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/ffttools.py ADDED
@@ -0,0 +1,168 @@
1
+ #!/usr/bin/env python
2
+ # -*- coding: utf-8 -*-
3
+ #
4
+ # Copyright 2016-2025 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 warnings
20
+
21
+ import numpy as np
22
+ from scipy import fftpack
23
+
24
+ with warnings.catch_warnings():
25
+ warnings.simplefilter("ignore")
26
+ try:
27
+ import pyfftw
28
+ except ImportError:
29
+ pyfftwpresent = False
30
+ else:
31
+ pyfftwpresent = True
32
+
33
+ if pyfftwpresent:
34
+ fftpack = pyfftw.interfaces.scipy_fftpack
35
+ pyfftw.interfaces.cache.enable()
36
+
37
+
38
+ def primefacs(thelen: int) -> list:
39
+ """
40
+ Compute the prime factorization of a given integer.
41
+
42
+ Parameters
43
+ ----------
44
+ thelen : int
45
+ The positive integer to factorize. Must be greater than 0.
46
+
47
+ Returns
48
+ -------
49
+ list
50
+ A list of prime factors of `thelen`, sorted in ascending order.
51
+ Each factor appears as many times as its multiplicity in the
52
+ prime factorization.
53
+
54
+ Notes
55
+ -----
56
+ This function implements trial division algorithm to find prime factors.
57
+ The algorithm starts with the smallest prime (2) and continues with
58
+ increasing integers until the square root of the remaining number.
59
+ The final remaining number (if greater than 1) is also a prime factor.
60
+
61
+ Examples
62
+ --------
63
+ >>> primefacs(12)
64
+ [2, 2, 3]
65
+
66
+ >>> primefacs(17)
67
+ [17]
68
+
69
+ >>> primefacs(100)
70
+ [2, 2, 5, 5]
71
+ """
72
+ i = 2
73
+ factors = []
74
+ while i * i <= thelen:
75
+ if thelen % i:
76
+ i += 1
77
+ else:
78
+ factors.append(i)
79
+ thelen //= i
80
+ factors.append(thelen)
81
+ return factors
82
+
83
+
84
+ lencache: dict = {}
85
+
86
+
87
+ def optfftlen(
88
+ thelen: np.uint64, padlen: np.uint64 = 0, _depth: int = 0, debug: bool = False
89
+ ) -> np.uint64:
90
+ """
91
+ Calculate optimal FFT length for given input length.
92
+
93
+ This function currently returns the input length as-is, but is designed
94
+ to be extended for optimal FFT length calculation based on hardware
95
+ constraints or performance considerations.
96
+
97
+ Parameters
98
+ ----------
99
+ thelen : int
100
+ The input length for which to calculate optimal FFT length.
101
+ Must be a positive integer.
102
+ padlen : optional, int
103
+ Number of points the data is symmetrically padded with. Ensure that
104
+ the optimal length accounts for symmetric padding. Default is 0.
105
+ _depth: optional, int
106
+ How deep we are in the recursion
107
+ debug :optional, bool
108
+ Print out detailed information about how the length is calculated. Default is False.
109
+
110
+ Returns
111
+ -------
112
+ int
113
+ The optimal FFT length. If not using pyfftw, this
114
+ simply returns the input `thelen` value.
115
+
116
+ Notes
117
+ -----
118
+ In a more complete implementation, this function would calculate
119
+ the optimal FFT length by finding the smallest number >= thelen
120
+ that has only small prime factors (2, 3, 5, 7) for optimal
121
+ performance on most FFT implementations.
122
+
123
+ Examples
124
+ --------
125
+ >>> optfftlen(1024)
126
+ 1024
127
+ >>> optfftlen(1000)
128
+ 1000
129
+ """
130
+ cachekey = f"{thelen}_{padlen}"
131
+ if debug:
132
+ print(
133
+ f"entering optfftlen with {thelen=}, {padlen=}, {_depth=}, {cachekey=} totallen={thelen + 2 * padlen}"
134
+ )
135
+ if pyfftwpresent:
136
+ try:
137
+ thelen = lencache[cachekey]
138
+ if debug:
139
+ print(f"cache hit for {cachekey} ({thelen})")
140
+ except KeyError:
141
+ if padlen == 0:
142
+ thelen = pyfftw.interfaces.scipy_fft.next_fast_len(thelen)
143
+ else:
144
+ startlen = thelen
145
+ optpadded = pyfftw.interfaces.scipy_fft.next_fast_len(thelen + 2 * padlen)
146
+ if debug:
147
+ print(f"{optpadded=}")
148
+ if (optpadded - thelen) % 2 == 0:
149
+ thelen = optpadded
150
+ else:
151
+ # we get here if the optimal value - the initial value is not divisible by 2
152
+ # so we need to start one greater than that and and go to the next highest value.
153
+ if _depth < 500:
154
+ newpadlen = int((optpadded + 1 - startlen) // 2)
155
+ thelen = optfftlen(thelen, padlen=newpadlen, _depth=(_depth + 1))
156
+ else:
157
+ thelen = initval
158
+
159
+ lencache[cachekey] = thelen
160
+ if debug:
161
+ print(f"optfftlen returning {thelen=}")
162
+ return thelen
163
+
164
+
165
+ def showfftcache() -> None:
166
+ print("FFT length cache entries:")
167
+ for key, value in enumerate(lencache):
168
+ print(f"\t{key}: {value}, {lencache[value]}, {primefacs(lencache[value])}")