def load_models(opt):
models = []
model_cnns = []
for iteration in opt.iterations:
print(iteration)
# Load infos
infos = load_infos(opt, iteration)
ignore = [
"id", "batch_size", "beam_size", "start_from_best", "input_json",
"input_h5", "input_anno", "images_root", "aic_caption_path",
"input_bu"
]
for k in vars(infos['opt']).keys():
if k not in ignore:
vars(opt).update({k: vars(infos['opt'])[k]})
# Setup cnn model
model_cnn = setup_cnn(opt, iteration)
# Setup model
model = setup(opt, iteration)
models.append(model)
model_cnns.append(model_cnn)
return models, model_cnns
def parse_texts(self):
url = "%s/text/" % self.base_url
content = self.request_content(url)
# print content
if content:
pattern = re.compile(
'<img.*?u-logo lazy".*?data-original="(.*?)".*?></a>.*?'
+ # user icon url
'<a.*?u-user-name.*?target="_blank">(.*?)</a>.*?'
+ # user name
'<span.*?f-ib f-fr">(.*?)</span>.*?' + # release time
'<div.*?j-r-list-c-desc">(.*?)</div>',
re.S) # text
items = re.findall(pattern, content)
models = []
for item in items:
# name, icon
user = User(item[0], item[1])
# user, time, text, content_from
model = TextModel(user, item[2], item[3], self.name)
models.append(model)
return models
else:
print 'request content error'
return None
def parse_texts(self):
url = "%s/" % self.base_url
content = self.request_content(url)
# print content
if content:
pattern = re.compile(
'<img.*?"user-img lazy-load left".*?data-src="(.*?)".*?onerror.*?>.*?'
+ # user icon url
'<div.*?class="name-time-wrapper left">.*?<span.*?class="name">(.*?)</span>.*?'
+ # user name
'<span.*?class="time timeago".*?>(.*?)</span>.*?'
+ # release time
'<div.*?class="upload-txt no-mb">.*?<p>(.*?)</p>',
re.S) # text
items = re.findall(pattern, content)
models = []
for item in items:
# name, icon
user = User(item[0], item[1])
# user, time, text, content_from
model = TextModel(user, item[2], item[3], self.name)
models.append(model)
return models
else:
print 'request content error'
return None
def __init__(self, posts):
m = []
n = []
fmap = posts.familyhash.copy()
for family in fmap.keys():
flist = fmap[family]
if len(flist) >= 3:
while (len(m)<=2):
try:
ele = flist.pop()
except Exception as e:
break
if (ele.syllables > 7 and ele.syllables < 11):
m.append(ele.text)
for family in fmap.keys():
flist = fmap[family]
if (len(flist)) >= 2:
while(len(n)<=1):
try:
ele = flist.pop()
except Exception as e:
break
if (ele.syllables > 4 and ele.syllables < 8):
n.append(ele.text)
if (len(m)+len(n)) < 5:
return #Not a poem!
self.poems += [[m[0],m[1],n[0],n[1],m[1]]]
def get_model_lists():
from django.utils.text import capfirst
from django.utils.html import escape
from django.contrib import admin
def no_auto_fields(field):
from django.db import models
return not isinstance(field[2], models.AutoField)
excluded_models = [Role, SupplyPlace, LateHealthPost]
models = []
for model, m_admin in admin.site._registry.items():
# fetch ALL fields (including those nested via
# foreign keys) for this model
fields = [{ "caption": escape(capt), "name": name, "help_text": field.help_text }
for name, capt, field in filter(no_auto_fields, nested_fields(model))]
# pass model metadata and fields array
# to the template to be rendered
#select models only related to rutfet
if model._meta.app_label == "rutfet" and model not in excluded_models:
models.append({
"caption": capfirst(model._meta.verbose_name_plural),
"name": model.__name__.lower(),
"app_label": model._meta.app_label,
"fields": fields
})
return models
def get_defined_models():
import models
import sqlalchemy
members = dict(inspect.getmembers(models))
members.pop('Base')
models = list()
for name, member in members.items():
if isinstance(member, sqlalchemy.ext.declarative.api.DeclarativeMeta):
models.append(member)
return models
def main(args):
print("Loading config file: ", args.config)
params = utils.load_config_file(args.config)
params["dataset_paths"] = utils.format_dataset_path(
params["dataset_paths"])
if "nyu" not in params:
params["nyu"] = False
# Data loading code
print("Creating data loaders...")
if params["nyu"]:
from dataloaders.nyu import NYUDataset
val_dataset = NYUDataset(params["dataset_paths"], split='val')
else:
val_dataset = Datasets.FastDepthDataset(params["dataset_paths"],
split='val',
depth_min=params["depth_min"],
depth_max=params["depth_max"],
input_shape_model=(224, 224),
random_crop=False)
# set batch size to be 1 for validation
data_loader = torch.utils.data.DataLoader(
val_dataset,
batch_size=1,
shuffle=False,
num_workers=params["num_workers"],
pin_memory=True)
# Set GPU
params["device"] = torch.device(
"cuda:{}".format(params["device"])
if params["device"] >= 0 and torch.cuda.is_available() else "cpu")
print("Using device", params["device"])
print("Loading models...")
models = []
model_names = []
for model_dict in params["models"]:
model_names.append(Path(model_dict["model_path"]).stem)
model, _ = utils.load_model(model_dict, model_dict["model_path"],
params["device"])
model.to(params["device"])
models.append(model)
# Create output directory
output_directory = os.path.join(params["save_folder"],
".".join(model_names))
if not os.path.exists(output_directory):
os.makedirs(output_directory)
params["output_directory"] = output_directory
print("Saving results to " + output_directory)
compare_models(params, data_loader, models)
def compile_all_results (scenarios, dir='../data'):
"""
Compiles the results across multiple scenarios produced by running run_on_cluster on each
one into a single sv file. The specified directory must be where where the results of
running run_on_cluster for each scenario are stored (each is a sub-directory named v0, v1, etc.)
and is also where the output from this function will be saved.
"""
models = []
causes = []
time = []
true_cf = []
true_std = []
std_bias = []
mean_abs_err = []
median_abs_err = []
mean_rel_err = []
median_rel_err = []
mean_csmf_accuracy = []
median_csmf_accuracy = []
mean_coverage_bycause = []
mean_coverage = []
percent_total_coverage = []
scenario = []
for i in range(scenarios):
for j in ['bad_model', 'latent_simplex']:
read = csv.reader(open('%s/v%s/%s_summary.csv' % (dir, i, j)))
read.next()
for row in read:
models.append(row[0])
causes.append(row[1])
time.append(row[2])
true_cf.append(row[3])
true_std.append(row[4])
std_bias.append(row[5])
mean_abs_err.append(row[6])
median_abs_err.append(row[7])
mean_rel_err.append(row[8])
median_rel_err.append(row[9])
mean_csmf_accuracy.append(row[10])
median_csmf_accuracy.append(row[11])
mean_coverage_bycause.append(row[12])
mean_coverage.append(row[13])
percent_total_coverage.append(row[14])
scenario.append(i)
all = pl.np.core.records.fromarrays([scenario, models, time, true_cf, true_std, causes, mean_abs_err, median_abs_err, mean_rel_err, median_rel_err,
mean_csmf_accuracy, median_csmf_accuracy, mean_coverage_bycause, mean_coverage, percent_total_coverage],
names=['scenario', 'model', 'time', 'true_cf', 'true_std', 'cause', 'mean_abs_err', 'median_abs_err',
'mean_rel_err', 'median_rel_err', 'mean_csmf_accuracy', 'median_csmf_accuracy',
'mean_covearge_bycause', 'mean_coverage', 'percent_total_coverage'])
pl.rec2csv(all, fname='%s/all_summary_metrics.csv' % (dir))
def fit(csv_file,
classifiers=None,
features=None,
svm_settings=None,
knn_settings=None,
lda_settings=None):
"""
Function gets user input of which features to perform the fitting on.
