bug fix with partition & data -access
This commit is contained in:
Steve Nyemba
parent
718e578401
commit
330d6b6ae6
41
data/gan.py
41
data/gan.py
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@ -532,10 +532,13 @@ class Predict(GNet):
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self.generator = Generator(**args)
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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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self.MISSING_VALUES = 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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self.ROW_COUNT = self.oROW_COUNT
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def apply(self,**args):
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# print (self.train_dir)
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# suffix = "-".join(self.ATTRIBUTES['synthetic']) if isinstance(self.ATTRIBUTES['synthetic'],list) else self.ATTRIBUTES['synthetic']
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@ -544,6 +547,7 @@ class Predict(GNet):
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demo = self._LABEL #np.zeros([self.ROW_COUNT,self.NUM_LABELS]) #args['de"shape":{"LABEL":list(self._LABEL.shape)} mo']
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tf.compat.v1.reset_default_graph()
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z = tf.random.normal(shape=[self.ROW_COUNT, self.Z_DIM])
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y = tf.compat.v1.placeholder(shape=[self.ROW_COUNT, self.NUM_LABELS], dtype=tf.int32)
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if self._LABEL is not None :
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ma = [[i] for i in np.arange(self.NUM_LABELS - 2)]
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@ -569,6 +573,8 @@ class Predict(GNet):
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found = []
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ratio = []
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__x__ = None
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__ratio=0
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for i in np.arange(CANDIDATE_COUNT) :
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if labels :
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f = sess.run(fake,feed_dict={y:labels})
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@ -590,7 +596,8 @@ class Predict(GNet):
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if i == CANDIDATE_COUNT:
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break
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else:
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__x__ = df if __x__ is None or np.where(x > 0)[0].size > np.where(__x__ > 0)[0].size else __x__
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__ratio = np.divide( np.sum(x), x.size) if __x__ is None or np.where(x > 0)[0].size > np.where(__x__ > 0)[0].size else __ratio
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continue
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# i = df.T.index.astype(np.int32) #-- These are numeric pseudonyms
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@ -600,23 +607,33 @@ class Predict(GNet):
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#
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N = len(found)
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_index = [i for i in range(0,N) if found[i].shape[1] == len(self.values)]
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if not _index :
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INDEX = np.random.choice(np.arange(len(found)),1)[0]
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INDEX = ratio.index(np.max(ratio))
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else:
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INDEX = _index[0]
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if not _index and not found :
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df = __x__
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INDEX = -1
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else :
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if not _index :
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INDEX = np.random.choice(np.arange(len(found)),1)[0]
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INDEX = ratio.index(np.max(ratio))
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else:
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INDEX = _index[0]
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df = found[INDEX]
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df = found[INDEX]
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columns = self.ATTRIBUTES['synthetic'] if isinstance(self.ATTRIBUTES['synthetic'],list)else [self.ATTRIBUTES['synthetic']]
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# r = np.zeros((self.ROW_COUNT,len(columns)))
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# r = np.zeros(self.ROW_COUNT)
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if self.logger :
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info = {"found":len(found),"selected":INDEX, "ratio": ratio[INDEX],"rows":df.shape[0],"cols":df.shape[1],"expected":len(self.values)}
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info = {"found":len(found),"rows":df.shape[0],"cols":df.shape[1],"expected":len(self.values)}
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if INDEX > 0 :
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info =dict(info ,**{"selected":INDEX, "ratio": ratio[INDEX] })
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else :
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info['selected'] = -1
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info['ratio'] = __ratio
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self.logger.write({"module":"gan-generate","action":"generate","input":info})
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df.columns = self.values
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if len(found):
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if len(found) or df.columns.size == len(self.values):
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# print (len(found),NTH_VALID_CANDIDATE)
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# x = df * self.values
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#
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@ -639,10 +656,14 @@ class Predict(GNet):
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df = pd.DataFrame( df.iloc[i].apply(lambda row: self.values[np.random.choice(np.where(row != 0)[0],1)[0]] ,axis=1))
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df.columns = columns
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df = df[columns[0]].append(pd.Series(missing))
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if self.logger :
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info= {"missing": i.size,"rows":df.shape[0],"cols":1}
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self.logger.write({"module":"gan-generate","action":"compile.io","input":info})
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# print(df.head())
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tf.compat.v1.reset_default_graph()
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df = pd.DataFrame(df)
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df.columns = columns
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@ -107,23 +107,33 @@ def train (**args) :
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# args['real'] = pd.get_dummies(df[col].fillna('')).astype(np.float32).values
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# if 'float' not in df[col].dtypes.name :
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# args['real'] = pd.get_dummies(df[col].fillna('')).astype(np.float32).values
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if 'float' in df[col].dtypes.name and col in CONTINUOUS:
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if col in CONTINUOUS:
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BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
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args['real'] = ContinuousToDiscrete.binary(df[col],BIN_SIZE).astype(np.float32)
