Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Y | Z _ __annotations__ (zensols.mimic.domain.MimicParseError attribute) (zensols.mimic.domain.RecordNotFoundError attribute) __init__() (zensols.mimic.adm.HospitalAdmission method) (zensols.mimic.adm.HospitalAdmissionDbFactoryStash method) (zensols.mimic.adm.HospitalAdmissionDbStash method) (zensols.mimic.adm.NoteDocumentPreemptiveStash method) (zensols.mimic.app.Application method) (zensols.mimic.cli.ApplicationFactory method) (zensols.mimic.corpus.Corpus method) (zensols.mimic.domain.Admission method) (zensols.mimic.domain.Diagnosis method) (zensols.mimic.domain.HospitalAdmissionContainer method) (zensols.mimic.domain.ICD9Container method) (zensols.mimic.domain.MimicContainer method) (zensols.mimic.domain.MimicParseError method) (zensols.mimic.domain.NoteEvent method) (zensols.mimic.domain.Patient method) (zensols.mimic.domain.Procedure method) (zensols.mimic.domain.RecordNotFoundError method) (zensols.mimic.note.DefaultNoteFactory method) (zensols.mimic.note.GapSectionContainer method) (zensols.mimic.note.Note method) (zensols.mimic.note.NoteFactory method) (zensols.mimic.note.ParagraphFactory method) (zensols.mimic.note.Section method) (zensols.mimic.note.SectionContainer method) (zensols.mimic.parafac.ChunkingParagraphFactory method) (zensols.mimic.persist.AdmissionPersister method) (zensols.mimic.persist.DiagnosisPersister method) (zensols.mimic.persist.NoteDocumentStash method) (zensols.mimic.persist.NoteEventPersister method) (zensols.mimic.persist.PatientPersister method) (zensols.mimic.persist.ProcedurePersister method) (zensols.mimic.regexnote.ConsultNote method) (zensols.mimic.regexnote.DischargeSummaryNote method) (zensols.mimic.regexnote.EchoNote method) (zensols.mimic.regexnote.NursingOtherNote method) (zensols.mimic.regexnote.PhysicianNote method) (zensols.mimic.regexnote.RadiologyNote method) (zensols.mimic.regexnote.RegexNote method) (zensols.mimic.tokenizer.MimicTokenDecorator method) (zensols.mimic.tokenizer.MimicTokenizerComponent method) __module__ (zensols.mimic.domain.MimicError attribute) (zensols.mimic.domain.MimicParseError attribute) (zensols.mimic.domain.RecordNotFoundError attribute) A adm_factory_stash (zensols.mimic.adm.NoteDocumentPreemptiveStash attribute) Admission (class in zensols.mimic.domain) admission (zensols.mimic.adm.HospitalAdmission attribute) admission_location (zensols.mimic.domain.Admission attribute) admission_persister (zensols.mimic.adm.HospitalAdmissionDbStash attribute) (zensols.mimic.corpus.Corpus attribute) admission_type (zensols.mimic.domain.Admission attribute) AdmissionPersister (class in zensols.mimic.persist) admittime (zensols.mimic.domain.Admission attribute) Application (class in zensols.mimic.app) ApplicationFactory (class in zensols.mimic.cli) B body (zensols.mimic.note.Section property) body_doc (zensols.mimic.note.Section property) body_span (zensols.mimic.note.Section attribute) body_tokens (zensols.mimic.note.Section property) C categories (zensols.mimic.persist.NoteEventPersister property) category (zensols.mimic.domain.NoteEvent attribute) CATEGORY (zensols.mimic.regexnote.ConsultNote attribute) (zensols.mimic.regexnote.DischargeSummaryNote attribute) (zensols.mimic.regexnote.EchoNote attribute) (zensols.mimic.regexnote.NursingOtherNote attribute) (zensols.mimic.regexnote.PhysicianNote attribute) (zensols.mimic.regexnote.RadiologyNote attribute) category_to_id() (zensols.mimic.note.SectionContainer static method) category_to_note (zensols.mimic.note.NoteFactory attribute) cgid (zensols.mimic.domain.NoteEvent attribute) chartdate (zensols.mimic.domain.NoteEvent