User can also choose which classifier to use
Arguments:
csv_file: the file path to csv file containing data. This is formatted and split into
training and control data
classifiers: the array of classifier names
Returns:
models: array of trained classifiers
control_data: data you can use to control the fit of the data per classifier
"""
if (classifiers == None):
classifiers = select_classifiers()
if (features == None):
features = select_features(csv_file)
training_data, control_data = data.get_dataframes(csv_file, features)
target_data = training_data['diabetes']
training_data = training_data.drop(columns=['diabetes'])
models = [] #The array containing trained models
for c in classifiers:
if c == 'svm':
model = get_model(c, training_data, target_data, svm_settings)
elif c == 'knn':
model = get_model(c, training_data, target_data, knn_settings)
elif c == 'lda':
model = get_model(c, training_data, target_data, lda_settings)
else:
model = get_model(c, training_data, target_data)
if model == None:
pass
else:
models.append((c, model))
return models, training_data, target_data, control_data
def parse_images(self):
url = '%s/pic/' % self.base_url
content = self.request_content(url)
# print content
if content:
pattern = re.compile(
'<img.*?"user-img lazy-load left".*?data-src="(.*?)".*?onerror.*?>.*?'
+
'<div.*?class="name-time-wrapper left">.*?<span.*?class="name">(.*?)</span>.*?'
+ '<span.*?class="time timeago".*?>(.*?)</span>.*?' +
'<div.*?class="upload-txt.*?<p>(.*?)</p>.*?' +
'<img.*?class="upload-img lazy".*?data-src="(.*?)".*?>',
re.S) #
items = re.findall(pattern, content)
models = []
for item in items:
user = User(item[0], item[1])
# (self, user, time, image_url, text, content_from):
model = ImageModel(user, item[2], item[3], item[4], self.name)
models.append(model)
return models
def parse_images(self):
url = '%s/pic/' % self.base_url
content = self.request_content(url)
# print content
if content:
pattern = re.compile(
'<img.*?u-logo lazy".*?data-original="(.*?)".*?></a>.*?'
+ # user icon url
'<a.*?u-user-name.*?target="_blank">(.*?)</a>.*?'
+ # user name
'<span.*?f-ib f-fr">(.*?)</span>.*?' + # release time
'<div.*?j-r-list-c-desc">(.*?)</div>.*?' + # text
'<img.*?class="lazy".*?data-original="(.*?)".*?>',
re.S) #image url
items = re.findall(pattern, content)
models = []
for item in items:
user = User(item[0], item[1])
# (self, user, time, image_url, text, content_from):
model = ImageModel(user, item[2], item[3], item[4], self.name)
models.append(model)
return models
def getRelatedModels(entry):
entries = {}
models = []
try:
for query, fk in reversed(list(entry.dependencies())):
#for x in dir(fk):
#print x
for x in fk.model_class.select().where(query):
#print 'here:'
#print x
modelname = fk.model_class.__name__
try:
entries[modelname].append(x)
except:
models.append(modelname)
entries[modelname] = []
entries[modelname].append(x)
#entries.append((fk.model_class.__name__, x))
except:
pass
return (models, entries)
def init():
if os.path.exists('./saliency_data/{}'.format(args.name)):
models = []
folds = []
for i in range(len(os.listdir('./saliency_data/{}/models'.format(args.name)))):
models.append(keras.models.load_model('./saliency_data/{}/models/model{}.hdf5'.format(args.name, i)))
folds.append((pd.read_pickle('./saliency_data/{}/data/train{}.p'.format(args.name, i)), pd.read_pickle('./saliency_data/{}/data/test{}.p'.format(args.name, i)), pd.read_pickle('./saliency_data/{}/data/val{}.p'.format(args.name, i))))
else:
models = []
folds = deepconv_kfold.get_data('min', 'max', cols, args.preprocessing, args.simple, args.test_split, args.runs)
if args.fold is not None:
folds = [folds[args.fold]]
for i, fold in enumerate(folds):
train, test, val = fold
model = deepconv_kfold.train_model_fold(train, val, args.model, args.epochs, i, use_keras=True)
models.append(model)
os.makedirs('./saliency_data/{}/models/'.format(args.name), exist_ok=True)
os.makedirs('./saliency_data/{}/data/'.format(args.name), exist_ok=True)
model.save('./saliency_data/{}/models/model{}.hdf5'.format(args.name, i))
test.to_pickle('./saliency_data/{}/data/test{}.p'.format(args.name, i))
train.to_pickle('./saliency_data/{}/data/train{}.p'.format(args.name, i))
val.to_pickle('./saliency_data/{}/data/val{}.p'.format(args.name, i))
return models, folds
def input_layer(sh_list, sh_test, sh_c_list, shm_list, train_loader,
test_loader, model, rank, split, batch_size, batch_num,
test_batch_num, epoch_num, lamda, lr, cv):
update = 0
feed_q1 = sh_list[rank]
grad_q1 = sh_list[rank + split - 1] #split = 3
send_output = sh_c_list[rank]
feed_test = sh_test[rank]
send_target = shm_list[0]
models = []
outputs = []
inputs = []
optim = []
n = -1 * (rank - (split - 1))
#num_of_models = 2*split - 1
#num_of_models = n + 1
num_of_models = split
#delay = n *(2)# + 1
delay = n
#model.reset_parameters()
for i in range(num_of_models):
models.append(copy.deepcopy(model))
outputs.append(0)
inputs.append(0)
optim.append(
torch.optim.SGD(models[i].parameters(),
lr=lr,
momentum=0.9,
weight_decay=0.0005,
nesterov=True))
#optim.append(torch.optim.Adam(models[i].parameters(),lr=1e-4))
#optim.append(torch.optim.SGD(models[i].parameters(),lr=lr))
for i in models:
i.cuda(rank)
model.cuda(rank)
#data = data_set[:,:-mnist_data.NUM_LABELS]
time_tot = 0
steps = int(batch_num / lamda)
if batch_num % lamda != 1:
steps += 1
lamda_back = lamda
for epoch in range(epoch_num):
#with torch.autograd.profiler.profile() as prof:
s_t_u = resource_usage(RUSAGE_SELF)
s_t = timestamp()
model.train()
for i in models:
i.train()
train_data = train_loader.__iter__()
t = 0
t1 = 0
t2 = 0
t3 = 0
