def do_all(options):
if options.k_max != "auto":
k_values = range_log2(np.minimum(int(options.k_max),
options.n_features), add_n=True)
else:
k_values = range_log2(options.n_features, add_n=True)
C_values = [1, 10]
random_state = 0
#print options
#sys.exit(0)
if options.trace:
from epac import conf
conf.TRACE_TOPDOWN = True
## 1) Build dataset
## ================
X, y = datasets.make_classification(n_samples=options.n_samples,
n_features=options.n_features,
n_informative=options.n_informative)
## 2) Build Workflow
## =================
time_start = time.time()
## CV + Grid search of a pipeline with a nested grid search
cls = Methods(*[Pipe(SelectKBest(k=k),
SVC(kernel="linear", C=C))
for C in C_values
for k in k_values])
pipeline = CVBestSearchRefit(cls,
n_folds=options.n_folds_nested, random_state=random_state)
wf = Perms(CV(pipeline, n_folds=options.n_folds),
n_perms=options.n_perms,
permute="y",
random_state=random_state)
print "Time ellapsed, tree construction:", time.time() - time_start
## 3) Run Workflow
## ===============
time_fit_predict = time.time()
## Run on local machine
sfw_engine = SomaWorkflowEngine(
tree_root=wf,
num_processes=options.n_cores
)
## Run on cluster
# sfw_engine = SomaWorkflowEngine(
# tree_root=wf,
# num_processes=options.n_cores,
# resource_id="jl237561@gabriel",
# login="******")
# You can use soma_workflow_gui to track your progress
wf = sfw_engine.run(X=X, y=y)
print "Time ellapsed, fit predict:", time.time() - time_fit_predict
time_reduce = time.time()
## 4) Reduce Workflow
## ==================
print wf.reduce()
print "Time ellapsed, reduce:", time.time() - time_reduce
def do_all(options):
if options.k_max != "auto":
k_values = range_log2(np.minimum(int(options.k_max),
options.n_features),
add_n=True)
else:
k_values = range_log2(options.n_features, add_n=True)
C_values = [1, 10]
random_state = 0
#print options
#sys.exit(0)
if options.trace:
from epac import conf
conf.TRACE_TOPDOWN = True
## 1) Build dataset
## ================
X, y = datasets.make_classification(n_samples=options.n_samples,
n_features=options.n_features,
n_informative=options.n_informative)
## 2) Build Workflow
## =================
time_start = time.time()
## CV + Grid search of a pipeline with a nested grid search
cls = Methods(*[
Pipe(SelectKBest(k=k), SVC(kernel="linear", C=C)) for C in C_values
for k in k_values
])
pipeline = CVBestSearchRefit(cls,
n_folds=options.n_folds_nested,
random_state=random_state)
wf = Perms(CV(pipeline, n_folds=options.n_folds),
n_perms=options.n_perms,
permute="y",
random_state=random_state)
print "Time ellapsed, tree construction:", time.time() - time_start
## 3) Run Workflow
## ===============
time_fit_predict = time.time()
## Run on local machine
sfw_engine = SomaWorkflowEngine(tree_root=wf,
num_processes=options.n_cores)
## Run on cluster
# sfw_engine = SomaWorkflowEngine(
# tree_root=wf,
# num_processes=options.n_cores,
# resource_id="jl237561@gabriel",
# login="******")
wf = sfw_engine.run(X=X, y=y)
print "Time ellapsed, fit predict:", time.time() - time_fit_predict
time_reduce = time.time()
## 4) Reduce Workflow
## ==================
print wf.reduce()
print "Time ellapsed, reduce:", time.time() - time_reduce
def do_all(options):
if options.k_max != "auto":
k_values = range_log2(np.minimum(int(options.k_max), options.n_features), add_n=True)
else:
k_values = range_log2(options.n_features, add_n=True)
C_values = [1, 10]
random_state = 0
# print options
# sys.exit(0)
if options.trace:
from epac import conf
conf.TRACE_TOPDOWN = True
## 1) Build dataset
## ================
X, y = datasets.make_classification(
n_samples=options.n_samples, n_features=options.n_features, n_informative=options.n_informative
)
## 2) Build Workflow
## =================
time_start = time.time()
## CV + Grid search of a pipeline with a nested grid search
cls = Methods(*[Pipe(SelectKBest(k=k), SVC(kernel="linear", C=C)) for C in C_values for k in k_values])
pipeline = CVBestSearchRefit(cls, n_folds=options.n_folds_nested, random_state=random_state)
wf = Perms(CV(pipeline, n_folds=options.n_folds), n_perms=options.n_perms, permute="y", random_state=random_state)
print "Time ellapsed, tree construction:", time.time() - time_start
