├── .gitignore ├── COPYING ├── README ├── setup-notes.txt ├── src ├── broad-wired.sh ├── chan1-filter.pl ├── chan2-filter.pl ├── devreader.sh ├── filter_coefs.yaml ├── freq-broad-bandpass.pl ├── freq-split-smooth.pl ├── generate_filter_coef.py ├── killreader.sh ├── plot_3chan.pl ├── plot_frames.pl ├── sample.sh ├── score_trial.pl ├── simple-capture.sh ├── stm.sh ├── throttle.pl ├── time-stamp.pl ├── visualize-signal-with-noise-test.sh ├── window.pl └── wired.sh └── test ├── freq-split-smooth.1.out └── generate-test-signals.R /.gitignore: -------------------------------------------------------------------------------- 1 | ################### 2 | # backup files 3 | ################### 4 | *.bak 5 | *.bck 6 | *cache.lib 7 | $* 8 | *.swp 9 | *.000 10 | *~ 11 | 12 | ################ 13 | # Output files 14 | ################ 15 | *.o 16 | *.a 17 | *.bin 18 | *.d 19 | *.elf 20 | *.hex 21 | *.list 22 | *.srec 23 | *.map 24 | 25 | #################### 26 | # R temporary files 27 | #################### 28 | .RData 29 | .Rhistory 30 | -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | 676 | -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | The eeg-mouse is a project to attempt to control an on-screen pointer with eeg signals. 2 | 3 | This has potential application for adaptive equipment. 4 | 5 | http://openelectronicslab.github.io/eeg-mouse/ 6 | 7 | Hardware can be found at: 8 | http://openelectronicslab.github.io/OpenHardwareExG/ 9 | and 10 | https://github.com/OpenElectronicsLab/ads1298-breakout 11 | 12 | Notes and data can be found at: 13 | https://github.com/OpenElectronicsLab/eeg-mouse-notes 14 | -------------------------------------------------------------------------------- /setup-notes.txt: -------------------------------------------------------------------------------- 1 | need to install the perl module Device/SerialPort.pm 2 | 3 | sudo apt-get install libdevice-serialport-perl 4 | 5 | need to verify the /dev/ttyACM0 (or adjust serial-reader.pl to match) 6 | 7 | need to have rights to tty device ("dialout" group on ubuntu) 8 | 9 | sudo apt-get install gnuplot 10 | -------------------------------------------------------------------------------- /src/broad-wired.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | EXG="../OpenHardwareExG/src" 4 | 5 | SAMPLE=`date +"%Y%m%d.%H%M%S"` 6 | 7 | # tee >(./plot_frames.pl) | 8 | 9 | $EXG/serial-reader.pl | 10 | $EXG/frame-parser.pl | 11 | tee -a sample-${USER}-${SAMPLE}.csv | 12 | ./chan2-filter.pl | 13 | ./freq-broad-bandpass.pl | 14 | ./window.pl | 15 | tee -a trial-${USER}-${SAMPLE}.csv | 16 | ./plot_3chan.pl 17 | -------------------------------------------------------------------------------- /src/chan1-filter.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | # turn off output buffering 6 | $| = 1; 7 | 8 | # C, 00, 00, 0, 0, 0, 0, -0.1136117, -0.1485806, -0.1476560, -0.1508017, -0.2974134, -0.2481733, -0.2990923, -0.9263688 9 | 10 | my $valid_row_regex = qr/ 11 | (?C),\s*.* 12 | (?[0-9A-F]{2}),\s* 13 | (?[0-9A-F]{2}),\s* 14 | (?[01]),\s* 15 | (?[01]),\s* 16 | (?[01]),\s* 17 | (?[01]),\s* 18 | (?-?