def main():
exitStatus = 0
try:
get_results.get_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
find_latest_results.find_latest_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
update_results.update_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
upload_results.upload_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
purge_results.purge_results()
except Exception as e:
logging.error(e)
exitStatus = 5
sys.exit(exitStatus)
def main():
exitStatus = 0
try:
get_results.get_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
find_latest_results.find_latest_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
update_results.update_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
upload_results.upload_results()
except Exception as e:
logging.error(e)
exitStatus = 1
try:
purge_results.purge_results()
except Exception as e:
logging.error(e)
exitStatus = 5
sys.exit(exitStatus)
def gen_outcomes():
"""
Generate all outcomes possible
"""
base_teams = get_survivors()
twoexp = len(base_teams) - 1
base_peeps = readm()
retv = {}
base_results = get_results()
pinfo = scorem(base_results, base_peeps)
for group in pinfo:
retv[group] = {}
for indx in range(0, 2**twoexp):
picks = gen_future(indx, twoexp, base_teams)
temp_res = copy.deepcopy(base_results)
rslts = loc_update(temp_res, picks)
pinfo = scorem(rslts, base_peeps)
for group in pinfo:
prev = 0
wlist = []
for bracket in pinfo[group]:
if bracket['score'] < prev:
break
wlist.append(bracket['name'])
prev = bracket['score']
if indx % 100 == 0:
print(indx)
for name in wlist:
if name not in retv[group]:
retv[group][name] = []
retv[group][name].append(0)
retv[group][name].append(gen_histo(twoexp))
retv[group][name][0] += 1 / len(wlist)
retv[group][name][1] = gupdate(retv[group][name][1], indx)
return retv
def download_day_source(source_name, date, source_day_total, authToken):
iter_list = construct_page_list(source_day_total)
results_list = []
# if source_day_total is 0, just pass?
for p in iter_list:
t = get_results(source_name, date, p[0], p[1], authToken)
results_list.append(t.text)
output_list = [] # keep outside the iter
junk_list = []
for t in results_list:
soup = BeautifulSoup(t)
for num, i in enumerate(soup.findAll("ns1:document")):
try:
t = i.text
# try:
d = extract_from_b64(t)
output_list.append(d)
except:
junk_list.append(t) # error handling ¯\_(ツ)_/¯
if junk_list:
print "There were problems getting text from the base 64 in download_day_source. {0}".format(
len(junk_list))
output = {"stories": output_list, "junk": junk_list}
return output
def get_source_day_total(source_name, date, authToken):
try:
t = get_results(source_name, date, 1, 10, authToken)
if t.status_code == 500:
#print "There was an error. Check the log file"
print "Error 500 from server on getting source-day total for {0} on {1}: {2}".format(
source_name, date, t.text)
return 0
c = re.findall('">(\d+?)</ns3:documentsFound', t.text)
if c != []:
try:
c_int = int(c[0])
except TypeError as e:
c_int = 0
print "Error for {0}, {1}: {2}".format(source_name, date, e)
return c_int
else:
print "In get_source_day_total, couldn't find total documents: {0}".format(
t.text)
return 0
except Exception as e:
print "Problem getting total for {0}, {1}: {2}".format(
source_name, date, e)
return 0
def download_day_source(source_name, date, source_day_total, authToken):
iter_list = construct_page_list(source_day_total)
results_list = []
# if source_day_total is 0, just pass?
for p in iter_list:
t = get_results(source_name, date, p[0], p[1], authToken)
results_list.append(t.text)
output_list = [] # keep outside the iter
junk_list = []
for t in results_list:
soup = BeautifulSoup(t)
for num, i in enumerate(soup.findAll("ns1:document")):
try:
t = i.text
# try:
d = extract_from_b64(t)
output_list.append(d)
except:
junk_list.append(t) # error handling ¯\_(ツ)_/¯
if junk_list:
print "There were problems getting text from the base 64 in download_day_source. {0}".format(len(junk_list))
output = {"stories" : output_list,
"junk" : junk_list}
return output
def main(args): file = args[0] M = read_input(file) k = int(args[1]) D = generate_solution(M,k) rgb.write_partitions(D,'random_player_solution.png') R = gr.get_results(D,M,k) rgb.write_results(R,'random_player_results.png')
def test_things():
"""
Run scorem and display the results
"""
results = scorem(get_results(), readm())
for group in results:
print(group)
