# -*- coding: utf-8 -*- # Authors: Eric Larson # # License: BSD-3-Clause import datetime as dt import pytest import numpy as np from numpy.testing import assert_allclose, assert_array_less from mne.channels import make_standard_montage from mne.io import read_raw_hitachi from mne.io.hitachi.hitachi import _compute_pairs from mne.io.tests.test_raw import _test_raw_reader from mne.preprocessing.nirs import (source_detector_distances, optical_density, tddr, beer_lambert_law, scalp_coupling_index) CONTENTS = dict() CONTENTS['1.18'] = b"""\ Header,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, File Version,1.18,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Patient Information,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ID,TestID,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Name,Test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Comment,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Age, 45y,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Sex,Female,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Analyze Information,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, AnalyzeMode,Continuous,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Pre Time[s],9,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Post Time[s],7,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Recovery Time[s],12,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Base Time[s],10,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Fitting Degree,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, HPF[Hz],No Filter,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, LPF[Hz],0.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Moving Average[s],0.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Measure Information,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Date,5/17/04 5:14,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Mode,3x5,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Wave[nm],695,830,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Wave Length,CH1(700.1),CH1(829.1),CH2(699.3),CH2(827.9),CH3(699.3),CH3(827.9),CH4(698.6),CH4(828.1),CH5(700.1),CH5(829.1),CH6(698.5),CH6(828.2),CH7(699.3),CH7(827.9),CH8(699.8),CH8(828.5),CH9(698.6),CH9(828.1),CH10(698.5),CH10(828.2),CH11(698.5),CH11(828.2),CH12(699.8),CH12(828.5),CH13(699.8),CH13(828.5),CH14(699.0),CH14(828.2),CH15(698.5),CH15(828.2),CH16(699.5),CH16(828.1),CH17(699.8),CH17(828.5),CH18(699.5),CH18(828.5),CH19(699.0),CH19(828.2),CH20(699.5),CH20(828.1),CH21(699.5),CH21(828.1),CH22(699.5),CH22(828.5),,,,, Analog Gain,30.117647,30.117647,30.117647,30.117647,94.117647,94.117647,94.117647,94.117647,10.27451,10.27451,30.117647,30.117647,59.607843,59.607843,94.117647,94.117647,110.588235,110.588235,10.27451,10.27451,59.607843,59.607843,59.607843,59.607843,110.588235,110.588235,10.27451,10.27451,41.176471,41.176471,59.607843,59.607843,9.333333,9.333333,110.588235,110.588235,41.176471,41.176471,41.176471,41.176471,9.333333,9.333333,9.333333,9.333333,,,,, Digital Gain,13.38,2.82,44.57,7.52,29.46,4.12,36.56,4.84,6.67,1.37,22.61,3.28,79.19,10.88,16.37,2.78,39.97,4.09,100,38.02,36.58,3.95,61.77,7.67,100,15.23,31.52,7.15,53.46,5.05,13.61,2.07,63.74,11.16,14.35,2.05,58.64,8.93,14.53,1.99,8.16,1.82,27.84,5.97,,,,, Sampling Period[s],0.