Added stim_part to word csv converter script

app.py

@@ -1,6 +1,6 @@
 import pathops
 import os
-from matrix_test.generate_matrix_stimulus import generateAudioStimulus
+from matrix_test.long_concat_stim.gen_long_stim import generateAudioStimulus
 import time
 
 import config

click_test_thread.py

@@ -1,7 +1,7 @@
 from threading import Thread, Event
 import os
 import numpy as np
-from matrix_test.filesystem import globDir
+from matrix_test.helper_modules.filesystem import globDir
 from pysndfile import PySndfile, sndio
 from random import randint, shuffle
 from shutil import copyfile
@@ -12,7 +12,7 @@ from shutil import copy2
 
 from test_base import BaseThread
 
-from matrix_test.signalops import play_wav
+from matrix_test.helper_modules.signalops import play_wav
 from scipy.special import logit
 from config import socketio
 import csv

da_test_thread.py

@@ -1,7 +1,7 @@
 from threading import Thread, Event
 import os
 import numpy as np
-from matrix_test.filesystem import globDir
+from matrix_test.helper_modules.filesystem import globDir
 from pysndfile import PySndfile, sndio
 from random import randint, shuffle
 from shutil import copyfile
@@ -12,7 +12,7 @@ from shutil import copy2
 
 from test_base import BaseThread
 
-from matrix_test.signalops import play_wav
+from matrix_test.helper_modules.signalops import play_wav
 from scipy.special import logit
 from config import socketio
 import csv

eeg_mat_train_thread.py

@@ -1,7 +1,7 @@
 from threading import Thread, Event
 import os
 import numpy as np
-from matrix_test.filesystem import globDir
+from matrix_test.helper_modules.filesystem import globDir
 from pysndfile import PySndfile, sndio
 from random import randint, shuffle
 from shutil import copyfile
@@ -10,9 +10,7 @@ import numpy as np
 import pandas as pd
 from shutil import copy2
 
-from test_base import BaseThread
+from test_base import BaseThread, run_test_thread
-
-from matrix_test.signalops import play_wav
 from scipy.special import logit
 from config import socketio
 import csv
@@ -24,6 +22,17 @@ symb_dict = {
     False: 10007
 }
 
+def roll_independant(A, r):
+    rows, column_indices = np.ogrid[:A.shape[0], :A.shape[1]]
+
+    # Use always a negative shift, so that column_indices are valid.
+    # (could also use module operation)
+    r[r < 0] += A.shape[1]
+    column_indices = column_indices - r[:,np.newaxis]
+
+    result = A[rows, column_indices]
+    return result
+
 def set_trace():
     import logging
     log = logging.getLogger('werkzeug')
@@ -38,25 +47,128 @@ class EEGMatTrainThread(BaseThread):
     Thread for running server side matrix test operations
     '''
     def __init__(self, sessionFilepath=None,
-                 stimFolder='./da_stim/', nTrials=2,
+                 listFolder="./matrix_test/short_concat_stim/out",
+                 noiseFilepath="./matrix_test/behavioural_stim/stimulus/wav/noise/noise.wav",
                  socketio=None, participant=None, srt_50=None, s_50=None):
-        self.wav_file = os.path.join(stimFolder, '3000_da.wav')
+        self.noise_path = noiseFilepath
+        self.listDir = listFolder
 
-        self.test_name = 'da_test'
+        self.wav_files = []
-        self.nTrials = nTrials
+        self.marker_files = []
+        self.question_files = []
+        self.question = []
+        self.response = []
+
+        # Percent speech inteligibility (estimated using behavioural measure)
+        # to present stimuli at
+        self.si = np.array([20.0, 35.0, 50.0, 65.0, 80.0, 90.0, 100.0])
         self.trial_ind = 0
         self._stopevent = Event()
 
-        super(DaTestThread, self).__init__(self.test_name,
+        super(EEGMatTrainThread, self).__init__('eeg_mat_train',
-                                           sessionFilepath=sessionFilepath,
+                                            sessionFilepath=sessionFilepath,
-                                           socketio=socketio,
+                                            socketio=socketio,
-                                           participant=participant)
+                                            participant=participant)
-
-        self.toSave = ['trial_ind', 'nTrials', 'wav_file', 'test_name']
 
