rapidtide 3.0.10__py3-none-any.whl → 3.1__py3-none-any.whl

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Files changed (141) hide show
  1. rapidtide/Colortables.py +492 -27
  2. rapidtide/OrthoImageItem.py +1053 -47
  3. rapidtide/RapidtideDataset.py +1533 -86
  4. rapidtide/_version.py +3 -3
  5. rapidtide/calccoherence.py +196 -29
  6. rapidtide/calcnullsimfunc.py +191 -40
  7. rapidtide/calcsimfunc.py +245 -42
  8. rapidtide/correlate.py +1210 -393
  9. rapidtide/data/examples/src/testLD +56 -0
  10. rapidtide/data/examples/src/testalign +1 -1
  11. rapidtide/data/examples/src/testdelayvar +0 -1
  12. rapidtide/data/examples/src/testfmri +19 -1
  13. rapidtide/data/examples/src/testglmfilt +5 -5
  14. rapidtide/data/examples/src/testhappy +30 -1
  15. rapidtide/data/examples/src/testppgproc +17 -0
  16. rapidtide/data/examples/src/testrolloff +11 -0
  17. rapidtide/data/models/model_cnn_pytorch/best_model.pth +0 -0
  18. rapidtide/data/models/model_cnn_pytorch/loss.png +0 -0
  19. rapidtide/data/models/model_cnn_pytorch/loss.txt +1 -0
  20. rapidtide/data/models/model_cnn_pytorch/model.pth +0 -0
  21. rapidtide/data/models/model_cnn_pytorch/model_meta.json +68 -0
  22. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm.nii.gz +0 -0
  23. rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm_mask.nii.gz +0 -0
  24. rapidtide/decorators.py +91 -0
  25. rapidtide/dlfilter.py +2225 -108
  26. rapidtide/dlfiltertorch.py +4843 -0
  27. rapidtide/externaltools.py +327 -12
  28. rapidtide/fMRIData_class.py +79 -40
  29. rapidtide/filter.py +1899 -810
  30. rapidtide/fit.py +2004 -574
  31. rapidtide/genericmultiproc.py +93 -18
  32. rapidtide/happy_supportfuncs.py +2044 -171
  33. rapidtide/helper_classes.py +584 -43
  34. rapidtide/io.py +2363 -370
  35. rapidtide/linfitfiltpass.py +341 -75
  36. rapidtide/makelaggedtcs.py +211 -20
  37. rapidtide/maskutil.py +423 -53
  38. rapidtide/miscmath.py +827 -121
  39. rapidtide/multiproc.py +210 -22
  40. rapidtide/patchmatch.py +234 -33
  41. rapidtide/peakeval.py +32 -30
  42. rapidtide/ppgproc.py +2203 -0
  43. rapidtide/qualitycheck.py +352 -39
  44. rapidtide/refinedelay.py +422 -57
  45. rapidtide/refineregressor.py +498 -184
  46. rapidtide/resample.py +671 -185
  47. rapidtide/scripts/applyppgproc.py +28 -0
  48. rapidtide/simFuncClasses.py +1052 -77
  49. rapidtide/simfuncfit.py +260 -46
  50. rapidtide/stats.py +540 -238
  51. rapidtide/tests/happycomp +9 -0
  52. rapidtide/tests/test_dlfiltertorch.py +627 -0
  53. rapidtide/tests/test_findmaxlag.py +24 -8
  54. rapidtide/tests/test_fullrunhappy_v1.py +0 -2
  55. rapidtide/tests/test_fullrunhappy_v2.py +0 -2
  56. rapidtide/tests/test_fullrunhappy_v3.py +1 -0
  57. rapidtide/tests/test_fullrunhappy_v4.py +2 -2
  58. rapidtide/tests/test_fullrunrapidtide_v7.py +1 -1
  59. rapidtide/tests/test_simroundtrip.py +8 -8
  60. rapidtide/tests/utils.py +9 -8
  61. rapidtide/tidepoolTemplate.py +142 -38
  62. rapidtide/tidepoolTemplate_alt.py +165 -44
  63. rapidtide/tidepoolTemplate_big.py +189 -52
  64. rapidtide/util.py +1217 -118
  65. rapidtide/voxelData.py +684 -37
  66. rapidtide/wiener.py +19 -12
  67. rapidtide/wiener2.py +113 -7
  68. rapidtide/wiener_doc.py +255 -0
  69. rapidtide/workflows/adjustoffset.py +105 -3
  70. rapidtide/workflows/aligntcs.py +85 -2
  71. rapidtide/workflows/applydlfilter.py +87 -10
  72. rapidtide/workflows/applyppgproc.py +522 -0
  73. rapidtide/workflows/atlasaverage.py +210 -47
  74. rapidtide/workflows/atlastool.py +100 -3
  75. rapidtide/workflows/calcSimFuncMap.py +294 -64
  76. rapidtide/workflows/calctexticc.py +201 -9
  77. rapidtide/workflows/ccorrica.py +97 -4
  78. rapidtide/workflows/cleanregressor.py +168 -29
  79. rapidtide/workflows/delayvar.py +163 -10
  80. rapidtide/workflows/diffrois.py +81 -3
  81. rapidtide/workflows/endtidalproc.py +144 -4
