def get_session_trials(animal_name, session_filename):
'''
Returns a time-ordered list of dicts, where each dict is info about a trial.
e.g. [{"trial_num": 1,
"behavior_outcome": "failure",
"stm_size": 40.0,
},
{"trial_num": 2,
"behavior_outcome": "success",
"stm_size": 35.0
}]
:param animal_name: name of the animal string
:param session_filename: filename for the session (string)
'''
#TODO: unfuck this: hard coded paths not ideal for code reuse
# path = 'input/' + animal_name + '/' + session_filename
path = os.path.join(input_dir, animal_name, session_filename)
df = pymworks.open_file(path)
events = df.get_events([
"Announce_TrialStart",
"Announce_TrialEnd",
"success",
"failure",
"ignore",
"stm_size"]
)
trials = []
trial_num = 1
for index, event in enumerate(events):
if (event.name == "Announce_TrialStart" and
event.value == 1):
trial = {
"trial_num": trial_num,
"stm_size": None,
"behavior_outcome": None
}
try:
if events[index - 1].name == "stm_size":
trial["stm_size"] = events[index - 1].value
except IndexError:
print "stm_size out of range for session", session_filename, \
index
try:
if events[index + 1].name in ["success", "failure", "ignore"]:
trial["behavior_outcome"] = events[index + 1].name
except IndexError:
print "beh_outcome out of range for session", session_filename,\
index
if (trial["stm_size"] is not None and
trial["behavior_outcome"] is not None):
trials.append(trial)
trial_num += 1
return trials
def get_session_statistics(animal_name, session_filename):
'''
Returns a time-ordered list of dicts, where each dict is info about a trial.
e.g. [{"trial_num": 1,
"behavior_outcome": "failure",
"stm_pos_x": 7.5,
},
{"trial_num": 2,
"behavior_outcome": "success",
"stm_pos_x": -7.5
}]
NOTE: trial_num: 1 corresponds to the FIRST trial in the session,
and trials occur when Announce_TrialStart and Announce_TrialEnd
events have success, failure, or ignore events between them with
value=1.
:param animal_name: name of the animal string
:param session_filename: filename for the session (string)
'''
#TODO: unfuck this: hard coded paths not ideal for code reuse
#path = 'input/' + animal_name + '/' + session_filename
path = os.path.join(data_dir, animal_name, session_filename)
df = pymworks.open_file(path)
events = df.get_events(["Announce_TrialStart", "Announce_TrialEnd",
"success", "failure", "ignore", "stm_pos_x"])
result = []
index = 0
temp_events = []
last_announce = None
trial_num = 0
while index < len(events):
if events[index].name == "Announce_TrialStart":
temp_events = []
last_announce = "Announce_TrialStart"
elif events[index].name == "Announce_TrialEnd":
if last_announce == "Announce_TrialStart":
trial_result = {}
for ev in temp_events:
if ev.name == "success" and ev.value == 1:
trial_result["behavior_outcome"] = "success"
elif ev.name == "failure" and ev.value == 1:
trial_result["behavior_outcome"] = "failure"
elif ev.name == "ignore" and ev.value == 1:
trial_result["behavior_outcome"] = "ignore"
elif ev.name == "stm_pos_x":
trial_result["stm_pos_x"] = ev.value
else:
pass
if "behavior_outcome" in trial_result:
trial_num += 1
trial_result["trial_num"] = trial_num
result.append(trial_result)
last_announce = "Announce_TrialEnd"
else:
temp_events.append(events[index])
index += 1
#FYI, testing showed some good filtering of weird events here...
#blah = df.get_events(["success", "failure", "ignore"])
#print "EVENTS EQUAL? ", len(result) == len(blah) - 6, session_filename
#subtract 6 because session initialization emits 2 behavior outcomes per
#outcome type
#print len(result), len(blah) - 6
#lines above unequal in 6/77 sessions for AB3&7 because of random behavior
#outcome events firing in rapid succession. They happens within a couple
#microseconds of one another so filtering these out is probably good
# save each animal's analyzed session info:
out_dir_by_animal = os.path.join(out_dir, '%s' % animal_name)
if not os.path.exists(out_dir_by_animal):
os.makedirs(out_dir_by_animal)
fname = os.path.join(out_dir_by_animal, '%s.pkl' % session_filename)
with open(fname, 'wb') as f:
pkl.dump(result, f, protocol=pkl.HIGHEST_PROTOCOL) #protocol=pkl.HIGHEST_PROTOCOL)
# make_a_figure(data_for_animal)
return result
import pymworks
input = 'grat10_ephys_160202_1622.mwk/grat10_ephys_160202_1622.mwk'
file = pymworks.open_file(input)
events = file.get_events('#announceStimulus')
# find all unique stimulus names so we know what we're dealing with:
stimuli_names = set([ev.value['name'] for ev in events if hasattr(ev.value, '__iter__')])
# take the name and times of a particular stimulus:
def get_stim_times(stim_name):
stim_times = [ev.time for ev in events if hasattr(ev.value, '__iter__') and ev.value['name'] == stim_name]
kwik_times = [tb.mworks_to_audio(x/1e6) for x in stim_times] #mworks times are in microseconds - convert to seconds
return kwik_times
# make dictionary of stimulus name and its times:
stimuli_kwik_times = {stimulus_name : get_stim_times(stimulus_name) for stimulus_name in stimuli_names}
