rapidtide 3.1__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 (70) hide show
  1. rapidtide/OrthoImageItem.py +4 -4
  2. rapidtide/_version.py +3 -3
  3. rapidtide/calccoherence.py +4 -4
  4. rapidtide/calcnullsimfunc.py +2 -5
  5. rapidtide/calcsimfunc.py +1 -4
  6. rapidtide/correlate.py +130 -127
  7. rapidtide/data/examples/src/testfmri +41 -9
  8. rapidtide/data/examples/src/testhappy +8 -8
  9. rapidtide/dlfilter.py +21 -22
  10. rapidtide/dlfiltertorch.py +18 -19
  11. rapidtide/filter.py +4 -4
  12. rapidtide/fit.py +18 -18
  13. rapidtide/happy_supportfuncs.py +84 -82
  14. rapidtide/helper_classes.py +2 -2
  15. rapidtide/io.py +88 -83
  16. rapidtide/linfitfiltpass.py +30 -49
  17. rapidtide/makelaggedtcs.py +11 -16
  18. rapidtide/maskutil.py +30 -14
  19. rapidtide/miscmath.py +2 -2
  20. rapidtide/patchmatch.py +10 -11
  21. rapidtide/peakeval.py +1 -3
  22. rapidtide/ppgproc.py +3 -3
  23. rapidtide/qualitycheck.py +2 -2
  24. rapidtide/refinedelay.py +12 -3
  25. rapidtide/refineregressor.py +20 -29
  26. rapidtide/scripts/showxcorr_legacy.py +7 -7
  27. rapidtide/scripts/stupidramtricks.py +15 -17
  28. rapidtide/simFuncClasses.py +2 -2
  29. rapidtide/simfuncfit.py +27 -41
  30. rapidtide/tests/test_cleanregressor.py +1 -2
  31. rapidtide/tests/test_fullrunhappy_v3.py +11 -5
  32. rapidtide/tests/test_fullrunhappy_v4.py +9 -1
  33. rapidtide/tests/test_getparsers.py +11 -3
  34. rapidtide/tests/test_refinedelay.py +0 -1
  35. rapidtide/tests/test_simroundtrip.py +8 -0
  36. rapidtide/tests/test_stcorrelate.py +3 -1
  37. rapidtide/util.py +6 -6
  38. rapidtide/voxelData.py +1 -1
  39. rapidtide/wiener.py +122 -16
  40. rapidtide/wiener2.py +3 -3
  41. rapidtide/workflows/applyppgproc.py +33 -15
  42. rapidtide/workflows/calcSimFuncMap.py +11 -22
  43. rapidtide/workflows/ccorrica.py +4 -2
  44. rapidtide/workflows/cleanregressor.py +6 -11
  45. rapidtide/workflows/delayvar.py +8 -13
  46. rapidtide/workflows/fitSimFuncMap.py +2 -9
  47. rapidtide/workflows/happy.py +6 -6
  48. rapidtide/workflows/happy_parser.py +36 -25
  49. rapidtide/workflows/pairproc.py +10 -2
  50. rapidtide/workflows/pixelcomp.py +1 -2
  51. rapidtide/workflows/rankimage.py +1 -1
  52. rapidtide/workflows/rapidtide.py +98 -63
  53. rapidtide/workflows/refineDelayMap.py +7 -6
  54. rapidtide/workflows/refineRegressor.py +6 -16
  55. rapidtide/workflows/regressfrommaps.py +9 -6
  56. rapidtide/workflows/retrolagtcs.py +5 -7
  57. rapidtide/workflows/retroregress.py +11 -17
  58. rapidtide/workflows/roisummarize.py +11 -10
  59. rapidtide/workflows/showarbcorr.py +2 -2
  60. rapidtide/workflows/showxcorrx.py +6 -6
  61. rapidtide/workflows/simdata.py +31 -31
  62. rapidtide/workflows/spatialmi.py +0 -1
  63. rapidtide/workflows/tidepool.py +6 -4
  64. {rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/METADATA +8 -7
  65. {rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/RECORD +69 -70
  66. rapidtide/wiener_doc.py +0 -255
  67. {rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/WHEEL +0 -0
  68. {rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/entry_points.txt +0 -0
  69. {rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/licenses/LICENSE +0 -0
  70. {rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/top_level.txt +0 -0
@@ -7,39 +7,39 @@ cloud/rapidtide-HCPYA,sha256=kqW8ENbOQhvVqZGz-HqiVbrbzHy4cfyy1rk8ejpJor0,963
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  cloud/rapidtide-cloud-test,sha256=SATOwGo4QYLvt-6hE0e3wyK9JjuDU5XzfLrfMoybvcY,466
