PyPI - rapidtide - Versions diffs - 2.9.6__py3-none-any.whl → 3.1.3__py3-none-any.whl - Mend

rapidtide 2.9.6py3-none-any.whl → 3.1.3py3-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

cloud/gmscalc-HCPYA +1 -1
cloud/mount-and-run +2 -0
cloud/rapidtide-HCPYA +3 -3
rapidtide/Colortables.py +538 -38
rapidtide/OrthoImageItem.py +1094 -51
rapidtide/RapidtideDataset.py +1709 -114
rapidtide/__init__.py +0 -8
rapidtide/_version.py +4 -4
rapidtide/calccoherence.py +242 -97
rapidtide/calcnullsimfunc.py +240 -140
rapidtide/calcsimfunc.py +314 -129
rapidtide/correlate.py +1211 -389
rapidtide/data/examples/src/testLD +56 -0
rapidtide/data/examples/src/test_findmaxlag.py +2 -2
rapidtide/data/examples/src/test_mlregressallt.py +32 -17
rapidtide/data/examples/src/testalign +1 -1
rapidtide/data/examples/src/testatlasaverage +35 -7
rapidtide/data/examples/src/testboth +21 -0
rapidtide/data/examples/src/testcifti +11 -0
rapidtide/data/examples/src/testdelayvar +13 -0
rapidtide/data/examples/src/testdlfilt +25 -0
rapidtide/data/examples/src/testfft +35 -0
rapidtide/data/examples/src/testfileorfloat +37 -0
rapidtide/data/examples/src/testfmri +92 -42
rapidtide/data/examples/src/testfuncs +3 -3
rapidtide/data/examples/src/testglmfilt +8 -6
rapidtide/data/examples/src/testhappy +84 -51
rapidtide/data/examples/src/testinitdelay +19 -0
rapidtide/data/examples/src/testmodels +33 -0
rapidtide/data/examples/src/testnewrefine +26 -0
rapidtide/data/examples/src/testnoiseamp +2 -2
rapidtide/data/examples/src/testppgproc +17 -0
rapidtide/data/examples/src/testrefineonly +22 -0
rapidtide/data/examples/src/testretro +26 -13
rapidtide/data/examples/src/testretrolagtcs +16 -0
rapidtide/data/examples/src/testrolloff +11 -0
rapidtide/data/examples/src/testsimdata +45 -28
rapidtide/data/models/model_cnn_pytorch/loss.png +0 -0
rapidtide/data/models/model_cnn_pytorch/loss.txt +1 -0
rapidtide/data/models/model_cnn_pytorch/model.pth +0 -0
rapidtide/data/models/model_cnn_pytorch/model_meta.json +68 -0
rapidtide/data/models/model_cnn_pytorch_fulldata/loss.png +0 -0
rapidtide/data/models/model_cnn_pytorch_fulldata/loss.txt +1 -0
rapidtide/data/models/model_cnn_pytorch_fulldata/model.pth +0 -0
rapidtide/data/models/model_cnn_pytorch_fulldata/model_meta.json +80 -0
rapidtide/data/models/model_cnnbp_pytorch_fullldata/loss.png +0 -0
rapidtide/data/models/model_cnnbp_pytorch_fullldata/loss.txt +1 -0
rapidtide/data/models/model_cnnbp_pytorch_fullldata/model.pth +0 -0
rapidtide/data/models/model_cnnbp_pytorch_fullldata/model_meta.json +138 -0
rapidtide/data/models/model_cnnfft_pytorch_fulldata/loss.png +0 -0
rapidtide/data/models/model_cnnfft_pytorch_fulldata/loss.txt +1 -0
rapidtide/data/models/model_cnnfft_pytorch_fulldata/model.pth +0 -0
rapidtide/data/models/model_cnnfft_pytorch_fulldata/model_meta.json +128 -0
rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/loss.png +0 -0
rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/loss.txt +1 -0
rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/model.pth +0 -0
rapidtide/data/models/model_ppgattention_pytorch_w128_fulldata/model_meta.json +49 -0
rapidtide/data/models/model_revised_tf2/model.keras +0 -0
rapidtide/data/models/{model_serdar → model_revised_tf2}/model_meta.json +1 -1
rapidtide/data/models/model_serdar2_tf2/model.keras +0 -0
rapidtide/data/models/{model_serdar2 → model_serdar2_tf2}/model_meta.json +1 -1
rapidtide/data/models/model_serdar_tf2/model.keras +0 -0
rapidtide/data/models/{model_revised → model_serdar_tf2}/model_meta.json +1 -1
rapidtide/data/reference/HCP1200v2_MTT_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_binmask_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_csf_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_gray_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_graylaghist.json +7 -0
rapidtide/data/reference/HCP1200v2_graylaghist.tsv.gz +0 -0
rapidtide/data/reference/HCP1200v2_laghist.json +7 -0
rapidtide/data/reference/HCP1200v2_laghist.tsv.gz +0 -0
rapidtide/data/reference/HCP1200v2_mask_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_maxcorr_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_maxtime_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_maxwidth_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_negmask_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_timepercentile_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_white_2mm.nii.gz +0 -0
rapidtide/data/reference/HCP1200v2_whitelaghist.json +7 -0
rapidtide/data/reference/HCP1200v2_whitelaghist.tsv.gz +0 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2.xml +131 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2_regions.txt +60 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2_space-MNI152NLin6Asym_2mm.nii.gz +0 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm.nii.gz +0 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm_mask.nii.gz +0 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin6Asym_2mm_mask.nii.gz +0 -0
rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL2_space-MNI152NLin6Asym_2mm_mask.nii.gz +0 -0
rapidtide/data/reference/MNI152_T1_1mm_Brain_FAST_seg.nii.gz +0 -0
rapidtide/data/reference/MNI152_T1_1mm_Brain_Mask.nii.gz +0 -0
rapidtide/data/reference/MNI152_T1_2mm_Brain_FAST_seg.nii.gz +0 -0
rapidtide/data/reference/MNI152_T1_2mm_Brain_Mask.nii.gz +0 -0
rapidtide/decorators.py +91 -0
rapidtide/dlfilter.py +2553 -414
rapidtide/dlfiltertorch.py +5201 -0
rapidtide/externaltools.py +328 -13
rapidtide/fMRIData_class.py +108 -92
rapidtide/ffttools.py +168 -0
rapidtide/filter.py +2704 -1462
rapidtide/fit.py +2361 -579
rapidtide/genericmultiproc.py +197 -0
rapidtide/happy_supportfuncs.py +3255 -548
rapidtide/helper_classes.py +587 -1116
rapidtide/io.py +2569 -468
rapidtide/linfitfiltpass.py +784 -0