t4 = 0
t5 = 0
t6 = 0
t7 = 0
t8 = 0
td1 = 0
td2 = 0
td3 = 0
td4 = 0
td5 = 0
td6 = 0
#for time in range(1,(batch_num + 2 * split - (rank + 1) - 1 + 1)):
for step in range(1, steps + 1):
#off = (step-1)*lamda
#cv.acquire()
#cv.wait()
#cv.notify_all()
#cv.release()
#cv.sync(rank)
lamda = lamda_back
if step == steps:
lamda = batch_num - (step - 1) * lamda
#print('step',step,'lamda',lamda)
for time in range(1, lamda + delay + 1):
#if time <= off + lamda :
if time <= lamda:
#offset = (time-1) * batch_size
t1 = timestamp()
#offset = t * batch_size
data, target = next(train_data)
send_target.send(target)
#print('rank',rank,time,target)
#x = x.view(-1,784)
#input_feat = Variable(data,requires_grad=True).to("cuda:0")
data = data.cuda(rank, non_blocking=True)
#input_feat = Variable(data[offset:offset+batch_size,:],requires_grad=True).cuda(rank)
t2 = timestamp()
#print(input_feat)
#print(input_feat.size())
model_idx = (time % num_of_models) - 1
#output = models[model_idx].forward(input_feat)
output = models[model_idx].forward(data)
#inputs[model_idx] = input_feat
outputs[model_idx] = output
t3 = timestamp()
#print(output.size())
#output_send = output.to("cpu")
feed_q1.send_wait()
send_output.copy_(output.data)
#print('send',t,send_output)
feed_q1.async_send_signal()
#feed_q1.send(output.data.to("cpu"))
t += 1
t4 = timestamp()
if time > delay: # t-(2K-k-1)
#if time >= 1+ delay : # t-(2K-k-1)
t5 = timestamp()
pg = grad_q1.recv()
pg = pg.cuda(rank)
t6 = timestamp()
output_idx = ((time - delay) % num_of_models) - 1
optimizer = optim[output_idx]
optimizer.zero_grad()
output = outputs[output_idx]
output.backward(pg)
#a = list(models[output_idx].parameters())[0].clone()
optimizer.step()
t7 = timestamp()
#b = list(models[output_idx].parameters())[0].clone()
#print(torch.equal(a.data,b.data))
td1 += t2 - t1
td2 += t3 - t2
td3 += t4 - t3
td4 += t6 - t5
td5 += t7 - t6
#print(time)
#feed_q1.init()
#grad_q1.init()
model.init_zero()
with torch.cuda.device(rank):
for i in range(num_of_models):
j = models[i].parameters()
for k in model.parameters():
#k = 0
l = j.__next__()
k.requires_grad_(False)
k.copy_(k.data + l.data / num_of_models)
for i in range(num_of_models):
j = model.parameters()
for k in models[i].parameters():
l = j.__next__()
k.requires_grad_(False)
k.copy_(l.data)
k.requires_grad_(True)
#print('average_done worker 1')
e_t_u = resource_usage(RUSAGE_SELF)
e_t = timestamp()
u_t = e_t_u.ru_stime - s_t_u.ru_stime
t = e_t - s_t
time_tot = time_tot + t
#print('node1 user time = %f time = %f time_tot = %f' % ( u_t , t, time_tot))
#print(prof)
print('rank =', rank, 'recv output =', td1)
print('rank =', rank, 'forward =', td2)
print('rank =', rank, 'send output', td3)
print('rank =', rank, 'recv grad =', td4)
print('rank =', rank, 'backward =', td5)
model.eval()
for i in models:
i.eval()
for data, target in test_loader:
#for i in range(test_batch_num):
#print(data,target)
#print('rank',rank,target)
#offset = i * batch_size
#x = Variable(test_set[offset:offset+batch_size,:])
x = Variable(data).cuda(rank)
#x = x.view(-1,784)
#x = x.to("cuda:0")
output = model.forward(x)
#output = output.to("cpu")
#print(output.size())
feed_test.send(output.data.to('cpu'))
#i += 1
if epoch == 150 or epoch == 225:
lr = lr * 0.1
for i in optim:
for j in i.param_groups:
j['lr'] = lr
def predict_fast(args):
transforms = Compose([])
dataset = OpenEDSDatasetTest(data_path=args.data_path,
labels_file=args.label_file,
save_path=args.save_dir,
transforms=transforms,
normalize={
"mean": [0.485, 0.456, 0.406],
"std": [0.229, 0.224, 0.225]
},
cumulative=True)
data_loader = DataLoader(dataset,
batch_size=1,
num_workers=8,
shuffle=False,
pin_memory=False)
models = []
for model_config in configs:
conf = load_config(model_config.config_path)
models_zoo = conf.get('models_zoo', 'selim')
if models_zoo == 'qubvel':
import segmentation_models_pytorch as smp
model = smp.Unet(encoder_name=conf['encoder'],
classes=conf['num_classes'])
else:
model = models.__dict__[conf['network']](
seg_classes=4, backbone_arch=conf['encoder'])
model = torch.nn.DataParallel(model).cuda()
checkpoint_path = model_config.weights_path
checkpoint = torch.load(checkpoint_path, map_location="cpu")
model.load_state_dict(checkpoint['state_dict'])
model.eval()
models.append([model, model_config])
with torch.no_grad():
for sample in tqdm(data_loader):
imgs = sample["image"].cuda().float()
preds_dict = {}
for model, model_config in models:
output = model(imgs)
output_flip = torch.flip(model(torch.flip(imgs, dims=(3, ))),
dims=(3, ))
output = (output + output_flip) / 2
output = output.cpu()
for i in range(output.shape[0]):
img_name = sample["img_name"][i]
if img_name not in preds_dict:
preds_dict[img_name] = {
'output': output[i] * model_config.weight,
'total_weight': model_config.weight
}
else:
preds_dict[img_name][
'output'] += output[i] * model_config.weight
preds_dict[img_name][
'total_weight'] += model_config.weight
preds_total = normalize_preds(preds_dict)
save_preds(args, preds_total)
for j in range(int((n_frames - n_trains[i])/10)):
(x, y) = next(test_gen)
test_preds[j*batch_size:(j+1)*batch_size, :] = net.forward(x).cpu().detach().numpy()
test_targets[j*batch_size:(j+1)*batch_size, :] = y.cpu().detach().numpy()
temp = pearsonr(train_preds.squeeze(), train_targets.squeeze())
train_pcc[i] = temp[0]
temp = pearsonr(test_preds.squeeze(), test_targets.squeeze())
test_pcc[i] = temp[0]
temp = spearmanr(train_preds.squeeze(), train_targets.squeeze())
train_srocc[i] = temp[0]
temp = spearmanr(test_preds.squeeze(), test_targets.squeeze())
test_srocc[i] = temp[0]
models.append(net)