+        self.socketio.on_event('submit_eeg_response', self.submitTestResponse, namespace='/main')
         self.socketio.on_event('finalise_results', self.finaliseResults, namespace='/main')
 
-        self.dev_mode = True
+    def loadStimulus(self):
+        '''
+        '''
+        self.participant.load('mat_test')
+        try:
+            srt_50=self.participant.data['mat_test']['srt_50']
+            s_50=self.participant.data['mat_test']['s_50']
+        except KeyError:
+            raise KeyError("Behavioural matrix test results not available, make "
+                           "sure the behavioural test has been run before "
+                           "running this test.")
+        # Estimate speech intelligibility thresholds using predicted
+        # psychometric function
+        reduction_coef = float(np.load(os.path.join(self.listDir, 'reduction_coef.npy')))
+        s_50 *= 0.01
+        x = logit(self.si * 0.01)
+        snrs = (x/(4*s_50))+srt_50
+        snr_map = pd.DataFrame({"speech_intel" : self.si, "snr": snrs})
+        save_dir = self.participant.data_paths['eeg_test/stimulus']
+        snr_map_path = os.path.join(save_dir, "snr_map.csv")
+        snr_map.to_csv(snr_map_path)
+        snrs = np.repeat(snrs[np.newaxis], 4, axis=0)
+        snrs = roll_independant(snrs, np.array([0,-1,-2,-3]))
+        noise_file = PySndfile(self.noise_path, 'r')
+        stim_dirs = [x for x in os.listdir(self.listDir) if os.path.isdir(os.path.join(self.listDir, x))]
+        shuffle(stim_dirs)
+        wav_files = []
+        question = []
+        marker_files = []
+        self.socketio.emit('test_stim_load', namespace='/main')
+        for ind, dir_name in enumerate(stim_dirs):
+            stim_dir = os.path.join(self.listDir, dir_name)
+            wav = globDir(stim_dir, "*.wav")[0]
+            csv_files = natsorted(globDir(stim_dir, "*.csv"))
+            marker_file = csv_files[0]
+            question_files = csv_files[1:]
+            rms_file = globDir(stim_dir, "*.npy")[0]
+            speech_rms = float(np.load(rms_file))
+            snr = snrs[:, ind]
+            audio, fs, enc, fmt = sndio.read(wav, return_format=True)
+
+            speech = audio[:, :2]
+            #triggers = audio[:, 2]
+            wf = []
+            for ind2, s in enumerate(snr):
+                start = randint(0, noise_file.frames()-speech.shape[0])
+                noise_file.seek(start)
+                noise = noise_file.read_frames(speech.shape[0])
+                noise_rms = np.sqrt(np.mean(noise**2))
+                snr_fs = 10**(-s/20)
+                if snr_fs == np.inf:
+                    snr_fs = 0.
+                elif snr_fs == -np.inf:
+                    raise ValueError("Noise infinitely louder than signal at snr: {}".format(snr))
+                noise = noise*(speech_rms/noise_rms)
+                out_wav_path = os.path.join(save_dir, "Stim_{0}_{1}.wav".format(ind, ind2))
+                out_meta_path = os.path.join(save_dir, "Stim_{0}_{1}.npy".format(ind, ind2))
+                with np.errstate(divide='raise'):
+                    try:
+                        out_wav = (speech+(np.stack([noise, noise], axis=1)*snr_fs))*reduction_coef
+                    except:
+                        set_trace()
+                #out_wav = np.concatenate([out_wav, triggers[:, np.newaxis]], axis=1)
+                sndio.write(out_wav_path, out_wav, fs, fmt, enc)
+                np.save(out_meta_path, snr)
+                wf.append(out_wav_path)
+            wav_files.append(wf)
+            out_marker_path = os.path.join(save_dir, "Marker_{0}.csv".format(ind))
+            marker_files.append(out_marker_path)
+            copyfile(marker_file, out_marker_path)
+            for q_file in question_files:
+                out_q_path = os.path.join(save_dir, "Questions_{0}_{1}.csv".format(ind, ind2))
+                self.question_files.append(out_q_path)
+                copyfile(q_file, out_q_path)
+
+            for q_file_path in question_files:
+                q = []
+                with open(q_file_path, 'r') as q_file:
+                    q_reader = csv.reader(q_file)
+                    for line in q_reader:
+                        q.append(line)
+                question.append(q)
+
+        self.wav_files = [item for sublist in wav_files for item in sublist]
+
+        self.question.extend(question)
+
+        for item in marker_files:
+            self.marker_files.extend([item] * 4)
+
+        c = list(zip(self.wav_files, self.marker_files, self.question))
+        shuffle(c)
+        self.wav_files, self.marker_files, self.question = zip(*c)
+
+        self.answers = np.empty(np.shape(self.question)[:2])
+        self.answers[:] = np.nan
 
