflows/showtc.py +172 -10
  307. rapidtide/workflows/showxcorrx.py +250 -62
  308. rapidtide/workflows/showxy.py +186 -16
  309. rapidtide/workflows/simdata.py +418 -112
  310. rapidtide/workflows/spatialfit.py +83 -8
  311. rapidtide/workflows/spatialmi.py +252 -29
  312. rapidtide/workflows/spectrogram.py +306 -33
  313. rapidtide/workflows/synthASL.py +157 -6
  314. rapidtide/workflows/tcfrom2col.py +77 -3
  315. rapidtide/workflows/tcfrom3col.py +75 -3
  316. rapidtide/workflows/tidepool.py +3829 -666
  317. rapidtide/workflows/utils.py +45 -19
  318. rapidtide/workflows/utils_doc.py +293 -0
  319. rapidtide/workflows/variabilityizer.py +118 -5
  320. {rapidtide-2.9.5.dist-info → rapidtide-3.1.3.dist-info}/METADATA +30 -223
  321. rapidtide-3.1.3.dist-info/RECORD +393 -0
  322. {rapidtide-2.9.5.dist-info → rapidtide-3.1.3.dist-info}/WHEEL +1 -1
  323. rapidtide-3.1.3.dist-info/entry_points.txt +65 -0
  324. rapidtide-3.1.3.dist-info/top_level.txt +2 -0
  325. rapidtide/calcandfitcorrpairs.py +0 -262
  326. rapidtide/data/examples/src/testoutputsize +0 -45
  327. rapidtide/data/models/model_revised/model.h5 +0 -0
  328. rapidtide/data/models/model_serdar/model.h5 +0 -0
  329. rapidtide/data/models/model_serdar2/model.h5 +0 -0
  330. rapidtide/data/reference/ASPECTS_nlin_asym_09c_2mm.nii.gz +0 -0
  331. rapidtide/data/reference/ASPECTS_nlin_asym_09c_2mm_mask.nii.gz +0 -0
  332. rapidtide/data/reference/ATTbasedFlowTerritories_split_nlin_asym_09c_2mm.nii.gz +0 -0
  333. rapidtide/data/reference/ATTbasedFlowTerritories_split_nlin_asym_09c_2mm_mask.nii.gz +0 -0
  334. rapidtide/data/reference/HCP1200_binmask_2mm_2009c_asym.nii.gz +0 -0
  335. rapidtide/data/reference/HCP1200_lag_2mm_2009c_asym.nii.gz +0 -0
  336. rapidtide/data/reference/HCP1200_mask_2mm_2009c_asym.nii.gz +0 -0
  337. rapidtide/data/reference/HCP1200_negmask_2mm_2009c_asym.nii.gz +0 -0
  338. rapidtide/data/reference/HCP1200_sigma_2mm_2009c_asym.nii.gz +0 -0
  339. rapidtide/data/reference/HCP1200_strength_2mm_2009c_asym.nii.gz +0 -0
  340. rapidtide/glmpass.py +0 -434
  341. rapidtide/refine_factored.py +0 -641
  342. rapidtide/scripts/retroglm +0 -23
  343. rapidtide/workflows/glmfrommaps.py +0 -202
  344. rapidtide/workflows/retroglm.py +0 -643
  345. rapidtide-2.9.5.data/scripts/adjustoffset +0 -23
  346. rapidtide-2.9.5.data/scripts/aligntcs +0 -23
  347. rapidtide-2.9.5.data/scripts/applydlfilter +0 -23
  348. rapidtide-2.9.5.data/scripts/atlasaverage +0 -23
  349. rapidtide-2.9.5.data/scripts/atlastool +0 -23
  350. rapidtide-2.9.5.data/scripts/calcicc +0 -22
  351. rapidtide-2.9.5.data/scripts/calctexticc +0 -23
  352. rapidtide-2.9.5.data/scripts/calcttest +0 -22
  353. rapidtide-2.9.5.data/scripts/ccorrica +0 -23
  354. rapidtide-2.9.5.data/scripts/diffrois +0 -23
  355. rapidtide-2.9.5.data/scripts/endtidalproc +0 -23
  356. rapidtide-2.9.5.data/scripts/filtnifti +0 -23
  357. rapidtide-2.9.5.data/scripts/filttc +0 -23
  358. rapidtide-2.9.5.data/scripts/fingerprint +0 -593
  359. rapidtide-2.9.5.data/scripts/fixtr +0 -23
  360. rapidtide-2.9.5.data/scripts/glmfilt +0 -24
  361. rapidtide-2.9.5.data/scripts/gmscalc +0 -22
  362. rapidtide-2.9.5.data/scripts/happy +0 -25
  363. rapidtide-2.9.5.data/scripts/happy2std +0 -23
  364. rapidtide-2.9.5.data/scripts/happywarp +0 -350
  365. rapidtide-2.9.5.data/scripts/histnifti +0 -23
  366. rapidtide-2.9.5.data/scripts/histtc +0 -23
  367. rapidtide-2.9.5.data/scripts/localflow +0 -23
  368. rapidtide-2.9.5.data/scripts/mergequality +0 -23
  369. rapidtide-2.9.5.data/scripts/pairproc +0 -23
  370. rapidtide-2.9.5.data/scripts/pairwisemergenifti +0 -23
  371. rapidtide-2.9.5.data/scripts/physiofreq +0 -23
  372. rapidtide-2.9.5.data/scripts/pixelcomp +0 -23
  373. rapidtide-2.9.5.data/scripts/plethquality +0 -23
  374. rapidtide-2.9.5.data/scripts/polyfitim +0 -23
  375. rapidtide-2.9.5.data/scripts/proj2flow +0 -23
  376. rapidtide-2.9.5.data/scripts/rankimage +0 -23
  377. rapidtide-2.9.5.data/scripts/rapidtide +0 -23
  378. rapidtide-2.9.5.data/scripts/rapidtide2std +0 -23
  379. rapidtide-2.9.5.data/scripts/resamplenifti +0 -23
  380. rapidtide-2.9.5.data/scripts/resampletc +0 -23
  381. rapidtide-2.9.5.data/scripts/retroglm +0 -23
  382. rapidtide-2.9.5.data/scripts/roisummarize +0 -23
  383. rapidtide-2.9.5.data/scripts/runqualitycheck +0 -23
