bug fix with ICD and some minor improvements
This commit is contained in:
Steve Nyemba
parent
2f6f43c9c6
commit
915601236c
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@ -535,8 +535,12 @@ class Predict(GNet):
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self.values = args['values']
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self.ROW_COUNT = args['row_count']
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self.oROW_COUNT = self.ROW_COUNT
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if args['no_value'] in ['na','','NA'] :
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self.MISSING_VALUES = np.nan
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else :
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self.MISSING_VALUES = args['no_value']
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# self.MISSING_VALUES = args['no_value']
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# self.MISSING_VALUES = int(args['no_value']) if args['no_value'].isnumeric() else np.na if args['no_value'] in ['na','NA','N/A'] else args['no_value']
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def load_meta(self, column):
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super().load_meta(column)
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self.generator.load_meta(column)
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@ -652,7 +656,8 @@ class Predict(GNet):
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if ii.shape[0] > 0 :
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#
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#@TODO Have this be a configurable variable
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missing = np.repeat(0, np.where(ii==1)[0].size)
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missing = np.repeat(self.MISSING_VALUES, np.where(ii==1)[0].size)
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else:
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missing = []
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#
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@ -62,21 +62,28 @@ class ContinuousToDiscrete :
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BOUNDS = ContinuousToDiscrete.bounds(X,BIN_SIZE)
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values = []
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_BINARY= ContinuousToDiscrete.binary(X,BIN_SIZE)
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# # print (BOUNDS)
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# _BINARY= ContinuousToDiscrete.binary(X,BIN_SIZE)
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# # # print (BOUNDS)
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l = {}
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for value in X :
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values += [ np.round(np.random.uniform(item.left,item.right),ContinuousToDiscrete.ROUND_UP) for item in BOUNDS if value >= item.left and value <= item.right ]
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# values = []
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for row in _BINARY :
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# ubound = BOUNDS[row.index(1)]
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index = np.where(row == 1)[0][0]
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ubound = BOUNDS[ index ].right
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lbound = BOUNDS[ index ].left
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x_ = np.round(np.random.uniform(lbound,ubound),ContinuousToDiscrete.ROUND_UP).astype(float)
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values.append(x_)
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# # values = []
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# for row in _BINARY :
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# # ubound = BOUNDS[row.index(1)]
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# index = np.where(row == 1)[0][0]
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lbound = ubound
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# ubound = BOUNDS[ index ].right
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# lbound = BOUNDS[ index ].left
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# x_ = np.round(np.random.uniform(lbound,ubound),ContinuousToDiscrete.ROUND_UP).astype(float)
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# values.append(x_)
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# lbound = ubound
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# values = [np.random.uniform() for item in BOUNDS]
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return values
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@ -173,6 +180,8 @@ def generate(**args):
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# If the identifier is not present, we should fine a way to determine or make one
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#
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BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
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NO_VALUE = dict(args['no_value']) if type(args['no_value']) == dict else args['no_value']
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_df = df.copy()
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for col in column :
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args['context'] = col
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@ -195,13 +204,29 @@ def generate(**args):
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args['values'] = values
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args['row_count'] = df.shape[0]
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if col in NO_VALUE :
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args['no_value'] = NO_VALUE[col]
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else:
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args['no_value'] = NO_VALUE
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#
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# we can determine the cardinalities here so we know what to allow or disallow
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handler = gan.Predict (**args)
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handler.load_meta(col)
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r = handler.apply()
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if col in CONTINUOUS :
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r[col] = np.array(r[col])
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MISSING= np.nan if args['no_value'] in ['na','','NA'] else args['no_value']
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_df[col] = ContinuousToDiscrete.continuous(r[col],BIN_SIZE) if col in CONTINUOUS else r[col]
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if np.isnan(MISSING):
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i = np.isnan(r[col])
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i = np.where (i == False)[0]
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else:
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i = np.where( r[col] != None)[0]
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_approx = ContinuousToDiscrete.continuous(r[col][i],BIN_SIZE)
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r[col][i] = _approx
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_df[col] = r[col] #ContinuousToDiscrete.continuous(r[col],BIN_SIZE) if col in CONTINUOUS else r[col]
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# _df[col] = r[col]
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#
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# @TODO: log basic stats about the synthetic attribute
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120
pipeline.py
120
pipeline.py
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@ -16,7 +16,12 @@ from data.params import SYS_ARGS
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DATASET='combined20191004v2_deid'
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class Components :
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class KEYS :
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PIPELINE_KEY = 'pipeline'
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SQL_FILTER = 'filter'
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@staticmethod
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def get_logger(**args) :