for bracket in results[group]:
print(bracket['name'], bracket['score'], bracket['best_poss'])
def recover(self):
try:
files = self.download_state()
if not files:
pass
else:
for job in files:
job.update()
self.text_box.config(state=NORMAL)
self.text_box.insert(
END, "Watching for results... (" +
datetime.now().strftime('%Y-%m-%d %H:%M:%S') + ')\n',
"cool")
self.text_box.see(END)
self.text_box.config(state=DISABLED)
self.text_box.update()
self.state = job.isDone()
if self.state:
get_results(self, job)
except IndexError:
pass
self.master.after(900000, self.recover)
def get_source_day_total(source_name, date, authToken):
try:
t = get_results(source_name, date, 1, 10, authToken)
if t.status_code == 500:
#print "There was an error. Check the log file"
print "Error 500 from server on getting source-day total for {0} on {1}: {2}".format(source_name, date, t.text)
return 0
c = re.findall('">(\d+?)</ns3:documentsFound', t.text)
if c != []:
try:
c_int = int(c[0])
except TypeError as e:
c_int = 0
print "Error for {0}, {1}: {2}".format(source_name, date, e)
return c_int
else:
print "In get_source_day_total, couldn't find total documents: {0}".format(t.text)
return 0
except Exception as e:
print "Problem getting total for {0}, {1}: {2}".format(source_name, date, e)
return 0
def dockit_vina(verbose, reset, minimization):
path = os.path.dirname(os.path.realpath(__file__))
logger = AppLogger.get(__name__,
os.path.join(path, 'dockit.logs'),
stream_level=logging.INFO)
app_dir = os.path.dirname(os.path.abspath(__file__))
root_dir, app = os.path.split(app_dir)
if verbose:
stdout = None
logger.info('Verbose=True. Set to False to silence console messages')
else:
stdout = open(os.devnull, 'w')
if reset:
logger.info('Resetting to pre-run state')
reset_(root_dir)
sys.exit()
logger.info('Creating ligands and targets directories')
ligands_dir = os.path.join(root_dir, 'ligands', 'PDB')
if not os.path.exists(ligands_dir):
os.makedirs(ligands_dir)
targets_dir = os.path.join(root_dir, 'targets', 'PDB')
if not os.path.exists(targets_dir):
os.makedirs(targets_dir)
logger.info('Checking for files in targets and ligands folders')
if len([
protein for protein in os.listdir(targets_dir)
if protein.lower().endswith('.pdb')
]) == 0:
logger.error(
'Failed to find PDB files in {0} directory'.format(targets_dir))
sys.exit()
if len([
ligand for ligand in os.listdir(ligands_dir)
if ligand.lower().endswith('.pdb')
]) == 0:
logger.error(
'Failed to find PDB files in {0} directory'.format(ligands_dir))
sys.exit()
logger.info('Checking input file formats')
for protein in os.listdir(targets_dir):
if protein.lower().endswith('.pdb') and not parse_pdb(
os.path.join(targets_dir, protein)):
logger.error('File {0} not in PDB format'.format(protein))
sys.exit()
for ligand in os.listdir(ligands_dir):
if ligand.lower().endswith('.pdb') and not parse_pdb(
os.path.join(ligands_dir, ligand)):
logger.error('File not in PDB format {0}'.format(ligand))
sys.exit()
# NOTE: sometimes the prepare_ligand will fail if pwd is not ligand PDB folder
os.chdir(ligands_dir)
if minimization is True:
logger.info('Minimizing ligands with obminimize')
try:
for ligand in os.listdir(ligands_dir):
subprocess.Popen(
'obminimize -o pdb {0} > min_{0}'.format(ligand),
shell=True,
stdout=stdout).wait()
os.remove(ligand)
os.rename('min_' + ligand, ligand)
except Exception as e:
logger.error('Failed to minimize ligands')
logger.debug('Creating ligand PDBQT dir')
ligands_pdbqt_dir = os.path.join(root_dir, 'ligands', 'PDBQT')
if not os.path.exists(ligands_pdbqt_dir):
os.makedirs(ligands_pdbqt_dir)
logger.info('Converting ligands to PDBQT')
for ligand in os.listdir(ligands_dir):
if not ligand.lower().endswith('.pdb'):
continue
subprocess.Popen('{0} -l {1} -o {2} -A hydrogens -U nphs -v'.format(
os.path.join(app_dir, 'prepare_ligand4.py'), ligand,
os.path.join(
ligands_pdbqt_dir,
ligand.replace('pdb', 'pdbqt').replace('.PDB', '.pdbqt'))),
shell=True,
stdout=stdout).wait()
logger.debug('Creating target PDBQT dir')
targets_pdbqt_dir = os.path.join(root_dir, 'targets', 'PDBQT')
if not os.path.exists(targets_pdbqt_dir):
os.makedirs(targets_pdbqt_dir)
logger.info('Converting targets to PDBQT')
os.chdir(targets_dir)
for target in os.listdir(targets_dir):
if not target.lower().endswith('.pdb'):
continue
subprocess.Popen(
'{0} -r {1} -o {2} -A checkhydrogens -U nphs -v'.format(
os.path.join(app_dir, 'prepare_receptor4.py'), target,