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else:
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args['real'] = pd.get_dummies(df[col].dropna()).astype(np.float32).values
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df.to_csv('tmp-'+args['logs'].replace('/','_')+'-'+col+'.csv',index=False)
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# print (df[col].dtypes)
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# print (df[col].dropna/(axis=1).unique())
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args['real'] = pd.get_dummies(df[col].dropna()).astype(np.float32).values
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args['column'] = col
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args['context'] = col
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context = args['context']
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if 'store' in args :
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args['store']['args']['doc'] = context
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logger = factory.instance(**args['store'])
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args['logger'] = logger
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info = {"rows":args['real'].shape[0],"cols":args['real'].shape[1],"name":col}
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logger.write({"module":"gan-train","action":"data-prep","input":info})
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else:
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logger = None
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args['column'] = col
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args['context'] = col
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#
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# If the s
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trainer = gan.Train(**args)
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trainer.apply()
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def post(**args):
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@ -149,6 +159,7 @@ def generate(**args):
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"""
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# df = args['data']
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df = args['data'] if not isinstance(args['data'],str) else pd.read_csv(args['data'])
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CONTINUOUS = args['continous'] if 'continuous' in args else []
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column = args['column'] if (isinstance(args['column'],list)) else [args['column']]
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# column_id = args['id']
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@ -168,7 +179,8 @@ def generate(**args):
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# values = ContinuousToDiscrete.continuous(df[col].values,BIN_SIZE)
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# # values = np.unique(values).tolist()
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# else:
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values = df[col].unique().tolist()
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values = df[col].dropna().unique().tolist()
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args['values'] = values
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args['row_count'] = df.shape[0]
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@ -178,8 +190,9 @@ def generate(**args):
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handler.load_meta(col)
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r = handler.apply()
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BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
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_df[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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# _df[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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#
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176
pipeline.py
176
pipeline.py
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@ -30,11 +30,13 @@ class Components :
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condition = ' '.join([args['condition']['field'],args['condition']['qualifier'],'(',args['condition']['value'],')'])
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SQL = " ".join([SQL,'WHERE',condition])
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SQL = SQL.replace(':dataset',args['dataset']) #+ " LIMIT 1000 "
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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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SQL = SQL + ' LIMIT ' + args['limit']
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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')
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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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# return lambda: pd.read_gbq(SQL,credentials=credentials,dialect='standard')[args['columns']].dropna()
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@ -51,7 +53,8 @@ class Components :
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#
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# @TODO: we need to log something here about the parameters being passed
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# pointer = args['reader'] if 'reader' in args else lambda: Components.get(**args)
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df = args['reader']()
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df = args['data']
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# if df.shape[0] == 0 :
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# print ("CAN NOT TRAIN EMPTY DATASET ")
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@ -62,85 +65,43 @@ class Components :
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logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
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log_folder = args['logs'] if 'logs' in args else 'logs'
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# _args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
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# _args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
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# _args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1
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# _args['gpu'] = args['gpu'] if 'gpu' in args else 0
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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'])
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partition = args['partition']
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log_folder = os.sep.join([log_folder,args['context'],str(partition)])
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_args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
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_args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
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_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1
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_args['gpu'] = args['gpu'] if 'gpu' in args else 0
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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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if 'partition' not in args:
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lbound = 0
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# bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
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# bounds = Components.split(df,MAX_ROWS,PART_SIZE)
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columns = args['columns']
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df = np.array_split(df[columns].values,PART_SIZE)
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qwriter = factory.instance(type='queue.QueueWriter',args={'queue':'aou.io'})
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part_index = 0
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#
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# let's start n processes to listen & train this mother ...
