rapidtide 2.9.6__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 +92 -42
  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 +2 -2
  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 +108 -92
  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 +587 -1116
  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 +835 -144
  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-2.9.6.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 +26 -14
  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 +1785 -1858
  292. rapidtide/workflows/rapidtide2std.py +101 -3
  293. rapidtide/workflows/rapidtide_parser.py +590 -389
  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-2.9.6.dist-info → rapidtide-3.1.3.dist-info}/METADATA +30 -223
  321. rapidtide-3.1.3.dist-info/RECORD +393 -0
  322. {rapidtide-2.9.6.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-2.9.6.data/scripts/adjustoffset +0 -23
  346. rapidtide-2.9.6.data/scripts/aligntcs +0 -23
  347. rapidtide-2.9.6.data/scripts/applydlfilter +0 -23
  348. rapidtide-2.9.6.data/scripts/atlasaverage +0 -23
  349. rapidtide-2.9.6.data/scripts/atlastool +0 -23
  350. rapidtide-2.9.6.data/scripts/calcicc +0 -22
  351. rapidtide-2.9.6.data/scripts/calctexticc +0 -23
  352. rapidtide-2.9.6.data/scripts/calcttest +0 -22
  353. rapidtide-2.9.6.data/scripts/ccorrica +0 -23
  354. rapidtide-2.9.6.data/scripts/diffrois +0 -23
  355. rapidtide-2.9.6.data/scripts/endtidalproc +0 -23
  356. rapidtide-2.9.6.data/scripts/filtnifti +0 -23
  357. rapidtide-2.9.6.data/scripts/filttc +0 -23
  358. rapidtide-2.9.6.data/scripts/fingerprint +0 -593
  359. rapidtide-2.9.6.data/scripts/fixtr +0 -23
  360. rapidtide-2.9.6.data/scripts/glmfilt +0 -24
  361. rapidtide-2.9.6.data/scripts/gmscalc +0 -22
  362. rapidtide-2.9.6.data/scripts/happy +0 -25
  363. rapidtide-2.9.6.data/scripts/happy2std +0 -23
  364. rapidtide-2.9.6.data/scripts/happywarp +0 -350
  365. rapidtide-2.9.6.data/scripts/histnifti +0 -23
  366. rapidtide-2.9.6.data/scripts/histtc +0 -23
  367. rapidtide-2.9.6.data/scripts/localflow +0 -23
  368. rapidtide-2.9.6.data/scripts/mergequality +0 -23
  369. rapidtide-2.9.6.data/scripts/pairproc +0 -23
  370. rapidtide-2.9.6.data/scripts/pairwisemergenifti +0 -23
  371. rapidtide-2.9.6.data/scripts/physiofreq +0 -23
  372. rapidtide-2.9.6.data/scripts/pixelcomp +0 -23
  373. rapidtide-2.9.6.data/scripts/plethquality +0 -23
  374. rapidtide-2.9.6.data/scripts/polyfitim +0 -23
  375. rapidtide-2.9.6.data/scripts/proj2flow +0 -23
  376. rapidtide-2.9.6.data/scripts/rankimage +0 -23
  377. rapidtide-2.9.6.data/scripts/rapidtide +0 -23
  378. rapidtide-2.9.6.data/scripts/rapidtide2std +0 -23
  379. rapidtide-2.9.6.data/scripts/resamplenifti +0 -23
  380. rapidtide-2.9.6.data/scripts/resampletc +0 -23
  381. rapidtide-2.9.6.data/scripts/retroglm +0 -23
  382. rapidtide-2.9.6.data/scripts/roisummarize +0 -23
  383. rapidtide-2.9.6.data/scripts/runqualitycheck +0 -23
  384. rapidtide-2.9.6.data/scripts/showarbcorr +0 -23
  385. rapidtide-2.9.6.data/scripts/showhist +0 -23
  386. rapidtide-2.9.6.data/scripts/showstxcorr +0 -23
  387. rapidtide-2.9.6.data/scripts/showtc +0 -23
  388. rapidtide-2.9.6.data/scripts/showxcorr_legacy +0 -536
  389. rapidtide-2.9.6.data/scripts/showxcorrx +0 -23
  390. rapidtide-2.9.6.data/scripts/showxy +0 -23
  391. rapidtide-2.9.6.data/scripts/simdata +0 -23
  392. rapidtide-2.9.6.data/scripts/spatialdecomp +0 -23
  393. rapidtide-2.9.6.data/scripts/spatialfit +0 -23
  394. rapidtide-2.9.6.data/scripts/spatialmi +0 -23
  395. rapidtide-2.9.6.data/scripts/spectrogram +0 -23
  396. rapidtide-2.9.6.data/scripts/synthASL +0 -23
  397. rapidtide-2.9.6.data/scripts/tcfrom2col +0 -23
  398. rapidtide-2.9.6.data/scripts/tcfrom3col +0 -23
  399. rapidtide-2.9.6.data/scripts/temporaldecomp +0 -23
  400. rapidtide-2.9.6.data/scripts/threeD +0 -236
  401. rapidtide-2.9.6.data/scripts/tidepool +0 -23
  402. rapidtide-2.9.6.data/scripts/variabilityizer +0 -23
  403. rapidtide-2.9.6.dist-info/RECORD +0 -359
  404. rapidtide-2.9.6.dist-info/top_level.txt +0 -86
  405. {rapidtide-2.9.6.dist-info → rapidtide-3.1.3.dist-info/licenses}/LICENSE +0 -0
rapidtide-2.9.6.data/scripts/applydlfilter 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.applydlfilter as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.applydlfilter)
rapidtide-2.9.6.data/scripts/atlasaverage 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.atlasaverage as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.atlasaverage)
rapidtide-2.9.6.data/scripts/atlastool 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.atlastool as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.atlastool)
rapidtide-2.9.6.data/scripts/calcicc DELETED
@@ -1,22 +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.niftistats
20
-
21
- if __name__ == "__main__":
22
- rapidtide.workflows.niftistats.niftistats_main(calctype="icc")
rapidtide-2.9.6.data/scripts/calctexticc 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.calctexticc as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.calctexticc)
rapidtide-2.9.6.data/scripts/calcttest DELETED
@@ -1,22 +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.niftistats
20
-
21
- if __name__ == "__main__":
22
- rapidtide.workflows.niftistats.niftistats_main(calctype="ttest")
rapidtide-2.9.6.data/scripts/ccorrica 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.ccorrica as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.ccorrica)
rapidtide-2.9.6.data/scripts/diffrois 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.diffrois as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.diffrois)
rapidtide-2.9.6.data/scripts/endtidalproc 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.endtidalproc as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.endtidalproc)
rapidtide-2.9.6.data/scripts/filtnifti 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.filtnifti as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.filtnifti)
rapidtide-2.9.6.data/scripts/filttc 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.filttc as theworkflow
20
- import rapidtide.workflows.parser_funcs as pf
21
-
22
- if __name__ == "__main__":
23
- pf.generic_init(theworkflow._get_parser, theworkflow.filttc)