os.path.join(
targets_pdbqt_dir,
target.replace('pdb', 'pdbqt').replace('.PDB', '.pdbqt'))),
shell=True,
stdout=stdout).wait()
logger.debug('Creating results folder')
results_dir = os.path.join(root_dir, 'results')
if not os.path.exists(results_dir):
os.makedirs(results_dir)
logger.debug('Reading dockit_param.csv')
param_dir = os.path.join(root_dir, 'dockit_param.csv')
param_dict = parse_param_csv(param_dir)
logger.debug('Checking if targets in param file exist')
for index, row in param_dict.items():
if row['target'] not in [
i.rstrip('.pdbqt') for i in os.listdir(targets_pdbqt_dir)
]:
raise ValueError('{} does not exist'.format(row['target']))
logger.info('Creating docking config files and initiating docking')
for index, row in param_dict.items():
for ligand in os.listdir(ligands_pdbqt_dir):
if not ligand.endswith('.pdbqt'):
continue
ligand_name = ligand.rstrip('.pdbqt')
# creating a dir to store individual target results
tar_result_dir = os.path.join(results_dir, row['target'],
ligand_name)
if not os.path.exists(tar_result_dir):
os.makedirs(tar_result_dir)
flex_resi = None
if row['flex_resi'] not in ('0', '', 'None', ' '):
logger.info('Creating flexible residue PDBQT')
try:
subprocess.Popen(
'{0} -r {1} -s {2} -g {3} -x {4} -v'.format(
os.path.join(app_dir, 'prepare_flexreceptor4.py'),
os.path.join(targets_pdbqt_dir,
row['target'] + '.pdbqt'),
row['flex_resi'],
os.path.join(targets_pdbqt_dir,
row['target'] + '.pdbqt'),
os.path.join(
targets_pdbqt_dir,
row['target'] + row['flex_resi'] + '.pdbqt')),
shell=True,
stdout=stdout).wait()
flex_resi = os.path.join(
targets_pdbqt_dir,
row['target'] + row['flex_resi'] + '.pdbqt')
except Exception as e:
logger.warning(
'Failed to assign flexible residues. Skipping')
flex_resi = None
if not os.path.isfile(flex_resi):
logger.warning(
'Failed to assign flexible residues. Skipping')
flex_resi = None
engine = os.path.split(row['engine'])[-1]
config_dir = os.path.join(
tar_result_dir,
'{0}_config_{1}-{2}.txt'.format(engine, row['target'],
ligand_name))
logger.debug('Creating config file')
vina_config(config_dir,
targets_pdbqt_dir,
ligands_pdbqt_dir,
tar_result_dir,
ligand,
row,
engine,
flex_resi=flex_resi)
logger.info('Docking {0} to {1} using {2}'.format(
ligand_name, row['target'], row['engine']))
vina_command = "{0} --config {1} > {2}.txt".format(
row['engine'], config_dir,
os.path.join(
tar_result_dir, engine + "_out_" + row['target'] + '-' +
ligand.rstrip('.pdbqt')))
def run_cmd(vina_command, shell, stdout):
subprocess.Popen(vina_command, shell=shell,
stdout=stdout).wait()
# creating a thread
t = threading.Thread(target=run_cmd,
args=(vina_command, True, stdout))
t.daemon = True
t.start()
# waiting for threads to finish
main_thread = threading.currentThread()
for t in threading.enumerate():
if t is main_thread:
continue
t.join()
logger.info('Parsing results and writting output as CSV')
get_results()
import pandas as pd from get_results import get_results #from predict_next_turn import predict_next_turn #from calc_stats import calc_stats #Import Current Results fileloc = 'D://Campeonato Brasileiro//resultados.txt' db_CB = get_results(fileloc) print(db_CB.head) #Generate Statistics #calc_stats() #Predict Next Turn #predict_next_turn()
import os
import sys
sys.path.append('/u/sciteam/gupta1/improving_genes/tools')
from get_results import get_results
numreplicates=10
numgenes=50
dataset_dir='/u/sciteam/gupta1/scratch/astra2_dataset'
models = ['model.200.10000000.0.0000001','model.200.2000000.0.0000001','model.200.500000.0.0000001']
parameters=['unimproved']
for i in range(1,numreplicates+1):
for midx in range(0,len(models)):
for p in parameters:
result_filepath=dataset_dir+'/'+models[midx]+'/'+str(i).zfill(2)+'/result_'+p+'.txt'
#if not os.path.isfile(result_filepath) :
if True:
print result_filepath," Not found"
rgenedir=dataset_dir+'/'+models[midx]+'/'+str(i).zfill(2)
reftreefilename='true_induced50.tree'
ogenedir=dataset_dir+'/'+models[midx]+'/'+str(i).zfill(2)
outputtreefilename='50t_50s_fasttree.tree'
outputfilename='/result_'+p+'.txt'
get_results(rgenedir, reftreefilename,ogenedir,outputtreefilename,numgenes,outputfilename)
from sacred.observers import FileStorageObserver
from get_results import get_results
from main_loop import ex
ex.observers.append(FileStorageObserver.create('cifar100_attention_runs'))
try:
get_results()
except:
print("No experiments have been done yet!")
