rapidtide 3.0.10__py3-none-any.whl → 3.1__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 (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
@@ -17,14 +17,40 @@
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  #
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  #
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  import argparse
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+ from argparse import Namespace
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+ from typing import Any, Callable, Dict, List, Optional, Tuple, Union
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  import numpy as np
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+ from numpy.typing import NDArray
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  import rapidtide.io as tide_io
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  import rapidtide.util as tide_util
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- def _get_parser():
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+ def _get_parser() -> Any:
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+ """
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+ Create and configure argument parser for command line interface.
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+
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+ This function initializes an ArgumentParser object with specific parameters
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+ required for processing three-column data files and generating time course output.
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+
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+ Returns
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+ -------
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+ argparse.ArgumentParser
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+ Configured argument parser object with all required and optional arguments
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+
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+ Notes
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+ -----
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+ The parser expects exactly four positional arguments followed by an optional
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+ debug flag. The function is designed for use with the tcfrom3col program.
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+
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+ Examples
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+ --------
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+ >>> parser = _get_parser()
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+ >>> args = parser.parse_args(['input.txt', '0.1', '100', 'output.txt'])
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+ >>> print(args.infilename)
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+ 'input.txt'
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+ """
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  # get the command line parameters
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  parser = argparse.ArgumentParser(
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  prog="tcfrom3col",
@@ -48,7 +74,53 @@ def _get_parser():
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  return parser
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- def tcfrom3col(args):
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+ def tcfrom3col(args: Any) -> None:
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+ """
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+ Convert three-column data to tidal constituent data.
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+
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+ This function reads three-column input data, processes it to extract tidal constituents,
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+ and writes the results to an output file. The input data is expected to contain time,
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+ latitude, and longitude columns, and the output contains tidal constituent information.
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+
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+ Parameters
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+ ----------
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+ args : Any
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+ An object containing the following attributes:
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+ - infilename : str
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+ Path to the input file containing three-column data
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+ - outfilename : str
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+ Path to the output file for writing tidal constituent data
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+ - numpoints : int
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+ Number of data points in the time series
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+ - timestep : float
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+ Time step between data points
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+ - debug : bool
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+ Flag to enable debug printing
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+
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+ Returns
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+ -------
102
+ None
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+ This function does not return a value but writes output to a file.
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+
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+ Notes
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+ -----
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+ The function uses `tide_io.readvecs` to read input data and `tide_util.maketcfrom3col`
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+ to perform the tidal constituent calculation. The time axis is generated using
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+ `np.arange` with the specified number of points and time step.
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+
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+ Examples
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+ --------
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+ >>> class Args:
114
+ ... def __init__(self):
115
+ ... self.infilename = 'input.dat'
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+ ... self.outfilename = 'output.dat'
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+ ... self.numpoints = 1000
118
+ ... self.timestep = 3600.0
119
+ ... self.debug = False
120
+ ...
121
+ >>> args = Args()
122
+ >>> tcfrom3col(args)
123
+ """
52
124
  if args.debug:
53
125
  print(args)
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