savemat('results/nn_' + str(args.n_feats) + '_train_size_analysis.mat', {'nn_' + str(args.n_feats) + '_train_pcc': train_pcc, 'nn_' + str(args.n_feats) + '_test_pcc': test_pcc,
'nn_' + str(args.n_feats) + '_train_srocc': train_srocc, 'nn_' + str(args.n_feats) + '_test_srocc': test_srocc})
elif args.mode == 'analyze_scale_qp':
n_train = args.train_size
Net = models.model_class[args.model]
data_gen_function = models.data_generator[args.model]
net = Net(n_feats, h_size).cuda()
train_gen = data_gen_function(n_train, n_feats, batch_size, args.data_path, 'train')
net.train(train_gen, int(n_train/10), int(args.epochs))
test_gen = data_gen_function(n_train, n_feats, batch_size, args.data_path, 'test')
if __name__ == '__main__':
args = argparser()
# model_types = sorted(Prediction_Gammas.keys())
# model_types = ['dphprg','dphprgln','dphpg','dppn']
# model_types = ['dppprg','dppprgln','dpppg','dpppgln','dppn']
model_types = [
'sdppprg', 'sdpppg', 'sdpppgln', 'sdppprgln', 'mdppprg', 'mdpppg'
]
models = []
for model_type in model_types:
mm = glob.glob(os.path.join(args.path, model_type, 'results*.db'))
for m in mm:
models.append((model_type, m))
pplrs = []
for model in models:
print('Processing model {} '.format(model[0]), end=' ')
try:
pplrs.append(ppl_generation(model))
print('Passed')
except pd.io.sql.DatabaseError:
print('Failed')
pass
df = pd.DataFrame(
pplrs,
# columns = ('type','name','PPL_L1','PPL_L2','PPL_Linf','ES_Linf'),
columns=('type', 'name', 'PPL_Linf', 'ES_Linf', 'PPL_Linf_F',
return kldr
if __name__ == '__main__':
args = argparser()
paths = glob.glob(os.path.join(args.path, 'sim_*'))
# model_types = ['dphpg','dphprg','dphprgln','dppn','vhpg']
model_types = ['dpppg', 'dppprg', 'dppprgln', 'dppn', 'vppg']
models = []
gens = []
for path in paths:
for model_type in model_types:
mm = glob.glob(os.path.join(path, model_type, 'results*.db'))
for m in mm:
models.append(m)
gg = glob.glob(os.path.join(path, 'data.db'))
for g in gg:
gens.append(g)
pool = Pool(processes=cpu_count(), initializer=limit_cpu)
kldrs = list(pool.map(kl_wrapper, models + gens))
pool.close()
df = pd.DataFrame(
[(x[0], x[1], *x[2]) for x in kldrs],
columns=['type', 'scenario'] +
['k_{}'.format(i) for i in range(len(kldrs[0][2]))],
)
df.to_csv(os.path.join(args.path, 'kl_divergence.csv'), index=False)
def make_predictions(file,modelPath):
trainingDataFiles = [file]#glob.glob("/scratch/staff/ak1774/shared_folder/data/train/*.h5")
data = data_loader.load_data_from_file(trainingDataFiles[0])
models = []
for i in range(1,2):
print(i)
models.append( load_pytorch_model('ModelData/' +str(i) +'/' +'model.model',
get_config('/' +str(i) +'/config.json'), data) )
#fullGameData,fullGameLabels = data_loader.getSequencialNaive(data,hero_feature_indicies,label_indicies)
xLims = data['time'].values
#¢health = data['player_4_m_iHealth'].values
#######################
# get original health
######################
norm_stats = None
with open("norm_stats.pickle", 'rb') as f:
norm_stats = pickle.load(f)
for label,min_value,max_value in normalization_stats:
if "_m_iHealth" in label:
health_min = min_value
health_max = max_value
if "m_iMaxHealth" in label:
maxhealth_min = min_value
maxhealth_max = max_value
healthes = []
max_healthes = []
relative_healthes = []
for i in range(0,10):
health_vals = data['player_' + str(i) + '_m_iHealth'].values
maxhealth_vals = data['player_' + str(i) + '_m_iMaxHealth'].values
health_vals = health_vals * (health_max - health_min) + health_min
maxhealth_vals = maxhealth_vals * (maxhealth_max - maxhealth_min) + maxhealth_min
relative_health_vals = health_vals / maxhealth_vals # hopefully maxhealth is never 0
healthes.append(health_vals)
max_healthes.append(maxhealth_vals)
relative_healthes.append(relative_health_vals)
#######################
# get death times
######################
labels = [(i,label) for i,label in enumerate(list(data))]
death_time_indicies = preprocess.labels_to_indicies(preprocess.select_features_by_name("time_until_next_death",labels))
death_times = data.values[:,death_time_indicies].astype(np.float32)
for m in models:
X = [torch.from_numpy(hero_X) for hero_X in m.fullGameData]
pred = model(X)
pred = torch.sigmoid(pred)
pred = pred.cpu().detach().numpy()
y = m.fullGameLabels
currentMeanTrueAccuracy = 0
currentMeanFalseAccuracy=0
numTruePos = 0
numFalsePos = 0
numTrueNeg = 0
numFalseNeg = 0
for i in range(0,data.shape[0]):
predX = 0
for m in models:
y = m.fullGameLabels[i]
y = np.array(y)
y = np.expand_dims(y,0)
X = [torch.from_numpy(hero_X[i:(i+1),:]) for hero_X in m.fullGameData]
print(i)
#predX = averagePred(models,X)
predX = modelPred(m.model,X) +predX
predX = predX/len(models)
'''
true_pos = ((predX > 0.5) == (y > 0.5)).reshape(-1).astype(np.float32)
true_neg = ((predX < 0.5) == (y <0.5)).reshape(-1).astype(np.float32)
false_pos = ((predX > 0.5) == (y < 0.5)).reshape(-1).astype(np.float32)
false_neg = ((predX < 0.5) == (y > 0.5)).reshape(-1).astype(np.float32)
for pos in true_neg:
if pos ==1:
numTrueNeg +=1
for pos in false_neg:
if pos ==1:
numFalseNeg +=1
for pos in true_pos:
if pos ==1:
numTruePos +=1
for pos in false_pos:
if pos ==1:
numFalsePos +=1
'''
prediction = predX
currentMeanTrueAccuracy += np.mean(true_pos)
currentMeanFalseAccuracy += np.mean(false_pos)
prediction = np.squeeze(prediction,0)
if i %3000 ==0:
print('Current true pos ' +str(currentMeanTrueAccuracy/(i+1)))
print('Current false pos ' +str(currentMeanFalseAccuracy/(i+1)))
heroStuff.append(prediction)
labelStuff.append(np.squeeze(y,0))
print()
print(numTruePos)
print(numTrueNeg)
print()
print(numFalsePos)
print(numFalseNeg)
print()
