rapidtide 3.0.11__py3-none-any.whl → 3.1.1__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 (144) hide show
  1. rapidtide/Colortables.py +492 -27
  2. rapidtide/OrthoImageItem.py +1049 -46
  3. rapidtide/RapidtideDataset.py +1533 -86
  4. rapidtide/_version.py +3 -3
  5. rapidtide/calccoherence.py +196 -29
  6. rapidtide/calcnullsimfunc.py +188 -40
  7. rapidtide/calcsimfunc.py +242 -42
  8. rapidtide/correlate.py +1203 -383
  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 +53 -3
  13. rapidtide/data/examples/src/testglmfilt +5 -5
  14. rapidtide/data/examples/src/testhappy +29 -7
  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/decorators.py +91 -0
  23. rapidtide/dlfilter.py +2226 -110
  24. rapidtide/dlfiltertorch.py +4842 -0
  25. rapidtide/externaltools.py +327 -12
  26. rapidtide/fMRIData_class.py +79 -40
  27. rapidtide/filter.py +1899 -810
  28. rapidtide/fit.py +2011 -581
  29. rapidtide/genericmultiproc.py +93 -18
  30. rapidtide/happy_supportfuncs.py +2047 -172
  31. rapidtide/helper_classes.py +584 -43
  32. rapidtide/io.py +2370 -372
  33. rapidtide/linfitfiltpass.py +346 -99
  34. rapidtide/makelaggedtcs.py +210 -24
  35. rapidtide/maskutil.py +448 -62
  36. rapidtide/miscmath.py +827 -121
  37. rapidtide/multiproc.py +210 -22
  38. rapidtide/patchmatch.py +242 -42
  39. rapidtide/peakeval.py +31 -31
  40. rapidtide/ppgproc.py +2203 -0
  41. rapidtide/qualitycheck.py +352 -39
  42. rapidtide/refinedelay.py +431 -57
  43. rapidtide/refineregressor.py +494 -189
  44. rapidtide/resample.py +671 -185
  45. rapidtide/scripts/applyppgproc.py +28 -0
  46. rapidtide/scripts/showxcorr_legacy.py +7 -7
  47. rapidtide/scripts/stupidramtricks.py +15 -17
  48. rapidtide/simFuncClasses.py +1052 -77
  49. rapidtide/simfuncfit.py +269 -69
  50. rapidtide/stats.py +540 -238
  51. rapidtide/tests/happycomp +9 -0
  52. rapidtide/tests/test_cleanregressor.py +1 -2
  53. rapidtide/tests/test_dlfiltertorch.py +627 -0
  54. rapidtide/tests/test_findmaxlag.py +24 -8
  55. rapidtide/tests/test_fullrunhappy_v1.py +0 -2
  56. rapidtide/tests/test_fullrunhappy_v2.py +0 -2
  57. rapidtide/tests/test_fullrunhappy_v3.py +11 -4
  58. rapidtide/tests/test_fullrunhappy_v4.py +10 -2
  59. rapidtide/tests/test_fullrunrapidtide_v7.py +1 -1
  60. rapidtide/tests/test_getparsers.py +11 -3
  61. rapidtide/tests/test_refinedelay.py +0 -1
  62. rapidtide/tests/test_simroundtrip.py +16 -8
  63. rapidtide/tests/test_stcorrelate.py +3 -1
  64. rapidtide/tests/utils.py +9 -8
  65. rapidtide/tidepoolTemplate.py +142 -38
  66. rapidtide/tidepoolTemplate_alt.py +165 -44
  67. rapidtide/tidepoolTemplate_big.py +189 -52
  68. rapidtide/util.py +1217 -118
  69. rapidtide/voxelData.py +684 -37
  70. rapidtide/wiener.py +136 -23
  71. rapidtide/wiener2.py +113 -7
  72. rapidtide/workflows/adjustoffset.py +105 -3
  73. rapidtide/workflows/aligntcs.py +85 -2
  74. rapidtide/workflows/applydlfilter.py +87 -10
  75. rapidtide/workflows/applyppgproc.py +540 -0
  76. rapidtide/workflows/atlasaverage.py +210 -47
  77. rapidtide/workflows/atlastool.py +100 -3
  78. rapidtide/workflows/calcSimFuncMap.py +288 -69
  79. rapidtide/workflows/calctexticc.py +201 -9
  80. rapidtide/workflows/ccorrica.py +101 -6
  81. rapidtide/workflows/cleanregressor.py +165 -31
  82. rapidtide/workflows/delayvar.py +171 -23
  83. rapidtide/workflows/diffrois.py +81 -3
  84. rapidtide/workflows/endtidalproc.py +144 -4
  85. rapidtide/workflows/fdica.py +195 -15
  86. rapidtide/workflows/filtnifti.py +70 -3
  87. rapidtide/workflows/filttc.py +74 -3
  88. rapidtide/workflows/fitSimFuncMap.py +202 -51
  89. rapidtide/workflows/fixtr.py +73 -3
  90. rapidtide/workflows/gmscalc.py +113 -3
  91. rapidtide/workflows/happy.py +801 -199
  92. rapidtide/workflows/happy2std.py +144 -12
  93. rapidtide/workflows/happy_parser.py +163 -23
  94. rapidtide/workflows/histnifti.py +118 -2
  95. rapidtide/workflows/histtc.py +84 -3
  96. rapidtide/workflows/linfitfilt.py +117 -4
  97. rapidtide/workflows/localflow.py +328 -28
  98. rapidtide/workflows/mergequality.py +79 -3
  99. rapidtide/workflows/niftidecomp.py +322 -18
  100. rapidtide/workflows/niftistats.py +174 -4
  101. rapidtide/workflows/pairproc.py +98 -4
  102. rapidtide/workflows/pairwisemergenifti.py +85 -2
  103. rapidtide/workflows/parser_funcs.py +1421 -40
  104. rapidtide/workflows/physiofreq.py +137 -11
  105. rapidtide/workflows/pixelcomp.py +207 -5
  106. rapidtide/workflows/plethquality.py +103 -21
  107. rapidtide/workflows/polyfitim.py +151 -11
  108. rapidtide/workflows/proj2flow.py +75 -2
  109. rapidtide/workflows/rankimage.py +111 -4
  110. rapidtide/workflows/rapidtide.py +368 -76
  111. rapidtide/workflows/rapidtide2std.py +98 -2
  112. rapidtide/workflows/rapidtide_parser.py +109 -9
  113. rapidtide/workflows/refineDelayMap.py +144 -33
  114. rapidtide/workflows/refineRegressor.py +675 -96
  115. rapidtide/workflows/regressfrommaps.py +161 -37
  116. rapidtide/workflows/resamplenifti.py +85 -3
  117. rapidtide/workflows/resampletc.py +91 -3
  118. rapidtide/workflows/retrolagtcs.py +99 -9
  119. rapidtide/workflows/retroregress.py +176 -26
  120. rapidtide/workflows/roisummarize.py +174 -5
  121. rapidtide/workflows/runqualitycheck.py +71 -3
  122. rapidtide/workflows/showarbcorr.py +149 -6
  123. rapidtide/workflows/showhist.py +86 -2
  124. rapidtide/workflows/showstxcorr.py +160 -3
  125. rapidtide/workflows/showtc.py +159 -3
  126. rapidtide/workflows/showxcorrx.py +190 -10
  127. rapidtide/workflows/showxy.py +185 -15
  128. rapidtide/workflows/simdata.py +264 -38
  129. rapidtide/workflows/spatialfit.py +77 -2
  130. rapidtide/workflows/spatialmi.py +250 -27
  131. rapidtide/workflows/spectrogram.py +305 -32
  132. rapidtide/workflows/synthASL.py +154 -3
  133. rapidtide/workflows/tcfrom2col.py +76 -2
  134. rapidtide/workflows/tcfrom3col.py +74 -2
  135. rapidtide/workflows/tidepool.py +2971 -130
  136. rapidtide/workflows/utils.py +19 -14
  137. rapidtide/workflows/utils_doc.py +293 -0
  138. rapidtide/workflows/variabilityizer.py +116 -3
  139. {rapidtide-3.0.11.dist-info → rapidtide-3.1.1.dist-info}/METADATA +10 -8
  140. {rapidtide-3.0.11.dist-info → rapidtide-3.1.1.dist-info}/RECORD +144 -128
  141. {rapidtide-3.0.11.dist-info → rapidtide-3.1.1.dist-info}/entry_points.txt +1 -0
  142. {rapidtide-3.0.11.dist-info → rapidtide-3.1.1.dist-info}/WHEEL +0 -0
  143. {rapidtide-3.0.11.dist-info → rapidtide-3.1.1.dist-info}/licenses/LICENSE +0 -0
  144. {rapidtide-3.0.11.dist-info → rapidtide-3.1.1.dist-info}/top_level.txt +0 -0
rapidtide/peakeval.py CHANGED
@@ -19,8 +19,10 @@
19
19
  import gc
20
20
  import logging
21
21
  import warnings
22
+ from typing import Any
22
23
 