ex.run()
get_results()
for position_embedding_version in ["rows_then_columns"]:
for segment_embedding_version in ["rows_columns"]:
get_results()
ex.run(config_updates={"position_embedding_version": position_embedding_version,
"segment_embedding_version": segment_embedding_version,
}
)
get_results()
# for n_heads in [1, 2, 4, 7]:
# for n_layers in [1, 2, 3, 4, 5]:
# ex.run(config_updates={"n_layers": n_layers,
# "n_heads": n_heads,
# }
# )
# get_results()
def dockit(verbose, reset, minimization):
path = os.path.dirname(os.path.realpath(__file__))
app_dir = os.path.dirname(os.path.abspath(__file__))
root_dir, app = os.path.split(app_dir)
if verbose:
stdout = None
logging.info('Verbose=True. Set to False to silence console messages')
else:
stdout = open(os.devnull, 'w')
if reset:
logging.info('Resetting to pre-run state')
reset_(root_dir)
sys.exit()
logging.debug('Reading dockit_param.csv')
param_dir = os.path.join(root_dir, 'dockit_param.csv')
param_dict = parse_param_csv(param_dir)
logging.info('Creating ligands directory')
ligands_dir = os.path.join(root_dir, 'ligands', 'PDB')
if not os.path.exists(ligands_dir):
os.makedirs(ligands_dir)
logging.info('Creating targets directory')
targets_dir = os.path.join(root_dir, 'targets', 'PDB')
if not os.path.exists(targets_dir):
os.makedirs(targets_dir)
logging.info('Checking for PDB files in targets and ligands folders')
if len([
protein for protein in os.listdir(targets_dir)
if protein.lower().endswith('.pdb')
]) == 0:
logging.error(
'Failed to find PDB files in {0} directory'.format(targets_dir))
sys.exit()
if len([
ligand for ligand in os.listdir(ligands_dir)
if ligand.lower().endswith('.pdb')
]) == 0:
logging.error(
'Failed to find PDB files in {0} directory'.format(ligands_dir))
sys.exit()
logging.info('Checking input files are in PDB format')
for protein in os.listdir(targets_dir):
if protein.lower().endswith('.pdb') and not parse_pdb(
os.path.join(targets_dir, protein)):
logging.error('File {0} not in PDB format'.format(protein))
sys.exit()
for ligand in os.listdir(ligands_dir):
if ligand.lower().endswith('.pdb') and not parse_pdb(
os.path.join(ligands_dir, ligand)):
logging.error('File not in PDB format {0}'.format(ligand))
sys.exit()
if minimization is True:
logging.info('Minimizing ligands with obminimize')
try:
for ligand in os.listdir(ligands_dir):
subprocess.Popen(
'obminimize -o pdb {0} > min_{0}'.format(ligand),
shell=True,
stdout=stdout).wait()
os.remove(ligand)
os.rename('min_' + ligand, ligand)
except Exception as e:
logging.error('Failed to minimize ligands')
dockit_vina(param_dict, root_dir, app_dir, ligands_dir, targets_dir,
stdout)
logging.info('Parsing results and writting output as CSV')
get_results()
def my_main(random_seed, lr, hidden_dim1, hidden_dim2, n_heads, n_layers,
n_epochs, batch_size, dropout, position_embedding_version,
segment_embedding_version, attention_version,
attention_indv_channels_merge_mode, use_cls):
# %% --------------------------------------- Set-Up ----------------------------------------------------------------
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
torch.manual_seed(random_seed)
np.random.seed(random_seed)
random.seed(random_seed)
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
N_CLASSES = 100
ONLY_BATCH_IN_GPU = True
COLOR = True
DATA_DIR = os.getcwd() + "/cifar-100-python/"
# %% -------------------------------------- Data Prep --------------------------------------------------------------
x_train, y_train = load_data(DATA_DIR + "train")
x_train, p_train, s_train, y_train = prep_data(
x_train, y_train, only_batch_in_gpu=ONLY_BATCH_IN_GPU, use_cls=use_cls)
x_test, y_test = load_data(DATA_DIR + "test")
x_test, p_test, s_test, y_test = prep_data(
x_test, y_test, only_batch_in_gpu=ONLY_BATCH_IN_GPU, use_cls=use_cls)
# %% -------------------------------------- Training Prep ----------------------------------------------------------
model = RowColumnAttention(COLOR, use_cls, x_train.shape[1], hidden_dim1,
hidden_dim2, n_layers, n_heads, N_CLASSES,
dropout, position_embedding_version,
segment_embedding_version, attention_version,
attention_indv_channels_merge_mode).to(device)
optimizer = torch.optim.Adam(model.parameters(), lr=lr)
criterion = nn.CrossEntropyLoss()
# %% -------------------------------------- Training Loop ----------------------------------------------------------
print(
"\n ------------ Doing run number {} with configuration ---------------"
.format(ex.current_run._id))
print(ex.current_run.config)
try: # Gets the best result so far, so that we only save the model if the result is better (test loss in this case)
get_results()
results_so_far = pd.read_excel(os.getcwd() + "/experiments.xlsx")
acc_test_best = min(results_so_far["test acc"].values)
except:
acc_test_best = 0
print("No results so far, will save the best model out of this run")
best_epoch, loss_best, acc_best = 0, 1000, 0
inds_list = list(range(len(x_train)))
print("Starting training loop...")