 
     def testLoop(self):
@@ -64,22 +176,81 @@ class EEGMatTrainThread(BaseThread):
         Main loop for iteratively finding the SRT
         '''
         self.waitForPageLoad()
-        self.socketio.emit('test_ready', namespace='/main')
+        self.loadResponse()
-        for self.trial_ind in range(self.nTrials):
+        self.socketio.emit(
+            'test_ready',
+            {'sentence_1': self.question[0][0][0], 'sentence_2':
+             self.question[0][1][0]}, namespace='/main'
+        )
+        # For each stimulus
+        trials = list(zip(self.wav_files, self.question))[self.trial_ind:]
+        for (wav, q) in trials:
             self.displayInstructions()
             self.waitForPartReady()
             if self._stopevent.isSet() or self.finishTest:
                 break
             # Play concatenated matrix sentences at set SNR
-            self.playStimulus(self.wav_file)
+            self.playStimulus(wav)
-            self.saveState(out=self.backupFilepath)
+            self.setMatrix(q)
+        self.saveState(out=self.backupFilepath)
         if not self._stopevent.isSet():
             self.unsetPageLoaded()
             self.socketio.emit('processing-complete', namespace='/main')
-
+            self.waitForPageLoad()
+            self.fillTable()
 
     def displayInstructions(self):
-        self.socketio.emit('display_instructions', namespace='/main')
+        self.socketio.emit(
+            'display_instructions',
+            {'sentence_1': self.question[self.trial_ind][0][0], 'sentence_2':
+            self.question[self.trial_ind][1][0]}, namespace='/main'
+        )
+
+    def fillTable(self):
+        '''
+        '''
+        symb = [[symb_dict[x], symb_dict[y]] for x, y in self.answers if not np.isnan([x, y]).any()]
+        self.socketio.emit('test_fill_table', {'data': symb}, namespace='/main')
+
+
+    def setMatrix(self, questions):
+        '''
+        '''
+        for self.q_ind, q in enumerate(questions):
+            self.answer = q[1]
+            question = q[0]
+            self.socketio.emit('set_matrix', {'data': question}, namespace='/main')
+            self.waitForResponse()
+            if self._stopevent.isSet() or self.finishTest:
+                return
+            self.processResponse()
+        self.trial_ind += 1
+        self.saveState(out=self.backupFilepath)
+
+    def processResponse(self):
+        '''
+        '''
+        self.newResp = False
+        self.answers[self.trial_ind, self.q_ind] = self.answer in self.response
+        symb = symb_dict[self.answers[self.trial_ind, self.q_ind]]
+        self.socketio.emit('test_resp', {'q_ind': self.q_ind, 'trial_ind': self.trial_ind, "ans": symb}, namespace='/main')
+
+    def loadResponse(self):
+        incomplete_responses = np.isnan(self.answers).any(axis=1)[:, np.newaxis].repeat(2, axis=1)
+        self.answers[incomplete_responses] = np.nan
+        self.fillTable()
+
+    def finaliseResults(self):
+        toSave = ['marker_files', 'clinPageLoaded', 'wav_files', 'participant',
+                  'response', 'backupFilepath', 'noise_path', 'question_files',
+                  'si', 'question', 'answers', 'trial_ind']
+        saveDict = {k:self.__dict__[k] for k in toSave}
+        self.participant['eeg_test'].update(saveDict)
+        self.participant.save("eeg_test")
+        backup_path = os.path.join(self.participant.data_paths['eeg_test'],
+                        'finalised_backup.pkl')
+        copy2(self.backupFilepath, backup_path)
+        self.finalised = True
 
