diff --git a/Marie/pathways.py b/Marie/pathways.py
index fba9d64a590c55ef06c7f341f8a7d11f8a741dc9..f78f797b983e26230d232cfdfeb8122958d62476 100644
--- a/Marie/pathways.py
+++ b/Marie/pathways.py
@@ -1,3 +1,16 @@
+"""
+Description of the VICAN pathways
+"""
+
+import warnings
+from datetime import date
+from dateutil.relativedelta import relativedelta
+
+import numpy as np
+import numpy.random as rd
+import pandas as pd
+
+
from SNDSGenerator.pathway_factory import pathwayInjector
from SNDSGenerator.database_model import (
Patient,
@@ -7,15 +20,15 @@ from SNDSGenerator.database_model import (
)
from SNDSGenerator.simulation import simulation
-from datetime import date
-from dateutil.relativedelta import relativedelta
-
-import warnings
-import numpy as np
-import numpy.random as rd
+# pylint: disable=C0103
class Surgery(pathwayInjector):
+ """Surgery pathway
+
+ This pathway includes only one specific surgery (short hospital stay).
+ """
+
def __init__(self, sim: simulation):
super().__init__(sim)
# CCAM codes for breast cancer surgeries
@@ -26,7 +39,6 @@ class Surgery(pathwayInjector):
"QEFA016",
"QEFA017",
"QEFA018",
-
"QEFA003",
"QEF005",
"QEFA010",
@@ -38,9 +50,8 @@ class Surgery(pathwayInjector):
"QEFA019",
]
-
def pathdesc(self, patient: Patient, d: date):
- hospit_reason = "Z51.1"
+ hospit_reason = "C50" # C50.9 Tumeur maligne du sein, sans précision
surgery_code = rd.choice(self.code_chir)
care = ShortHospStay(patient, self.sim.etablissements[0], hospit_reason)
@@ -53,13 +64,12 @@ class Surgery(pathwayInjector):
class ET_uni(pathwayInjector):
- """Endocrino Therapy"""
+ """Endocrino Therapy pathway"""
def __init__(self, sim: simulation):
super().__init__(sim)
code_ET_ATC_AI = ["L02BA01"]
code_ET_ATC_Tamoxifen = ["L02BG03", "L02BG06", "L02BG04"]
-
# SELECT PHA_CIP_C13 from IR_PHA_r where PHA_ATC_C07 like "L02BA01" or PHA_ATC_C07 like "L02BG03" or PHA_ATC_C07 like "L02BG06" or PHA_ATC_C07 like "L02BG04" or PHA_ATC_C07 like "L02AE03" or PHA_ATC_C07 like "L02AE02" or PHA_ATC_C07 like "L02AE04";
self.code_ET_CIP_L02BA01 = [
@@ -228,7 +238,7 @@ class ET_uni(pathwayInjector):
def pathdesc(self, patient: Patient, d: date):
# tirage d'un sur les deux
- if rd.choice([0, 1], p=[0.255,0.745]):
+ if rd.choice([0, 1], p=[0.255, 0.745]):
ET_code = rd.choice(self.code_ET_CIP_L02BA01)
else:
ET_code = rd.choice(self.code_ET_CIP_Tamoxifen)
@@ -251,7 +261,10 @@ class ET_bi(pathwayInjector):
code_ET_ATC_AI = ["L02BA01"]
code_ET_ATC_Tamoxifen = ["L02BG03", "L02BG06", "L02BG04"]
- # SELECT PHA_CIP_C13 from IR_PHA_r where PHA_ATC_C07 like "L02BA01" or PHA_ATC_C07 like "L02BG03" or PHA_ATC_C07 like "L02BG06" or PHA_ATC_C07 like "L02BG04" or PHA_ATC_C07 like "L02AE03" or PHA_ATC_C07 like "L02AE02" or PHA_ATC_C07 like "L02AE04";
+ # SELECT PHA_CIP_C13 from IR_PHA_r where PHA_ATC_C07 like "L02BA01" or PHA_ATC_C07
+ # like "L02BG03" or PHA_ATC_C07 like "L02BG06" or PHA_ATC_C07 like "L02BG04" or
+ # PHA_ATC_C07 like "L02AE03" or PHA_ATC_C07 like "L02AE02" or
+ # PHA_ATC_C07 like "L02AE04";
self.code_ET_CIP_L02BA01 = [
"3400932059324",
"3400932865284",
@@ -415,18 +428,42 @@ class ET_bi(pathwayInjector):
"3400949980994",
"3400949982028",
]
- self.code_ET_CIP_agonist = ["3400930020005", "3400930122112", "3400930122129", "3400932829217", "3400932850037", "3400932850266", "3400932932672", "3400933129125", "3400933943769", "3400933963811", "3400934125423", "3400934125652", "3400935844675", "3400936690868", "3400936690929", "3400937575256", "3400937575317", "3400938081459", "3400938263381", "3400938458381", "3400939262123", "3400939890173", "3400949002634", "3400949002818"]
-
+ self.code_ET_CIP_agonist = [
+ "3400930020005",
+ "3400930122112",
+ "3400930122129",
+ "3400932829217",
+ "3400932850037",
+ "3400932850266",
+ "3400932932672",
+ "3400933129125",
+ "3400933943769",
+ "3400933963811",
+ "3400934125423",
+ "3400934125652",
+ "3400935844675",
+ "3400936690868",
+ "3400936690929",
+ "3400937575256",
+ "3400937575317",
+ "3400938081459",
