def visual_delete_one_by_one(heap_type, title):
heap = heap_type()
# generate random numbers and add them to the heap
nodes = []
values = random.sample(range(max_key), node_amount)
for n in values:
node = heap.insert(n) # add node to heap
nodes.append(node)
visualize(
heap,
title=f"{title}: 0. Inserted values",
highlight=min(nodes, key=lambda n: n.key),
)
# remove nodes from heap one be one
nodes = sorted(nodes, key=lambda n: n.key, reverse=True)
delete_next = nodes.pop()
for i in range(1, delete_amount + 1):
heap.delete(delete_next)
if i % 3 == 0:
delete_next = nodes.pop()
else:
delete_next = nodes.pop(random.randrange(len(nodes)))
visualize(
heap,
title=f"{title}: {i}. Deleting the node {delete_next.key}",
highlight=delete_next,
)
def visualize_voc_unet():
from data.voc2012_loader_segmentation import PascalVOCSegmentation
from torch.utils.data.dataloader import DataLoader
from visualize.visualize import visualize
from models.unet import UNet
dataloader = DataLoader(PascalVOCSegmentation('val'),
batch_size=16,
shuffle=False,
num_workers=0)
model = UNet(outputs=21, name='voc_unet')
model.load()
visualize(model, dataloader, model.name + '_visualization/')
def visualize_voc_wass():
from data.voc2012_loader_segmentation import PascalVOCSegmentation
from torch.utils.data.dataloader import DataLoader
from visualize.visualize import visualize
from models.wass import WASS
dataloader = DataLoader(PascalVOCSegmentation('val'),
batch_size=32,
shuffle=False,
num_workers=6)
model = WASS(name='voc_wass')
model.load()
visualize(model, dataloader, model.name + '_visualization/')
def visualize_voc_vgg16():
from data.voc2012_loader_segmentation import PascalVOCSegmentation
from torch.utils.data.dataloader import DataLoader
from visualize.visualize import visualize
from models.vgg16 import Vgg16GAP
dataloader = DataLoader(PascalVOCSegmentation('val'),
batch_size=32,
shuffle=False,
num_workers=6)
model = Vgg16GAP(outputs=21, name='voc_vgg16')
model.load()
visualize(model, dataloader, model.name + '_visualization/')
def main(args):
config = parse_configs(args)
mode = args.mode
for m in mode:
if m == MODE_STATS:
stats(config[MODE_STATS])
elif m == MODE_PERTURB:
perturb(config[MODE_PERTURB])
elif m == MODE_CHECK:
check(config[MODE_CHECK])
elif m == MODE_TOLERANCE:
tolerance(config[MODE_TOLERANCE])
elif m == MODE_RUN_ENSEMBLE:
run_ensemble(config[MODE_RUN_ENSEMBLE])
elif m == MODE_VISUALIZE:
visualize(config)
else:
sys.exit("invalid mode '{}' selected. must be '{}', '{}', '{}', '{}' or '{}'"
.format(mode, MODE_PERTURB, MODE_CHECK, MODE_STATS, MODE_TOLERANCE, MODE_RUN_ENSEMBLE,
MODE_VISUALIZE))
def all(args):
# Go filtering
#
# Why I'm NOT using .gz ext here even I have implemented this:
# 1. flate2 is slow, it takes much compressing data if single-threaded.
# 2. plug in a SSD is much more easier than adding a CPU.
# 3. Some method uses only plain text data, so you need an extra (de)compression
# but it means nothing in the process.
# 4. Some further codes may only accept plain-text input, and I'm not adding
# support of gzip to it.
args.cleanq1 = 'clean.1.fq'
args.cleanq2 = 'clean.2.fq'
if configurations.filter_rawdata.compress_output_in_all:
args.cleanq1 += '.gz'
args.cleanq2 += '.gz'
if not args.disable_filter:
args.fastq1, args.fastq2 = filter(args)
args.fastafile = assemble(args)
args.fastafile = findmitoscaf(args)
if not args.disable_annotation:
(args.pos_json, args.circular,
args.annotated_cds, args.annotated_rna) = annotate(args)
# Visualization is of no way if not annotated.
args.circos_png, args.circos_svg = visualize(
args) if not args.disable_visualization else (None, None)