## 3) Export Workflow to soma_workflow_gui
## ===============
time_fit_predict = time.time()
if os.path.isdir(options.soma_workflow_dir):
shutil.rmtree(options.soma_workflow_dir)
sfw_engine = SomaWorkflowEngine(tree_root=wf, num_processes=options.n_cores)
sfw_engine.export_to_gui(options.soma_workflow_dir, X=X, y=y)
print "Time ellapsed, fit predict:", time.time() - time_fit_predict
# ## 6) Load Epac tree & Reduce
# ## ==========================
reduce_filename = os.path.join(options.soma_workflow_dir, "reduce.py")
f = open(reduce_filename, "w")
reduce_str = (
"""from epac.map_reduce.engine import SomaWorkflowEngine
wf = SomaWorkflowEngine.load_from_gui("%s")
print wf.reduce()
"""
% options.soma_workflow_dir
)
f.write(reduce_str)
f.close()
print "#First run\n" "soma_workflow_gui\n" "\t(1)Open %s\n" "\t(2)Submit\n" "\t(3)Transfer Input Files\n" "\t...wait...\n" "\t(4)Transfer Output Files\n" "#When done run:\npython %s" % (
os.path.join(options.soma_workflow_dir, sfw_engine.open_me_by_soma_workflow_gui),
reduce_filename,
)
def test_mysvc_reducer(self):
## 1) Build dataset
## ===================================================================
X, y = datasets.make_classification(n_samples=12,
n_features=10,
n_informative=2,
random_state=1)
## 2) run with Methods
## ===================================================================
my_svc1 = MySVC(C=1.0)
my_svc2 = MySVC(C=2.0)
two_svc_single = Methods(my_svc1, my_svc2)
two_svc_local = Methods(my_svc1, my_svc2)
two_svc_swf = Methods(my_svc1, my_svc2)
two_svc_single.reducer = MyReducer()
two_svc_local.reducer = MyReducer()
two_svc_swf.reducer = MyReducer()
for leaf in two_svc_single.walk_leaves():
print leaf.get_key()
for leaf in two_svc_local.walk_leaves():
print leaf.get_key()
for leaf in two_svc_swf.walk_leaves():
print leaf.get_key()
# top-down process to call transform
two_svc_single.run(X=X, y=y)
# buttom-up process to compute scores
res_single = two_svc_single.reduce()
### You can get below results:
### ==================================================================
### [{'MySVC(C=1.0)': array([ 1., 1.])}, {'MySVC(C=2.0)': array([ 1., 1.])}]
### 3) Run using local multi-processes
### ==================================================================
from epac.map_reduce.engine import LocalEngine
local_engine = LocalEngine(two_svc_local, num_processes=2)
two_svc_local = local_engine.run(**dict(X=X, y=y))
res_local = two_svc_local.reduce()
### 4) Run using soma-workflow
### ==================================================================
from epac.map_reduce.engine import SomaWorkflowEngine
sfw_engine = SomaWorkflowEngine(tree_root=two_svc_swf,
num_processes=2)
two_svc_swf = sfw_engine.run(**dict(X=X, y=y))
res_swf = two_svc_swf.reduce()
if not repr(res_swf) == repr(res_local):
raise ValueError("Cannot dump class definition")
if not repr(res_swf) == repr(res_single):
raise ValueError("Cannot dump class definition")
def test_mysvc_reducer(self):
## 1) Build dataset
## ===================================================================
X, y = datasets.make_classification(n_samples=12,
n_features=10,
n_informative=2,
random_state=1)
## 2) run with Methods
## ===================================================================
my_svc1 = MySVC(C=1.0)
my_svc2 = MySVC(C=2.0)
two_svc_single = Methods(my_svc1, my_svc2)
two_svc_local = Methods(my_svc1, my_svc2)
two_svc_swf = Methods(my_svc1, my_svc2)
two_svc_single.reducer = MyReducer()
two_svc_local.reducer = MyReducer()
two_svc_swf.reducer = MyReducer()
for leaf in two_svc_single.walk_leaves():
print(leaf.get_key())
for leaf in two_svc_local.walk_leaves():
print(leaf.get_key())
for leaf in two_svc_swf.walk_leaves():
print(leaf.get_key())
# top-down process to call transform
two_svc_single.run(X=X, y=y)
# buttom-up process to compute scores
res_single = two_svc_single.reduce()
### You can get below results:
### ==================================================================
### [{'MySVC(C=1.0)': array([ 1., 1.])}, {'MySVC(C=2.0)': array([ 1., 1.])}]
### 3) Run using local multi-processes
### ==================================================================
from epac.map_reduce.engine import LocalEngine
local_engine = LocalEngine(two_svc_local, num_processes=2)