attribute) charttime (zensols.mimic.domain.NoteEvent attribute) ChunkingParagraphFactory (class in zensols.mimic.parafac) clear() (zensols.mimic.adm.HospitalAdmissionDbFactoryStash method) (zensols.mimic.app.Application method) (zensols.mimic.corpus.Corpus method) clone() (zensols.mimic.note.Section method) config_factory (zensols.mimic.adm.HospitalAdmissionDbStash attribute) (zensols.mimic.app.Application attribute) (zensols.mimic.corpus.Corpus attribute) (zensols.mimic.note.NoteFactory attribute) ConsultNote (class in zensols.mimic.regexnote) container (zensols.mimic.note.Section attribute) context (zensols.mimic.domain.NoteEvent attribute) Corpus (class in zensols.mimic.corpus) corpus (zensols.mimic.app.Application attribute) corpus_stats() (zensols.mimic.app.Application method) create() (zensols.mimic.note.DefaultNoteFactory method) (zensols.mimic.note.NoteFactory method) (zensols.mimic.note.ParagraphFactory method) (zensols.mimic.parafac.ChunkingParagraphFactory method) (zensols.mimic.parafac.WhitespaceParagraphFactory method) create_default() (zensols.mimic.note.NoteFactory method) D deathtime (zensols.mimic.domain.Admission attribute) decorate() (zensols.mimic.tokenizer.MimicTokenDecorator method) DEFAULT_SECTION_NAME (zensols.mimic.note.SectionContainer attribute) DefaultNoteFactory (class in zensols.mimic.note) delegate (zensols.mimic.note.GapSectionContainer attribute) description (zensols.mimic.domain.NoteEvent attribute) diagnoses (zensols.mimic.adm.HospitalAdmission attribute) Diagnosis (class in zensols.mimic.domain) diagnosis (zensols.mimic.domain.Admission attribute) diagnosis_persister (zensols.mimic.adm.HospitalAdmissionDbStash attribute) (zensols.mimic.corpus.Corpus attribute) DiagnosisPersister (class in zensols.mimic.persist) discharge_location (zensols.mimic.domain.Admission attribute) DischargeSummaryNote (class in zensols.mimic.regexnote) dischtime (zensols.mimic.domain.Admission attribute) dob (zensols.mimic.domain.Patient attribute) doc (zensols.mimic.domain.NoteEvent property) (zensols.mimic.note.Section property) doc_parser (zensols.mimic.app.Application attribute) (zensols.mimic.persist.NoteDocumentStash attribute) doc_stash (zensols.mimic.adm.HospitalAdmissionDbFactoryStash attribute) dod (zensols.mimic.domain.Patient attribute) dod_hosp (zensols.mimic.domain.Patient attribute) dod_ssn (zensols.mimic.domain.Patient attribute) E EchoNote (class in zensols.mimic.regexnote) edouttime (zensols.mimic.domain.Admission attribute) edregtime (zensols.mimic.domain.Admission attribute) ethnicity (zensols.mimic.domain.Admission attribute) exists() (zensols.mimic.adm.HospitalAdmissionDbStash method) (zensols.mimic.persist.NoteDocumentStash method) expire_flag (zensols.mimic.domain.Patient attribute) ext (zensols.mimic.note.NoteFormat property) F feature_dataframe (zensols.mimic.adm.HospitalAdmission property) (zensols.mimic.note.SectionContainer property) filter_empty (zensols.mimic.note.GapSectionContainer attribute) FILTER_ENUMS (zensols.mimic.note.Section attribute) filter_sent_text (zensols.mimic.parafac.ChunkingParagraphFactory attribute) G GapSectionContainer (class in zensols.mimic.note) gender (zensols.mimic.domain.Patient attribute) get_admission_counts() (zensols.mimic.persist.AdmissionPersister method) get_by_hadm_id() (zensols.mimic.persist.AdmissionPersister method) (zensols.mimic.persist.DiagnosisPersister method) (zensols.mimic.persist.ProcedurePersister method) get_by_subject_id() (zensols.mimic.persist.AdmissionPersister method) (zensols.mimic.persist.PatientPersister method) get_corpus() (zensols.mimic.cli.ApplicationFactory class