+ "3400938263381",
+ "3400938458381",
+ "3400939262123",
+ "3400939890173",
+ "3400949002634",
+ "3400949002818",
+ ]
def pathdesc(self, patient: Patient, d: date):
nb_tot = 12
- seq_type = rd.choice([1,2,3,4], p=[0.5167, 0.4, 0.05, 0.0333])
- if seq_type==1:
+ seq_type = rd.choice([1, 2, 3, 4], p=[0.5167, 0.4, 0.05, 0.0333])
+ if seq_type == 1:
ET_code_AI = rd.choice(self.code_ET_CIP_L02BA01)
ET_code_Tamoxifen = rd.choice(self.code_ET_CIP_Tamoxifen)
- nb=rd.randint(1,nb_tot-1)
+ nb = rd.randint(1, nb_tot - 1)
for i in range(nb):
care = DrugDelivery(ET_code_Tamoxifen, patient, self.sim.pharms[0])
care.date_debut = d
@@ -434,7 +471,7 @@ class ET_bi(pathwayInjector):
patient.append(care)
if i != nb - 1:
d = d + relativedelta(months=1)
- for i in range(nb_tot-nb):
+ for i in range(nb_tot - nb):
care = DrugDelivery(ET_code_AI, patient, self.sim.pharms[0])
care.date_debut = d
care.date_fin = d
@@ -442,11 +479,11 @@ class ET_bi(pathwayInjector):
if i != nb - 1:
d = d + relativedelta(months=1)
- elif seq_type==2:
+ elif seq_type == 2:
- ET_code_AI = rd.choice(self.code_ET_CIP_L02BA01)
- ET_code_Tamoxifen = rd.choice(self.code_ET_CIP_Tamoxifen)
- nb=rd.randint(1,nb_tot-1)
+ ET_code_AI = rd.choice(self.code_ET_CIP_L02BA01)
+ ET_code_Tamoxifen = rd.choice(self.code_ET_CIP_Tamoxifen)
+ nb = rd.randint(1, nb_tot - 1)
for i in range(nb):
care = DrugDelivery(ET_code_AI, patient, self.sim.pharms[0])
care.date_debut = d
@@ -454,7 +491,7 @@ class ET_bi(pathwayInjector):
patient.append(care)
if i != nb - 1:
d = d + relativedelta(months=1)
- for i in range(nb_tot-nb):
+ for i in range(nb_tot - nb):
care = DrugDelivery(ET_code_Tamoxifen, patient, self.sim.pharms[0])
care.date_debut = d
care.date_fin = d
@@ -462,7 +499,7 @@ class ET_bi(pathwayInjector):
if i != nb - 1:
d = d + relativedelta(months=1)
- elif seq_type==3:
+ elif seq_type == 3:
ET_code_Tamoxifen = rd.choice(self.code_ET_CIP_Tamoxifen)
ET_code_AI = rd.choice(self.code_ET_CIP_agonist)
for i in range(nb_tot): # combien de temps ??
@@ -477,7 +514,7 @@ class ET_bi(pathwayInjector):
if i != nb - 1:
d = d + relativedelta(months=1)
- elif seq_type==4:
+ elif seq_type == 4:
ET_code_L02BA01 = rd.choice(self.code_ET_CIP_L02BA01)
ET_code_AI = rd.choice(self.code_ET_CIP_agonist)
for i in range(nb_tot): # combien de temps ??
@@ -523,43 +560,45 @@ class RT_outHospital(pathwayInjector):
def __init__(self, sim: simulation):
super().__init__(sim)
- codes = {"YYYY166":5326,
- "YYYY047":4280,
- "YYYY152":3758,
- "YYYY128":2863,
- "YYYY048":2299,
- "YYYY323":2006,
- "YYYY334":1562,
- "YYYY050":837,
- "YYYY049":829,
- "YYYY109":779,
- "YYYY244":756,
- "YYYY197":732,
- "YYYY387":412,
- "YYYY356":354,
- "YYYY347":353,
- "YYYY345":314,
- "YYYY469":308,
- "YYYY081":298,
- "YYYY080":246,
- "YYYY380":246,
- "YYYY307":228,
- "YYYY337":218,
- "YYYY151":212,
- "YYYY304":205,
- "YYYY458":186,
- "YYYY460":185,
- "YYYY369":168,
- "YYYY331":154,
- "YYYY225":148,
- "YYYY370":138,
- "YYYY377":133,
- "YYYY491":129,
- "YYYY398":122,
- "YYYY391":115,
- "YYYY299":111,
- "YYYY459":108,
- "YYYY358":104}
+ codes = {
+ "YYYY166": 5326,
+ "YYYY047": 4280,
+ "YYYY152": 3758,
+ "YYYY128": 2863,
+ "YYYY048": 2299,
+ "YYYY323": 2006,
+ "YYYY334": 1562,
+ "YYYY050": 837,
+ "YYYY049": 829,
+ "YYYY109": 779,
+ "YYYY244": 756,
+ "YYYY197": 732,
+ "YYYY387": 412,
+ "YYYY356": 354,
+ "YYYY347": 353,
+ "YYYY345": 314,
+ "YYYY469": 308,
+ "YYYY081": 298,
+ "YYYY080": 246,
+ "YYYY380": 246,
+ "YYYY307": 228,
+ "YYYY337": 218,
+ "YYYY151": 212,
+ "YYYY304": 205,
+ "YYYY458": 186,
+ "YYYY460": 185,
+ "YYYY369": 168,
+ "YYYY331": 154,
+ "YYYY225": 148,
+ "YYYY370": 138,
+ "YYYY377": 133,
+ "YYYY491": 129,
+ "YYYY398": 122,
+ "YYYY391": 115,
+ "YYYY299": 111,
+ "YYYY459": 108,
+ "YYYY358": 104,
+ }
# draw the CCAM code used for this patient all along the RT
p = np.array(list(codes.values()))
@@ -587,52 +626,54 @@ class RT_inHospital(pathwayInjector):
The RT is organised as one first visit and then a collection of sessions.