[0-9]+(?:\.[0-9]*)),\s* 19 | (?-?[0-9]+(?:\.[0-9]*)),\s* 20 | (?-?[0-9]+(?:\.[0-9]*)),\s* 21 | (?-?[0-9]+(?:\.[0-9]*)),\s* 22 | (?-?[0-9]+(?:\.[0-9]*)),\s* 23 | (?-?[0-9]+(?:\.[0-9]*)),\s* 24 | (?-?[0-9]+(?:\.[0-9]*)),\s* 25 | (?-?[0-9]+(?:\.[0-9]*))\s* 26 | /x; 27 | 28 | while () { 29 | 30 | # parse the data 31 | if ( $_ =~ m/$valid_row_regex/ ) { 32 | print $+{chan1}, "\n"; 33 | } 34 | else { 35 | warn "unrecognized data string:\n", $_, "\n"; 36 | } 37 | } 38 | -------------------------------------------------------------------------------- /src/chan2-filter.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | # turn off output buffering 6 | $| = 1; 7 | 8 | # C, 00, 00, 0, 0, 0, 0, -0.1136117, -0.1485806, -0.1476560, -0.1508017, -0.2974134, -0.2481733, -0.2990923, -0.9263688 9 | 10 | my $valid_row_regex = qr/ 11 | (?C),\s*.* 12 | (?[0-9A-F]{2}),\s* 13 | (?[0-9A-F]{2}),\s* 14 | (?[01]),\s* 15 | (?[01]),\s* 16 | (?[01]),\s* 17 | (?[01]),\s* 18 | (?-?[0-9]+(?:\.[0-9]*)),\s* 19 | (?-?[0-9]+(?:\.[0-9]*)),\s* 20 | (?-?[0-9]+(?:\.[0-9]*)),\s* 21 | (?-?[0-9]+(?:\.[0-9]*)),\s* 22 | (?-?[0-9]+(?:\.[0-9]*)),\s* 23 | (?-?[0-9]+(?:\.[0-9]*)),\s* 24 | (?-?[0-9]+(?:\.[0-9]*)),\s* 25 | (?-?[0-9]+(?:\.[0-9]*))\s* 26 | /x; 27 | 28 | while () { 29 | 30 | # parse the data 31 | if ( $_ =~ m/$valid_row_regex/ ) { 32 | print $+{chan1}, ',', $+{chan2}, "\n"; 33 | } 34 | else { 35 | warn "unrecognized data string:\n", $_, "\n"; 36 | } 37 | } 38 | -------------------------------------------------------------------------------- /src/devreader.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | echo "g" > /dev/ttyACM0 3 | cat /dev/ttyACM0 4 | 5 | -------------------------------------------------------------------------------- /src/filter_coefs.yaml: -------------------------------------------------------------------------------- 1 | x_filter: 2 | in_coef: [0.00477952850316041, -0.017827843732432628, 0.02133463381903281, 0.0, -0.02133463381903281, 0.017827843732432624, -0.00477952850316041] 3 | out_coef: [-5.691356164442124, 13.6929827386752, -17.818776437449383, 13.22611247371713, -5.3100044118982845, 0.901263913122391] 4 | y_filter: 5 | in_coef: [0.004089453810784436, -0.013354414837795602, 0.014847937497981823, 0.0, -0.014847937497981823, 0.013354414837795602, -0.004089453810784436] 6 | out_coef: [-4.950151699635935, 11.074514320959294, -14.093607485952553, 10.750243222185905, -4.6644901480190075, 0.9147439680658163] 7 | baseline_filter: 8 | in_coef: [0.000689782274448917, -0.0025092973678783304, 0.002971490889697712, 0.0, -0.002971490889697712, 0.0025092973678783304, -0.000689782274448917] 9 | out_coef: [-5.447102955119436, 12.87540194547167, -16.826181095869945, 12.811807423618697, -5.3934270892516425, 0.9852556650491906] 10 | smooth_filter: 11 | in_coef: [0.003406439119826039, -0.003139475150201823, -0.003139475150201823, 0.003406439119826039] 12 | out_coef: [-2.9137129783371485, 2.8426746259167683, -0.9284277196403714] 13 | broad_bandpass_filter: 14 | in_coef: [1.6909095781919097e-06, 0.0, -1.5218186203726985e-05, -4.248935548711965e-20, 