rapidtide 3.0a11__py3-none-any.whl → 3.0a13__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 (73) hide show
  1. cloud/gmscalc-HCPYA +1 -1
  2. cloud/rapidtide-HCPYA +3 -3
  3. rapidtide/Colortables.py +10 -10
  4. rapidtide/DerivativeDelay.py +211 -0
  5. rapidtide/RegressorRefiner.py +464 -0
  6. rapidtide/__init__.py +2 -1
  7. rapidtide/_version.py +1 -1
  8. rapidtide/data/examples/src/test_mlregressallt.py +32 -17
  9. rapidtide/data/examples/src/testalign +1 -1
  10. rapidtide/data/examples/src/testboth +1 -1
  11. rapidtide/data/examples/src/testcifti +11 -0
  12. rapidtide/data/examples/src/testdelayvar +13 -0
  13. rapidtide/data/examples/src/testfmri +3 -124
  14. rapidtide/data/examples/src/testglmfilt +8 -6
  15. rapidtide/data/examples/src/testhappy +1 -1
  16. rapidtide/data/examples/src/testinitdelay +19 -0
  17. rapidtide/data/examples/src/testnewrefine +49 -0
  18. rapidtide/data/examples/src/testnoiseamp +2 -2
  19. rapidtide/data/examples/src/testrefineonly +22 -0
  20. rapidtide/data/examples/src/testretro +16 -7
  21. rapidtide/data/examples/src/testretrolagtcs +1 -1
  22. rapidtide/dlfilter.py +0 -1
  23. rapidtide/fit.py +41 -9
  24. rapidtide/happy_supportfuncs.py +5 -0
  25. rapidtide/io.py +13 -2
  26. rapidtide/{glmpass.py → linfitfiltpass.py} +29 -20
  27. rapidtide/refinedelay.py +133 -55
  28. rapidtide/refineregressor.py +38 -24
  29. rapidtide/resample.py +3 -0
  30. rapidtide/scripts/{retroglm.py → delayvar.py} +2 -2
  31. rapidtide/scripts/{glmfilt.py → linfitfilt.py} +2 -2
  32. rapidtide/scripts/retroregress.py +28 -0
  33. rapidtide/scripts/stupidramtricks.py +9 -7
  34. rapidtide/simfuncfit.py +1 -1
  35. rapidtide/tests/cleanposttest +21 -0
  36. rapidtide/tests/test_delayestimation.py +3 -3
  37. rapidtide/tests/test_fastresampler.py +1 -2
  38. rapidtide/tests/test_fullrunhappy_v1.py +1 -1
  39. rapidtide/tests/test_fullrunhappy_v2.py +1 -1
  40. rapidtide/tests/test_fullrunrapidtide_v1.py +2 -2
  41. rapidtide/tests/test_fullrunrapidtide_v3.py +1 -1
  42. rapidtide/tests/test_fullrunrapidtide_v5.py +1 -1
  43. rapidtide/tests/test_fullrunrapidtide_v6.py +11 -11
  44. rapidtide/tests/{test_glmpass.py → test_linfitfiltpass.py} +9 -9
  45. rapidtide/tests/test_motionregress.py +3 -3
  46. rapidtide/tests/test_refinedelay.py +12 -12
  47. rapidtide/tidepoolTemplate.py +1 -0
  48. rapidtide/tidepoolTemplate.ui +1 -0
  49. rapidtide/tidepoolTemplate_alt.py +5 -4
  50. rapidtide/tidepoolTemplate_alt.ui +3 -2
  51. rapidtide/tidepoolTemplate_alt_qt6.py +177 -49
  52. rapidtide/tidepoolTemplate_big.py +1 -0
  53. rapidtide/tidepoolTemplate_big.ui +1 -0
  54. rapidtide/tidepoolTemplate_big_qt6.py +197 -53
  55. rapidtide/tidepoolTemplate_qt6.py +151 -39
  56. rapidtide/workflows/delayvar.py +1048 -0
  57. rapidtide/workflows/happy.py +37 -11
  58. rapidtide/workflows/happy_parser.py +4 -4
  59. rapidtide/workflows/{glmfilt.py → linfitfilt.py} +4 -4
  60. rapidtide/workflows/parser_funcs.py +10 -2
  61. rapidtide/workflows/rapidtide.py +388 -452
  62. rapidtide/workflows/rapidtide_parser.py +129 -90
  63. rapidtide/workflows/{glmfrommaps.py → regressfrommaps.py} +28 -26
  64. rapidtide/workflows/retrolagtcs.py +12 -12
  65. rapidtide/workflows/{retroglm.py → retroregress.py} +243 -141
  66. rapidtide/workflows/tidepool.py +2 -2
  67. {rapidtide-3.0a11.dist-info → rapidtide-3.0a13.dist-info}/METADATA +3 -2
  68. {rapidtide-3.0a11.dist-info → rapidtide-3.0a13.dist-info}/RECORD +72 -63
  69. {rapidtide-3.0a11.dist-info → rapidtide-3.0a13.dist-info}/WHEEL +1 -1
  70. {rapidtide-3.0a11.dist-info → rapidtide-3.0a13.dist-info}/entry_points.txt +3 -2
  71. rapidtide/data/examples/src/testoutputsize +0 -45
  72. {rapidtide-3.0a11.dist-info → rapidtide-3.0a13.dist-info/licenses}/LICENSE +0 -0
  73. {rapidtide-3.0a11.dist-info → rapidtide-3.0a13.dist-info}/top_level.txt +0 -0
rapidtide/workflows/retrolagtcs.py CHANGED
@@ -24,8 +24,8 @@ import sys
24
24
 