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  cloud/simple-cp-test,sha256=5ef8wmLfcKdny59BV6_DnAPj7O_mi0rOHdFZVN2iiLA,421
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  rapidtide/Colortables.py,sha256=wKglfM9bOoHDlD_neHoATk29TP0auQBM7dw_qxsDyr4,22131
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- rapidtide/OrthoImageItem.py,sha256=EDzw4RAb2DtmY5E-qaVheoDu_iD53TdaFqYPNhB5mBU,58087
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+ rapidtide/OrthoImageItem.py,sha256=r4dYk5--AFHvRgmdx5HDa7uqlvsJlfcORFk9Fo2jcS8,58063
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  rapidtide/RapidtideDataset.py,sha256=SUt9k1EJaiHDJcAvw9-vbQ9sIfgBMuHb8I0tk7EoUv4,107153
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  rapidtide/__init__.py,sha256=cECnPfGNIWXETiummGLjKcNXLROSDiFlLp-RpZSavwc,97
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- rapidtide/_version.py,sha256=AOw8UIaSZZHWGTUynJUi-6RAwCgEmtgn5cvjfpRYRL0,495
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- rapidtide/calccoherence.py,sha256=5SYEKT8c7lSdH1FuCUcCSphjN4qZ7zi14EE5p5yzHFs,9946
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- rapidtide/calcnullsimfunc.py,sha256=diEx143QTS3__tPdOiSmd-erMoSw03kAn-wuoEPV_DM,10776
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- rapidtide/calcsimfunc.py,sha256=5NGVoGi8W9C5vzneZQBqgr315Ih1eUQ7NzpBR3Od7HA,13231
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- rapidtide/correlate.py,sha256=eJbWFyqg3ydOQ_bn9H_eRZcTflXPfkxhKGsakS9WBa8,71597
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+ rapidtide/_version.py,sha256=iCXaQ4XVA3ovtGOSUbEaLjq5J2X2frLAqvLJfv5rusA,497
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+ rapidtide/calccoherence.py,sha256=gwib99_1kSD-ebgFF-huAxXfSD9yjzNaE82GjIKOYi8,9922
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+ rapidtide/calcnullsimfunc.py,sha256=bfEMRUVdnwfe-Zr6a2xF_gikOimLtqSky2K5Zm_lsbA,10625
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+ rapidtide/calcsimfunc.py,sha256=Ydx7_k6YeEzrJMSpUDy1jFey1w4u_FoH2h_ehYPtwx8,13090
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+ rapidtide/correlate.py,sha256=jVtV6Wc_VErPR-vvQoCll2ZHahOl77bXyo89RiYgGak,71213
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  rapidtide/decorators.py,sha256=k-83nDT1sv6q6tP-xDqfqQdMh1d7V4mRJNBz7uZ3rkk,2628
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- rapidtide/dlfilter.py,sha256=kKSCwu3PoTQenUX3qg9YBfjoPdciYVCQed3TpxJXRDY,141123
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- rapidtide/dlfiltertorch.py,sha256=tmOaEh2n0lCHaqmjsXt8oQviT9fKoauv8XLdJyMun9w,176234
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+ rapidtide/dlfilter.py,sha256=khsFvRGcjfmUW-HuVUJzLvZP9avtpLydQ1zGDsIst24,140992
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+ rapidtide/dlfiltertorch.py,sha256=gHH4uJz-k9eJdMM2GAAg3iG4FZu7-deXZ7-l5qr8AjM,176121
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  rapidtide/externaltools.py,sha256=WdAZcFyqHnCYxauLuHFJlBwCkc14E438Wf9PRqp9vQI,14775
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- rapidtide/filter.py,sha256=AasOnO4_eTSPs9dkrGOypS6IZzUquNGXVlG0zz5zWCQ,114553
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- rapidtide/fit.py,sha256=Z9XgRpRs9D78bSRRG6tfwNWVYwRlpFT5PjR-w_3XsP0,151526
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+ rapidtide/filter.py,sha256=OFmMXG8SPY5UzzKM-yQoI0gy8cleXCLzLqu-2qMveJk,114529
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+ rapidtide/fit.py,sha256=0SvcxGEhWwHtJ5w6RBHtUW2vaQYA9zRcU2wQsdgdt5I,151307