Each session has its own RSS (MCO stay)
-
+
"""
def __init__(self, sim: simulation):
super().__init__(sim)
- codes = {"ZZNL065":34192,
- "ZZNL063":14296,
- "YYYY047":11402,
- "ZZNL062":5858,
- "ZZNL064":5207,
- "YYYY152":4953,
- "YYYY166":4639,
- "ZZNL053":3001,
- "YYYY307":2318,
- "YYYY048":1992,
- "ZZNL050":1739,
- "ZZNL037":1507,
- "YYYY049":1301,
- "ZZNL040":1266,
- "YYYY450":1144,
- "YYYY128":1113,
- "YYYY347":1012,
- "ZZNL031":936,
- "ZZNL048":833,
- "ZZNL054":791,
- "ZZNL039":753,
- "ZZNL043":675,
- "YYYY459":552,
- "YYYY197":528,
- "YYYY387":488,
- "YYYY050":479,
- "ZZNL036":478,
- "ZZNL051":456,
- "ZZNL061":363,
- "YYYY046":343,
- "ZZNL030":325,
- "YYYY304":290,
- "YYYY337":229,
- "YYYY081":223,
- "YYYY492":211,
- "YYYY109":166,
- "YYYY151":164,
- "ZZNL042":156,
- "YYYY080":118,
- "YYYY136":114}
+ codes = {
+ "ZZNL065": 34192,
+ "ZZNL063": 14296,
+ "YYYY047": 11402,
+ "ZZNL062": 5858,
+ "ZZNL064": 5207,
+ "YYYY152": 4953,
+ "YYYY166": 4639,
+ "ZZNL053": 3001,
+ "YYYY307": 2318,
+ "YYYY048": 1992,
+ "ZZNL050": 1739,
+ "ZZNL037": 1507,
+ "YYYY049": 1301,
+ "ZZNL040": 1266,
+ "YYYY450": 1144,
+ "YYYY128": 1113,
+ "YYYY347": 1012,
+ "ZZNL031": 936,
+ "ZZNL048": 833,
+ "ZZNL054": 791,
+ "ZZNL039": 753,
+ "ZZNL043": 675,
+ "YYYY459": 552,
+ "YYYY197": 528,
+ "YYYY387": 488,
+ "YYYY050": 479,
+ "ZZNL036": 478,
+ "ZZNL051": 456,
+ "ZZNL061": 363,
+ "YYYY046": 343,
+ "ZZNL030": 325,
+ "YYYY304": 290,
+ "YYYY337": 229,
+ "YYYY081": 223,
+ "YYYY492": 211,
+ "YYYY109": 166,
+ "YYYY151": 164,
+ "ZZNL042": 156,
+ "YYYY080": 118,
+ "YYYY136": 114,
+ }
# draw the CCAM code used for this patient all along the RT
p = np.array(list(codes.values()))
@@ -642,7 +683,7 @@ class RT_inHospital(pathwayInjector):
def pathdesc(self, patient: Patient, d: date):
# create the stay initiating the Radio therapy
care = ShortHospStay(patient, self.sim.etablissements[0], "Z5100")
- care.DRel = "Z50"
+ care.DRel = "C50"
if date.weekday(d) == 5: # Saturday
d += relativedelta(days=2)
@@ -650,33 +691,36 @@ class RT_inHospital(pathwayInjector):
d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
-
- #add a RUM
+
+ # add a RUM
rum = ShortHospStay.hospRUM(42, "Z5101")
- rum.length=1
- rum.DRel = "Z5100"
- care.RUMs.append( rum )
+ rum.length = 1
+ rum.DRel = "C50"
+ care.RUMs.append(rum)
patient.append(care)
- #next event
+ # next event
if date.weekday(d) == 4: # d was a Friday
d += relativedelta(days=3)
else:
d += relativedelta(days=1)
- nb = rd.randint(5,8) #5 to 7 week of treatment
+ nb = rd.randint(5, 8) # 5 to 7 week of treatment
# create one MCO (RSS) per RT session (Z5101: irradiation session)
# The first session in the same day
- for _ in range(nb*5-1):
+ for _ in range(nb * 5 - 1):
# session everyday, except the weekend
care = ShortHospStay(patient, self.sim.etablissements[0], "Z5101")
+ care.DRel = "C50"
care.start_date = d
care.finish_date = d
care.ccam.append(self.act_code)
- care.RUMs.append(ShortHospStay.hospRUM(42, "Z5101")) # add the corresponding RUM in a ambulatory service
+ care.RUMs.append(
+ ShortHospStay.hospRUM(42, "Z5101")
+ ) # add the corresponding RUM in a ambulatory service
patient.append(care)
-
+
if date.weekday(d) == 6: # d was a Sunday, might never happen!!
d += relativedelta(days=1)
elif date.weekday(d) == 5: # d was a Saturday, might never happen!!