method) get_discharge_reports() (zensols.mimic.persist.NoteEventPersister method) get_duplicate_notes() (zensols.mimic.adm.HospitalAdmission method) get_hadm_id() (zensols.mimic.persist.NoteEventPersister method) get_hadm_ids() (zensols.mimic.persist.AdmissionPersister method) (zensols.mimic.persist.NoteEventPersister method) get_hadm_ids_all() (zensols.mimic.persist.NoteEventPersister method) get_heart_failure_hadm_ids() (zensols.mimic.persist.DiagnosisPersister method) get_hospital_adm_by_id() (zensols.mimic.corpus.Corpus method) get_hospital_adm_for_note() (zensols.mimic.corpus.Corpus method) get_non_duplicate_notes() (zensols.mimic.adm.HospitalAdmission method) get_normal_name() (zensols.mimic.domain.NoteEvent method) get_note_by_id() (zensols.mimic.corpus.Corpus method) get_note_count() (zensols.mimic.persist.NoteEventPersister method) get_note_counts() (zensols.mimic.persist.NoteEventPersister method) get_note_counts_by_subject_id() (zensols.mimic.persist.NoteEventPersister method) get_notes_by_category() (zensols.mimic.persist.NoteEventPersister method) get_notes_by_hadm_id() (zensols.mimic.persist.NoteEventPersister method) get_row_ids_by_category() (zensols.mimic.persist.NoteEventPersister method) get_row_ids_by_hadm_id() (zensols.mimic.persist.NoteEventPersister method) get_row_ids_with_admissions() (zensols.mimic.persist.NoteEventPersister method) H hadm_id (zensols.mimic.adm.HospitalAdmission property) (zensols.mimic.domain.Admission attribute) (zensols.mimic.domain.HospitalAdmissionContainer attribute) (zensols.mimic.domain.NoteEvent attribute) hadm_row_chunk_size (zensols.mimic.persist.NoteEventPersister attribute) has_chartevents_data (zensols.mimic.domain.Admission attribute) header_spans (zensols.mimic.note.Section attribute) header_to_name() (zensols.mimic.note.Section static method) header_tokens (zensols.mimic.note.Section property) headers (zensols.mimic.note.Section property) hospital_adm_name (zensols.mimic.adm.HospitalAdmissionDbStash attribute) hospital_adm_stash (zensols.mimic.corpus.Corpus attribute) hospital_expire_flag (zensols.mimic.domain.Admission attribute) HospitalAdmission (class in zensols.mimic.adm) HospitalAdmissionContainer (class in zensols.mimic.domain) HospitalAdmissionDbFactoryStash (class in zensols.mimic.adm) HospitalAdmissionDbStash (class in zensols.mimic.adm) HUMAN (zensols.mimic.note.SectionAnnotatorType attribute) I icd9_code (zensols.mimic.domain.ICD9Container attribute) ICD9Container (class in zensols.mimic.domain) id (zensols.mimic.domain.NoteEvent property) (zensols.mimic.note.Section attribute) id_to_category() (zensols.mimic.note.SectionContainer static method) include_section_headers (zensols.mimic.parafac.ChunkingParagraphFactory attribute) init() (zensols.mimic.tokenizer.MimicTokenizerComponent method) insurance (zensols.mimic.domain.Admission attribute) is_empty (zensols.mimic.note.Section property) iserror (zensols.mimic.domain.NoteEvent attribute) J json (zensols.mimic.note.NoteFormat attribute) K keys() (zensols.mimic.adm.HospitalAdmission method) (zensols.mimic.adm.HospitalAdmissionDbStash method) (zensols.mimic.persist.NoteDocumentStash method) L language (zensols.mimic.domain.Admission attribute) lexspan (zensols.mimic.note.Section property) load() (zensols.mimic.adm.HospitalAdmissionDbFactoryStash method) (zensols.mimic.adm.HospitalAdmissionDbStash method) (zensols.mimic.persist.NoteDocumentStash method) long_title (zensols.mimic.domain.ICD9Container attribute) M main() (in module zensols.mimic.cli) marital_status (zensols.mimic.domain.Admission attribute) markdown (zensols.mimic.note.NoteFormat attribute) MASK_REGEX (zensols.mimic.tokenizer.MimicTokenDecorator