rapidtide/makelaggedtcs.py +267 -97
rapidtide/maskutil.py +555 -25
rapidtide/miscmath.py +835 -144
rapidtide/multiproc.py +217 -44
rapidtide/patchmatch.py +752 -0
rapidtide/peakeval.py +32 -32
rapidtide/ppgproc.py +2205 -0
rapidtide/qualitycheck.py +353 -40
rapidtide/refinedelay.py +854 -0
rapidtide/refineregressor.py +939 -0
rapidtide/resample.py +725 -204
rapidtide/scripts/__init__.py +1 -0
rapidtide/scripts/{adjustoffset → adjustoffset.py} +7 -2
rapidtide/scripts/{aligntcs → aligntcs.py} +7 -2
rapidtide/scripts/{applydlfilter → applydlfilter.py} +7 -2
rapidtide/scripts/applyppgproc.py +28 -0
rapidtide/scripts/{atlasaverage → atlasaverage.py} +7 -2
rapidtide/scripts/{atlastool → atlastool.py} +7 -2
rapidtide/scripts/{calcicc → calcicc.py} +7 -2
rapidtide/scripts/{calctexticc → calctexticc.py} +7 -2
rapidtide/scripts/{calcttest → calcttest.py} +7 -2
rapidtide/scripts/{ccorrica → ccorrica.py} +7 -2
rapidtide/scripts/delayvar.py +28 -0
rapidtide/scripts/{diffrois → diffrois.py} +7 -2
rapidtide/scripts/{endtidalproc → endtidalproc.py} +7 -2
rapidtide/scripts/{fdica → fdica.py} +7 -2
rapidtide/scripts/{filtnifti → filtnifti.py} +7 -2
rapidtide/scripts/{filttc → filttc.py} +7 -2
rapidtide/scripts/{fingerprint → fingerprint.py} +20 -16
rapidtide/scripts/{fixtr → fixtr.py} +7 -2
rapidtide/scripts/{gmscalc → gmscalc.py} +7 -2
rapidtide/scripts/{happy → happy.py} +7 -2
rapidtide/scripts/{happy2std → happy2std.py} +7 -2
rapidtide/scripts/{happywarp → happywarp.py} +8 -4
rapidtide/scripts/{histnifti → histnifti.py} +7 -2
rapidtide/scripts/{histtc → histtc.py} +7 -2
rapidtide/scripts/{glmfilt → linfitfilt.py} +7 -4
rapidtide/scripts/{localflow → localflow.py} +7 -2
rapidtide/scripts/{mergequality → mergequality.py} +7 -2
rapidtide/scripts/{pairproc → pairproc.py} +7 -2
rapidtide/scripts/{pairwisemergenifti → pairwisemergenifti.py} +7 -2
rapidtide/scripts/{physiofreq → physiofreq.py} +7 -2
rapidtide/scripts/{pixelcomp → pixelcomp.py} +7 -2
rapidtide/scripts/{plethquality → plethquality.py} +7 -2
rapidtide/scripts/{polyfitim → polyfitim.py} +7 -2
rapidtide/scripts/{proj2flow → proj2flow.py} +7 -2
rapidtide/scripts/{rankimage → rankimage.py} +7 -2
rapidtide/scripts/{rapidtide → rapidtide.py} +7 -2
rapidtide/scripts/{rapidtide2std → rapidtide2std.py} +7 -2
rapidtide/scripts/{resamplenifti → resamplenifti.py} +7 -2
rapidtide/scripts/{resampletc → resampletc.py} +7 -2
rapidtide/scripts/retrolagtcs.py +28 -0
rapidtide/scripts/retroregress.py +28 -0
rapidtide/scripts/{roisummarize → roisummarize.py} +7 -2
rapidtide/scripts/{runqualitycheck → runqualitycheck.py} +7 -2
rapidtide/scripts/{showarbcorr → showarbcorr.py} +7 -2
rapidtide/scripts/{showhist → showhist.py} +7 -2
rapidtide/scripts/{showstxcorr → showstxcorr.py} +7 -2
rapidtide/scripts/{showtc → showtc.py} +7 -2
rapidtide/scripts/{showxcorr_legacy → showxcorr_legacy.py} +8 -8