6.087274481490756e-05, -4.2489355487119655e-19, -0.00014203640456813882, -1.593350830766987e-19, 0.00021305460685212612, -5.158473314608121e-19, -0.0002130546068522077, -1.593350830766987e-19, 0.00014203640456812524, -2.1244677743559827e-19, -6.087274481490794e-05, -4.248935548711965e-20, 1.5218186203726985e-05, 0.0, -1.6909095781919097e-06] 15 | out_coef: [-12.488419783387014, 75.5259633299214, -293.59256131504253, 821.4082163802806, -1755.3376196749905, 2967.871867129326, -4057.9677927582748, 4547.419553523908, -4207.072207090399, 3220.7606344046203, -2035.594853027713, 1054.4216977096867, -441.6983742975524, 146.40647224590808, -37.074934176982985, 6.760223378255063, -0.7929598071891343, 0.04510354827065592] 16 | -------------------------------------------------------------------------------- /src/freq-broad-bandpass.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | use Getopt::Long; 6 | use Math::Trig; 7 | use YAML qw( LoadFile ); 8 | 9 | my $pi = Math::Trig::pi; 10 | 11 | # turn off channel buffering 12 | $| = 1; 13 | 14 | 15 | my $skipsmooth = 0; 16 | my $samplerate = 250; # SPS 17 | 18 | GetOptions("skipsmooth" => \$skipsmooth); 19 | 20 | my $dt = 1.0 / $samplerate; 21 | 22 | # IIR filtering coefficients designed using scipy.signal with the specified 23 | # function call. The first set of each pair is used to take a weighted sum of 24 | # the previous input values to the filter, and the second set of each pair is 25 | # used for taking the weighted sum of the previous channels of the filter. 26 | # N.B.: These need to be kept at high precision; pasting these with nine 27 | # significant figures produced an unstable filter (!) 28 | my $filter_coef = LoadFile('filter_coefs.yaml'); 29 | 30 | # old input and output values for each filter 31 | my @old_filter_in_vals = ( 32 | [ map { 0.0 } @{ $filter_coef->{broad_bandpass_filter}->{in_coef} } ], 33 | [ map { 0.0 } @{ $filter_coef->{broad_bandpass_filter}->{in_coef} } ], 34 | [ map { 0.0 } @{ $filter_coef->{baseline_filter}->{in_coef} } ], 35 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{in_coef} } ], 36 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{in_coef} } ], 37 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{in_coef} } ], 38 | ); 39 | my @old_filter_out_vals = ( 40 | [ map { 0.0 } @{ $filter_coef->{broad_bandpass_filter}->{out_coef} } ], 41 | [ map { 0.0 } @{ $filter_coef->{broad_bandpass_filter}->{out_coef} } ], 42 | [ map { 0.0 } @{ $filter_coef->{baseline_filter}->{out_coef} } ], 43 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{out_coef} } ], 44 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{out_coef} } ], 45 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{out_coef} } ], 46 | ); 47 | 48 | 49 | sub linear_filter { 50 | my ( $buffer_number, $coef_name, $in_val ) = @_; 51 | my $order = @{ $filter_coef->{$coef_name}->{out_coef} }; 52 | 53 | # update the input value list with the new input value 54 | pop @{ $old_filter_in_vals[$buffer_number] }; 55 | unshift @{ $old_filter_in_vals[$buffer_number] }, $in_val; 56 | 57 | # calculate a weighted sum of the old inputs minus the old outputs 58 | my $total = 0; 59 | my $i; 60 | for ($i = 0; $i < $order + 1; $i++) { 61 | $total += $filter_coef->{$coef_name}->{in_coef}[$i] 62 | * $old_filter_in_vals[$buffer_number][$i]; 63 | } 64 | for ($i = 0; $i < $order; $i++) { 65 | $total -= $filter_coef->{$coef_name}->{out_coef}[$i] 66 | * $old_filter_out_vals[$buffer_number][$i]; 67 | } 68 | 69 | # update the output value list with the new output value 70 | pop @{ $old_filter_out_vals[$buffer_number] }; 71 | unshift @{ $old_filter_out_vals[$buffer_number] }, $total; 72 | 73 | # print "@{ $old_filter_out_vals[$channel] }\n"; 74 | 75 | return $total; 76 | } 77 | 78 | sub smooth { 79 | my ( $buffer_number, $coef_name, $in_val ) = @_; 80 | my $rough_val = linear_filter( $buffer_number, $coef_name, $in_val ); 81 | if ($skipsmooth) { 82 | return sprintf( "%13.9f", $rough_val ); 83 | } 84 | my $rectified = abs($rough_val); 85 | my $bufoffset = $buffer_number + (( scalar @old_filter_in_vals ) / 2); 86 | my $out_val = linear_filter( $bufoffset, 'smooth_filter', $rectified ); 87 | return sprintf( "%13.9f", $out_val ); 88 | } 89 | 90 | my $valid_row_regex = qr/ 91 | (?-?[0-9]+(?:\.[0-9]*)?(?:e[+-]?[0-9]+)?)\s*,\s* 92 | (?-?[0-9]+(?:\.[0-9]*)?(?:e[+-]?[0-9]+)?)\s* 93 | /x; 94 | 95 | my @row; 96 | while () { 97 | 98 | # parse the data 99 | if ( $_ =~ m/$valid_row_regex/ ) { 100 | my $val1 = $+{val1}; 101 | my $val2 = $+{val2}; 102 | print join( ", ", 103 | smooth( 0, 'broad_bandpass_filter', $val1 ), 104 | smooth( 1, 'broad_bandpass_filter', $val2 ), 105 | "0.0", 106 | ), "\n"; 107 | } 108 | else { 109 | die "unrecognized data string:\n", $_, "\n"; 110 | } 111 | } 112 | -------------------------------------------------------------------------------- /src/freq-split-smooth.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | use Getopt::Long; 6 | use Math::Trig; 7 | use YAML qw( LoadFile ); 8 | 9 | my $pi = Math::Trig::pi; 10 | 11 | # turn off channel buffering 12 | $| = 1; 13 | 14 | 15 | my $skipsmooth = 0; 16 | my $samplerate = 250; # SPS 17 | 18 | GetOptions("skipsmooth" => \$skipsmooth); 19 | 20 | my $dt = 1.0 / $samplerate; 21 | 22 | # IIR filtering coefficients designed using scipy.signal with the specified 23 | # function call. The first set of each pair is used to take a weighted sum of 24 | # the previous input values to the filter, and the second set of each pair is 25 | # used for taking the weighted sum of the previous channels of the filter. 26 | # N.B.: These need to be kept at high precision; pasting these with nine 27 | # significant figures produced an unstable filter (!) 28 | my $filter_coef = LoadFile('filter_coefs.yaml'); 29 | 30 | # old input and output values for each filter 31 | my @old_filter_in_vals = ( 32 | [ map { 0.0 } @{ $filter_coef->{x_filter}->{in_coef} } ], 33 | [ map { 0.0 } @{ $filter_coef->{y_filter}->{in_coef} } ], 34 | [ map { 0.0 } @{ $filter_coef->{baseline_filter}->{in_coef} } ], 35 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{in_coef} } ], 36 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{in_coef} } ], 37 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{in_coef} } ], 