  82. rapidtide/workflows/fdica.py +195 -15
  83. rapidtide/workflows/filtnifti.py +70 -3
  84. rapidtide/workflows/filttc.py +74 -3
  85. rapidtide/workflows/fitSimFuncMap.py +206 -48
  86. rapidtide/workflows/fixtr.py +73 -3
  87. rapidtide/workflows/gmscalc.py +113 -3
  88. rapidtide/workflows/happy.py +813 -201
  89. rapidtide/workflows/happy2std.py +144 -12
  90. rapidtide/workflows/happy_parser.py +149 -8
  91. rapidtide/workflows/histnifti.py +118 -2
  92. rapidtide/workflows/histtc.py +84 -3
  93. rapidtide/workflows/linfitfilt.py +117 -4
  94. rapidtide/workflows/localflow.py +328 -28
  95. rapidtide/workflows/mergequality.py +79 -3
  96. rapidtide/workflows/niftidecomp.py +322 -18
  97. rapidtide/workflows/niftistats.py +174 -4
  98. rapidtide/workflows/pairproc.py +88 -2
  99. rapidtide/workflows/pairwisemergenifti.py +85 -2
  100. rapidtide/workflows/parser_funcs.py +1421 -40
  101. rapidtide/workflows/physiofreq.py +137 -11
  102. rapidtide/workflows/pixelcomp.py +208 -5
  103. rapidtide/workflows/plethquality.py +103 -21
  104. rapidtide/workflows/polyfitim.py +151 -11
  105. rapidtide/workflows/proj2flow.py +75 -2
  106. rapidtide/workflows/rankimage.py +111 -4
  107. rapidtide/workflows/rapidtide.py +272 -15
  108. rapidtide/workflows/rapidtide2std.py +98 -2
  109. rapidtide/workflows/rapidtide_parser.py +109 -9
  110. rapidtide/workflows/refineDelayMap.py +143 -33
  111. rapidtide/workflows/refineRegressor.py +682 -93
  112. rapidtide/workflows/regressfrommaps.py +152 -31
  113. rapidtide/workflows/resamplenifti.py +85 -3
  114. rapidtide/workflows/resampletc.py +91 -3
  115. rapidtide/workflows/retrolagtcs.py +98 -6
  116. rapidtide/workflows/retroregress.py +165 -9
  117. rapidtide/workflows/roisummarize.py +173 -5
  118. rapidtide/workflows/runqualitycheck.py +71 -3
  119. rapidtide/workflows/showarbcorr.py +147 -4
  120. rapidtide/workflows/showhist.py +86 -2
  121. rapidtide/workflows/showstxcorr.py +160 -3
  122. rapidtide/workflows/showtc.py +159 -3
  123. rapidtide/workflows/showxcorrx.py +184 -4
  124. rapidtide/workflows/showxy.py +185 -15
  125. rapidtide/workflows/simdata.py +262 -36
  126. rapidtide/workflows/spatialfit.py +77 -2
  127. rapidtide/workflows/spatialmi.py +251 -27
  128. rapidtide/workflows/spectrogram.py +305 -32
  129. rapidtide/workflows/synthASL.py +154 -3
  130. rapidtide/workflows/tcfrom2col.py +76 -2
  131. rapidtide/workflows/tcfrom3col.py +74 -2
  132. rapidtide/workflows/tidepool.py +2972 -133
  133. rapidtide/workflows/utils.py +19 -14
  134. rapidtide/workflows/utils_doc.py +293 -0
  135. rapidtide/workflows/variabilityizer.py +116 -3
  136. {rapidtide-3.0.10.dist-info → rapidtide-3.1.dist-info}/METADATA +10 -9
  137. {rapidtide-3.0.10.dist-info → rapidtide-3.1.dist-info}/RECORD +141 -122
  138. {rapidtide-3.0.10.dist-info → rapidtide-3.1.dist-info}/entry_points.txt +1 -0
  139. {rapidtide-3.0.10.dist-info → rapidtide-3.1.dist-info}/WHEEL +0 -0
  140. {rapidtide-3.0.10.dist-info → rapidtide-3.1.dist-info}/licenses/LICENSE +0 -0
  141. {rapidtide-3.0.10.dist-info → rapidtide-3.1.dist-info}/top_level.txt +0 -0
rapidtide/peakeval.py CHANGED
@@ -19,8 +19,10 @@
19
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  import gc
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  import logging
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  import warnings
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+ from typing import Any
22
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  import numpy as np
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+ from numpy.typing import NDArray
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  from tqdm import tqdm
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  import rapidtide.fit as tide_fit
@@ -32,19 +34,19 @@ LGR = logging.getLogger("GENERAL")
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34
 