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, StimType,BLOCK,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Stim Time[s],20,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, F1,15,F2,15,F3,15,F4,15,F5,15,F6,15,F7,15,F8,15,F9,15,M,15,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Repeat Count,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Exception Ch,0,0,0,0,0,0,1,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Data,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Probe1,CH1(700.1),CH1(829.1),CH2(699.3),CH2(827.9),CH3(699.3),CH3(827.9),CH4(698.6),CH4(828.1),CH5(700.1),CH5(829.1),CH6(698.5),CH6(828.2),CH7(699.3),CH7(827.9),CH8(699.8),CH8(828.5),CH9(698.6),CH9(828.1),CH10(698.5),CH10(828.2),CH11(698.5),CH11(828.2),CH12(699.8),CH12(828.5),CH13(699.8),CH13(828.5),CH14(699.0),CH14(828.2),CH15(698.5),CH15(828.2),CH16(699.5),CH16(828.1),CH17(699.8),CH17(828.5),CH18(699.5),CH18(828.5),CH19(699.0),CH19(828.2),CH20(699.5),CH20(828.1),CH21(699.5),CH21(828.1),CH22(699.5),CH22(828.5),Mark,Time,BodyMovement,RemovalMark,PreScan 1,1.99371338,1.95037842,2.24243164,2.17483521,2.2052002,2.16384888,2.18017578,2.10418701,1.75735474,1.63879395,1.99432373,1.88644409,2.1307373,2.05368042,2.08358765,1.96212769,1.89682007,1.97311401,0.6993103,1.8006897,2.01049805,1.86462402,1.95968628,1.87988281,1.59408569,1.97891235,1.9392395,1.73034668,2.18307495,2.00424194,1.90841675,1.87286377,1.89331055,1.79077148,1.82418823,1.82601929,2.44125366,2.05291748,2.09381104,2.03796387,1.92672729,1.90353394,2.10266113,2.0401001,0,14:08.2,0,0,1 2,1.97433472,1.94091797,2.31689453,2.16079712,2.22290039,2.15209961,2.12936401,2.08328247,1.75445557,1.63269043,2.01126099,1.88186646,2.11425781,2.04345703,2.07015991,1.95236206,1.90826416,1.95266724,0.71853638,1.78970337,2.03872681,1.8572998,1.95602417,1.86798096,1.59118652,1.94122314,1.93054199,1.72439575,2.21435547,2.00531006,1.90200806,1.86508179,1.87957764,1.78085327,1.81564331,1.81365967,2.33200073,2.02987671,2.0980835,2.02682495,1.92520142,1.8939209,2.10327148,2.01843262,0,14:08.4,0,0,1 3,1.97616577,1.93359375,2.2819519,2.15866089,2.19512939,2.15301514,2.10266113,2.07931519,1.74468994,1.62582397,2.04330444,1.87774658,2.06222534,2.0425415,2.06008911,1.95098877,1.94946289,1.94793701,0.69549561,1.76803589,1.9909668,1.85028076,1.93374634,1.86599731,1.60140991,1.92367554,1.92260742,1.72225952,2.16796875,1.99523926,1.89208984,1.86080933,1.88095093,1.78207397,1.80541992,1.81091309,2.32818604,2.01675415,2.10418701,2.01965332,1.92001343,1.88995361,2.08648682,2.01065063,0,14:08.4,0,0,1 4,1.97799683,1.93695068,2.25875854,2.16461182,2.23007202,2.15774536,2.12554932,2.08068848,1.73980713,1.62155151,2.02072144,1.87957764,2.09320068,2.0401001,2.06558228,1.95327759,1.90414429,1.953125,0.66207886,1.77108765,2.01797485,1.85043335,1.98562622,1.86843872,1.48071289,1.93771362,1.92520142,1.71554565,2.18002319,1.98654175,1.89208984,1.85958862,1.88766479,1.78253174,1.81396484,1.80923462,2.34085083,2.01660156,2.09869385,2.0211792,1.92108154,1.89041138,2.07946777,2.01278687,0,14:08.6,0,0,1 5,1.97219849,1.93847656,2.315979,2.16430664,2.20230103,2.15713501,2.07458496,2.07824707,1.73614502,1.62399292,2.00408936,1.87652588,2.1005249,2.03887939,2.07061768,1.95220947,1.89361572,1.95129395,0.72784424,1.79977417,2.01309204,1.85089111,1.88674927,1.86035156,1.40136719,1.97387695,1.91711426,1.71966553,2.16247559,1.99234009,1.8737793,1.86035156,1.8989563,1.78543091,1.83700562,1.80877686,2.39151001,2.02896118,2.08709717,2.02224731,1.92138672,1.89025879,2.09014893,2.01431274,0,14:08.6,0,0,1 6,1.96807861,1.93969727,2.27905273,2.15988159,2.22793579,2.15789795,2.10266113,2.08618164,1.73950195,1.62445068,2.01156616,1.87728882,2.08847046,2.03811646,2.06420898,1.95617676,1.91879272,1.95541382,0.7019043,1.77963257,1.98974609,1.85195923,1.93954468,1.86630249,1.57897949,2.00317383,1.91040039,1.72515869,2.24868774,1.99157715,1.89849854,1.86218262,1.90658569,1.78634644,1.82495117,1.81427002,2.45651245,2.03353882,2.10083008,2.02758789,1.92184448,1.89331055,2.09686279,2.01980591,0,14:08.8,0,0,1 