print('True Pos = ' + str(currentMeanTrueAccuracy/19326))
print('False pos = ' + str(currentMeanFalseAccuracy/19326))
heroStuff1 = np.swapaxes(heroStuff,0,1)
labelStuff1= np.swapaxes(labelStuff,0,1)
xLims = xLims - xLims[0] - 90
np.save('hero.npy', np.array(heroStuff1))
np.save('label.npy', np.array(labelStuff1))
np.save('xLims.npy', np.array(xLims))
np.save('health.npy',np.array(healthes))
def hidden_layer(sh_list, sh_test, sh_c_list, model, rank, split, batch_num,
test_batch_num, epoch_num, lamda, lr, cv):
feed_q1 = sh_list[rank - 1]
grad_q1 = sh_list[rank + split - 2]
send_output = sh_c_list[2 * rank]
send_grad = sh_c_list[2 * rank - 1]
feed_test = sh_test[rank - 1]
if split > 2:
feed_q2 = sh_list[rank]
grad_q2 = sh_list[rank + split - 1]
feed_test2 = sh_test[rank]
models = []
outputs = []
inputs = []
optim = []
n = -1 * (rank - (split - 1))
#num_of_models = 2*split - 1
num_of_models = split
#delay = n *(2)# + 1
#delay = 2* split -(rank+1) #- 1
delay = n
#model.reset_parameters()
for i in range(2 * split - 1):
models.append(copy.deepcopy(model))
outputs.append(0)
inputs.append(0)
optim.append(
torch.optim.SGD(models[i].parameters(),
lr=lr,
momentum=0.9,
weight_decay=0.0005,
nesterov=True))
#optim.append(torch.optim.Adam(models[i].parameters(),lr=1e-4))
#optim.append(torch.optim.SGD(models[i].parameters(),lr=lr))
for i in models:
i.cuda(rank)
model.cuda(rank)
time_tot = 0
steps = int(batch_num / lamda)
if batch_num % lamda != 0:
steps += 1
lamda_back = lamda
t = 0
for epoch in range(epoch_num):
#with torch.autograd.profiler.profile() as prof:
s_t_u = resource_usage(RUSAGE_SELF)
s_t = timestamp()
model.train()
for i in models:
i.train()
t = 0
t1 = 0
t2 = 0
t3 = 0
t4 = 0
t5 = 0
t6 = 0
t7 = 0
t8 = 0
td1 = 0
td2 = 0
td3 = 0
td4 = 0
td5 = 0
td6 = 0
##########################################################################################################
#for time in range(1,(batch_num + 2*split - (rank + 1) -1 + 1)):
for step in range(1, steps + 1):
#off = (step-1)*lamda
#for time in range(off+1 , off+lamda + delay ):
#cv.acquire()
#cv.wait()
#cv.release()
#cv.sync(rank)
lamda = lamda_back
if step == steps:
lamda = batch_num - (step - 1) * lamda
#print(rank,'steps',steps,'step',step,'lamda',lamda)
for time in range(1, lamda + delay + 1):
#if time <= off + lamda: # k = 2 ; t >= k
if time <= lamda: # k = 2 ; t >= k
t1 = timestamp()
x = feed_q1.recv()
x = x.cuda(rank, non_blocking=True)
#print('recv',x)
t2 = timestamp()
input_feat = Variable(x, requires_grad=True)
#input_feat = input_feat.to("cuda:1")
model_idx = (time % num_of_models) - 1
output = models[model_idx].forward(input_feat)
inputs[model_idx] = input_feat
outputs[model_idx] = output
t3 = timestamp()
feed_q2.send_wait()
send_output.copy_(output.data)
feed_q2.async_send_signal()
t += 1
t4 = timestamp()
#pg = grad_q2.get()
#if len(pg) > 0:
#if time > delay: # t-(2K-k-1)
if time > delay: # t-(2K-k-1)
t5 = timestamp()
pg = grad_q2.recv()
pg = pg.cuda(rank)
t6 = timestamp()
output_idx = ((time - delay) % num_of_models) - 1
optimizer = optim[output_idx]
optimizer.zero_grad()
output = outputs[output_idx]
output.backward(pg)
#outputs[output_idx].backward(pg)
#a = list(models[output_idx].parameters())[0].clone()
optimizer.step()
t7 = timestamp()
#outputs[output_idx].backward(pg)
#b = list(models[output_idx].parameters())[0].clone()
#print(torch.equal(a.data,b.data))
#grad = inputs[output_idx].grad.data.to('cpu')
grad_q1.send_wait()
send_grad.copy_(inputs[output_idx].grad.data)
#grad = pg
grad_q1.async_send_signal()
t8 = timestamp()
#outputs[output_idx].backward(pg)
td1 += t2 - t1
td2 += t3 - t2
td3 += t4 - t3
td4 += t6 - t5
td5 += t7 - t6
td6 += t8 - t7
###############################################################################################################
#feed_q2.init()
#grad_q2.init()
#print(time)
model.init_zero()
with torch.cuda.device(rank):
for i in range(num_of_models):
j = models[i].parameters()
for k in model.parameters():
#k = 0
l = j.__next__()
k.requires_grad_(False)
k.copy_(k.data + l.data / num_of_models)
for i in range(num_of_models):
j = model.parameters()
for k in models[i].parameters():
l = j.__next__()
k.requires_grad_(False)
k.copy_(l.data)
k.requires_grad_(True)
#print('average_done')
e_t_u = resource_usage(RUSAGE_SELF)
e_t = timestamp()
u_t = e_t_u.ru_stime - s_t_u.ru_stime
t = e_t - s_t
time_tot = time_tot + t
#print('node2 user time = %f time = %f tot_time = %f' % ( u_t , t, time_tot))
#print(prof)
print('rank =', rank, 'recv output =', td1)
print('rank =', rank, 'forward =', td2)
print('rank =', rank, 'send output', td3)
print('rank =', rank, 'recv grad =', td4)
print('rank =', rank, 'backward =', td5)
print('rank =', rank, 'send grad =', td6)
model.eval()
for i in models:
i.eval()
#for data,target in test_loader:
for i in range(test_batch_num):
x = feed_test.recv()
x = x.cuda(rank)
output = model.forward(x)
#output = output.to('cpu')
feed_test2.send(output.data.to('cpu'))
if epoch == 150 or epoch == 225:
lr = lr * 0.1
for i in optim:
for j in i.param_groups:
j['lr'] = lr
def generate_models(self, queue=None, output_fits=True):
""" gblend.generate_models( queue=None, output_fits=True )
Generate all the high resolution models used in the fitting process.
The high resolution catalog must be set before models can be generated.
If output_fits = True then a fits file will be generated with the inital models. This will be created in the model_dir.
queue is used to return models when run in parallel mode. """
if not self.hres_loaded:
raise ValueError(
'You must set the high resolution catalog with gblend.set_hres_catalog() before generating models!'