38 | ); 39 | my @old_filter_out_vals = ( 40 | [ map { 0.0 } @{ $filter_coef->{x_filter}->{out_coef} } ], 41 | [ map { 0.0 } @{ $filter_coef->{y_filter}->{out_coef} } ], 42 | [ map { 0.0 } @{ $filter_coef->{baseline_filter}->{out_coef} } ], 43 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{out_coef} } ], 44 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{out_coef} } ], 45 | [ map { 0.0 } @{ $filter_coef->{smooth_filter}->{out_coef} } ], 46 | ); 47 | 48 | 49 | sub linear_filter { 50 | my ( $buffer_number, $coef_name, $in_val ) = @_; 51 | my $order = @{ $filter_coef->{$coef_name}->{out_coef} }; 52 | 53 | # update the input value list with the new input value 54 | pop @{ $old_filter_in_vals[$buffer_number] }; 55 | unshift @{ $old_filter_in_vals[$buffer_number] }, $in_val; 56 | 57 | # calculate a weighted sum of the old inputs minus the old outputs 58 | my $total = 0; 59 | my $i; 60 | for ($i = 0; $i < $order + 1; $i++) { 61 | $total += $filter_coef->{$coef_name}->{in_coef}[$i] 62 | * $old_filter_in_vals[$buffer_number][$i]; 63 | } 64 | for ($i = 0; $i < $order; $i++) { 65 | $total -= $filter_coef->{$coef_name}->{out_coef}[$i] 66 | * $old_filter_out_vals[$buffer_number][$i]; 67 | } 68 | 69 | # update the output value list with the new output value 70 | pop @{ $old_filter_out_vals[$buffer_number] }; 71 | unshift @{ $old_filter_out_vals[$buffer_number] }, $total; 72 | 73 | # print "@{ $old_filter_out_vals[$channel] }\n"; 74 | 75 | return $total; 76 | } 77 | 78 | sub smooth { 79 | my ( $buffer_number, $coef_name, $in_val ) = @_; 80 | my $rough_val = linear_filter( $buffer_number, $coef_name, $in_val ); 81 | if ($skipsmooth) { 82 | return sprintf( "%13.9f", $rough_val ); 83 | } 84 | my $rectified = abs($rough_val); 85 | my $bufoffset = $buffer_number + (( scalar @old_filter_in_vals ) / 2); 86 | my $out_val = linear_filter( $bufoffset, 'smooth_filter', $rectified ); 87 | return sprintf( "%13.9f", $out_val ); 88 | } 89 | 90 | my $valid_row_regex = qr/ 91 | (?-?[0-9]+(?:\.[0-9]*)?(?:e[+-]?[0-9]+)?)\s* 92 | /x; 93 | 94 | my @row; 95 | while () { 96 | 97 | # parse the data 98 | if ( $_ =~ m/$valid_row_regex/ ) { 99 | my $val = $+{val}; 100 | print join( ", ", 101 | smooth( 0, 'x_filter', $val ), 102 | smooth( 1, 'y_filter', $val ), 103 | smooth( 2, 'baseline_filter', $val ), 104 | ), "\n"; 105 | } 106 | else { 107 | die "unrecognized data string:\n", $_, "\n"; 108 | } 109 | } 110 | -------------------------------------------------------------------------------- /src/generate_filter_coef.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import numpy as np 3 | from scipy import signal 4 | from matplotlib import pyplot as plt 5 | 6 | nyquest_freq = 250./2; 7 | 8 | # 7-14 Hz elliptic bandpass filter 9 | x_filter = signal.iirdesign( 10 | wp = [7./nyquest_freq, 14./nyquest_freq], 11 | ws = [4./nyquest_freq, 20./nyquest_freq], 12 | gstop=40, gpass=3, ftype='ellip' 13 | ) 14 | 15 | # 20-26 Hz elliptic bandpass filter 16 | y_filter = signal.iirdesign( 17 | wp = [20.0/nyquest_freq, 26.0/nyquest_freq], 18 | ws = [16./nyquest_freq, 32./nyquest_freq], 19 | gstop=40, gpass=3, ftype='ellip' 20 | ) 21 | 22 | # 16.5-17.5 Hz elliptic bandpass filter 23 | baseline_filter = signal.iirdesign( 24 | wp = [16.5/nyquest_freq, 17.5/nyquest_freq], 25 | ws = [15.5/nyquest_freq, 18.5/nyquest_freq], 26 | gstop=40, gpass=3, ftype='ellip' 27 | ) 28 | 29 | # 5 Hz elliptic lowpass filter 30 | smooth_filter = signal.iirdesign( 31 | wp = 5./ nyquest_freq, 32 | ws = 10./ nyquest_freq, gstop=40, 33 | gpass=3, ftype='ellip' 34 | ) 35 | 36 | # 15-35 Hz band-pass filter 37 | broad_bandpass_filter = signal.iirdesign( 38 | wp = [15/nyquest_freq, 35/nyquest_freq], 39 | ws = [5/nyquest_freq, 45/nyquest_freq], 40 | gstop=40, gpass=3, ftype='butterworth' 41 | ) 42 | 43 | 44 | fig = plt.figure() 45 | for filter in [x_filter, y_filter, baseline_filter, smooth_filter, broad_bandpass_filter]: 46 | w,h = signal.freqz(*filter) 47 | plt.plot(w*(nyquest_freq/max(w)), np.abs(h)) 48 | plt.xlim(0,40) 49 | plt.xlabel('frequency (Hz)'); 50 | plt.ylabel('response'); 51 | fig.savefig("test.png") 52 | 53 | with open('filter_coefs.yaml','wt') as f: 54 | f.write('x_filter:\n'); 55 | f.write(' in_coef: ' + str(x_filter[0].tolist()) + '\n'); 56 | f.write(' out_coef: ' + str(x_filter[1][1:].tolist()) + '\n'); 57 | f.write('y_filter:\n'); 58 | f.write(' in_coef: ' + str(y_filter[0].tolist()) + '\n'); 59 | f.write(' out_coef: ' + str(y_filter[1][1:].tolist()) + '\n'); 60 | f.write('baseline_filter:\n'); 61 | f.write(' in_coef: ' + str(baseline_filter[0].tolist()) + '\n'); 62 | f.write(' out_coef: ' + str(baseline_filter[1][1:].tolist()) + '\n'); 63 | f.write('smooth_filter:\n'); 64 | f.write(' in_coef: ' + str(smooth_filter[0].tolist()) + '\n'); 65 | f.write(' out_coef: ' + str(smooth_filter[1][1:].tolist()) + '\n'); 66 | f.write('broad_bandpass_filter:\n'); 67 | f.write(' in_coef: ' + str(broad_bandpass_filter[0].tolist()) + '\n'); 68 | f.write(' out_coef: ' + str(broad_bandpass_filter[1][1:].tolist()) + '\n'); 69 | 70 | -------------------------------------------------------------------------------- /src/killreader.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | sleep $1 3 | # 4 | # killall on some systems works only with the first 15 characters 5 | # this killall tries both the full name and the 15 character name 6 | # 7 | killall serial-reader.p 2>/dev/null 8 | killall serial-reader.pl 2>/dev/null 9 | -------------------------------------------------------------------------------- /src/plot_3chan.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | # Inspired by Thanassis Tsiodras's script here: 6 | # http://users.softlab.ece.ntua.gr/~ttsiod/gnuplotStreaming.html 7 | # and Andreas Bernauer's extension here: 8 | # http://www.lysium.de/blog/index.php?