7,1.98776245,1.94198608,2.2895813,2.15759277,2.21405029,2.16812134,2.15332031,2.09991455,1.74499512,1.62765503,2.01919556,1.87911987,2.2026062,2.04589844,2.05276489,1.96105957,1.93862915,1.96105957,0.67474365,1.78604126,1.99249268,1.84967041,1.89849854,1.86676025,1.39373779,1.95846558,1.90979004,1.72698975,2.27798462,1.99798584,1.91055298,1.86172485,1.91375732,1.78375244,1.78024292,1.8157959,2.30819702,2.05245972,2.1043396,2.03079224,1.925354,1.89697266,2.11288452,2.02545166,0,14:08.9,0,0,1 8,1.98364258,1.94488525,2.28744507,2.16598511,2.20123291,2.17254639,2.13745117,2.10357666,1.75003052,1.63162231,2.00790405,1.87637329,2.20916748,2.05444336,2.05459595,1.95983887,1.90536499,1.96777344,0.72494507,1.78741455,1.98318481,1.85516357,1.89605713,1.86798096,1.4453125,1.95663452,1.91436768,1.73355103,2.22427368,2.00180054,1.89605713,1.86599731,1.86950684,1.79077148,1.79962158,1.82327271,2.31536865,2.06726074,2.09564209,2.03521729,1.92459106,1.90078735,2.10281372,2.03353882,0,14:08.9,0,0,1 9,1.97967529,1.95297241,2.34939575,2.18048096,2.22961426,2.1711731,2.10784912,2.10617065,1.75308228,1.6368103,2.00836182,1.87728882,2.07595825,2.04437256,2.04742432,1.96411133,1.92672729,1.97036743,0.65322876,1.78192139,2.00515747,1.85562134,1.99584961,1.86828613,1.41708374,1.91955566,1.92321777,1.73690796,2.25341797,1.99813843,1.89788818,1.86904907,1.8699646,1.79336548,1.80130005,1.82952881,2.44827271,2.08602905,2.10388184,2.03964233,1.9291687,1.90505981,2.0980835,2.0401001,0,14:09.1,0,0,1 10,1.96777344,1.95663452,2.3046875,2.17712402,2.26348877,2.17590332,2.14691162,2.11624146,1.75506592,1.64108276,2.01538086,1.88278198,2.21374512,2.04696655,2.07824707,1.96838379,1.94854736,1.97387695,0.64300537,1.80709839,2.03277588,1.86340332,1.96380615,1.87942505,1.38870239,1.95419312,1.92611694,1.74087524,2.30636597,2.00012207,1.90124512,1.87103271,1.88766479,1.79397583,1.81411743,1.83273315,2.38845825,2.09106445,2.12188721,2.04544067,1.93237305,1.90994263,2.12310791,2.04696655,0,14:09.1,0,0,1 11,1.98181152,1.96182251,2.2883606,2.1812439,2.25265503,2.18231201,2.12814331,2.11181641,1.75842285,1.64596558,2.0135498,1.88995361,2.15209961,2.05230713,2.07077026,1.97387695,1.86767578,1.98471069,0.69610596,1.80511475,1.9960022,1.87103271,1.90963745,1.8838501,1.41983032,1.98654175,1.91070557,1.74255371,2.22869873,2.00119019,1.8977356,1.87103271,1.87271118,1.80007935,1.83288574,1.83670044,2.45758057,2.09213257,2.08786011,2.04910278,1.93267822,1.90963745,2.10998535,2.05307007,0,14:09.2,0,0,1 12,1.9909668,1.95526123,2.2756958,2.17941284,2.26486206,2.17056274,2.14797974,2.09945679,1.75415039,1.64199829,2.02407837,1.8913269,2.07015991,2.05383301,2.05596924,1.96411133,1.85272217,1.96365356,0.62423706,1.79443359,1.99417114,1.86538696,1.96487427,1.87637329,1.50161743,1.97616577,1.92626953,1.73583984,2.29568481,2.00210571,1.90765381,1.86904907,1.87347412,1.79473877,1.81488037,1.82327271,2.35809326,2.07244873,2.09411621,2.03353882,1.92932129,1.90338135,2.10510254,2.03475952,0,14:09.4,0,0,1 13,1.98287964,1.94839478,2.24395752,2.18048096,2.22961426,2.16156006,2.13409424,2.08709717,1.74362183,1.62902832,2.0111084,1.89331055,2.10952759,2.05001831,2.06558228,1.95846558,1.92581177,1.95098877,0.67565918,1.77017212,1.96060181,1.85882568,1.95159912,1.8762207,1.68884277,1.97921753,1.92855835,1.73416138,2.23876953,2.00210571,1.90200806,1.86828613,1.88858032,1.78710938,1.83029175,1.81137085,2.3526001,2.04116821,2.10769653,2.02423096,1.92565918,1.90002441,2.09457397,2.01904297,0,14:09.5,0,0,1 