292 lines
11 KiB
Python
292 lines
11 KiB
Python
from threading import Thread, Event
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import os
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import numpy as np
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from matrix_test.helper_modules.filesystem import globDir
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from pysndfile import PySndfile, sndio
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from random import randint, shuffle
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from shutil import copyfile
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from natsort import natsorted
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import numpy as np
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import pandas as pd
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from shutil import copy2
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from test_base import BaseThread, run_test_thread
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from scipy.special import logit
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from config import socketio
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import csv
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import pdb
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import dill
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symb_dict = {
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True: 10003,
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False: 10007
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}
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def roll_independant(A, r):
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rows, column_indices = np.ogrid[:A.shape[0], :A.shape[1]]
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# Use always a negative shift, so that column_indices are valid.
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# (could also use module operation)
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r[r < 0] += A.shape[1]
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column_indices = column_indices - r[:,np.newaxis]
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result = A[rows, column_indices]
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return result
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def set_trace():
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import logging
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log = logging.getLogger('werkzeug')
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log.setLevel(logging.ERROR)
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log = logging.getLogger('engineio')
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log.setLevel(logging.ERROR)
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pdb.set_trace()
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class EEGTestThread(BaseThread):
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'''
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Thread for running server side matrix test operations
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'''
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def __init__(self, sessionFilepath=None,
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listFolder="./matrix_test/short_concat_stim/out",
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noiseFilepath="./matrix_test/behavioural_stim/stimulus/wav/noise/noise.wav",
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red_coef="./calibration/out/reduction_coefficients/mat_red_coef.npy",
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cal_coef="./calibration/out/calibration_coefficients/mat_cal_coef.npy",
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socketio=None, participant=None, srt_50=None, s_50=None):
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self.test_name = 'eeg_test'
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self.noise_path = noiseFilepath
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self.listDir = listFolder
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self.wav_files = []
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self.marker_files = []
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self.question_files = []
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self.question = []
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self.response = []
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with open('./test_params.json') as json_file:
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self.params = json.load(json_file)
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self.reduction_coef = np.load(red_coef)*np.load(cal_coef)
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# Percent speech inteligibility (estimated using behavioural measure)
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# to present stimuli at
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self.trial_ind = 0
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self._stopevent = Event()
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super(EEGTestThread, self).__init__('eeg_test',
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sessionFilepath=sessionFilepath,
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socketio=socketio,
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participant=participant)
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self.socketio.on_event('submit_eeg_response', self.submitTestResponse, namespace='/main')
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self.socketio.on_event('finalise_results', self.finaliseResults, namespace='/main')
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self.dev_mode = False
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def testLoop(self):
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'''
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Main loop for iteratively finding the SRT
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'''
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self.waitForPageLoad()
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self.loadResponse()
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self.socketio.emit(
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'test_ready',
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{'sentence_1': self.question[0][0][0], 'sentence_2':
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self.question[0][1][0]}, namespace='/main'
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)
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# For each stimulus
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trials = list(zip(self.wav_files, self.question))[self.trial_ind:]
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for (wav, q) in trials:
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self.saveState(out=self.backupFilepath)
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self.displayInstructions()
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self.waitForPartReady()
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if self._stopevent.isSet() or self.finishTest:
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break
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# Play concatenated matrix sentences at set SNR
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self.playStimulusWav(wav)
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self.setMatrix(q)
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self.saveState(out=self.backupFilepath)
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if not self._stopevent.isSet():
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self.unsetPageLoaded()
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self.socketio.emit('processing-complete', namespace='/main')
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self.waitForPageLoad()
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self.fillTable()
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self.waitForFinalise()
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def displayInstructions(self):
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self.socketio.emit(
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'display_instructions',
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{'sentence_1': self.question[self.trial_ind][0][0], 'sentence_2':
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self.question[self.trial_ind][1][0]}, namespace='/main'
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)
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def fillTable(self):
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'''
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'''
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symb = [[symb_dict[x], symb_dict[y]] for x, y in self.answers if not np.isnan([x, y]).any()]
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self.socketio.emit('eeg_test_fill_table', {'data': symb}, namespace='/main')
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def setMatrix(self, questions):
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'''
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'''
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for self.q_ind, q in enumerate(questions):
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self.answer = q[1]
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question = q[0]
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self.socketio.emit('set_matrix', {'data': question}, namespace='/main')
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self.waitForResponse()
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if self._stopevent.isSet() or self.finishTest:
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return
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self.processResponse()
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self.trial_ind += 1
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self.saveState(out=self.backupFilepath)
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def processResponse(self):
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'''
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'''
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self.newResp = False
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self.answers[self.trial_ind, self.q_ind] = self.answer in self.response
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symb = symb_dict[self.answers[self.trial_ind, self.q_ind]]
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self.socketio.emit('test_resp', {'q_ind': self.q_ind, 'trial_ind': self.trial_ind, "ans": symb}, namespace='/main')
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def loadResponse(self):
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incomplete_responses = np.isnan(self.answers).any(axis=1)[:, np.newaxis].repeat(2, axis=1)
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self.answers[incomplete_responses] = np.nan
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self.fillTable()
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def finaliseResults(self):
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toSave = ['marker_files', 'clinPageLoaded', 'wav_files', 'participant',
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'response', 'backupFilepath', 'noise_path', 'question_files',
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'si', 'question', 'answers', 'trial_ind']
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saveDict = {k:self.__dict__[k] for k in toSave}
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self.participant['eeg_test'].update(saveDict)
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self.participant.save("eeg_test")
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backup_path = os.path.join(self.participant.data_paths['eeg_test'],
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'finalised_backup.pkl')
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copy2(self.backupFilepath, backup_path)
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self.finalised = True
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@staticmethod
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def logisticFunction(L, L_50, s_50):
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'''
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Calculate logistic function for SNRs L, 50% SRT point L_50, and slope
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s_50
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'''
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return 1./(1.+np.exp(4.*s_50*(L_50-L)))
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def loadStimulus(self):
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'''
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'''
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self.participant.load('mat_test')
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try:
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srt_50=self.participant.data['mat_test']['srt_50']
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s_50=self.participant.data['mat_test']['s_50']
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except KeyError:
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raise KeyError("Behavioural matrix test results not available, make "
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"sure the behavioural test has been run before "
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"running this test.")