rapidtide/scripts/{showxcorrx → showxcorrx.py} +7 -2
rapidtide/scripts/{showxy → showxy.py} +7 -2
rapidtide/scripts/{simdata → simdata.py} +7 -2
rapidtide/scripts/{spatialdecomp → spatialdecomp.py} +7 -2
rapidtide/scripts/{spatialfit → spatialfit.py} +7 -2
rapidtide/scripts/{spatialmi → spatialmi.py} +7 -2
rapidtide/scripts/{spectrogram → spectrogram.py} +7 -2
rapidtide/scripts/stupidramtricks.py +238 -0
rapidtide/scripts/{synthASL → synthASL.py} +7 -2
rapidtide/scripts/{tcfrom2col → tcfrom2col.py} +7 -2
rapidtide/scripts/{tcfrom3col → tcfrom3col.py} +7 -2
rapidtide/scripts/{temporaldecomp → temporaldecomp.py} +7 -2
rapidtide/scripts/{testhrv → testhrv.py} +1 -1
rapidtide/scripts/{threeD → threeD.py} +7 -2
rapidtide/scripts/{tidepool → tidepool.py} +7 -2
rapidtide/scripts/{variabilityizer → variabilityizer.py} +7 -2
rapidtide/simFuncClasses.py +2113 -0
rapidtide/simfuncfit.py +312 -108
rapidtide/stats.py +579 -247
rapidtide/tests/.coveragerc +27 -6
rapidtide-2.9.6.data/scripts/fdica → rapidtide/tests/cleanposttest +4 -6
rapidtide/tests/happycomp +9 -0
rapidtide/tests/resethappytargets +1 -1
rapidtide/tests/resetrapidtidetargets +1 -1
rapidtide/tests/resettargets +1 -1
rapidtide/tests/runlocaltest +3 -3
rapidtide/tests/showkernels +1 -1
rapidtide/tests/test_aliasedcorrelate.py +4 -4
rapidtide/tests/test_aligntcs.py +1 -1
rapidtide/tests/test_calcicc.py +1 -1
rapidtide/tests/test_cleanregressor.py +184 -0
rapidtide/tests/test_congrid.py +70 -81
rapidtide/tests/test_correlate.py +1 -1
rapidtide/tests/test_corrpass.py +4 -4
rapidtide/tests/test_delayestimation.py +54 -59
rapidtide/tests/test_dlfiltertorch.py +437 -0
rapidtide/tests/test_doresample.py +2 -2
rapidtide/tests/test_externaltools.py +69 -0
rapidtide/tests/test_fastresampler.py +9 -5
rapidtide/tests/test_filter.py +96 -57
rapidtide/tests/test_findmaxlag.py +50 -19
rapidtide/tests/test_fullrunhappy_v1.py +15 -10
rapidtide/tests/test_fullrunhappy_v2.py +19 -13
rapidtide/tests/test_fullrunhappy_v3.py +28 -13
rapidtide/tests/test_fullrunhappy_v4.py +30 -11
rapidtide/tests/test_fullrunhappy_v5.py +62 -0
rapidtide/tests/test_fullrunrapidtide_v1.py +61 -7
rapidtide/tests/test_fullrunrapidtide_v2.py +26 -14
rapidtide/tests/test_fullrunrapidtide_v3.py +28 -8
rapidtide/tests/test_fullrunrapidtide_v4.py +16 -8
rapidtide/tests/test_fullrunrapidtide_v5.py +15 -6
rapidtide/tests/test_fullrunrapidtide_v6.py +142 -0
rapidtide/tests/test_fullrunrapidtide_v7.py +114 -0
rapidtide/tests/test_fullrunrapidtide_v8.py +66 -0
rapidtide/tests/test_getparsers.py +158 -0
rapidtide/tests/test_io.py +59 -18
rapidtide/tests/{test_glmpass.py → test_linfitfiltpass.py} +10 -10
rapidtide/tests/test_mi.py +1 -1
rapidtide/tests/test_miscmath.py +1 -1
rapidtide/tests/test_motionregress.py +5 -5
rapidtide/tests/test_nullcorr.py +6 -9
rapidtide/tests/test_padvec.py +216 -0
rapidtide/tests/test_parserfuncs.py +101 -0
