def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
adm_conds = []
icu_conds = []
pat_cond = None
if self.subject_ids is not None:
pat_cond = 'SUBJECT_ID IN ( {} )'.format(', '.join(map(str, self.subject_ids)))
adm_conds.append(pat_cond)
icu_conds.append(pat_cond)
if self.hadm_ids is not None:
adm_cond = 'HADM_ID IN ( {} )'.format(', '.join(map(str, self.hadm_ids)))
adm_conds.append(adm_cond)
icu_conds.append(adm_cond)
if self.icustay_ids is not None:
icu_cond = 'ICUSTAY_ID IN ( {} )'.format(', '.join(map(str, self.icustay_ids)))
icu_conds.append(icu_cond)
if 'admissions' not in incr_data:
adm_cond = ' and '.join(adm_conds) or None
incr_data['admissions'] = mimic_common.load_table(admissions_schema, adm_cond)
if 'icustayevents' not in incr_data:
icu_cond = ' and '.join(icu_conds) or None
incr_data['icustayevents'] = mimic_common.load_table(icustayevents_schema, icu_cond)
if 'patients' not in incr_data:
incr_data['patients'] = mimic_common.load_table(patients_schema, pat_cond)
return incr_data
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
if 'icustayevents' not in incr_data:
incr_data['icustayevents'] = mimic_common.load_table(mimic_schema.icustayevents_schema)
if 'admissions' not in incr_data:
incr_data['admissions'] = mimic_common.load_table(mimic_schema.admissions_schema)
return incr_data
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
if 'ioevents' not in incr_data:
cond = 'itemid IN ( {} )'.format(', '.join(map(str, self.ioevent_item_ids)))
incr_data['ioevents'] = mimic_common.load_table(mimic_schema.ioevents_schema, cond)
if 'icustayevents' not in incr_data:
incr_data['icustayevents'] = mimic_common.load_table(mimic_schema.icustayevents_schema)
return incr_data
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
if 'icustayevents' not in incr_data:
incr_data['icustayevents'] = mimic_common.load_table(
mimic_schema.icustayevents_schema)
if 'admissions' not in incr_data:
incr_data['admissions'] = mimic_common.load_table(
mimic_schema.admissions_schema)
return incr_data
def _load(self):
conds = []
if self.subject_ids is not None:
conds.append('SUBJECT_ID IN ( {} )'.format(', '.join(map(str, self.subject_ids))))
if self.hadm_ids is not None:
conds.append('HADM_ID IN ( {} )'.format(', '.join(map(str, self.hadm_ids))))
cpt_cond = ' and '.join(conds + [self.cpt_cond]) or None
cptevents = mimic_common.load_table(cptevents_schema, cpt_cond)
icu_cond = ' and '.join(conds) or None
icustayevents = mimic_common.load_table(icustayevents_schema, icu_cond)
return {'cptevents': cptevents, 'icustayevents': icustayevents}
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
if 'ioevents' not in incr_data:
cond = 'itemid IN ( {} )'.format(', '.join(
map(str, self.ioevent_item_ids)))
incr_data['ioevents'] = mimic_common.load_table(
mimic_schema.ioevents_schema, cond)
if 'icustayevents' not in incr_data:
incr_data['icustayevents'] = mimic_common.load_table(
mimic_schema.icustayevents_schema)
return incr_data
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
if 'diagnoses_icd' not in incr_data:
cond = 'icd9_code IN ( {} )'.format(', '.join(map(repr, self.icd9_codes)))
incr_data['diagnoses_icd'] = mimic_common.load_table(mimic_schema.diagnoses_icd_schema, cond)
if 'procedures_icd' not in incr_data:
cond = 'icd9_code IN ( {} )'.format(', '.join(map(repr, self.icd9_codes)))
incr_data['procedures_icd'] = mimic_common.load_table(mimic_schema.procedures_icd_schema, cond)
if 'icustayevents' not in incr_data:
incr_data['icustayevents'] = mimic_common.load_table(mimic_schema.icustayevents_schema)
return incr_data
def _load(self):
conds = []
if self.subject_ids is not None:
conds.append('SUBJECT_ID IN ( {} )'.format(', '.join(
map(str, self.subject_ids))))
if self.hadm_ids is not None:
conds.append('HADM_ID IN ( {} )'.format(', '.join(
map(str, self.hadm_ids))))
cpt_cond = ' and '.join(conds + [self.cpt_cond]) or None
cptevents = mimic_common.load_table(cptevents_schema, cpt_cond)
icu_cond = ' and '.join(conds) or None
icustayevents = mimic_common.load_table(icustayevents_schema, icu_cond)
return {'cptevents': cptevents, 'icustayevents': icustayevents}
def _load(self):
valid_vaso_ids = []
if self.metavision:
valid_vaso_ids.extend(VasoIOEventsMetavision.valid_vaso_ids)
if self.carevue:
valid_vaso_ids.extend(VasoIOEventsCarevue.valid_vaso_ids)
ioevents_cond = "itemid in ( {} )".format(', '.join(map(str, sorted(valid_vaso_ids))))
ioevents_cond += " and ((rate is not null and rate != 0) or (volume is not null and volume != 0))"
ioevents = mimic_common.load_table(ioevents_schema, ioevents_cond)
return ioevents
def _load(self):
valid_vaso_ids = []
if self.metavision:
valid_vaso_ids.extend(VasoIOEventsMetavision.valid_vaso_ids)