14,1.99539185,1.93984985,2.27966309,2.16644287,2.20947266,2.16186523,2.12966919,2.08984375,1.73339844,1.61865234,2.02865601,1.89239502,2.11593628,2.05337524,2.05307007,1.95632935,1.9682312,1.95175171,0.69198608,1.7729187,1.95541382,1.85348511,1.95953369,1.86935425,1.55059814,1.9203186,1.91192627,1.73065186,2.30255127,1.99172974,1.89743042,1.86325073,1.87255859,1.7855835,1.83547974,1.81137085,2.35107422,2.0413208,2.09243774,2.01477051,1.92810059,1.89575195,2.10174561,2.01538086,0,14:09.6,0,0,1 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# noqa: E501 CONTENTS['1.25'] = b"""\ Header File Version,1.25 Patient Information ID,REDACTED Name, Comment,sentence,, Birth Date,1999/09/09 Age, 99y Sex,Male Analyze Information AnalyzeMode,Continuous Pre Time[s],9.0 Post Time[s],7.0 Recovery Time[s],12.0 Base Time[s],5 Fitting Degree,1 HPF[Hz],No Filter LPF[Hz],No Filter Moving Average[s],0.1 Measure Information Date,2020/02/02 11:20 Probe Type,adult Mode,3x11 Wave[nm],695,830 Wave Length,CH1(703.6),CH1(829.0),CH2(703.9),CH2(829.3),CH3(703.9),CH3(829.3),CH4(703.9),CH4(828.8),CH5(703.9),CH5(828.8),CH6(703.1),CH6(828.8),CH7(703.1),CH7(828.8),CH8(702.9),CH8(829.0),CH9(702.9),CH9(829.0),CH10(703.6),CH10(829.0),CH11(703.6),CH11(829.0),CH12(703.4),CH12(829.0),CH13(703.9),CH13(829.3),CH14(703.6),CH14(828.5),CH15(703.9),CH15(828.8),CH16(704.1),CH16(829.8),CH17(703.1),CH17(828.8),CH18(704.4),CH18(829.0),CH19(702.9),CH19(829.0),CH20(703.9),CH20(828.8),CH21(703.6),CH21(829.0),CH22(703.4),CH22(829.0),CH23(703.4),CH23(829.0),CH24(703.6),CH24(828.5),CH25(703.6),CH25(828.5),CH26(704.1),CH26(829.8),CH27(704.1),CH27(829.8),CH28(704.4),CH28(829.0),CH29(704.4),CH29(829.0),CH30(703.9),CH30(828.8),CH31(703.9),CH31(828.8),CH32(704.1),CH32(828.8),CH33(703.4),CH33(829.0),CH34(703.1),CH34(828.8),CH35(703.6),CH35(828.5),CH36(704.4),CH36(828.8),CH37(704.1),CH37(829.8),CH38(703.6),CH38(828.5),CH39(704.4),CH39(829.0),CH40(703.9),CH40(829.0),CH41(703.9),CH41(828.8),CH42(704.4),CH42(829.0),CH43(704.1),CH43(828.8),CH44(703.1),CH44(828.8),CH45(703.1),CH45(828.8),CH46(704.4),CH46(828.8),CH47(704.4),CH47(828.8),CH48(703.6),CH48(828.5),CH49(703.6),CH49(828.5),CH50(703.9),CH50(829.0),CH51(703.9),CH51(829.0),CH52(704.4),CH52(829.0) Analog Gain,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,6.58823500,6.58823500,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,6.58823500,6.58823500,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,6.58823500,6.58823500,2.74509800,2.74509800,1.25490200,1.25490200,4.07843100,4.07843100,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,2.74509800,2.74509800,2.74509800,2.74509800,4.07843100,4.07843100,4.07843100,4.07843100,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200,1.25490200 Digital Gain,5.99000000,3.61000000,1.93000000,1.12000000,5.43000000,3.20000000,7.11000000,4.02000000,11.82000000,6.06000000,16.42000000,7.48000000,15.82000000,7.56000000,12.13000000,6.80000000,14.62000000,7.78000000,5.35000000,2.57000000,10.27000000,5.01000000,52.84000000,26.95000000,9.75000000,6.12000000,6.97000000,3.99000000,11.31000000,5.91000000,2.26000000,1.15000000,9.49000000,4.58000000,3.21000000,2.25000000,2.97000000,1.65000000,12.34000000,6.77000000,33.81000000,17.23000000,7.10000000,2.92000000,12.78000000,7.02000000,17.47000000,9.94000000,16.93000000,9.55000000,6.87000000,3.47000000,5.96000000,3.07000000,20.56000000,13.42000000,3.67000000,2.53000000,17.39000000,8.72000000,2.96000000,1.61000000,14.25000000,5.67000000,8.87000000,4.21000000,21.68000000,11.89000000,12.24000000,6.47000000,28.07000000,16.60000000,13.95000000,7.05000000,9.37000000,5.53000000,18.15000000,11.62000000,39.72000000,19.87000000,20.78000000,9.56000000,91.12000000,43.86000000,17.86000000,7.84000000,5.47000000,3.40000000,4.83000000,3.38000000,7.61000000,5.15000000,4.65000000,2.86000000,1.33000000,0.88000000,16.06000000,11.46000000,11.94000000,6.47000000,25.92000000,12.83000000,4.35000000,2.44000000 