# give kwik times to..... .raw.kwd file....
# 1. determine which .raw.kwd file(s) we'll need - compare stimulus times with .kwik files' stamps.
stimuli_kwik_times['0']
# collect the raw.kwd files:
def get_kwd_files():
input_file_path = os.getcwd()
kwd_files = []
for file in os.listdir(input_file_path):
import flask
import pymworks
#MAXEVENTS = 10000000
MAXEVENTS = None
fn = '/home/graham/Repositories/braingram/pymworks/test/error.mwk'
if len(sys.argv) > 1:
fn = sys.argv[1]
debug = False
if len(sys.argv) > 2:
debug = True
datafile = pymworks.open_file(fn)
app = flask.Flask(__name__)
def events_to_json(events):
if (MAXEVENTS is not None) and (len(events) > MAXEVENTS):
s = slice(0, len(events), len(events) / MAXEVENTS + 1)
else:
s = slice(len(events))
return json.dumps([{'code': e.code, 'time': e.time / float(1E6), \
'value': e.value, 'name': datafile.to_name(e.code)} \
for e in events[s]])
def get_session_statistics(animal_name, session_filename):
'''
Returns a time-ordered list of dicts, where each dict is info about a trial.
e.g. [{"trial_num": 1,
"behavior_outcome": "failure",
"stm_pos_x": 7.5,
},
{"trial_num": 2,
"behavior_outcome": "success",
"stm_pos_x": -7.5
}]
NOTE: trial_num: 1 corresponds to the FIRST trial in the session,
and trials occur when Announce_TrialStart and Announce_TrialEnd
events have success, failure, or ignore events between them with
value = 1.
:param animal_name: name of the animal string
:param session_filename: filename for the session (string)
'''
#TODO: unfuck this: hard coded paths not ideal for code reuse
path = 'input/' + 'phase1/' + animal_name + '/' + session_filename
# events_we_want = ['#stimDisplayUpdate','Announce_TrialStart', 'Announce_TrialEnd','success', 'failure', 'ignore']
df = pymworks.open_file(path)
# Start by getting the pixel clock / bit code data
stimulus_announces = df.get_events['#announceStimulus']
# bit_codes is a list of (time, code) tuples
bit_codes = [(e.time, e.value['bit_code']) for e in stimuli if 'bit_code' in e.value]
# ok, now let's grab the pixel clock events out of the open-ephys file
result = []
index = 0
temp_events = []
last_announce = None
trial_num = 0
while index < len(events):
if events[index].name == 'Announce_TrialStart':
temp_events = []
last_announce = 'Announce_TrialStart'
elif events[index].name == 'Announce_TrialEnd':
if last_announce == 'Announce_TrialStart':
trial_result = {}
for ev in temp_events:
### ANIMAL RESPONSE ###
if ev.name == 'success' and ev.value == 1:
trial_result['behavior_outcome'] = 'success'
trial_result['time_trial_response'] = ev.time
elif ev.name == 'failure' and ev.value == 1:
trial_result['behavior_outcome'] = 'failure'
trial_result['time_trial_response'] = ev.time
elif ev.name == 'ignore' and ev.value == 1:
trial_result['behavior_outcome'] = 'ignore'
trial_result['time_trial_response'] = ev.time
### SCREEN INFORMATION ###
#elif ev.name == '#stimDisplayUpdate':
# print ev.value[0]['name']
elif ev.name == '#stimDisplayUpdate' and len(ev.value) == 1: # this won't actually happen
pass
elif ev.name == '#stimDisplayUpdate' and len(ev.value) == 2: # if blank screen with pixel clock on.