# Add command check if there's something further
# If you wrapped the 'all' module in other task or workflow
# the results will be retained since we don't know what you
# want.
if args.__calling == 'all':
def move_to_result(*files):
for file in files:
if path.isfile(str(file)):
os.rename(file, path.join(
args.result_dir, path.basename(file)))
# Iteratively collects all the results generated in the whole process
move_to_result(args.circos_png, args.circos_svg,
args.pos_json, args.fastafile,
args.annotated_cds, args.annotated_rna)
logger.log(2, f'Results dumped at {args.result_dir}')
sys.path.insert(0, os.path.abspath('../'))
from visualize.visualize import visualize
from torch.utils.data.dataloader import DataLoader
from data.voc2012_loaders import PascalVOCSegmentation
from models.vgg16_gap_feat import Vgg16GAP
from data import voc2012
model = Vgg16GAP('voc_classification_epoch_1', voc2012.get_class_count() - 1)
model.load()
visualize(model=model,
dataloaders={
'val':
DataLoader(PascalVOCSegmentation('val'),
batch_size=1,
shuffle=False,
num_workers=0),
},
palette=voc2012.color_map(256))
model = Vgg16GAP('voc_classification_epoch_5', voc2012.get_class_count() - 1)
model.load()
visualize(model=model,
dataloaders={
'val':
DataLoader(PascalVOCSegmentation('val'),
batch_size=1,
shuffle=False,
num_workers=0),
},
"""
return self.data
def getPruned(self):
"""
Get the list of Data objects after pruning.
"""
return self.pruned
def removeRtree(self):
"""
remove rtree data and index file
"""
try:
os.remove(str(self.dim) + 'd_index.data')
os.remove(str(self.dim) + 'd_index.index')
print('Files removed')
except:
print('No such files')
if __name__ == '__main__':
test = prunePSky(3, drange=[0, 100], radius=2)
test.loadData('test_30_dim2_pos3_rad2_0100.csv')
test.createIndex(2)
test.pruning()
test.calculateUSky()
visualize(test.getOrigin(), 3, [0, 100])
visualize(test.getPruned(), 3, [0, 100])
visualize(test.getCandidate(), 3, [0, 100])
test.removeRtree()
def main():
global args
args = parser.parse_args()
use_gpu = torch.cuda.is_available()
# Load and process data
time_data = time.time()
SRC, TRG, train_iter, val_iter = preprocess(args.v, args.b)
print('Loaded data. |TRG| = {}. Time: {:.2f}.'.format(
len(TRG.vocab),
time.time() - time_data))
# Load embeddings if available
LOAD_EMBEDDINGS = True
if LOAD_EMBEDDINGS:
np_de_file = 'scripts/emb-{}-de.npy'.format(len(SRC.vocab))
np_en_file = 'scripts/emb-{}-en.npy'.format(len(TRG.vocab))
embedding_src, embedding_trg = load_embeddings(SRC, TRG, np_de_file,
np_en_file)
print('Loaded embedding vectors from np files')
else:
embedding_src = (torch.rand(len(SRC.vocab), args.emb) - 0.5) * 2
embedding_trg = (torch.rand(len(TRG.vocab), args.emb) - 0.5) * 2
print('Initialized embedding vectors')
# Create model
tokens = [TRG.vocab.stoi[x] for x in ['<s>', '</s>', '<pad>', '<unk>']]
model = Seq2seq(embedding_src,
embedding_trg,
args.hs,
args.nlayers,
args.dp,
args.bi,
args.attn,
tokens_bos_eos_pad_unk=tokens,
reverse_input=args.reverse_input)
# Load pretrained model
if args.model is not None and os.path.isfile(args.model):
model.load_state_dict(torch.load(args.model))
print('Loaded pretrained model.')
model = model.cuda() if use_gpu else model
# Create weight to mask padding tokens for loss function
weight = torch.ones(len(TRG.vocab))
weight[TRG.vocab.stoi['<pad>']] = 0
weight = weight.cuda() if use_gpu else weight
# Create loss function and optimizer
criterion = nn.CrossEntropyLoss(weight=weight)
optimizer = torch.optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.lr)
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
'max',
patience=30,
factor=0.25,
verbose=True,
cooldown=6)
# scheduler = torch.optim.lr_scheduler.MultiStepLR(optimizer, milestones=[10,13,16,19], gamma=0.5)
# Create directory for logs, create logger, log hyperparameters
path = os.path.join('saves',
datetime.datetime.now().strftime("%m-%d-%H-%M-%S"))
os.makedirs(path, exist_ok=True)
logger = Logger(path)
logger.log('COMMAND ' + ' '.join(sys.argv), stdout=False)
logger.log(
'ARGS: {}\nOPTIMIZER: {}\nLEARNING RATE: {}\nSCHEDULER: {}\nMODEL: {}\n'
.format(args, optimizer, args.lr, vars(scheduler), model),
stdout=False)
# Train, validate, or predict
start_time = time.time()
if args.predict_from_input is not None:
predict.predict_from_input(model, args.predict_from_input, SRC, TRG,
logger)
elif args.predict is not None:
predict.predict(model, args.predict, args.predict_outfile, SRC, TRG,
logger)
elif args.visualize:
visualize.visualize(train_iter, model, SRC, TRG, logger)
elif args.evaluate:
valid.validate(val_iter, model, criterion, SRC, TRG, logger)
else:
train.train(train_iter, val_iter, model, criterion, optimizer,
scheduler, SRC, TRG, args.epochs, logger)
logger.log('Finished in {}'.format(time.time() - start_time))
return