Sampling Period[s],0.1 StimType,STIM Stim Time[s] A,15,B,15,C,15,D,15,E,15,F,15,G,15,H,15,I,15,J,15 Repeat Count,20 Exception Ch,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 Data Probe1,CH1(703.6),CH1(829.0),CH2(703.9),CH2(829.3),CH3(703.9),CH3(829.3),CH4(703.9),CH4(828.8),CH5(703.9),CH5(828.8),CH6(703.1),CH6(828.8),CH7(703.1),CH7(828.8),CH8(702.9),CH8(829.0),CH9(702.9),CH9(829.0),CH10(703.6),CH10(829.0),CH11(703.6),CH11(829.0),CH12(703.4),CH12(829.0),CH13(703.9),CH13(829.3),CH14(703.6),CH14(828.5),CH15(703.9),CH15(828.8),CH16(704.1),CH16(829.8),CH17(703.1),CH17(828.8),CH18(704.4),CH18(829.0),CH19(702.9),CH19(829.0),CH20(703.9),CH20(828.8),CH21(703.6),CH21(829.0),CH22(703.4),CH22(829.0),CH23(703.4),CH23(829.0),CH24(703.6),CH24(828.5),CH25(703.6),CH25(828.5),CH26(704.1),CH26(829.8),CH27(704.1),CH27(829.8),CH28(704.4),CH28(829.0),CH29(704.4),CH29(829.0),CH30(703.9),CH30(828.8),CH31(703.9),CH31(828.8),CH32(704.1),CH32(828.8),CH33(703.4),CH33(829.0),CH34(703.1),CH34(828.8),CH35(703.6),CH35(828.5),CH36(704.4),CH36(828.8),CH37(704.1),CH37(829.8),CH38(703.6),CH38(828.5),CH39(704.4),CH39(829.0),CH40(703.9),CH40(829.0),CH41(703.9),CH41(828.8),CH42(704.4),CH42(829.0),CH43(704.1),CH43(828.8),CH44(703.1),CH44(828.8),CH45(703.1),CH45(828.8),CH46(704.4),CH46(828.8),CH47(704.4),CH47(828.8),CH48(703.6),CH48(828.5),CH49(703.6),CH49(828.5),CH50(703.9),CH50(829.0),CH51(703.9),CH51(829.0),CH52(704.4),CH52(829.0),Mark,Time,BodyMovement,RemovalMark,PreScan 1,2.01614380,2.01263428,2.01354980,2.01248169,2.02392578,2.01644897,2.02453613,2.01934814,2.01873779,2.01919556,2.02087402,2.01889038,2.02621460,2.03781128,2.02423096,2.02011108,2.00881958,2.00637817,2.02087402,2.01644897,2.02209473,2.00988770,2.03155518,2.01919556,2.02148438,2.01370239,2.01324463,2.00973511,2.00973511,2.01477051,2.02117920,2.02636719,2.00805664,2.01583862,2.02529907,2.03033447,2.00424194,1.99935913,2.01202393,2.01568604,2.01583862,2.01095581,2.02545166,2.01721191,2.02758789,2.02957153,2.00622559,2.00073242,2.00759888,2.00485229,2.02041626,2.03094482,2.01782227,2.01675415,2.00820923,2.01110840,2.01354980,2.00637817,2.01538086,2.00271606,2.01156616,2.01217651,2.01736450,1.99386597,2.03353882,2.02362061,2.03598022,2.02728271,2.00866699,1.99676514,2.00714111,2.00744629,2.02087402,2.01492310,2.01202393,2.01644897,2.00057983,1.99584961,2.01370239,1.99050903,1.99783325,1.99371338,2.01431274,1.99920654,1.99630737,1.97814941,2.02545166,2.01126099,2.02102661,2.00790405,2.00912476,1.99813843,2.01156616,1.99981689,1.99829102,1.99523926,2.01141357,2.00424194,2.00164795,1.98730469,2.03948975,2.00637817,2.00958252,1.99615479,0,15:40:49.15,0,0,1 2,2.02087402,2.02194214,2.01782227,2.02026367,2.02743530,2.02453613,2.02789307,2.02758789,2.02255249,2.02880859,2.02819824,2.02880859,2.03445435,2.04879761,2.02850342,2.02865601,2.01583862,2.01477051,2.02529907,2.02499390,2.03033447,2.02178955,2.03308105,2.02636719,2.02545166,2.02224731,2.01690674,2.01751709,2.01522827,2.02423096,2.02590942,2.03536987,2.01507568,2.02850342,2.03033447,2.04040527,2.00729370,2.00546265,2.01431274,2.02407837,2.02224731,2.02346802,2.02972412,2.02682495,2.03186035,2.03720093,2.01171875,2.00851440,2.00897217,2.01370239,2.02468872,2.04177856,2.02224731,2.02606201,2.01339722,2.02499390,2.01766968,2.01583862,2.01690674,2.00851440,2.01568604,2.02117920,2.02087402,2.00164795,2.03689575,2.03247070,2.04132080,2.03613281,2.01110840,2.00332642,2.01293945,2.01583862,2.02560425,2.02224731,2.01828003,2.02621460,2.00637817,2.00607300,2.01431274,1.99890137,2.00714111,1.99813843,2.01721191,2.00942993,1.99874878,1.98593140,2.02941895,2.02087402,2.02743530,2.01690674,2.01263428,2.00668335,2.01690674,2.00592041,2.00210571,2.00210571,2.01568604,2.01110840,2.00378418,1.99447632,2.04177856,2.01278687,2.01217651,2.00210571,0,15:40:49.26,0,0,1 