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return factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
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@staticmethod
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def get(args):
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"""
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@ -26,15 +31,19 @@ class Components :
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:condition optional condition and filters
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"""
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SQL = args['sql']
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if 'condition' in args :
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condition = ' '.join([args['condition']['field'],args['condition']['qualifier'],'(',args['condition']['value'],')'])
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if Components.KEYS.SQL_FILTER in args :
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SQL_FILTER = Components.KEYS.SQL_FILTER
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condition = ' '.join([args[SQL_FILTER]['field'],args[SQL_FILTER]['qualifier'],'(',args[SQL_FILTER]['value'],')'])
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SQL = " ".join([SQL,'WHERE',condition])
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SQL = SQL.replace(':dataset',args['dataset']) #+ " LI "
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if 'limit' in args :
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SQL = SQL + ' LIMIT ' + args['limit']
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#
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# let's log the sql query that has been performed here
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logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
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logger.write({"module":"bigquery","action":"read","input":{"sql":SQL}})
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credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
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df = pd.read_gbq(SQL,credentials=credentials,dialect='standard').astype(object)
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return df
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@ -131,6 +140,7 @@ class Components :
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_args['num_gpu'] = 1
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os.environ['CUDA_VISIBLE_DEVICES'] = str(args['gpu'])
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_args['no_value']= args['no_value']
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# MAX_ROWS = args['max_rows'] if 'max_rows' in args else 0
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PART_SIZE = int(args['part_size']) if 'part_size' in args else 8
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@ -166,19 +176,27 @@ class Components :
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#
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# performing basic analytics on the synthetic data generated (easy to quickly asses)
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#
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info = {"module":"generate","action":"io-stats","input":{"rows":data_comp.shape[0],"partition":partition,"logs":[]}}
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logs = []
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for name in data_comp.columns.tolist() :
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g = pd.DataFrame(data_comp.groupby([name]).size())
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g.columns = ['counts']
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g[name] = g.index.tolist()
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g.index = np.arange(g.shape[0])
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logs.append({"name":name,"counts": g.to_dict(orient='records')})
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info['input']['logs'] = logs
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info = {"module":"generate","action":"io.metrics","input":{"rows":data_comp.shape[0],"partition":partition,"logs":[]}}
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x = {}
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for name in args['columns'] :
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ident = data_comp.apply(lambda row: 1*(row[name]==row[name+'_io']),axis=1).sum()
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count = data_comp[name].unique().size
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_ident= data_comp.shape[1] - ident
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_count= data_comp[name+'_io'].unique().size
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info['input']['logs'] += [{"name":name,"identical":int(ident),"no_identical":int(_ident),"original_count":count,"synthetic_count":_count}]
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# for name in data_comp.columns.tolist() :
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# g = pd.DataFrame(data_comp.groupby([name]).size())
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# g.columns = ['counts']
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# g[name] = g.index.tolist()
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# g.index = np.arange(g.shape[0])
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# logs.append({"name":name,"counts": g.to_dict(orient='records')})
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# info['input']['logs'] = logs
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logger.write(info)
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base_cols = list(set(_args['data'].columns) - set(args['columns'])) #-- rebuilt the dataset (and store it)
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cols = _dc.columns.tolist()
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for name in cols :
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_args['data'][name] = _dc[name]
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info = {"module":"generate","action":"io","input":{"rows":_dc[name].shape[0],"name":name}}
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@ -223,43 +241,14 @@ class Components :
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info ['partition'] = int(partition)
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logger.write({"module":"generate","action":"write","input":info} )
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@staticmethod
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def callback(channel,method,header,stream):
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if stream.decode('utf8') in ['QUIT','EXIT','END'] :
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channel.close()
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channel.connection.close()
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info = json.loads(stream)
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logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':SYS_ARGS['context']})
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logger.write({'module':'process','action':'read-partition','input':info['input']})
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df = pd.DataFrame(info['data'])
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args = info['args']
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if args['num_gpu'] > 1 :
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args['gpu'] = int(info['input']['partition']) if info['input']['partition'] < 8 else np.random.choice(np.arange(8)).astype(int)
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else:
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args['gpu'] = 0
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args['num_gpu'] = 1
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# if int(args['num_gpu']) > 1 and args['gpu'] > 0:
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# args['gpu'] = args['gpu'] + args['num_gpu'] if args['gpu'] + args['num_gpu'] < 8 else args['gpu'] #-- 8 max gpus
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args['reader'] = lambda: df
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#
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# @TODO: Fix
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# There is an inconsistency in column/columns ... fix this shit!