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  rapidtide/genericmultiproc.py,sha256=MxwYMhBHbrzZke5NUKTcpkM38DG63yvdkSv2ckvA8HA,6490
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- rapidtide/happy_supportfuncs.py,sha256=wMB_qY61v3y1DfSrlgtaJU3dF_8ycEElqf-JJxxNN3Y,126576
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- rapidtide/helper_classes.py,sha256=w49qpQn8EGjlj0EId2TpV43MITiso8385YktmRgw0Ck,30045
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- rapidtide/io.py,sha256=EhIjY6hPd0Thc5O_yqlirrFpCOixasYnYjNaVcqTrxA,154114
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- rapidtide/linfitfiltpass.py,sha256=NCcCenYYlpYYuY0LA-PU4VEZV-KhE1Ku1jSv2nYycCc,31590
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- rapidtide/makelaggedtcs.py,sha256=9SALNwHYZmGLn33z-ce_ndERKi6ReaLzAEpMoJEnq_E,10007
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- rapidtide/maskutil.py,sha256=WAK2zx8mhRB-IwdNDST-iKWPHs4Jbm-By54xs5MaBAk,25777
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- rapidtide/miscmath.py,sha256=LNz8hziOJPG5OUK78XT-9dXYyHnJ4g5oym8lN4b6yXU,42617
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+ rapidtide/happy_supportfuncs.py,sha256=LnAApwmSZ1LeZRyqFvWEU2takjV5dbAz8Ca-LMLDBas,126274
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+ rapidtide/helper_classes.py,sha256=DwjG7oHZG-bGWO0lPvju2ibvzsKI0ULkxQANIthHr9g,30033
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+ rapidtide/io.py,sha256=h0h_pKLFEvCuWo4DXviboan_27tLnBYnQQeX-4KAvfY,154004
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+ rapidtide/linfitfiltpass.py,sha256=Ix4IrjecEoKT27ntPqTV6tUnbVTB-DmUMPAaeRq5GdY,30574
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+ rapidtide/makelaggedtcs.py,sha256=sbNjiHe9iiqJ-vrWmtvQI1Upf6T61DrMpeK3RO4EWfo,9794
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+ rapidtide/maskutil.py,sha256=Wh0KJoBTUVuYn8gKc5wWSO6cgPTgkNoAIRHPZjwNCWw,26505
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+ rapidtide/miscmath.py,sha256=lG0gMp1JgAR_ecC8ao4aUFeggFDGGi3oeJNZcbHVtjA,42605
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- rapidtide/patchmatch.py,sha256=fl09AU3uU3RJN2EVuma7emvRlF_x2y2xbOZ_CwTUXX4,26709
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- rapidtide/peakeval.py,sha256=quAQ1B7_AJiAUg8Szr_qKV-6qkagy1ZuBI0uKJ0UF8w,5514
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- rapidtide/ppgproc.py,sha256=3YY8pHD-NW9dkOUeITF4eTCo7ba9jTGa-opFWEBU-3A,78697
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- rapidtide/qualitycheck.py,sha256=F1VQ1uet3t6OlZ0G3kNYheFSWr1Yftj1lHRVMNZmlo4,23991
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- rapidtide/refinedelay.py,sha256=lqiBp1c4omkTdR_UQ7D3SR4izIgpjJWV_tqGlAacSKc,29886
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- rapidtide/refineregressor.py,sha256=izu-IYznn0zJ3HESuUeg-IXtlHUekewWA2mnfn7x37Q,36310
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+ rapidtide/patchmatch.py,sha256=Rc2QtODMFkWTq6T3l_HblRBC0zX6LQ4LYloIBPLbdU4,26638
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+ rapidtide/peakeval.py,sha256=MCCilwbiT2FuUJTAtF2MyXS9Gk-i9WBYTCjly9n_0H4,5468
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+ rapidtide/ppgproc.py,sha256=zK5cjNBNwUI_ThhCGg_g9JVf4xNqdiDCak8BF7h_QoU,78679
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+ rapidtide/qualitycheck.py,sha256=oym8F11z5ERFK0vAfMy7d2L708GtRE0ErN5OIJM0Hbg,23979
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+ rapidtide/refinedelay.py,sha256=0c_d5lzLf3Er7gdxSqLFmYt-J8TUdAjK-8QXQnuzMvg,30165
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+ rapidtide/refineregressor.py,sha256=echFnWDgCfjBuqbV9aUlQeN3BvPqevueGvvYcU1UiH8,35825