/archives/234-Plotting-data-with-gnuplot-in-real-time.html 9 | 10 | use IO::Handle; 11 | 12 | my $samplerate = 250; # SPS 13 | my $duration_visible = 4; # seconds 14 | my $refresh_rate = 10; # Hz 15 | my $numchannels = 3; #8; 16 | 17 | # start gnuplot 18 | my $pipe; 19 | open( $pipe, "|-", "gnuplot -geometry 800x600" ) 20 | or die "failed to start gnuplot: $!"; 21 | print $pipe "set xtics\n"; 22 | print $pipe "set ytics\n"; 23 | print $pipe "set style data lines\n"; 24 | print $pipe "set grid\n"; 25 | print $pipe "set term x11\n"; 26 | 27 | #print $pipe "set yrange [-0.005:0.005]\n"; 28 | #print $pipe "set yrange [-0.5:0.5]\n"; 29 | #print $pipe "set yrange [-5.0:5.0]\n"; 30 | print $pipe "set xrange [0:" . ( $samplerate * $duration_visible ) . "]\n"; 31 | 32 | # set up a list of lists for buffering the incoming data 33 | my @data; 34 | for ( my $i = 0 ; $i < $numchannels ; $i++ ) { 35 | push @data, []; 36 | } 37 | 38 | # generate a plot command for the appropriate number of channels (but don't sent it yet) 39 | my $plotcommand = "plot \"-\" title 'channel 1'"; 40 | for ( my $i = 2 ; $i <= $numchannels ; $i++ ) { 41 | $plotcommand = $plotcommand . ", \"-\" title 'channel $i'"; 42 | } 43 | $plotcommand = $plotcommand . "\n"; 44 | 45 | our $valid_row_regex = qr/ 46 | (?-?[0-9]+(?:\.[0-9]*)),\s* 47 | (?-?[0-9]+(?:\.[0-9]*)),\s*[.]* 48 | (?-?[0-9]+(?:\.[0-9]*))[.]* 49 | /x; 50 | my $samples_since_last_update = 0; 51 | while () { 52 | next if $_ eq "\n"; 53 | 54 | # parse the data 55 | if ( $_ =~ m/$valid_row_regex/ ) { 56 | my $chan_1 = $+{chan1}; 57 | my $chan_2 = $+{chan2}; 58 | my $chan_3 = $+{chan3}; 59 | 60 | push( @{ $data[0] }, $chan_1 ); 61 | push( @{ $data[1] }, $chan_2 ); 62 | push( @{ $data[2] }, $chan_3 ); 63 | } 64 | else { 65 | warn "unrecognized data string: '" . $_ . "'\n"; 66 | } 67 | 68 | # Drop any data that's older than the interval of time we're showing 69 | for ( my $i = 0 ; $i < $numchannels ; $i++ ) { 70 | if ( scalar( @{ $data[$i] } ) > $samplerate * $duration_visible ) { 71 | shift @{ $data[$i] }; 72 | } 73 | } 74 | 75 | $samples_since_last_update++; 76 | if ( $samples_since_last_update > $samplerate * 1. / $refresh_rate ) { 77 | $samples_since_last_update = 0; 78 | 79 | # generate the plot 80 | my @sorted = sort { $b <=> $a } @{ $data[0] }; 81 | my $padding = 0.05 * ( $sorted[0] - $sorted[-1] ); 82 | my $onemin = $sorted[-1] - $padding; 83 | my $onemax = $sorted[0] + $padding; 84 | print $pipe "set yrange [$onemin:$onemax]\n"; 85 | print $pipe $plotcommand; 86 | for ( my $i = 0 ; $i < $numchannels ; $i++ ) { 87 | print $pipe join( "\n", @{ $data[$i] } ) . "\ne\n"; 88 | } 89 | $pipe->flush; 90 | } 91 | } 92 | 93 | print $pipe, "exit;"; 94 | -------------------------------------------------------------------------------- /src/plot_frames.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | # Inspired by Thanassis Tsiodras's script here: 6 | # http://users.softlab.ece.ntua.gr/~ttsiod/gnuplotStreaming.html 7 | # and Andreas Bernauer's extension here: 8 | # http://www.lysium.de/blog/index.php?/archives/234-Plotting-data-with-gnuplot-in-real-time.html 9 | 10 | use IO::Handle; 11 | 12 | my $samplerate = 250; # SPS 13 | my $duration_visible = 4; # seconds 14 | my $refresh_rate = 10; # Hz 15 | my $numchannels = 1; #8; 16 | 17 | # start gnuplot 18 | my $pipe; 19 | open($pipe, "|-", "gnuplot -geometry 800x600") or die "failed to start gnuplot: $!"; 20 | print $pipe "set xtics\n"; 21 | print $pipe "set ytics\n"; 22 | print $pipe "set style data lines\n"; 23 | print $pipe "set grid\n"; 24 | print $pipe "set term x11\n"; 25 | #print $pipe "set yrange [-0.005:0.005]\n"; 26 | #print $pipe "set yrange [-0.5:0.5]\n"; 27 | #print $pipe "set yrange [-5.0:5.0]\n"; 28 | print $pipe "set xrange [0:".