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#
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#-- hopefully they learn as daemons
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for _df in df:
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# _args['logs'] = os.sep.join([log_folder,str(part_index)])
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_args['partition'] = str(part_index)
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_args['logger'] = {'args':{'dbname':'aou','doc':args['context']},'type':'mongo.MongoWriter'}
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#
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# We should post the the partitions to a queue server (at least the instructions on ):
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# - where to get the data
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# - and athe arguments to use (partition #,columns,gpu,epochs)
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#
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_df = pd.DataFrame(_df,columns=columns)
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# print (columns)
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info = {"rows":_df.shape[0],"cols":_df.shape[1], "partition":part_index,"logs":_args['logs'],"num_gpu":1,"part_size":PART_SIZE}
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p = {"args":_args,"data":_df.to_dict(orient="records"),"input":info}
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part_index += 1
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qwriter.write(p)
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#
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# @TODO:
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# - Notify that information was just posted to the queue
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# In case we want slow-mode, we can store the partitions in mongodb and process (Yes|No)?
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#
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logger.write({"module":"train","action":"setup-partition","input":info})
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pass
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#
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# We ask the process to assume 1 gpu given the system number of GPU and that these tasks can run in parallel
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#
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if int(args['num_gpu']) > 1 :
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_args['gpu'] = int(args['gpu']) if int(args['gpu']) < 8 else np.random.choice(np.arange(8)).astype(int)[0]
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else:
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print ('.....')
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partition = args['partition'] if 'partition' in args else ''
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log_folder = os.sep.join([log_folder,args['context'],str(partition)])
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_args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
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_args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
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_args['gpu'] = 0
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_args['num_gpu'] = 1
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os.environ['CUDA_VISIBLE_DEVICES'] = str(args['gpu'])
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#
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# We ask the process to assume 1 gpu given the system number of GPU and that these tasks can run in parallel
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#
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if int(args['num_gpu']) > 1 :
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_args['gpu'] = int(args['gpu']) if int(args['gpu']) < 8 else np.random.choice(np.arange(8)).astype(int)[0]
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else:
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_args['gpu'] = 0
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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['store'] = {'type':'mongo.MongoWriter','args':{'dbname':'aou','doc':args['context']}}
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_args['data'] = args['data']
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# print (['partition ',partition,df.value_source_concept_id.unique()])
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#
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# @log :
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# Logging information about the training process for this partition (or not)
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#
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_args['data'] = df
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#
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# @log :
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# Logging information about the training process for this partition (or not)
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#
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info = {"rows":df.shape[0],"cols":df.shape[1], "partition":int(partition),"logs":_args['logs']}
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info = {"rows":df.shape[0],"cols":df.shape[1], "partition":int(partition),"logs":_args['logs']}
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logger.write({"module":"train","action":"train","input":info})
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data.maker.train(**_args)
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logger.write({"module":"train","action":"train","input":info})
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data.maker.train(**_args)
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pass
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@ -210,6 +171,7 @@ class Components :
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#
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#-- Let us store all of this into bigquery
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prefix = args['notify']+'.'+_args['context']
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partition = str(partition)
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table = '_'.join([prefix,partition,'io']).replace('__','_')
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folder = os.sep.join([args['logs'],args['context'],partition,'output'])
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if 'file' in args :
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@ -219,17 +181,19 @@ class Components :
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data_comp.to_csv( _pname,index=False)
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_args['data'].to_csv(_fname,index=False)
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_id = 'path'
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else:
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credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
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_pname = os.sep.join([folder,table+'.csv'])
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_fname = table.replace('_io','_full_io')
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data_comp.to_gbq(if_exists='replace',destination_table=_pname,credentials='credentials',chunk_size=50000)
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partial = '.'.join(['io',args['context']+'_partial_io'])
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complete= '.'.join(['io',args['context']+'_full_io'])
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data_comp.to_gbq(if_exists='append',destination_table=partial,credentials=credentials,chunksize=50000)
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data_comp.to_csv(_pname,index=False)
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INSERT_FLAG = 'replace' if 'partition' not in args or 'segment' not in args else 'append'
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_args['data'].to_gbq(if_exists=INSERT_FLAG,destination_table=_fname,credentials='credentials',chunk_size=50000)
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info = {"full":{"path":_fname,"rows":_args['data'].shape[0]},"compare":{"name":_pname,"rows":data_comp.shape[0]} }
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_args['data'].to_gbq(if_exists=INSERT_FLAG,destination_table=complete,credentials=credentials,chunksize=50000)
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_id = 'dataset'
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info = {"full":{_id:_fname,"rows":_args['data'].shape[0]},"partial":{"path":_pname,"rows":data_comp.shape[0]} }
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if partition :
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info ['partition'] = int(partition)
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logger.write({"module":"generate","action":"write","input":info} )
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@ -280,18 +244,18 @@ if __name__ == '__main__' :
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args['logs'] = args['logs'] if 'logs' in args else 'logs'
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if 'dataset' not in args :
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args['dataset'] = 'combined20191004v2_deid'
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PART_SIZE = int(args['part_size']) if 'part_size' in args else 8
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#
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# @TODO:
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# Log what was initiated so we have context of this processing ...