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- rapidtide/simFuncClasses.py,sha256=0eHKlY4jrTcUmi-pRujpRqWejnO6KaokvboKgQwEjP0,79927
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- rapidtide/simfuncfit.py,sha256=CtaCrE5GIU-0kgsvh-9pDaT34CcuigtmpXB3yrBbnxo,21108
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+ rapidtide/simFuncClasses.py,sha256=FbNZw6A6nZsAktIGKKYGTR0wchU3_zYntQ849DqPa0U,79915
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+ rapidtide/simfuncfit.py,sha256=zD1VfsdQD16jJMDyWlIg6GjElWsy7dMTL2mS3i6yqUg,20375
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@@ -50,11 +50,10 @@ rapidtide/tidepoolTemplate_big.py,sha256=vTNk6bJe_QN3EsvSte1F8u2duXSj6zpfn0RObbG
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- rapidtide/util.py,sha256=4vnCfw6D_5n3EJMCQP3sTBy7LZvLUdMojOOI119g8sc,78359
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- rapidtide/voxelData.py,sha256=DCThUyFu5uDet2oVqf7ntCpywPuJCLLEAafjU51RF5k,37830
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- rapidtide/wiener.py,sha256=SDhHR_CaAjd1AWZzo6bYhuV25MWHW5FAygw-CNoxH4s,4384
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- rapidtide/wiener2.py,sha256=LNKYew5Ggy-iBHnfdouKqpvO_aodhlUGMcCINnhX1NI,7074
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- rapidtide/wiener_doc.py,sha256=kkTCcAjAS6dIfLH0Z1hC0m1krJoS7KDVSfgfIgRu6O0,8701
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+ rapidtide/util.py,sha256=BWXUwgOgoZZDxP1qK9_2e4RvoxfpCeGIXBJPzunlWk8,78360
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+ rapidtide/voxelData.py,sha256=veRRDLJZR2h0auJy2MGRvEYlMrN3f-vHS-6VVNB00lA,37824
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+ rapidtide/wiener.py,sha256=RDOPaWU1Zn-tjkQiMP0EU2Von2N9kfusG2vN7KZL400,8207
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+ rapidtide/wiener2.py,sha256=8uYBDfhPmrFtPkf4uJkZqlfDoM7njfpv_6tBykR2Ek0,7056
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- rapidtide/data/examples/src/testfmri,sha256=ywiL4kCKjMpdolajjRrMVTiJVV_QaKwT1taJoo3QdHc,1890
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+ rapidtide/data/examples/src/testfmri,sha256=r84404u8Kr34aAUWcF5r97-LRRBoafmmkpsn4OI66PQ,2979
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@@ -235,7 +234,7 @@ rapidtide/tests/showkernels,sha256=h9bge8uIPFq1mTPal8Uqs_drwVrN1qyIbZGFLK-ez2s,1
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- rapidtide/workflows/calcSimFuncMap.py,sha256=P1JkZkiE7mqv2mWsTHRc6Fvoty4Wge1cDXO8XQk9G0o,17836
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+ rapidtide/workflows/ccorrica.py,sha256=N7LLfdZ3L2mmRtXvWGrxW5aG7cUKFL009a4aNi9UTJc,14223
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+ rapidtide/workflows/cleanregressor.py,sha256=Ozkn6zWjCIf02Y-sgnFs-YCsTbHL7j2yuJfh83UGtHI,15534
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+ rapidtide/workflows/happy.py,sha256=tOVLl6UVzarF5M4muNp3g_JVzbcw-RHiwb7Ic2ra-7g,93456
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+ rapidtide/workflows/happy_parser.py,sha256=62aCmPqpzXyKIXeP0q7Bs8XVTY8w1v09oq8PoZX_guY,32617
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@@ -334,47 +333,47 @@ rapidtide/workflows/localflow.py,sha256=s11r9b_T_IKU3P2jce4ZOlRUuKIwvlPFucbzsp_u
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- rapidtide/workflows/pairproc.py,sha256=-s9CjpE6XUkYt0NU6cDqLbbHUL-WqofqiwqTieRTxg8,9799
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+ rapidtide/workflows/pairproc.py,sha256=nfzyBcjiiogaEB9fdzZqqkNN1iUf0mWaB8W3-z6tsrU,10063
