def add_patient_clicked(self):
text, ok = QtGui.QInputDialog.getText(self, '', 'Enter patient name:')
if ok:
new_file_name = os.path.join(PATIENT_DIR, str(text) + '.pkl')
if os.path.exists(new_file_name):
QtGui.QMessageBox.about(self, 'Error', 'Name already exists!')
else:
new_patient = Patient(str(text))
else:
return
text, ok = QtGui.QInputDialog.getInt(self, '', 'Enter patient age:')
if ok:
new_patient.age = int(text)
else:
return
text, ok = QtGui.QInputDialog.getText(self, '', 'Enter patient diagnosis:')
if ok:
new_patient.diagnosis = str(text)
else:
return
text, ok = QtGui.QInputDialog.getItem(self, '', 'Enter patient gender:', ['Female', 'Male', 'Other'])
if ok:
new_patient.gender = str(text)
else:
return
pickle.dump(new_patient, open(new_file_name, 'wb'))
self.update_patient_list()
def load_demographics(self, file):
f = codecs.open(file, 'r', 'utf-8')
reader = csv.reader(f)
line_ctr = 0
for row in reader:
# table title
if line_ctr < 1:
table_ttl = dict(zip(row, range(len(row))))
line_ctr += 1
continue
if len(row) == 0:
continue
pval = Patient()
pid = row[table_ttl['ID']]
pval.age = row[table_ttl['AGE']]
pval.gender = row[table_ttl['GENDER']]
pval.edu_year = row[table_ttl['EDUCATION YEAR']]
pval.duration = row[table_ttl['DURATION(MONTH)']]
self.patient_info[pid] = pval
line_ctr += 1
f.close()
def parse_events(patients,
event_collection,
event_type_names,
models_to_run,
remove_xyz_null=False,
remove_loc_empty=False):
# Populates patients dic with event entries (From HFO collection)
# Modifies patients
for evt in event_collection:
# Patient level
patient_id = evt['patient_id']
if patient_id not in patients.keys():
# raise RuntimeWarning('The parse_electrodes may should have had the patient created first')
patient = Patient(id=patient_id, age=parse_age(evt))
# moment
patients[patient.id] = patient
else:
patient = patients[patient_id]
# Check consistency of patient attributes
age = parse_age(evt)
if age != patient.age:
log('Warning, age should be consistent among events of the same patient'
)
if patient.age != 0 or age != 0:
patient.age = max(age, patient.age)
assert (patient is patients[patient_id]
) # They refer to the same object, but we use the short one
# Electrode level
e_name = parse_elec_name(evt)
soz = parse_soz_field(evt['soz'])
file_block = int(evt['file_block'])
block_duration = float(evt['r_duration'])
x, y, z = parse_coord(evt['x']), parse_coord(evt['y']), parse_coord(
evt['z'])
loc1, loc2, loc3, loc4, loc5 = parse_loc(evt, 1), parse_loc(
evt, 2), parse_loc(evt, 3), parse_loc(evt, 4), parse_loc(evt, 5)
if e_name not in patient.electrode_names():
# raise RuntimeWarning('The parse_electrodes should have created the electrode for this event')
# The code below would create a new a electrode from the HFO info
electrode = Electrode(name=e_name,
soz=soz,
blocks={file_block: block_duration},
x=x,
y=y,
z=z,
soz_sc=parse_soz_field(evt['soz_sc']),
loc1=loc1,
loc2=loc2,
loc3=loc3,
loc4=loc4,
loc5=loc5,
event_type_names=event_type_names)
patient.add_electrode(electrode)
else:
electrode = patient.get_electrode(e_name)
# Check consistency
# SOZ
if soz != electrode.soz:
log(msg=('Warning, soz disagreement among event and electrode'
'running OR between values'),
msg_type='elec_evt_SOZ_conflict',
patient=patient.id,
electrode=electrode.name)
electrode.soz = electrode.soz or soz # Fixs db bug of event nsoz and electrode.soz
electrode.soz_sc = electrode.soz_sc or parse_soz_field(
evt['soz_sc'])
# File block and duration
if file_block not in electrode.blocks.keys(
) or electrode.blocks[file_block] is None:
electrode.blocks[file_block] = block_duration
else:
if (block_duration != electrode.blocks[file_block]):
raise NotImplementedError(
'Implement which duration must be saved if they differ.'
)
# X Y Z
if electrode.x is None:
electrode.x = x
if electrode.y is None:
electrode.y = y
if electrode.z is None:
electrode.z = z
if x is not None and electrode.x != x:
raise RuntimeError(
'X disagreement (both not null) in event/electrode')
##Locations
if electrode.loc1 == 'empty':
electrode.loc1 = loc1
if electrode.loc2 == 'empty':
electrode.loc2 = loc2
if electrode.loc3 == 'empty':
electrode.loc3 = loc3
if electrode.loc4 == 'empty':
electrode.loc4 = loc4
if electrode.loc5 == 'empty':
electrode.loc5 = loc5
# Elec count update
evt_type = decode_type_name(evt['type'])
if file_block not in electrode.evt_count[evt_type].keys():
electrode.evt_count[evt_type][file_block] = 1
else:
electrode.evt_count[evt_type][file_block] += 1
# HFO_level
info = dict(
x=x,
y=y,
z=z,
prediction={m: []
for m in models_to_run},
# for saving results of a model
proba={m: []
for m in models_to_run},
# for saving results of a model
soz=soz,
type=decode_type_name(evt['type']),
file_block=int(evt['file_block']),
start_t=float(evt['start_t']),
finish_t=float(evt['finish_t']),
duration=float(evt['duration']) * 1000, # duration to milliseconds
fr_duration=float(evt['fr_duration']),
r_duration=float(evt['r_duration']),
freq_av=float(evt['freq_av']),
freq_pk=float(evt['freq_pk']), # spikes have 0 frec and power but
# they aren't used in ml so we just leave a None there
power_av=None if evt['power_av'] == 0 else mt.log10(
float(evt['power_av'])),
power_pk=None if evt['power_pk'] == 0 else mt.log10(
float(evt['power_pk'])),
loc1=loc1, # electrode.