attribute) MASK_TOKEN_FEATURE (zensols.mimic.tokenizer.MimicTokenDecorator attribute) max_sent_list_len (zensols.mimic.parafac.ChunkingParagraphFactory attribute) mimic_default_note_section (zensols.mimic.note.NoteFactory attribute) mimic_note_context (zensols.mimic.adm.HospitalAdmissionDbFactoryStash attribute) (zensols.mimic.persist.NoteEventPersister attribute) mimic_note_factory (zensols.mimic.adm.HospitalAdmissionDbStash attribute) MIMIC_SPAN_PATTERN (zensols.mimic.parafac.ChunkingParagraphFactory attribute) MimicContainer (class in zensols.mimic.domain) MimicError MimicParseError MimicTokenDecorator (class in zensols.mimic.tokenizer) MimicTokenizerComponent (class in zensols.mimic.tokenizer) min_list_norm_matches (zensols.mimic.parafac.ChunkingParagraphFactory attribute) min_sent_len (zensols.mimic.parafac.ChunkingParagraphFactory attribute) MODEL (zensols.mimic.note.SectionAnnotatorType attribute) module zensols.mimic zensols.mimic.adm zensols.mimic.app zensols.mimic.cli zensols.mimic.corpus zensols.mimic.domain zensols.mimic.note zensols.mimic.parafac zensols.mimic.persist zensols.mimic.regexnote zensols.mimic.tokenizer N name (zensols.mimic.note.Section attribute) name_to_header() (zensols.mimic.note.Section static method) NONE (zensols.mimic.note.SectionAnnotatorType attribute) normal_name (zensols.mimic.domain.NoteEvent property) Note (class in zensols.mimic.note) note_db_persister (zensols.mimic.persist.NoteDocumentStash attribute) note_event_persister (zensols.mimic.adm.HospitalAdmissionDbStash attribute) (zensols.mimic.adm.NoteDocumentPreemptiveStash attribute) (zensols.mimic.corpus.Corpus attribute) note_stash (zensols.mimic.adm.HospitalAdmissionDbStash attribute) note_text (zensols.mimic.note.Section property) NoteDocumentPreemptiveStash (class in zensols.mimic.adm) NoteDocumentStash (class in zensols.mimic.persist) NoteEvent (class in zensols.mimic.domain) NoteEventPersister (class in zensols.mimic.persist) NoteFactory (class in zensols.mimic.note) NoteFormat (class in zensols.mimic.note) notes (zensols.mimic.adm.HospitalAdmission property) notes_by_category (zensols.mimic.adm.HospitalAdmission property) NursingOtherNote (class in zensols.mimic.regexnote) O ONTO_FEATURE_ID (zensols.mimic.tokenizer.MimicTokenDecorator attribute) P ParagraphFactory (class in zensols.mimic.note) paragraphs (zensols.mimic.note.Section property) Patient (class in zensols.mimic.domain) patient (zensols.mimic.adm.HospitalAdmission attribute) patient_persister (zensols.mimic.adm.HospitalAdmissionDbStash attribute) (zensols.mimic.corpus.Corpus attribute) PatientPersister (class in zensols.mimic.persist) PhysicianNote (class in zensols.mimic.regexnote) preempt_notes() (zensols.mimic.app.Application method) preempt_stash (zensols.mimic.app.Application attribute) prime() (zensols.mimic.adm.HospitalAdmissionDbFactoryStash method) (zensols.mimic.adm.HospitalAdmissionDbStash method) (zensols.mimic.adm.NoteDocumentPreemptiveStash method) (zensols.mimic.note.NoteFactory method) Procedure (class in zensols.mimic.domain) procedure_persister (zensols.mimic.adm.HospitalAdmissionDbStash attribute) ProcedurePersister (class in zensols.mimic.persist) procedures (zensols.mimic.adm.HospitalAdmission attribute) process_keys() (zensols.mimic.adm.NoteDocumentPreemptiveStash method) R RadiologyNote (class in zensols.mimic.regexnote) raw (zensols.mimic.note.NoteFormat attribute) RecordNotFoundError RegexNote (class in zensols.mimic.regexnote) REGULAR_EXPRESSION (zensols.mimic.note.SectionAnnotatorType attribute) religion (zensols.mimic.domain.Admission attribute) row_id (zensols.mimic.domain.MimicContainer