@@ -725,64 +769,225 @@ class CT_uni(pathwayInjector):
"HPLB003": 4,
"HPLB007": 0,
"ZZLF004": 10,
- "ZZLF900": 0,
}
-
- #UCD codes: obtained from the requests: "select PHA_CIP_UCD from IR_PHA_R where PHA_ATC_C07="L01AA01""
+
+ # UCD codes: obtained from the requests: "select PHA_CIP_UCD from IR_PHA_R where PHA_ATC_C07="L01AA01""
+ # complemented with UCD codes deduced from the NU_UCD_R table (Reference table for UCD) using the drug name (ATC code)
+ # L01AA01: CYCLOPHOSPHAMIDE -> ??
+ # L01CD02: TAXOTERE -> "9178082","9178099"
+ # L01DB03: EPIRUBICINE -> "9284306","9284312","9284329","9284335","9284341","9284358","9284364","9284370","9284387","9284393","9284401","9284418","9284424","9285257","9285263","9285286","9285292","9285300","9285317","9285323","9285346","9285352","9293357","9293363","9293386","9293392","9304457","9304463","9304486","9304492","9305095","9305103","9305126","9305132","9306605","9306611","9306628","9306634","9306640","9306657","9306663","9306686","9313137","9313143","9313166","9313172","9313189","9316058","9316064","9316070","9319708","9319714","9328481","9332637","9332643","9337913","9337936","9337942","9337959","9343724","9343730","9343747","9343753"
+ # L01BC02: Fluorouracile -> "9191527","9191533","9191556","9192107","9192113","9192136","9196163","9196186","9196192","9196200","9216925","9227685","9227691","9227716","9227722","9247191","9247216","9247222","9247239","9257315","9268276","9268282","9334866","9334872","9334889","9334895","9340950","9340967","9340973","9340996","9341004"
+ # L01CD01: paclitaxel -> "9278091","9278116","9278122","9282744","9282750","9282767","9282773","9284499","9284507","9284513","9284536","9285381","9285398","9285406","9285412","9290459","9290465","9290471","9296829","9296835","9296841","9296858","9299443","9299466","9299472","9299489","9305379","9305385","9305391","9308254","9308923","9308946","9308952","9308969","9319022","9327903","9327926","9327932","9327949","9332809","9332815","9332821","9363282","9363299","9363307","9366441","9366458","9401350","9401367",
+
self.code_CT_ATC = {
- "L01AA01":["9031083","9031077","9031114"],
- "L01CD02":[],
- "L01DB03":["9145332", "9145361"],
- "L01BC02":["9224505", "9030534", "9224505", "9303995"],
- "L01CD01":[]
- }
- #NB: the UCD codes does not necessarily exist in the NU_UCD_R table (Reference table for UCD)
- # pick up a random UCD code:
- self.ucd = "9031083"
+ "L01AA01": ["9031083", "9031077", "9031114"],
+ "L01CD02": ["9178082", "9178099"],
+ "L01DB03": [
+ "9145332",
+ "9145361",
+ "9284306",
+ "9284312",
+ "9284329",
+ "9284335",
+ "9284341",
+ "9284358",
+ "9284364",
+ "9284370",
+ "9284387",
+ "9284393",
+ "9284401",
+ "9284418",
+ "9284424",
+ "9285257",
+ "9285263",
+ "9285286",
+ "9285292",
+ "9285300",
+ "9285317",
+ "9285323",
+ "9285346",
+ "9285352",
+ "9293357",
+ "9293363",
+ "9293386",
+ "9293392",
+ "9304457",
+ "9304463",
+ "9304486",
+ "9304492",
+ "9305095",
+ "9305103",
+ "9305126",
+ "9305132",
+ "9306605",
+ "9306611",
+ "9306628",
+ "9306634",
+ "9306640",
+ "9306657",
+ "9306663",
+ "9306686",
+ "9313137",
+ "9313143",
+ "9313166",
+ "9313172",
+ "9313189",
+ "9316058",
+ "9316064",
+ "9316070",
+ "9319708",
+ "9319714",
+ "9328481",
+ "9332637",
+ "9332643",
+ "9337913",
+ "9337936",
+ "9337942",
+ "9337959",
+ "9343724",
+ "9343730",
+ "9343747",
+ "9343753",
+ ],
+ "L01BC02": [
+ "9224505",
+ "9030534",
+ "9224505",
+ "9303995",
+ "9191527",
+ "9191533",
+ "9191556",
+ "9192107",
+ "9192113",
+ "9192136",
+ "9196163",
+ "9196186",
+ "9196192",
+ "9196200",
+ "9216925",
+ "9227685",
+ "9227691",
+ "9227716",
+ "9227722",
+ "9247191",
+ "9247216",
+ "9247222",
+ "9247239",
+ "9257315",
+ "9268276",
+ "9268282",
+ "9334866",
+ "9334872",
+ "9334889",
+ "9334895",
+ "9340950",
+ "9340967",
+ "9340973",
+ "9340996",
+ "9341004",
+ ],
+ "L01CD01": [
+ "9278091",
+ "9278116",
+ "9278122",
+ "9282744",
+ "9282750",
+ "9282767",
+ "9282773",
+ "9284499",
+ "9284507",
+ "9284513",
+ "9284536",
+ "9285381",
+ "9285398",
+ "9285406",
+ "9285412",
+ "9290459",
+ "9290465",
+ "9290471",
+ "9296829",
+ "9296835",
+ "9296841",
+ "9296858",
+ "9299443",
+ "9299466",
+ "9299472",
+ "9299489",
+ "9305379",
+ "9305385",
+ "9305391",
+ "9308254",
+ "9308923",
+ "9308946",
+ "9308952",
+ "9308969",
+ "9319022",
+ "9327903",
+ "9327926",
+ "9327932",
+ "9327949",
+ "9332809",
+ "9332815",
+ "9332821",
+ "9363282",
+ "9363299",
+ "9363307",
+ "9366441",
+ "9366458",
+ "9401350",
+ "9401367",
+ ],
+ }
# table T_MCOaaMED **not yet implemented**
- if nb is None:
+ if nb is None or nb <= 0:
self.nb = int(rd.uniform(3, 10))
else:
self.nb = nb
-
+
self.delay = delay
self.CT_code = None
+ self.ucd_atc = None
+ self.ucd = None
def pathdesc(self, patient: Patient, d: date):
+ # then, pick up a random UCD code, through the choice of an ATC code:
+ self.ucd_atc = rd.choice(list(self.code_CT_ATC.keys()))
+ self.ucd = rd.choice(self.code_CT_ATC[self.ucd_atc])
- care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
- care.DRel = "Z50"
- if date.weekday(d) == 5: # Saturday
- d += relativedelta(days=-1)
- elif date.weekday(d) == 6: # Sunday
- d += relativedelta(days=1)
- care.start_date = d
- care.finish_date = d
- patient.append(care)
-
+ # choose the type of medical act
p = np.array(list(self.code_CT_CCAM.values()))
p /= np.sum(p)
if self.CT_code is None:
self.CT_code = rd.choice(list(self.code_CT_CCAM.keys()), p=p)
-
+ oldd = d
for _ in range(self.nb):
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "Z50"
care.ccam.append(self.CT_code)
- care.UCDs.append( ShortHospStay.UCD(self.ucd) )
+ care.UCDs.append(ShortHospStay.UCD(self.ucd))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
patient.append(care)
+ oldd = d
d = d + relativedelta(days=self.delay)
- d = d - relativedelta(days=self.delay)
- return d
+ return oldd
class CT_bi(pathwayInjector):
- """Chimiotherapy pathway, bitherapy"""
+ """Chimiotherapy (CT) pathway, bitherapy
+
+ In a bitherapy, the patient starts with one type of drugs for CT, and at some point
+ of the therapy, the injected drug is changed.
+ In our model, we change the ATC type of the drugs delivered to patient though CT sessions.
+ """
- def __init__(self, sim: simulation, nb:int = None, delays:int = (14,21)):
+ def __init__(self, sim: simulation, nb: int = None, delays: int = (14, 21)):
super().__init__(sim)
self.code_CT_CIM10 = ["Z511", "Z512"]
self.code_CT_CCAM = {
@@ -811,56 +1016,236 @@ class CT_bi(pathwayInjector):
"HPLB003": 4,
"HPLB007": 0,
"ZZLF004": 10,
- "ZZLF900": 0,
}
- self.code_CT_ATC = ["L01AA01", "L01CD02", "L01DB03", "L01BC02", "L01CD01"]
+ self.code_CT_ATC = {
+ "L01AA01": ["9031083", "9031077", "9031114"],
+ "L01CD02": ["9178082", "9178099"],
+ "L01DB03": [
+ "9145332",
+ "9145361",
+ "9284306",
+ "9284312",
+ "9284329",
+ "9284335",
+ "9284341",
+ "9284358",
+ "9284364",
+ "9284370",
+ "9284387",
+ "9284393",
+ "9284401",
+ "9284418",
+ "9284424",
+ "9285257",
+ "9285263",
+ "9285286",
+ "9285292",
+ "9285300",
+ "9285317",
+ "9285323",
+ "9285346",
+ "9285352",
+ "9293357",
+ "9293363",
+ "9293386",
+ "9293392",
+ "9304457",
+ "9304463",
+ "9304486",
+ "9304492",
+ "9305095",
+ "9305103",
+ "9305126",
+ "9305132",
+ "9306605",
+ "9306611",
+ "9306628",
+ "9306634",
+ "9306640",
+ "9306657",
+ "9306663",
+ "9306686",
+ "9313137",
+ "9313143",
+ "9313166",
+ "9313172",
+ "9313189",
+ "9316058",
+ "9316064",
+ "9316070",
+ "9319708",
+ "9319714",
+ "9328481",
+ "9332637",
+ "9332643",
+ "9337913",
+ "9337936",
+ "9337942",
+ "9337959",
+ "9343724",
+ "9343730",
+ "9343747",
+ "9343753",
+ ],
+ "L01BC02": [
+ "9224505",
+ "9030534",
+ "9224505",
+ "9303995",
+ "9191527",
+ "9191533",
+ "9191556",
+ "9192107",
+ "9192113",
+ "9192136",
+ "9196163",
+ "9196186",
+ "9196192",
+ "9196200",
+ "9216925",
+ "9227685",
+ "9227691",
+ "9227716",
+ "9227722",
+ "9247191",
+ "9247216",
+ "9247222",
+ "9247239",
+ "9257315",
+ "9268276",
+ "9268282",
+ "9334866",
+ "9334872",
+ "9334889",
+ "9334895",
+ "9340950",
+ "9340967",
+ "9340973",
+ "9340996",
+ "9341004",
+ ],
+ "L01CD01": [
+ "9278091",
+ "9278116",
+ "9278122",
+ "9282744",
+ "9282750",
+ "9282767",
+ "9282773",
+ "9284499",
+ "9284507",
+ "9284513",
+ "9284536",
+ "9285381",
+ "9285398",
+ "9285406",
+ "9285412",
+ "9290459",
+ "9290465",
+ "9290471",
+ "9296829",
+ "9296835",
+ "9296841",
+ "9296858",
+ "9299443",
+ "9299466",
+ "9299472",
+ "9299489",
+ "9305379",
+ "9305385",
+ "9305391",
+ "9308254",
+ "9308923",
+ "9308946",
+ "9308952",
+ "9308969",
+ "9319022",
+ "9327903",
+ "9327926",
+ "9327932",
+ "9327949",
+ "9332809",
+ "9332815",
+ "9332821",
+ "9363282",
+ "9363299",
+ "9363307",
+ "9366441",
+ "9366458",
+ "9401350",
+ "9401367",
+ ],
+ }
if nb is None:
self.nb = int(rd.uniform(3, 6))
else:
- self.nb=nb
+ self.nb = nb
+
+ # pick up a random UCD code, through the choice of an ATC code:
+ self.ucd_atc = None
+ self.ucd = None
self.delays = delays
self.CT_code = None
def pathdesc(self, patient: Patient, d: date):
- care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
- care.DRel = "Z50"