loc2=loc2,
loc3=loc3,
loc4=loc4,
loc5=loc5,
age=patient.age)
if decode_type_name(evt['type']) in ['RonO', 'Fast RonO']:
# Compass sample --> 37% has slow == [] or None, map to None
parse_freq(info, 'slow', evt)
parse_freq(info, 'delta', evt)
parse_freq(info, 'theta', evt)
parse_freq(info, 'spindle', evt)
else:
parse_freq(info, 'spike', evt)
event = Event(info)
electrode.add(event)
# Removes electrodes with None coords or empty loc if requested by parameter
# Notice that here elec fields are ok here after parsing events, soz has been 'or' and if a coord or loc is None/empty all their events too
patient_ids_to_remove = set()
for patient in patients.values():
if remove_xyz_null:
remove_elec_xyz_null(patient)
if len(patient.electrodes) == 0: # If all electrodes were removed
patient_ids_to_remove.add(patient.id)
check_elec_xyz_not_null(patient)
if remove_loc_empty:
remove_elec_loc_empty(patient)
if len(patient.electrodes) == 0: # If all electrodes were removed
patient_ids_to_remove.add(patient.id)
check_elec_loc_not_empty(patient)
for p_name in patient_ids_to_remove:
patients.pop(p_name)
# Fixs EVENT inconsistencies to their electrodes
# We know that here all electrodes have their fields ok
evts_with_wrong_empty_loc = dict()
for patient in patients.values():
fix_elec_evt_soz_consistency(patient)
fix_elec_evt_xyz_consistency(patient)
fix_elec_evt_loc_consistency(patient, evts_with_wrong_empty_loc)
# Just to check that the above was well done, else raise errors
check_elec_evt_soz_consistency(patient)
check_elec_evt_xyz_consistency(patient)
check_elec_evt_loc_consistency(patient)
def parse_electrodes(patients, elec_cursor, event_type_names):
# Populates patients dic with electrode entries (From Electrodes collection)
# Modifies patients
for e in elec_cursor:
# Patient level
patient_id = e['patient_id']
if patient_id not in patients.keys():
patient = Patient(id=patient_id, age=parse_age(e))
patients[patient_id] = patient
else:
patient = patients[patient_id]
# Check consistency of patient attributes
age = parse_age(e)
if age != patient.age:
log('Warning, age should agree among electrodes of the same patient'
)
if patient.age != 0 or age != 0:
patient.age = max(age, patient.age)
# Electrode level
e_name = parse_elec_name(e)
file_block = int(e['file_block'])
x, y, z = parse_coord(e['x']), parse_coord(e['y']), parse_coord(e['z'])
loc1, loc2, loc3, loc4, loc5 = parse_loc(e, 1), parse_loc(e, 2), \
parse_loc(e, 3), parse_loc(e, 4), \
parse_loc(e, 5)
first_time_seen = e_name not in patient.electrode_names()
if first_time_seen:
electrode = Electrode(name=e_name,
soz=parse_soz_field(e['soz']),
blocks={file_block: None},
x=x,
y=y,
z=z,
soz_sc=(e['soz_sc']),
loc1=loc1,
loc2=loc2,
loc3=loc3,
loc4=loc4,
loc5=loc5,
event_type_names=event_type_names)
patient.add_electrode(electrode)
else: # The electrode exists probably because there are many blocks for the electrodes
electrode = patient.get_electrode(e_name)
# Check consistency
assert (electrode.name == e_name and patient.id == e['patient_id'])
if parse_soz_field(e['soz']) != electrode.soz:
log(msg=('Warning, soz disagreement among blocks of '
'the same patient_id, electrode, '
'running OR between values'),
msg_type='elec_blocks_SOZ_conflict',
patient=patient.id,
electrode=electrode.name)
electrode.soz = electrode.soz or parse_soz_field(e['soz'])
electrode.soz_sc = electrode.soz_sc or parse_soz_field(e['soz_sc'])
if file_block not in electrode.blocks.keys():
electrode.blocks[
file_block] = None # here we will save the time of the block that is given in the HFO db...
##Locations
if electrode.loc1 == 'empty':
electrode.loc1 = loc1
if electrode.loc2 == 'empty':
electrode.loc2 = loc2
if electrode.loc3 == 'empty':
electrode.loc3 = loc3
if electrode.loc4 == 'empty':
electrode.loc4 = loc4
if electrode.loc5 == 'empty':
electrode.loc5 = loc5
if electrode.x is None:
electrode.x = x
if electrode.y is None:
electrode.y = y
if electrode.z is None:
electrode.z = z
if x is not None and electrode.x != x:
raise RuntimeError(
'X disagreement (both not null) in electrode blocks')
if loc5 != 'empty' and electrode.loc5 != loc5:
RuntimeError(
'This shouldnt happen, says that blocks of the same electrode have dif names none empty'
)
log(msg=(
'Warning, loc5 disagreement among blocks for the same (patient_id, electrode)'
),
msg_type='LOC5',
patient=patient.id,
electrode=electrode.name)
if loc5 == 'Hippocampus': # Priority
electrode.loc5 = loc5