3,2.01614380,2.01263428,2.01354980,2.01248169,2.02392578,2.01644897,2.02453613,2.01934814,2.01873779,2.01919556,2.02087402,2.01889038,2.02621460,2.03781128,2.02423096,2.02011108,2.00881958,2.00637817,2.02087402,2.01644897,2.02209473,2.00988770,2.03155518,2.01919556,2.02148438,2.01370239,2.01324463,2.00973511,2.00973511,2.01477051,2.02117920,2.02636719,2.00805664,2.01583862,2.02529907,2.03033447,2.00424194,1.99935913,2.01202393,2.01568604,2.01583862,2.01095581,2.02545166,2.01721191,2.02758789,2.02957153,2.00622559,2.00073242,2.00759888,2.00485229,2.02041626,2.03094482,2.01782227,2.01675415,2.00820923,2.01110840,2.01354980,2.00637817,2.01538086,2.00271606,2.01156616,2.01217651,2.01736450,1.99386597,2.03353882,2.02362061,2.03598022,2.02728271,2.00866699,1.99676514,2.00714111,2.00744629,2.02087402,2.01492310,2.01202393,2.01644897,2.00057983,1.99584961,2.01370239,1.99050903,1.99783325,1.99371338,2.01431274,1.99920654,1.99630737,1.97814941,2.02545166,2.01126099,2.02102661,2.00790405,2.00912476,1.99813843,2.01156616,1.99981689,1.99829102,1.99523926,2.01141357,2.00424194,2.00164795,1.98730469,2.03948975,2.00637817,2.00958252,1.99615479,0,15:40:49.15,0,0,1 4,2.02087402,2.02194214,2.01782227,2.02026367,2.02743530,2.02453613,2.02789307,2.02758789,2.02255249,2.02880859,2.02819824,2.02880859,2.03445435,2.04879761,2.02850342,2.02865601,2.01583862,2.01477051,2.02529907,2.02499390,2.03033447,2.02178955,2.03308105,2.02636719,2.02545166,2.02224731,2.01690674,2.01751709,2.01522827,2.02423096,2.02590942,2.03536987,2.01507568,2.02850342,2.03033447,2.04040527,2.00729370,2.00546265,2.01431274,2.02407837,2.02224731,2.02346802,2.02972412,2.02682495,2.03186035,2.03720093,2.01171875,2.00851440,2.00897217,2.01370239,2.02468872,2.04177856,2.02224731,2.02606201,2.01339722,2.02499390,2.01766968,2.01583862,2.01690674,2.00851440,2.01568604,2.02117920,2.02087402,2.00164795,2.03689575,2.03247070,2.04132080,2.03613281,2.01110840,2.00332642,2.01293945,2.01583862,2.02560425,2.02224731,2.01828003,2.02621460,2.00637817,2.00607300,2.01431274,1.99890137,2.00714111,1.99813843,2.01721191,2.00942993,1.99874878,1.98593140,2.02941895,2.02087402,2.02743530,2.01690674,2.01263428,2.00668335,2.01690674,2.00592041,2.00210571,2.00210571,2.01568604,2.01110840,2.00378418,1.99447632,2.04177856,2.01278687,2.01217651,2.00210571,0,15:40:49.26,0,0,1 5,2.01614380,2.01263428,2.01354980,2.01248169,2.02392578,2.01644897,2.02453613,2.01934814,2.01873779,2.01919556,2.02087402,2.01889038,2.02621460,2.03781128,2.02423096,2.02011108,2.00881958,2.00637817,2.02087402,2.01644897,2.02209473,2.00988770,2.03155518,2.01919556,2.02148438,2.01370239,2.01324463,2.00973511,2.00973511,2.01477051,2.02117920,2.02636719,2.00805664,2.01583862,2.02529907,2.03033447,2.00424194,1.99935913,2.01202393,2.01568604,2.01583862,2.01095581,2.02545166,2.01721191,2.02758789,2.02957153,2.00622559,2.00073242,2.00759888,2.00485229,2.02041626,2.03094482,2.01782227,2.01675415,2.00820923,2.01110840,2.01354980,2.00637817,2.01538086,2.00271606,2.01156616,2.01217651,2.01736450,1.99386597,2.03353882,2.02362061,2.03598022,2.02728271,2.00866699,1.99676514,2.00714111,2.00744629,2.02087402,2.01492310,2.01202393,2.01644897,2.00057983,1.99584961,2.01370239,1.99050903,1.99783325,1.99371338,2.01431274,1.99920654,1.99630737,1.97814941,2.02545166,2.01126099,2.02102661,2.00790405,2.00912476,1.99813843,2.01156616,1.99981689,1.99829102,1.99523926,2.01141357,2.00424194,2.00164795,1.98730469,2.03948975,2.00637817,2.00958252,1.99615479,0,15:40:49.15,0,0,1 