- care.start_date = d
- care.finish_date = d
- patient.append(care)
+ # start by choosing the type of medical act for the sessions
p = np.array(list(self.code_CT_CCAM.values()))
p /= np.sum(p)
if self.CT_code is None:
self.CT_code = rd.choice(list(self.code_CT_CCAM.keys()), p=p)
+ # then, pick up a random UCD code, through the choice of an ATC code:
+ self.ucd_atc = rd.choice(list(self.code_CT_ATC.keys()))
+ self.ucd = rd.choice(self.code_CT_ATC[self.ucd_atc])
+
+ oldd = d
nb = int(rd.uniform(3, 5))
for _ in range(nb):
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "C50"
care.ccam.append(self.CT_code)
+ care.UCDs.append(ShortHospStay.UCD(self.ucd))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
patient.append(care)
+ oldd = d
d = d + relativedelta(days=self.delays[0])
+
+ # change the type of ATC drugs (bitherapy)
+ self.ucd_atc = rd.choice(list(self.code_CT_ATC.keys()).remove(self.ucd_atc))
+ self.ucd = rd.choice(self.code_CT_ATC[self.ucd_atc])
nb = int(rd.uniform(2, 5))
for _ in range(nb):
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "C50"
care.ccam.append(self.CT_code)
+ care.UCDs.append(ShortHospStay.UCD(self.ucd))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
patient.append(care)
+ oldd = d
d = d + relativedelta(days=self.delays[1])
- d = d - relativedelta(days=self.delays[1])
- return d
+
+ return oldd
class TT(pathwayInjector):
"""Targeted Therapy pathway"""
- def __init__(self, sim: simulation, nb:int = 3):
+ def __init__(self, sim: simulation, nb: int = 3):
super().__init__(sim)
- self.code_TT_ATC = ["L01XC03"] # L01XE07 L01XC13, L01XC03, L01XC14 ???
+ self.code_TT_ATC = ["L01XC03"] # L01XE07 L01XC13, L01XC03, L01XC14 ???
self.code_TT_CIP13 = [
"3400938379457",
"3400938379518",
@@ -888,14 +1273,12 @@ class TT(pathwayInjector):
# implementation of a breast cancer pathway (P1)
class P1(pathwayInjector):
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
- # The starting date of thiscare pathway is not triggered by an
- # external event : it is randomly generated !
+ """
+ The starting date of this care pathway is not triggered by an
+ external event: it is randomly generated !
+ """
def pathdesc(self, patient: Patient, d: date):
- """"""
if len(self.sim.etablissements) == 0:
warnings.warn(
@@ -903,31 +1286,27 @@ class P1(pathwayInjector):
)
return
- Surgery(self.sim).pathdesc(patient, d)
+ d = Surgery(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P1"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
class P2(pathwayInjector):
- """Rmplementation of a breast cancer pathway (P2)
+ """Implementation of a breast cancer pathway (P2)
This profil corresponds to patients having a treatment pathway with [S+ET].
The starting date of this care pathway is uniformly random generated within the simulation year.
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
- """"""
-
if len(self.sim.etablissements) == 0:
warnings.warn(
"Warning (Pathway): no etablissement available to create the pathway"
@@ -940,12 +1319,13 @@ class P2(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# inject ET
- ET_uni(self.sim).pathdesc(patient, d)
+ d = ET_uni(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P2"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -959,12 +1339,7 @@ class P3(pathwayInjector):
The starting date of this care pathway is uniformly random generated within the simulation year.
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
- """"""
-
if len(self.sim.etablissements) == 0:
warnings.warn(
"Warning (Pathway): no etablissement available to create the pathway"
@@ -977,12 +1352,13 @@ class P3(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# Radiotherapy
- RT(self.sim).pathdesc(patient, d)
+ d = RT(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P3"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -996,12 +1372,7 @@ class P4(pathwayInjector):
The starting date of this care pathway is uniformly random generated within the simulation year.
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
- """"""
-
if len(self.sim.etablissements) == 0:
warnings.warn(
"Warning (Pathway): no etablissement available to create the pathway"
@@ -1020,12 +1391,13 @@ class P4(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# ET
- ET_uni(self.sim).pathdesc(patient, d)
+ d = ET_uni(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P4"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -1036,15 +1408,10 @@ class P5(pathwayInjector):
This profil corresponds to patients having a treatment pathway with [CT+S+RT+ET].