start = time()
for epoch in range(n_epochs):
random.shuffle(inds_list)
loss_train, train_steps = 0, 0
model.train()
total = len(x_train) // batch_size + 1
pred_labels, real_labels = [], [
] # Need to get the real labels because we are shuffling after each epoch
with tqdm(total=total, desc=f"Epoch {epoch}") as pbar:
for inds in [
inds_list[batch * batch_size:(batch + 1) * batch_size]
for batch in range(len(inds_list) // batch_size + 1)
]:
if not inds:
break
optimizer.zero_grad()
if ONLY_BATCH_IN_GPU:
logits = model(x_train[inds].to(device),
p_train[inds].to(device),
s_train[inds].to(device))
loss = criterion(logits, y_train[inds].to(device))
else:
logits = model(x_train[inds], p_train[inds], s_train[inds])
loss = criterion(logits, y_train[inds])
loss.backward()
optimizer.step()
loss_train += loss.item()
train_steps += 1
pbar.update(1)
pbar.set_postfix_str(
f"Training Loss: {loss_train / train_steps:.5f}")
pred_labels += list(
np.argmax(logits.detach().cpu().numpy(),
axis=1).reshape(-1))
real_labels += list(y_train[inds].cpu().numpy().reshape(-1))
acc_train = 100 * accuracy_score(np.array(real_labels),
np.array(pred_labels))
with torch.no_grad():
loss_test, test_steps = 0, 0
model.eval()
total = len(x_test) // batch_size + 1
pred_labels = []
with tqdm(total=total, desc=f"Epoch {epoch}") as pbar:
for batch in range(len(x_test) // batch_size + 1):
inds = slice(batch * batch_size, (batch + 1) * batch_size)
if len(x_test[inds]) == 0:
break
if ONLY_BATCH_IN_GPU:
logits = model(x_test[inds].to(device),
p_test[inds].to(device),
s_test[inds].to(device))
loss = criterion(logits, y_test[inds].to(device))
else:
logits = model(x_test[inds], p_test[inds],
s_test[inds])
loss = criterion(logits, y_test[inds])
loss_test += loss.item()
test_steps += 1
pbar.update(1)
pbar.set_postfix_str(
f"Testing Loss: {loss_test / test_steps:.5f}")
pred_labels += list(
np.argmax(logits.cpu().numpy(), axis=1).reshape(-1))
acc_test = 100 * accuracy_score(y_test.cpu().numpy(),
np.array(pred_labels))
print(
"Epoch {} | Train Loss {:.5f}, Train Acc {:.2f} - Test Loss {:.5f}, Test Acc {:.2f}"
.format(epoch, loss_train / train_steps, acc_train,
loss_test / test_steps, acc_test))
# Only saves the model if it's better than the models from all of the other experiments
if acc_test > acc_test_best:
torch.save(model.state_dict(), "PixelAttentionv2_cifar100.pt")
print("A new model has been saved!")
acc_test_best = acc_test
if acc_test > acc_best:
best_epoch, loss_best, acc_best = epoch, loss_test / test_steps, acc_test
# To keep track of the metrics during the training process on metrics.json
ex.log_scalar("training loss", loss_train / train_steps, epoch)
ex.log_scalar("training acc", acc_train, epoch)
ex.log_scalar("testing loss", loss_test / test_steps, epoch)
ex.log_scalar("testing acc", acc_test, epoch)
# To save the best results of this run to info.json. This is used by get_results() to generate the spreadsheet
ex.info["epoch"], ex.info["test loss"], ex.info[
"test acc"] = best_epoch, loss_best, acc_best
ex.info["train loss"], ex.info[
"train acc"] = loss_train / train_steps, acc_train
ex.info["time (min)"], ex.info["actual epochs"] = (
time() - start) / 60, epoch + 1
import get_results
import sqlite3 as lite
import csv
import thorobred as tb
import sys
filename = sys.argv[1]
con = lite.connect('TB.db')
myfile = open(filename, 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
#church hill downs and gulfstream park last month
CD_results = get_results.get_results('CD')
GP_results = get_results.get_results('GP')
AP_results = get_results.get_results('AP')
PIM_results = get_results.get_results('PIM')
cur = con.cursor()
#do the same for other results
def write_train(results):
for race in results:
date = race[1].split('-')
#writes track date race number
cur.execute('SELECT ID FROM HORSE WHERE NAME="{}"'.format(race[3]))
x = cur.fetchone()
def main(expdir, plot_speakers, plot_types):
'''main function'''
#lowess parameters
smooth = lambda y, x: lowess(y,
x + 1e-12 * np.random.randn(len(x)),
frac=1.0 / 3,
it=0,
delta=1.0,
return_sorted=True)
typestyle = dict()
typestyle['f1'] = '-'
typestyle['precision'] = '--'
typestyle['recal'] = ':'
results = dict()
results['f1'] = get_results(expdir, 'f1')
if plot_types:
results['precision'] = get_results(expdir, 'precision')
results['recal'] = get_results(expdir, 'recal')
speakers = results['f1'].keys()
#do LOWESS smooting per speaker
numexamples = {
s: np.array(r.values())[:, 0]
for s, r in results['f1'].items()
}
results = {
t: {s: np.array(r.values())[:, 1]
for s, r in results[t].items()}
for t in results
}
#lowess fit all the results for all the speakers speakers
fits = {
t: {s: smooth(a, numexamples[s])
for s, a in r.items()}
for t, r in results.items()
}
if plot_speakers:
#plot all the speakers
for s in speakers:
plt.figure(s)
for t in fits:
if t != 'f1' and not plot_types:
continue
plt.plot(fits[t][s][:, 0], fits[t][s][:, 1], label=t)
plt.scatter(numexamples[s], results['f1'][s])
plt.legend()