if self.carevue:
valid_vaso_ids.extend(VasoIOEventsCarevue.valid_vaso_ids)
ioevents_cond = "itemid in ( {} )".format(', '.join(
map(str, sorted(valid_vaso_ids))))
ioevents_cond += " and ((rate is not null and rate != 0) or (volume is not null and volume != 0))"
ioevents = mimic_common.load_table(ioevents_schema, ioevents_cond)
return ioevents
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
if 'diagnoses_icd' not in incr_data:
cond = 'icd9_code IN ( {} )'.format(', '.join(
map(repr, self.icd9_codes)))
incr_data['diagnoses_icd'] = mimic_common.load_table(
mimic_schema.diagnoses_icd_schema, cond)
if 'procedures_icd' not in incr_data:
cond = 'icd9_code IN ( {} )'.format(', '.join(
map(repr, self.icd9_codes)))
incr_data['procedures_icd'] = mimic_common.load_table(
mimic_schema.procedures_icd_schema, cond)
if 'icustayevents' not in incr_data:
incr_data['icustayevents'] = mimic_common.load_table(
mimic_schema.icustayevents_schema)
return incr_data
def _load(self, incr_data=None):
if incr_data is None:
incr_data = {}
adm_conds = []
icu_conds = []
pat_cond = None
if self.subject_ids is not None:
pat_cond = 'SUBJECT_ID IN ( {} )'.format(', '.join(
map(str, self.subject_ids)))
adm_conds.append(pat_cond)
icu_conds.append(pat_cond)
if self.hadm_ids is not None:
adm_cond = 'HADM_ID IN ( {} )'.format(', '.join(
map(str, self.hadm_ids)))
adm_conds.append(adm_cond)
icu_conds.append(adm_cond)
if self.icustay_ids is not None:
icu_cond = 'ICUSTAY_ID IN ( {} )'.format(', '.join(
map(str, self.icustay_ids)))
icu_conds.append(icu_cond)
if 'admissions' not in incr_data:
adm_cond = ' and '.join(adm_conds) or None
incr_data['admissions'] = mimic_common.load_table(
admissions_schema, adm_cond)
if 'icustayevents' not in incr_data:
icu_cond = ' and '.join(icu_conds) or None
incr_data['icustayevents'] = mimic_common.load_table(
icustayevents_schema, icu_cond)
if 'patients' not in incr_data:
incr_data['patients'] = mimic_common.load_table(
patients_schema, pat_cond)
return incr_data
def load(self):
incr_result = None
if self.medications is not None:
icustayevents = self.medications.load_transform()
incr_result = {"icustayevents": icustayevents}
if self.labevents is not None:
icustayevents = self.labevents.load_transform(incr_result)
incr_result = {"icustayevents": icustayevents}
if self.death is not None:
icustayevents = self.death.load_transform(incr_result)
incr_result = {"icustayevents": icustayevents}
if self.icd9_codes is not None:
icd9_codes = self.icd9_codes.load_transform()
icustayevents = cohorts.Icd9Filter(icd9_codes["icd9_codes"].values).load_transform(incr_result)
incr_result = {"icustayevents": icustayevents}
if incr_result is None:
icustayevents = mimic_common.load_table(mimic_schema.icustayevents_schema)
incr_result = {"icustayevents": icustayevents}
return incr_result["icustayevents"]
def load(self):
incr_result = None
if self.medications is not None:
icustayevents = self.medications.load_transform()
incr_result = {'icustayevents': icustayevents}
if self.labevents is not None:
icustayevents = self.labevents.load_transform(incr_result)
incr_result = {'icustayevents': icustayevents}
if self.death is not None:
icustayevents = self.death.load_transform(incr_result)
incr_result = {'icustayevents': icustayevents}
if self.icd9_codes is not None:
icd9_codes = self.icd9_codes.load_transform()
icustayevents = cohorts.Icd9Filter(icd9_codes['icd9_codes'].values).load_transform(incr_result)
incr_result = {'icustayevents': icustayevents}
if incr_result is None:
icustayevents = mimic_common.load_table(mimic_schema.icustayevents_schema)
incr_result = {'icustayevents': icustayevents}
return incr_result['icustayevents']
def valid_meditems(cls):
meditems = mimic_common.load_table(mimic_schema.d_items_schema,
"linksto = 'ioevents'")
return meditems
def valid_labitems(cls):
labitems = mimic_common.load_table(mimic_schema.d_labitems_schema)
return labitems
def _load(self):
ioevents_cond = "itemid in ( {} )".format(', '.join(map(str, sorted(self.valid_vaso_ids))))
ioevents_cond += " and ((rate is not null and rate != 0) or (volume is not null and volume != 0))"
ioevents = mimic_common.load_table(ioevents_schema, ioevents_cond)
return ioevents
def _load(self):
ioevents_cond = "itemid in ( {} )".format(', '.join(
map(str, sorted(self.valid_vaso_ids))))
ioevents_cond += " and ((rate is not null and rate != 0) or (volume is not null and volume != 0))"
ioevents = mimic_common.load_table(ioevents_schema, ioevents_cond)
return ioevents
def valid_labitems(cls):
labitems = mimic_common.load_table(mimic_schema.d_labitems_schema)
return labitems
def valid_meditems(cls):
meditems = mimic_common.load_table(mimic_schema.d_items_schema, "linksto = 'ioevents'")
return meditems