- The starting date of this care pathway is uniformly random generated within the simulation year.
+ The starting date of this care path
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
- """"""
-
if len(self.sim.etablissements) == 0:
warnings.warn(
"Warning (Pathway): no etablissement available to create the pathway"
@@ -1083,12 +1450,13 @@ class P5(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# ET
- ET_uni(self.sim).pathdesc(patient, d)
+ d = ET_uni(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P5"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -1102,12 +1470,7 @@ class P6(pathwayInjector):
The starting date of this care pathway is uniformly random generated within the simulation year.
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
- """"""
-
if len(self.sim.etablissements) == 0:
warnings.warn(
"Warning (Pathway): no etablissement available to create the pathway"
@@ -1141,12 +1504,13 @@ class P6(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(15, 61)))
# Radiotherapy
- RT(self.sim).pathdesc(patient, d)
+ d = RT(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P6"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -1164,6 +1528,8 @@ class P7(pathwayInjector):
def __init__(self, sim: simulation):
super().__init__(sim)
+ # self.code_TT_ATC = ["L01XC03"] # code pour Herceptin
+ self.code_TT_UCD = ["9220097", "9400037"] # version UCD de l'Herceptin
def pathdesc(self, patient: Patient, d: date):
"""
@@ -1191,42 +1557,76 @@ class P7(pathwayInjector):
else:
unict = rd.binomial(1, 1)
- #init the treatment with 4 sessions
- therapy_phase1= CT_uni(self.sim)
- d = therapy_phase1.pathdesc(patient, d, nb=4, delay=15)
+ # init the treatment with 4 sessions of CT alone
+ therapy_phase1 = CT_uni(self.sim, nb=4, delay=15)
+ d = therapy_phase1.pathdesc(patient, d)
- dcomb = d + relativedelta(days=15)
-
- #continue in association with TT
+ # CT continue in association with TT
+ TT_code = rd.choice(self.code_TT_UCD)
if unict:
# CT unitherapy
therapy = CT_uni(self.sim)
therapy.CT_code = therapy_phase1.CT_code
- d = therapy.pathdesc(patient, dcomb, nb=8, delay=15)
+
+ for i in range(12):
+ care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "Z50"
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
+ care.start_date = d
+ care.finish_date = d
+ care.ccam.append(therapy_phase1.CT_code) # same codes as before for CT
+ care.UCDs.append(ShortHospStay.UCD(therapy_phase1.ucd))
+ if i % 3 == 0:
+ care.UCDs.append(ShortHospStay.UCD(TT_code))
+ patient.append(care)
+ d = d + relativedelta(days=7)
+ d = d - relativedelta(days=7)
else:
- d = dcomb
+ # bi-therapy
nb = int(rd.uniform(1, 10))
- for _ in range(nb):
+ i = 0
+ while i < nb:
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "C50"
care.ccam.append(therapy_phase1.CT_code)
+ care.UCDs.append(ShortHospStay.UCD(therapy_phase1.ucd))
+ if i % 3 == 0: # combinaison with TT
+ care.UCDs.append(ShortHospStay.UCD(TT_code))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
patient.append(care)
- d = d + relativedelta(days=15)
+ d = d + relativedelta(days=7)
+ i += 1
- p = np.array(list(therapy_phase1.code_CT_CCAM.values()))
- p /= np.sum(p)
- CT_code = rd.choice(list(therapy_phase1.code_CT_CCAM.keys()), p=p)
- for _ in range(12-nb):
+ # choose another drug code for CT (bitherapy)
+ ucd_atc = rd.choice(
+ list(therapy_phase1.code_CT_ATC.keys()).remove(therapy_phase1.ucd_atc)
+ )
+ ucd = rd.choice(therapy_phase1.code_CT_ATC[ucd_atc])
+ while i < 12:
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
- care.ccam.append(CT_code)
+ care.DRel = "C50"
+ care.ccam.append(therapy_phase1.CT_code)
+ care.UCDs.append(ShortHospStay.UCD(ucd))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
+ if i % 3 == 0:
+ care.UCDs.append(ShortHospStay.UCD(TT_code))
patient.append(care)
- d = d + relativedelta(days=15)
- d = d - relativedelta(days=15)
-
- TT(self.sim, nb=4).pathdesc(patient, dcomb)
+ d = d + relativedelta(days=7)
+ i += 1
+ d = d - relativedelta(days=7)
# Surgery
dch = d + relativedelta(days=int(rd.uniform(7, 21)))
@@ -1238,7 +1638,7 @@ class P7(pathwayInjector):
# TT
d = TT(self.sim, nb=10).pathdesc(patient, d)
- # restart from surgery, no synchronized
+ # restart from surgery, not synchronized
d = dch + relativedelta(days=int(rd.uniform(3, 31)))
# RT
@@ -1248,12 +1648,13 @@ class P7(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# ET bitherapy
- ET_bi(self.sim).pathdesc(patient, d)
+ d = ET_bi(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P7"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -1270,6 +1671,16 @@ class P8(pathwayInjector):
def __init__(self, sim: simulation):
super().__init__(sim)
+ self.code_TT_ATC = ["L01XC03"] # L01XE07 L01XC13, L01XC03, L01XC14 ???