6,2.02087402,2.02194214,2.01782227,2.02026367,2.02743530,2.02453613,2.02789307,2.02758789,2.02255249,2.02880859,2.02819824,2.02880859,2.03445435,2.04879761,2.02850342,2.02865601,2.01583862,2.01477051,2.02529907,2.02499390,2.03033447,2.02178955,2.03308105,2.02636719,2.02545166,2.02224731,2.01690674,2.01751709,2.01522827,2.02423096,2.02590942,2.03536987,2.01507568,2.02850342,2.03033447,2.04040527,2.00729370,2.00546265,2.01431274,2.02407837,2.02224731,2.02346802,2.02972412,2.02682495,2.03186035,2.03720093,2.01171875,2.00851440,2.00897217,2.01370239,2.02468872,2.04177856,2.02224731,2.02606201,2.01339722,2.02499390,2.01766968,2.01583862,2.01690674,2.00851440,2.01568604,2.02117920,2.02087402,2.00164795,2.03689575,2.03247070,2.04132080,2.03613281,2.01110840,2.00332642,2.01293945,2.01583862,2.02560425,2.02224731,2.01828003,2.02621460,2.00637817,2.00607300,2.01431274,1.99890137,2.00714111,1.99813843,2.01721191,2.00942993,1.99874878,1.98593140,2.02941895,2.02087402,2.02743530,2.01690674,2.01263428,2.00668335,2.01690674,2.00592041,2.00210571,2.00210571,2.01568604,2.01110840,2.00378418,1.99447632,2.04177856,2.01278687,2.01217651,2.00210571,0,15:40:49.26,0,0,1 7,2.01614380,2.01263428,2.01354980,2.01248169,2.02392578,2.01644897,2.02453613,2.01934814,2.01873779,2.01919556,2.02087402,2.01889038,2.02621460,2.03781128,2.02423096,2.02011108,2.00881958,2.00637817,2.02087402,2.01644897,2.02209473,2.00988770,2.03155518,2.01919556,2.02148438,2.01370239,2.01324463,2.00973511,2.00973511,2.01477051,2.02117920,2.02636719,2.00805664,2.01583862,2.02529907,2.03033447,2.00424194,1.99935913,2.01202393,2.01568604,2.01583862,2.01095581,2.02545166,2.01721191,2.02758789,2.02957153,2.00622559,2.00073242,2.00759888,2.00485229,2.02041626,2.03094482,2.01782227,2.01675415,2.00820923,2.01110840,2.01354980,2.00637817,2.01538086,2.00271606,2.01156616,2.01217651,2.01736450,1.99386597,2.03353882,2.02362061,2.03598022,2.02728271,2.00866699,1.99676514,2.00714111,2.00744629,2.02087402,2.01492310,2.01202393,2.01644897,2.00057983,1.99584961,2.01370239,1.99050903,1.99783325,1.99371338,2.01431274,1.99920654,1.99630737,1.97814941,2.02545166,2.01126099,2.02102661,2.00790405,2.00912476,1.99813843,2.01156616,1.99981689,1.99829102,1.99523926,2.01141357,2.00424194,2.00164795,1.98730469,2.03948975,2.00637817,2.00958252,1.99615479,0,15:40:49.15,0,0,1 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""" # noqa: E501 @pytest.mark.parametrize('preload', (True, False)) @pytest.mark.parametrize('version, n_ch, n_times, lowpass, sex, date, end', [ ('1.18', 48, 60, 0.1, 2, (2004, 5, 17, 5, 14, 0, 0), None), ('1.25', 108, 10, 5., 1, (2020, 2, 2, 11, 20, 0, 0), b'\r'), ('1.25', 108, 10, 5., 1, (2020, 2, 2, 11, 20, 0, 0), b'\n'), ('1.25', 108, 10, 5., 1, (2020, 2, 2, 11, 20, 0, 0), b'\r\n'), ]) def test_hitachi_basic(preload, version, n_ch, n_times, lowpass, sex, date, end, tmp_path): """Test NIRSport1 file with no saturation.""" fname = tmp_path / 'test.csv' contents = CONTENTS[version] if end is not None: contents = contents.replace(b'\r', b'\n').replace(b'\n\n', b'\n') contents = contents.replace(b'\n', end) with open(fname, 'wb') as fid: fid.write(CONTENTS[version]) raw = read_raw_hitachi(fname, preload=preload, verbose=True) data = raw.get_data() assert data.shape == (n_ch, n_times) assert raw.info['sfreq'] == 10 assert raw.info['lowpass'] == lowpass assert raw.info['subject_info']['sex'] == sex assert np.isfinite(raw.get_data()).all() assert raw.info['meas_date'] == dt.datetime(*date, tzinfo=dt.timezone.utc) # bad distances (zero) distances = source_detector_distances(raw.info) want = [0.] * (n_ch - 4) assert_allclose(distances, want, atol=0.) raw_od_bad = optical_density(raw) with