def rp(psa_dates, psa_vals, rp_date):
rp_date = filter(None, rp_date)
result = []
if len(psa_dates) > 0:
for date in rp_date:
psd = equal_or_after(psa_dates, date)
if len(psd) != 0:
for j in range(psa_dates.index(psd), len(psa_dates)):
cur = psa_vals[j]
if (j + 1) < len(psa_dates):
nex = psa_vals[j + 1]
else:
break
if float(cur) >= 0.2 and float(nex) >= 0.2:
result.append([
'Radical Prostatectomy', 'Curative',
psa_dates[j + 1], nex
])
break
if len(result) > 0:
return result
else:
return [['NULL', 'NULL', 'NULL', 'NULL']]
def chemo(psa_dates, psa_vals, chemo_start, chemo_intent):
result = []
if len(psa_dates) > 0:
#intent_dic = {'2': 'Curative', '3': 'Life prolonging', '4': 'Symptom control', '5': 'Adjuvant'}
#chemo_intent = [intent_dic[x] if x in intent_dic.keys() else '' for x in chemo_intent]
#indices = [i for i, x in enumerate(chemo_intent) if x in intent_dic.values()]
indices = [
i for i, x in enumerate(chemo_intent)
if (x == "Curative" or x == "2")
]
for i in indices:
date = chemo_start[i]
psd = equal_or_after(psa_dates, date)
if len(psd) != 0:
j = psa_dates.index(psd)
while j < len(psa_dates):
cur = psa_vals[j]
if (j + 1) < len(psa_dates):
nex = psa_vals[j + 1]
else:
break
if float(nex) > float(cur):
nadir = float(cur)
zenith = float(cur) * 1.25
for k in range((j + 1), len(psa_dates)):
p = psa_vals[k]
if float(p) <= nadir:
j = k
break
elif float(p) >= zenith:
result.append([
'Chemotherapy', 'Curative', psa_dates[k], p
])
break
if j != k:
break
else:
j = j + 1
if len(result) > 0:
return result
else:
return [['NULL', 'NULL', 'NULL', 'NULL']]
def cryo(psa_dates, psa_vals, cryo_start, cryo_intent):
result = []
if len(psa_dates) > 0:
indices = [
i for i, x in enumerate(cryo_intent)
if (x == "Primary" or x == "1")
]
for i in indices:
date = cryo_start[i]
psd = equal_or_after(psa_dates, date)
if len(psd) != 0:
j = psa_dates.index(psd)
while j < len(psa_dates):
cur = psa_vals[j]
if (j + 1) < len(psa_dates):
nex = psa_vals[j + 1]
else:
break
if float(nex) > float(cur):
nadir = float(cur)
zenith = float(cur) + 2
for k in range((j + 1), len(psa_dates)):
p = psa_vals[k]
if float(p) <= nadir:
j = k
break
elif float(p) >= zenith:
result.append([
'Cryotherapy', 'Primary', psa_dates[k], p
])
break
if j != k:
break
else:
j = j + 1
if len(result) > 0:
return result
else:
return [['NULL', 'NULL', 'NULL', 'NULL']]
def rt(psa_dates, psa_vals, rt_start, rt_intent, all_tx):
all_tx = filter(None, all_tx)
result = []
if len(psa_dates) > 0:
indices = [
i for i, x in enumerate(rt_intent) if (x == "Curative" or x == "2")
]
# Add non-curative RT txs to all_tx
all_tx.extend(
[rt_start[i] for i in range(len(rt_start)) if i not in indices])
all_tx = sorted(
all_tx, key=lambda x: datetime.datetime.strptime(x, date_match))
for i in indices:
date = rt_start[i]
psd = equal_or_after(psa_dates, date)
if len(psd) != 0:
terminus = ''
if len(all_tx) != 0:
terminus = equal_or_after(all_tx, date)
if len(terminus) == 0:
terminus = datetime.datetime.strftime(
(datetime.datetime.strptime(psa_dates[-1], date_match)
+ datetime.timedelta(days=1)), date_match)
bounce = False
nadir_set = False
j = psa_dates.index(psd)
while j < len(psa_dates):
cur = psa_vals[j]
if (j + 1) < len(psa_dates):
nex = psa_vals[j + 1]
else:
break
if float(nex) > float(cur):
nadir = float(cur)
zenith = nadir + 2
for k in range((j + 1), len(psa_dates)):
p = psa_vals[k]
if float(p) <= nadir:
if nadir_set:
bounce = True
nadir_set = False
#print 'Benign bounce'
j = k
break
elif float(p) >= zenith:
if not bounce and not nadir_set:
break_val = p
break_date = psa_dates[k]
nadir = 0.5
zenith = nadir + 2
nadir_set = True
if bounce or (k == len(psa_vals) - 1) or (
datetime.datetime.strptime(
psa_dates[k + 1], date_match) >=
datetime.datetime.strptime(
terminus, date_match)):
if bounce:
result.append([
'Radiation Therapy', 'Curative',
psa_dates[k], p
])
else:
result.append([
'Radiation Therapy', 'Curative',
break_date, break_val
])
break
if j != k:
break
else:
j = j + 1
if len(result) > 0:
return result
else:
return [['NULL', 'NULL', 'NULL', 'NULL']]
def lhrh(psa_dates, psa_vals, lhrh_start, lhrh_stop, lhrh_intent):
result = []
if len(psa_dates) > 0:
intent_dic = {
'1': 'Neo-adjuvant',
'2': 'Curative',
'3': 'Salvage',
'4': 'Metastatic',
'5': 'Life prolonging',
'6': 'Symptom control',
'7': 'Adjuvant'
}
# this line allows tx periods to have no stop date, IE, tx periods which may be in process.
lhrh_stop = [psa_dates[-1] if x == '' else x for x in lhrh_stop]
for i, date in enumerate(lhrh_start):
start = equal_or_after(psa_dates, date)
stop = equal_or_before(psa_dates,
lhrh_stop[lhrh_start.index(date)])
if len(start) != 0 and len(stop) != 0 and psa_dates.index(
start) < psa_dates.index(stop):
j = psa_dates.index(start)
while j < len(psa_dates) and equal_or_before([psa_dates[j]],
stop) != '':
cur = psa_vals[j]
if (j + 1) < len(psa_dates) and equal_or_before(
[psa_dates[j + 1]], stop) != '':
nex = psa_vals[j + 1]
else:
break
if float(nex) > float(cur):
nadir = float(cur)
zenith = float(nex)
zenith_date = datetime.datetime.strptime(
psa_dates[j + 1], date_match)
for k in range((j + 1), len(psa_dates)):
if equal_or_before([psa_dates[k]], stop) == '':
break
p = psa_vals[k]
p_date = datetime.datetime.strptime(
psa_dates[k], date_match)
if float(p) <= nadir:
j = k
break
elif float(p) > zenith and (p_date -
zenith_date).days >= 7:
result.append([
'LHRH',
intent_dic.get(lhrh_intent[i], 'NULL'),
psa_dates[k], p
])
break
if j != k:
break
else:
j = j + 1
if len(result) > 0:
return result
else:
return [['NULL', 'NULL', 'NULL', 'NULL']]