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#
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if 'listen' not in SYS_ARGS :
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if 'file' in args :
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reader = lambda: pd.read_csv(args['file']) ;
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DATA = pd.read_csv(args['file']) ;
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else:
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DATA = Components().get(args)
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reader = lambda: DATA
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args['reader'] = reader
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COLUMNS = DATA.columns
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DATA = np.array_split(DATA,PART_SIZE)
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if 'generate' in SYS_ARGS :
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#
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@ -299,32 +263,34 @@ if __name__ == '__main__' :
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content = os.listdir( os.sep.join([args['logs'],args['context']]))
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generator = Components()
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DATA = reader()
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if ''.join(content).isnumeric() :
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#
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# we have partitions we are working with
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jobs = []
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del args['reader']
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columns = DATA.columns.tolist()
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DATA = np.array_split(DATA[args['columns']],len(content))
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for id in ''.join(content) :
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if 'focus' in args and int(args['focus']) != int(id) :
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# columns = DATA.columns.tolist()
|
||||
|
||||
# DATA = np.array_split(DATA,PART_SIZE)
|
||||
|
||||
for index in range(0,PART_SIZE) :
|
||||
if 'focus' in args and int(args['focus']) != index :
|
||||
#
|
||||
# This handles failures/recoveries for whatever reason
|
||||
# If we are only interested in generating data for a given partition
|
||||
continue
|
||||
# index = id.index(id)
|
||||
|
||||
args['partition'] = id
|
||||
args['data'] = pd.DataFrame(DATA[(int(id))],columns=args['columns'])
|
||||
args['partition'] = index
|
||||
args['data'] = DATA[index]
|
||||
if int(args['num_gpu']) > 1 :
|
||||
args['gpu'] = id
|
||||
args['gpu'] = index
|
||||
else:
|
||||
args['gpu']=0
|
||||
make = lambda _args: (Components()).generate(_args)
|
||||
job = Process(target=make,args=(args,))
|
||||
job.name = 'generator # '+str(id)
|
||||
job.name = 'generator # '+str(index)
|
||||
job.start()
|
||||
jobs.append(job)
|
||||
|
||||
|
|
@ -370,18 +336,26 @@ if __name__ == '__main__' :
|
|||
# qreader.read(1)
|
||||
pass
|
||||
else:
|
||||
PART_SIZE = int(args['jobs']) if 'jobs' in args else 8
|
||||
DATA = reader()
|
||||
DATA = np.array_split(DATA[args['columns']],PART_SIZE)
|
||||
|
||||
# DATA = np.array_split(DATA,PART_SIZE)
|
||||
|
||||
jobs = []
|
||||
for index in range(0,int(args['jobs'])) :
|
||||
for index in range(0,PART_SIZE) :
|
||||
if 'focus' in args and int(args['focus']) != index :
|
||||
continue
|
||||
args['part_size'] = PART_SIZE
|
||||
args['partition'] = index
|
||||
_df = pd.DataFrame(DATA[index],columns=args['columns'])
|
||||
args['reader'] = lambda: _df
|
||||
# _df = pd.DataFrame(DATA[index],columns=args['columns'])
|
||||
args['data'] = DATA[index]
|
||||
args['data'].to_csv('aou-'+str(index)+'csv',index=False)
|
||||
# args['reader'] = lambda: _df
|
||||
if int(args['num_gpu']) > 1 :
|
||||
args['gpu'] = index
|
||||
else:
|
||||
args['gpu']=0
|
||||
|
||||
make = lambda _args: (Components()).train(**_args)
|
||||
job = Process(target=make,args=(args,))
|
||||
job = Process(target=make,args=( dict(args),))
|
||||
job.name = 'Trainer # ' + str(index)
|
||||
job.start()
|
||||
jobs.append(job)
|
||||
|
|
|
|||
Loading…
Reference in New Issue