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Z d Z Gd d ä d â Z d S)z! It reads and process variables.
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FeatureParser)┌ CONSTANTS┌ DataFramer zMohsen Mesgarpourz-Copyright 2016, https://github.com/mesgarpour┌GPLz1.1zmohsen.mesgarpour@gmail.com┌Releasec
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input_path┌ output_path┌input_features_configs┌ output_tablec C sô t j t j â | _ | j j t â | | _ | | _ | | _ t
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| j â | _ | j â | _ | j | | â d S)aF Initialise the objects and constants.
:param model_features_table: the feature table name.
:param input_path: the input path.
:param output_path: the output path.
:param input_features_configs: the input features' configuration file.
:param output_table: the output table name.
N)┌logging┌ getLoggerr ┌app_name┌_Variables__logger┌debug┌__name__┌ _Variables__model_features_table┌_Variables__output_path┌_Variables__output_tabler ┌_Variables__readers_writers┌_Variables__init_settings┌ _Variables__variables_settings┌ _Variables__init_features_names┌ _Variables__features_dic_names┌ _Variables__init_features_dtypes┌ _Variables__features_dic_dtypes┌_Variables__init_output)┌selfr
r r r r ę r$ ˙JC:\Users\eagle\Documents\GitHub\Analytics_UoW\TCARER\Features\Variables.py┌__init__+ s
zVariables.__init__)┌
input_schemas┌ input_tables┌history_tables┌ column_index┌query_batch_sizec C sô | j j t â | j | d | d â \ } } | j â \ } } | j | | â | j | | | â }
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d S)aW Set the variables by reading the selected features from MySQL database.
:param input_schemas: the mysql database schemas.
:param input_tables: the mysql table names.
:param history_tables: the source tables' alias names (a.k.a. history table name) that features belong to
(e.g. inpatient, or outpatient).
:param column_index: the name of index column (unique integer value) in the database table, which is used
for batch reading the input.
:param query_batch_size: the number of rows to be read in each batch.
:return:
r N)r r r ┌_Variables__init_batch┌$_Variables__set_features_names_types┌ _Variables__validate_mysql_names┌_Variables__init_prevalence┌_Variables__set_batch) r# r' r( r) r* r+ ┌query_batch_start┌query_batch_max┌features_names┌features_dtypes┌
prevalencer$ r$ r% ┌setD s z
Variables.set)r r ┌returnc C sc | j j t â | j j | | d d â } | j | d d k | d | j k @} | j â } | S)zřRead and set the settings of input variables that are selected.
:param input_path: the path of the input file.
:param input_features_configs: the input features' configuration file.
:return: the input variables settings.
r TZSelectedÚ ZTable_Reference_Name)r r r r Zload_csv┌locr ┌ reset_index)r# r r ┌variables_settingsr$ r$ r% Z__init_settings\ s
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z╚Generate the features names, based on variable name, source table alias name (a.k.a. history table
name), and the aggregation function name.
:return: the name of features.
┌Table_History_Namec S s g | ] } g Ĺ q Sr$ r$ )┌.0┌_r$ r$ r% ˙
<listcomp>s s z3Variables.__init_features_names.<locals>.<listcomp>┌Variable_Aggregation˙ ┌ ˙,┌
Variable_Namer> )r r r r6 r ┌dict┌zip┌range┌len┌iterrows┌pd┌isnull┌replace┌split┌append)r# ┌table_history_namesr3 r> ┌row┌ postfixes┌postfixr$ r$ r% Z__init_features_namesl s .
( z Variables.__init_features_namesc C s║ | j j t â t | j d â } t t | d d ä t t | â â Dâ â â } xb | j j â D]Q \ } } | d j
d d â j d â } x# | D] } | | d j | â qô Wqa W| S)zuGenerate the features types, based on the input configuration file.
:return: the dtypes of features.
r< c S s g | ] } g Ĺ q Sr$ r$ )r= r> r$ r$ r% r? â s z4Variables.__init_features_dtypes.<locals>.<listcomp>ZVariable_dTyperA rB rC )
r r r r6 r rE rF rG rH rI rL rM rN )r# rO r4 r> rP Z
feature_typesZ feature_typer$ r$ r% Z__init_features_dtypes} s .
z Variables.__init_features_dtypes)r r c sq ł j j t â t ł j j â â } ç f d d ć | Dâ } ł j j | | â ł j j | | | d d âd S)zčInitialise the output file by writing the header row.