plt.xlabel('# Examples')
plt.ylabel('Accuracy')
#concatenate all the results
cnumex = np.concatenate(numexamples.values())
conc = {t: np.concatenate(r.values()) for t, r in results.items()}
#fit all the results
cfits = {t: smooth(conc[t], cnumex) for t in conc}
#plot averages
plt.figure('averages')
for t in cfits:
if t != 'f1' and not plot_types:
continue
plt.plot(cfits[t][:, 0],
cfits[t][:, 1],
color='black',
linestyle=typestyle[t],
linewidth=2,
label=t)
for s in speakers:
plt.plot(fits['f1'][s][:, 0], fits['f1'][s][:, 1], label=s)
plt.legend()
plt.xlabel('# Examples')
plt.ylabel('Accuracy')
plt.show()
def run_import(user_project_list, timestamp, initial_setup):
print(os.getcwd())
# print('start run import: ', get_memory_consumption())
logging.basicConfig(filename='import.log',
level=logging.WARNING,
format='%(asctime)s %(levelname)-8s %(message)s',
datefmt='%m-%d %H:%M:%S',
filemode='a')
logging.warning('>>> start of script import.py')
# check if the user provided an argument to set up the database
if initial_setup:
print('start the initial setup')
logging.warning('start the initial setup')
project_table_name, results_table_name, task_table_name = create_database_and_tables(
)
users_table_name = 'users'
else:
# define some variables that are related to the configuration of the psql database
project_table_name = 'projects'
results_table_name = 'results'
task_table_name = 'tasks'
users_table_name = 'users'
# get list of all project_ids if no list of projects is provided
if not user_project_list:
project_list = get_all_projects()
project_list = check_projects(project_list)
print('got all projects from firebase: ', project_list)
logging.warning('got all projects from firebase: %s' % project_list)
else:
print('user provided project ids: ', user_project_list)
logging.warning('user provided project ids: %s' % user_project_list)
project_list = check_projects(user_project_list)
if not project_list:
print('there are no projects to process. stop here.')
logging.warning('there are no projects to process. stop here.')
sys.exit(0)
# get project information
new_projects, updated_projects, project_dict = get_projects(
project_list, project_table_name)
print('new projects in firebase: ', new_projects)
logging.warning('new projects in firebase: %s' % new_projects)
print('updated projects in firebase: ', updated_projects)
logging.warning('updated projects in firebase: %s' % updated_projects)
logging.warning('get_projects() was successfull')
# check if the user provided a timestamp for the processing
if timestamp:
print('use timestamp provided by user')
logging.warning('use timestamp provided by user')
pass
else:
# print('get timestamp from database')
timestamp = get_last_timestamp(results_table_name)
# timestamp = 1509637220000
# timestamp = int((time.time() - 3600)*1000) # this creates a timestamp representing the last 1 hour, in milliseconds
print(timestamp)
# get latest results, retrieve a list object with project id's of latest results
changed_projects = get_results(results_table_name, timestamp, 500000)
print('projects with new results: ', changed_projects)
logging.warning('get_results() was successfull')
# add the projects which need a update based on results to the ones based on contr. | progres | state
# basidally merge the two lists with changed projects and remove the duplicates
# merge updated projects from get_projects and get_results
updated_projects = updated_projects + list(
set(changed_projects) - set(updated_projects))
# remove new projects from updated projects list
# when importing new projects, we already get the latest completed count
updated_projects = list(set(updated_projects) - set(new_projects))
print('new projects: ', new_projects)
logging.warning('new projects: %s' % new_projects)
print('updated projects: ', updated_projects)
logging.warning('updated projects: %s' % updated_projects)
# get tasks for new projects
get_tasks(new_projects, task_table_name)
logging.warning('get_tasks() was successfull')
# update projects that need an update
# get latest completed count for projects that need an update
get_tasks_completed_count(updated_projects, task_table_name)
logging.warning('get_tasks_completed_count() was successfull')
# save project data in psql database
save_projects_psql(project_table_name, project_dict)
print('saved project info to psql')
logging.warning('saved project info to psql')
# get user information
get_users(users_table_name)
logging.warning('get_users() was successfull')
logging.warning('<<< end of script import.py')
# print('after garbage collection: ', get_memory_consumption())
# garbage collection
for i in range(2):
n = gc.collect()
return new_projects, updated_projects
def main(result, sweepfile, expdir):
'''main function'''
colorlist = [
'red', 'blue', 'cyan', 'green', 'yellow', 'magenta', 'purple', 'pink',
'gold', 'navy', 'olive', 'grey'
]
linestyles = ['-']
#read the sweepfile
sweep = ConfigParser()
sweep.read(sweepfile)
#colorlist = ['black']
#linestyles = ['-', '--', ':', '-.']