 
     def playStimulus(self, wav_file, replay=False):
@@ -96,14 +267,18 @@ class EEGMatTrainThread(BaseThread):
 
         self.socketio.emit("stim_done", namespace="/main")
 
-
+    def submitTestResponse(self, msg):
-    def loadStimulus(self):
         '''
+        Get and store participant response for current trial
         '''
-        #audio, fs, enc, fmt = sndio.read(wav, return_format=True)
+        self.response = [x.upper() for x in msg['resp']]
+        self.newResp = True
 
 
-    def saveState(self, out="test_state.pkl"):
+    def saveState(self, out="eeg_test_state.pkl"):
-        saveDict = {k:self.__dict__[k] for k in self.toSave}
+        toSave = ['marker_files', 'wav_files', 'participant', 'response',
+                  'backupFilepath', 'noise_path', 'question_files', 'si',
+                  'question', 'answers', 'trial_ind']
+        saveDict = {k:self.__dict__[k] for k in toSave}
         with open(out, 'wb') as f:
             dill.dump(saveDict, f)

eeg_story_train_thread.py

@@ -1,7 +1,6 @@
 from threading import Thread, Event
 import os
 import numpy as np
-from matrix_test.filesystem import globDir
 from pysndfile import PySndfile, sndio
 from random import randint, shuffle
 from shutil import copyfile
@@ -12,7 +11,8 @@ from shutil import copy2
 
 from test_base import BaseThread
 
-from matrix_test.signalops import play_wav
+from matrix_test.helper_modules.signalops import play_wav
+from matrix_test.helper_modules.filesystem import globDir
 from scipy.special import logit
 from config import socketio
 import csv
@@ -65,11 +65,10 @@ class EEGStoryTrainThread(BaseThread):
         self.socketio.on_event('finalise_results', self.finaliseResults, namespace='/main')
         self.loadStimulus()
 
-        self.dev_mode = True
+        self.dev_mode = False
 
     def setQuestion(self, q):
         self.socketio.emit('set_question', data=q[0], namespace='/main')
-        set_trace()
 
     def testLoop(self):
         '''

eeg_test_thread.py

@@ -1,7 +1,7 @@
 from threading import Thread, Event
 import os
 import numpy as np
-from matrix_test.filesystem import globDir
+from matrix_test.helper_modules.filesystem import globDir
 from pysndfile import PySndfile, sndio
 from random import randint, shuffle
 from shutil import copyfile
@@ -47,7 +47,7 @@ class EEGTestThread(BaseThread):
     Thread for running server side matrix test operations
     '''
     def __init__(self, sessionFilepath=None,
-                 listFolder="./matrix_test/short_concat_stim/",
+                 listFolder="./matrix_test/short_concat_stim/out",
                  noiseFilepath="./matrix_test/stimulus/wav/noise/noise.wav",
                  socketio=None, participant=None, srt_50=None, s_50=None):
         self.noise_path = noiseFilepath

matrix_test/__init__.py

@@ -1 +0,0 @@
-from .pathtype import PathType

matrix_test/long_concat_stim/gen_long_stim.py

@@ -22,7 +22,7 @@ from pathops import dir_must_exist
 try:
     from signalops import rolling_window_lastaxis, block_lfilter
 except ImportError:
-    from .signalops import rolling_window_lastaxis, block_lfilter
+    from ..helper_modules.signalops import rolling_window_lastaxis, block_lfilter
 
 import scipy.signal as sgnl
 from scipy.stats import pearsonr
@@ -32,12 +32,12 @@ from pyswarm import pso
 try:
     from lpc import lpc
 except ImportError:
-    from .lpc import lpc
+    from ..helper_modules.lpc import lpc
 