  384. rapidtide-2.9.5.data/scripts/showarbcorr +0 -23
  385. rapidtide-2.9.5.data/scripts/showhist +0 -23
  386. rapidtide-2.9.5.data/scripts/showstxcorr +0 -23
  387. rapidtide-2.9.5.data/scripts/showtc +0 -23
  388. rapidtide-2.9.5.data/scripts/showxcorr_legacy +0 -536
  389. rapidtide-2.9.5.data/scripts/showxcorrx +0 -23
  390. rapidtide-2.9.5.data/scripts/showxy +0 -23
  391. rapidtide-2.9.5.data/scripts/simdata +0 -23
  392. rapidtide-2.9.5.data/scripts/spatialdecomp +0 -23
  393. rapidtide-2.9.5.data/scripts/spatialfit +0 -23
  394. rapidtide-2.9.5.data/scripts/spatialmi +0 -23
  395. rapidtide-2.9.5.data/scripts/spectrogram +0 -23
  396. rapidtide-2.9.5.data/scripts/synthASL +0 -23
  397. rapidtide-2.9.5.data/scripts/tcfrom2col +0 -23
  398. rapidtide-2.9.5.data/scripts/tcfrom3col +0 -23
  399. rapidtide-2.9.5.data/scripts/temporaldecomp +0 -23
  400. rapidtide-2.9.5.data/scripts/threeD +0 -236
  401. rapidtide-2.9.5.data/scripts/tidepool +0 -23
  402. rapidtide-2.9.5.data/scripts/variabilityizer +0 -23
  403. rapidtide-2.9.5.dist-info/RECORD +0 -357
  404. rapidtide-2.9.5.dist-info/top_level.txt +0 -86
  405. {rapidtide-2.9.5.dist-info → rapidtide-3.1.3.dist-info/licenses}/LICENSE +0 -0
rapidtide-2.9.5.data/scripts/rapidtide DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
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- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.rapidtide as rapidtide_workflow
20
- import rapidtide.workflows.rapidtide_parser as rapidtide_parser
21
-
22
- if __name__ == "__main__":
23
- rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=None))
rapidtide-2.9.5.data/scripts/rapidtide2std DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
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- #
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- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
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- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.rapidtide2std as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.rapidtide2std)
rapidtide-2.9.5.data/scripts/resamplenifti DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.resamplenifti as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.resamplenifti)
rapidtide-2.9.5.data/scripts/resampletc DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.resampletc as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.resampletc)
rapidtide-2.9.5.data/scripts/retroglm DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.retroglm as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.retroglm)
rapidtide-2.9.5.data/scripts/roisummarize DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.roisummarize as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.roisummarize)
rapidtide-2.9.5.data/scripts/runqualitycheck DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.runqualitycheck as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.runqualitycheck)
rapidtide-2.9.5.data/scripts/showarbcorr DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.showarbcorr as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.showarbcorr)
rapidtide-2.9.5.data/scripts/showhist DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.showhist as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.showhist)
rapidtide-2.9.5.data/scripts/showstxcorr DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.showstxcorr as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.showstxcorr)
rapidtide-2.9.5.data/scripts/showtc DELETED
@@ -1,23 +0,0 @@
1
- #!python
2
- # -*- coding: utf-8 -*-
3
- #
4
- # Copyright 2016-2024 Blaise Frederick
5
- #
6
- # Licensed under the Apache License, Version 2.0 (the "License");
7
- # you may not use this file except in compliance with the License.
8
- # You may obtain a copy of the License at
9
- #
10
- # http://www.apache.org/licenses/LICENSE-2.0
11
- #
12
- # Unless required by applicable law or agreed to in writing, software
13
- # distributed under the License is distributed on an "AS IS" BASIS,
14
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
- # See the License for the specific language governing permissions and
16
- # limitations under the License.
17
- #
18
- #
19
- import rapidtide.workflows.parser_funcs as pf
20
- import rapidtide.workflows.showtc as theworkflow
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.showtc)