:py:mod:`medcat.utils.helpers`
==============================

.. py:module:: medcat.utils.helpers


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   medcat.utils.helpers.get_important_config_parameters
   medcat.utils.helpers.cui2tuis
   medcat.utils.helpers.tui2name
   medcat.utils.helpers.to_json_simple
   medcat.utils.helpers.to_json_sumithra
   medcat.utils.helpers.doc2html
   medcat.utils.helpers.json2html
   medcat.utils.helpers.prepare_name
   medcat.utils.helpers.get_all_from_name
   medcat.utils.helpers.tkn_inds_from_doc
   medcat.utils.helpers.tkns_from_doc
   medcat.utils.helpers.filter_cdb_by_icd10
   medcat.utils.helpers.umls_to_icd10cm
   medcat.utils.helpers.umls_to_icd10_over_snomed
   medcat.utils.helpers.umls_to_icd10_ext
   medcat.utils.helpers.umls_to_icd10
   medcat.utils.helpers.umls_to_snomed
   medcat.utils.helpers.snomed_to_umls
   medcat.utils.helpers.snomed_to_icd10
   medcat.utils.helpers.snomed_to_desc
   medcat.utils.helpers.filter_only_icd10
   medcat.utils.helpers.add_names_icd10
   medcat.utils.helpers.add_names_icd10cm
   medcat.utils.helpers.remove_icd10_ranges
   medcat.utils.helpers.dep_check_scispacy
   medcat.utils.helpers.run_cv
   medcat.utils.helpers.has_new_spacy
   medcat.utils.helpers.has_spacy_model
   medcat.utils.helpers.ensure_spacy_model



Attributes
~~~~~~~~~~

.. autoapisummary::

   medcat.utils.helpers.logger


.. py:data:: logger

   

.. py:function:: get_important_config_parameters(config)


.. py:function:: cui2tuis(cdb, cui)


.. py:function:: tui2name(cdb, tui)


.. py:function:: to_json_simple(docs, cdb)

   output:  [{'text': <text>, 'entities': [<start,end,type>, ]}]

   :param docs: The list of documents.
   :param cdb: The concept database
   :type cdb: CDB

   :Returns: **List[Dict]** -- The output dict.


.. py:function:: to_json_sumithra(docs, cdb)

   output:  [
             [ text, {'entities': [<start,end,type>, ]} ],
             ...]

   :param docs: The list of documents.
   :param cdb: The concept database
   :type cdb: CDB

   :Returns: **List[List]** -- The output list.


.. py:function:: doc2html(doc)


.. py:function:: json2html(doc)


.. py:function:: prepare_name(cat, name, version='CLEAN')

   Cleans up the name.

   :param cat: The model pack.
   :param name: The name to prepare.
   :param version: The version of prepare to use.

   :Returns: **Tuple[str, List]** -- The name and tokens


.. py:function:: get_all_from_name(name, nlp, source_value, SEP='', version='clean')


.. py:function:: tkn_inds_from_doc(spacy_doc, text_inds=None, source_val=None)


.. py:function:: tkns_from_doc(spacy_doc, start, end)


.. py:function:: filter_cdb_by_icd10(cdb)

   Filters an existing CDB to only contain concepts that have an associated ICD-10 code.
   Can be used for snomed orr UMLS CDBs.

   :param cdb: The input CDB
   :type cdb: CDB

   :Returns: **CDB** -- The filtered CDB


.. py:function:: umls_to_icd10cm(cdb, csv_path)


.. py:function:: umls_to_icd10_over_snomed(cdb, pickle_path)


.. py:function:: umls_to_icd10_ext(cdb, pickle_path)


.. py:function:: umls_to_icd10(cdb, csv_path)

   Map UMLS CDB to ICD10 concepts.

   :param cdb: The CDB
   :type cdb: CDB
   :param csv_path: The path to the file to load.


.. py:function:: umls_to_snomed(cdb, pickle_path)

   Map UMLS CDB to SNOMED concepts.

   :param cdb: The CDB
   :type cdb: CDB
   :param pickle_path: The path to the file to load.


.. py:function:: snomed_to_umls(cdb, pickle_path)

   Map SNOMED CDB to UMLS concepts.

   :param cdb: The concept database.
   :type cdb: CDB
   :param pickle_path: The file path.
   :type pickle_path: str


.. py:function:: snomed_to_icd10(cdb, csv_path)

   Add map from cui to icd10 for concepts.

   :param cdb: The concept database.
   :type cdb: CDB
   :param csv_path: The file path.
   :type csv_path: str


.. py:function:: snomed_to_desc(cdb, csv_path)

   Add descriptions to the concepts.

   :param cdb: The concept database.
   :type cdb: CDB
   :param csv_path: The file path.
   :type csv_path: str


.. py:function:: filter_only_icd10(doc, cat)


.. py:function:: add_names_icd10(csv_path, cat)


.. py:function:: add_names_icd10cm(cdb, csv_path, cat)


.. py:function:: remove_icd10_ranges(cdb)


.. py:function:: dep_check_scispacy()


.. py:function:: run_cv(cdb_path, data_path, vocab_path, cv=100, nepochs=16, test_size=0.1, lr=1, groups=None, **kwargs)


.. py:function:: has_new_spacy()

   Figures out whether or not a newer version of spacy is installed.

   This plays a role in how some parts of the Span needs to be interacted with.

   As of writing, the new version starts at v3.3.1.

   :Returns: **bool** -- Whether new version was detected.


.. py:function:: has_spacy_model(model_name)

   Checks if the spacy model is available.

   :param model_name: The model name.
   :type model_name: str

   :Returns: **bool** -- True if the model is available, False otherwise.


.. py:function:: ensure_spacy_model(model_name)

   Ensure the specified spacy model exists.

   If the model does not currently exist, it will attempt downloading it.

   :param model_name: The spacy model name.
   :type model_name: str