:param output_path: the output path.
:param output_table: the output table name.
c s* g | ] } ł j | D] } | Ĺ q q Sr$ )r )r= ┌k┌f)r# r$ r% r? ô s z+Variables.__init_output.<locals>.<listcomp>rN FN) r r r ┌sortedr ┌keysr Z reset_csv┌save_csv)r# r r rV r3 r$ )r# r% Z
__init_outputŐ s
zVariables.__init_output)r' r( r) r7 c C sş | j j | j | j d d g d d d d â| j j | j | j d d g d d d d ât | j | j | j â } t â } x&t t | â â D]} | j | j d | | k } t â | | | <x┌| j â D]╠\ } } | j
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| g d d d d âq▓WqŇ Wqô W| S)aą Generate the prevalence dictionary of values for all the variables.
:param input_schemas: the mysql database schemas.
:param input_tables: the mysql table names.
:param history_tables: the source tables' alias names (a.k.a. history table name) that features belong to
(e.g. inpatient, or outpatient).
:return: the prevalence dictionary of values for all the variables.
z Feature NamezTop Prevalence Feature NamerN F┌ext┌inizPrevalence & Freq.┌txtr< z Prevalence: rD z ...r@ Nr rA rB rC r> Ú Z prevalence_r8 ┌NoneT)r Z save_textr r r r rE rG rH rI r ┌inforJ rK ┌ _Variables__init_prevalence_readr5 rL rM ┌int┌str)r# r' r( r) ┌feature_parserr5 ┌table_ir; r> rP ┌ variablesrQ ┌pZ feature_name┌indexZfeature_name_prevalencer$ r$ r% Z__init_prevalenceŚ sB . 0!"! zVariables.__init_prevalence)┌ input_schema┌ input_table┌
variable_namer7 c C s/ d | d | d } | j j | | d d âS)a Read a variable from database, to calculate the prevalence of the values.
:param input_schema: the mysql database schema.
:param input_table: the mysql database table.
:param variable_name: the variable name.
:return: the selected variable.
zSELECT `z` FROM `z`;┌ dataframingT)r ┌load_mysql_query)r# rf rg rh ┌queryr$ r$ r% Z__init_prevalence_readĎ s
z Variables.__init_prevalence_read)rf rg r7 c C s┬ | j j t â d | d } t | j j | | d d ââ } d d ä | Dâ d d k r~ | j j t d | â t j â t d
d ä | Dâ d â } t d d ä | Dâ d â } | | f S) a% Find the minimum and maximum value of the index column, to use when reading mysql tables in
batches.
:param input_schema: the mysql database schema.
:param input_table: the mysql database table.
:return: the minimum and maximum of the index column.
z(select min(localID), max(localID) from `z`;ri Fc S s g | ] } | d Ĺ q S)r r$ )r= ┌rr$ r$ r% r? Ű s z*Variables.__init_batch.<locals>.<listcomp>r Nz No data is found: c S s g | ] } | d Ĺ q S)r r$ )r= rl r$ r$ r% r? ´ s c S s g | ] } | d Ĺ q S)r8 r$ )r= rl r$ r$ r% r? s )
r r r ┌listr rj ┌error┌sys┌exitr_ )r# rf rg rk ┌outputr1 r2 r$ r$ r% Z __init_batch▀ s !
zVariables.__init_batchc sé ł j j t â t ł j j â â } ç f d d ć | Dâ } ç f d d ć | Dâ } t j t t | | â â â j
} | | f S)zĹProduce the sorted lists of features names and features dtypes.
:return: the sorted lists of features names and features dtypes.
c s* g | ] } ł j | D] } | Ĺ q q Sr$ )r )r= rS rT )r# r$ r% r? ¨ s z8Variables.__set_features_names_types.<locals>.<listcomp>c s6 g | ], } ł j | D] } t j d | â Ĺ q q S)┌dtype)r! rJ ┌Series)r= rS rT )r# r$ r% r? ˙ s ) r r r rU r rV rJ r rE rF ┌dtypes)r# rV r3 r4 r$ )r# r% Z__set_features_names_typesˇ s !z$Variables.__set_features_names_types)
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| â } | j | â q: Wd S) aŇ Using batch processing first read variables, then generate features and write them into output.