#lowess parameters
smooth = lambda y, x: lowess(y,
x + 1e-12 * np.random.randn(len(x)),
frac=2.0 / 3,
it=0,
delta=1.0,
return_sorted=True)
plot_speakers = True
#read all the results
results = [
get_results(os.path.join(expdir, section), result)
for section in sweep.sections()
]
expnames = sweep.sections()
if plot_speakers:
for speaker in results[0]:
plt.figure(speaker)
for i, result in enumerate(results):
if speaker not in result:
continue
sort = np.array(result[speaker])
sort = sort[np.argsort(sort[:, 0], axis=0), :]
fit = smooth(sort[:, 1], sort[:, 0])
plt.plot(fit[:, 0],
fit[:, 1],
color=colorlist[i % len(colorlist)],
linestyle=linestyles[i % len(linestyles)],
label=expnames[i])
plt.legend(loc='lower right')
plt.xlabel('# Examples')
plt.ylabel('Accuracy')
#concatenate all the results
concatenated = [
np.array(list(itertools.chain.from_iterable(result.values())))
for result in results
]
#sort the concatenated data
sort = [
c[np.argsort(c[:, 0], axis=0), :] if c.size else None
for c in concatenated
]
#smooth all the results
fit = [smooth(s[:, 1], s[:, 0]) if s is not None else None for s in sort]
plt.figure('result')
for i, f in enumerate(fit):
if f is None:
continue
plt.plot(f[:, 0],
f[:, 1],
color=colorlist[i % len(colorlist)],
linestyle=linestyles[i % len(linestyles)],
label=expnames[i])
plt.legend(loc='lower right')
plt.xlabel('# Examples')
plt.ylabel('Accuracy')
plt.show()
def main(expdirs, result):
'''main function'''
expdirs = [os.path.normpath(expdir) for expdir in expdirs]
#colorlist = ['red', 'blue', 'cyan', 'green', 'yellow', 'magenta',
# 'purple', 'pink', 'gold', 'navy', 'olive', 'grey']
#linestyles = ['-']
colorlist = ['black']
linestyles = ['-', '--', ':', '-.']
#colorlist = ['green', 'dimgrey', 'darkorange']
#linestyles = ['-']
plot_speakers = True
remove_uncomplete = True
#tick parameters
tick_params = {
'size': 'x-large',
#'color': 'dimgrey'
}
#axis properties
ax_params = {'color': 'black'}
#label properties
label_params = {'color': 'black', 'size': 'x-large'}
#legend properties
legend_params = {
'loc': 'lower right',
'edgecolor': 'black',
'fontsize': 'x-large'
}
lcolor = 'black'
#lowess parameters
smooth = lambda y, x: lowess(y,
x + 1e-12 * np.random.randn(len(x)),
frac=2.0 / 3,
it=0,
delta=1.0,
return_sorted=True)
#read all the results
results = [get_results(expdir, result) for expdir in expdirs]
expnames = [os.path.basename(expdir) for expdir in expdirs]
#remove experiments that are not performed in all experiments
if remove_uncomplete:
speakers = set(results[0].keys())
for result in results[1:]:
speakers = speakers & set(result.keys())
results = [{s: result[s] for s in speakers} for result in results]
for speaker in speakers:
experiments = set(results[0][speaker].keys())
for result in results[1:]:
experiments = experiments & set(result[speaker].keys())
if not experiments:
for result in results:
del result[speaker]
else:
for result in results:
result[speaker] = {
e: result[speaker][e]
for e in experiments
}
if plot_speakers:
for speaker in results[0]:
plt.figure(speaker)
for i, result in enumerate(results):
if speaker not in result:
continue
sort = np.array(result[speaker].values())
sort = sort[np.argsort(sort[:, 0], axis=0), :]
fit = smooth(sort[:, 1], sort[:, 0])
plot = plt.plot(fit[:, 0],
fit[:, 1],
color=colorlist[i % len(colorlist)],
linestyle=linestyles[i % len(linestyles)],
label=expnames[i])
plt.yticks(**tick_params)
plt.xticks(**tick_params)
plt.axis(**ax_params)
l = plt.legend(**legend_params)
for text in l.get_texts():
text.set_color(lcolor)
plt.xlabel('# Examples', **label_params)
plt.ylabel('Accuracy', **label_params)
#concatenate all the results
concatenated = [
np.array(
list(
itertools.chain.from_iterable(
[r.values() for r in result.values()])))
for result in results
]
#sort the concatenated data
sort = [c[np.argsort(c[:, 0], axis=0), :] for c in concatenated]
#smooth all the results
fit = [smooth(s[:, 1], s[:, 0]) for s in sort]
plt.figure('result')
for i, f in enumerate(fit):
plt.plot(f[:, 0],
f[:, 1],
color=colorlist[i % len(colorlist)],
linestyle=linestyles[i % len(linestyles)],
label=expnames[i])
plt.yticks(**tick_params)
plt.xticks(**tick_params)
plt.axis(**ax_params)
l = plt.legend(**legend_params)
for text in l.get_texts():
text.set_color(lcolor)
plt.xlabel('# Examples', **label_params)