)
imgs = []
# loop through high resolution models
for (i, model_obj) in enumerate(self):
# catch any and all errors
try:
# generate models
model_obj.generate_model(
self.pad, (self.ny, self.nx),
self.psf.copy(),
use_integration=self.config['use_integration'])
# the rest is for outputting fits files of input models - skip if output_fits==False
if not output_fits: continue
# generate extension for outputting to fits
imgs.append(pyfits.ImageHDU(model_obj.model_img.copy()))
# add to complete model
if i == 0:
full_model = model_obj.model_img.copy()
else:
full_model += model_obj.model_img.copy()
except KeyboardInterrupt:
raise
except:
# on exception return the traceback string. Also return the traceback string to the queue if was passed
trace = traceback.format_exc()
if queue is not None: queue.put((self.number, trace))
return trace
# output a fits file for the full model and individual models
if output_fits:
# prepare hdulist
hdus = [pyfits.PrimaryHDU(full_model)]
hdus.extend(imgs)
hdulist = pyfits.HDUList(hdus)
# write out file - delete first
file = '%s%d_input.fits' % (self.config['model_dir'], self.number)
if os.path.isfile(file): os.remove(file)
hdulist.writeto(file)
# if queue is not None, then it is an ouput queue used to return the models to pygfit when running in parallel mode
# that means I have to fetch the model from every model object and return them through the queue.
# whatever I set in the queue will be passed back through gblend.set_models()
if queue is not None:
models = []
for model_obj in self:
models.append(model_obj.model_img)
# and send it off!
queue.put((self.number, models))
# now we are ready for fitting!
self.ready = True
return True
if model_type == 'rf':
m = RandomForestRegressor(n_estimators=100, random_state=1)
elif model_type == 'dt':
m = DecisionTreeRegressor()
elif model_type == 'linear':
m = LinearRegression()
elif model_type == 'ridge':
m = RidgeCV()
elif model_type == 'svm':
m = SVR(gamma='scale')
elif model_type == 'gb':
m = GradientBoostingRegressor(random_state=1)
for feat_set in ['basic', 'dasc']:
models.append(f'{model_type}_{feat_set}')
if feat_set == 'basic':
feat_set = feat_names[1:]
elif feat_set == 'dasc':
feat_set = ['X_d1', 'X_d2', 'X_d3']
m.fit(df_full[feat_set], df_full['Y_sig_mean_normalized'].values)
for i, (k, v) in enumerate(ds.keys()):
if v == 'test':
df = ds[(k, v)]
#if k == 'clath_aux+gak_a7d2_new':
# df = df.dropna()
X = df[feat_set]
X = X.fillna(X.mean())
#y = df['Y_sig_mean_normalized']
def output_layer(sh_list, sh_test, sh_c_list, shm_list, train_loader,
test_loader, model, loss_function, rank, split, batch_size,
batch_num, test_batch_num, test_num, epoch_num, lamda, lr,
cv):
feed_q2 = sh_list[rank - 1]
grad_q2 = sh_list[rank + split - 2]
send_grad = sh_c_list[rank + split - 2]
feed_test = sh_test[rank - 1]
send_target = shm_list[0]
start = torch.cuda.Event(enable_timing=True)
end = torch.cuda.Event(enable_timing=True)
models = []
outputs = []
inputs = []
optim = []
loss_tot = 0
time_tot = 0
cuda_time = 0
#test_num = test_set_labels.size(0)
#num_of_models = 1#2*n + 1
n = -1 * (rank - (split - 1))
#num_of_models = 2*split - 1
num_of_models = split
#delay = n *(2)# + 1
#delay = 2* split -(rank+1) #- 1
delay = n
#model.reset_parameters()
for i in range(num_of_models):
models.append(copy.deepcopy(model))
outputs.append(0)
inputs.append(0)
optim.append(
torch.optim.SGD(models[i].parameters(),
lr=lr,
momentum=0.9,
weight_decay=0.0005,
nesterov=True))
#optim.append(torch.optim.Adam(models[i].parameters(),lr=1e-4))
#optim.append(torch.optim.SGD(models[i].parameters(),lr=lr))
for i in models:
i.cuda(rank)
model.cuda(rank)
#labels = data_set[:,-mnist_data.NUM_LABELS:].cuda(rank) ######### if have a error, cuda(rank) add
steps = int(batch_num / lamda)
if batch_num % lamda != 0:
steps += 1
lamda_back = lamda
t = 0
for epoch in range(epoch_num):
#with torch.autograd.profiler.profile() as prof:
s_t_u = resource_usage(RUSAGE_SELF)
s_t = timestamp()
start.record()
loss_sum = 0
model.train()
t = 0
t1 = 0
t2 = 0
t3 = 0
t4 = 0
t5 = 0
t6 = 0
t7 = 0
t8 = 0
td1 = 0
td2 = 0
td3 = 0
td4 = 0
td5 = 0
td6 = 0
train_data = train_loader.__iter__()
#for time in range(1,(batch_num + 2*split - (rank+1) -1 + 1 )):
for step in range(1, steps + 1):
#for time in range(step , step+lamda + 2*split -(rank+1)- 1 + 1 ):
#off = (step-1)*lamda
#cv.acquire()
#cv.wait()
#cv.notify_all()
#cv.release()
#cv.sync(rank)
lamda = lamda_back
if step == steps:
lamda = batch_num - (step - 1) * lamda
#print(rank,'steps',steps,'step',step,'lamda',lamda)
#print('sync',step,steps)
for time in range(1, lamda + 1):
#if time >= (rank +) : # t >= k ; k = 3
t1 = timestamp()
# recv output
offset = t * batch_size
#data,target = next(train_data)
#offset = (time - 1) * batch_size
x = feed_q2.recv()
x = x.cuda(rank, non_blocking=True)
#print('recv',t,x)
# label gpu load
#data,target = next(train_data)
#target = target.cuda(rank).long()
target = send_target.recv()
target = target.cuda(rank, non_blocking=True).long()
#target = Variable(labels[offset:offset + batch_size,:]).long()
#target = Variable(labels[offset:offset + batch_size,:]).cuda(rank)
t2 = timestamp()
model_idx = (
time % num_of_models
) - 1 ########################################### model idx correct
#model_idx = 0
input_feat = Variable(x, requires_grad=True)
output = models[model_idx].forward(input_feat)
#print('rank',rank,time,target)
#print(target.size())
loss = loss_function(output, target)
t3 = timestamp()
#loss = loss_function(output,torch.max(target,1)[1])
optimizer = optim[model_idx]
optimizer.zero_grad()
loss.backward()
#a = list(models[model_idx].parameters())[0].clone()
optimizer.step()
t4 = timestamp()
#b = list(models[model_idx].parameters())[0].clone()
#print(torch.equal(a.data,b.data))
#grad = input_feat.grad.data.to('cpu')
grad_q2.send_wait()
send_grad.copy_(input_feat.grad.data)
grad_q2.async_send_signal()
t5 = timestamp()
loss_sum = loss_sum + loss.data
t += 1
td1 += t2 - t1
td2 += t3 - t2
td3 += t4 - t3
td4 += t5 - t4
#print(time)
model.init_zero()
with torch.cuda.device(rank):
for i in range(num_of_models):
j = models[i].parameters()
for k in model.parameters():
#k = 0
l = j.__next__()
k.requires_grad_(False)
k.copy_(k.data + l.data / num_of_models)
for i in range(num_of_models):
j = model.parameters()
for k in models[i].parameters():
l = j.__next__()
k.requires_grad_(False)
k.copy_(l.data)
k.requires_grad_(True)
loss_tot = loss_sum / batch_num
e_t_u = resource_usage(RUSAGE_SELF)
e_t = timestamp()
u_t = e_t_u.ru_stime - s_t_u.ru_stime
t = e_t - s_t