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- rapidtide/workflows/pixelcomp.py,sha256=VIWWkA9Pmq1jhj36trxB2GFxBJ9nEktTase-zG7cM44,13830
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+ rapidtide/workflows/pixelcomp.py,sha256=ZfjkxG8f7tISg9cpfhW_80LMt6wWb29mOi0ALY1lIZw,13793
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+ rapidtide/workflows/rankimage.py,sha256=0BcNHVcrztHBEbHvTWdtIIEYn0j_aPAjLeuFZ4Uo4-8,7107
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+ rapidtide/workflows/rapidtide.py,sha256=d5iaiBKC1dk_X6XzhNQfe1B6s9GKuvv3aAUPdYRiDzs,143891
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- rapidtide/workflows/regressfrommaps.py,sha256=Pkdrg-BiHo8Hf3wIoiN-RYDdHtWh7Ct0jqsAoly4M10,10059
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+ rapidtide/workflows/refineDelayMap.py,sha256=qgMNWUymkNYUdGVlnHUVmumsDfPcUwtdrs65KqH4O00,7882
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+ rapidtide/workflows/refineRegressor.py,sha256=9P8rtZv7nvf-msKBXXR0NDcxptkCownigrlcLhPBsMw,46983
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+ rapidtide/workflows/regressfrommaps.py,sha256=BwyXxXBOLokQfS_LjdICaCclKMi9HorpTYVjbguAvDI,10192
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+ rapidtide/workflows/retrolagtcs.py,sha256=cOYsJ5ZNiviQ29wwFJETS_2LIUzToi8Sd46P-6_9yHI,13936
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+ rapidtide/workflows/retroregress.py,sha256=XcEEfsfaTEz8mhk3PVgZR0p-NRzGx6COIWjU0AhmSyE,52765
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+ rapidtide/workflows/roisummarize.py,sha256=JEsIwqIawlQGaSo_a2fNXFBzFDIqWfpvTVamR1OG8Jk,13017
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- rapidtide/workflows/showxcorrx.py,sha256=wY5XVQ_tv1KvaIoQqsAaAKVhul5Zbud-ZqEA141nhKE,37614
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+ rapidtide/workflows/showxcorrx.py,sha256=_r5_1nOEZIga9k13NBesAZNmf4rcBxScxmGg6Z_jaso,37666
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- rapidtide/workflows/simdata.py,sha256=7GjQCrPc3Z-s-Q5W5nY-uqwK1BP0x_juIW6yapzeCqc,26612
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+ rapidtide/workflows/simdata.py,sha256=tvR-Sz-8ygDfLTWFxxIl_sDJmFMqqImKOxNRnniI6Ps,26613
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- rapidtide/workflows/spatialmi.py,sha256=qS131Dk3cDhHCyDze20itR07bCZb1tP_6q2usOUnkh0,22173
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+ rapidtide/workflows/spatialmi.py,sha256=eosMBe_WflSAAxC9NsoHisWTcTcuimNTNiIYTDLeTkA,22172
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+ rapidtide/workflows/tidepool.py,sha256=ViQBR9FeVXg77JSNZa0k78Bx7oxF1IDnWzgEPqZwz7A,187919
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  rapidtide/workflows/variabilityizer.py,sha256=_AY16UY9_1cVjkUMFWPTufTQWLxhUFNpG1PAangvThw,7576
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- rapidtide-3.1.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
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- rapidtide-3.1.dist-info/METADATA,sha256=0Wn2UujZPrs3-CSFAXim0JWRljfMhBLbHJw_z-5YLcI,15717
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- rapidtide-3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- rapidtide-3.1.dist-info/entry_points.txt,sha256=dVXEEfqnv_eUNdn02PfZTTd5KK4vZwumP8HCfhUVhag,3380
379
- rapidtide-3.1.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
380
- rapidtide-3.1.dist-info/RECORD,,
374
+ rapidtide-3.1.1.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
375
+ rapidtide-3.1.1.dist-info/METADATA,sha256=Td-ko8Sgzy3JVaq9DVLefi5wcitlyfsgw10g0QtyHdM,15746
376