rapidtide/tests/test_phaseanalysis.py +1 -1
rapidtide/tests/test_rapidtideparser.py +59 -53
rapidtide/tests/test_refinedelay.py +296 -0
rapidtide/tests/test_runmisc.py +5 -5
rapidtide/tests/test_sharedmem.py +60 -0
rapidtide/tests/test_simroundtrip.py +132 -0
rapidtide/tests/test_simulate.py +1 -1
rapidtide/tests/test_stcorrelate.py +4 -2
rapidtide/tests/test_timeshift.py +2 -2
rapidtide/tests/test_valtoindex.py +1 -1
rapidtide/tests/test_zRapidtideDataset.py +5 -3
rapidtide/tests/utils.py +10 -9
rapidtide/tidepoolTemplate.py +88 -70
rapidtide/tidepoolTemplate.ui +60 -46
rapidtide/tidepoolTemplate_alt.py +88 -53
rapidtide/tidepoolTemplate_alt.ui +62 -52
rapidtide/tidepoolTemplate_alt_qt6.py +921 -0
rapidtide/tidepoolTemplate_big.py +1125 -0
rapidtide/tidepoolTemplate_big.ui +2386 -0
rapidtide/tidepoolTemplate_big_qt6.py +1129 -0
rapidtide/tidepoolTemplate_qt6.py +793 -0
rapidtide/util.py +1389 -148
rapidtide/voxelData.py +1048 -0
rapidtide/wiener.py +138 -25
rapidtide/wiener2.py +114 -8
rapidtide/workflows/adjustoffset.py +107 -5
rapidtide/workflows/aligntcs.py +86 -3
rapidtide/workflows/applydlfilter.py +231 -89
rapidtide/workflows/applyppgproc.py +540 -0
rapidtide/workflows/atlasaverage.py +309 -48
rapidtide/workflows/atlastool.py +130 -9
rapidtide/workflows/calcSimFuncMap.py +490 -0
rapidtide/workflows/calctexticc.py +202 -10
rapidtide/workflows/ccorrica.py +123 -15
rapidtide/workflows/cleanregressor.py +415 -0
rapidtide/workflows/delayvar.py +1268 -0
rapidtide/workflows/diffrois.py +84 -6
rapidtide/workflows/endtidalproc.py +149 -9
rapidtide/workflows/fdica.py +197 -17
rapidtide/workflows/filtnifti.py +71 -4
rapidtide/workflows/filttc.py +76 -5
rapidtide/workflows/fitSimFuncMap.py +578 -0
rapidtide/workflows/fixtr.py +74 -4
rapidtide/workflows/gmscalc.py +116 -6
rapidtide/workflows/happy.py +1242 -480
rapidtide/workflows/happy2std.py +145 -13
rapidtide/workflows/happy_parser.py +277 -59
rapidtide/workflows/histnifti.py +120 -4
rapidtide/workflows/histtc.py +85 -4
rapidtide/workflows/{glmfilt.py → linfitfilt.py} +128 -14
rapidtide/workflows/localflow.py +329 -29
rapidtide/workflows/mergequality.py +80 -4
rapidtide/workflows/niftidecomp.py +323 -19
rapidtide/workflows/niftistats.py +178 -8
rapidtide/workflows/pairproc.py +99 -5
rapidtide/workflows/pairwisemergenifti.py +86 -3
rapidtide/workflows/parser_funcs.py +1488 -56
rapidtide/workflows/physiofreq.py +139 -12
rapidtide/workflows/pixelcomp.py +211 -9
rapidtide/workflows/plethquality.py +105 -23
rapidtide/workflows/polyfitim.py +159 -19
rapidtide/workflows/proj2flow.py +76 -3
rapidtide/workflows/rankimage.py +115 -8
rapidtide/workflows/rapidtide.py +1785 -1858
rapidtide/workflows/rapidtide2std.py +101 -3
rapidtide/workflows/rapidtide_parser.py +590 -389
rapidtide/workflows/refineDelayMap.py +249 -0
rapidtide/workflows/refineRegressor.py +1215 -0
rapidtide/workflows/regressfrommaps.py +308 -0
