healthcareio
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data-maker
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bug fix and upgrades to base functionalities

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dev
Steve L. Nyemba 5 years ago
parent a2988a5972
commit 8e722d5bf1
3 changed files with 313 additions and 125 deletions
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15
data/gan.py
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@ -550,6 +550,7 @@ class Predict(GNet):
label = y[:, 1] * len(ma) + tf.squeeze(tf.matmul(y[:, 2:], tf.constant(ma, dtype=tf.int32)))
else:
label = None
fake = self.generator.network(inputs=z, label=label)
init = tf.compat.v1.global_variables_initializer()
saver = tf.compat.v1.train.Saver()
@ -577,11 +578,13 @@ class Predict(GNet):
# if we are dealing with numeric values only we can perform a simple marginal sum against the indexes
# The code below will insure we have some acceptable cardinal relationships between id and synthetic values
#
df = ( pd.DataFrame(np.round(f).astype(np.int32)))
df = pd.DataFrame(np.round(f).astype(np.int32))
p = 0 not in df.sum(axis=1).values
x = df.sum(axis=1).values
if np.divide( np.sum(x), x.size) > .9 or p:
if np.divide( np.sum(x), x.size) > .9 or p and np.sum(x) == x.size:
ratio.append(np.divide( np.sum(x), x.size))
found.append(df)
if i == CANDIDATE_COUNT:
@ -597,11 +600,13 @@ class Predict(GNet):
INDEX = np.random.choice(np.arange(len(found)),1)[0]
INDEX = ratio.index(np.max(ratio))
df = found[INDEX]
columns = self.ATTRIBUTES['synthetic'] if isinstance(self.ATTRIBUTES['synthetic'],list)else [self.ATTRIBUTES['synthetic']]
# r = np.zeros((self.ROW_COUNT,len(columns)))
r = np.zeros(self.ROW_COUNT)
# r = np.zeros(self.ROW_COUNT)
df.columns = self.values
if len(found):
# print (len(found),NTH_VALID_CANDIDATE)
@ -618,6 +623,10 @@ class Predict(GNet):
missing = np.repeat(0, np.where(ii==1)[0].size)
else:
missing = []
#
# @TODO:
# Log the findings here in terms of ratio, missing, candidate count
# print ([np.max(ratio),len(missing),len(found),i])
i = np.where(ii == 0)[0]
df = pd.DataFrame( df.iloc[i].apply(lambda row: self.values[np.random.choice(np.where(row != 0)[0],1)[0]] ,axis=1))
df.columns = columns

29
data/maker/__init__.py
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@ -15,6 +15,7 @@ from transport import factory
from data.bridge import Binary
import threading as thread
class ContinuousToDiscrete :
ROUND_UP = 2
@staticmethod
def binary(X,n=4) :
"""
@ -22,7 +23,7 @@ class ContinuousToDiscrete :
"""
# BOUNDS = np.repeat(np.divide(X.max(),n),n).cumsum().tolist()
BOUNDS = ContinuousToDiscrete.bounds(X,n)
BOUNDS = ContinuousToDiscrete.bounds(np.round(X,ContinuousToDiscrete.ROUND_UP),n)
# _map = [{"index":BOUNDS.index(i),"ubound":i} for i in BOUNDS]
_matrix = []
@ -41,7 +42,7 @@ class ContinuousToDiscrete :
@staticmethod
def bounds(x,n):
return list(pd.cut(np.array(x),n).categories)
return list(pd.cut(np.array( np.round(x,ContinuousToDiscrete.ROUND_UP) ),n).categories)
@ -66,7 +67,7 @@ class ContinuousToDiscrete :
ubound = BOUNDS[ index ].right
lbound = BOUNDS[ index ].left
x_ = np.round(np.random.uniform(lbound,ubound),3).astype(float)
x_ = np.round(np.random.uniform(lbound,ubound),ContinuousToDiscrete.ROUND_UP).astype(float)
values.append(x_)
lbound = ubound
@ -104,10 +105,10 @@ def train (**args) :
# if 'float' not in df[col].dtypes.name :
# args['real'] = pd.get_dummies(df[col].fillna('')).astype(np.float32).values
if 'float' in df[col].dtypes.name and col in CONTINUOUS:
BIN_SIZE = 10 if 'bin_size' not in args else int(args['bin_size'])
BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
args['real'] = ContinuousToDiscrete.binary(df[col],BIN_SIZE).astype(np.float32)
else:
args['real'] = pd.get_dummies(df[col].fillna('')).astype(np.float32).values
args['real'] = pd.get_dummies(df[col].dropna()).astype(np.float32).values
args['column'] = col
@ -157,12 +158,13 @@ def generate(**args):
args['context'] = col
args['column'] = col
if 'float' in df[col].dtypes.name or col in CONTINUOUS :
#
# We should create the bins for the values we are observing here
BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
values = ContinuousToDiscrete.continuous(df[col].values,BIN_SIZE)
else:
# if 'float' in df[col].dtypes.name or col in CONTINUOUS :
# #
# # We should create the bins for the values we are observing here
# BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
# values = ContinuousToDiscrete.continuous(df[col].values,BIN_SIZE)
# # values = np.unique(values).tolist()
# else:
values = df[col].unique().tolist()