+ rapidtide-3.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
377
+ rapidtide-3.1.1.dist-info/entry_points.txt,sha256=dVXEEfqnv_eUNdn02PfZTTd5KK4vZwumP8HCfhUVhag,3380
378
+ rapidtide-3.1.1.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
379
+ rapidtide-3.1.1.dist-info/RECORD,,
rapidtide/wiener_doc.py DELETED
@@ -1,255 +0,0 @@
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- #!/usr/bin/env python
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- # -*- coding: utf-8 -*-
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- #
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- # Copyright 2016-2025 Blaise Frederick
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- #
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- # Licensed under the Apache License, Version 2.0 (the "License");
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- # you may not use this file except in compliance with the License.
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- # You may obtain a copy of the License at
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- #
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- # http://www.apache.org/licenses/LICENSE-2.0
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- #
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- # Unless required by applicable law or agreed to in writing, software
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- # distributed under the License is distributed on an "AS IS" BASIS,
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- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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- # See the License for the specific language governing permissions and
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- # limitations under the License.
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- #
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- #
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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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-
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- import rapidtide.fit as tide_fit
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- import rapidtide.multiproc as tide_multiproc
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-
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-
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- def _procOneVoxelWiener(
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- vox: int,
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- lagtc: NDArray,
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- inittc: NDArray,
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- rt_floatset: type = np.float64,
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- rt_floattype: str = "float64",
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- ) -> tuple[int, NDArray, NDArray, NDArray, NDArray, NDArray, NDArray, NDArray]:
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- """
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- Perform Wiener filter processing on a single voxel time series.
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-
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- This function applies a Wiener filter to remove the lagged component from
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- the initial time course, returning both the filtered and unfiltered results
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- along with fitting statistics.