($samplerate * $duration_visible)."]\n"; 29 | 30 | # set up a list of lists for buffering the incoming data 31 | my @data; 32 | for (my $i = 0; $i < $numchannels; $i++) { 33 | push @data, []; 34 | } 35 | 36 | # generate a plot command for the appropriate number of channels (but don't sent it yet) 37 | my $plotcommand = "plot \"-\" title 'channel 1'"; 38 | for (my $i = 2; $i <= $numchannels; $i++) { 39 | $plotcommand = $plotcommand . ", \"-\" title 'channel $i'"; 40 | } 41 | $plotcommand = $plotcommand . "\n"; 42 | 43 | my $valid_row_regex = 44 | qr/C,\s*(?:\d{1,2},\s*+){6}(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?),\s*(-?\d+(?:\.\d*)?)/; 45 | my $samples_since_last_update = 0; 46 | while () { 47 | next if $_ eq "\n"; 48 | 49 | # parse the data 50 | if ( $_ =~ m/$valid_row_regex/ ) { 51 | push (@{$data[0]}, $1); 52 | push (@{$data[1]}, $2); 53 | push (@{$data[2]}, $3); 54 | push (@{$data[3]}, $4); 55 | push (@{$data[4]}, $5); 56 | push (@{$data[5]}, $6); 57 | push (@{$data[6]}, $7); 58 | push (@{$data[7]}, $8); 59 | } else { 60 | warn "unrecognized data string: '" . $_ . "'\n"; 61 | } 62 | 63 | # Drop any data that's older than the interval of time we're showing 64 | for (my $i = 0; $i < $numchannels; $i++) { 65 | if (scalar(@{$data[$i]}) > $samplerate * $duration_visible) { 66 | shift @{$data[$i]} 67 | } 68 | } 69 | 70 | $samples_since_last_update++; 71 | if ($samples_since_last_update > $samplerate * 1. / $refresh_rate) { 72 | $samples_since_last_update = 0; 73 | 74 | # generate the plot 75 | my @sorted = sort { $b <=> $a } @{$data[0]}; 76 | my $padding = 0.05 * ($sorted[0] - $sorted[-1]); 77 | my $onemin = $sorted[-1] - $padding; 78 | my $onemax = $sorted[0] + $padding; 79 | print $pipe "set yrange [$onemin:$onemax]\n"; 80 | print $pipe $plotcommand; 81 | for (my $i = 0; $i < $numchannels; $i++) { 82 | print $pipe join("\n", @{$data[$i]})."\ne\n"; 83 | } 84 | $pipe->flush; 85 | } 86 | } 87 | 88 | print $pipe, "exit;"; 89 | -------------------------------------------------------------------------------- /src/sample.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | EXG="../OpenHardwareExG/src" 4 | SAMPLE=`date +"%Y%m%d.%H%M%S"` 5 | 6 | ./killreader.sh $1 & 7 | $EXG/serial-reader.pl | 8 | $EXG/frame-parser.pl | 9 | ./parsed-frame-filter.pl | 10 | tee sample-${USER}-${SAMPLE}.csv | 11 | ./plot.pl 12 | -------------------------------------------------------------------------------- /src/score_trial.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | use Getopt::Long; 6 | 7 | my $shuffle = 0; 8 | my $lacks_basechan = 0; 9 | 10 | GetOptions("shuffle" => \$shuffle); 11 | GetOptions("lacks_basechan" => \$lacks_basechan); 12 | 13 | our $without_basechan = qr/ 14 | (?-?[0-9]+(?:\.[0-9]*)),\s* 15 | (?-?[0-9]+(?:\.[0-9]*)),\s* 16 | (?<_x>[0-9]*),\s*(?[0-9]*),\s* 17 | (?<_y>[0-9]*),\s*(?[0-9]*),\s* 18 | (?