+ self.code_TT_CIP13 = [
+ "3400938379457",
+ "3400938379518",
+ "3400941701764",
+ "3400941701825",
+ "3400941701993",
+ "3400949164349",
+ ]
+ self.code_TT_UCD = ["9220097", "9400037"] # version UCD de l'Herceptin
def pathdesc(self, patient: Patient, d: date):
"""
@@ -1303,59 +1714,95 @@ class P8(pathwayInjector):
else:
unict = 1
+ # init the treatment with 4 sessions of CT alone
+ therapy_phase1 = CT_uni(self.sim, nb=4, delay=15)
+ d = therapy_phase1.pathdesc(patient, d)
- #init the treatment with 4 sessions
- therapy_phase1= CT_uni(self.sim)
- d = therapy_phase1.pathdesc(patient, d, nb=4, delay=15)
-
- dcomb = d + relativedelta(days=15)
-
- #continue in association with TT
+ # CT continue in association with TT
+ TT_code = rd.choice(self.code_TT_UCD)
if unict:
# CT unitherapy
therapy = CT_uni(self.sim)
therapy.CT_code = therapy_phase1.CT_code
- d = therapy.pathdesc(patient, dcomb, nb=8, delay=15)
+
+ for i in range(12):
+ care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "Z50"
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
+ care.start_date = d
+ care.finish_date = d
+ care.ccam.append(therapy_phase1.CT_code) # same codes as before for CT
+ care.UCDs.append(ShortHospStay.UCD(therapy_phase1.ucd))
+ if i % 3 == 0:
+ care.UCDs.append(ShortHospStay.UCD(TT_code))
+ patient.append(care)
+ d = d + relativedelta(days=7)
+ d = d - relativedelta(days=7)
else:
- d = dcomb
+ # bi-therapy
nb = int(rd.uniform(1, 10))
- for _ in range(nb):
+ i = 0
+ while i < nb:
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
+ care.DRel = "C50"
care.ccam.append(therapy_phase1.CT_code)
+ care.UCDs.append(ShortHospStay.UCD(therapy_phase1.ucd))
+ if i % 3 == 0: # combinaison with TT
+ care.UCDs.append(ShortHospStay.UCD(TT_code))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
patient.append(care)
- d = d + relativedelta(days=15)
+ d = d + relativedelta(days=7)
+ i += 1
- p = np.array(list(therapy_phase1.code_CT_CCAM.values()))
- p /= np.sum(p)
- CT_code = rd.choice(list(therapy_phase1.code_CT_CCAM.keys()), p=p)
- for _ in range(12-nb):
+ # choose another drug code for CT (bitherapy)
+ ucd_atc = rd.choice(
+ list(therapy_phase1.code_CT_ATC.keys()).remove(therapy_phase1.ucd_atc)
+ )
+ ucd = rd.choice(therapy_phase1.code_CT_ATC[ucd_atc])
+ while i < 12:
care = ShortHospStay(patient, self.sim.etablissements[0], "Z511")
- care.ccam.append(CT_code)
+ care.DRel = "C50"
+ care.ccam.append(therapy_phase1.CT_code)
+ care.UCDs.append(ShortHospStay.UCD(ucd))
+ if date.weekday(d) == 5: # Saturday
+ d += relativedelta(days=-1)
+ elif date.weekday(d) == 6: # Sunday
+ d += relativedelta(days=1)
care.start_date = d
care.finish_date = d
+ if i % 3 == 0:
+ care.UCDs.append(ShortHospStay.UCD(TT_code))
patient.append(care)
- d = d + relativedelta(days=15)
-
- TT(self.sim, nb=10).pathdesc(patient, dcomb)
+ d = d + relativedelta(days=7)
+ i += 1
+ d = d - relativedelta(days=7)
# break
- d = dcomb + relativedelta(days=int(rd.uniform(3, 31)))
+ d = d + relativedelta(days=int(rd.uniform(3, 31)))
# RT
- d= RT(self.sim).pathdesc(patient, d)
+ d = RT(self.sim).pathdesc(patient, d)
# break
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# ET bitherapy
- ET_bi(self.sim).pathdesc(patient, d)
+ d = ET_bi(self.sim).pathdesc(patient, d)
+
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P8"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -1370,9 +1817,6 @@ class P9(pathwayInjector):
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
"""
- d is the starting date of the pathway
@@ -1416,12 +1860,13 @@ class P9(pathwayInjector):
d = d + relativedelta(days=int(rd.uniform(3, 31)))
# RT
- RT(self.sim).pathdesc(patient, d)
+ d = RT(self.sim).pathdesc(patient, d)
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P9"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)
@@ -1436,9 +1881,6 @@ class P10(pathwayInjector):
"""
- def __init__(self, sim: simulation):
- super().__init__(sim)
-
def pathdesc(self, patient: Patient, d: date):
"""
- d is the starting date of the pathway
@@ -1499,15 +1941,17 @@ class P10(pathwayInjector):
if uniet:
# ET unitherapy
- ET_uni(self.sim).pathdesc(patient, d)
+ d = ET_uni(self.sim).pathdesc(patient, d)
else:
# ET bitherapy
- ET_bi(self.sim).pathdesc(patient, d)
+ d = ET_bi(self.sim).pathdesc(patient, d)
+
+ return d
def __precondition__(self, patient: Patient) -> bool:
return patient.raw_data["pathway"] == "P10"
- def __index_date__(self, patient: Patient):
+ def __index_date__(self, patient: Patient, d: date = pd.NaT):
return date(day=1, month=1, year=self.sim.year) + relativedelta(
days=int(rd.uniform(0, 364))
)