25
25
  import numpy as np
26
26
 
27
- import rapidtide.glmpass as tide_glmpass
28
27
  import rapidtide.io as tide_io
28
+ import rapidtide.linfitfiltpass as tide_linfitfiltpass
29
29
  import rapidtide.makelaggedtcs as tide_makelagged
30
30
  import rapidtide.multiproc as tide_multiproc
31
31
  import rapidtide.resample as tide_resample
@@ -36,7 +36,7 @@ LGR = logging.getLogger("GENERAL")
36
36
  ErrorLGR = logging.getLogger("ERROR")
37
37
  TimingLGR = logging.getLogger("TIMING")
38
38
 
39
- DEFAULT_GLMDERIVS = 0
39
+ DEFAULT_REGRESSIONFILTDERIVS = 0
40
40
 
41
41
 
42
42
  def _get_parser():
@@ -76,15 +76,15 @@ def _get_parser():
76
76
  help="Output root.",
77
77
  )
78
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  parser.add_argument(
79
- "--glmderivs",
80
- dest="glmderivs",
79
+ "--regressderivs",
80
+ dest="regressderivs",
81
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  action="store",
82
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  type=int,
83
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  metavar="NDERIVS",
84
84
  help=(
85
- f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_GLMDERIVS}"
85
+ f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_REGRESSIONFILTDERIVS}"
86
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  ),
87
- default=DEFAULT_GLMDERIVS,
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+ default=DEFAULT_REGRESSIONFILTDERIVS,
88
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  )
89
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  parser.add_argument(
90
90
  "--nprocs",
@@ -209,7 +209,7 @@ def retrolagtcs(args):
209
209
  internalvalidspaceshape = numvalidspatiallocs
210
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  internalvalidspaceshapederivs = (
211
211
  internalvalidspaceshape,
212
- args.glmderivs + 1,
212
+ args.regressderivs + 1,
213
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  )
214
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  internalvalidfmrishape = (numvalidspatiallocs, np.shape(initial_fmri_x)[0])
215
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  if args.debug:
@@ -250,7 +250,7 @@ def retrolagtcs(args):
250
250
  "CommandLineArgs": thecommandline,
251
251
  }
252
252
 
253
- print("calling glmmfrommaps")
253
+ print("calling makelaggedtcs")
254
254
  voxelsprocessed_makelagged = tide_makelagged.makelaggedtcs(
255
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  genlagtc,
256
256
  initial_fmri_x,
@@ -293,10 +293,10 @@ def retrolagtcs(args):
293
293
  theheader = copy.deepcopy(fmri_header)
294
294
  maplist = []
295
295
 
296
- if args.glmderivs > 0:
296
+ if args.regressderivs > 0:
297
297
  if args.debug:
298
- print(f"adding derivatives up to order {args.glmderivs} prior to regression")
299
- regressorset = tide_glmpass.makevoxelspecificderivs(lagtc, args.glmderivs)
298
+ print(f"adding derivatives up to order {args.regressderivs} prior to regression")
299
+ regressorset = tide_linfitfiltpass.makevoxelspecificderivs(lagtc, args.regressderivs)
300
300
 
301
301
  if args.debug:
302
302
  print("going down the multiple EV path")
@@ -310,7 +310,7 @@ def retrolagtcs(args):
310
310
  "Shifted sLFO regressor to filter",
311
311
  ),
312
312
  ]
313
- for thederiv in range(1, args.glmderivs + 1):
313
+ for thederiv in range(1, args.regressderivs + 1):
314
314
  if args.debug:
315
315
  print(f"{regressorset[:, :, thederiv].shape=}")
316
316
  maplist += [