 try:
     from filesystem import globDir, organiseWavs, prepareOutDir
 except ImportError:
-    from .filesystem import globDir, organiseWavs, prepareOutDir
+    from ..helper_modules.filesystem import globDir, organiseWavs, prepareOutDir
 
 
 def synthesizeTrial(wavFileMatrix, indexes):

matrix_test/long_concat_stim/gen_part_words.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+import sys
+sys.path.insert(0, "../helper_modules/")
+
+import csv
+from tokens_to_words import tokens_to_words, load_component_map
+import pdb
+
+def main():
+    component_map_file = "../speech_components/component_map.json"
+    stim_parts = "./out/parts/stim_parts.csv"
+    stim_words = "./out/parts/stim_words.csv"
+    component_map = load_component_map(component_map_file)
+    lines = []
+    with open(stim_parts, 'r') as csvfile:
+        for line in csv.reader(csvfile):
+            lines.append(tokens_to_words(line, component_map))
+    with open(stim_words, 'w') as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerows(lines)
+
+
+if __name__ == "__main__":
+    main()

matrix_test_thread.py

@@ -11,7 +11,7 @@ import csv
 from shutil import copy2
 
 from pysndfile import sndio, PySndfile
-from matrix_test.filesystem import globDir
+from matrix_test.helper_modules.filesystem import globDir
 from test_base import BaseThread
 import sounddevice as sd
 import pdb

route.py

@@ -21,7 +21,7 @@ from pysndfile import sndio
 from scipy.optimize import minimize
 
 from app import generate_matrix_stimulus
-from matrix_test.filesystem import globDir, organiseWavs, prepareOutDir
+from matrix_test.helper_modules.filesystem import globDir, organiseWavs, prepareOutDir
 from matrix_test_thread import MatTestThread
 from pathops import dir_must_exist
 from participant import Participant, find_participants, gen_participant_num

server.py

@@ -27,7 +27,7 @@ from pysndfile import sndio
 from scipy.optimize import minimize
 
 from app import generate_matrix_stimulus
-from matrix_test.filesystem import globDir, organiseWavs, prepareOutDir
+from matrix_test.helper_modules.filesystem import globDir, organiseWavs, prepareOutDir
 from matrix_test_thread import MatTestThread
 from pathops import dir_must_exist
 from participant import Participant

socket_handlers.py

@@ -23,11 +23,11 @@ from scipy.optimize import minimize
 from WavPlayer import play_wav_async
 
 from app import generate_matrix_stimulus
-from matrix_test.filesystem import globDir, organiseWavs, prepareOutDir
+from matrix_test.helper_modules.filesystem import globDir, organiseWavs, prepareOutDir
 from matrix_test_thread import MatTestThread
 from pathops import dir_must_exist
 from participant import Participant
-from matrix_test.signalops import play_wav
+from matrix_test.helper_modules.signalops import play_wav
 
 from config import server, socketio, participants
 
@@ -126,13 +126,13 @@ def start_test(msg):
     test_name = msg.pop('test_name')
     part_key = msg.pop('part_key')
     thread_type = thread_types[test_name]
-    socketio.emit('participant_start_{}'.format(test_name), namespace='/main')
 
     if part_key != "--":
         participant = participants[part_key]
     else:
         raise ValueError("Participant must be selected...")
 
+    socketio.emit('participant_start_{}'.format(test_name), namespace='/main')
     socketio.emit('participant_start', test_name, namespace='/main', broadcast=True)
     run_test_thread(test_name, thread_type, participant=participant, **msg)
 

templates/participant_index.html

@@ -69,7 +69,8 @@
             'eeg_test': "/eeg/test/run",
             'da_test': "/da/run",
             'click_test': "/click/run",
-            'eeg_story_train': "/eeg/train/story/run"
+            'eeg_story_train': "/eeg/train/story/run",
+            'eeg_mat_train': "/eeg/train/mat/run"
         }
 
         socket.on('participant_start', function(msg) {