args['values'] = values
@ -172,10 +174,11 @@ def generate(**args):
handler = gan.Predict (**args)
handler.load_meta(col)
r = handler.apply()
_df[col] = r[col]
BIN_SIZE = 4 if 'bin_size' not in args else int(args['bin_size'])
_df[col] = ContinuousToDiscrete.continuous(r[col],BIN_SIZE) if 'float' in df[col].dtypes.name or col in CONTINUOUS else r[col]
#
# @TODO: log basic stats about the synthetic attribute
#
# print (r)s
# break
return _df

290
pipeline.py
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@ -1,5 +1,6 @@
import json
from transport import factory
import numpy as np
import os
from multiprocessing import Process
import pandas as pd
@ -8,116 +9,291 @@ import data.maker
from data.params import SYS_ARGS
f = open ('config.json')
PIPELINE = json.loads(f.read())
f.close()
#
# The configuration array is now loaded and we will execute the pipe line as follows
DATASET='combined20190510_deid'
DATASET='combined20190510'
class Components :
@staticmethod
def get(args):
"""
This function returns a data-frame provided a bigquery sql statement with conditions (and limits for testing purposes)
The function must be wrapped around a lambda this makes testing easier and changing data stores transparent to the rest of the code. (Vital when testing)
:sql basic sql statement
:condition optional condition and filters
"""
SQL = args['sql']
if 'condition' in args :
condition = ' '.join([args['condition']['field'],args['condition']['qualifier'],'(',args['condition']['value'],')'])
SQL = " ".join([SQL,'WHERE',condition])
SQL = SQL.replace(':dataset',args['dataset']) #+ " LIMIT 1000 "
return SQL #+ " LIMIT 10000 "
if 'limit' in args :
SQL = SQL + 'LIMIT ' + args['limit']
credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
df = pd.read_gbq(SQL,credentials=credentials,dialect='standard').dropna()
return df
# return lambda: pd.read_gbq(SQL,credentials=credentials,dialect='standard')[args['columns']].dropna()
@staticmethod
def train(args):
def split(X,MAX_ROWS=3,PART_SIZE=3):
return list(pd.cut( np.arange(X.shape[0]+1),PART_SIZE).categories)
def train(self,**args):
"""
This function will instanciate a worker that will train given a message that is provided to it
This is/will be a separate process that will
This function will perform training on the basis of a given pointer that reads data
"""
print (['starting .... ',args['notify'],args['context']] )
#SQL = args['sql']
#if 'condition' in args :
# condition = ' '.join([args['condition']['field'],args['condition']['qualifier'],'(',args['condition']['value'],')'])
# SQL = " ".join([SQL,'WHERE',condition])
print ( args['context'])
#
# @TODO: we need to log something here about the parameters being passed
pointer = args['reader'] if 'reader' in args else lambda: Components.get(**args)
df = pointer()
#
# Now we can parse the arguments and submit the entire thing to training
#
logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
log_folder = os.sep.join(["logs",args['context']])
_args = {"batch_size":2000,"logs":log_folder,"context":args['context'],"max_epochs":250,"num_gpus":2,"column":args['columns'],"id":"person_id","logger":logger}
os.environ['CUDA_VISIBLE_DEVICES'] = args['gpu']
#SQL = SQL.replace(':dataset',args['dataset']) #+ " LIMIT 1000 "
SQL = Components.get(args)
if 'limit' in args :
SQL = ' '.join([SQL,'limit',args['limit'] ])
_args['max_epochs'] = 250 if 'max_epochs' not in args else args['max_epochs']
credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
_args['data'] = pd.read_gbq(SQL,credentials=credentials,dialect='standard')
#_args['data'] = _args['data'].astype(object)
log_folder = args['logs'] if 'logs' in args else 'logs'
_args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
_args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1
MAX_ROWS = args['max_rows'] if 'max_rows' in args else 0
PART_SIZE = args['part_size'] if 'part_size' in args else 0
if df.shape[0] > MAX_ROWS and 'partition' not in args:
lbound = 0
bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
# bounds = Components.split(df,MAX_ROWS,PART_SIZE)
qwriter = factory.instance(type='queue.QueueWriter',args={'queue':'aou.io'})
for b in bounds :
part_index = bounds.index(b)
ubound = int(b.right)
_data = df.iloc[lbound:ubound][args['columns']]
lbound = ubound