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# Estimate speech intelligibility thresholds using predicted
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# psychometric function
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s_50 *= 0.01
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x = logit(self.si * 0.01)
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snrs = (x/(4*s_50))+srt_50
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snrs = np.append(snrs, np.inf)
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snr_map = pd.DataFrame({"speech_intel" : np.append(self.si, 0.0), "snr": snrs})
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save_dir = self.participant.data_paths['eeg_test/stimulus']
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snr_map_path = os.path.join(save_dir, "snr_map.csv")
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snr_map.to_csv(snr_map_path)
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snrs = np.repeat(snrs[np.newaxis], 4, axis=0)
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snrs = roll_independant(snrs, np.array([0,-1,-2,-3]))
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noise_file = PySndfile(self.noise_path, 'r')
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stim_dirs = [x for x in os.listdir(self.listDir) if os.path.isdir(os.path.join(self.listDir, x))]
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shuffle(stim_dirs)
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wav_files = []
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question = []
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marker_files = []
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self.socketio.emit('test_stim_load', namespace='/main')
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for ind, dir_name in enumerate(stim_dirs):
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stim_dir = os.path.join(self.listDir, dir_name)
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wav = globDir(stim_dir, "*.wav")[0]
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csv_files = natsorted(globDir(stim_dir, "*.csv"))
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marker_file = csv_files[0]
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question_files = csv_files[1:]
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rms_file = globDir(stim_dir, "*.npy")[0]
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speech_rms = float(np.load(rms_file))
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snr = snrs[:, ind]
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audio, fs, enc, fmt = sndio.read(wav, return_format=True)
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speech = audio[:, :2]
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triggers = audio[:, 2]
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wf = []
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for ind2, s in enumerate(snr):
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start = randint(0, noise_file.frames()-speech.shape[0])
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noise_file.seek(start)
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noise = noise_file.read_frames(speech.shape[0])
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noise_rms = np.sqrt(np.mean(noise**2))
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snr_fs = 10**(-s/20)
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if snr_fs == np.inf:
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snr_fs = 0.
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elif snr_fs == -np.inf:
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raise ValueError("Noise infinitely louder than signal at snr: {}".format(snr))
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noise = noise*(speech_rms/noise_rms)
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out_wav_path = os.path.join(save_dir, "Stim_{0}_{1}.wav".format(ind, ind2))
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out_meta_path = os.path.join(save_dir, "Stim_{0}_{1}.npy".format(ind, ind2))
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with np.errstate(divide='raise'):
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try:
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out_wav = (speech+(np.stack([noise, noise], axis=1)*snr_fs))*self.reduction_coef
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except:
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set_trace()
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out_wav = np.concatenate([out_wav, triggers[:, np.newaxis]], axis=1)
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sndio.write(out_wav_path, out_wav, fs, fmt, enc)
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np.save(out_meta_path, snr)
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wf.append(out_wav_path)
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wav_files.append(wf)
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out_marker_path = os.path.join(save_dir, "Marker_{0}.csv".format(ind))
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marker_files.append(out_marker_path)
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copyfile(marker_file, out_marker_path)
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for q_file in question_files:
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out_q_path = os.path.join(save_dir, "Questions_{0}_{1}.csv".format(ind, ind2))
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self.question_files.append(out_q_path)
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copyfile(q_file, out_q_path)
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for q_file_path in question_files:
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q = []
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with open(q_file_path, 'r') as q_file:
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q_reader = csv.reader(q_file)
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for line in q_reader:
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q.append(line)
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question.append(q)
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self.wav_files = [item for sublist in wav_files for item in sublist]
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self.question.extend(question)
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for item in marker_files:
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self.marker_files.extend([item] * 4)
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c = list(zip(self.wav_files, self.marker_files, self.question))
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shuffle(c)
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self.wav_files, self.marker_files, self.question = zip(*c)
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self.answers = np.empty(np.shape(self.question)[:2])
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self.answers[:] = np.nan
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def submitTestResponse(self, msg):
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'''
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Get and store participant response for current trial
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'''
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self.response = [x.upper() for x in msg['resp']]
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self.newResp = True
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def saveState(self, out="eeg_test_state.pkl"):
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toSave = ['marker_files', 'wav_files', 'participant', 'response',
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'backupFilepath', 'noise_path', 'question_files', 'si',
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'question', 'answers', 'trial_ind']
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saveDict = {k:self.__dict__[k] for k in toSave}
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with open(out, 'wb') as f:
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dill.dump(saveDict, f)
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