attribute) (zensols.mimic.domain.Patient attribute) S Section (class in zensols.mimic.note) section_annotator_type (zensols.mimic.note.Note property) section_dataframe (zensols.mimic.note.SectionContainer property) SectionAnnotatorType (class in zensols.mimic.note) SectionContainer (class in zensols.mimic.note) sections (zensols.mimic.note.SectionContainer property) sections_by_name (zensols.mimic.note.SectionContainer property) sections_ordered (zensols.mimic.note.SectionContainer property) SEP_REGEX (zensols.mimic.tokenizer.MimicTokenDecorator attribute) SEPARATOR_REGEX (zensols.mimic.parafac.WhitespaceParagraphFactory attribute) SEPARATOR_TOKEN_FEATURE (zensols.mimic.tokenizer.MimicTokenDecorator attribute) short_title (zensols.mimic.domain.ICD9Container attribute) show() (zensols.mimic.app.Application method) storetime (zensols.mimic.domain.NoteEvent attribute) subject_id (zensols.mimic.domain.Admission attribute) (zensols.mimic.domain.NoteEvent attribute) (zensols.mimic.domain.Patient attribute) summary (zensols.mimic.note.NoteFormat attribute) T temporary_results_dir (zensols.mimic.corpus.Corpus attribute) text (zensols.mimic.domain.NoteEvent attribute) (zensols.mimic.note.NoteFormat attribute) (zensols.mimic.note.Section property) token_entities (zensols.mimic.tokenizer.MimicTokenDecorator attribute) TOKEN_FEATURE_ID (zensols.mimic.tokenizer.MimicTokenDecorator attribute) token_replacements (zensols.mimic.tokenizer.MimicTokenDecorator attribute) truncted_text (zensols.mimic.domain.NoteEvent property) U uniform_sample_hadm_ids() (zensols.mimic.app.Application method) (zensols.mimic.persist.AdmissionPersister method) UNKNOWN_ENTITY (zensols.mimic.tokenizer.MimicTokenDecorator attribute) V verbose (zensols.mimic.note.NoteFormat attribute) W WhitespaceParagraphFactory (class in zensols.mimic.parafac) write() (zensols.mimic.adm.HospitalAdmission method) (zensols.mimic.corpus.Corpus method) (zensols.mimic.domain.MimicContainer method) (zensols.mimic.domain.NoteEvent method) (zensols.mimic.note.Note method) (zensols.mimic.note.Section method) (zensols.mimic.note.SectionContainer method) write_admission() (zensols.mimic.app.Application method) write_admission_summary() (zensols.mimic.app.Application method) write_as_item() (zensols.mimic.note.Section method) write_by_format() (zensols.mimic.note.SectionContainer method) write_discharge_reports() (zensols.mimic.app.Application method) write_features() (zensols.mimic.app.Application method) write_fields() (zensols.mimic.note.Note method) (zensols.mimic.note.SectionContainer method) write_full() (zensols.mimic.adm.HospitalAdmission method) (zensols.mimic.note.Note method) (zensols.mimic.note.SectionContainer method) write_hadm_id_for_note() (zensols.mimic.app.Application method) write_hospital_admission() (zensols.mimic.corpus.Corpus method) write_hosptial_count_admission() (zensols.mimic.corpus.Corpus method) write_human() (zensols.mimic.note.SectionContainer method) write_markdown() (zensols.mimic.note.SectionContainer method) write_note() (zensols.mimic.app.Application method) write_note_event_counts() (zensols.mimic.corpus.Corpus method) write_notes() (zensols.mimic.adm.HospitalAdmission method) write_sections() (zensols.mimic.note.SectionContainer method) write_sentences() (zensols.mimic.note.Section method) Y yaml (zensols.mimic.note.NoteFormat attribute) Z zensols.mimic module zensols.mimic.adm module zensols.mimic.app module zensols.mimic.cli module zensols.mimic.corpus module zensols.mimic.domain module zensols.mimic.note module zensols.mimic.parafac module zensols.mimic.persist module zensols.mimic.regexnote module zensols.mimic.tokenizer module