pytest.warns(RuntimeWarning, match='will be zero'): beer_lambert_law(raw_od_bad, ppf=6) # bad distances (too big) if version == '1.18': need = sum(([f'S{ii}', f'D{ii}'] for ii in range(1, 9)), [])[:-1] have = 'P7 FC3 C3 CP3 P3 F5 FC5 C5 CP5 P5 F7 FT7 T7 TP7 F3'.split() assert len(need) == len(have) mon = make_standard_montage('standard_1020') mon.rename_channels(dict(zip(have, need))) raw.set_montage(mon) raw_od_bad = optical_density(raw) with pytest.warns(RuntimeWarning, match='greater than 10 cm'): beer_lambert_law(raw_od_bad, ppf=6) # good distances mon = make_standard_montage('standard_1020') if version == '1.18': need = sum(([f'S{ii}', f'D{ii}'] for ii in range(1, 9)), [])[:-1] have = 'F3 FC3 C3 CP3 P3 F5 FC5 C5 CP5 P5 F7 FT7 T7 TP7 P7'.split() else: need = sum(([f'S{ii}', f'D{ii}'] for ii in range(1, 18)), [])[:-1] have = ('FT9 FT7 FC5 FC3 FC1 FCz FC2 FC4 FC6 FT8 FT10 ' 'T9 T7 C5 C3 C1 Cz C2 C4 C6 T8 T10 ' 'TP9 TP7 CP5 CP3 CP1 CPz CP2 CP4 CP6 TP8 TP10').split() assert len(need) == len(have) mon.rename_channels(dict(zip(have, need))) raw.set_montage(mon) distances = source_detector_distances(raw.info) want = [0.03] * (n_ch - 4) assert_allclose(distances, want, atol=0.01) test_rank = 'less' if n_times < n_ch else True _test_raw_reader(read_raw_hitachi, fname=fname, boundary_decimal=1, test_rank=test_rank) # low fs # TODO: eventually we should refactor these to be in # mne/io/tests/test_raw.py and run them for all fNIRS readers # OD raw_od = optical_density(raw) assert np.isfinite(raw_od.get_data()).all() sci = scalp_coupling_index(raw_od, verbose='error') lo, mi, hi = np.percentile(sci, [5, 50, 95]) if version == '1.18': assert -0.1 < lo < 0.1 # not great assert 0.4 < mi < 0.5 assert 0.8 < hi < 0.9 else: assert 0.99 <= lo <= hi <= 1 # TDDR raw_tddr = tddr(raw_od) data = raw_tddr.get_data('fnirs') assert np.isfinite(data.all()) peaks = np.ptp(data, axis=-1) assert_array_less(1e-4, peaks, err_msg='TDDR too small') assert_array_less(peaks, 1, err_msg='TDDR too big') # HbO/HbR raw_tddr.set_montage(mon) raw_h = beer_lambert_law(raw_tddr, ppf=6) data = raw_h.get_data('fnirs') assert np.isfinite(data).all() assert data.shape == (n_ch - 4, n_times) peaks = np.ptp(data, axis=-1) assert_array_less(1e-10, peaks, err_msg='Beer-Lambert too small') assert_array_less(peaks, 1e-5, err_msg='Beer-Lambert too big') # From Hitachi 2 Homer KNOWN_PAIRS = { (3, 3, 2): ( (0, 0), (1, 0), (0, 1), (2, 0), (1, 2), (2, 1), (2, 2), (3, 1), (2, 3), (4, 2), (3, 3), (4, 3), (5, 4), (6, 4), (5, 5), (7, 4), (6, 6), (7, 5), (7, 6), (8, 5), (7, 7), (9, 6), (8, 7), (9, 7)), (3, 5, 1): ( (0, 0), (1, 0), (1, 1), (2, 1), (0, 2), (3, 0), (1, 3), (4, 1), (2, 4), (3, 2), (3, 3), (4, 3), (4, 4), (5, 2), (3, 5), (6, 3), (4, 6), (7, 4), (5, 5), (6, 5), (6, 6), (7, 6)), (4, 4, 1): ( (0, 0), (1, 0), (1, 1), (0, 2), (2, 0), (1, 3), (3, 1), (2, 2), (2, 3), (3, 3), (4, 2), (2, 4), (5, 3), (3, 5), (4, 4), (5, 4), (5, 5), (4, 6), (6, 4), (5, 7), (7, 5), (6, 6), (6, 7), (7, 7)), (3, 11, 1): ( (0, 0), (1, 0), (1, 1), (2, 1), (2, 2), (3, 2), (3, 3), (4, 3), (4, 4), (5, 4), (0, 5), (6, 0), (1, 6), (7, 1), (2, 7), (8, 2), (3, 8), (9, 3), (4, 9), (10, 4), (5, 10), (6, 5), (6, 6), (7, 6), (7, 7), (8, 7), (8, 8), (9, 8), (9, 9), (10, 9), (10, 10), (11, 5), (6, 11), (12, 6), (7, 12), (13, 7), (8, 13), (14, 8), (9, 14), (15, 9), (10, 15), (16, 10), (11, 11), (12, 11), (12, 12), (13, 12), (13, 13), (14, 13), (14, 14), (15, 14), (15, 15), (16, 15)), } @pytest.mark.parametrize('n_rows, n_cols, n', list(KNOWN_PAIRS)) def test_compute_pairs(n_rows, n_cols, n): """Test computation of S-D pairings.""" want = KNOWN_PAIRS[(n_rows, n_cols, n)] got = _compute_pairs(n_rows, n_cols, n) assert got == want