two_svc_local = local_engine.run(**dict(X=X, y=y))
res_local = two_svc_local.reduce()
### 4) Run using soma-workflow
### ==================================================================
from epac.map_reduce.engine import SomaWorkflowEngine
sfw_engine = SomaWorkflowEngine(tree_root=two_svc_swf, num_processes=2)
two_svc_swf = sfw_engine.run(**dict(X=X, y=y))
res_swf = two_svc_swf.reduce()
if not repr(res_swf) == repr(res_local):
raise ValueError("Cannot dump class definition")
if not repr(res_swf) == repr(res_single):
raise ValueError("Cannot dump class definition")
def do_all(options):
if options.k_max != "auto":
k_values = range_log2(np.minimum(int(options.k_max),
options.n_features),
add_n=True)
else:
k_values = range_log2(options.n_features, add_n=True)
C_values = [1, 10]
random_state = 0
#print options
#sys.exit(0)
if options.trace:
from epac import conf
conf.TRACE_TOPDOWN = True
## 1) Build dataset
## ================
X, y = datasets.make_classification(n_samples=options.n_samples,
n_features=options.n_features,
n_informative=options.n_informative)
## 2) Build Workflow
## =================
time_start = time.time()
## CV + Grid search of a pipeline with a nested grid search
cls = Methods(*[
Pipe(SelectKBest(k=k), SVC(kernel="linear", C=C)) for C in C_values
for k in k_values
])
pipeline = CVBestSearchRefit(cls,
n_folds=options.n_folds_nested,
random_state=random_state)
wf = Perms(CV(pipeline, n_folds=options.n_folds),
n_perms=options.n_perms,
permute="y",
random_state=random_state)
print "Time ellapsed, tree construction:", time.time() - time_start
## 3) Export Workflow to soma_workflow_gui
## ===============
time_fit_predict = time.time()
if os.path.isdir(options.soma_workflow_dir):
shutil.rmtree(options.soma_workflow_dir)
sfw_engine = SomaWorkflowEngine(tree_root=wf,
num_processes=options.n_cores)
sfw_engine.export_to_gui(options.soma_workflow_dir, X=X, y=y)
print "Time ellapsed, fit predict:", time.time() - time_fit_predict
# ## 6) Load Epac tree & Reduce
# ## ==========================
reduce_filename = os.path.join(options.soma_workflow_dir, "reduce.py")
f = open(reduce_filename, 'w')
reduce_str = """from epac.map_reduce.engine import SomaWorkflowEngine
wf = SomaWorkflowEngine.load_from_gui("%s")
print wf.reduce()
""" % options.soma_workflow_dir
f.write(reduce_str)
f.close()
print "#First run\n"\
"soma_workflow_gui\n"\
"\t(1)Open %s\n"\
"\t(2)Submit\n"\
"\t(3)Transfer Input Files\n"\
"\t...wait...\n"\
"\t(4)Transfer Output Files\n"\
"#When done run:\npython %s" % (
os.path.join(options.soma_workflow_dir,
sfw_engine.open_me_by_soma_workflow_gui),
reduce_filename)
n_perms=n_perms,
permute="y",
random_state=random_state)
# wf.run(X=X, y=y)
# for leaf in wf.walk_leaves():
# print leaf.load_results()
# wf.reduce()
# from epac.map_reduce.engine import LocalEngine
# local_engine = LocalEngine(tree_root=wf, num_processes=2)
# wf = local_engine.run(X=X, y=y)
# for leaf in wf.walk_leaves():
# print leaf.load_results()
# wf.reduce()
from epac.map_reduce.engine import SomaWorkflowEngine
sfw_engine = SomaWorkflowEngine(
tree_root=wf,
num_processes=3,
remove_finished_wf=False,
remove_local_tree=False)
wf = sfw_engine.run(X=X, y=y)
#for leaf in wf.walk_leaves():
# print leaf.load_results()
#for node in wf.walk_true_nodes():
# print node
# print node.load_results()
print wf.reduce()
from sklearn.svm import SVC
svc = SVC(C=self.C)
svc.fit(X, y)
# "transform" should return a dictionary: ie.: a result, keys are abritrary
return {"y/pred": svc.predict(X), "y/true": y}
best_svc_tranform = Methods(SVMTransform(C=1.0), SVMTransform(C=2.0))
cv = CV(best_svc_tranform, cv_key="y", cv_type="stratified", n_folds=2,
reducer=None)
cv.run(X=X, y=y) # top-down process to call transform
cv.reduce() # buttom-up process
#
## 4) Run using local multi-processes
## ==================================
from epac.map_reduce.engine import LocalEngine
local_engine = LocalEngine(best_svc, num_processes=2)
best_svc = local_engine.run(**dict(X=X, y=y))
best_svc_tranform.reduce()
## 5) Run using soma-workflow
## ==========================
from epac.map_reduce.engine import SomaWorkflowEngine
sfw_engine = SomaWorkflowEngine(tree_root=best_svc,
num_processes=2)
best_svc = sfw_engine.run(**dict(X=X, y=y))
best_svc.reduce()