end.record()
torch.cuda.synchronize()
cuda_time = cuda_time + start.elapsed_time(end)
print(
'node3 user time = %f time = %f cuda time = %f cuda tot time = %f loss_tot = %f'
% (u_t, t, start.elapsed_time(end), cuda_time, loss_tot))
#print('node3 user time = %f time = %f loss_tot = %f' % ( u_t , t,loss_tot))
#print(prof)
time_tot = time_tot + t
print('rank =', rank, 'recv output =', td1)
print('rank =', rank, 'forward =', td2)
print('rank =', rank, 'backward =', td3)
print('rank =', rank, 'send grad =', td4)
model.eval()
total = 0
correct = 0
dev_loss_tot = 0
for data, target in test_loader:
#for i in range(test_batch_num) :
offset = i * batch_size #####################################
#print('rank',rank,i,target)
x = feed_test.recv()
#print(x)
x = x.cuda(rank)
target = target.cuda(rank)
#target = Variable(test_set_labels[offset:offset+batch_size,:]).long()
#target = Variable(test_set_labels[offset:offset+batch_size,:])
output = model.forward(x)
_, pred = torch.max(output.data, 1)
#dev_loss = loss_function(output,torch.max(target,1)[1])
dev_loss = loss_function(output, target)
dev_loss_tot += dev_loss.item()
#print('rank',rank,i,pred)
#print(target,pred)
#total += target.size(0)
#print(total)
#correct += (pred == torch.max(target,1)[1]).sum()
correct += (pred == target).sum()
#print('correct',correct)
#i += 1
print('epoch=', epoch, 'tot_time =', time_tot, 'accuracy =',
(100 * correct / test_num), 'test_loss',
dev_loss_tot / test_batch_num)
if epoch == 150 or epoch == 225:
lr = lr * 0.1
for i in optim:
for j in i.param_groups:
j['lr'] = lr
def find_best_segmentation(model_funct,
folder,
validation_frac,
metric="choose",
raw_vol=raw,
gt_vol=gt,
aff_vol=aff,
top_n_valid=3,
gpus=1):
l = custom_loss.loss()
weights = np.zeros((3, 2))
weights[0] = [2.6960856, 0.61383891]
weights[1] = [4.05724285, 0.57027915]
weights[2] = [4.09752934, 0.56949214]
models = []
model_keys = []
print("\nGrabbing models...\n")
for file in os.listdir(folder):
model = model_funct(verbose=0)
try:
model.load_weights(folder + "/" + file)
models.append(model)
model_keys.append(file)
except OSError:
print("\n%s is invalid\n" % file)
continue
print("\nLoaded %i models.\n" % len(models))
for key in model_keys:
print("\t" + key)
proc = process.process(l.weighted_cross,
raw_vol,
gt_vol,
aff_vol,
model=models[0],
validation_frac=validation_frac,
gpus=gpus)
valid_loss = []
print("\nGetting validation loss for all models...\n")
for model in models:
proc.model = model
valid_loss.append(proc.calc_validation_loss())
top_models = []
top_model_keys = []
top_indexs = np.asarray(valid_loss).argsort()[-top_n_valid:][::-1]
for index in top_indexs:
top_models.append(models[index])
top_model_keys.append(model_keys[index])
print("\nFound top %i models.\n" % top_n_valid)
for key in top_model_keys:
print("\t%s" % key)
print("\nWatershed sweep...\n")
segs, metrics = predict_and_watershed_on_list_of_models(top_models,
metric=metric)
if metric != "choose":
index = np.where(metrics == np.max(metrics))
index = index[0]
print("BEST PERFORMANCE WAS =" + str(np.max(metrics)))
seg = segs[int(index)]
else:
n = 0
for metric in metrics:
print("\tSegmentation %i: " % n)
print("\t\tSplit: " + str(metric[0]))
print("\t\tMerge: " + str(metric[1]))
n += 1
index = input("\n\nWhich model?")
seg = segs[int(index)]
model_key = top_model_keys[math.floor(
(int(index) / len(segs)) * len(top_models))]
print("Model %s is the choice" % model_key)
save_segmentation_tifs(gt_vol, seg)
def parse_args_and_settings():
parser = argparse.ArgumentParser()
parser.add_argument(
"-p",
"--phase",
default=None,
help=
"can be train, deploy (by default includes evaluate) or evaluate. Automatically inferred if not specified."
)
# Only for training:
# TODO @Future Make parser give warnings when wrong combination of arguments is given (standard feature of argparse perhaps?)
parser.add_argument(
"-c",
"--conf_file",
default=None,
help=
"Path to config file including .ini; can be left None only in deploy/evaluation, in which case it is derived from model/answers path.",
metavar="FILE")
parser.add_argument(
"-r",
"--random",
action=
'store_true', # Note: also kinda used, but overwritten, during deploy/evaluate
help="To sample values randomly from intervals in config file.")
parser.add_argument(
"-d",
"--subdir",
default=None, # Note: also used, but overwritten, during deploy
help=
"(training phase) use /models/<subdir> for output; by default set to year_month."
)
parser.add_argument(
"-n",
"--run_name",
default=None, # Note: also used, but overwritten, during deploy/evaluate
help=
"(training phase) by default set to time stamp; always automatically appended by randomly sampled params."
)
# For deployment/evaluation:
parser.add_argument(
"-t",
"--deploy_data",
default=None,
help=
"Default is data on which the model was trained; can be 'train', 'test' or 'trial', abbreviations as defined in config_utils. During evaluation this can be omitted: it will be read from the predictions .csv file."
)
parser.add_argument(
"-l",
"--deploy_level",
default=None,
help=
"Scene or episode; default is the level on which the model was trained. During evaluation this can be omitted: it will be read from the predictions .csv file."
)
# Only for deployment
parser.add_argument(
"-m",
"--model",
default=None,
help=
"(deployment phase) path to model, with base name (though without .pt suffix); if fold number is included, only that fold is considered."
)
parser.add_argument(
"--answers_per_fold",
action='store_true',
help=
"To write an answers.txt file for each fold separately (in addition to their merger)."
)
parser.add_argument(
"--no_cv",
action='store_true',
help=
"Option to prevent respecting cross-validation (which is done by default when deployed on training data)."
)
parser.add_argument(
"-s",
"--no_eval",
action='store_true',
help=
"If data includes keys, evaluation phase is run automatically after deployment; this option prevents that."
)
# Only for evaluation
parser.add_argument(
"-a",
"--answer_file",
default=None,
help="Evaluates an answer file, outputting interesting statistics.")
parser.add_argument(
"--no_semeval",
action='store_true',
help=
"To turn off the SemEval filter for evaluation (filter which groups infrequent (< 3) entities together as 'other')."
)
# Meta:
parser.add_argument(
"--no_cuda",
action='store_true',
help="Forces not using cuda; otherwise cuda is used whenever available."
)
parser.add_argument(
"-v",
"--verbosity",
type=int,
default=3,
help=
"Sets verbosity regarding console output (default 3; lower to print less)."