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#
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channel.close()
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channel.connection.close()
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args['columns'] = args['column']
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(Components()).train(**args)
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logger.write({"module":"process","action":"exit","input":info["input"]})
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pass
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if __name__ == '__main__' :
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filename = SYS_ARGS['config'] if 'config' in SYS_ARGS else 'config.json'
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f = open (filename)
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PIPELINE = json.loads(f.read())
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_config = json.loads(f.read())
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f.close()
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PIPELINE = _config['pipeline']
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index = SYS_ARGS['index']
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if index.isnumeric() :
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index = int(SYS_ARGS['index'])
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@ -274,10 +263,17 @@ if __name__ == '__main__' :
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# print
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print ("..::: ",PIPELINE[index]['context'])
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args = (PIPELINE[index])
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for key in _config :
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if key == 'pipeline' or key in args:
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#
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# skip in case of pipeline or if key exists in the selected pipeline (provided by index)
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#
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continue
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args[key] = _config[key]
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args = dict(args,**SYS_ARGS)
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args['logs'] = args['logs'] if 'logs' in args else 'logs'
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args['batch_size'] = 2000 if 'batch_size' not in args else int(args['batch_size'])
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if 'dataset' not in args :
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args['dataset'] = 'combined20191004v2_deid'
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@ -340,38 +336,14 @@ if __name__ == '__main__' :
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else:
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generator.generate(args)
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# Components.generate(args)
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elif 'listen' in args :
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elif 'finalize' in args :
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#
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# This will start a worker just in case to listen to a queue
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SYS_ARGS = dict(args) #-- things get lost in context
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if 'read' in SYS_ARGS :
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QUEUE_TYPE = 'queue.QueueReader'
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pointer = lambda qreader: qreader.read()
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else:
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QUEUE_TYPE = 'queue.QueueListener'
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pointer = lambda qlistener: qlistener.listen()
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N = int(SYS_ARGS['jobs']) if 'jobs' in SYS_ARGS else 1
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qhandlers = [factory.instance(type=QUEUE_TYPE,args={'queue':'aou.io'}) for i in np.arange(N)]
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jobs = []
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for qhandler in qhandlers :
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qhandler.callback = Components.callback
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job = Process(target=pointer,args=(qhandler,))
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job.start()
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jobs.append(job)
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# This will finalize a given set of synthetic operations into a table
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#
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# let us wait for the jobs
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print (["Started ",len(jobs)," trainers"])
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while len(jobs) > 0 :
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idataset = args['input'] if 'input' in args else 'io' #-- input dataset
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odataset = args['output'] #-- output dataset
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labels = [name.strip() for name in args['labels'].split(',') ]
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jobs = [job for job in jobs if job.is_alive()]
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time.sleep(2)
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# pointer(qhandler)
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# qreader.read(1)
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pass
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else:
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# DATA = np.array_split(DATA,PART_SIZE)
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2
setup.py
2
setup.py
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@ -4,7 +4,7 @@ import sys
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def read(fname):
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return open(os.path.join(os.path.dirname(__file__), fname)).read()
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args = {"name":"data-maker","version":"1.2.4","author":"Vanderbilt University Medical Center","author_email":"steve.l.nyemba@vanderbilt.edu","license":"MIT",
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args = {"name":"data-maker","version":"1.2.5","author":"Vanderbilt University Medical Center","author_email":"steve.l.nyemba@vanderbilt.edu","license":"MIT",
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"packages":find_packages(),"keywords":["healthcare","data","transport","protocol"]}
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args["install_requires"] = ['data-transport@git+https://dev.the-phi.com/git/steve/data-transport.git','tensorflow==1.15','pandas','pandas-gbq','pymongo']
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args['url'] = 'https://hiplab.mc.vanderbilt.edu/git/aou/data-maker.git'
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