rapidtide/workflows/resamplenifti.py +86 -4
rapidtide/workflows/resampletc.py +92 -4
rapidtide/workflows/retrolagtcs.py +442 -0
rapidtide/workflows/retroregress.py +1501 -0
rapidtide/workflows/roisummarize.py +176 -7
rapidtide/workflows/runqualitycheck.py +72 -7
rapidtide/workflows/showarbcorr.py +172 -16
rapidtide/workflows/showhist.py +87 -3
rapidtide/workflows/showstxcorr.py +161 -4
rapidtide/workflows/showtc.py +172 -10
rapidtide/workflows/showxcorrx.py +250 -62
rapidtide/workflows/showxy.py +186 -16
rapidtide/workflows/simdata.py +418 -112
rapidtide/workflows/spatialfit.py +83 -8
rapidtide/workflows/spatialmi.py +252 -29
rapidtide/workflows/spectrogram.py +306 -33
rapidtide/workflows/synthASL.py +157 -6
rapidtide/workflows/tcfrom2col.py +77 -3
rapidtide/workflows/tcfrom3col.py +75 -3
rapidtide/workflows/tidepool.py +3829 -666
rapidtide/workflows/utils.py +45 -19
rapidtide/workflows/utils_doc.py +293 -0
rapidtide/workflows/variabilityizer.py +118 -5
{rapidtide-2.9.6.dist-info → rapidtide-3.1.3.dist-info}/METADATA +30 -223
rapidtide-3.1.3.dist-info/RECORD +393 -0
{rapidtide-2.9.6.dist-info → rapidtide-3.1.3.dist-info}/WHEEL +1 -1
rapidtide-3.1.3.dist-info/entry_points.txt +65 -0
rapidtide-3.1.3.dist-info/top_level.txt +2 -0
rapidtide/calcandfitcorrpairs.py +0 -262
rapidtide/data/examples/src/testoutputsize +0 -45
rapidtide/data/models/model_revised/model.h5 +0 -0
rapidtide/data/models/model_serdar/model.h5 +0 -0
rapidtide/data/models/model_serdar2/model.h5 +0 -0
rapidtide/data/reference/ASPECTS_nlin_asym_09c_2mm.nii.gz +0 -0
rapidtide/data/reference/ASPECTS_nlin_asym_09c_2mm_mask.nii.gz +0 -0
rapidtide/data/reference/ATTbasedFlowTerritories_split_nlin_asym_09c_2mm.nii.gz +0 -0
rapidtide/data/reference/ATTbasedFlowTerritories_split_nlin_asym_09c_2mm_mask.nii.gz +0 -0
rapidtide/data/reference/HCP1200_binmask_2mm_2009c_asym.nii.gz +0 -0
rapidtide/data/reference/HCP1200_lag_2mm_2009c_asym.nii.gz +0 -0
rapidtide/data/reference/HCP1200_mask_2mm_2009c_asym.nii.gz +0 -0
rapidtide/data/reference/HCP1200_negmask_2mm_2009c_asym.nii.gz +0 -0
rapidtide/data/reference/HCP1200_sigma_2mm_2009c_asym.nii.gz +0 -0
rapidtide/data/reference/HCP1200_strength_2mm_2009c_asym.nii.gz +0 -0
rapidtide/glmpass.py +0 -434
rapidtide/refine_factored.py +0 -641
rapidtide/scripts/retroglm +0 -23
rapidtide/workflows/glmfrommaps.py +0 -202
rapidtide/workflows/retroglm.py +0 -643
rapidtide-2.9.6.data/scripts/adjustoffset +0 -23
rapidtide-2.9.6.data/scripts/aligntcs +0 -23
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{rapidtide-2.9.6.dist-info → rapidtide-3.1.3.dist-info/licenses}/LICENSE +0 -0

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{rapidtide-2.9.6.dist-info → rapidtide-3.1.3.dist-info/licenses}/LICENSE RENAMED Viewed

File without changes

rapidtide 2.9.6__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide 2.9.6py3-none-any.whl → 3.1.3py3-none-any.whl