23
24
  import numpy as np
25
+ from numpy.typing import NDArray
24
26
  from tqdm import tqdm
25
27
 
26
28
  import rapidtide.fit as tide_fit
@@ -32,19 +34,19 @@ LGR = logging.getLogger("GENERAL")
32
34
 
33
35
 
34
36
  def _procOneVoxelPeaks(
35
- vox,
36
- thetc,
37
- theMutualInformationator,
38
- fmri_x,
39
- fmritc,
40
- os_fmri_x,
41
- xcorr_x,
42
- thexcorr,
43
- bipolar=False,
44
- oversampfactor=1,
45
- sort=True,
46
- interptype="univariate",
47
- ):
37
+ vox: int,
38
+ thetc: NDArray,
39
+ theMutualInformationator: Any,
40
+ fmri_x: NDArray,
41
+ fmritc: NDArray,
42
+ os_fmri_x: NDArray,
43
+ xcorr_x: NDArray,
44
+ thexcorr: NDArray,
45
+ bipolar: bool = False,
46
+ oversampfactor: int = 1,
47
+ sort: bool = True,
48
+ interptype: str = "univariate",
49
+ ) -> 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 +65,22 @@ 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_floattype: np.dtype = np.float64,
83
+ ) -> tuple[int, dict]:
83
84
  """
84
85
 
85
86
  Parameters
@@ -98,7 +99,6 @@ def peakevalpass(
98
99
  interptype
99
100
  showprogressbar
100
101
  chunksize
101
- rt_floatset
102
102
  rt_floattype
103
103
 
104
104
  Returns