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-
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- Parameters
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- ----------
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- vox : int
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- Voxel index identifier
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- lagtc : NDArray
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- Lagged time course data (input signal)
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- inittc : NDArray
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- Initial time course data (target signal)
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- rt_floatset : type, optional
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- Real-time float type for output arrays, default is np.float64
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- rt_floattype : str, optional
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- String representation of the real-time float type, default is "float64"
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-
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- Returns
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- -------
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- tuple[int, NDArray, NDArray, NDArray, NDArray, NDArray, NDArray, NDArray]
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- A tuple containing:
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- - vox (int): Input voxel index
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- - intercept (NDArray): Regression intercept term
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- - sqrt_R2 (NDArray): Square root of coefficient of determination
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- - R2 (NDArray): Coefficient of determination
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- - fitcoff (NDArray): Fitting coefficient
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- - ratio (NDArray): Ratio of slope to intercept
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- - datatoremove (NDArray): Data to be removed (filtered signal)
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- - residual (NDArray): Residual signal (unfiltered data)
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-
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- Notes
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- -----
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- This function uses maximum likelihood regression to estimate the relationship
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- between lagged and initial time courses, then applies the Wiener filter
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- to remove the lagged component from the initial signal.
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-
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- Examples
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- --------
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- >>> import numpy as np
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- >>> lagtc = np.array([1.0, 2.0, 3.0, 4.0])
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- >>> inittc = np.array([2.0, 4.0, 6.0, 8.0])
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- >>> result = _procOneVoxelWiener(0, lagtc, inittc)
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- >>> print(result[0]) # voxel index
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- 0
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- >>> print(result[4]) # fitting coefficient
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- 2.0
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- """
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- thefit, R2 = tide_fit.mlregress(lagtc, inittc)
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- fitcoff = rt_floatset(thefit[0, 1])
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- datatoremove = rt_floatset(fitcoff * lagtc)
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- return (
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- vox,
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- rt_floatset(thefit[0, 0]),
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- rt_floatset(np.sqrt(R2)),
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- rt_floatset(R2),
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- fitcoff,
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- rt_floatset(thefit[0, 1] / thefit[0, 0]),
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- datatoremove,
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- rt_floatset(inittc - datatoremove),
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- )
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-
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-
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- def wienerpass(
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- numspatiallocs: int,
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- fmri_data: NDArray,
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- threshval: float,
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- lagtc: NDArray,
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- optiondict: dict,
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- wienerdeconv: NDArray,
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- wpeak: NDArray,
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- resampref_y: NDArray,
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- rt_floatset: type = np.float64,
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- rt_floattype: str = "float64",
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- ) -> int:
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- """
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- Perform Wiener deconvolution on fMRI data voxels.
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-
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- This function applies Wiener deconvolution to each voxel in the fMRI data
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- based on the provided lagged time course and threshold. It supports both
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- single-threaded and multi-threaded processing depending on the configuration
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- in `optiondict`.
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-
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- Parameters
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- ----------
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- numspatiallocs : int
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- Number of spatial locations (voxels) in the fMRI data.
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- fmri_data : numpy.ndarray
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- 2D array of fMRI data with shape (numspatiallocs, timepoints).
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- threshval : float
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- Threshold value for masking voxels based on mean signal intensity.
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- lagtc : numpy.ndarray
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- 2D array of lagged time courses with shape (numspatiallocs, timepoints).
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- optiondict : dict
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- Dictionary containing processing options including:
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- - 'nprocs': number of processors to use (default: 1)
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- - 'showprogressbar': whether to show progress bar (default: True)
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- - 'mp_chunksize': chunk size for multiprocessing (default: 10)
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- wienerdeconv : numpy.ndarray
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- Wiener deconvolution kernel or filter.
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- wpeak : numpy.ndarray
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- Peak values associated with the Wiener deconvolution.