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34
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  def _procOneVoxelPeaks(
35
- vox,
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- thetc,
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- theMutualInformationator,
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- fmri_x,
39
- fmritc,
40
- os_fmri_x,
41
- xcorr_x,
42
- thexcorr,
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- bipolar=False,
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- oversampfactor=1,
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- sort=True,
46
- interptype="univariate",
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- ):
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+ vox: int,
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+ thetc: NDArray,
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+ theMutualInformationator: Any,
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+ fmri_x: NDArray,
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+ fmritc: NDArray,
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+ os_fmri_x: NDArray,
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+ xcorr_x: NDArray,
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+ thexcorr: NDArray,
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+ bipolar: bool = False,
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+ oversampfactor: int = 1,
47
+ sort: bool = True,
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+ interptype: str = "univariate",
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+ ) -> tuple[int, list]:
48
50
  if oversampfactor >= 1:
49
51
  thetc[:] = tide_resample.doresample(fmri_x, fmritc, os_fmri_x, method=interptype)
50
52
  else:
@@ -63,23 +65,23 @@ def _procOneVoxelPeaks(
63
65
 
64
66
 
65
67
  def peakevalpass(
66
- fmridata,
67
- referencetc,
68
- fmri_x,
69
- os_fmri_x,
70
- theMutualInformationator,
71
- xcorr_x,
72
- corrdata,
73
- nprocs=1,
74
- alwaysmultiproc=False,
75
- bipolar=False,
76
- oversampfactor=1,
77
- interptype="univariate",
78
- showprogressbar=True,
79
- chunksize=1000,
80
- rt_floatset=np.float64,
81
- rt_floattype="float64",
82
- ):
68
+ fmridata: NDArray,
69
+ referencetc: NDArray,
70
+ fmri_x: NDArray,
71
+ os_fmri_x: NDArray,
72
+ theMutualInformationator: Any,
73
+ xcorr_x: NDArray,
74
+ corrdata: NDArray,
75
+ nprocs: int = 1,
76
+ alwaysmultiproc: bool = False,
77
+ bipolar: bool = False,
78
+ oversampfactor: int = 1,
79
+ interptype: str = "univariate",
80
+ showprogressbar: bool = True,
81
+ chunksize: int = 1000,
82
+ rt_floatset: type = np.float64,
83
+ rt_floattype: str = "float64",
84
+ ) -> tuple[int, dict]:
83
85
  """
84
86
 
85
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  Parameters