plt.ylabel('Accuracy', **label_params)
plt.show()
def main(expdirs, result):
'''main function'''
## delete the line matplotlib.use('Agg') if you want to show the plots
toplot = result
resultdir = expdirs
expdirs = [os.path.normpath(expdir) for expdir in expdirs]
#colorlist = ['red', 'blue', 'cyan', 'green', 'yellow', 'magenta',
# 'purple', 'pink', 'gold', 'navy', 'olive', 'grey']
#linestyles = ['-']
colorlist = ['black']
linestyles = ['-', '--', ':', '-.', (0, (5, 10))]
#colorlist = ['green', 'dimgrey', 'darkorange']
#linestyles = ['-']
plot_speakers = False # True
remove_uncomplete = True #False
#tick parameters
tick_params = {
'size': 'x-large',
#'color': 'dimgrey'
}
#axis properties
ax_params = {'color': 'black'}
#label properties
label_params = {'color': 'black', 'size': 'x-large'}
#legend properties
legend_params = {
'loc': 'lower right',
'edgecolor': 'black',
'fontsize': 'x-large'
}
lcolor = 'black'
#lowess parameters
def smooth1(y, x):
return lowess(y,
x + 1e-12 * np.random.randn(len(x)),
frac=2.0 / 3,
it=0,
delta=1.0,
return_sorted=True)
#weighted moving average
def smooth2(y, x, step_size=0.1, width=50):
bin_centers = np.arange(np.min(x),
np.max(x) - 0.5 * step_size,
step_size) + 0.5 * step_size
bin_avg = np.zeros(len(bin_centers))
#weight with a Gaussian function
def gaussian(x, amp=1, mean=0, sigma=1):
return amp * np.exp(-(x - mean)**2 / (2 * sigma**2))
for index in range(0, len(bin_centers)):
bin_center = bin_centers[index]
weights = gaussian(x, mean=bin_center, sigma=width)
bin_avg[index] = np.average(y, weights=weights)
yvals = np.sort(bin_avg)
xvals = [bin_centers[i] for i in list(np.argsort(bin_avg))]
return np.transpose(np.array([xvals, yvals]))
#read all the results
results = [get_results(expdir, result) for expdir in expdirs]
expnames = [os.path.basename(expdir) for expdir in expdirs]
labelnames = ['pccn', 'rccn', 'nmf', 'encoder-decoder']
#labelnames = ['pccn-multi', 'rccn-multi', 'pccn', 'rccn']
smooth = smooth2
pickylabel = 'f1'
if toplot == 'word_f1':
pickylabel = 'word_f1'
elif toplot == 'speakerperformance':
pickylabel = '% correctly decoded speakers'
spkweights = []
wordweights = []
wordthresholds = []
#remove experiments that are not performed in all experiments
if remove_uncomplete:
speakers = set(results[0].keys())
for result in results[1:]:
speakers = speakers & set(result.keys())
results = [{s: result[s] for s in speakers} for result in results]
for speaker in speakers:
experiments = set(results[0][speaker].keys())
for result in results[1:]:
experiments = experiments & set(result[speaker].keys())
if not experiments:
for result in results:
del result[speaker]
else:
for result in results:
result[speaker] = {
e: result[speaker][e]
for e in experiments
}
wordweights = [1, 10, 100]
if plot_speakers:
for speaker in results[0]:
plt.figure(speaker)
for i, result in enumerate(results):
if speaker not in result:
continue
sort = np.array(result[speaker].values())
sort = sort[np.argsort(sort[:, 0], axis=0), :]
fit = smooth(sort[:, 1], sort[:, 0])
plot = plt.plot(fit[:, 0],
fit[:, 1],
color=colorlist[i % len(colorlist)],
linestyle=linestyles[i % len(linestyles)])
# label=expnames[i])
plt.yticks(**tick_params)
plt.xticks(**tick_params)
plt.axis(**ax_params)
l = plt.legend(**legend_params)
for text in l.get_texts():
text.set_color(lcolor)
plt.xlabel('# Trainingsvoorbeelden', **label_params)
plt.ylabel('Accuracy', **label_params)
#concatenate all the results
concatenated = [
np.array(
list(
itertools.chain.from_iterable(
[r.values() for r in result.values()])))
for result in results
]
#sort the concatenated data
sort = [c[np.argsort(c[:, 0], axis=0), :] for c in concatenated]
#smooth all the results
fit = [smooth(s[:, 1], s[:, 0]) for s in sort]
plt.figure('result ' + str(toplot))
for i, f in enumerate(fit):
plt.plot(f[:, 0],
f[:, 1],
color=colorlist[i % len(colorlist)],
linestyle=linestyles[i % len(linestyles)],
label=labelnames[i])
plt.yticks(**tick_params)
plt.xticks(**tick_params)
plt.axis(**ax_params)
l = plt.legend(**legend_params)
for text in l.get_texts():
text.set_color(lcolor)
plt.xlabel('# Examples', **label_params)
plt.ylabel(str(pickylabel), **label_params)
print 'Figure of result saved in: ', resultdir[0]
plt.savefig(os.path.join(resultdir[0], 'result_' + str(toplot) + '.pdf'),
format='pdf')
plt.show()