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- resampref_y : numpy.ndarray
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- Resampled reference signal for filtering.
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- rt_floatset : type, optional
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- Data type for floating-point numbers, default is `np.float64`.
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- rt_floattype : str, optional
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- String representation of the floating-point data type, default is "float64".
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-
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- Returns
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- -------
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- int
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- Total number of voxels processed.
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-
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- Notes
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- -----
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- - Voxels are masked based on their mean signal intensity exceeding `threshval`.
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- - If `nprocs` > 1, multiprocessing is used to process voxels in parallel.
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- - The function modifies global variables such as `meanvalue`, `rvalue`, etc.,
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- which are assumed to be defined in the outer scope.
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-
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- Examples
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- --------
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- >>> import numpy as np
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- >>> fmri_data = np.random.rand(100, 50)
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- >>> lagtc = np.random.rand(100, 50)
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- >>> optiondict = {'nprocs': 4, 'showprogressbar': True, 'mp_chunksize': 5}
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- >>> result = wienerpass(
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- ... numspatiallocs=100,
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- ... fmri_data=fmri_data,
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- ... threshval=0.1,
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- ... lagtc=lagtc,
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- ... optiondict=optiondict,
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- ... wienerdeconv=np.array([1, 2, 1]),
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- ... wpeak=np.array([0.5]),
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- ... resampref_y=np.array([1, 1, 1])
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- ... )
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- >>> print(result)
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- 100
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- """
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- rt_floatset = (rt_floatset,)
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- rt_floattype = rt_floattype
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- inputshape = np.shape(fmri_data)
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- themask = np.where(np.mean(fmri_data, axis=1) > threshval, 1, 0)
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- if optiondict["nprocs"] > 1:
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- # define the consumer function here so it inherits most of the arguments
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- def Wiener_consumer(inQ, outQ):
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- while True:
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- try:
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- # get a new message
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- val = inQ.get()
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-
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- # this is the 'TERM' signal
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- if val is None:
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- break
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-
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- # process and send the data
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- outQ.put(
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- _procOneVoxelWiener(
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- val,
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- lagtc[val, :],
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- fmri_data[val, :],
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- rt_floatset=rt_floatset,
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- rt_floattype=rt_floattype,
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- )
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- )
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-
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- except Exception as e:
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- print("error!", e)
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- break
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-
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- data_out = tide_multiproc.run_multiproc(
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- Wiener_consumer,
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- inputshape,
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- themask,
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- nprocs=optiondict["nprocs"],
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- showprogressbar=True,
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- chunksize=optiondict["mp_chunksize"],
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- )
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- # unpack the data
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- volumetotal = 0
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- for voxel in data_out:
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- meanvalue[voxel[0]] = voxel[1]
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- rvalue[voxel[0]] = voxel[2]
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- r2value[voxel[0]] = voxel[3]
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- fitcoff[voxel[0]] = voxel[4]
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- fitNorm[voxel[0]] = voxel[5]
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- datatoremove[voxel[0], :] = voxel[6]
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- filtereddata[voxel[0], :] = voxel[7]
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- volumetotal += 1
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- data_out = []
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- else:
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- volumetotal = 0
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- for vox in tqdm(
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- range(0, numspatiallocs),
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- desc="Voxel",
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- unit="voxels",
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- disable=(not optiondict["showprogressbar"]),
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- ):
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- inittc = fmri_data[vox, :].copy()
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- if np.mean(inittc) >= threshval:
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- (
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- dummy,
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- meanvalue[vox],
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- rvalue[vox],
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- r2value[vox],
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- fitcoff[vox],
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- fitNorm[vox],
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- datatoremove[vox],
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- filtereddata[vox],
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- ) = _procOneVoxelWiener(
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- vox,
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- lagtc[vox, :],
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- inittc,
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- rt_floatset=rt_floatset,
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- t_floattype=rt_floattype,
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- )
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- volumetotal += 1
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-
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- return volumetotal