:param features_names: the name of features that are selected.
:param features_dtypes: the dtypes of features that are selected.
:param input_schemas: the mysql database schemas.
:param input_tables: the mysql table names.
:param history_tables: the source tables' alias names (a.k.a. history table name) that features belong to
(e.g. inpatient, or outpatient).
:param column_index: the name of index column (unique integer value) in the database table, which is used
for batch reading the input.
:param prevalence: the prevalence dictionary of values for all the variables.
:param query_batch_start: the minimum value of the column index.
:param query_batch_max: the maximum value of the column index.
:param query_batch_size: the number of rows to be read in each batch.
r8 FNzBatch: z ; Table: Tr re ┌columnsrr Ú )r r r r r r r rG rH r] r` ┌_Variables__set_batch_readrJ r ┌astype┌ _Variables__set_batch_process┌_Variables__set_batch_write)r# r3 r4 r' r( r) r* r5 r1 r2 r+ ra ┌stepZ batch_break┌featuresrb rc r$ r$ r% Z __set_batch■ s0
& '% zVariables.__set_batchN)rf rg r{ r* r1 r2 r+ r7 c C sç | | | } | | } | | k r( d Sd | d t | â d t | â d t | â d t | â d }
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aV Read the queried variables.
:param input_schema: the mysql database schema.
:param input_table: the mysql database table.
:param step: the batch id.
:param column_index: the name of index column (unique integer value) in the database table, which is used
for batch reading the input.
:param query_batch_start: the minimum value of the column index.
:param query_batch_max: the maximum value of the column index.
:param query_batch_size: the number of rows to be read in each batch.
:return: the queried variables.
NzSELECT * FROM `z ` WHERE `z` >= z AND `z` < ˙;ri T)r` r rj ) r# rf rg r{ r* r1 r2 r+ Z
step_startZstep_endrk r$ r$ r% Z__set_batch_read9 s
FzVariables.__set_batch_read)ra ┌
history_tabler| rc r5 r7 c C s | j | | | | â S)aă Process variables and generate features.
:param feature_parser:
:param history_table: the source table alias name (a.k.a. history table name) that features belong to
(e.g. inpatient, or outpatient).
:param features: the output features.
:param variables: the input variables.
:param prevalence: the prevalence dictionary of values for all the variables.
:return: the generated features.
)┌generate)r# ra r~ r| rc r5 r$ r$ r% Z__set_batch_processV s z Variables.__set_batch_process)r| c C s& | j j | j | j | d d âd S)z^Write the features into an output file.
:param features: the output features.
rN TN)r rW r r )r# r| r$ r$ r% Z__set_batch_writeg s zVariables.__set_batch_write)r' r) c C sÚ xÔ t t | â â D]╬ } | j | j d | | k } | j j | | | | â sz | j j t d | | â t j â xd | j
â D]V \ } } | j j | | | | | d â sç | j j t d | d â t j â qç Wq Wd S)aB Validate mysql tables and their columns, and generate exception if table/column name is invalid.
:param input_schemas: the mysql database schemas.
:param history_tables: the source tables' alias names (a.k.a. history table name) that features belong to
(e.g. inpatient, or outpatient).
r< z - Table does not exist: rD z - Column does not exist: N) rG rH r r Z exists_mysqlr rn r ro rp rI Zexists_mysql_column)r# r' r) rb r; r> rP r$ r$ r% Z__validate_mysql_namesn s
z Variables.__validate_mysql_names)r ┌
__module__┌ __qualname__r` r& r r_ r6 ┌PandasDataFramer r r r r" r/ r^ r, r- rm r0 r rw ┌FeaturesFeatureParserry rz r. r$ r$ r$ r% r * sd 9 2(
r )┌__doc__┌typingr r r r ro r ┌pandasrJ ┌ ReadersWriters.ReadersWritersr ZFeatures.FeatureParserr ┌Configs.CONSTANTSr ré râ ┌
__author__┌
__copyright__┌ __credits__┌ __license__┌ __version__┌__maintainer__┌ __email__┌
__status__r r$ r$ r$ r% ┌<module> s$ "