)
parser.add_argument(
"-f",
"--no_files",
action='store_true',
help="Prevents generation of folders and files (log, model, answer).")
args = parser.parse_args()
# If phase is not specified, this can usually be inferred from other arguments:
if args.phase is None:
if args.model is not None:
args.phase = 'deploy'
elif args.answer_file is not None:
args.phase = 'evaluate'
else:
args.phase = 'train'
# Use CUDA only if available:
if not args.no_cuda and not torch.cuda.is_available:
print(
'WARNING: CUDA requested but unavailable; running on cpu instead.')
args.no_cuda = True
# Deploy either a single model or a set of models (of the same type).
# Also, from the model file arg.model also extract model_dir and run_name:
if args.phase == 'deploy':
if '.pt' in args.model:
# A single model file .pt was provided, so deploy only on that:
runs_path, args.run_name = os.path.split(args.model)
args.model_dir, args.subdir = os.path.split(runs_path)
args.run_name = args.run_name[:-3] # removes the .pt
if '--fold' in args.run_name:
args.run_name = args.run_name.split('--fold')[0]
args.model = [args.model]
else:
# model name doesn't contain .pt (i.e., either directory, or directory+run_name:
if os.path.isdir(args.model):
# model is a directory
runs_path = args.model
args.run_name = None # To be extracted below
else:
# model is not a directory, nor .pt; hence only run_name of model is given:
runs_path, args.run_name = os.path.split(args.model)
args.model_dir, args.subdir = os.path.split(runs_path)
# Get all model paths from directory (with run_name):
models = []
for file in os.listdir(runs_path):
if file.endswith(".pt"):
if args.run_name is None:
args.run_name = file[:-3] # removes the .pt
if '--fold' in args.run_name:
args.run_name = args.run_name.split('--fold')[0]
if file.startswith(args.run_name):
models.append(os.path.join(runs_path, file))
elif os.path.isdir(args.model):
print(
"ERROR: run_name could not be inferred; directory contains multiple runs.\n Rerun with more specific --model (i.e., including model file name, minus .pt and minus --fold#)."
)
quit()
args.model = sorted(models)
# When evaluating, obtain run name etcetera from the provided answers .csv file:
if args.phase == 'evaluate':
args.run_name = os.path.basename(args.answer_file)[:-4]
if args.run_name.endswith('--ensemble'):
args.run_name = args.run_name[:
-10] # removes the --ensemble suffix
if '--fold' in args.run_name:
args.run_name = args.run_name.split('--fold')[0]
if '--cv' in args.run_name:
args.run_name = args.run_name.split('--cv')[0]
args.model_dir = None # This is kinda ugly.
# For train phase a config file is mandatory; otherwise it can be automatically obtained:
if args.conf_file is None:
if args.phase == 'train':
print(
'ERROR: training requires a config file (try including -c config.ini)'
)
quit()
elif args.phase == 'deploy':
args.conf_file = os.path.join(runs_path, args.run_name + '.ini')
elif args.phase == 'evaluate':
args.conf_file = os.path.join(os.path.dirname(args.answer_file),
args.run_name + '.ini')
# Read the config file (either given as argument, or obtained from pre-trained model or its predictions file:
if args.phase == 'deploy' or args.phase == 'evaluate':
# Of course don't randomly sample when deploying or evaluating.
args.random = False
settings, fixed_params, sampled_params = config_utils.settings_from_config(
args.conf_file, args.random)
# NOTE: Which params were fixed or sampled determines the subdir and run_name in case of training.
# If no level and data for deployment are given, these are taken from training data/level in config file
if args.phase == 'deploy':
args.deploy_level = args.deploy_level or settings.data.level
args.deploy_data = args.deploy_data or settings.data.dataset
if args.deploy_data in config_utils.data_paths:
args.deploy_data = config_utils.data_paths[args.deploy_data][
args.deploy_level]
# For evaluate, if deploy_data is not provided, attempt to read it from the answer_file:
# (The alternative, of reading it from directory structure, seems too unsafe.)
if args.phase == 'evaluate' and args.deploy_data is None:
with open(args.answer_file) as file:
firstline = file.readline()
if firstline.startswith('#'):
args.deploy_data = firstline.strip('# \n')
# When deploying on a new dataset (not training data), cross-validation doesn't apply:
if args.deploy_data != settings.data.dataset:
args.no_cv = True
# When training, create runs dir, id and run name if none were given (mostly time stamps).
if args.phase == 'train':
args.model_dir = 'models' # Default for training output.
args.subdir = args.subdir or time.strftime("%Y_%m")
args.run_name = args.run_name or time.strftime("%Y_%m_%d_%H_%M_%S")
if not sampled_params:
args.run_name = 'fixed--' + args.run_name
else:
# TODO @Future: Automatic run naming can be considerably improved wrt. readability.
sampled_params_strings = sorted([
k[0:3] + "--" + str(sampled_params[k])[0:5].replace(",", "-")
for k in sampled_params
])
args.run_name = '{0}--{1}'.format(
args.run_name, "--".join(sampled_params_strings))
# Within the settings Namespace, which is subject to overwriting, make sure to include a backup,
# so that original settings can at any time be saved to a new config file.
settings.orig = copy.deepcopy(settings)
print('--------------Setttings---------------------')
print('[phase] ', args.phase)
print('[deploy_data] ', args.deploy_data)
print('[settings.data.datasets] ', settings.data.dataset)
print('--------------------------------------------')
return args, settings
def compile_all_results(scenarios, dir='../data'):
"""
Compiles the results across multiple scenarios produced by running run_on_cluster on each
one into a single sv file. The specified directory must be where where the results of
running run_on_cluster for each scenario are stored (each is a sub-directory named v0, v1, etc.)
and is also where the output from this function will be saved.
"""
models = []
causes = []
time = []
true_cf = []
true_std = []
std_bias = []
mean_abs_err = []
median_abs_err = []
mean_rel_err = []
median_rel_err = []
mean_csmf_accuracy = []
median_csmf_accuracy = []
mean_coverage_bycause = []
mean_coverage = []
percent_total_coverage = []
scenario = []
for i in range(scenarios):
for j in ['bad_model', 'latent_simplex']:
read = csv.reader(open('%s/v%s/%s_summary.csv' % (dir, i, j)))
read.next()
for row in read:
models.append(row[0])
causes.append(row[1])
time.append(row[2])
true_cf.append(row[3])
true_std.append(row[4])
std_bias.append(row[5])
mean_abs_err.append(row[6])
median_abs_err.append(row[7])
mean_rel_err.append(row[8])
median_rel_err.append(row[9])
mean_csmf_accuracy.append(row[10])
median_csmf_accuracy.append(row[11])
mean_coverage_bycause.append(row[12])
mean_coverage.append(row[13])
percent_total_coverage.append(row[14])
scenario.append(i)
all = pl.np.core.records.fromarrays(
[
scenario, models, time, true_cf, true_std, causes, mean_abs_err,
median_abs_err, mean_rel_err, median_rel_err, mean_csmf_accuracy,
median_csmf_accuracy, mean_coverage_bycause, mean_coverage,
percent_total_coverage
],
names=[
'scenario', 'model', 'time', 'true_cf', 'true_std', 'cause',
'mean_abs_err', 'median_abs_err', 'mean_rel_err', 'median_rel_err',
'mean_csmf_accuracy', 'median_csmf_accuracy',
'mean_covearge_bycause', 'mean_coverage', 'percent_total_coverage'
])
pl.rec2csv(all, fname='%s/all_summary_metrics.csv' % (dir))
