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