# _args['logs'] = os.sep.join([log_folder,str(part_index)])
_args['partition'] = str(part_index)
_args['logger'] = {'args':{'dbname':'aou','doc':args['context']},'type':'mongo.MongoWriter'}
#
# We should post the the partitions to a queue server (at least the instructions on ):
# - where to get the data
# - and athe arguments to use (partition #,columns,gpu,epochs)
#
info = {"rows":_data.shape[0],"cols":_data.shape[1], "paritition":part_index,"logs":_args['logs']}
p = {"args":_args,"data":_data.to_dict(orient="records"),"info":info}
qwriter.write(p)
#
# @TODO:
# - Notify that information was just posted to the queue
info['max_rows'] = MAX_ROWS
info['part_size'] = PART_SIZE
logger.write({"module":"train","action":"setup-partition","input":info})
pass
else:
partition = args['partition'] if 'partition' in args else ''
log_folder = os.sep.join([log_folder,args['context'],partition])
_args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
_args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1
os.environ['CUDA_VISIBLE_DEVICES'] = str(args['gpu']) if 'gpu' in args else '0'
_args['data'] = df
#
# @log :
# Logging information about the training process for this partition (or not)
#
info = {"rows":df.shape[0],"cols":df.shape[1], "partition":partition,"logs":_args['logs']}
logger.write({"module":"train","action":"train","input":info})
data.maker.train(**_args)
@staticmethod
def generate(args):
pass
# @staticmethod
def generate(self,args):
"""
This function will generate data and store it to a given,
"""
logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
log_folder = os.sep.join(["logs",args['context']])
_args = {"batch_size":2000,"logs":log_folder,"context":args['context'],"max_epochs":250,"num_gpus":2,"column":args['columns'],"id":"person_id","logger":logger}
os.environ['CUDA_VISIBLE_DEVICES'] = args['gpu']
SQL = Components.get(args)
if 'limit' in args :
SQL = " ".join([SQL ,'limit', args['limit'] ])
credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
_args['data'] = pd.read_gbq(SQL,credentials=credentials,dialect='standard').fillna('')
#_args['data'] = _args['data'].astype(object)
log_folder = args['logs'] if 'logs' in args else 'logs'
partition = args['partition'] if 'partition' in args else ''
log_folder = os.sep.join([log_folder,args['context'],partition])
_args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
_args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1
os.environ['CUDA_VISIBLE_DEVICES'] = str(args['gpu']) if 'gpu' in args else '0'
_args['no_value']= args['no_value']
MAX_ROWS = args['max_rows'] if 'max_rows' in args else 0
PART_SIZE = args['part_size'] if 'part_size' in args else 0
_args['max_epochs'] = 250 if 'max_epochs' not in args else args['max_epochs']
_args['no_value'] = args['no_value'] if 'no_value' in args else ''
#credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
#_args['data'] = pd.read_gbq(SQL,credentials=credentials,dialect='standard')
# credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
# _args['data'] = pd.read_gbq(SQL,credentials=credentials,dialect='standard').dropna()
reader = args['reader']
df = reader()
if 'partition' in args :
bounds = Components.split(df,MAX_ROWS,PART_SIZE)
# bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
lbound = int(bounds[int(partition)].left)
ubound = int(bounds[int(partition)].right)
df = df.iloc[lbound:ubound]
_args['data'] = df
# _args['data'] = reader()
#_args['data'] = _args['data'].astype(object)
_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1
_dc = data.maker.generate(**_args)
#
# We need to post the generate the data in order to :
# 1. compare immediately
# 2. synthetic copy
#
cols = _dc.columns.tolist()
print (args['columns'])
data_comp = _args['data'][args['columns']].join(_dc[args['columns']],rsuffix='_io') #-- will be used for comparison (store this in big query)
base_cols = list(set(_args['data'].columns) - set(args['columns'])) #-- rebuilt the dataset (and store it)
print (_args['data'].shape)
print (_args['data'].shape)
for name in cols :
_args['data'][name] = _dc[name]
info = {"module":"generate","action":"io","input":{"rows":_dc[name].shape[0],"name":name}}
if partition != '' :
info['partition'] = partition
logger.write(info)
# filename = os.sep.join([log_folder,'output',name+'.csv'])
# data_comp[[name]].to_csv(filename,index=False)
#
#-- Let us store all of this into bigquery
prefix = args['notify']+'.'+_args['context']
table = '_'.join([prefix,'compare','io'])