trial_result['bit_code'] = ev.value[1]['bit_code'] # this is the actual bit code on this screen
trial_result['stim_name'] = ev.value[0]['name'] # this should be BlankScreen
# print 'stim: ', trial_result['stim_name'], ' and bit code: ', trial_result['bit_code']
elif ev.name == 'get_#stimDisplayUpdate' and len(ev.value) == 3:
# two options here: 1)blank screen, stimulus, and pixel clock
# or 2) blank, pixel, grayscreen (error trial)
# if [2] element of ev.value is bit code, do this:
if ev.value[2]['name'] == 'pixel clock':
trial_result['time_trial_start'] = ev.time
trial_result['stim_name'] = ev.value[1]['name']
trial_result['bit_code'] = ev.value[2]['bit_code']
#print "bit code as ev.value[2]['name']"
# elif [2] value of ev.value is gray screen (i.e. this is an error trial),
elif ev.value[2]['name'] == 'BlankScreenGray':
# bit code is under ev.value[1]
trial_result['bit_code'] = ev.value[1]['bit_code']
trial_result['stim_name'] = ev.value[2]['name']
#print "gray screen as ev.value[2]['name']"
else:
#print ev.value[2]['name']
pass
### STIMULUS PROPERTIES ###
# elif ev.name == 'stm_size':
# trial_result['stm_size'] = ev.value
# elif ev.name == 'stm_rotation':
# trial_result['stm_rotation'] = ev.value
# elif ev.name == 'stm_rotation_in_depth':
# trial_result['stm_rotation_in_depth'] = ev.value
# elif ev.name == 'stm_pos_x':
# if trial_result['stm_pos_x'] == -0.0: #weird MWorks protocol thing where some of the 0.0s come out negative, so just correcting that
# trial_result['stm_pos_x'] = abs(ev.value)
# else:
# trial_result['stm_pos_x'] = ev.value
# elif ev.name == 'stm_pos_y':
# trial_result['stm_pos_y'] = ev.value
else:
pass
print 'bit code was: ', trial_result['bit_code'], 'and stim was: ', trial_result['stim_name']
if 'behavior_outcome' in trial_result:
trial_num += 1
trial_result['trial_num'] = trial_num
result.append(trial_result)
last_announce = 'Announce_TrialEnd'
else:
temp_events.append(events[index])
index += 1
#FYI, testing showed some good filtering of weird events here...
#blah = df.get_events(["success", "failure", "ignore"])
#print "EVENTS EQUAL? ", len(result) == len(blah) - 6, session_filename
#subtract 6 because session initialization emits 2 behavior outcomes per
#outcome type
#print len(result), len(blah) - 6
#lines above unequal in 6/77 sessions for AB3&7 because of random behavior
#outcome events firing in rapid succession. They happen within a couple
#microseconds of one another so filtering these out is probably good
return result
print result
def get_bitcode_simple(animal_name, session_filename):
path = '/Volumes/Mac HD/Dropbox (coxlab)/Behavior/3-port-analysis-master/' + 'input/' + 'phase1/' + animal_name + '/' + session_filename
display_events = ['#stimDisplayUpdate']
df = pymworks.open_file(path)
events = df.get_events(display_events)
temp_events = []
last_announce = None
trial_num = 0
result = {'bit_code': [], 'stim_name': [], 'time': []}
index = 0
while index < len(events):
# result['bit_code'].append()
trial_result = {'bit_code': [], 'stim_name': [], 'time': []}
if events[index].name == '#stimDisplayUpdate' and len(
events[index].value) == 1: # this won't actually happen
pass
elif events[index].name == '#stimDisplayUpdate' and len(
events[index].value) == 2:
trial_result['bit_code'] = events[index].value[1][
'bit_code'] # this is the actual bit code on this screen
trial_result['stim_name'] = events[index].value[0][
'name'] # this should be BlankScreen
trial_result['time'] = events[index].time
elif events[index].name == '#stimDisplayUpdate' and len(
events[index].value) == 3:
if events[index].value[2]['name'] == 'pixel clock':
trial_result['stim_name'] = events[index].value[1]['name']
trial_result['bit_code'] = events[index].value[2]['bit_code']
trial_result['time'] = events[index].time
# elif [2] value of ev.value is gray screen (i.e. this is an error trial),
elif events[index].value[2]['name'] == 'BlankScreenGray':
# bit code is under ev.value[1]
trial_result['bit_code'] = events[index].value[1]['bit_code']
trial_result['stim_name'] = events[index].value[2]['name']
trial_result['time'] = events[index].time
else:
#print ev.value[2]['name']
pass
result['bit_code'].append(trial_result['bit_code'])
result['stim_name'].append(trial_result['stim_name'])
result['time'].append(trial_result['time'])
index += 1
#print result
return result
def load_mworks(filename):
pyfilename = "%s/%s" % (filename, os.path.basename(filename))
mf = MworksFile(filename)
pf = pymworks.open_file(pyfilename)
return mf, pf
def load_h5(filename):
h5filename = os.path.splitext(filename)[0] + '.h5'
mf = TableFile(h5filename)
pf = pymworks.open_file(filename)
return mf, pf
#!/usr/bin/env python import datautils.grouping import pymworks import pymworks.events import gaze.io.mworks import gaze.ops.check.check import gaze.ops.check.trials import gaze.opts.clean.constrain fn = "test.mwk" # open file df = pymworks.open_file(fn) # read gaze data & info (g = 2 tuple) g = gaze.io.mworks.read(df) # find valid gaze data c = gaze.ops.check.check.check_validity(*g) # min_error_mask = gaze.ops.check.check.find_minimum_error_mask(*g) # remove invalid data cg = g[0][c == 0] # remove data outside of 'reasonable' bounds ccg = gaze.ops.clean.constrain.constrain(cg) # read trial data