data_comp.to_gbq(if_exists='replace',destination_table=table,credentials=credentials,chunksize=50000)
_args['data'].to_gbq(if_exists='replace',destination_table=table.replace('compare','full'),credentials=credentials,chunksize=50000)
data_comp.to_csv(os.sep.join([log_folder,table+'.csv']),index=False)
table = '_'.join([prefix,partition,'io']).replace('__','_')
folder = os.sep.join([args['logs'],args['context'],partition,'output'])
if 'file' in args :
_fname = os.sep.join([folder,table.replace('_io','_full_io.csv')])
_pname = os.sep.join([folder,table])+'.csv'
data_comp.to_csv( _pname,index=False)
_args['data'].to_csv(_fname,index=False)
else:
credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
_pname = os.sep.join([folder,table+'.csv'])
_fname = table.replace('_io','_full_io')
data_comp.to_gbq(if_exists='replace',destination_table=_pname,credentials='credentials',chunk_size=50000)
data_comp.to_csv(_pname,index=False)
INSERT_FLAG = 'replace' if 'partition' not in args else 'append'
_args['data'].to_gbq(if_exists=INSERT_FLAG,destination_table=_fname,credentials='credentials',chunk_size=50000)
info = {"full":{"path":_fname,"rows":_args['data'].shape[0]},"compare":{"name":_pname,"rows":data_comp.shape[0]} }
if partition :
info ['partition'] = partition
logger.write({"module":"generate","action":"write","info":info} )
@staticmethod
def callback(channel,method,header,stream):
info = json.loads(stream)
logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':SYS_ARGS['context']})
logger.write({'module':'process','action':'read-partition','input':info['info']})
df = pd.DataFrame(info['data'])
args = info['args']
if int(args['num_gpu']) > 1 and args['gpu'] > 0:
args['gpu'] = args['gpu'] + args['num_gpu']
args['reader'] = lambda: df
#
# @TODO: Fix
# There is an inconsistency in column/columns ... fix this shit!
#
args['columns'] = args['column']
(Components()).train(**args)
logger.write({"module":"process","action":"exit","info":info["info"]})
channel.close()
channel.connection.close()
pass
if __name__ == '__main__' :
index = int(SYS_ARGS['index'])
filename = SYS_ARGS['config'] if 'config' in SYS_ARGS else 'config.json'
f = open (filename)
PIPELINE = json.loads(f.read())
f.close()
index = int(SYS_ARGS['index']) if 'index' in SYS_ARGS else 0
args = (PIPELINE[index])
#if 'limit' in SYS_ARGS :
# args['limit'] = SYS_ARGS['limit']
#args['dataset'] = 'combined20190510'
SYS_ARGS['dataset'] = 'combined20190510_deid' if 'dataset' not in SYS_ARGS else SYS_ARGS['dataset']
#if 'max_epochs' in SYS_ARGS :
# args['max_epochs'] = SYS_ARGS['max_epochs']
args['dataset'] = 'combined20190510'
args = dict(args,**SYS_ARGS)
args['max_rows'] = int(args['max_rows']) if 'max_rows' in args else 3
args['part_size']= int(args['part_size']) if 'part_size' in args else 3
#
# @TODO:
# Log what was initiated so we have context of this processing ...
#
if 'listen' not in SYS_ARGS :
if 'file' in args :
reader = lambda: pd.read_csv(args['file']) ;
else:
reader = lambda: Components().get(args)
args['reader'] = reader
if 'generate' in SYS_ARGS :
Components.generate(args)
#
# Let us see if we have partitions given the log folder
content = os.listdir( os.sep.join([args['logs'],args['context']]))
generator = Components()
if ''.join(content).isnumeric() :
#
# we have partitions we are working with
for id in ''.join(content) :
args['partition'] = id
generator.generate(args)
else:
generator.generate(args)
# Components.generate(args)
elif 'listen' in args :
#
# This will start a worker just in case to listen to a queue
if 'read' in SYS_ARGS :
QUEUE_TYPE = 'queue.QueueReader'
pointer = lambda qreader: qreader.read(1)
else:
QUEUE_TYPE = 'queue.QueueListener'
pointer = lambda qlistener: qlistener.listen()
N = int(SYS_ARGS['jobs']) if 'jobs' in SYS_ARGS else 1
qhandlers = [factory.instance(type=QUEUE_TYPE,args={'queue':'aou.io'}) for i in np.arange(N)]
jobs = []
for qhandler in qhandlers :
qhandler.callback = Components.callback
job = Process(target=pointer,args=(qhandler,))
job.start()
jobs.append(job)
#
# let us wait for the jobs
print (["Started ",len(jobs)," trainers"])
while len(jobs) > 0 :
jobs = [job for job in jobs if job.is_alive()]
# pointer(qhandler)
# qreader.read(1)
pass
else:
Components.train(args)
trainer = Components()
trainer.train(**args)
# Components.train(**args)
#for args in PIPELINE :
#args['dataset'] = 'combined20190510'
#process = Process(target=Components.train,args=(args,))

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